@article {pmid30453059,
year = {2018},
author = {Hatton, GB and Madla, CM and Rabbie, SC and Basit, AW},
title = {Gut reaction: impact of systemic diseases on gastrointestinal physiology and drug absorption.},
journal = {Drug discovery today},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.drudis.2018.11.009},
pmid = {30453059},
issn = {1878-5832},
abstract = {It was in 400 BC that Hippocrates reportedly stated that "death sits in the colon". The growth in our knowledge of the intestinal microbiome and the gut-brain axis, their function and imbalance, has distinctly uncovered the complex relationship between the gut to disease predisposition and development, heralding the problem and the solution to disease pathology. Human studies of new drug molecules are typically performed in healthy volunteers and their specific disease indication. Approved drugs, however, are used by patients with diverse disease backgrounds. Here, we review the current literature of the gastrointestinal tract reacting to systemic disease pathology that elicits physiological and functional changes that consequently affect oral drug product performance.},
}
@article {pmid30452879,
year = {2018},
author = {Röth, D and Chiang, AJ and Hu, W and Gugiu, GB and Morra, CN and Versalovic, J and Kalkum, M},
title = {Two-carbon folate cycle of commensal Lactobacillus reuteri 6475 gives rise to immunomodulatory ethionine, a source for histone ethylation.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {},
number = {},
pages = {fj201801848R},
doi = {10.1096/fj.201801848R},
pmid = {30452879},
issn = {1530-6860},
abstract = {Colonization of the gut by certain probiotic Lactobacillus reuteri strains has been associated with reduced risk of inflammatory diseases and colorectal cancer. Previous studies pointed to a functional link between immunomodulation, histamine production, and folate metabolism, the central 1-carbon pathway for the transfer of methyl groups. Using mass spectrometry and NMR spectroscopy, we analyzed folate metabolites of L. reuteri strain 6475 and discovered that the bacterium produces a 2-carbon-transporting folate in the form of 5,10-ethenyl-tetrahydrofolyl polyglutamate. Isotopic labeling permitted us to trace the source of the 2-carbon unit back to acetate of the culture medium. We show that the 2C folate cycle of L. reuteri is capable of transferring 2 carbon atoms to homocysteine to generate the unconventional amino acid ethionine, a known immunomodulator. When we treated monocytic THP-1 cells with ethionine, their transcription of TNF-α was inhibited and cell proliferation reduced. Mass spectrometry of THP-1 histones revealed incorporation of ethionine instead of methionine into proteins, a reduction of histone-methylation, and ethylation of histone lysine residues. Our findings suggest that the microbiome can expose the host to ethionine through a novel 2-carbon transporting variant of the folate cycle and modify human chromatin via ethylation.-Röth, D., Chiang, A. J., Hu, W., Gugiu, G. B., Morra, C. N., Versalovic, J., Kalkum, M. The two-carbon folate cycle of commensal Lactobacillus reuteri 6475 gives rise to immunomodulatory ethionine, a source for histone ethylation.},
}
@article {pmid30452717,
year = {2018},
author = {Whelan, RA and Doranalli, K and Rinttilä, T and Vienola, K and Jurgens, G and Apajalahti, J},
title = {The impact of Bacillus subtilis DSM 32315 on the pathology, performance, and intestinal microbiome of broiler chickens in a necrotic enteritis challenge.},
journal = {Poultry science},
volume = {},
number = {},
pages = {},
doi = {10.3382/ps/pey500},
pmid = {30452717},
issn = {1525-3171},
abstract = {It was hypothesized that dietary inclusion of Bacillus subtilis DSM 32315 could inhibit Clostridium perfringens induced necrotic enteritis (NE), thereby improving broiler performance. Male, d 0 chicks were randomly assigned 14 birds/pen, 11 pens/treatment in 3 treatments: a basal diet (control), a coccidiostat fed control (Narasin), and a direct fed microbial (DFM) B. subtilis DSM 32315 treatment. Necrotic enteritis was induced in all birds by oral inoculation of Eimeria maxima oocysts on d 12 and a virulent C. perfringens on d 16. Mortality was reduced (P < 0.001) in DFM and Narasin compared to control. DFM reduced (P < 0.001) feed conversion ratio (FCR) compared to control. Furthermore, DFM and Narasin reduced (P < 0.001) footpad lesions. The DFM was shown to increase (P < 0.05) Bacillus spp. and decrease (P < 0.05) C. perfringens in the ileum and cecum at several time points. To investigate microbiome changes in the cecum, digesta samples were analyzed with % guanine and cytosine (%G+C) microbial profiling which fractionates bacterial chromosomes based on the %G+C in DNA. The method revealed treatment profile peaks in low (27.0 to 34.5%), mid (40.5 to 54.0%), and high (59.0 to 68.0%) G+C fractions. 16S rRNA gene amplification and high throughput sequencing was conducted on each of these fractions in order to elucidate specific bacterial population differences. In the low and mid %G+C fractions, DFM had greater abundance of Lactobacillaceae family members (P = 0.03 and P = 0.01, respectively) and Lactobacillus salivarius (P = 0.04 and P = 0.01, respectively) than control or Narasin. Lactobacillus johnsonii was also greater in the low %G+C fraction compared to control and Narasin (P = 0.01). Lachnospiraceae (P = 0.04) and Ruminococcaceae (P < 0.01) in the mid %G+C fraction were reduced in the DFM compared to control. Positive alterations to the microbial populations in the gut of broilers may at least be a partial mechanism by which B. subtilis DSM 32315 reduced pathology and improved performance of broilers in the NE challenge.},
}
@article {pmid30452699,
year = {2018},
author = {Kok, CR and Hutkins, R},
title = {Yogurt and other fermented foods as sources of health-promoting bacteria.},
journal = {Nutrition reviews},
volume = {76},
number = {Supplement_1},
pages = {4-15},
doi = {10.1093/nutrit/nuy056},
pmid = {30452699},
issn = {1753-4887},
abstract = {Increased consumption of yogurt, kefir, and other fermented foods has been driven, in part, by the health benefits these products may confer. Epidemiological studies have shown that the consumption of fermented foods is associated with reduced risks of type 2 diabetes, metabolic syndrome, and heart disease, along with improved weight management. The microorganisms present in these foods are suggested to contribute to these health benefits. Among these are the yogurt starter culture organisms Streptococcus thermophilus and Lactobacillus delbrueckii subsp bulgaricus as well as Bifidobacterium and Lactobacillus strains that are added for their probiotic properties. In contrast, for other fermented foods, such as sauerkraut, kimchi, and miso, fermentation is initiated by autochthonous microbes present in the raw material. In both cases, for these fermentation-associated microbes to influence the gut microbiome and contribute to host health, they must overcome, at least transiently, colonization resistance and other host defense factors. Culture and culture-independent methods have now clearly established that many of these microbes present in fermented dairy and nondairy foods do reach the gastrointestinal tract. Several studies have shown that consumption of yogurt and other fermented foods may improve intestinal and extraintestinal health and might be useful in improving lactose malabsorption, treating infectious diarrhea, reducing the duration and incidence of respiratory infections, and enhancing immune and anti-inflammatory responses.},
}
@article {pmid30452680,
year = {2018},
author = {Jin, T and Wang, Y and Huang, Y and Xu, J and Zhang, P and Wang, N and Liu, X and Chu, H and Liu, G and Jiang, H and Li, Y and Xu, J and Kristiansen, K and Xiao, L and Zhang, Y and Zhang, G and Du, G and Zhang, H and Zou, H and Zhang, H and Jie, Z and Liang, S and Jia, H and Wan, J and Lin, D and Li, J and Fan, G and Yang, H and Wang, J and Bai, Y and Xu, X},
title = {Erratum to: Taxonomic structure and functional association of foxtail millet root microbiome.},
journal = {GigaScience},
volume = {7},
number = {11},
pages = {},
doi = {10.1093/gigascience/giy099},
pmid = {30452680},
issn = {2047-217X},
}
@article {pmid30452101,
year = {2018},
author = {Bednarz, VN and van de Water, JAJM and Rabouille, S and Maguer, JF and Grover, R and Ferrier-Pagès, C},
title = {Diazotrophic community and associated dinitrogen fixation within the temperate coral Oculina patagonica.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14480},
pmid = {30452101},
issn = {1462-2920},
abstract = {Dinitrogen (N2) fixing bacteria (diazotrophs) are an important source of new nitrogen in oligotrophic environments and represent stable members of the microbiome in tropical corals, while information on corals from temperate oligotrophic regions is lacking. Therefore, this study provides new insights into the diversity and activity of diazotrophs associated with the temperate coral Oculina patagonica from the Mediterranean Sea by combining metabarcoding sequencing of amplicons of both the 16S rRNA and nifH genes and 15 N2 stable isotope tracer analysis to assess diazotroph-derived nitrogen (DDN) assimilation by the coral. Results show that the diazotrophic community of O. patagonica is dominated by autotrophic bacteria (i.e. Cyanobacteria and Chlorobia). The majority of DDN was assimilated into the tissue and skeletal matrix, and DDN assimilation significantly increased in bleached corals. Thus, diazotrophs may constitute an additional nitrogen source for the coral host, when nutrient exchange with Symbiodinium is disrupted (e.g. bleaching) and external food supply is limited (e.g. oligotrophic summer season). Furthermore, we hypothesize that DDN can facilitate the fast proliferation of endolithic algae, which provide an alternative carbon source for bleached O. patagonica. Overall, O. patagonica could serve as a good model for investigating the importance of diazotrophs in coral recovery from bleaching. This article is protected by copyright. All rights reserved.},
}
@article {pmid30452039,
year = {2018},
author = {Rajakovich, LJ and Balskus, EP},
title = {Metabolic functions of the human gut microbiota: the role of metalloenzymes.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/c8np00074c},
pmid = {30452039},
issn = {1460-4752},
abstract = {Covering: up to the end of 2017The human body is composed of an equal number of human and microbial cells. While the microbial community inhabiting the human gastrointestinal tract plays an essential role in host health, these organisms have also been connected to various diseases. Yet, the gut microbial functions that modulate host biology are not well established. In this review, we describe metabolic functions of the human gut microbiota that involve metalloenzymes. These activities enable gut microbial colonization, mediate interactions with the host, and impact human health and disease. We highlight cases in which enzyme characterization has advanced our understanding of the gut microbiota and examples that illustrate the diverse ways in which metalloenzymes facilitate both essential and unique functions of this community. Finally, we analyze Human Microbiome Project sequencing datasets to assess the distribution of a prominent family of metalloenzymes in human-associated microbial communities, guiding future enzyme characterization efforts.},
}
@article {pmid30451673,
year = {2018},
author = {Côté, N and Pasquier, JC},
title = {[Spontaneous preterm birth and the maternal microbiome].},
journal = {Medecine sciences : M/S},
volume = {34},
number = {10},
pages = {799-805},
doi = {10.1051/medsci/2018205},
pmid = {30451673},
issn = {1958-5381},
abstract = {Preterm birth is the leading cause of perinatal mortality and morbidity. Despite the efforts spent over the past 40 years to solve the physiopathological processes involved in the triggering of prematurity, efficient therapeutics are still lacking. Recently, growing body of evidence suggests that the maternal microbiome is a major player for a normal pregnancy and that dysbiosis is associated with preterm birth. The vaginal microbiome and its commensal Lactobacillus species may protect the uterus of ascending dissemination of pathogens. The uterus can also be contaminated with oral bacteria by the blood stream. Thus, the maternal microbiome can play both a protective role or a causal role in the triggering of preterm birth.},
}
@article {pmid30451146,
year = {2018},
author = {Matsuyama, M and Gomez-Arango, LF and Fukuma, NM and Morrison, M and Davies, PSW and Hill, RJ},
title = {Breastfeeding: a key modulator of gut microbiota characteristics in late infancy.},
journal = {Journal of developmental origins of health and disease},
volume = {},
number = {},
pages = {1-8},
doi = {10.1017/S2040174418000624},
pmid = {30451146},
issn = {2040-1752},
abstract = {The objective of this study was to investigate the impact of the most commonly cited factors that may have influenced infants' gut microbiota profiles at one year of age: mode of delivery, breastfeeding duration and antibiotic exposure. Barcoded V3/V4 amplicons of bacterial 16S-rRNA gene were prepared from the stool samples of 52 healthy 1-year-old Australian children and sequenced using the Illumina MiSeq platform. Following the quality checks, the data were processed using the Quantitative Insights Into Microbial Ecology pipeline and analysed using the Calypso package for microbiome data analysis. The stool microbiota profiles of children still breastfed were significantly different from that of children weaned earlier (P<0.05), independent of the age of solid food introduction. Among children still breastfed, Veillonella spp. abundance was higher. Children no longer breastfed possessed a more 'mature' microbiota, with notable increases of Firmicutes. The microbiota profiles of the children could not be differentiated by delivery mode or antibiotic exposure. Further analysis based on children's feeding patterns found children who were breastfed alongside solid food had significantly different microbiota profiles compared to that of children who were receiving both breastmilk and formula milk alongside solid food. This study provided evidence that breastfeeding continues to influence gut microbial community even at late infancy when these children are also consuming table foods. At this age, any impacts from mode of delivery or antibiotic exposure did not appear to be discernible imprints on the microbial community profiles of these healthy children.},
}
@article {pmid30450942,
year = {2018},
author = {Brown, CC and Manis, MM and Bohm, NM and Curry, SR},
title = {Oral Vancomycin for Secondary Prophylaxis of Clostridium difficile Infection.},
journal = {The Annals of pharmacotherapy},
volume = {},
number = {},
pages = {1060028018815170},
doi = {10.1177/1060028018815170},
pmid = {30450942},
issn = {1542-6270},
abstract = {OBJECTIVE: To summarize and critically appraise the evidence regarding oral vancomycin prophylaxis (OVP) to prevent recurrent Clostridium difficile infections (RCDIs), identify potential consequences of this emerging practice, and highlight future directions of study.<br><br>DATA SOURCES: A MEDLINE literature search of English-language publications from 1947 through September 2018 was performed using the search terms vancomycin and C difficile and prophylaxis. Clinical trials were identified on the National Library of Medicine clinical trials registry.<br><br>All clinical studies (n = 3) assessing oral vancomycin for secondary prophylaxis of C difficile infection (CDI) were evaluated by all authors. Other search results and references in selected publications were used for background and discussion.<br><br>DATA SYNTHESIS: OVP reduced the risk of RCDI in high-risk patients taking systemic antibiotics. Variable dosing regimens and lack of safety data are limitations. OVP may have an adverse impact on the gastrointestinal microbiome, but this was not examined in the clinical studies. Relevance to Patient Care and Clinical Practice: Although current studies are limited by methodological concerns, clinicians can consider vancomycin 125 mg orally once or twice daily in high-risk patients receiving broad-spectrum antibacterial agents. Results of ongoing trials will define the most appropriate regimen and its impact on outcomes, including collateral damage.<br><br>CONCLUSIONS: OVP reduces the risk of RCDIs and should be considered on a case-by-case basis. Caution is warranted before routine use is implemented because the impact on long-term outcomes has not been assessed and the optimal regimen has not been defined.},
}
@article {pmid30450723,
year = {2018},
author = {Prazeres, M and Renema, W},
title = {Evolutionary significance of the microbial assemblages of large benthic Foraminifera.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.12482},
pmid = {30450723},
issn = {1469-185X},
support = {//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; },
abstract = {Large benthic Foraminifera (LBF) are major carbonate producers on coral reefs, and are hosts to a diverse symbiotic microbial community. During warm episodes in the geological past, these reef-building organisms expanded their geographical ranges as subtropical and tropical belts moved into higher latitudes. During these range-expansion periods, LBF were the most prolific carbonate producers on reefs, dominating shallow carbonate platforms over reef-building corals. Even though the fossil and modern distributions of groups of species that harbour different types of symbionts are known, the nature, mechanisms, and factors that influence their occurrence remain elusive. Furthermore, the presence of a diverse and persistent bacterial community has only recently gained attention. We examined recent advances in molecular identification of prokaryotic (i.e. bacteria) and eukaryotic (i.e. microalgae) associates, and palaeoecology, and place the partnership with bacteria and algae in the context of climate change. In critically reviewing the available fossil and modern data on symbiosis, we reveal a crucial role of microalgae in the response of LBF to ocean warming, and their capacity to colonise a variety of habitats, across both latitudes and broad depth ranges. Symbiont identity is a key factor enabling LBF to expand their geographic ranges when the sea-surface temperature increases. Our analyses showed that over the past 66 million years (My), diatom-bearing species were dominant in reef environments. The modern record shows that these species display a stable, persistent eukaryotic assemblage across their geographic distribution range, and are less dependent on symbiotic photosynthesis for survival. By contrast, dinoflagellate and chlorophytic species, which show a provincial distribution, tend to have a more flexible eukaryotic community throughout their range. This group is more dependent on their symbionts, and flexibility in their symbiosis is likely to be the driving force behind their evolutionary history, as they form a monophyletic group originating from a rhodophyte-bearing ancestor. The study of bacterial assemblages, while still in its infancy, is a promising field of study. Bacterial communities are likely to be shaped by the local environment, although a core bacterial microbiome is found in species with global distributions. Cryptic speciation is also an important factor that must be taken into consideration. As global warming intensifies, genetic divergence in hosts in addition to the range of flexibility/specificity within host-symbiont associations will be important elements in the continued evolutionary success of LBF species in a wide range of environments. Based on fossil and modern data, we conclude that the microbiome, which includes both algal and bacterial partners, is a key factor influencing the evolution of LBF. As a result, the microbiome assists LBF in colonising a wide range of habitats, and allowed them to become the most important calcifiers on shallow platforms worldwide during periods of ocean warming in the geologic past. Since LBF are crucial ecosystem engineers and prolific carbonate producers, the microbiome is a critical component that will play a central role in the responses of LBF to a changing ocean, and ultimately in shaping the future of coral reefs.},
}
@article {pmid30450669,
year = {2018},
author = {Corwin, EJ and Jones, DP and Dunlop, AL},
title = {Symptom Science Research in the Era of Big Data: Leveraging Interdisciplinary Resources and Partners to Make It Happen.},
journal = {Journal of nursing scholarship : an official publication of Sigma Theta Tau International Honor Society of Nursing},
volume = {},
number = {},
pages = {},
doi = {10.1111/jnu.12446},
pmid = {30450669},
issn = {1547-5069},
support = {//National Institutes of Health/ ; R01NR014800//National Institutes of Nursing Research/ ; 3R01NR014800//National Institutes of Nursing Research/ ; },
abstract = {PURPOSE: The purpose of this article is to review the concept of team science as well as its benefits and challenges, within the framework of how including new ways of knowing can advance nursing science.<br><br>DESIGN: An exemplar highlights the experiences and strategies utilized by researchers at one school of nursing as they increasingly became involved in team science.<br><br>METHODS: Presented are the steps and processes that occurred as team science became the norm, expanding to include a network of linked investigators.<br><br>CONCLUSIONS: Although challenges to conducting team science exist, a reflection on how team science fits into the theoretical framework of Carper's Patterns of Knowing highlights its potential to drive nursing research forward.<br><br>CLINICAL RELEVANCE: Leading or participating in team science can expand the lens by which nursing scientists conduct research that is meaningful to patients and families.},
}
@article {pmid30450127,
year = {2018},
author = {Efimova, D and Tyakht, A and Popenko, A and Vasilyev, A and Altukhov, I and Dovidchenko, N and Odintsova, V and Klimenko, N and Loshkarev, R and Pashkova, M and Elizarova, A and Voroshilova, V and Slavskii, S and Pekov, Y and Filippova, E and Shashkova, T and Levin, E and Alexeev, D},
title = {Knomics-Biota - a system for exploratory analysis of human gut microbiota data.},
journal = {BioData mining},
volume = {11},
number = {},
pages = {25},
doi = {10.1186/s13040-018-0187-3},
pmid = {30450127},
issn = {1756-0381},
abstract = {Background: Metagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for investigating experimental data are of high interest to researchers.<br><br>Results: Knomics-Biota is a web-based resource for exploratory analysis of human gut metagenomes. Users can generate and share analytical reports corresponding to common experimental schemes (like case-control study or paired comparison). Interactive visualizations and statistical analysis are provided in association with the external factors and in the context of thousands of publicly available datasets arranged into thematic collections. The web-service is available at https://biota.knomics.ru.<br><br>Conclusions: Knomics-Biota web service is a comprehensive tool for interactive metagenomic data analysis.},
}
@article {pmid30450088,
year = {2018},
author = {Li, X and Gao, X and Hu, H and Xiao, Y and Li, D and Yu, G and Yu, D and Zhang, T and Wang, Y},
title = {Clinical Efficacy and Microbiome Changes Following Fecal Microbiota Transplantation in Children With Recurrent Clostridium Difficile Infection.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2622},
doi = {10.3389/fmicb.2018.02622},
pmid = {30450088},
issn = {1664-302X},
abstract = {Fecal microbiota transplantation (FMT) has been shown as an effective treatment for recurrent clostridium difficile infection (RCDI) in adults. In this study, we aim to evaluate the clinical efficacy of FMT in treating children with RCDI, and explore fecal microbiota changes during FMT treatment. A total of 11 RCDI subjects with a median age of 3.5 years were enrolled in this single-center prospective pilot study. All patients were cured (11/11, 100%) by FMT either through upper gastrointestinal tract route with a nasointestinal tube (13/16, 81.2%) or lower gastrointestinal tract route with a rectal tube (3/16, 18.8%). The cure rate of single FMT was 63.6% (7/11), and 4 (4/11, 36.4%) cases were performed with 2 or 3 times of FMT. Mild adverse events were reported in 4 children (4/11, 36.4%), including transient diarrhea, mild abdominal pain, transient fever and vomit. Gut microbiota composition analysis of 59 fecal samples collected from 34 participants (9 RCDI children, 9 donors and 16 health controls) showed that the alpha diversity was lower in pediatric RCDI patients before FMT than the healthy controls and donors, and fecal microbial community of pre-FMT samples (beta diversity) was apart from that of healthy controls and donors. No significant differences in alpha diversity, beta diversity or phylogenetic distance were detected between donors and healthy controls. Both the richness and diversity of gut microbiota were improved in the pediatric RCDI patients after FMT, and the bacteria community was shifted closer to the donor and healthy control group. Furthermore, FMT re-directed gut microbiome functions of pediatric RCDI toward a health state. Our results indicate that it is safe and tolerant to use FMT in treating pediatric RCDI. FMT shifted the gut microbiome composition and function in children with RCDI toward a healthy state.},
}
@article {pmid30449316,
year = {2018},
author = {Guerin, E and Shkoporov, A and Stockdale, SR and Clooney, AG and Ryan, FJ and Sutton, TDS and Draper, LA and Gonzalez-Tortuero, E and Ross, RP and Hill, C},
title = {Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut.},
journal = {Cell host &amp; microbe},
volume = {24},
number = {5},
pages = {653-664.e6},
doi = {10.1016/j.chom.2018.10.002},
pmid = {30449316},
issn = {1934-6069},
abstract = {CrAssphages represent the most abundant virus in the human gut microbiota, but the lack of available genome sequences for comparison has kept them enigmatic. Recently, sequence-based classification of distantly related crAss-like phages from multiple environments was reported, leading to a proposed familial-level taxonomic group. Here, we assembled the metagenomic sequencing reads from 702 human fecal virome/phageome samples and analyzed 99 complete circular crAss-like phage genomes and 150 contigs ≥70 kb. In silico comparative genomics and taxonomic analysis enabled a classification scheme of crAss-like phages from human fecal microbiomes into four candidate subfamilies composed of ten candidate genera. Laboratory analysis was performed on fecal samples from an individual harboring seven distinct crAss-like phages. We achieved crAss-like phage propagation in ex vivo human fecal fermentations and visualized short-tailed podoviruses by electron microscopy. Mass spectrometry of a crAss-like phage capsid protein could be linked to metagenomic sequencing data, confirming crAss-like phage structural annotations.},
}
@article {pmid30449315,
year = {2018},
author = {Teng, Y and Ren, Y and Sayed, M and Hu, X and Lei, C and Kumar, A and Hutchins, E and Mu, J and Deng, Z and Luo, C and Sundaram, K and Sriwastva, MK and Zhang, L and Hsieh, M and Reiman, R and Haribabu, B and Yan, J and Jala, VR and Miller, DM and Van Keuren-Jensen, K and Merchant, ML and McClain, CJ and Park, JW and Egilmez, NK and Zhang, HG},
title = {Plant-Derived Exosomal MicroRNAs Shape the Gut Microbiota.},
journal = {Cell host &amp; microbe},
volume = {24},
number = {5},
pages = {637-652.e8},
doi = {10.1016/j.chom.2018.10.001},
pmid = {30449315},
issn = {1934-6069},
abstract = {The gut microbiota can be altered by dietary interventions to prevent and treat various diseases. However, the mechanisms by which food products modulate commensals remain largely unknown. We demonstrate that plant-derived exosome-like nanoparticles (ELNs) are taken up by the gut microbiota and contain RNAs that alter microbiome composition and host physiology. Ginger ELNs (GELNs) are preferentially taken up by Lactobacillaceae in a GELN lipid-dependent manner and contain microRNAs that target various genes in Lactobacillus rhamnosus (LGG). Among these, GELN mdo-miR7267-3p-mediated targeting of the LGG monooxygenase ycnE yields increased indole-3-carboxaldehyde (I3A). GELN-RNAs or I3A, a ligand for aryl hydrocarbon receptor, are sufficient to induce production of IL-22, which is linked to barrier function improvement. These functions of GELN-RNAs can ameliorate mouse colitis via IL-22-dependent mechanisms. These findings reveal how plant products and their effects on the microbiome may be used to target specific host processes to alleviate disease.},
}
@article {pmid30449244,
year = {2018},
author = {Sterlin, D and Fieschi, C and Malphettes, M and Larsen, M and Gorochov, G and Fadlallah, J},
title = {Immune/microbial interface perturbation in human IgA deficiency.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-5},
doi = {10.1080/19490976.2018.1546520},
pmid = {30449244},
issn = {1949-0984},
abstract = {In a recently published article we report the metagenomic analysis of human gut microbiomes evolved in the absence of immunoglobulin A (IgA). We show that human IgA deficiency is not associated with massive quantitative perturbations of gut microbial ecology. While our study underlines a rather expected pathobiont expansion, we at the same time highlight a less expected depletion in some typically beneficial symbionts. We also show that IgM partially supply IgA deficiency, explaining the relatively mild clinical phenotype associated with the early steps of this condition. Microbiome studies in patients should consider potential issues such as cohort size, human genetic polymorphism and treatments. In this commentary, we discuss how such issues were taken into account in our own study.},
}
@article {pmid30448776,
year = {2018},
author = {Paganini, D and Uyoga, MA and Kortman, GAM and Cercamondi, CI and Winkler, HC and Boekhorst, J and Moretti, D and Lacroix, C and Karanja, S and Zimmermann, MB},
title = {Iron-containing micronutrient powders modify the effect of oral antibiotics on the infant gut microbiome and increase post-antibiotic diarrhoea risk: a controlled study in Kenya.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2018-317399},
pmid = {30448776},
issn = {1468-3288},
abstract = {OBJECTIVE: Many African infants receiving iron fortificants also receive antibiotics. Antibiotic efficacy against enteropathogens may be modified by high colonic iron concentrations. In this study, we evaluated the effect of antibiotics on the infant gut microbiome and diarrhoea when given with or without iron-containing micronutrient powders (MNPs).<br><br>DESIGN: In a controlled intervention trial, four groups of community-dwelling infants (n=28; aged 8-10 months) received either: (A) antibiotics for 5 days and iron-MNPs for 40 days (Fe+Ab+); (B) antibiotics and no-iron-MNPs (Fe-Ab+); (C) no antibiotics and iron-MNPs (Fe+Ab-); or (D) no antibiotics and no-iron-MNPs (Fe-Ab-). We collected a faecal sample before the first antibiotic dose (D0) and after 5, 10, 20 and 40 days (D5-D40) to assess the gut microbiome composition by 16S profiling, enteropathogens by quantitative PCR, faecal calprotectin and pH and assessed morbidity over the 40-day study period.<br><br>RESULTS: In Fe+Ab+, there was a decrease in Bifidobacterium abundances (p<0.05), but no decrease in Fe-Ab+. In Fe-Ab+, there was a decrease in abundances of pathogenic Escherichia coli (p<0.05), but no decrease in Fe+Ab+. In Fe-Ab+, there was a decrease in pH (p<0.05), but no decrease in Fe+Ab+. Longitudinal prevalence of diarrhoea was higher in Fe+Ab+ (19.6%) compared with Fe-Ab+ (12.4%) (p=0.04) and compared with Fe+Ab- (5.2%) (p=0.00).<br><br>CONCLUSION: Our findings need confirmation in a larger study but suggest that, in African infants, iron fortification modifies the response to broad-spectrum antibiotics: iron may reduce their efficacy against potential enteropathogens, particularly pathogenic E. coli, and may increase risk for diarrhoea.<br><br>TRIAL REGISTRATION NUMBER: NCT02118402; Pre-results.},
}
@article {pmid30448775,
year = {2018},
author = {Hendrikx, T and Duan, Y and Wang, Y and Oh, JH and Alexander, LM and Huang, W and Stärkel, P and Ho, SB and Gao, B and Fiehn, O and Emond, P and Sokol, H and van Pijkeren, JP and Schnabl, B},
title = {Bacteria engineered to produce IL-22 in intestine induce expression of REG3G to reduce ethanol-induced liver disease in mice.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2018-317232},
pmid = {30448775},
issn = {1468-3288},
abstract = {OBJECTIVE: Antimicrobial C-type lectin regenerating islet-derived 3 gamma (REG3G) is suppressed in the small intestine during chronic ethanol feeding. Our aim was to determine the mechanism that underlies REG3G suppression during experimental alcoholic liver disease.<br><br>DESIGN: Interleukin 22 (IL-22) regulates expression of REG3G. Therefore, we investigated the role of IL-22 in mice subjected to chronic-binge ethanol feeding (NIAAA model).<br><br>RESULTS: In a mouse model of alcoholic liver disease, we found that type 3 innate lymphoid cells produce lower levels of IL-22. Reduced IL-22 production was the result of ethanol-induced dysbiosis and lower intestinal levels of indole-3-acetic acid (IAA), a microbiota-derived ligand of the aryl hydrocarbon receptor (AHR), which regulates expression of IL-22. Importantly, faecal levels of IAA were also found to be lower in patients with alcoholic hepatitis compared with healthy controls. Supplementation to restore intestinal levels of IAA protected mice from ethanol-induced steatohepatitis by inducing intestinal expression of IL-22 and REG3G, which prevented translocation of bacteria to liver. We engineered Lactobacillus reuteri to produce IL-22 (L. reuteri/IL-22) and fed them to mice along with the ethanol diet; these mice had reduced liver damage, inflammation and bacterial translocation to the liver compared with mice fed an isogenic control strain and upregulated expression of REG3G in intestine. However, L. reuteri/IL-22 did not reduce ethanol-induced liver disease in Reg3g-/- mice.<br><br>CONCLUSION: Ethanol-associated dysbiosis reduces levels of IAA and activation of the AHR to decrease expression of IL-22 in the intestine, leading to reduced expression of REG3G; this results in bacterial translocation to the liver and steatohepatitis. Bacteria engineered to produce IL-22 induce expression of REG3G to reduce ethanol-induced steatohepatitis.},
}
@article {pmid30448747,
year = {2018},
author = {Wan, Z and Wang, C and Zhou, J and Shen, M and Wang, X and Fu, Z and Jin, Y},
title = {Effects of polystyrene microplastics on the composition of the microbiome and metabolism in larval zebrafish.},
journal = {Chemosphere},
volume = {217},
number = {},
pages = {646-658},
doi = {10.1016/j.chemosphere.2018.11.070},
pmid = {30448747},
issn = {1879-1298},
abstract = {Microplastics are major pollutants in marine environment and may have health effects on aquatic organisms. In this study, we used two sizes (5 and 50 μm diameter) of fluorescent and virgin polystyrene microplastics to analyze the adverse effects on larval zebrafish. In our study, we evaluated the effects on larval zebrafish after exposure to 100 and 1000 μg/L of two sizes of polystyrene microplastics for 7 days. Our results show that polystyrene microplastics could cause alterations in the microbiome at the phylum and genus levels in larval zebrafish, including changes in abundance and diversity of the microbiome. In addition, metabolomic analysis suggested that exposure to polystyrene microplastics induced alterations of metabolic profiles in larval zebrafish, and differential metabolites were involved in energy metabolism, glycolipid metabolism, inflammatory response, neurotoxic response, nucleic acid metabolism, oxidative stress. Polystyrene microplastics also significantly decreased the activities of catalase and the content of glutathione. In addition, the results of gene transcription analysis showed that exposure to polystyrene microplastics induced changes in glycolysis-related genes and lipid metabolism-related genes, confirming that polystyrene microplastics disturbed glycolipid and energy metabolism. Taken together, the results obtained in the present study indicated that the potential effects of environmental microplastics on aquatic organisms should not be ignored.},
}
@article {pmid30448529,
year = {2018},
author = {Metcalf, JL},
title = {Estimating the postmortem interval using microbes: Knowledge gaps and a path to technology adoption.},
journal = {Forensic science international. Genetics},
volume = {38},
number = {},
pages = {211-218},
doi = {10.1016/j.fsigen.2018.11.004},
pmid = {30448529},
issn = {1878-0326},
abstract = {Microbes have potential to be used as physical evidence for forensic science because they are ubiquitous and have predictable ecologies. With the advent of next generation sequencing technology and the subsequent boost to microbiome science (study of the genes and molecules of microbial communities), it has become possible to develop new microbial-based tools for forensic science. One promising approach is the use of microbial succession during the ecological process of decomposition to estimate the time since death, or postmortem interval (PMI). This microbial clock of death is developed by building a regression model using microbiome data collected from postmortem samples (e.g. swab of skin) with known PMIs. In a death investigation, a similar sample type (e.g. swab of skin) would be collected, the microbes profiled using DNA sequencing, and the microbes would be matched to a point on the clock (i.e. the regression model). Recent research by several independent scientific teams has provided a proof of concept for this new microbiome forensic tool. However, developing and transitioning new forensic science technologies into the justice system requires overcoming scientific, investigative, and legal hurdles. In this article, I address the apparent knowledge gaps in the science of microbiome technology to estimate PMI, and discuss a path for bringing this technology into the justice system.},
}
@article {pmid30448038,
year = {2018},
author = {Schlomann, BH and Wiles, TJ and Wall, ES and Guillemin, K and Parthasarathy, R},
title = {Bacterial Cohesion Predicts Spatial Distribution in the Larval Zebrafish Intestine.},
journal = {Biophysical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bpj.2018.10.017},
pmid = {30448038},
issn = {1542-0086},
abstract = {Are there general biophysical relationships governing the spatial organization of the gut microbiome? Despite growing realization that spatial structure is important for population stability, interbacterial competition, and host functions, it is unclear in any animal gut whether such structure is subject to predictive, unifying rules or if it results from contextual, species-specific behaviors. To explore this, we used light sheet fluorescence microscopy to conduct a high-resolution comparative study of bacterial distribution patterns throughout the entire intestinal volume of live, larval zebrafish. Fluorescently tagged strains of seven bacterial symbionts, representing six different species native to zebrafish, were each separately monoassociated with animals that had been raised initially germ-free. The strains showed large differences in both cohesion-the degree to which they auto-aggregate-and spatial distribution. We uncovered a striking correlation between each strain's mean position and its cohesion, whether quantified as the fraction of cells existing as planktonic individuals, the average aggregate size, or the total number of aggregates. Moreover, these correlations held within species as well; aggregates of different sizes localized as predicted from the pan-species observations. Together, our findings indicate that bacteria within the zebrafish intestine are subject to generic processes that organize populations by their cohesive properties. The likely drivers of this relationship-peristaltic fluid flow, tubular anatomy, and bacterial growth and aggregation kinetics-are common throughout animals. We therefore suggest that the framework introduced here of biophysical links between bacterial cohesion and spatial organization should be useful for directing explorations in other host-microbe systems, formulating detailed models that can quantitatively map onto experimental data, and developing new tools that manipulate cohesion to engineer microbiome function.},
}
@article {pmid30447983,
year = {2018},
author = {Vasquez, AK and Ganda, EK and Capel, MB and Eicker, S and Virkler, PD and Bicalho, RC and Nydam, DV},
title = {The microbiome of Escherichia coli and culture-negative nonsevere clinical mastitis: Characterization and associations with linear score and milk production.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2018-15062},
pmid = {30447983},
issn = {1525-3198},
abstract = {Culture-negative and Escherichia coli cases are uncommonly treated in pathogen-based protocols for nonsevere mastitis. High-throughput 16S rRNA sequencing might reveal the presence of other pathogens and can provide information on microbial diversity. The objective was to explore the milk microbiome at the time of the mastitis event (enrollment) and its association with survival in the herd, milk production, and postevent linear score (LS) for cows with clinical mastitis characterized as negative or E. coli by culture. Fifty E. coli-positive and 35 culture-negative samples from cases were enrolled. No cases were treated with antimicrobials. All E. coli-positive quarters were characterized as transient; microbiological culture of samples taken 15 d postmastitis were negative for this organism. However, a difference in α-diversity (Shannon index) was present between enrollment and follow-up samples (3.8 vs. 5.1). When α-diversity was explored for enrollment E. coli samples, no relationship was observed between the Shannon indices of these samples and postmastitis LS. Alpha-diversity of the enrollment samples was lower for E. coli-positive cows that subsequently had greater losses in milk production. This difference was explained by a greater relative abundance of the family Enterobacteriaceae (67.8 vs. 38.4%) for cows that dropped in production. Analysis of composition of the microbiome identified one phylum, Proteobacteria, that differed between E. coli-positive cows that dropped in production and those that did not. Evaluation of β-diversity found no statistical relationship between postmastitis LS and the microbiome. When evaluating α- and β-diversities and composition of the microbiomes for culture-negative quarters, no associations were found for milk production changes and postmastitis LS. Three cows did not remain in the herd, limiting the ability to analyze survival. The findings suggest that a contributing factor to negative outcomes in E. coli-positive cows is relative abundance of this pathogen, and that no single or collective group of bacterial families is associated with milk production changes or postmastitis LS in culture-negative quarters. Although additional studies should be performed, the absence of associations between outcomes explored and microbial profiles in this study suggests that we are not missing opportunities by not treating nonsevere E. coli or culture-negative mastitis cases.},
}
@article {pmid30447602,
year = {2018},
author = {Ma, J and Zhu, D and Chen, QL and Ding, J and Zhu, YG and Sheng, GD and Qiu, YP},
title = {Exposure to tetracycline perturbs the microbiome of soil oligochaete Enchytraeus crypticus.},
journal = {The Science of the total environment},
volume = {654},
number = {},
pages = {643-650},
doi = {10.1016/j.scitotenv.2018.11.154},
pmid = {30447602},
issn = {1879-1026},
abstract = {Microbial symbiosis is essential for the normal development and growth of hosts. Past attention has mostly been paid to its effects on plants and vertebrates. The effects of environmental pressures such as antibiotics on the microbiome of soil fauna remain largely elusive. We used bacterial 16S rRNA gene high-throughput sequencing to examine the response of microbiome of soil invertebrate Enchytraeus crypticus to oral tetracycline exposure. After two-week exposure, tetracycline-free oat was used as food to monitor the restoration of E. crypticus microbiome. The results showed that Proteobacteria, Actinobacteria and Planctomycetes were the three dominant phyla in all samples, Rhizobiaceae and Kaistia were the most abundant family and genus in all samples, respectively. After 14 days tetracycline exposure, Planctomycetes declined dramatically from 33.05% to 3.28% (P = 0.016), but Actinobacteria elevated substantially from 2.47% to 23.65% (P = 0.004). The alpha-diversity of microbial community increased significantly after tetracycline exposure compared to the control (P = 0.014). Terminating tetracycline exposure led to the recovery of E. crypticus microbiome back to the background level within 14 days. Our results suggest that while tetracycline can disturb the microbiome in E. crypticus significantly, the effects of the antibiotic on E. crypticus microbiome may not be permanent but reversibly diminish after stopping exposure for a period of time. The results may contribute to extending our understanding of the effect of antibiotics on microbiome of soil invertebrates. CAPSULE: The microbiome of E. crypticus exposed to tetracycline is perturbed and reversibly restored after terminating the exposure.},
}
@article {pmid30447213,
year = {2018},
author = {Greenbaum, S and Greenbaum, G and Moran-Gilad, J and Weintruab, AY},
title = {Ecological dynamics of the vaginal microbiome in relation to health and disease.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2018.11.1089},
pmid = {30447213},
issn = {1097-6868},
abstract = {The bacterial composition of the vaginal microbiome is thought to be related to health and disease states of women. This microbiome is particularly dynamic, with compositional changes related to pregnancy, menstruation, and disease states such as bacterial vaginosis. In order to understand these dynamics and their impact on health and disease, ecological theories have been introduced to study the complex interactions between the many taxa in the vaginal bacterial ecosystem. The goal of this review is to introduce the ecological principles that are used in the study of the vaginal microbiome and its dynamics, and to review the application of ecology to vaginal microbial communities with respect to health and disease. While applications of vaginal microbiome analysis and modulation have not yet been introduced into the routine clinical setting, a deeper understanding of its dynamics has the potential to facilitate development of future practices, for example in the context of postmenopausal vaginal symptoms, stratifying risk for obstetric complications, and control of sexually transmitted infections.},
}
@article {pmid30446559,
year = {2018},
author = {Parris, DJ and Morgan, MM and Stewart, FJ},
title = {Feeding rapidly alters microbiome composition and gene transcription in the clownfish gut.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02479-18},
pmid = {30446559},
issn = {1098-5336},
abstract = {BackgroundDiet is a major determinant of intestinal microbiome composition. While studies have evaluated microbiome responses to diet variation, less is understood of how the act of feeding influences the microbiome, independent of diet type. Here, we use the clownfish Premnas biaculeatus, a species reared commonly in ornamental marine aquaculture, to test how the diversity, predicted gene content, and gene transcription of the microbiome vary over a two-day diurnal period with a single daily feeding event. This study used fish fed four times daily, once daily, or every three days prior to the diurnal period, allowing us also to test how feeding frequency affected microbiome diversity. The amount of time between feedings had no affect on baseline diversity of the microbiome. In contrast, the act of feeding itself caused a significant short term change in the microbiome, with microbiome diversity, predicted gene content, and gene transcription varying significantly between time points immediately before and 1.5 hours post feeding. Variation was driven by abundance shifts involving exact sequence variants (ESVs), with one ESV identified as Photobacterium sp. increasing from <0.5% of sequences immediately pre-feeding to 34% at 1.5 hours post-feeding. Other ESVs from a range of microbial groups also increased dramatically after feeding, with the majority also detected in the food. One ESV identified as Clostridium perfringens represented up to 55% of sequences but did not vary significantly over the diurnal period and was not detected in the food. Post-feeding samples were enriched in transcripts and predicted genes for social interactions, cell motility, and coping with foreign DNA, whereas time points farther from feeding were enriched in genes of diverse catabolic and biosynthetic functions. These results confirm feeding as a significant destabilizing force in clownfish intestinal microbiomes, likely due to both input of cells attached to food and stimulation of resident microbes. Microbes such as Photobacterium may episodically transition from environmental reservoirs to growth in the gut, likely in association with food particles. This transition may be facilitated by functions for navigating a new environment and interacting with neighboring microbes and host cells. Other taxa, such as Clostridium, are comparatively stable intestinal members and less likely to be affected by passing food. Conclusions about microbiome ecology may therefore differ based on when samples were collected relative to the last feeding.ImportanceDespite extensive study of intestinal microbiome diversity and the role of diet type in structuring gut microbial communities, we know very little about short-term changes in the intestinal microbiome as a result of feeding alone. Sampling microbiomes over a feeding cycle will allow us to differentiate opportunistic, feeding-responsive microbes from resident, potentially commensal members of the gut community. Also, since feeding has the potential to alter microbiome structure, sampling at different points relative to the last feeding event will likely yield different conclusions about microbiome composition and function. This variation should be addressed in comparative microbiome studies. Our study contributes to knowledge of short-term changes in the gut microbiome associated with feeding events.},
}
@article {pmid30446434,
year = {2018},
author = {Lucking, EF and O'Connor, KM and Strain, CR and Fouhy, F and Bastiaanssen, TFS and Burns, DP and Golubeva, AV and Stanton, C and Clarke, G and Cryan, JF and O'Halloran, KD},
title = {Chronic intermittent hypoxia disrupts cardiorespiratory homeostasis and gut microbiota composition in adult male guinea-pigs.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ebiom.2018.11.010},
pmid = {30446434},
issn = {2352-3964},
abstract = {BACKGROUND: Carotid body (peripheral oxygen sensor) sensitisation is pivotal in the development of chronic intermittent hypoxia (CIH)-induced hypertension. We sought to determine if exposure to CIH, modelling human sleep apnoea, adversely affects cardiorespiratory control in guinea-pigs, a species with hypoxia-insensitive carotid bodies. We reasoned that CIH-induced disruption of gut microbiota would evoke cardiorespiratory morbidity.<br><br>METHODS: Adult male guinea-pigs were exposed to CIH (6.5% O2 at nadir, 6 cycles.hour-1) for 8 h.day-1 for 12 consecutive days.<br><br>FINDINGS: CIH-exposed animals established reduced faecal microbiota species richness, with increased relative abundance of Bacteroidetes and reduced relative abundance of Firmicutes bacteria. Urinary corticosterone and noradrenaline levels were unchanged in CIH-exposed animals, but brainstem noradrenaline concentrations were lower compared with sham. Baseline ventilation was equivalent in CIH-exposed and sham animals; however, respiratory timing variability, sigh frequency and ventilation during hypoxic breathing were all lower in CIH-exposed animals. Baseline arterial blood pressure was unaffected by exposure to CIH, but β-adrenoceptor-dependent tachycardia and blunted bradycardia during phenylephrine-induced pressor responses was evident compared with sham controls.<br><br>INTERPRETATION: Increased carotid body chemo-afferent signalling appears obligatory for the development of CIH-induced hypertension and elevated chemoreflex control of breathing commonly reported in mammals, with hypoxia-sensitive carotid bodies. However, we reveal that exposure to modest CIH alters gut microbiota richness and composition, brainstem neurochemistry, and autonomic control of heart rate, independent of carotid body sensitisation, suggesting modulation of breathing and autonomic homeostasis via the microbiota-gut-brainstem axis. The findings have relevance to human sleep-disordered breathing.<br><br>FUNDING: The Department of Physiology, and APC Microbiome Ireland, UCC.},
}
@article {pmid30446306,
year = {2018},
author = {Gao, Z and Karlsson, I and Geisen, S and Kowalchuk, G and Jousset, A},
title = {Protists: Puppet Masters of the Rhizosphere Microbiome.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2018.10.011},
pmid = {30446306},
issn = {1878-4372},
abstract = {The rhizosphere microbiome is a central determinant of plant performance. Microbiome assembly has traditionally been investigated from a bottom-up perspective, assessing how resources such as root exudates drive microbiome assembly. However, the importance of predation as a driver of microbiome structure has to date largely remained overlooked. Here we review the importance of protists, a paraphyletic group of unicellular eukaryotes, as a key regulator of microbiome assembly. Protists can promote plant-beneficial functions within the microbiome, accelerate nutrient cycling, and remove pathogens. We conclude that protists form an essential component of the rhizosphere microbiome and that accounting for predator-prey interactions would greatly improve our ability to predict and manage microbiome function at the service of plant growth and health.},
}
@article {pmid30446179,
year = {2018},
author = {Brey, CW and Akbari-Alavijeh, S and Ling, J and Sheagley, J and Shaikh, B and Al-Mohanna, F and Wang, Y and Gaugler, R and Hashmi, S},
title = {Salts and energy balance: A special role for dietary salts in metabolic syndrome.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnu.2018.10.021},
pmid = {30446179},
issn = {1532-1983},
abstract = {BACKGROUND: Dietary salts sodium (Na+), potassium (K+), magnesium (Mg2+), and calcium (Ca2+) are important in metabolic diseases. Yet, we do not have sufficient understanding on the salts global molecular network in these diseases. In this systematic review we have pooled information to identify the general effect of salts on obesity, insulin resistance and hypertension.<br><br>AIMS: To assess the roles of salts in metabolic disorders by focusing on their individual effect and the network effect among these salts.<br><br>METHODS: We searched articles in PubMed, EMBASE and Google Scholar. We selected original laboratory research, systematic reviews, clinical trials, observational studies and epidemiological data that focused on dietary salts and followed the preferred reporting items for systematic review in designing the present systematic review.<br><br>RESULTS: From the initial search of 2898 studies we selected a total of 199 articles that met our inclusion criteria and data extraction. Alterations in metabolic pathways associated with the sensitivity of sodium, potassium, magnesium and calcium may lead to obesity, hypertension, and insulin resistance. We found that the results of most laboratory research, animal studies and clinical trials are coherent but some research outcome are either inconsistent or inconclusive.<br><br>CONCLUSION: Important of salts in metabolic disorder is evident. In order to assess the effects of dietary salts in metablic diseases, environmental factors, dietary habits, physical activity, and the microbiome, should be considered in any study. Although interest in this area of research continues to grow, the challenge is to integrate the action of these salts in metabolic syndrom.},
}
@article {pmid30445993,
year = {2018},
author = {Breitwieser, FP and Baker, DN and Salzberg, SL},
title = {KrakenUniq: confident and fast metagenomics classification using unique k-mer counts.},
journal = {Genome biology},
volume = {19},
number = {1},
pages = {198},
doi = {10.1186/s13059-018-1568-0},
pmid = {30445993},
issn = {1474-760X},
support = {W911NF-14-1-0490//Army Research Office (US)/ ; R01-HG006677//National Human Genome Research Institute (US)/ ; R01-GM083873//National Institute of General Medical Sciences/ ; R01-GM118568//National Institute of General Medical Sciences/ ; },
abstract = {False-positive identifications are a significant problem in metagenomics classification. We present KrakenUniq, a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory. KrakenUniq is freely available at https://github.com/fbreitwieser/krakenuniq .},
}
@article {pmid30445918,
year = {2018},
author = {Wakita, Y and Shimomura, Y and Kitada, Y and Yamamoto, H and Ohashi, Y and Matsumoto, M},
title = {Taxonomic classification for microbiome analysis, which correlates well with the metabolite milieu of the gut.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {188},
doi = {10.1186/s12866-018-1311-8},
pmid = {30445918},
issn = {1471-2180},
abstract = {BACKGROUND: 16S rRNA gene amplicon sequencing analysis (16S amplicon sequencing) has provided considerable information regarding the ecology of the intestinal microbiome. Recently, metabolomics has been used for investigating the crosstalk between the intestinal microbiome and the host via metabolites. In the present study, we determined the accuracy with which 16S rRNA gene data at different classification levels correspond to the metabolome data for an in-depth understanding of the intestinal environment.<br><br>RESULTS: Over 200 metabolites were identified using capillary electrophoresis and time-of-flight mass spectrometry (CE-TOFMS)-based metabolomics in the feces of antibiotic-treated and untreated mice. 16S amplicon sequencing, followed by principal component analysis (PCA) of the intestinal microbiome at each taxonomic rank, revealed differences between the antibiotic-treated and untreated groups in the first principal component in the family-, genus, and species-level analyses. These differences were similar to those observed in the PCA of the metabolome. Furthermore, a strong correlation between principal component (PC) scores of the metabolome and microbiome was observed in family-, genus-, and species-level analyses.<br><br>CONCLUSIONS: Lower taxonomic ranks such as family, genus, or species are preferable for 16S amplicon sequencing to investigate the correlation between the microbiome and metabolome. The correlation of PC scores between the microbiome and metabolome at lower taxonomic levels yield a simple method of integrating different &quot;-omics&quot; data, which provides insights regarding crosstalk between the intestinal microbiome and the host.},
}
@article {pmid30445722,
year = {2018},
author = {Harhala, M and Nelson, DC and Miernikiewicz, P and Heselpoth, RD and Brzezicka, B and Majewska, J and Linden, SB and Shang, X and Szymczak, A and Lecion, D and Marek-Bukowiec, K and Kłak, M and Wojciechowicz, B and Lahutta, K and Konieczny, A and Dąbrowska, K},
title = {Safety Studies of Pneumococcal Endolysins Cpl-1 and Pal.},
journal = {Viruses},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/v10110638},
pmid = {30445722},
issn = {1999-4915},
support = {UMO-2015/18/M/NZ6/00412//Narodowe Centrum Nauki/ ; 2014-2018//Krajowy Naukowy Osrodek Wiodacy/ ; },
abstract = {Bacteriophage-derived endolysins have gained increasing attention as potent antimicrobial agents and numerous publications document the in vivo efficacy of these enzymes in various rodent models. However, little has been documented about their safety and toxicity profiles. Here, we present preclinical safety and toxicity data for two pneumococcal endolysins, Pal and Cpl-1. Microarray, and gene profiling was performed on human macrophages and pharyngeal cells exposed to 0.5 µM of each endolysin for six hours and no change in gene expression was noted. Likewise, in mice injected with 15 mg/kg of each endolysin, no physical or behavioral changes were noted, pro-inflammatory cytokine levels remained constant, and there were no significant changes in the fecal microbiome. Neither endolysin caused complement activation via the classic pathway, the alternative pathway, or the mannose-binding lectin pathway. In cellular response assays, IgG levels in mice exposed to Pal or Cpl-1 gradually increased for the first 30 days post exposure, but IgE levels never rose above baseline, suggesting that hypersensitivity or allergic reaction is unlikely. Collectively, the safety and toxicity profiles of Pal and Cpl-1 support further preclinical studies.},
}
@article {pmid30445599,
year = {2018},
author = {Zakrzewski, M and Simms, LA and Brown, A and Appleyard, M and Irwin, J and Waddell, N and Radford-Smith, GL},
title = {IL23R-protective coding variant promotes beneficial bacteria and diversity in the ileal microbiome in healthy individuals without inflammatory bowel disease.},
journal = {Journal of Crohn's &amp; colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjy188},
pmid = {30445599},
issn = {1876-4479},
abstract = {Background and aims: This study aimed to characterise the mucosa-associated microbiota in ileal Crohn's disease (CD) patients and in healthy controls in terms of host genotype and inflammation status.<br><br>Methods: The mucosa-associated microbiota of intestinal pinch biopsies from 15 ileal CD patients with mild and moderate disease and from 58 healthy controls were analysed by 16S ribosomal sequencing to determine microbial profile differences between (1) IL23R, NOD2 and ATG16L1 genotypes in healthy subjects, (2) ileal CD patients and control subjects, and (3) inflamed and non-inflamed mucosal tissue in CD patients.<br><br>Results: The protective variant of the IL23R gene (rs11209026) significantly impacted the microbial composition in the ileum of healthy subjects and was associated with an increased abundance of phylotypes within the Christensenellaceae family as well as increases in diversity and richness. Comparative analysis of healthy and non-inflamed CD microbiome samples indicated notable decrease in the abundance of Faecalibacterium prausnitzii as well as Shannon diversity and richness. Inflamed and non-inflamed ileal samples of CD subjects had high intra-individual stability and inter-individual variability but no significant alterations in diversity, richness and taxa were identified. Calprotectin correlated positively with Proteobacteria abundance and negatively with diversity in the samples from healthy subjects.<br><br>Conclusions: The observation of low diversity and low abundance of beneficial bacteria in healthy control subjects carrying the IL23R (rs11209026) wild-type GG genotype indicates that the gut microbiome is influenced by host genetics and is altered prior to disease diagnosis. Fecal calprotectin may be a potential non-invasive screening tool for dysbiosis in subjects without disorders of intestinal inflammation.},
}
@article {pmid30445563,
year = {2018},
author = {Ramos-Sevillano, E and Wade, WG and Mann, A and Gilbert, A and Lambkin-Williams, R and Killingley, B and Nguyen-Van-Tam, JS and Tang, CM},
title = {The Effect of Influenza Virus on the Human Oropharyngeal Microbiome.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciy821},
pmid = {30445563},
issn = {1537-6591},
abstract = {Background: Secondary bacterial infections are an important cause of morbidity and mortality associated with influenza infections. As bacterial disease can be caused by a disturbance of the host microbiome, we examined the impact of influenza on the upper respiratory tract microbiome in a human challenge study.<br><br>Methods: The dynamics and ecology of the throat microbiome were examined following an experimental influenza challenge of 52 previously-healthy adult volunteers with influenza A/Wisconsin/67/2005 (H3N2) by intranasal inoculation; 35 healthy control subjects were not subjected to the viral challenge. Serial oropharyngeal samples were taken over a 30-day period, and the V1-V3 region of the bacterial 16S ribosomal RNA sequences were amplified and sequenced to determine the composition of the microbiome. The carriage of pathogens was also detected.<br><br>Results: Of the 52 challenged individuals, 43 developed proven influenza infections, 33 of whom became symptomatic. None of the controls developed influenza, although 22% reported symptoms. The diversity of bacterial communities remained remarkably stable following the acquisition of influenza, with no significant differences over time between individuals with influenza and those in the control group. Influenza infection was not associated with perturbation of the microbiome at the level of phylum or genus. There was no change in colonization rates with Streptococcus pneumoniae or Neisseria meningitidis.<br><br>Conclusions: The throat microbiota is resilient to influenza infection, indicating the robustness of the upper-airway microbiome.},
}
@article {pmid30445178,
year = {2018},
author = {Ozkan, J and Willcox, M and Wemheuer, B and Wilcsek, G and Coroneo, M and Thomas, T},
title = {Biogeography of the human ocular microbiota.},
journal = {The ocular surface},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtos.2018.11.005},
pmid = {30445178},
issn = {1937-5913},
abstract = {PURPOSE: The human eye is composed of numerous microhabitats. The aim of this study was to understand the communality and differences in the microbiomes of various regions of the eye.<br><br>METHODS: Four ocular sites from different subject groups were assessed including the eyelid margin tissue from patients with lid abnormalities (n = 20), fornix and limbus conjunctival tissue from patients with pterygia (n = 23), ocular (conjunctival) surface swabs (n = 45) and facial skin swabs (n = 16). Microbial communities were analysed by extracting total DNA from samples and sequencing the 16S ribosomal(r)RNA gene using the Illumina MiSeq platform. Sequences were quality filtered, clustered into unique sequences (zOTUs) using the UNOISE pipeline in USEARCH and taxonomically classified using SILVA.<br><br>RESULTS: A difference in bacterial richness and diversity was found between sites (P < 0.001) and for age (P < 0.035) but not for sex (P > 0.05). There was a difference in bacterial community structure and composition between sites (P < 0.001). Bacterial distribution could be broadly classified into three groups - zOTUs resident on the skin and lid margin but with low abundances at other sites (Corynebacterium, Staphylococcus), zOTUs found mainly on the ocular surface (Acinetobacter, Aeribacillus) and zOTUs mostly present in the conjunctiva and lid margin (Pseudomonas).<br><br>CONCLUSION: The microhabitats of the human eye (ocular surface, conjunctiva, lid margin and skin) have a distinct bacterial biogeography with some bacteria shared between multiple regions while other bacteria occupy a more confined niche.},
}
@article {pmid30445141,
year = {2018},
author = {Avgerinos, KI and Spyrou, N and Mantzoros, CS and Dalamaga, M},
title = {Obesity and Cancer Risk: Emerging biological mechanisms and perspectives.},
journal = {Metabolism: clinical and experimental},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.metabol.2018.11.001},
pmid = {30445141},
issn = {1532-8600},
abstract = {Continuously rising trends in obesity-related malignancies render this disease spectrum a public health priority. Worldwide, the burden of cancer attributable to obesity, expressed as population attributable fraction, is 11.9% in men and 13.1% in women. There is convincing evidence that excess body weight is associated with an increased risk for cancer of at least 13 anatomic sites, including endometrial, esophageal, renal and pancreatic adenocarcinomas; hepatocellular carcinoma; gastric cardia cancer; meningioma; multiple myeloma; colorectal, postmenopausal breast, ovarian, gallbladder and thyroid cancers. We first synopsize current epidemiologic evidence; the obesity paradox in cancer risk and mortality; the role of weight gain and weight loss in the modulation of cancer risk; reliable somatometric indicators for obesity and cancer research; and gender differences in obesity related cancers. We critically summarize emerging biological mechanisms linking obesity to cancer encompassing insulin resistance and abnormalities of the IGF-I system and signaling; sex hormones biosynthesis and pathway; subclinical chronic low-grade inflammation and oxidative stress; alterations in adipokine pathophysiology; factors deriving from ectopic fat deposition; microenvironment and cellular perturbations including vascular perturbations, epithelial-mesenchymal transition, endoplasmic reticulum stress and migrating adipose progenitor cells; disruption of circadian rhythms; dietary nutrients; factors with potential significance such as the altered intestinal microbiome; and mechanic factors in obesity and cancer. Future perspectives regarding prevention, diagnosis and therapeutics are discussed. The aim of this review is to investigate how the interplay of these main potential mechanisms and risk factors, exerts their effects on target tissues provoking them to acquire a cancerous phenotype.},
}
@article {pmid30445014,
year = {2018},
author = {Albaugh, VL and Banan, B and Antoun, J and Xiong, Y and Guo, Y and Ping, J and Alikhan, M and Clements, BA and Abumrad, NN and Flynn, CR},
title = {Role of Bile Acids and GLP-1 in Mediating the Metabolic Improvements of Bariatric Surgery.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2018.11.017},
pmid = {30445014},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: Bile diversion to the ileum (GB-IL) has strikingly similar metabolic and satiating effects to Roux-en-Y gastric bypass (RYGB) in rodent obesity models. The metabolic benefits of these procedures are thought to be mediated by increased bile acids, though parallel changes in body weight and other confounding variables limits this interpretation.<br><br>METHODS: Global G protein-coupled bile acid receptor-1 null (Tgr5-/-) and intestinal-specific farnesoid X receptor null (FxrΔ/E) mice on high-fat diet as well as wild-type C57BL/6 and glucagon-like polypeptide 1 receptor deficient (Glp-1r-/-) mice on chow diet were characterized following bile diversion to the ileum (GB-IL).<br><br>RESULTS: GB-IL induced weight loss and improved oral glucose tolerance in HFD-fed Tgr5-/-, but not FxrΔ/E mice, suggesting a role for intestinal Fxr. GB-IL in wild-type, chow-fed mice prompted weight-independent improvements in glycemia and glucose tolerance secondary to augmented insulin responsiveness. Improvements were concomitant with increased levels of lymphatic GLP-1 in the fasted state and increased levels of intestinal Akkermansia muciniphila. Improvements in fasting glycemia after GB-IL were mitigated with Ex-9, a GLP-1 receptor antagonist, or cholestyramine, a bile acid sequestrant. The glucoregulatory effects of GB-IL were lost in whole body Glp-1r-/- mice.<br><br>CONCLUSIONS: Bile diversion to the ileum improves glucose homeostasis via an intestinal Fxr-Glp-1 axis. Altered intestinal bile acid availability, independent of weight loss, and intestinal Akkermansia muciniphila appear to mediate the metabolic changes observed after bariatric surgery and might be manipulated for treatment of obesity and diabetes.},
}
@article {pmid30444291,
year = {2018},
author = {O'Malley, D},
title = {Endocrine regulation of gut function - a role for glucagon-like peptide-1 in the pathophysiology of irritable bowel syndrome.},
journal = {Experimental physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/EP087443},
pmid = {30444291},
issn = {1469-445X},
abstract = {NEW FINDINGS: Pathophysiological changes linked to Irritable Bowel Syndrome (IBS) include stress and immune activation, changes in gastrointestinal microbial and bile acids profiles and sensitisation of extrinsic and intrinsic gut neurons. This review explores the potential role for L-cells in these pathophysiological changes. L-cells, which secrete glucagon-like peptide-1 (GLP-1) in response to nutrients, microbial factors, bile acids and short-chain fatty acids, may sense IBS-related changes in the luminal environment. Glucagon-like peptide 1 can act as a hormone, a paracrine factor or a neuromodulatory factor and through its actions on central or peripheral neurons, may play a role in gastrointestinal dysfunction.<br><br>ABSTRACT: The prevalent and debilitating functional bowel disorder Irritable Bowel Syndrome (IBS), is characterized by symptoms which include abdominal pain, bloating, diarrhoea and/or constipation. The heterogeneity of IBS underscores a complex multifactorial pathophysiology, which is not completely understood, but involves dysfunction of the bidirectional signalling axis between the brain and the gut. This axis incorporates efferent and afferent branches of the autonomic nervous system, circulating endocrine hormones and immune factors, local paracrine and neurocrine factors and microbial metabolites. L-cells, which are electrically excitable biosensors embedded in the gastrointestinal epithelium, secrete glucagon-like peptide-1 (GLP-1) in response to nutrients in the small intestine. However, they appear to function differently more distally in the gastrointestinal tract, where they are activated by luminal factors including short-chain fatty acids, bile acids and microbial metabolic products, all of which are altered in IBS patients. GLP-1 can also interact with the hypothalamic-pituitary-adrenal stress axis and immune system, both of which are activated in IBS. Given that a GLP-1 mimetic has been found to alleviate acute pain symptoms in IBS patients, GLP-1 may be important in the manifestation of IBS symptoms. This review assessed the current knowledge on the role of GLP-1 in IBS pathophysiology and its potential role as a signal transducer in the microbiome-gut-brain signalling axis. This article is protected by copyright. All rights reserved.},
}
@article {pmid30444134,
year = {2018},
author = {Adolph, TE and Effenberger, M and Tilg, H},
title = {How our understanding of the microbiome has changed the way we look at liver diseases.},
journal = {Biomarkers in medicine},
volume = {},
number = {},
pages = {},
doi = {10.2217/bmm-2018-0266},
pmid = {30444134},
issn = {1752-0371},
}
@article {pmid30443963,
year = {2018},
author = {Hattori, N and Niwa, T and Ishida, T and Kobayashi, K and Imai, T and Mori, A and Kimura, K and Mori, T and Asami, Y and Ushijima, T},
title = {Antibiotics Suppress Colon Tumorigenesis Through Inhibition of Aberrant DNA Methylation in an AOM/DSS Colitis Model.},
journal = {Cancer science},
volume = {},
number = {},
pages = {},
doi = {10.1111/cas.13880},
pmid = {30443963},
issn = {1349-7006},
abstract = {Chronic inflammation is involved in the development of colon cancer by inducing mutations and aberrant DNA methylation in colon epithelial cells. Furthermore, there is growing evidence showing that the colonic microbiota modulates the inflammation response in the host and influences colon tumorigenesis. However, the influence of the colonic microbiota on aberrant DNA methylation remains unknown. Here, we show the effect of colonic microbes on DNA methylation and tumorigenicity using a mouse model of human ulcerative colitis. Mice treated with azoxymethane (AOM) and dextran sulfate sodium (DSS) showed an increase in degree of colitis, as estimated by body weight, occult blood, and stool consistency/diarrhea at 2 weeks after treatment, but treatment with antibiotics markedly reduced the severity of the colitis. Although mucosal hyperplasia and increased inflammation-related genes were observed in the colonic epithelial cells of the AOM/DSS-treated mice, treatment with antibiotics abrogated these changes. In addition, treatment with antibiotics significantly decreased the number of mucosal nodules from 5.9 ± 5.3 to 0.2 ± 0.6 (P < 0.01) and area of occupancy from 50.1 ± 57.4 to 0.5 ± 1.4 mm2 (P < 0.01). Aberrant DNA methylation of three marker CpG islands (Cbln4, Fosb and Msx1) was induced by AOM/DSS treatment in colonic mucosae, but this increase was suppressed by 50% to 92% (P < 0.05) with antibiotic treatment. Microbiome analysis showed that this change was associated with a decrease of the Clostridium leptum subgroup. These data demonstrate that antibiotics suppressed tumorigenesis through inhibition of aberrant DNA methylation induced by chronic inflammation. This article is protected by copyright. All rights reserved.},
}
@article {pmid30443932,
year = {2018},
author = {Chen, J and Thomsen, M and Vitetta, L},
title = {Interaction of gut microbiota with dysregulation of bile acids in the pathogenesis of nonalcoholic fatty liver disease and potential therapeutic implications of probiotics.},
journal = {Journal of cellular biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/jcb.27635},
pmid = {30443932},
issn = {1097-4644},
abstract = {The intestinal microbiota is now recognised to play key roles in health due to its involvement in many aspects of human physiology. Disturbance in gut microbiota (dysbiosis) is thus associated with many diseases including nonalcoholic fatty liver disease (NAFLD) which includes nonalcoholic fatty liver and nonalcoholic steatohepatitis. The mechanisms for the effect of dysbiosis in NAFLD pathogenesis are not completely elucidated. Many explanations have been proposed to trigger dysbiosis, leading to NAFLD including inflammation, ethanol produced by the gut bacteria and lipotoxicity. Recently the roles of bile acids and nuclear receptors are highly regarded. It is well known that gut microbes produce enzymes that convert primary bile acids into secondary bile acids in the intestines. Several studies have demonstrated that disturbance of the intestinal microbiota leads to decreased synthesis of secondary bile acids, which in turn decreases activation of nuclear receptors such as farnesoid X receptor (FXR), pregnane X receptor, Takeda G-protein-coupled bile acid protein 5 and vitamin D receptor. These receptors are important in energy regulation and their dysregulation can cause NAFLD. Therefore, stimulation of nuclear receptors especially FXR has been extensively explored for the amelioration of NAFLD. However, paradoxical effects of nuclear receptor activation are a major problem for the clinical application of nuclear receptor stimuli. We further posit that microbiome restoration could be an alternative approach for the treatment of NAFLD. Several gut bacteria are now known to be involved in bile acid metabolism. It will be necessary to identify which one/ones is/are feasible. Careful selection of commensal bacteria for probiotics may lead to an effective therapy for NAFLD.},
}
@article {pmid30443602,
year = {2018},
author = {Hillmann, B and Al-Ghalith, GA and Shields-Cutler, RR and Zhu, Q and Gohl, DM and Beckman, KB and Knight, R and Knights, D},
title = {Evaluating the Information Content of Shallow Shotgun Metagenomics.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00069-18},
pmid = {30443602},
issn = {2379-5077},
abstract = {Although microbial communities are associated with human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes in such communities. While deep whole-metagenome shotgun (WMS) sequencing provides high taxonomic and functional resolution, it is often prohibitively expensive for large-scale studies. The prevailing alternative, 16S rRNA gene amplicon (16S) sequencing, often does not resolve taxonomy past the genus level and provides only moderately accurate predictions of the functional profile; thus, there is currently no widely accepted approach to affordable, high-resolution, taxonomic, and functional microbiome analysis. To address this technology gap, we evaluated the information content of shallow shotgun sequencing with as low as 0.5 million sequences per sample as an alternative to 16S sequencing for large human microbiome studies. We describe a library preparation protocol enabling shallow shotgun sequencing at approximately the same per-sample cost as 16S sequencing. We analyzed multiple real and simulated biological data sets, including two novel human stool samples with ultradeep sequencing of 2.5 billion sequences per sample, and found that shallow shotgun sequencing recovers more-accurate species-level taxonomic and functional profiles of the human microbiome than 16S sequencing. We discuss the inherent limitations of shallow shotgun sequencing and note that 16S sequencing remains a valuable and important method for taxonomic profiling of novel environments. Although deep WMS sequencing remains the gold standard for high-resolution microbiome analysis, we recommend that researchers consider shallow shotgun sequencing as a useful alternative to 16S sequencing for large-scale human microbiome research studies where WMS sequencing may be cost-prohibitive. IMPORTANCE A common refrain in recent microbiome-related academic meetings is that the field needs to move away from broad taxonomic surveys using 16S sequencing and toward more powerful longitudinal studies using shotgun sequencing. However, performing deep shotgun sequencing in large longitudinal studies remains prohibitively expensive for all but the most well-funded research labs and consortia, which leads many researchers to choose 16S sequencing for large studies, followed by deep shotgun sequencing on a subset of targeted samples. Here, we show that shallow- or moderate-depth shotgun sequencing may be used by researchers to obtain species-level taxonomic and functional data at approximately the same cost as amplicon sequencing. While shallow shotgun sequencing is not intended to replace deep shotgun sequencing for strain-level characterization, we recommend that microbiome scientists consider using shallow shotgun sequencing instead of 16S sequencing for large-scale human microbiome studies.},
}
@article {pmid30443249,
year = {2018},
author = {Suwal, S and Wu, Q and Liu, W and Liu, Q and Sun, H and Liang, M and Gao, J and Zhang, B and Kou, Y and Liu, Z and Wei, Y and Wang, Y and Zheng, K},
title = {The Probiotic Effectiveness in Preventing Experimental Colitis Is Correlated With Host Gut Microbiota.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2675},
doi = {10.3389/fmicb.2018.02675},
pmid = {30443249},
issn = {1664-302X},
abstract = {Current evidence to support extensive use of probiotics in inflammatory bowel disease is limited and factors that contribute to the inconsistent effectiveness of clinical probiotic therapy are not completely known. Here, we used Bifidobacterium longum JDM 301 as a model probiotic to study potential factors that may influence the effect of probiotics in experimental colitis. We found that the effect of B. longum JDM 301 in tempering experimental colitis varied across individual mice even with the same genetic background. The probiotic efficacy was highly correlated with the host gut microbial community features. Consumption of a diet rich in fat could exacerbate mucosal injury-induced colitis but could not change the host responsiveness to B. longum JDM 301 treatment, suggesting of potential mechanistic differences between regulating colitis pathogenesis, and modulating probiotic efficacies by the gut microbiota. Together, our results suggest that personalized microbiome features may modify the probiotic therapeutic effect and support the idea of personalized probiotic medicine in inflammatory bowel disease.},
}
@article {pmid30443248,
year = {2018},
author = {Peng, M and Tabashsum, Z and Patel, P and Bernhardt, C and Biswas, D},
title = {Linoleic Acids Overproducing Lactobacillus casei Limits Growth, Survival, and Virulence of Salmonella Typhimurium and Enterohaemorrhagic Escherichia coli.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2663},
doi = {10.3389/fmicb.2018.02663},
pmid = {30443248},
issn = {1664-302X},
abstract = {Probiotics, particularly lactic acid bacteria, are biologic agents which limit the growth, virulence, and survival/colonization of various enteric bacterial pathogens and serve as potential alternatives to antibiotics. Mechanisms that contribute to this antimicrobial effect include producing bioactive metabolites/acids, increasing nutrient and receptor-mediated competition, and modulating gut microbiome ecology. However, these functions of common probiotic strains are limited due to the finite quantity of metabolites they produce and their total number in the gut ecosystem. Conjugated linoleic acids (CLAs), critical metabolites of Lactobacillus, have multiple beneficial effects on human health including anti-carcinogenesis, anti-inflammation, anti-oxidation, and anti-pathogenicity. In this study, we aim to overexpress the myosin cross-reactive antigen gene (mcra) in Lactobacillus casei (LC) to enhance the production of CLA and investigate its effectiveness against enteric bacterial pathogens, specifically Salmonella enterica serovar Typhimurium (ST) and enterohaemorrhagic Escherichia coli (EHEC). By inserting mcra in L. casei, we generated LC-CLA and found the total linoleic acid production by an individual bacterial cell was raised by 21-fold. The adherence ability of LC-CLA on human epithelial cells increased significantly and LC-CLA competitively excluded both ST and EHEC in a mixed-culture condition. Furthermore, LC-CLA significantly altered the physicochemical properties, biofilm formation abilities, interactions with host cells of both ST and EHEC, and triggered anti-inflammatory activities of host cells. These findings offer insights on applying a genetically engineered probiotic to control gut intestinal infections caused by ST and EHEC and prevent foodborne enteric illness in human.},
}
@article {pmid30443242,
year = {2018},
author = {O'Brien, PA and Smith, HA and Fallon, S and Fabricius, K and Willis, BL and Morrow, KM and Bourne, DG},
title = {Elevated CO2 Has Little Influence on the Bacterial Communities Associated With the pH-Tolerant Coral, Massive Porites spp.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2621},
doi = {10.3389/fmicb.2018.02621},
pmid = {30443242},
issn = {1664-302X},
abstract = {Ocean acidification (OA) as a result of increased anthropogenic CO2 input into the atmosphere carries consequences for all ocean life. Low pH can cause a shift in coral-associated microbial communities of pCO2-sensitive corals, however, it remains unknown whether the microbial community is also influenced in corals known to be more tolerant to high pCO2/low pH. This study profiles the bacterial communities associated with the tissues of the pCO2-tolerant coral, massive Porites spp., from two natural CO2 seep sites in Papua New Guinea. Amplicon sequencing of the hypervariable V3-V4 regions of the 16S rRNA gene revealed that microbial communities remained stable across CO2 seep sites (pH = 7.44-7.85) and adjacent control sites (ambient pH = 8.0-8.1). Microbial communities were more significantly influenced by reef location than pH, with the relative abundance of dominant microbial taxa differing between reefs. These results directly contrast with previous findings that increased CO2 has a strong effect on structuring microbial communities. The stable structure of microbial communities associated with the tissues of massive Porites spp. under high pCO2/low pH conditions confirms a high degree of tolerance by the whole Porites holobiont to OA, and suggest that pH tolerant corals such as Porites may dominate reef assemblages in an increasingly acidic ocean.},
}
@article {pmid30443241,
year = {2018},
author = {Chander, AM and Yadav, H and Jain, S and Bhadada, SK and Dhawan, DK},
title = {Cross-Talk Between Gluten, Intestinal Microbiota and Intestinal Mucosa in Celiac Disease: Recent Advances and Basis of Autoimmunity.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2597},
doi = {10.3389/fmicb.2018.02597},
pmid = {30443241},
issn = {1664-302X},
abstract = {Celiac disease (CD) is an autoimmune disorder of the small intestine, caused by gluten induced inflammation in some individuals susceptible to genetic and environmental influences. To date, pathophysiology of CD in relation to intestinal microbiota is not known well. This review relies on contribution of intestinal microbiome and oral microbiome in pathogenesis of CD based on their interactions with gluten, thereby highlighting the role of upper gastrointestinal microbiota. It has been hypothesized that CD might be triggered by additive effects of immunotoxic gluten peptides and intestinal dysbiosis (microbial imbalance) in the people with or without genetic susceptibilities, where antibiotics may be deriving dysbiotic agents. In contrast to the intestinal dysbiosis, genetic factors even seem secondary in disease outcome thus suggesting the importance of interaction between microbes and dietary factors in immune regulation at intestinal mucosa. Moreover, association of imbalanced counts of some commensal microbes in intestine of CD patients suggests the scope for probiotic therapies. Lactobacilli and specific intestinal and oral bacteria are potent source of gluten degrading enzymes (glutenases) that may contribute to commercialization of a novel glutenase therapy. In this review, we shall discuss advantages and disadvantages of food based therapies along with probiotic therapies where probiotic therapies are expected to emerge as the safest biotherapies among other in-process therapies. In addition, this review emphasizes on differential targets of probiotics that make them suitable to manage CD as along with glutenase activity, they also exhibit immunomodulatory and intestinal microbiome modulatory properties.},
}
@article {pmid30442926,
year = {2018},
author = {Vieira-Potter, VJ and Cross, TL and Swanson, KS and Sarma, SJ and Lei, Z and Sumner, LW and Rosenfeld, CS},
title = {Soy-Induced Fecal Metabolome Changes in Ovariectomized and Intact Female Rats: Relationship with Cardiometabolic Health.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16896},
doi = {10.1038/s41598-018-35171-3},
pmid = {30442926},
issn = {2045-2322},
support = {P50AT006273//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 1340058//National Science Foundation (NSF)/ ; 1139489//National Science Foundation (NSF)/ ; 1R01ES025547//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; },
abstract = {Phytoestrogens are plant-derived compounds found in a variety of foods, most notably, soy. These compounds have been shown to improve immuno-metabolic health, yet mechanisms remain uncertain. We demonstrated previously that dietary phytoestrogen-rich soy (SOY) rescued metabolic dysfunction/inflammation following ovariectomy (OVX) in female rats; we also noted remarkable shifts in gut microbiota in SOY vs control diet-fed rats. Importantly, specific bacteria that significantly increased in those fed the SOY correlated positively with several favorable host metabolic parameters. One mechanism by which gut microbes might lead to such host effects is through production of bacterial metabolites. To test this possibility, we utilized non-targeted gas chromatography-mass spectrometry (GCMS) to assess the fecal metabolome in those previously studied animals. Partial least square discriminant analysis (PLSDA) revealed clear separation of fecal metabolomes based on diet and ovarian state. In particular, SOY-fed animals had greater fecal concentrations of the beneficial bacterial metabolite, S-equol, which was positively associated with several of the bacteria upregulated in the SOY group. S-equol was inversely correlated with important indicators of metabolic dysfunction and inflammation, suggesting that this metabolite might be a key mediator between SOY and gut microbiome-positive host health outcomes.},
}
@article {pmid30442671,
year = {2018},
author = {Bor, B and McLean, JS and Foster, KR and Cen, L and To, TT and Serrato-Guillen, A and Dewhirst, FE and Shi, W and He, X},
title = {Rapid evolution of decreased host susceptibility drives a stable relationship between ultrasmall parasite TM7x and its bacterial host.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1810625115},
pmid = {30442671},
issn = {1091-6490},
abstract = {Around one-quarter of bacterial diversity comprises a single radiation with reduced genomes, known collectively as the Candidate Phyla Radiation. Recently, we coisolated TM7x, an ultrasmall strain of the Candidate Phyla Radiation phylum Saccharibacteria, with its bacterial host Actinomyces odontolyticus strain XH001 from human oral cavity and stably maintained as a coculture. Our current work demonstrates that within the coculture, TM7x cells establish a long-term parasitic association with host cells by infecting only a subset of the population, which stay viable yet exhibit severely inhibited cell division. In contrast, exposure of a naïve A. odontolyticus isolate, XH001n, to TM7x cells leads to high numbers of TM7x cells binding to each host cell, massive host cell death, and a host population crash. However, further passaging reveals that XH001n becomes less susceptible to TM7x over time and enters a long-term stable relationship similar to that of XH001. We show that this reduced susceptibility is driven by rapid host evolution that, in contrast to many forms of phage resistance, offers only partial protection. The result is a stalemate where infected hosts cannot shed their parasites; nevertheless, parasite load is sufficiently low that the host population persists. Finally, we show that TM7x can infect and form stable long-term relationships with other species in a single clade of Actinomyces, displaying a narrow host range. This system serves as a model to understand how parasitic bacteria with reduced genomes such as those of the Candidate Phyla Radiation have persisted with their hosts and ultimately expanded in their diversity.},
}
@article {pmid30442371,
year = {2018},
author = {Nocera, AL and Mueller, SK and Stephan, JR and Hing, L and Seifert, P and Han, X and Lin, DT and Amiji, MM and Libermann, T and Bleier, BS},
title = {Exosome swarms eliminate airway pathogens and provide passive epithelial immunoprotection through nitric oxide.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2018.08.046},
pmid = {30442371},
issn = {1097-6825},
abstract = {BACKGROUND: Nasal mucosa-derived exosomes (NMDEs) harbor immunodefensive proteins and are capable of rapid interepithelial protein transfer.<br><br>OBJECTIVES: We sought to determine whether mucosal exposure to inhaled pathogens stimulates a defensive swarm of microbiocidal exosomes, which also donate their antimicrobial cargo to adjacent epithelial cells.<br><br>METHODS: We performed an institutional review board-approved study of healthy NMDE secretion after Toll-like receptor (TLR) 4 stimulation by LPS (12.5 μg/mL) in the presence of TLR4 inhibitors. Interepithelial transfer of exosomal nitric oxide (NO) synthase and nitric oxide was measured by using ELISAs and NO activity assays. Exosomal antimicrobial assays were performed with Pseudomonas aeruginosa. Proteomic analyses were performed by using SOMAscan.<br><br>RESULTS: In vivo and in vitro LPS exposure induced a 2-fold increase in NMDE secretion along with a 2-fold increase in exosomal inducible nitric oxide synthase expression and function through TLR4 and inhibitor of nuclear factor κB kinase activation. LPS stimulation increased exosomal microbiocidal activity against P aeruginosa by almost 2 orders of magnitude. LPS-stimulated exosomes induced a 4-fold increase in NO production within autologous epithelial cells with protein transfer within 5 minutes of contact. Pathway analysis of the NMDE proteome revealed 44 additional proteins associated with NO signaling and innate immune function.<br><br>CONCLUSIONS: We provide direct in vivo evidence for a novel exosome-mediated innate immunosurveillance and defense mechanism of the human upper airway. These findings have implications for lower airway innate immunity, delivery of airway therapeutics, and host microbiome regulation.},
}
@article {pmid30442309,
year = {2018},
author = {Laha, T and Brindley, PJ and Suyapoh, W and Suttiprapa, S},
title = {RNA Interference as an Approach to Functional Genomics Genetic Manipulation of Opisthorchis viverrini.},
journal = {Advances in parasitology},
volume = {102},
number = {},
pages = {25-43},
doi = {10.1016/bs.apar.2018.06.001},
pmid = {30442309},
issn = {2163-6079},
abstract = {The availability of genome and transcriptome data of the liver fluke Opisthorchis viverrini provides the foundation for exploration of gene function and its effect on host-parasite interactions and pathogenesis of O. viverrini-associated bile duct cancer. Functional genomics approaches address the function of DNA at levels of the gene, RNA transcript and protein product using informative manipulations of the genome, epigenome, transcriptome, proteome, microbiome and metabolome. Advances in functional genomics for O. viverrini have thus far focused on RNA interference. The flukes have been transfected with double-stranded RNAs aiming to silence target gene expression. In general, this approach for functional genomics investigation of this pathogen has been found to be tractable and efficient: suppression of messenger RNA expression in O. viverrini results in reduction of protein activity and phenotypic changes. Future perspectives for functional genomics of this liver fluke and close phylogenetic relatives are also discussed.},
}
@article {pmid30442306,
year = {2018},
author = {Saltykova, IV and Petrov, VA and Brindley, PJ},
title = {Opisthorchiasis and the Microbiome.},
journal = {Advances in parasitology},
volume = {102},
number = {},
pages = {1-23},
doi = {10.1016/bs.apar.2018.07.001},
pmid = {30442306},
issn = {2163-6079},
abstract = {The liver flukes Opisthorchis viverrini, O. felineus, and Clonorchis sinensis are closely related fish-borne trematodes endemic in East Asia, Eurasia, and Siberia. Following ingestion, the parasites locate to the biliary tree, where chronic infection frequently leads to cholangiocarcinoma (CCA). Infection with C. sinensis or O. viverrini is classified as a Group 1 carcinogen by the International Agency for Research on Cancer. Infection with O. felineus may also be carcinogenic. The mechanism(s) by which infection with these liver flukes culminates in CCA remain elusive, although they are likely to be multi-factorial. Not yet well studied is the influence of opisthorchiasis on the microbiome of the host despite reports that helminth parasites are capable of affecting the microbiome, potentially modulating gastrointestinal inflammation in response to the appearance of pathogenic strains of bacteria. Here, we review recent findings related to opisthorchiasis and the microbiome and related issues. In the hamster, a tractable model of infection with liver fluke and of infection-induced biliary morbidity and CCA, infection with O. viverrini perturbs the microbiome of the gastrointestinal tract, including increasing numbers of Lachnospiraceae, Ruminococcaceae, Lactobacillaceae, and others, while decreasing Porphyromonadaceae, Erysipelotrichaceae, and Eubacteriaceae. In addition, a complex microbial community associates with the parasites within the biliary tree, including Helicobacter pylori and related bacteria. Moreover, higher rates of infection with Helicobacter occur in Thailand in persons with opisthorchiasis in a liver fluke infection intensity-dependent manner. Experimental infection of hamsters with Opisthorchis felineus results in increased alpha diversity of the microbiota diversity in the biliary tract. In humans, infection with O. felineus modifies the composition of the biliary microbiome, with increasing numbers of species of Klebsiella, Aggregatibacter, Lactobacillus, Treponema, and others. Several phylotypes of Archaea occurred solely in bile from persons infected with O. felineus.},
}
@article {pmid30442070,
year = {2018},
author = {Barnett, JA and Gibson, DL},
title = {H2Oh No! The importance of reporting your water source in your in vivo microbiome studies.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/19490976.2018.1539599},
pmid = {30442070},
issn = {1949-0984},
abstract = {Water is a fundamental part of any in vivo microbiome experiment however, it is also one of the most overlooked and underreported variables within the literature. Currently there is no established standard for drinking water quality set by the Canadian Council on Animal Care. Most water treatment methods focus on inhibiting bacterial growth within the water while prolonging the shelf-life of bottles once poured. When reviewing the literature, it is clear that some water treatment methods, such as water acidification, alter the gut microbiome of experimental animals resulting in dramatic differences in disease phenotype progression. Furthermore, The Jackson Lab, one of the world's leading animal vendors, provides acidified water to their in-house animals and is often cited in the literature as having a dramatically different gut microbiome than animals acquired from either Charles River or Taconic. While we recognize that it is impossible to standardize water across all animal facilities currently conducting microbiome research, we hope that by drawing attention to the issue in this commentary, researchers will consider water source as an experimental variable and report their own water sources to facilitate experimental reproducibility. Moreover, researchers should be cognisant of potential phenotypic differences observed between commercial animal vendors due to changes in the gut microbiome as a result of various sources of water used.},
}
@article {pmid30440884,
year = {2018},
author = {Gao, Z and Chen, KY and Mueller, O and Zhang, H and Rakhilin, N and Chen, J and Shen, X},
title = {Microbiota of Inflammatory Bowel Disease Models.},
journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference},
volume = {2018},
number = {},
pages = {2374-2377},
doi = {10.1109/EMBC.2018.8512848},
pmid = {30440884},
issn = {1557-170X},
abstract = {Gut microbiome plays an important role in inflammatory bowel disease (IBD), a group of intestinal chronic inflammation conditions that affect a large population. The animal models of IBD have long been established on basis of pathological features, but their ability to recapitulate patient gut microbiota is unknown. We investigated and compared the composition and biodiversity of bacterial population in the fecal samples from rat models of the two IBD subtypes, and compared them with patient samples. Our analyses revealed that inflammation reduces overall microbiome diversity and increased variation between individuals. We identified specific microbial signatures associated with the two IBD subtypes that were consistent between the animal models and human IBD patients, suggesting that the animal models can partially recapitulate the microbiota in human diseases. Furthermore, metagenome prediction analysis suggested microbial functions that were likely altered by host-microbiota interactions in IBD models.},
}
@article {pmid30440093,
year = {2018},
author = {Park, CH and Lee, AR and Lee, YR and Eun, CS and Lee, SK and Han, DS},
title = {Evaluation of gastric microbiome and metagenomic function in patients with intestinal metaplasia using 16S rRNA gene sequencing.},
journal = {Helicobacter},
volume = {},
number = {},
pages = {e12547},
doi = {10.1111/hel.12547},
pmid = {30440093},
issn = {1523-5378},
support = {//National Research Foundation of Korea (NRF)/ ; NRF-2017R1C1B5015928//Korea government (MSIP; Ministry of Science, ICT &amp; Future Planning)/ ; },
abstract = {BACKGROUND: Despite recent advances in studies on the gastric microbiome, the role of the non-Helicobacter pylori gastric microbiome in gastric carcinogenesis remains unclear. We evaluated the characteristics of the gastric microbiome and metagenomic functions in patients with IM.<br><br>METHODS: Participants were classified into six groups according to disease status (chronic superficial gastritis [CSG], intestinal metaplasia [IM], and cancer) and H. pylori- infection status (H. pylori-positive and H. pylori-negative). The gastric microbiome was analyzed in mucosal tissues at the gastric antrum by 16S rRNA gene sequencing. Moreover, we assessed the metagenome including the type IV secretion system (T4SS) gene, as T4SS proteins are essential for transferring CagA from H. pylori- into the human gastric epithelium.<br><br>RESULTS: Among the 138 included patients, 48, 9, 23, 14, 12, and 32 were classified into the H. pylori-negative CSG, H. pylori-negative IM, H. pylori-negative cancer, H. pylori-positive CSG, H. pylori-positive IM, and H. pylori-positive cancer groups, respectively. Cyanobacteria were predominant in the H. pylori-negative CSG group compared to in the H. pylori-negative IM and H. pylori-negative cancer groups (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 14.0% vs 4.2% vs 0.04%, P < 0.001). In contrast, Rhizobiales were commonly observed in the H. pylori-negative IM group (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 1.9% vs 15.4% vs 2.8%, P < 0.001). The relative abundance of Rhizobiales increased as H. pylori-infected stomachs progressed from gastritis to IM. In the H. pylori-negative IM group, genes encoding T4SS were prevalent among the metagenome. Additionally, after H. pylori- eradication therapy, the gastric microbiome was similar to the microbiome observed after spontaneous clearance of H. pylori-.<br><br>CONCLUSIONS: The relative abundance of Rhizobiales was higher in patients with H. pylori-negative IM than in those with H. pylori-negative CSG or cancer. Additionally, T4SS genes were highly observed in the metagenome of patients with IM. Highly abundant T4SS proteins in these patients may promote gastric carcinogenesis.},
}
@article {pmid30439937,
year = {2018},
author = {Jha, AR and Davenport, ER and Gautam, Y and Bhandari, D and Tandukar, S and Ng, KM and Fragiadakis, GK and Holmes, S and Gautam, GP and Leach, J and Sherchand, JB and Bustamante, CD and Sonnenburg, JL},
title = {Gut microbiome transition across a lifestyle gradient in Himalaya.},
journal = {PLoS biology},
volume = {16},
number = {11},
pages = {e2005396},
doi = {10.1371/journal.pbio.2005396},
pmid = {30439937},
issn = {1545-7885},
abstract = {The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle. Whether shifts away from the foraging lifestyle that characterize much of humanity's past influence the gut microbiome, and to what degree, remains unclear. Here, we characterize the stool bacterial composition of four Himalayan populations to investigate how the gut community changes in response to shifts in traditional human lifestyles. These groups led seminomadic hunting-gathering lifestyles until transitioning to varying levels of agricultural dependence upon farming. The Tharu began farming 250-300 years ago, the Raute and Raji transitioned 30-40 years ago, and the Chepang retain many aspects of a foraging lifestyle. We assess the contributions of dietary and environmental factors on their gut-associated microbes and find that differences in the lifestyles of Himalayan foragers and farmers are strongly correlated with microbial community variation. Furthermore, the gut microbiomes of all four traditional Himalayan populations are distinct from that of the Americans, indicating that industrialization may further exacerbate differences in the gut community. The Chepang foragers harbor an elevated abundance of taxa associated with foragers around the world. Conversely, the gut microbiomes of the populations that have transitioned to farming are more similar to those of Americans, with agricultural dependence and several associated lifestyle and environmental factors correlating with the extent of microbiome divergence from the foraging population. The gut microbiomes of Raute and Raji reveal an intermediate state between the Chepang and Tharu, indicating that divergence from a stereotypical foraging microbiome can occur within a single generation. Our results also show that environmental factors such as drinking water source and solid cooking fuel are significantly associated with the gut microbiome. Despite the pronounced differences in gut bacterial composition across populations, we found little differences in alpha diversity across lifestyles. These findings in genetically similar populations living in the same geographical region establish the key role of lifestyle in determining human gut microbiome composition and point to the next challenging steps of determining how large-scale gut microbiome reconfiguration impacts human biology.},
}
@article {pmid30431239,
year = {2018},
author = {Berry, D},
title = {Up-close-and-personal with the human microbiome.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12709},
pmid = {30431239},
issn = {1758-2229},
}
@article {pmid30430765,
year = {2018},
author = {Minakova, E and Warner, BB},
title = {Maternal immune activation, central nervous system development and behavioral phenotypes.},
journal = {Birth defects research},
volume = {},
number = {},
pages = {},
doi = {10.1002/bdr2.1416},
pmid = {30430765},
issn = {2472-1727},
support = {MD-II-2018-725//Children's Discovery Institute at Washington University in St. Louis/ ; },
abstract = {Maternal immune activation (MIA) refers to a maternal immune system triggered by infectious or infectious-like stimuli. A cascade of cytokines and immunologic alterations are transmitted to the fetus, resulting in adverse phenotypes most notably in the central nervous system. Epidemiologic studies implicate maternal infections in a variety of neuropsychiatric disorders, most commonly autism spectrum disorders and schizophrenia. In animal models, MIA causes neurochemical and anatomic changes in the brain that correspond to those found in humans with the disorders. As our understanding of the interactions between environment, genetics, and immune system grows, the role of alternative, noninfectious risk factors, such as prenatal stress, obesity, and the gut microbiome also becomes clearer. This review considers how infectious and noninfectious etiologies activate the maternal immune system. Their impact on fetal programming and neuropsychiatric disorders in offspring is examined in the context of human and animal studies.},
}
@article {pmid30430538,
year = {2018},
author = {Frew, JW},
title = {Complement, Hidradenitis Suppurativa and Pathogen-Driven Positive Selection.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bjd.17426},
pmid = {30430538},
issn = {1365-2133},
abstract = {The precise pathogenesis of Hidradenitis Suppurativa (HS) remains unclear. Kanni et al1 provides novel data implicating C5a and the membrane attack complex in HS pathogenesis. This opens the possibility of therapeutic blockade of C5a for the treatment of HS, although the results do require replication in larger patient cohorts. The current HS pathogenic paradigm involves dysregulation of the Th17:T-reg axis with contribution from genetic polymorphisms, metabolic syndrome, the microbiome and smoking, so data implicating complement is somewhat unexpected, stimulating the need for reconsideration of the current pathogenic paradigm. This article is protected by copyright. All rights reserved.},
}
@article {pmid30430061,
year = {2018},
author = {Schultz, J and Schröttner, P and Leupold, S and Dragu, A and Sußmann, S and Haase, M and Fitze, G},
title = {Conservative treatment of fingertip injuries in children - first experiences with a novel silicone finger cap that enables woundfluid analysis.},
journal = {GMS Interdisciplinary plastic and reconstructive surgery DGPW},
volume = {7},
number = {},
pages = {Doc05},
doi = {10.3205/iprs000125},
pmid = {30430061},
issn = {2193-8091},
abstract = {Introduction: Human fingertips are able to regenerate soft tissue and skin after amputation injuries with excellent cosmetic and functional results when treated with semiocclusive dressings. Despite bacterial colonizations, proceeding infections are not reported with this management. The underlying mechanisms for this form of regenerative healing as well as for the resilience to infections are not known. Due to the lack of mechanical protection, the leakage of maloderous woundfluid and the sometimes challenging application, conventional film dressings have their problems, especially in treating young children. We therefore treated selected patients with a novel silicone finger cap with an integrated wound fluid reservoir that enables atraumatic routine wound fluid aspiration. Methods: We report on 34 patients in between 1 and 13 years with traumatic fingertip amputations primarily treated with occlusive dressings. 12 patients were treated with a novel silicone finger cap. We summarized clinical data for each patient. This included photographs and microbiological results from wound fluid analyses, whenever available. Results: The results of both, conventional film dressing and silicone finger cap treatment, were excellent with no hypersensitivity and no restrictions in sensibility and motility. Even larger pulp defects were rearranged in a round shape and good soft tissue coverage of the distal phalanx was achieved. Nail deformities were not observed. We detected a wide spectrum of both aerobic and anaerobic bacteria in the wound fluids but infections were not observed. Epithelialization times did not differ significantly and no severe complications were seen in all primarily conservatively treated patients. Conclusion: This study provides preliminary data demonstrating that the treatment with the silicone finger cap leads to excellent clinical results in wound healing. Interestingly, the wounds were colonized with a wide range of bacteria including species that may cause wound infections. However, we saw no proceeding inflammation and the regeneration was undisturbed. In the future, the efficacy of this new management should be evaluated in randomized, controlled clinical trials to confirm the results under standard conditions and get more insight into the role of the wound microbiome as well as other factors that may promote regeneration. The aspirable Reservoir of the finger cap will enable easy atraumatic sampling of wound fluids both for diagnostic and for research purposes as well as possibly allowing direct administration of pro-regenerative drugs in the future.},
}
@article {pmid30429843,
year = {2018},
author = {Chen, C and Huang, X and Fang, S and Yang, H and He, M and Zhao, Y and Huang, L},
title = {Contribution of Host Genetics to the Variation of Microbial Composition of Cecum Lumen and Feces in Pigs.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2626},
doi = {10.3389/fmicb.2018.02626},
pmid = {30429843},
issn = {1664-302X},
abstract = {Pigs are a perfect model for studying the interaction between host genetics and gut microbiome due to the high similarity of gastrointestine and digestive system with humans, and the easily controlled feeding conditions. In this study, two pig populations which were raised in uniformed farm conditions and provided with the same commercial formula diet were used as the experimental animals. A systematical investigation of host genetic effect on the gut microbial composition was separately performed in porcine cecum lumen and feces samples through the comparison of microbial composition among full-sibs, half-sibs and unrelated members, heritability estimate (h2), and genome-wide association study (GWAS). The results showed that full-sib members had a higher similarity of microbial composition than unrelated individuals. A significant correlation was observed between the microbial composition-based kinship and the host SNP-based kinship in both populations (P < 9.9 × 10-5). We identified 81 and 67 microbial taxa having h2 > 0.15 in fecal and cecum luminal samples, respectively, including 31 taxa with h2 > 0.15 in both types of samples. GWAS identified 40 and 34 significant associations between host genomic loci and the abundance or presence/absence of bacterial taxa in the fecal and cecum luminal samples. Functional classifications of host candidate genes related to microbial taxa are mainly associated with metabolism, immunity functions and response, and signal transduction. The high similarity of heritable taxa and functional categories of candidate genes among pig, human and mouse suggests the similar mechanism of the host genetic effect on gut microbiome across mammalian species. The results from this study provided another evidence that host genetics contributes significantly to the gut microbiome.},
}
@article {pmid30429840,
year = {2018},
author = {Mas-Carrió, E and Dini-Andreote, F and Brossi, MJL and Salles, JF and Olff, H},
title = {Organic Amendment Under Increasing Agricultural Intensification: Effects on Soil Bacterial Communities and Plant Productivity.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2612},
doi = {10.3389/fmicb.2018.02612},
pmid = {30429840},
issn = {1664-302X},
abstract = {The soil microbiome is a complex living network that plays essential roles in agricultural systems, regardless of the level of intensification. However, the effects of agricultural management on the soil microbiome and the association with plant productivity remain largely unclear. Here, we studied the responses of three soil systems displaying distinct levels of agriculture intensiveness (i.e., natural, organic, and conventional soil management regimes) to experimentally manipulated organic farming amendments (i.e., dung and earthworms). We aimed at (i) identifying the effect on plant productivity and (ii) elucidating the degree of shifts in bacterial communities in response to the applied organic amendments. We found plant productivity to be lower with increasing agricultural intensification. Bacterial communities shifted distinctively for each soil management regime to the organic amendments applied. In brief, greater changes were observed in the Conventional management comparatively to the Organic and Natural management, an effect largely driven by dung addition. Moreover, we found evidence that the level of agricultural intensiveness also affects the timespan for these shifts. For instance, while the Natural system reached a relatively stable community composition before the end of the experiment, treatments on the conventional soil management regime did not. Random forest analyses further revealed an increasing impact of introduced taxa from dung addition aligned with increasing agricultural intensification. These analyses suggested that earthworms regulate the introduction of species from dung into the soil bacterial community. Collectively, our results contribute to a better understanding of the outcomes of organic amendments on soils under distinct levels of agriculture intensiveness, with implications for further development in soil restorations practices.},
}
@article {pmid30429832,
year = {2018},
author = {Bruno, A and Sandionigi, A and Bernasconi, M and Panio, A and Labra, M and Casiraghi, M},
title = {Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy).},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2557},
doi = {10.3389/fmicb.2018.02557},
pmid = {30429832},
issn = {1664-302X},
abstract = {While safe and of high quality, drinking water can host an astounding biodiversity of microorganisms, dismantling the belief of its &quot;biological simplicity.&quot; During the very few years, we are witnessing an exponential growth in scientific publications, exploring the ecology hidden in drinking water treatment plants (DWTPs) and drinking water distribution system (DWDS). We focused on what happens to the microbial communities from source water (groundwater) throughout the main steps of the potabilization process of a DWTP, located in an urbanized area in Northern Italy. Samples were processed by a stringent water filtration to retain even the smallest environmental bacteria and then analyzed with High-Throughput DNA Sequencing (HTS) techniques. We showed that carbon filters harbored a microbial community seeding and shaping water microbiota downstream, introducing a significant variation on incoming (groundwater) microbial community. Chlorination did not instantly affect the altered microbiota. We were also able to correctly predict (through machine learning analysis) samples belonging to groundwater (overall accuracy was 0.71), but the assignation was not reliable with carbon filter samples, which were incorrectly predicted as chlorination samples. The presence and abundance of specific microorganisms allowed us to hypothesize their role as indicators. In particular, Candidatus Adlerbacteria (Parcubacteria), together with microorganisms belonging to Alphaproteobacteria and Gammaproteobacteria, characterized treated water, but not raw water. An exception, confirming our hypothesis, is given by the samples downstream the filters renewal, which had a composition resembling groundwater. Volatility analysis illustrated how carbon filters represented an ecosystem that is stable over time, probably bearing the environmental conditions that promote the survival and growth of this peculiar microbial community.},
}
@article {pmid30429801,
year = {2018},
author = {Kennedy, EA and King, KY and Baldridge, MT},
title = {Mouse Microbiota Models: Comparing Germ-Free Mice and Antibiotics Treatment as Tools for Modifying Gut Bacteria.},
journal = {Frontiers in physiology},
volume = {9},
number = {},
pages = {1534},
doi = {10.3389/fphys.2018.01534},
pmid = {30429801},
issn = {1664-042X},
abstract = {As the intestinal microbiota has become better appreciated as necessary for maintenance of physiologic homeostasis and also as a modulator of disease processes, there has been a corresponding increase in manipulation of the microbiota in mouse models. While germ-free mouse models are generally considered to be the gold standard for studies of the microbiota, many investigators turn to antibiotics treatment models as a rapid, inexpensive, and accessible alternative. Here we describe and compare these two approaches, detailing advantages and disadvantages to both. Further, we detail what is known about the effects of antibiotics treatment on cell populations, cytokines, and organs, and clarify how this compares to germ-free models. Finally, we briefly describe recent findings regarding microbiota regulation of infectious diseases and other immunologic challenges by the microbiota, and highlight important future directions and considerations for the use of antibiotics treatment in manipulation of the microbiota.},
}
@article {pmid30429438,
year = {2018},
author = {Takeuchi, K and Asakawa, M and Hashiba, T and Takeshita, T and Saeki, Y and Yamashita, Y},
title = {Effects of xylitol-containing chewing gum on the oral microbiota.},
journal = {Journal of oral science},
volume = {},
number = {},
pages = {},
doi = {10.2334/josnusd.17-0446},
pmid = {30429438},
issn = {1880-4926},
abstract = {In this interventional study, a randomized controlled trial was used to evaluate the short-term effects of xylitol-containing chewing gum on the salivary microbiota. In total, 70 healthy adult men recruited from the Japan Ground Self Defense Force participated in the study during a 2-day training at Yamaguchi camp, Yamaguchi Prefecture, Japan. The men were randomly divided into two groups: one group chewed two pieces of xylitol-containing chewing gum 7 times/day for 2 days (n = 34) and the other did not (n = 36). Baseline and follow-up stimulated saliva samples were collected and the salivary microbial composition was assessed using the 16S rRNA gene next-generation sequencing analysis. The total salivary bacterial count was quantified using a quantitative real-time PCR system. No statistically significant difference was found between the two groups regarding any parameter analyzed in the baseline samples; however, the follow-up samples of the test group showed significantly lower total salivary bacterial count than those of the control group. Conversely, no significant difference was observed in the overall composition of the salivary microbiota between the baseline and follow-up samples of the two groups. These results indicate that xylitol-containing chewing gum inhibits the increase in total salivary bacteria over a short time during which the salivary microbial composition is not affected.},
}
@article {pmid30429354,
year = {2018},
author = {Bodogai, M and O'Connell, J and Kim, K and Kim, Y and Moritoh, K and Chen, C and Gusev, F and Vaughan, K and Shulzhenko, N and Mattison, JA and Lee-Chang, C and Chen, W and Carlson, O and Becker, KG and Gurung, M and Morgun, A and White, J and Meade, T and Perdue, K and Mack, M and Ferrucci, L and Trinchieri, G and de Cabo, R and Rogaev, E and Egan, J and Wu, J and Biragyn, A},
title = {Commensal bacteria contribute to insulin resistance in aging by activating innate B1a cells.},
journal = {Science translational medicine},
volume = {10},
number = {467},
pages = {},
doi = {10.1126/scitranslmed.aat4271},
pmid = {30429354},
issn = {1946-6242},
abstract = {Aging in humans is associated with increased hyperglycemia and insulin resistance (collectively termed IR) and dysregulation of the immune system. However, the causative factors underlying their association remain unknown. Here, using &quot;healthy&quot; aged mice and macaques, we found that IR was induced by activated innate 4-1BBL+ B1a cells. These cells (also known as 4BL cells) accumulated in aging in response to changes in gut commensals and a decrease in beneficial metabolites such as butyrate. We found evidence suggesting that loss of the commensal bacterium Akkermansia muciniphila impaired intestinal integrity, causing leakage of bacterial products such as endotoxin, which activated CCR2+ monocytes when butyrate was decreased. Upon infiltration into the omentum, CCR2+ monocytes converted B1a cells into 4BL cells, which, in turn, induced IR by expressing 4-1BBL, presumably to trigger 4-1BB receptor signaling as in obesity-induced metabolic disorders. This pathway and IR were reversible, as supplementation with either A. muciniphila or the antibiotic enrofloxacin, which increased the abundance of A. muciniphila, restored normal insulin response in aged mice and macaques. In addition, treatment with butyrate or antibodies that depleted CCR2+ monocytes or 4BL cells had the same effect on IR. These results underscore the pathological function of B1a cells and suggest that the microbiome-monocyte-B cell axis could potentially be targeted to reverse age-associated IR.},
}
@article {pmid30429285,
year = {2018},
author = {Mahadik, K and Yadav, P and Bhatt, B and Shah, RA and Balaji, KN},
title = {Deregulated AUF1 Assists BMP-EZH2-Mediated Delayed Wound Healing during Candida albicans Infection.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {},
number = {},
pages = {},
doi = {10.4049/jimmunol.1800688},
pmid = {30429285},
issn = {1550-6606},
abstract = {Tissue repair is a complex process that necessitates an interplay of cellular processes, now known to be dictated by epigenetics. Intriguingly, macrophages are testimony to a large repertoire of evolving functions in this process. We identified a role for BMP signaling in regulating macrophage responses to Candida albicans infection during wound repair in a murine model. In this study, the RNA binding protein, AU-rich element-binding factor 1, was posttranslationally destabilized to bring about ubiquitin ligase, NEDD4-directed activation of BMP signaling. Concomitantly, PI3K/PKCδ mobilized the rapid phosphorylation of BMP-responsive Smad1/5/8. Activated BMP pathway orchestrated the elevated recruitment of EZH2 at promoters of genes assisting timely wound closure. In vivo, the repressive H3K27 trimethylation was observed to persist, accompanied by a robust upregulation of BMP pathway upon infection with C. albicans, culminating in delayed wound healing. Altogether, we uncovered the signaling networks coordinated by fungal colonies that are now increasingly associated with the infected wound microbiome, resulting in altered wound fate.},
}
@article {pmid30428546,
year = {2018},
author = {Limborg, MT and Heeb, P},
title = {Special Issue: Coevolution of Hosts and Their Microbiome.},
journal = {Genes},
volume = {9},
number = {11},
pages = {},
doi = {10.3390/genes9110549},
pmid = {30428546},
issn = {2073-4425},
abstract = {The evolution of life-history traits in plants and animals has taken place in the midst of complex microbial communities. [...].},
}
@article {pmid30406656,
year = {2018},
author = {Tuncil, YE and Thakkar, RD and Arioglu-Tuncil, S and Hamaker, BR and Lindemann, SR},
title = {Fecal Microbiota Responses to Bran Particles Are Specific to Cereal Type and In Vitro Digestion Methods That Mimic Upper Gastrointestinal Tract Passage.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.8b03469},
pmid = {30406656},
issn = {1520-5118},
abstract = {Although in vitro studies to identify interactions between food components and the colonic microbiota employ distinct methods to mimic upper gastrointestinal (GI) tract digestion, the effects of differences in protocols on fermentation have not been rigorously addressed. Here, we compared two widely used upper GI tract digestion methods on four different cereal brans in fermentations by fecal microbiota to test the hypotheses that (1) different methods are varyingly efficient in removing accessible starches and proteins from dietary components and (2) these result in cereal-specific differences in fermentation by fecal microbiota. Our results supported both hypotheses, in that the methods differed significantly in bran starch and protein retention and that the effects were cereal-specific. Furthermore, these differences impacted fermentation by the fecal microbiota of healthy donors, altering both short-chain fatty acid production and microbial community composition. These data suggest that digestion methods should be standardized across laboratories for in vitro fiber fermentation studies.},
}
@article {pmid30427852,
year = {2018},
author = {Brito, TL and Campos, AB and Bastiaan von Meijenfeldt, FA and Daniel, JP and Ribeiro, GB and Silva, GGZ and Wilke, DV and de Moraes, DT and Dutilh, BE and Meirelles, PM and Trindade-Silva, AE},
title = {The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0200437},
doi = {10.1371/journal.pone.0200437},
pmid = {30427852},
issn = {1932-6203},
abstract = {Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae &quot;clade I&quot; strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills' metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.},
}
@article {pmid30426401,
year = {2018},
author = {Ver Heul, A and Planer, J and Kau, AL},
title = {The Human Microbiota and Asthma.},
journal = {Clinical reviews in allergy &amp; immunology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12016-018-8719-7},
pmid = {30426401},
issn = {1559-0267},
support = {K08AI113184//National Institute of Allergy and Infectious Diseases (US)/ ; 5T32DK077653-27//National Institute of Diabetes and Digestive and Kidney Diseases/ ; Faculty Development Award//AAAAI Foundation/ ; },
abstract = {Over the last few decades, advances in our understanding of microbial ecology have allowed us to appreciate the important role of microbial communities in maintaining human health. While much of this research has focused on gut microbes, microbial communities in other body sites and from the environment are increasingly recognized in human disease. Here, we discuss recent advances in our understanding of host-microbiota interactions in the development and manifestation of asthma focusing on three distinct microbial compartments. First, environmental microbes originating from house dust, pets, and farm animals have been linked to asthma pathogenesis, which is often connected to their production of bioactive molecules such as lipopolysaccharide. Second, respiratory microbial communities, including newly appreciated populations of microbes in the lung have been associated with allergic airway inflammation. Current evidence suggests that the presence of particular microbes, especially Streptococcus, Haemophilus, and Morexella species within the airway may shape local immune responses and alter the severity and manifestations of airway inflammation. Third, the gut microbiota has been implicated in both experimental models and clinical studies in predisposing to asthma. There appears to be a &quot;critical window&quot; of colonization that occurs during early infancy in which gut microbial communities shape immune maturation and confer susceptibility to allergic airway inflammation. The mechanisms by which gut microbial communities influence lung immune responses and physiology, the &quot;gut-lung axis,&quot; are still being defined but include the altered differentiation of immune cell populations important in asthma and the local production of metabolites that affect distal sites. Together, these findings suggest an intimate association of microbial communities with host immune development and the development of allergic airway inflammation. Improved understanding of these relationships raises the possibility of microbiota-directed therapies to improve or prevent asthma.},
}
@article {pmid30425946,
year = {2018},
author = {David Spence, J},
title = {Advances in Stroke Prevention.},
journal = {Journal of translational internal medicine},
volume = {6},
number = {3},
pages = {105-114},
doi = {10.2478/jtim-2018-0024},
pmid = {30425946},
issn = {2450-131X},
abstract = {There have been recent advances in stroke prevention in nutrition, blood pressure control, antiplatelet therapy, anticoagulation, identification of high-risk asymptomatic carotid stenosis, and percutaneous closure of patent foramen ovale. There is evidence that the Mediterranean diet significantly reduces the risk of stroke and that B vitamins lower homocysteine, thus preventing stroke. The benefit of B vitamins to lower homocysteine was masked by harm from cyanocobalamin among study participants with impaired renal function; we should be using methylcobalamin instead of cyanocobalamin. Blood pressure control can be markedly improved by individualized therapy based on phenotyping by plasma renin and aldosterone. Loss of function mutations of CYP2D19 impair activation of clopidogrel and limits its efficacy; ticagrelor can avoid this problem. New oral anticoagulants that are not significantly more likely than aspirin to cause severe bleeding, and prolonged monitoring for atrial fibrillation (AF), have revolutionized the prevention of cardioembolic stroke. Most patients (~90%) with asymptomatic carotid stenosis are better treated with intensive medical therapy; the few that could benefit from stenting or endarterectomy can be identified by a number of approaches, the best validated of which is transcranial Doppler (TCD) embolus detection. Percutaneous closure of patent foramen ovale has been shown to be efficacious but should only be implemented in selected patients; they can be identified by clinical clues to paradoxical embolism and by TCD estimation of shunt grade. &quot;Treating arteries instead of treating risk factors,&quot; and recent findings related to the intestinal microbiome and atherosclerosis point the way to promising advances in future.},
}
@article {pmid30425923,
year = {2018},
author = {Berger, FK and Schwab, N and Glanemann, M and Bohle, RM and Gärtner, B and Groesdonk, HV},
title = {Flavonifractor (Eubacterium) plautii bloodstream infection following acute cholecystitis.},
journal = {IDCases},
volume = {14},
number = {},
pages = {e00461},
doi = {10.1016/j.idcr.2018.e00461},
pmid = {30425923},
issn = {2214-2509},
abstract = {Flavonifractor plautii (formerly Eubacterium plautii) is an anaerobic gram positive rod shaped bacterium belonging to the family of Clostridiales, and a common member of the human gut microbiome. However, it is very rarely isolated from clinical human specimens, so data about its clinical significance are scarce. Here we report of a bloodstream infection due to F. plautii following gangrenous cholecystitis in a 69 year old man. After cholecystectomy and empirical antimicrobial treatment with ceftriaxone and metronidazole the patient recovered. F. plautii was the only bacterium detected in blood culture, suggesting that it might have been causative for cholecystitis. Antimicrobial resistance testing identified decreased susceptibilities against linezolid and penicillin indicating that a targeted therapy might be necessary. F. plautii can be considered a potential pathogen for cholecystitis.},
}
@article {pmid30425894,
year = {2018},
author = {Ornelas-García, P and Pajares, S and Sosa-Jiménez, VM and Rétaux, S and Miranda-Gamboa, RA},
title = {Microbiome differences between river-dwelling and cave-adapted populations of the fish Astyanax mexicanus (De Filippi, 1853).},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5906},
doi = {10.7717/peerj.5906},
pmid = {30425894},
issn = {2167-8359},
abstract = {Symbiotic relationships between host and microbiome can play a major role in local adaptation. Previous studies with freshwater organisms have shown that microbiome performs numerous important biochemical functions for the host, playing a key role in metabolism, physiology or health. Experimental studies in fish groups have found an effect of enzymatic activity of gut microbiota on a variety of metabolic processes. The goal of this study was to compare stomach microbiome from cave and surface Astyanax mexicanus, in order to evaluate the potential response of microbiota to contrasting environmental conditions and physiological adaptations of the host. Stomach microbiota was obtained from three different populations: Pachón cave, and two surface rivers (Rascón and Micos rivers). The stomach microbiome was analyzed using the Ion 16S Metagenomic kit considering seven variable regions: V2, V3, V4, V6-7, V8 and V9. A high diversity was observed across samples, including 16 phyla, 120 families and 178 genera. Gammaproteobacteria, Firmicutes, Bacteroidetes and Betaproteobacteria were the most abundant phyla across the samples. Although the relative abundance of the core OTUs at genus level were highly contrasting among populations, we did not recover differences in stomach microbiome between contrasting habitats (cave vs. surface rivers). Rather, we observed a consistent association between β-diversity and dissolved oxygen concentration in water. Therefore, and unexpectedly, the microbiota of A. mexicanus is not linked with the contrasting conditions of the habitat considered here but is related to water parameters.},
}
@article {pmid30425805,
year = {2018},
author = {Ong, J and Bath, MF and Swift, C and Al-Naeeb, Y},
title = {Does colectomy affect the progression of primary sclerosing cholangitis? A systematic review and meta-analysis.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {11},
number = {4},
pages = {277-283},
pmid = {30425805},
issn = {2008-2258},
abstract = {Aim: The aim of this systematic review was to determine if the human colon, through the lower gut-liver axis, drives PSC activity by assessing the progression of the disease in patients with and without colectomy for colonic disease.<br><br>Background: The gut-liver axis is involved in the pathogenesis of liver disease. Abnormal immune-mediated responses to intestinal microbiome are implicated in primary sclerosing cholangitis (PSC) however the mechanisms remain poorly understood. Currently, no single animal model recapitulates all attributes of PSC in humans and this limits further studies of gut-liver interactions.<br><br>Methods: A systematic search of PubMed, Medline, and Scopus was performed for articles that contained the terms &quot;colectomy&quot; or &quot;bowel resection&quot; AND &quot;primary sclerosing cholangitis&quot; up to 15th April 2018. Articles were reviewed by 2 reviewers and raw data collated. A Forest plot was used to illustrate the effect of colectomy on subsequent liver transplantation for PSC. Linear regression was used to estimate mortality risk.<br><br>Results: Colectomy appeared to have no effect on PSC progression, although high-quality studies were lacking. Rates of liver transplantation or transjugular intrahepatic portosystemic shunt for PSC were not affected by colectomy (OR 0.59, 95% CI 0.14 - 2.53, p=0.48). Mortality risk following colectomy in patients with PSC is 2.11% per year (95% CI 0.03% - 4.18%, p=0.032, R2 = 0.722).<br><br>Conclusion: Current evidence is limited but suggests colectomy does not affect the progression of PSC in patients with colonic disease. Pathogenic micro-organisms or antigens that drive PSC may not be limited to the lower gut.},
}
@article {pmid30425700,
year = {2018},
author = {Hubert, J and Nesvorna, M and Sopko, B and Smrz, J and Klimov, P and Erban, T},
title = {Two Populations of Mites (Tyrophagus putrescentiae) Differ in Response to Feeding on Feces-Containing Diets.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2590},
doi = {10.3389/fmicb.2018.02590},
pmid = {30425700},
issn = {1664-302X},
abstract = {Background:Tyrophagus putrescentiae is a ubiquitous mite species in soil, stored products and house dust and infests food and causes allergies in people. T. putrescentiae populations harbor different bacterial communities, including intracellular symbionts and gut bacteria. The spread of microorganisms via the fecal pellets of T. putrescentiae is a possibility that has not been studied in detail but may be an important means by which gut bacteria colonize subsequent generations of mites. Feces in soil may be a vector for the spread of microorganisms. Methods: Extracts from used mite culture medium (i.e., residual food, mite feces, and dead mite bodies) were used as a source of feces-inhabiting microorganisms as food for the mites. Two T. putrescentiae populations (L and P) were used for experiments, and they hosted the intracellular bacteria Cardinium and Wolbachia, respectively. The effects of the fecal fraction on respiration in a mite microcosm, mite nutrient contents, population growth and microbiome composition were evaluated. Results: Feces from the P population comprised more than 90% Bartonella-like sequences. Feces from the L population feces hosted Staphylococcus, Virgibacillus, Brevibacterium, Enterobacteriaceae, and Bacillus. The mites from the P population, but not the L population, exhibited increased bacterial respiration in the microcosms in comparison to no-mite controls. Both L- and P-feces extracts had an inhibitory effect on the respiration of the microcosms, indicating antagonistic interactions within feces-associated bacteria. The mite microbiomes were resistant to the acquisition of new bacterial species from the feces, but their bacterial profiles were affected. Feeding of P mites on P-feces-enriched diets resulted in an increase in Bartonella abundance from 6 to 20% of the total bacterial sequences and a decrease in Bacillus abundance. The population growth was fivefold accelerated on P-feces extracts in comparison to the control. Conclusion: The mite microbiome, to a certain extent, resists the acquisition of new bacteria when mites are fed on feces of the same species. However, a Bartonella-like bacteria-feces-enriched diet seems to be beneficial for mite populations with symbiotic Bartonella-like bacteria. Coprophagy on the feces of its own population may be a mechanism of bacterial acquisition in T. putrescentiae.},
}
@article {pmid30425690,
year = {2018},
author = {Fang, X and Monk, JM and Nurk, S and Akseshina, M and Zhu, Q and Gemmell, C and Gianetto-Hill, C and Leung, N and Szubin, R and Sanders, J and Beck, PL and Li, W and Sandborn, WJ and Gray-Owen, SD and Knight, R and Allen-Vercoe, E and Palsson, BO and Smarr, L},
title = {Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2559},
doi = {10.3389/fmicb.2018.02559},
pmid = {30425690},
issn = {1664-302X},
abstract = {Dysbiosis of the gut microbiome, including elevated abundance of putative leading bacterial triggers such as E. coli in inflammatory bowel disease (IBD) patients, is of great interest. To date, most E. coli studies in IBD patients are focused on clinical isolates, overlooking their relative abundances and turnover over time. Metagenomics-based studies, on the other hand, are less focused on strain-level investigations. Here, using recently developed bioinformatic tools, we analyzed the abundance and properties of specific E. coli strains in a Crohns disease (CD) patient longitudinally, while also considering the composition of the entire community over time. In this report, we conducted a pilot study on metagenomic-based, strain-level analysis of a time-series of E. coli strains in a left-sided CD patient, who exhibited sustained levels of E. coli greater than 100X healthy controls. We: (1) mapped out the composition of the gut microbiome over time, particularly the presence of E. coli strains, and found that the abundance and dominance of specific E. coli strains in the community varied over time; (2) performed strain-level de novo assemblies of seven dominant E. coli strains, and illustrated disparity between these strains in both phylogenetic origin and genomic content; (3) observed that strain ST1 (recovered during peak inflammation) is highly similar to known pathogenic AIEC strains NC101 and LF82 in both virulence factors and metabolic functions, while other strains (ST2-ST7) that were collected during more stable states displayed diverse characteristics; (4) isolated, sequenced, experimentally characterized ST1, and confirmed the accuracy of the de novo assembly; and (5) assessed growth capability of ST1 with a newly reconstructed genome-scale metabolic model of the strain, and showed its potential to use substrates found abundantly in the human gut to outcompete other microbes. In conclusion, inflammation status (assessed by the blood C-reactive protein and stool calprotectin) is likely correlated with the abundance of a subgroup of E. coli strains with specific traits. Therefore, strain-level time-series analysis of dominant E. coli strains in a CD patient is highly informative, and motivates a study of a larger cohort of IBD patients.},
}
@article {pmid30425612,
year = {2018},
author = {Miller, I},
title = {The gut-brain axis: historical reflections.},
journal = {Microbial ecology in health and disease},
volume = {29},
number = {1},
pages = {1542921},
doi = {10.1080/16512235.2018.1542921},
pmid = {30425612},
issn = {0891-060X},
abstract = {The gut-brain axis and the microbiome have recently acquired an important position in explaining a wide range of human behaviours and emotions. Researchers have typically presented developments in understandings of the microbiome as radical and new, offering huge potential for better understandings of our bodies and what it means to be human. Without refuting the value of this research, this article insists that, traditionally, doctors and patients acknowledged the complex interactions between their guts and emotions, although using alternative models often based on nerves or psychology. For example, nineteenth-century doctors and patients would have been well acquainted with the idea that their stomachs and minds were somehow connected, and that this interaction could produce positive or negative physical and mental health impacts. To demonstrate this, this article offers a snapshot of medical and public thought on (what we currently call) the gut-brain axis in the nineteenth and twentieth centuries, using Britain as a key case study due to the prevalence of gastric problems in that country. It commences by exploring how nineteenth-century doctors and patients took for granted the intimate relations between gut and mind and used their ideas on this to debate personal health, medical theory and social and political discourse. The article then moves on to argue that various medical sub-disciplines emerged (anatomy, physiology, surgery) that threatened to reduce the stomach to a physiologically complex organ but, in doing so, inadvertently began to erase ideas of a gut-mind connection. However, these new models proved unsatisfactory, allowing more holistic ideas of the body-mind relationship to continue to carry currency in twentieth-century psychological and medical thought. In the late century, pharmacological developments once again threatened to minimise the gut-brain axis, before it once again became popular in the early twenty-first century, now debated through a new language of microbiology.},
}
@article {pmid30425247,
year = {2018},
author = {Hansen, LBS and Roager, HM and Søndertoft, NB and Gøbel, RJ and Kristensen, M and Vallès-Colomer, M and Vieira-Silva, S and Ibrügger, S and Lind, MV and Mærkedahl, RB and Bahl, MI and Madsen, ML and Havelund, J and Falony, G and Tetens, I and Nielsen, T and Allin, KH and Frandsen, HL and Hartmann, B and Holst, JJ and Sparholt, MH and Holck, J and Blennow, A and Moll, JM and Meyer, AS and Hoppe, C and Poulsen, JH and Carvalho, V and Sagnelli, D and Dalgaard, MD and Christensen, AF and Lydolph, MC and Ross, AB and Villas-Bôas, S and Brix, S and Sicheritz-Pontén, T and Buschard, K and Linneberg, A and Rumessen, JJ and Ekstrøm, CT and Ritz, C and Kristiansen, K and Nielsen, HB and Vestergaard, H and Færgeman, NJ and Raes, J and Frøkiær, H and Hansen, T and Lauritzen, L and Gupta, R and Licht, TR and Pedersen, O},
title = {A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {4630},
doi = {10.1038/s41467-018-07019-x},
pmid = {30425247},
issn = {2041-1723},
abstract = {Adherence to a low-gluten diet has become increasingly common in parts of the general population. However, the effects of reducing gluten-rich food items including wheat, barley and rye cereals in healthy adults are unclear. Here, we undertook a randomised, controlled, cross-over trial involving 60 middle-aged Danish adults without known disorders with two 8-week interventions comparing a low-gluten diet (2 g gluten per day) and a high-gluten diet (18 g gluten per day), separated by a washout period of at least six weeks with habitual diet (12 g gluten per day). We find that, in comparison with a high-gluten diet, a low-gluten diet induces moderate changes in the intestinal microbiome, reduces fasting and postprandial hydrogen exhalation, and leads to improvements in self-reported bloating. These observations suggest that most of the effects of a low-gluten diet in non-coeliac adults may be driven by qualitative changes in dietary fibres.},
}
@article {pmid30425147,
year = {2018},
author = {Su, X and Jing, G and McDonald, D and Wang, H and Wang, Z and Gonzalez, A and Sun, Z and Huang, S and Navas, J and Knight, R and Xu, J},
title = {Identifying and Predicting Novelty in Microbiome Studies.},
journal = {mBio},
volume = {9},
number = {6},
pages = {},
doi = {10.1128/mBio.02099-18},
pmid = {30425147},
issn = {2150-7511},
abstract = {With the expansion of microbiome sequencing globally, a key challenge is to relate new microbiome samples to the existing space of microbiome samples. Here, we present Microbiome Search Engine (MSE), which enables the rapid search of query microbiome samples against a large, well-curated reference microbiome database organized by taxonomic similarity at the whole-microbiome level. Tracking the microbiome novelty score (MNS) over 8 years of microbiome depositions based on searching in more than 100,000 global 16S rRNA gene amplicon samples, we detected that the structural novelty of human microbiomes is approaching saturation and likely bounded, whereas that in environmental habitats remains 5 times higher. Via the microbiome focus index (MFI), which is derived from the MNS and microbiome attention score (MAS), we objectively track and compare the structural-novelty and attracted-attention scores of individual microbiome samples and projects, and we predict future trends in the field. For example, marine and indoor environments and mother-baby interactions are likely to receive disproportionate additional attention based on recent trends. Therefore, MNS, MAS, and MFI are proposed &quot;alt-metrics&quot; for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.IMPORTANCE We introduce two concepts to quantify the novelty of a microbiome. The first, the microbiome novelty score (MNS), allows identification of microbiomes that are especially different from what is already sequenced. The second, the microbiome attention score (MAS), allows identification of microbiomes that have many close neighbors, implying that considerable scientific attention is devoted to their study. By computing a microbiome focus index based on the MNS and MAS, we objectively track and compare the novelty and attention scores of individual microbiome samples and projects over time and predict future trends in the field; i.e., we work toward yielding fundamentally new microbiomes rather than filling in the details. Therefore, MNS, MAS, and MFI can serve as &quot;alt-metrics&quot; for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.},
}
@article {pmid30424933,
year = {2018},
author = {Castillo-Álvarez, F and Marzo-Sola, ME},
title = {Disease of the holobiont, the example of multiple sclerosis.},
journal = {Medicina clinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.medcli.2018.08.019},
pmid = {30424933},
issn = {1578-8989},
abstract = {In recent years there has been a revolution regarding the role of the microbiota in different diseases, most of them within the spectrum of inflammatory and autoimmune diseases, associated with the development of metagenomics and the concept of holobiont, a large organism together with its microbiota. Specifically, in Multiple Sclerosis, multiple evidence points to the role of the microbiota in experimental autoimmune encephalomyelitis, animal model of the disease, and several articles have been published in recent years about differences in intestinal microbiota among patients with multiple sclerosis and control subjects. We review in this article the concept of holobiont and the gut microbiota functions, as well as the evidence accumulated about the role of the microbiota in experimental autoimmune encephalomyelitis and multiple sclerosis. Nowadays, there is a lot of evidence showing the role of the microbiota in the genesis, prevention and treatment of experimental autoimmune encephalomyelitis based mainly on three immunological pillars, the Th1-Th17 / Th2 balance, the Treg cells and the humoral immunity. It is also well documented that there are differences in the microbiota of patients with MS that are associated with a different expression of genes related to inflammation.},
}
@article {pmid30424824,
year = {2018},
author = {Haney, MM and Ericsson, AC and Lever, TE},
title = {Effects of Intraoperative Vagal Nerve Stimulation on the Gastrointestinal Microbiome in a Mouse Model of Amyotrophic Lateral Sclerosis.},
journal = {Comparative medicine},
volume = {},
number = {},
pages = {},
doi = {10.30802/AALAS-CM-18-000039},
pmid = {30424824},
issn = {1532-0820},
abstract = {The gastrointestinal microbiota (GM) plays a fundamental role in health and disease and contributes to the bidirectional signaling between the gastrointestinal system and brain. The direct line of communication between these organ systems is through the vagus nerve. Therefore, vagal nerve stimulation (VNS), a commonly used technique for multiple disorders, has potential to modulate the enteric microbiota, enabling investigation and possibly treatment of numerous neurologic disorders in which the microbiota has been linked with disease. Here we investigate the effect of VNS in a mouse model of amyotrophic lateral sclerosis (ALS). B6SJL-Tg(SOD1*G93A)dl1Gur (SOD1dl) and wildtype mice underwent ventral neck surgeryto access the vagus nerve. During surgery, the experimental group received 1 h of VNS, whereas the sham group underwent 1 h of sham treatment. The third (control) group did not undergo any surgical manipulation. Fecal samples were collected before surgery and at 8 d after the initial collection. Microbial DNA was sequenced to determine the GM profiles at both time points. GM profiles did not differ between genotypes at either the initial or end point. In addition, VNS did not alter GM populations, according to the parameters chosen in this study, indicating that this short intraoperative treatment is safeand has no lasting effects on the GM. Future studies are warranted to determine whether different stimulation parametersor chronic use of VNS affect GM profiles.},
}
@article {pmid30424821,
year = {2018},
author = {Singh, NK and Wood, JM and Karouia, F and Venkateswaran, K},
title = {Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {204},
doi = {10.1186/s40168-018-0585-2},
pmid = {30424821},
issn = {2049-2618},
support = {19-12829-26//2012 Space Biology NNH12ZTT001N/ ; },
abstract = {BACKGROUND: The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms.<br><br>RESULTS: The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii, and Aspergillus lentulus. Even though Rhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3. The AMR signatures associated with β-lactam, cationic antimicrobial peptide, and vancomycin were detected. Prominent virulence factors were cobalt-zinc-cadmium resistance and multidrug-resistance efflux pumps.<br><br>CONCLUSIONS: There was an increase in AMR and virulence gene factors detected over the period sampled, and metagenome sequences of human pathogens persisted over time. Comparative analysis of the microbial compositions of ISS with Earth analogs revealed that the ISS environmental surfaces were different in microbial composition. Metagenomics coupled with PMA treatment would help future space missions to estimate problematic risk group microbial pathogens. Cataloging AMR/virulence characteristics, succession, accumulation, and persistence of microorganisms would facilitate the development of suitable countermeasures to reduce their presence in the closed built environment.},
}
@article {pmid30424806,
year = {2018},
author = {Kaliannan, K and Robertson, RC and Murphy, K and Stanton, C and Kang, C and Wang, B and Hao, L and Bhan, AK and Kang, JX},
title = {Estrogen-mediated gut microbiome alterations influence sexual dimorphism in metabolic syndrome in mice.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {205},
doi = {10.1186/s40168-018-0587-0},
pmid = {30424806},
issn = {2049-2618},
abstract = {BACKGROUND: Understanding the mechanism of the sexual dimorphism in susceptibility to obesity and metabolic syndrome (MS) is important for the development of effective interventions for MS.<br><br>RESULTS: Here we show that gut microbiome mediates the preventive effect of estrogen (17β-estradiol) on metabolic endotoxemia (ME) and low-grade chronic inflammation (LGCI), the underlying causes of MS and chronic diseases. The characteristic profiles of gut microbiome observed in female and 17β-estradiol-treated male and ovariectomized mice, such as decreased Proteobacteria and lipopolysaccharide biosynthesis, were associated with a lower susceptibility to ME, LGCI, and MS in these animals. Interestingly, fecal microbiota-transplant from male mice transferred the MS phenotype to female mice, while antibiotic treatment eliminated the sexual dimorphism in MS, suggesting a causative role of the gut microbiome in this condition. Moreover, estrogenic compounds such as isoflavones exerted microbiome-modulating effects similar to those of 17β-estradiol and reversed symptoms of MS in the male mice. Finally, both expression and activity of intestinal alkaline phosphatase (IAP), a gut microbiota-modifying non-classical anti-microbial peptide, were upregulated by 17β-estradiol and isoflavones, whereas inhibition of IAP induced ME and LGCI in female mice, indicating a critical role of IAP in mediating the effects of estrogen on these parameters.<br><br>CONCLUSIONS: In summary, we have identified a previously uncharacterized microbiome-based mechanism that sheds light upon sexual dimorphism in the incidence of MS and that suggests novel therapeutic targets and strategies for the management of obesity and MS in males and postmenopausal women.},
}
@article {pmid30424722,
year = {2018},
author = {Sharaf, LK and Sharma, M and Chandel, D and Shukla, G},
title = {Prophylactic intervention of probiotics (L.acidophilus, L.rhamnosus GG) and celecoxib modulate Bax-mediated apoptosis in 1,2-dimethylhydrazine-induced experimental colon carcinogenesis.},
journal = {BMC cancer},
volume = {18},
number = {1},
pages = {1111},
doi = {10.1186/s12885-018-4999-9},
pmid = {30424722},
issn = {1471-2407},
abstract = {BACKGROUND: Colorectal cancer has been found to be attenuated either with prophylactic manipulation of gut microbiome with probiotics or celecoxib, a non-steroidal anti-inflammatory drug mainly by suppressing early pro-carcinogenic markers in various experimental studies. Therefore, the present study was designed to assess the prophylactic potential of combinatorial administration of probiotics (Lactobacillus rhamnosus GG, Lactobacillus acidophilus) and celecoxib in experimental colon carcinogenesis.<br><br>METHODS: Six groups of Spraugue Dawely rats received probiotics L.rhamnosus GG or/and L.acidophilus in combination with celecoxib one week prior to the inducement of tumor by 1,2-dimethylhydrazine (DMH) and the treatment continued for 18 weeks. Prophylactic potentials of probiotics and celecoxib were determined by employing various methods such as tumor incidence, tumor burden, tumor multiplicity, apoptosis, caspase activity, expression of proto-oncogene K-ras and tumor suppressor p53 gene in colonic tumors.<br><br>RESULTS: Interestingly, it was found that one week prior supplementation of both probiotics and celecoxib reduced tumor burden, tumor multiplicity, down-regulated the expression of anti-apoptotic Bcl-2, proto-oncogene K-ras and up-regulated pro-apoptotic Bax as well as tumor suppressor p53 in L.rhamnosus GG + celecoxib+DMH animals compared with counter controls and DMH-treated.<br><br>CONCLUSIONS: It can be concluded that such combinatorial approach may be useful in reducing the burden and severity of disease in highly susceptible individuals but needs to be validated clinically.},
}
@article {pmid30424581,
year = {2018},
author = {Teschke, R},
title = {Alcoholic Liver Disease: Alcohol Metabolism, Cascade of Molecular Mechanisms, Cellular Targets, and Clinical Aspects.},
journal = {Biomedicines},
volume = {6},
number = {4},
pages = {},
doi = {10.3390/biomedicines6040106},
pmid = {30424581},
issn = {2227-9059},
abstract = {Alcoholic liver disease is the result of cascade events, which clinically first lead to alcoholic fatty liver, and then mostly via alcoholic steatohepatitis or alcoholic hepatitis potentially to cirrhosis and hepatocellular carcinoma. Pathogenetic events are linked to the metabolism of ethanol and acetaldehyde as its first oxidation product generated via hepatic alcohol dehydrogenase (ADH) and the microsomal ethanol-oxidizing system (MEOS), which depends on cytochrome P450 2E1 (CYP 2E1), and is inducible by chronic alcohol use. MEOS induction accelerates the metabolism of ethanol to acetaldehyde that facilitates organ injury including the liver, and it produces via CYP 2E1 many reactive oxygen species (ROS) such as ethoxy radical, hydroxyethyl radical, acetyl radical, singlet radical, superoxide radical, hydrogen peroxide, hydroxyl radical, alkoxyl radical, and peroxyl radical. These attack hepatocytes, Kupffer cells, stellate cells, and liver sinusoidal endothelial cells, and their signaling mediators such as interleukins, interferons, and growth factors, help to initiate liver injury including fibrosis and cirrhosis in susceptible individuals with specific risk factors. Through CYP 2E1-dependent ROS, more evidence is emerging that alcohol generates lipid peroxides and modifies the intestinal microbiome, thereby stimulating actions of endotoxins produced by intestinal bacteria; lipid peroxides and endotoxins are potential causes that are involved in alcoholic liver injury. Alcohol modifies SIRT1 (Sirtuin-1; derived from Silent mating type Information Regulation) and SIRT2, and most importantly, the innate and adapted immune systems, which may explain the individual differences of injury susceptibility. Metabolic pathways are also influenced by circadian rhythms, specific conditions known from living organisms including plants. Open for discussion is a 5-hit working hypothesis, attempting to define key elements involved in injury progression. In essence, although abundant biochemical mechanisms are proposed for the initiation and perpetuation of liver injury, patients with an alcohol problem benefit from permanent alcohol abstinence alone.},
}
@article {pmid30424006,
year = {2018},
author = {Solano-Aguilar, GI and Jang, S and Lakshman, S and Gupta, R and Beshah, E and Sikaroodi, M and Vinyard, B and Molokin, A and Gillevet, PM and Urban, JF},
title = {The Effect of Dietary Mushroom Agaricus bisporus on Intestinal Microbiota Composition and Host Immunological Function.},
journal = {Nutrients},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/nu10111721},
pmid = {30424006},
issn = {2072-6643},
support = {58-8040-5-018//Mushroom Council/ ; },
abstract = {A study was designed to determine the potential prebiotic effect of dietary mushrooms on the host immune response, and intestinal microbiota composition and function. Thirty-one six-week-old pigs were fed a pig grower diet alone or supplemented with either three or six servings of freeze-dried white button (WB)-mushrooms for six weeks. Host immune response was evaluated in peripheral blood mononuclear cells (PBMC), and alveolar macrophages (AM) after stimulation with Salmonella typhymurium-Lipopolysaccharide (LPS). Isolated DNA from fecal and proximal colon contents were used for 16S rDNA taxonomic analysis and linear discriminant analysis effect size (LEfSe) to determine bacterial abundance and metabolic function. Pigs gained weight with no difference in body composition or intestinal permeability. Feeding mushrooms reduced LPS-induced IL-1β gene expression in AM (P < 0.05) with no change in LPS-stimulated PBMC or the intestinal mucosa transcriptome. LEfSe indicated increases in Lachnospiraceae, Ruminococcaceae within the order Clostridiales with a shift in bacterial carbohydrate metabolism and biosynthesis of secondary metabolites in the mushroom-fed pigs. These results suggested that feeding WB mushrooms significantly reduced the LPS-induced inflammatory response in AM and positively modulated the host microbiota metabolism by increasing the abundance of Clostridiales taxa that are associated with improved intestinal health.},
}
@article {pmid30423913,
year = {2018},
author = {Lee, SH and Lee, Y and Park, JS and Cho, YJ and Yoon, HI and Lee, CT and Lee, JH},
title = {Characterization of Microbiota in Bronchiectasis Patients with Different Disease Severities.},
journal = {Journal of clinical medicine},
volume = {7},
number = {11},
pages = {},
doi = {10.3390/jcm7110429},
pmid = {30423913},
issn = {2077-0383},
abstract = {The applications of the 16S rRNA gene pyrosequencing has expanded our knowledge of the respiratory tract microbiome originally obtained using conventional, culture-based methods. In this study, we employed DNA-based molecular techniques for examining the sputum microbiome in bronchiectasis patients, in relation to disease severity. Of the sixty-three study subjects, forty-two had mild and twenty-one had moderate or severe bronchiectasis, which was classified by calculating the FACED score, based on the FEV₁ (forced expiratory volume in 1 s, %) (F, 0⁻2 points), age (A, 0⁻2 points), chronic colonization by Pseudomonas aeruginosa (C, 0⁻1 point), radiographic extension (E, 0⁻1 point), and dyspnoea (D, 0⁻1 point). Bronchiectasis was defined as mild, at 0⁻2 points, moderate at 3⁻4 points, and severe at 5⁻7 points. The mean age was 68.0 ± 9.3 years; thirty-three patients were women. Haemophilus (p = 0.005) and Rothia (p = 0.043) were significantly more abundant in the mild bronchiectasis group, whereas Pseudomonas (p = 0.031) was significantly more abundant in the moderate or severe group. However, in terms of the alpha and beta diversity, the sputum microbiota of the two groups did not significantly differ, i.e., the same dominant genera were found in all samples. Further large-scale studies are needed to investigate the sputum microbiome in bronchiectasis.},
}
@article {pmid30423561,
year = {2018},
author = {Cruz-Aguliar, RM and Wantia, N and Clavel, T and Vehreschild, MJGT and Buch, T and Bajbouj, M and Haller, D and Busch, D and Schmid, RM and Stein-Thoeringer, CK},
title = {An Open-Labeled Study on Fecal Microbiota Transfer in Irritable Bowel Syndrome Patients Reveals Improvement in Abdominal Pain Associated with the Relative Abundance of Akkermansia Muciniphila.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-12},
doi = {10.1159/000494252},
pmid = {30423561},
issn = {1421-9867},
abstract = {BACKGROUND/AIMS: The gut microbiota is altered in irritable bowel syndrome (IBS), and microbiota manipulations by diet or antibiotics can reduce its symptoms. As fecal microbiota transfer (FMT) in IBS is still controversial, we investigated the clinical and side effects of FMT in a cohort of IBS patients with recurrent, treatment refractory symptoms, and studied gut microbiota signatures.<br><br>METHODS: Using an observational, prospective study design, we applied FMTs from one unrelated, healthy donor to 13 IBS patients. Fecal samples of patients and the donor were analyzed by 16S ribosomal RNA amplicon sequencing.<br><br>RESULTS: On a symptom level, primarily abdominal pain symptoms were reduced after FMT, and no adverse effects were observed. Studying the microbiome, we found an increase in alpha diversity and changes in the composition of the gut microbiota after FMT. Beta diversity changes after FMT were prominent in a subset of 7 patients with microbiota profiles coming very close to the donor. These patients also showed most pronounced visceral pain reduction. The relative abundance of Akkermansia muciniphila was inversely correlated with pain reduction in our cohort.<br><br>CONCLUSION: Although exploratory in nature and with a pilot character, this study highlights the potential role of microbiota manipulations in IBS and describes a novel association of intestinal Akkermansia and pain modulation.},
}
@article {pmid30423465,
year = {2018},
author = {Okubo, R and Koga, M and Katsumata, N and Odamaki, T and Matsuyama, S and Oka, M and Narita, H and Hashimoto, N and Kusumi, I and Xiao, J and Matsuoka, YJ},
title = {Effect of bifidobacterium breve A-1 on anxiety and depressive symptoms in schizophrenia: A proof-of-concept study.},
journal = {Journal of affective disorders},
volume = {245},
number = {},
pages = {377-385},
doi = {10.1016/j.jad.2018.11.011},
pmid = {30423465},
issn = {1573-2517},
abstract = {BACKGROUND: Studies of probiotics have suggested they have a positive effect on anxiety and depressive symptoms in humans. This study investigated the effect of consuming the probiotic Bifidobacterium breve A-1 on anxiety and depressive symptoms in patients with schizophrenia and explored its effect on immune products such as cytokines and chemokines.<br><br>METHODS: In this open-label single-arm study, all participants received B. breve strain A-1 (1011 cfu/day) for 4 weeks followed by 4 weeks of observation. The primary outcome was the Hospital Anxiety and Depression Scale (HADS) score. Secondary outcomes were anxiety and depressive symptoms on the Positive and Negative Syndrome Scale (PANSS), blood test findings, and fecal microbiome composition.<br><br>RESULTS: Twenty-nine outpatients completed the study. HADS total score and PANSS anxiety/depression score were significantly improved at 4 weeks. Based on the criterion of a greater than 25% reduction in HADS total score at 4 weeks from baseline, there were 12 responders and 17 non-responders. Responders were found to have fewer negative symptoms, reduced intake of dairy products, and higher relative abundance of Parabacteroides in the gut microbiome than non-responders. Moreover, IL-22 and TRANCE expression was significantly increased at 4 weeks from baseline in responders but not in non-responders.<br><br>LIMITATIONS: This open-label, single-arm study cannot exclude a placebo effect.<br><br>CONCLUSIONS: The results suggest the potential effect of B. breve A-1 in improving anxiety and depressive symptoms in patients with schizophrenia. Further studies should investigate this effect in patients with other psychiatric conditions and assess dietary habits and the gut microbiome.},
}
@article {pmid30423107,
year = {2018},
author = {García-Jiménez, B and de la Rosa, T and Wilkinson, MD},
title = {MDPbiome: microbiome engineering through prescriptive perturbations.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {17},
pages = {i838-i847},
doi = {10.1093/bioinformatics/bty562},
pmid = {30423107},
issn = {1367-4811},
abstract = {Motivation: Recent microbiome dynamics studies highlight the current inability to predict the effects of external perturbations on complex microbial populations. To do so would be particularly advantageous in fields such as medicine, bioremediation or industrial scenarios.<br><br>Results: MDPbiome statistically models longitudinal metagenomics samples undergoing perturbations as a Markov Decision Process (MDP). Given a starting microbial composition, our MDPbiome system suggests the sequence of external perturbation(s) that will engineer that microbiome to a goal state, for example, a healthier or more performant composition. It also estimates intermediate microbiome states along the path, thus making it possible to avoid particularly undesirable/unhealthy states. We demonstrate MDPbiome performance over three real and distinct datasets, proving its flexibility, and the reliability and universality of its output 'optimal perturbation policy'. For example, an MDP created using a vaginal microbiome time series, with a goal of recovering from bacterial vaginosis, suggested avoidance of perturbations such as lubricants or sex toys; while another MDP provided a quantitative explanation for why salmonella vaccine accelerates gut microbiome maturation in chicks. This novel analytical approach has clear applications in medicine, where it could suggest low-impact clinical interventions that will lead to achievement or maintenance of a healthy microbial population, or alternately, the sequence of interventions necessary to avoid strongly negative microbiome states.<br><br>Code (https://github.com/beatrizgj/MDPbiome) and result files (https://tomdelarosa.shinyapps.io/MDPbiome/) are available online.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.},
}
@article {pmid30423063,
year = {2018},
author = {Frioux, C and Fremy, E and Trottier, C and Siegel, A},
title = {Scalable and exhaustive screening of metabolic functions carried out by microbial consortia.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {17},
pages = {i934-i943},
doi = {10.1093/bioinformatics/bty588},
pmid = {30423063},
issn = {1367-4811},
abstract = {Motivation: The selection of species exhibiting metabolic behaviors of interest is a challenging step when switching from the investigation of a large microbiota to the study of functions effectiveness. Approaches based on a compartmentalized framework are not scalable. The output of scalable approaches based on a non-compartmentalized modeling may be so large that it has neither been explored nor handled so far.<br><br>Results: We present the Miscoto tool to facilitate the selection of a community optimizing a desired function in a microbiome by reporting several possibilities which can be then sorted according to biological criteria. Communities are exhaustively identified using logical programming and by combining the non-compartmentalized and the compartmentalized frameworks. The benchmarking of 4.9 million metabolic functions associated with the Human Microbiome Project, shows that Miscoto is suited to screen and classify metabolic producibility in terms of feasibility, functional redundancy and cooperation processes involved. As an illustration of a host-microbial system, screening the Recon 2.2 human metabolism highlights the role of different consortia within a family of 773 intestinal bacteria.<br><br>Miscoto source code, instructions for use and examples are available at: https://github.com/cfrioux/miscoto.},
}
@article {pmid30421297,
year = {2018},
author = {Shah, A and Morrison, M and Holtmann, GJ},
title = {Gastroduodenal &quot;Dysbiosis&quot;: a New Clinical Entity.},
journal = {Current treatment options in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11938-018-0207-x},
pmid = {30421297},
issn = {1092-8472},
abstract = {PURPOSE OF REVIEW: Like the rest of the gastrointestinal tract, the small intestine is colonised by microbes, but how this &quot;microbiome&quot; affects the immune system and digestive functions has largely been overlooked, especially in the &quot;omics&quot; era. Here, we present recent findings that show that the diversity, density and interactions of these microbes in the small intestine can play an important role in the pathogenesis of a number of gastrointestinal and extraintestinal disorders.<br><br>RECENT FINDINGS: Changes in the small intestinal mucosa-associated microbiota (SI-MAM) have been shown to occur with inflammatory bowel diseases, functional gastrointestinal disorders, metabolic disorders such as obesity and type 2 diabetes. More recently, there is emerging evidence that small intestinal dysbiosis can be a driver for the progression of chronic liver disease. Initially believed that small intestinal dysbiosis (e.g. SIBO) is mainly due to alterations of luminal conditions (e.g. after surgical resections of the ileocecal valve), there is now enough evidence to conclude that small intestinal dysbiosis can occur without underlying structural abnormalities. Alterations of the SI-MAM appear to play a key role for the manifestation and progression of inflammatory and metabolic disorders.},
}
@article {pmid30421194,
year = {2018},
author = {Malfertheiner, P and Mayerle, J},
title = {[Gastrointestinal innovations].},
journal = {MMW Fortschritte der Medizin},
volume = {160},
number = {Suppl 3},
pages = {58-63},
doi = {10.1007/s15006-018-1124-6},
pmid = {30421194},
issn = {1613-3560},
}
@article {pmid30421155,
year = {2018},
author = {Macut, D and Milutinović, DV and Rašić-Marković, A and Nestorov, J and Bjekić-Macut, J and Stanojlović, O},
title = {A decade in female reproduction: an endocrine view of the past and into the future.},
journal = {Hormones (Athens, Greece)},
volume = {},
number = {},
pages = {},
doi = {10.1007/s42000-018-0073-x},
pmid = {30421155},
issn = {2520-8721},
abstract = {Over the last decade, huge achievements have been made in the fields of neurophysiology, molecular endocrinology, and biochemistry, as well as in the successful translation of clinical research into diseases into clinical practice. As regards female reproduction, most of the advances made in this area were achieved in gonadal axis regulation, regulation of behavior through sex steroids, reproductive genetics, preservation of ovarian reproductive function, steroid profiling, and metabolic and overall reproductive outcomes. The coming years are expected to bring further understanding of the relationships between nutrition, energy metabolism, and reproductive function and to succeed in identifying new genetic markers linked to adverse metabolic and unfavorable cardiovascular outcomes in women. From our perspective, future research in the field of female reproduction should be directed toward doing research into genetic reproductive abnormalities and neuroendocrine diseases, pathophysiology, long-term health outcomes for oligo/amenorrhea, hyperandrogenism, and ovulatory dysfunction. It is additionally expected that a better understanding will be gained of the endocrinology of the placenta and of pregnancy, the role of the microbiome in female reproduction, the role of insulin sensitizers, anti-obesity and anti-diabetic drugs, and various advances in the prevention of ovarian damage caused by various oncology therapies, while new therapeutic options for the treatment of infertility, including kisspeptin, will be developed.},
}
@article {pmid30421135,
year = {2018},
author = {Cortez, RV and Taddei, CR and Sparvoli, LG and Ângelo, AGS and Padilha, M and Mattar, R and Daher, S},
title = {Microbiome and its relation to gestational diabetes.},
journal = {Endocrine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12020-018-1813-z},
pmid = {30421135},
issn = {1559-0100},
support = {444174/2014-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 303306/2016-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {PURPOSE: Gestational diabetes mellitus (GDM), the major endocrine pathology in pregnancy, has been associated with the development of an intense inflammatory process and increased insulin resistance. The maternal microbiota is involved in several metabolic functions; however, its role in GDM physiopathology remains unclear. The aim of this study was to assess the composition of the microbiota at different sites and evaluate its relationship with the occurrence of GDM.<br><br>METHODS: This cross-sectional study recruited women in the third trimester of gestation with and without GDM. Oral, vaginal, and stool samples were evaluated using next-generation sequencing. We included 68 participants: 26 with and 42 without GDM.<br><br>RESULTS: The analysis of the oral microbiome did not show significant differences in phyla and genus among the studied groups. In contrast, GDM patients presented a specific vaginal and intestinal microbiome composition, which was less diverse than those found in the control group, showing genera related to dysbiosis.<br><br>CONCLUSIONS: Our findings suggest that changes in the composition of the vaginal and intestinal microbiome might be involved in the development of GDM. The follow-up of these patients in order to evaluate vaginal and intestinal samples after delivery may contribute to understanding the development of metabolic disease in women with previous GDM.},
}
@article {pmid30420850,
year = {2018},
author = {López Nadal, A and Peggs, D and Wiegertjes, GF and Brugman, S},
title = {Exposure to Antibiotics Affects Saponin Immersion-Induced Immune Stimulation and Shift in Microbial Composition in Zebrafish Larvae.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2588},
doi = {10.3389/fmicb.2018.02588},
pmid = {30420850},
issn = {1664-302X},
abstract = {In the last decades, pollution of the environment by large scale use of antibiotics in agriculture and human medicine have led to increased antimicrobial resistance in both the environment and the host animal microbiome. Disturbances in the host microbiome can result in impaired immunity and reduced resilience of aquaculture species. Here, we investigated whether environmentally measured levels of the commonly used antibiotics ciprofloxacin and oxytetracycline influences the host microbiome and susceptibility toward saponin-induced immune stimulation in larval zebrafish. Firstly, neutrophil and macrophage reporter zebrafish larvae were exposed to different concentrations of soy saponin by immersion. A dose-dependent increase in neutrophil presence in the intestinal area was observed together with increased expression of immune genes il1b, tnfa, il22 and mmp9. To investigate the effect of antibiotics, larval zebrafish were immersed in ciprofloxacin or oxytetracycline in the presence or absence of a low dose of saponin. In vivo imaging revealed that antibiotic treatment did not reduce the number of neutrophils that were recruited to the intestinal area upon saponin exposure, although it did tend to lower pro-inflammatory cytokine levels. Microbial sequencing of whole larvae revealed that exposure to a low dose of saponin already shifted the microbial composition. The combination of oxytetracycline and saponin significantly increased α-diversity compared to the controls. In conclusion, the current study provides evidence that the combination of low levels of antibiotics with low levels of anti-nutritional factors (saponin) can induce inflammatory phenotypes and can modify the microbiota, which might lead to altered disease susceptibility.},
}
@article {pmid30420845,
year = {2018},
author = {De Vrieze, M and Germanier, F and Vuille, N and Weisskopf, L},
title = {Combining Different Potato-Associated Pseudomonas Strains for Improved Biocontrol of Phytophthora infestans.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2573},
doi = {10.3389/fmicb.2018.02573},
pmid = {30420845},
issn = {1664-302X},
abstract = {Late blight caused by Phytophthora infestans is considered as the most devastating disease of potato and is a re-emerging problem worldwide. Current late blight control practices rely mostly on synthetic fungicides or copper-based products, but growing awareness of the negative impact of these compounds on the environment has led to the search for alternative control measures. A collection of Pseudomonas strains isolated from both the rhizosphere and the phyllosphere of potato was recently characterized for in vitro protective effects against P. infestans. In the present study, we used a leaf disk assay with three different potato cultivars to compare the disease inhibition capacity of nine selected Pseudomonas strains when applied alone or in all possible dual and triple combinations. Results showed a strong cultivar effect and identified strains previously thought to be inactive based on in vitro assays as the best biocontrol candidates. One strain was much more active alone than in combination with other strains, while two other strains provided significantly better protection in dual combination than when applied alone. A subset of five strains was then further selected to determine their mutual influence on each other's survival and growth, as well as to characterize their activity against P. infestans in more details. This revealed that the two strains whose dual combination was particularly efficient were only weakly interfering with each other's growth and had complementary modes of action. Our results highlight the potential to harness the crop's native rhizosphere and phyllosphere microbiome through re-assembling strains with differing modes of action into small communities, thereby providing more consistent protection than with the application of single strains. We consider this as a first step toward more elaborate microbiome management efforts, which shall be integrated into global strategies for sustainable control of potato late blight.},
}
@article {pmid30420844,
year = {2018},
author = {Galand, PE and Chapron, L and Meistertzheim, AL and Peru, E and Lartaud, F},
title = {The Effect of Captivity on the Dynamics of Active Bacterial Communities Differs Between Two Deep-Sea Coral Species.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2565},
doi = {10.3389/fmicb.2018.02565},
pmid = {30420844},
issn = {1664-302X},
abstract = {Microbes play a crucial role in sustaining the coral holobiont's functions and in particular under the pressure of environmental stressors. The effect of a changing environment on coral health is now a major branch of research that relies heavily on aquarium experiments. However, the effect of captivity on the coral microbiome remains poorly known. Here we show that different cold-water corals species have different microbiome responses to captivity. For both the DNA and the RNA fraction, Madrepora oculata bacterial communities were maintained for at least 6 months of aquarium rearing, while Lophelia pertusa bacteria changed within a day. Interestingly, bacteria from the genus Endozoicomonas, a ubiquitous symbiont of numerous marine hosts, were resilient and remained active in M. oculata for several months. Our results demonstrate that a good knowledge of the coral microbiome and an understanding of the ecological strategy of the holobiont is needed before designing aquarium experiments.},
}
@article {pmid30420841,
year = {2018},
author = {Levy, B and Jami, E},
title = {Exploring the Prokaryotic Community Associated With the Rumen Ciliate Protozoa Population.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2526},
doi = {10.3389/fmicb.2018.02526},
pmid = {30420841},
issn = {1664-302X},
abstract = {Ciliate protozoa are an integral part of the rumen microbiome and were found to exert a large effect on the rumen ecosystem itself as well as their host animal physiology. Part of these effects have been attributed to their ability to harbor a diverse ecto- and endo-symbiotic community of prokaryotic cells. Studies on the relationship between the protozoa population and their associated prokaryotic community in the rumen mainly focused on the methanogens, revealing that protozoa play a major role in enhancing methanogenesis potential. In contrast, little is known about the composition and function of the bacteria associated with rumen protozoa and the extent of this association. In this study, we characterize the prokaryotic communities associated with different protozoa populations and compare their structure to the free-living prokaryotic population residing in the cow rumen. We show that the overall protozoa associated prokaryotic community structure differs significantly compared to the free-living community in terms of richness and composition. The methanogens proportion was significantly higher in all protozoa populations compared to the free-living fraction, while the Lachnospiraceae was the most prevalent bacterial family in the protozoa associated bacterial communities. Several taxa not detected or detected in extremely low abundance in the free-living community were enriched in the protozoa associated bacterial community. These include members of the Endomicrobia class, previously identified as protozoa symbionts in the termite gut. Our results show that rumen protozoa harbor prokaryotic communities that are compositionally different from their surroundings, which may be the result of specific tropism between the prokaryotic community and protozoa.},
}
@article {pmid30420838,
year = {2018},
author = {Li, W and Yuan, Y and Xia, Y and Sun, Y and Miao, Y and Ma, S},
title = {A Cross-Scale Neutral Theory Approach to the Influence of Obesity on Community Assembly of Human Gut Microbiome.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2320},
doi = {10.3389/fmicb.2018.02320},
pmid = {30420838},
issn = {1664-302X},
abstract = {Background: The implications of gut microbiome to obesity have been extensively investigated in recent years although the exact mechanism is still unclear. The question whether or not obesity influences gut microbiome assembly has not been addressed. The question is significant because it is fundamental for investigating the diversity maintenance and stability of gut microbiome, and the latter should hold a key for understanding the etiological implications of gut microbiome to obesity. Methods: In this study, we adopt a dual neutral theory modeling strategy to address this question from both species and community perspectives, with both discrete and continuous neutral theory models. The first neutral theory model we apply is Hubbell's neutral theory of biodiversity that has been extensively tested in macro-ecology of plants and animals, and the second we apply is Sloan's neutral theory model that was developed particularly for microbial communities based on metagenomic sequencing data. Both the neutral models are complementary to each other and integrated together offering a comprehensive approach to more accurately revealing the possible influence of obesity on gut microbiome assembly. This is not only because the focus of both neutral theory models is different (community vs. species), but also because they adopted two different modeling strategies (discrete vs. continuous). Results: We test both the neutral theory models with datasets from Turnbaugh et al. (2009). Our tests showed that the species abundance distributions of more than ½ species (59-69%) in gut microbiome satisfied the prediction of Sloan's neutral theory, although at the community level, the number of communities satisfied the Hubbell's neutral theory was negligible (2 out of 278). Conclusion: The apparently contradictory findings above suggest that both stochastic neutral effects and deterministic environmental (host) factors play important roles in shaping the assembly and diversity of gut microbiome. Furthermore, obesity may just be one of the host factors, but its influence may not be strong enough to tip the balance between stochastic and deterministic forces that shape the community assembly. Finally, the apparent contradiction from both the neutral theories should not be surprising given that there are still near 30-40% species that do not obey the neutral law.},
}
@article {pmid30420754,
year = {2018},
author = {Wang, Y and Wiesnoski, DH and Helmink, BA and Gopalakrishnan, V and Choi, K and DuPont, HL and Jiang, ZD and Abu-Sbeih, H and Sanchez, CA and Chang, CC and Parra, ER and Francisco-Cruz, A and Raju, GS and Stroehlein, JR and Campbell, MT and Gao, J and Subudhi, SK and Maru, DM and Blando, JM and Allison, JP and Sharma, P and Tetzlaff, MT and Wargo, JA and Jenq, RR},
title = {Fecal microbiota transplantation for refractory immune checkpoint inhibitor-associated colitis.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-018-0238-9},
pmid = {30420754},
issn = {1546-170X},
abstract = {We report the first case series of immune checkpoint inhibitors (ICI)-associated colitis successfully treated with fecal microbiota transplantation, with reconstitution of the gut microbiome and a relative increase in the proportion of regulatory T-cells within the colonic mucosa. These preliminary data provide evidence that modulation of the gut microbiome may abrogate ICI-associated colitis.},
}
@article {pmid30420594,
year = {2018},
author = {Yost, S and Stashenko, P and Choi, Y and Kukuruzinska, M and Genco, CA and Salama, A and Weinberg, EO and Kramer, CD and Frias-Lopez, J},
title = {Increased virulence of the oral microbiome in oral squamous cell carcinoma revealed by metatranscriptome analyses.},
journal = {International journal of oral science},
volume = {10},
number = {4},
pages = {32},
doi = {10.1038/s41368-018-0037-7},
pmid = {30420594},
issn = {2049-3169},
support = {Evans Center for Interdisciplinary Biomedical Research ARC//Boston University (BU)/ ; Evans Center for Interdisciplinary Biomedical Research ARC//Boston University (BU)/ ; Evans Center for Interdisciplinary Biomedical Research ARC//Boston University (BU)/ ; Evans Center for Interdisciplinary Biomedical Research ARC//Boston University (BU)/ ; Evans Center for Interdisciplinary Biomedical Research ARC//Boston University (BU)/ ; Evans Center for Interdisciplinary Biomedical Research ARC//Boston University (BU)/ ; Evans Center for Interdisciplinary Biomedical Research ARC//Boston University (BU)/ ; Evans Center for Interdisciplinary Biomedical Research ARC//Boston University (BU)/ ; Evans Center for Interdisciplinary Biomedical Research ARC//Boston University (BU)/ ; },
abstract = {Oral squamous cell carcinoma (OSCC) is the most prevalent and most commonly studied oral cancer. However, there is a void regarding the role that the oral microbiome may play in OSCC. Although the relationship between microbial community composition and OSCC has been thoroughly investigated, microbial profiles of the human microbiome in cancer are understudied. Here we performed a small pilot study of community-wide metatranscriptome analysis to profile mRNA expression in the entire oral microbiome in OSCC to reveal molecular functions associated with this disease. Fusobacteria showed a statistically significantly higher number of transcripts at tumour sites and tumour-adjacent sites of cancer patients compared to the healthy controls analysed. Regardless of the community composition, specific metabolic signatures were consistently found in disease. Activities such as iron ion transport, tryptophanase activity, peptidase activities and superoxide dismutase were over-represented in tumour and tumour-adjacent samples when compared to the healthy controls. The expression of putative virulence factors in the oral communities associated with OSCC showed that activities related to capsule biosynthesis, flagellum synthesis and assembly, chemotaxis, iron transport, haemolysins and adhesins were upregulated at tumour sites. Moreover, activities associated with protection against reactive nitrogen intermediates, chemotaxis, flagellar and capsule biosynthesis were also upregulated in non-tumour sites of cancer patients. Although they are preliminary, our results further suggest that Fusobacteria may be the leading phylogenetic group responsible for the increase in expression of virulence factors in the oral microbiome of OSCC patients.},
}
@article {pmid30420587,
year = {2018},
author = {Gay, MCL and Koleva, PT and Slupsky, CM and Toit, ED and Eggesbo, M and Johnson, CC and Wegienka, G and Shimojo, N and Campbell, DE and Prescott, SL and Munblit, D and Geddes, DT and Kozyrskyj, AL and , },
title = {Worldwide Variation in Human Milk Metabolome: Indicators of Breast Physiology and Maternal Lifestyle?.},
journal = {Nutrients},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/nu10091151},
pmid = {30420587},
issn = {2072-6643},
support = {-//World Universities Network (WUN)/ ; -//Canadian Institutes of Health Research/Canada ; unrestricted research grant//Medela AG/ ; },
abstract = {Human milk provides essential substrates for the optimal growth and development of a breastfed infant. Besides providing nutrients to the infant, human milk also contains metabolites which form an intricate system between maternal lifestyle, such as the mother's diet and the gut microbiome, and infant outcomes. This study investigates the variation of these human milk metabolites from five different countries. Human milk samples (n = 109) were collected one month postpartum from Australia, Japan, the USA, Norway, and South Africa and were analyzed by nuclear magnetic resonance. The partial least squares discriminant analysis (PLS-DA) showed separation between either maternal countries of origin or ethnicities. Variation between countries in concentration of metabolites, such as 2-oxoglutarate, creatine, and glutamine, in human milk, between countries, could provide insights into problems, such as mastitis and/or impaired functions of the mammary glands. Several important markers of milk production, such as lactose, betaine, creatine, glutamate, and glutamine, showed good correlation between each metabolite. This work highlights the importance of milk metabolites with respect to maternal lifestyle and the environment, and also provides the framework for future breastfeeding and microbiome studies in a global context.},
}
@article {pmid30420511,
year = {2018},
author = {Cáliz, J and Triadó-Margarit, X and Camarero, L and Casamayor, EO},
title = {A long-term survey unveils strong seasonal patterns in the airborne microbiome coupled to general and regional atmospheric circulations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1812826115},
pmid = {30420511},
issn = {1091-6490},
abstract = {Airborne microbes (bacteria, archaea, protists, and fungi) were surveyed over a 7-y period via high-throughput massive sequencing of 16S and 18S rRNA genes in rain and snow samples collected fortnightly at a high-elevation mountain Long-Term Ecological Research (LTER) Network site (LTER-Aigüestortes, Central Pyrenees, Spain). This survey constitutes the most comprehensive mountain-top aerobiology study reported to date. The air mass origins were tracked through modeled back-trajectories and analysis of rain water chemical composition. Consistent microbial seasonal patterns were observed with highly divergent summer and winter communities recurrent in time. Indicative microbial taxa were unveiled as a forensic signature, and ubiquitous taxa were observed as common atmosphere inhabitants, highlighting aerosols as a potentially successful mechanism for global microbial dispersal. Source-tracking analyses identified freshwater, cropland, and urban biomes as the most important sources for airborne bacteria in summer, while marine and forest biomes prevailed in winter, in agreement with air mass retrotrajectories and the prevailing general and regional atmospheric circulation.},
}
@article {pmid30420331,
year = {2018},
author = {de Souza Moraes, B and Mary Dos Santos, G and Palladino Delforno, T and Tadeu Fuess, L and José da Silva, A},
title = {Enriched microbial consortia for dark fermentation of sugarcane vinasse towards value-added short-chain organic acids and alcohol production.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2018.10.008},
pmid = {30420331},
issn = {1347-4421},
abstract = {The role of sugarcane vinasse as a nutrient source and the impacts of different inoculum pretreatment methods (acid-thermal and thermal treatment) were assessed in acidogenic systems aiming to produce value-added short-chain organic acids (SCOA) and alcohols. In-depth microbiome characterization was also conducted by high-throughput sequencing of the 16S rRNA gene using the Miseq Illumina platform. SCOA production was 47.3 % higher in vinasse-fed reactors, with isobutyric (up to 10.3 g L-1) and butyric (up to 10.6 g L-1) acids as the primary metabolites most likely resulting from lactate conversion. Ethanol comprised the main product from solventogenic pathways in all conditions, with values ranging between 2.7 and 5.2 g L-1, whereas no butanol was detected. Microbial analyses revealed high relative abundance values for the Clostridium, Lactobacillus, Bacillus and Ruminococcus genera, with the predominance of the Clostridium genus (17%) in acid-thermal treatment reactors and the Lactobacillus genus (37%) in thermal treatment reactors. Overall, vinasse proved to be a suitable substrate for value-added SCOA production, which characterizes a potential management approach to this wastewater stream. In this sense, the biochemical production of butyrate from vinasse could diversify the product portfolio of sugarcane biorefineries, also minimizing bioenergy losses by converting residual carbon fractions.},
}
@article {pmid30420263,
year = {2018},
author = {Lamprecht, P and Fischer, N and Huang, J and Burkhardt, L and Lütgehetmann, M and Arndt, F and Rolfs, I and Kerstein, A and Iking-Konert, C and Laudien, M},
title = {Changes in the composition of the upper respiratory tract microbial community in granulomatosis with polyangiitis.},
journal = {Journal of autoimmunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaut.2018.10.005},
pmid = {30420263},
issn = {1095-9157},
abstract = {Dysbiosis¸ i.e. changes in microbial composition at a mucosal interface, is implicated in the pathogenesis of many chronic inflammatory and autoimmune diseases. To assess the composition of the microbial upper respiratory tract (URT) community in patients with granulomatosis with polyangiitis (GPA), we used culture-independent high-throughput methods. In this prospective clinical study, nasal swabs were collected from patients with GPA, patients with rheumatoid arthritis (RA, disease control), and healthy controls. Nasal bacterial taxa were assessed using V3-V4 region 16S rRNA amplicon sequencing. Staphylococcus aureus, Haemophilus influenza, and entero- and rhinoviruses were detected using qPCR. Unbiased metagenomic RNA sequencing (UMERS) was performed in a subset of samples to determine the relative abundance of bacterial, fungal, and viral species. A trend toward reduced microbiome diversity was detected in GPA samples compared with healthy controls. The abundance of bacterial taxa and microbial richness were significantly decreased in GPA samples compared with RA samples. The relative abundance of bacterial families shifted, with increased Planococcaceae and decreased Moraxellaceae, Tissierellaceae, Staphylococcaceae, and Propionibacteriaceae in GPA and RA. Further, decreased abundance of Corynebacteriaceae, and Aerococcaceae was observed in GPA samples. Significantly more colonization of S. aureus was seen in the nasal microbiome of GPA compared with RA and healthy control samples. H. influenzae colonization was also observed in GPA samples. UMERS detected the presence of rhinoviral sequences in some GPA samples. Thus, our study uncovered changes in the URT microbial composition in patients with GPA and RA, suggesting that both immunosuppression and disease background affect the URT microbiome. Complex alterations of host-microbiome interactions in the URT could influence chronic endonasal inflammation in GPA.},
}
@article {pmid30420171,
year = {2018},
author = {Frugé, AD and Van der Pol, W and Rogers, LQ and Morrow, CD and Tsuruta, Y and Demark-Wahnefried, W},
title = {Fecal Akkermansia muciniphila Is Associated with Body Composition and Microbiota Diversity in Overweight and Obese Women with Breast Cancer Participating in a Presurgical Weight Loss Trial.},
journal = {Journal of the Academy of Nutrition and Dietetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jand.2018.08.164},
pmid = {30420171},
issn = {2212-2672},
abstract = {BACKGROUND: Akkermansia muciniphila (AM) is a gram-negative, mucin-degrading bacteria inhabiting the gastrointestinal tract associated with host phenotypes and disease states.<br><br>OBJECTIVE: Explore characteristics of overweight and obese female early-stage (0 to II) breast cancer patients with low AM relative abundance (LAM) vs high (HAM) enrolled in a presurgical weight-loss trial.<br><br>DESIGN: Secondary analysis of pooled participants in a randomized controlled trial (NCT02224807).<br><br>PARTICIPANTS/SETTING: During the period from 2014 to 2017, 32 female patients with breast cancer were randomized to weight-loss or attention-control arms from time of diagnosis-to-lumpectomy (mean=30±9 days).<br><br>INTERVENTION: All were instructed to correct nutrient deficiencies via food sources and on upper-body exercises. The weight-loss group received additional guidance to promote 0.5 to 1 kg/wk weight-loss via energy restriction and aerobic exercise.<br><br>MAIN OUTCOME MEASURES: At baseline and follow-up, sera, fecal samples, two-24 hour dietary recalls and dual x-ray absorptiometry were obtained. Bacterial DNA was isolated from feces and polymerase chain reaction (16S) amplified. Inflammatory cytokines were measured in sera.<br><br>Differences between LAM and HAM participants were analyzed using t tests and nonparametric tests. Spearman correlations explored relationships between continuous variables.<br><br>RESULTS: Participants were aged 61±9 years with body mass index 34.8±6. Mean AM relative abundance was 0.02% (0.007% to 0.06%) and 1.59% (0.59% to 13.57%) for LAM and HAM participants, respectively. At baseline, women with HAM vs LAM had lower fat mass (38.9±11.2 kg vs 46.4±9.0 kg; P=0.044). Alpha diversity (ie, species richness) was higher in women with HAM (360.8±84.8 vs 282.4±69.6; P=0.008) at baseline, but attenuated after weight-loss (P=0.058). At baseline, interleukin-6 level was associated with species richness (ρ=-0.471, P=0.008) and fat mass (ρ=0.529, P=0.002), but not AM. Change in total dietary fiber was positively associated with AM in LAM (ρ=0.626, P=0.002), but not HAM (ρ=0.436, P=0.180) participants.<br><br>CONCLUSIONS: Among women with early-stage breast cancer, body composition is associated with AM, microbiota diversity, and interleukin-6 level. AM may mediate the effects of dietary fiber in improving microbiota composition.},
}
@article {pmid30419949,
year = {2018},
author = {Silverman, JD and Durand, HK and Bloom, RJ and Mukherjee, S and David, LA},
title = {Dynamic linear models guide design and analysis of microbiota studies within artificial human guts.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {202},
doi = {10.1186/s40168-018-0584-3},
pmid = {30419949},
issn = {2049-2618},
support = {1R01DK116187//National Institutes of Health/ ; IIS-1546331//National Science Foundation/ ; DMS-1418261//National Science Foundation/ ; IIS-1320357//National Science Foundation (US)/ ; DMS-1045153//National Science Foundation (US)/ ; DMS1613261//National Science Foundation (US)/ ; None//University of North Carolina Center for Gastrointestinal Biology and Disease/ ; None//Hartwell Foundation/ ; NNX16AO69A//Translational Research Institute/ ; },
abstract = {BACKGROUND: Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models' fundamental biology include the timescales on which microbiota vary and the factors that drive such change. Answering these questions though requires overcoming analytical obstacles like estimating the effects of technical variation on observed microbiota dynamics, as well as the lack of appropriate benchmark datasets.<br><br>RESULTS: To address these obstacles, we created a modeling framework based on multinomial logistic-normal dynamic linear models (MALLARDs) and performed dense longitudinal sampling of four replicate artificial human guts over the course of 1 month. The resulting analyses revealed how the ratio of biological variation to technical variation from sample processing depends on sampling frequency. In particular, we find that at hourly sampling frequencies, 76% of observed variation could be ascribed to technical sources, which could also skew the observed covariation between taxa. We also found that the artificial guts demonstrated replicable trajectories even after a recovery from a transient feed disruption. Additionally, we observed irregular sub-daily oscillatory dynamics associated with the bacterial family Enterobacteriaceae within all four replicate vessels.<br><br>CONCLUSIONS: Our analyses suggest that, beyond variation due to sequence counting, technical variation from sample processing can obscure temporal variation from biological sources in artificial gut studies. Our analyses also supported hypotheses that human gut microbiota fluctuates on sub-daily timescales in the absence of a host and that microbiota can follow replicable trajectories in the presence of environmental driving forces. Finally, multiple aspects of our approach are generalizable and could ultimately be used to facilitate the design and analysis of longitudinal microbiota studies in vivo.},
}
@article {pmid30389414,
year = {2018},
author = {Fatkhullina, AR and Peshkova, IO and Dzutsev, A and Aghayev, T and McCulloch, JA and Thovarai, V and Badger, JH and Vats, R and Sundd, P and Tang, HY and Kossenkov, AV and Hazen, SL and Trinchieri, G and Grivennikov, SI and Koltsova, EK},
title = {An Interleukin-23-Interleukin-22 Axis Regulates Intestinal Microbial Homeostasis to Protect from Diet-Induced Atherosclerosis.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2018.09.011},
pmid = {30389414},
issn = {1097-4180},
abstract = {Although commensal flora is involved in the regulation of immunity, the interplay between cytokine signaling and microbiota in atherosclerosis remains unknown. We found that interleukin (IL)-23 and its downstream target IL-22 restricted atherosclerosis by repressing pro-atherogenic microbiota. Inactivation of IL-23-IL-22 signaling led to deterioration of the intestinal barrier, dysbiosis, and expansion of pathogenic bacteria with distinct biosynthetic and metabolic properties, causing systemic increase in pro-atherogenic metabolites such as lipopolysaccharide (LPS) and trimethylamine N-oxide (TMAO). Augmented disease in the absence of the IL-23-IL-22 pathway was mediated in part by pro-atherogenic osteopontin, controlled by microbial metabolites. Microbiota transfer from IL-23-deficient mice accelerated atherosclerosis, whereas microbial depletion or IL-22 supplementation reduced inflammation and ameliorated disease. Our work uncovers the IL-23-IL-22 signaling as a regulator of atherosclerosis that restrains expansion of pro-atherogenic microbiota and argues for informed use of cytokine blockers to avoid cardiovascular side effects driven by microbiota and inflammation.},
}
@article {pmid30419580,
year = {2018},
author = {Stallmach, A and Reuken, PA and Teich, N},
title = {[Advances in the diagnosis and treatment of Clostridioides [Clostridium] difficile infections in inflammatory bowel disease].},
journal = {Zeitschrift fur Gastroenterologie},
volume = {56},
number = {11},
pages = {1369-1377},
doi = {10.1055/a-0729-3168},
pmid = {30419580},
issn = {1439-7803},
abstract = {Patients with chronic inflammatory bowel disease (IBD) have a significantly increased risk of clinically relevant clostridial infection (CDI). In turn, CDI can increase IBD activity. Therefore, rapid diagnosis and therapy is required. Many diagnostic and treatment studies on patients with CDI without inflammatory bowel disease are not congruent with IBD patients. This overview summarizes the everyday data of recent years and condenses these into four guiding principles. 1) patients with IBD present a risk population for a CDI. A CDI not only worsens the disease activity in the short term, but also causes increased morbidity and mortality in the long term. 2) If a CDI is suspected, glutamate-dehydrogenase (GDH) detection should be carried out quickly. If this is positive, and the disease activity is high, a therapy against C. difficile already may be initiated and-if necessary-terminated in cases of negative confirmation tests. 3) IBD patients with a proven CDI should be treated primarily with vancomycin. 4) In a relapsing CDI, fecal microbiome transfer is an effective therapeutic measure. However, activation of the IBD must be expected in about 15 % of cases. Consistent adherence to these guidelines may help treat a CDI in IBD patients.},
}
@article {pmid30419503,
year = {2018},
author = {Salazar, AM and Resnik-Docampo, M and Ulgherait, M and Clark, RI and Shirasu-Hiza, M and Jones, DL and Walker, DW},
title = {Intestinal Snakeskin Limits Microbial Dysbiosis during Aging and Promotes Longevity.},
journal = {iScience},
volume = {9},
number = {},
pages = {229-243},
doi = {10.1016/j.isci.2018.10.022},
pmid = {30419503},
issn = {2589-0042},
abstract = {Intestinal barrier dysfunction is an evolutionarily conserved hallmark of aging, which has been linked to microbial dysbiosis, altered expression of occluding junction proteins, and impending mortality. However, the interplay between intestinal junction proteins, age-onset dysbiosis, and lifespan determination remains unclear. Here, we show that altered expression of Snakeskin (Ssk), a septate junction-specific protein, can modulate intestinal homeostasis, microbial dynamics, immune activity, and lifespan in Drosophila. Loss of Ssk leads to rapid and reversible intestinal barrier dysfunction, altered gut morphology, dysbiosis, and dramatically reduced lifespan. Remarkably, restoration of Ssk expression in flies showing intestinal barrier dysfunction rescues each of these phenotypes previously linked to aging. Intestinal up-regulation of Ssk protects against microbial translocation following oral infection with pathogenic bacteria. Furthermore, intestinal up-regulation of Ssk improves intestinal barrier function during aging, limits dysbiosis, and extends lifespan. Our findings indicate that intestinal occluding junctions may represent prolongevity targets in mammals.},
}
@article {pmid30419494,
year = {2018},
author = {Ventura Spagnolo, E and Stassi, C and Mondello, C and Zerbo, S and Milone, L and Argo, A},
title = {Forensic microbiology applications: A systematic review.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {36},
number = {},
pages = {73-80},
doi = {10.1016/j.legalmed.2018.11.002},
pmid = {30419494},
issn = {1873-4162},
abstract = {According to the Human Microbiome Project (HMP), a healthy human body contains ten times more microbes than human cells. Microbial communities colonize different organs of the body, playing fundamental roles both in human health and disease. Despite the vast scientific knowledge of the role of microbial communities in a living body, little is known at present about microbial changes occurring after death, thus leading many authors to investigate the composition of the thanatomicrobiome and its potential applications in the forensic field. The aim of the following review is to provide a general overview of the advances of postmortem microbiology research, mainly focusing on the role of microbiological investigations carried out on internal organs and fluids. To this end, a total of 19 studies have been sistematically reviewed, each one chosen according to specific inclusion/exclusion criteria. The selected studies assess the contribution of contamination, postmortem transmigration and agonal spread to microbial isolation from dead body samples, and shed light on the role of postmortem microbiological investigations in several forensic fields, such as cause of death or PMI determination.},
}
@article {pmid30419320,
year = {2018},
author = {Zhuo, C and Yao, Y and Xu, Y and Liu, C and Chen, M and Ji, F and Li, J and Tian, H and Jiang, D and Lin, C and Chen, C},
title = {Schizophrenia and gut-flora related epigenetic factors.},
journal = {Progress in neuro-psychopharmacology &amp; biological psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pnpbp.2018.11.005},
pmid = {30419320},
issn = {1878-4216},
abstract = {BACKGROUND: Schizophrenia (SZ) is a complex psychiatric disorder and the exact mechanisms that underpin SZ remain poorly understood despite decades of research. Genetic, epigenetic, and environmental factors are all considered to play a role. The importance of gut flora and its influence on the central nervous system has been recognized in recent years. We hypothesize that gut flora may be a converging point where environmental factors interact with epigenetic factors and contribute to SZ pathogenesis.<br><br>AIM: To summarize the current understanding of genetic and epigenetic factors and the possible involvement of gut flora in the pathogenesis of schizophrenia.<br><br>RESULTS: We searched PubMed and Medline with a combination of the key words schizophrenia, microbiome, epigenetic factors to identify studies of genetic and epigenetic factors in the pathogenesis of schizophrenia. Numerous genes that encode key proteins in neuronal signaling pathways have been linked to SZ. Epigenetic modifications, particularly, methylation and acetylation profiles, have been found to differ in individuals that present with SZ from those that don't. Gut flora may affect epigenetic modifications by regulation of key metabolic pathway molecules, including methionine, florate, biotin, and metabolites that are acetyl group donors. Despite a lack of direct studies on the subject, it is possible that gut flora may influence genetic and epigenetic expression and thereby contribute to the pathogenesis of SZ.<br><br>CONCLUSION: Gut flora is sensitive to both internal and environmental stimuli and the synthesis of some key molecules that participate in the epigenetic modulation of gene expression. Therefore, it is possible that gut flora is a converging point where environmental factors interact with genetic and epigenetic factors in the pathogenesis of SZ.},
}
@article {pmid30419166,
year = {2018},
author = {Hellauer, K and Uhl, J and Lucio, M and Schmitt-Kopplin, P and Wibberg, D and Huebner, U and Drewes, JE},
title = {Microbiome triggered transformations of trace organic chemicals in the presence of effluent organic matter in managed aquifer recharge (MAR) systems.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.8b04559},
pmid = {30419166},
issn = {1520-5851},
abstract = {It is widely assumed that biodegradation of trace organic chemicals (TOrCs) in managed aquifer recharge (MAR) systems occurs via a co-metabolic transformation with dissolved organic carbon serving as primary substrate. Hence, the composition facilitating bioavailability of the organic matter seems to have a great impact on TOrCs transformation in MAR systems. The aim of this study was to elucidate the character of effluent organic matter present in the feed water of a simulated sequential MAR system throughout the infiltration by use of FT-ICR-MS analyses as well as spectroscopic methods. Furthermore, compositional changes were correlated with TOrCs targeted throughout the system as well as the abundance of different microbial phyla. Based on their behavior throughout the infiltration system in which different redox and substrate conditions prevailed, TOrCs were classified in four groups: easily degradable, redox insensitive, redox sensitive, and persistent. Masses correlating with persistent TOrCs were mainly comprised of CHNO containing molecules, but also of CHO which are known as carboxyl-rich alicyclic molecules, while CHOS and CHNOS can be neglected. Easily degradable TOrCs could be associated with CHNO, CHO and CHOS containing compounds. However, a shift of molecular compounds to mostly CHOS was observed for redox insensitive TOrCs. 338 masses correlated with removal of redox sensitive TOrCs, but no distinct clustering was identified.},
}
@article {pmid30419047,
year = {2018},
author = {Compo, NR and Gomez, DE and Tapscott, B and Weese, JS and Turner, PV},
title = {Fecal bacterial microbiota of Canadian commercial mink (Neovison vison): Yearly, life stage, and seasonal comparisons.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0207111},
doi = {10.1371/journal.pone.0207111},
pmid = {30419047},
issn = {1932-6203},
abstract = {The gastrointestinal microbiome is known to play a critical role in animal health but has been relatively poorly characterized in commercial mink, an obligate carnivore. Whether the microbiota can be manipulated in mink to improve pelt quality, health, and well-being is unknown. The objectives of this study were to characterize the fecal microbiota of commercial mink, and to evaluate potential changes due to year (2014 vs 2015), life stage (adult female vs weaned kit), season (summer vs winter), and between Canadian farms. Pooled fecal samples were collected from adult females and weaned kits in the summers of 2014 (n = 173) and 2015 (n = 168), and from females in the winter of 2016 (n = 39), a time when females undergo marked calorie restriction, from 49 mink farms in Ontario. Bacterial DNA was extracted and the V4 region of the 16S rRNA gene was amplified. Approximately 22 million sequences were identified following quality control filtering. A total of 31 bacterial phyla were identified; however, only 3 comprised >1% of the total sequences identified, with Firmicutes and Proteobacteria together comprising 95% of the total sequences. Comparisons were made by life stage, season and year; no differences were found in the relative abundance of any taxa between samples collected from adult females and weaned kits from the same year and the greatest number of differences at each taxonomic level were noted between 2014 and 2015. Significantly more operational taxonomic units (OTUs) were found in 2014 than 2015 or 2016 (p<0.05) and samples from 2014 were more even, but less diverse than in 2015 (p = 0.002 and 0.001, respectively). There were significant differences in community population and structure by year and season (all p-values <0.001). The predominant phyla and genera at the farm level were similar from year to year. Together, these indicate that mink environment, season, and time are important factors in the stability of gastrointestinal microbiota, once mink reach maturity.},
}
@article {pmid30418545,
year = {2018},
author = {Meng, X and Dunsmore, G and Koleva, P and Elloumi, Y and Wu, RY and Sutton, RT and Ambrosio, L and Hotte, N and Nguyen, V and Madsen, KL and Dieleman, LA and Chen, H and Huang, V and Elahi, S},
title = {The profile of human milk metabolome, cytokines and antibodies in inflammatory bowel diseases versus healthy mothers and potential impact on the newborn.},
journal = {Journal of Crohn's &amp; colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjy186},
pmid = {30418545},
issn = {1876-4479},
abstract = {Background and Aims: For women with inflammatory bowel disease (IBD), it is not very well known how IBD or IBD treatment impacts their breastmilk components. We aimed to investigate whether breastmilk composition differs in healthy control (HC) versus IBD mothers in terms of antibodies, cytokines and metabolites to identify potential impact of IBD breastmilk on neonatal immune system.<br><br>Methods: Breastmilk specimens from HC (n=17) and IBD (n=31 for Crohn's disease (CD); n=41 for ulcerative colitis (UC)) were collected at 3 and 6 months post-partum (PP3) and (PP6), respectively. Fecal samples were also collected. Cytokines and immunoglobulins (IgA/IgG/IgE) were analyzed by multiplex Meso Scale Discovery (MSD) and commercial kits. Moreover, breastmilk metabolites were analyzed by 1H nuclear magnetic resonance (NMR).<br><br>Results: We found breastmilk from IBD mothers showed significantly lower levels of IgA, sugar metabolite (lactose) and 2-aminobutyrate. In contrast, we observed breastmilk from mothers with IBD had increased levels of pro-inflammatory cytokines and higher energy metabolites (lactate and succinate) than milk from healthy mothers. In addition, we noticed that the type of treatment (5-ASA versus Biologics) influenced the milk cytokines and metabolites profile.<br><br>Conclusions: The reduction in immunoprotective components of IBD breastmilk such as sIgA and lactose theoretically may modulate the potential protective effects of breastfeeding. On the other hand, presence of higher levels of pro-inflammatory cytokines, lactate and succinate may predispose the offspring to an inflammatory condition or impact the gut microbiome. Better understanding the role of succinate in infants and its potential effects on microbiome or mucosal immunity merits further investigations.},
}
@article {pmid30418163,
year = {2018},
author = {Sams-Dodd, J and Sams-Dodd, F},
title = {Time to Abandon Antimicrobial Approaches in Wound Healing: A Paradigm Shift.},
journal = {Wounds : a compendium of clinical research and practice},
volume = {30},
number = {11},
pages = {345-352},
pmid = {30418163},
issn = {1943-2704},
abstract = {Antimicrobial approaches (eg, antibiotics and antiseptics) have been used for decades in the treatment of infected wounds, ulcers, and burns. However, an increasing number of meta-analyses have raised questions regarding the therapeutic value of these approaches. Newer findings show that the body actively hosts an ecosystem of bacteria, fungi, viruses, and mites on its outer surfaces, known as the microbiome, as part of its defense against pathogens. Antimicrobials would disrupt this system and thereby work against the strategy the body has chosen. Recently, a new technology, micropore particle technology (MPPT), has been identified; it is not an antimicrobial but instead acts as a passive immunotherapy that disrupts the weaponry bacteria and fungi use to inhibit the immune system, allowing the immune system to recover. Clinical findings show MPPT removes wound infections 60% quicker than antibiotics and antiseptics and promotes the healing of chronic wounds that have not responded to antimicrobials. These effects are achieved without antimicrobial action and, considering the limited therapeutic benefits of antibiotics and antiseptics for wound infections, it is valid to question the use of antimicrobial approaches in wound care and the dogma that a reduction in microbial burden will lead to a reduction in infection. Instead, it may be time to consider a paradigm shift in wound healing away from antimicrobials and towards therapies that support the immune system and the microbiome. This review covers the increasing evidence that infections on external surfaces have to be treated fundamentally differently to internal infections.},
}
@article {pmid30418043,
year = {2018},
author = {Muleviciene, A and D'Amico, F and Turroni, S and Candela, M and Jankauskiene, A},
title = {Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {1-14},
doi = {10.1556/030.65.2018.045},
pmid = {30418043},
issn = {1217-8950},
abstract = {Nutritional iron deficiency (ID) causes not only anemia but also malfunction of the entire human organism. Recently, a role of the gut microbiota has been hypothesized, but limited data are available especially in infants. Here, we performed a pilot study to explore the gut microbiota in 10 patients with iron deficiency anemia (IDA) and 10 healthy controls aged 6-34 months. Fresh stool samples were collected from diapers, and the fecal microbiota was profiled by next-generation sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Except for diet diversity, the breastfeeding status at the enrollment, the exclusive breastfeeding duration, and the introduction of complementary foods did not differ between groups. Distinct microbial signatures were found in IDA patients, with increased relative abundance of Enterobacteriaceae (mean relative abundance, patients vs. controls, 4.4% vs. 3.0%) and Veillonellaceae (13.7% vs. 3.6%), and reduced abundance of Coriobacteriaceae (3.5% vs. 8.8%) compared to healthy controls. A decreased Bifidobacteriaceae/Enterobacteriaceae ratio was observed in IDA patients. Notwithstanding the low sample size, our data highlight microbiota dysbalance in IDA worth for further investigations, aimed at unraveling the ID impact on the microbiome trajectory in early life, and the possible long-term consequences.},
}
@article {pmid30417889,
year = {2018},
author = {Hyeon, JY and Mann, DA and Townsend, AM and Deng, X},
title = {Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {140},
pages = {},
doi = {10.3791/58612},
pmid = {30417889},
issn = {1940-087X},
abstract = {Quasi-metagenomics sequencing refers to the sequencing-based analysis of modified microbiomes of food and environmental samples. In this protocol, microbiome modification is designed to concentrate genomic DNA of a target foodborne pathogen contaminant to facilitate the detection and subtyping of the pathogen in a single workflow. Here, we explain and demonstrate the sample preparation steps for the quasi-metagenomics analysis of Salmonella enterica from representative food and environmental samples including alfalfa sprouts, ground black pepper, ground beef, chicken breast and environmental swabs. Samples are first subjected to the culture enrichment of Salmonella for a shortened and adjustable duration (4-24 h). Salmonella cells are then selectively captured from the enrichment culture by immunomagnetic separation (IMS). Finally, multiple displacement amplification (MDA) is performed to amplify DNA from IMS-captured cells. The DNA output of this protocol can be sequenced by high throughput sequencing platforms. An optional quantitative PCR analysis can be performed to replace sequencing for Salmonella detection or assess the concentration of Salmonella DNA before sequencing.},
}
@article {pmid30417656,
year = {2018},
author = {Fonkou, MD and Dufour, JC and Dubourg, G and Raoult, D},
title = {Repertoire of bacterial species cultured from the human oral cavity and respiratory tract.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {},
doi = {10.2217/fmb-2018-0181},
pmid = {30417656},
issn = {1746-0921},
abstract = {While the gut microbiota is currently in the spotlight, the airway microbiome has been recently associated with several pulmonary diseases and carcinogenesis. As there are several biases associated with high-throughput sequencing methods, cultivation techniques are crucial for the investigation of the human microbiome. We thus aimed to build an exhaustive database, including a list of microbes isolated by culture from respiratory specimens, by performing a review of the literature. Herein, we have listed a total of 756 species cultured from the human respiratory tract. This represents 27.23% of the overall bacterial richness captured from human being by culture methods. This repertoire could be valuable for the elucidation of the interactions between the respiratory microbiome and human health.},
}
@article {pmid30417145,
year = {2018},
author = {Cordero, OJ and Varela-Calviño, R},
title = {Oral hygiene might prevent cancer.},
journal = {Heliyon},
volume = {4},
number = {10},
pages = {e00879},
doi = {10.1016/j.heliyon.2018.e00879},
pmid = {30417145},
issn = {2405-8440},
abstract = {Many evidences support that species from the Human Oral Microbiome Database such as Fusobacterium nucleatum or Bacteroides, linked previously to periodontitis and appendicitis, play a role in colorectal cancer (CRC), including metastasis. These typically oral species are invasive anaerobes that form biofilms in their virulent state. Aspirin (a NSAID) has been recently included into routine CRC prevention rationale. NSAIDs can prevent the growth of neoplastic lesions by inhibiting COX enzymes and another set of recently identified COX-independent targets, which include the WNT, AMPK and MTOR signaling pathways, the crosstalk between nucleoli and NF-κB transcriptional activity in apoptosis, and the biochemistry of platelets. These are signaling pathways related to tumor-promoting inflammation. In this process, pathogens or simple deregulation of the microbiota play an important role in CRC. Aspirin and other NSAIDs are efficient inhibitors of biofilm formation and able to control periodontitis development preventing inflammation related to the microbiota of the gingival tissue, so its seems plausible to include this pathway in the mechanisms that aspirin uses to prevent CRC. We propose arguments suggesting that current oral hygiene methods and other future developments against periodontitis might prevent CRC and probably other cancers, alone or in combination with other options; and that the multidisciplinary studies needed to prove this hypothesis might be relevant for cancer prevention.},
}
@article {pmid30417115,
year = {2018},
author = {Cai, J and Nichols, RG and Koo, I and Kalikow, ZA and Zhang, L and Tian, Y and Zhang, J and Smith, PB and Patterson, AD},
title = {Multiplatform Physiologic and Metabolic Phenotyping Reveals Microbial Toxicity.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00123-18},
pmid = {30417115},
issn = {2379-5077},
abstract = {The gut microbiota is susceptible to modulation by environmental stimuli and therefore can serve as a biological sensor. Recent evidence suggests that xenobiotics can disrupt the interaction between the microbiota and host. Here, we describe an approach that combines in vitro microbial incubation (isolated cecal contents from mice), flow cytometry, and mass spectrometry- and 1H nuclear magnetic resonance (NMR)-based metabolomics to evaluate xenobiotic-induced microbial toxicity. Tempol, a stabilized free radical scavenger known to remodel the microbial community structure and function in vivo, was studied to assess its direct effect on the gut microbiota. The microbiota was isolated from mouse cecum and was exposed to tempol for 4 h under strict anaerobic conditions. The flow cytometry data suggested that short-term tempol exposure to the microbiota is associated with disrupted membrane physiology as well as compromised metabolic activity. Mass spectrometry and NMR metabolomics revealed that tempol exposure significantly disrupted microbial metabolic activity, specifically indicated by changes in short-chain fatty acids, branched-chain amino acids, amino acids, nucleotides, glucose, and oligosaccharides. In addition, a mouse study with tempol (5 days gavage) showed similar microbial physiologic and metabolic changes, indicating that the in vitro approach reflected in vivo conditions. Our results, through evaluation of microbial viability, physiology, and metabolism and a comparison of in vitro and in vivo exposures with tempol, suggest that physiologic and metabolic phenotyping can provide unique insight into gut microbiota toxicity. IMPORTANCE The gut microbiota is modulated physiologically, compositionally, and metabolically by xenobiotics, potentially causing metabolic consequences to the host. We recently reported that tempol, a stabilized free radical nitroxide, can exert beneficial effects on the host through modulation of the microbiome community structure and function. Here, we investigated a multiplatform phenotyping approach that combines high-throughput global metabolomics with flow cytometry to evaluate the direct effect of tempol on the microbiota. This approach may be useful in deciphering how other xenobiotics directly influence the microbiota.},
}
@article {pmid30417113,
year = {2018},
author = {Cekanaviciute, E and Pröbstel, AK and Thomann, A and Runia, TF and Casaccia, P and Katz Sand, I and Crabtree, E and Singh, S and Morrissey, J and Barba, P and Gomez, R and Knight, R and Mazmanian, S and Graves, J and Cree, BAC and Zamvil, SS and Baranzini, SE},
title = {Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00083-18},
pmid = {30417113},
issn = {2379-5077},
abstract = {Multiple sclerosis (MS) is an autoimmune disease of the central nervous system characterized by adaptive and innate immune system dysregulation. Recent work has revealed moderate alteration of gut microbial communities in subjects with MS and in experimental, induced models. However, a mechanistic understanding linking the observed changes in the microbiota and the presence of the disease is still missing. Chloroform-resistant, spore-forming bacteria, which primarily belong to the classes Bacilli and Clostridia in the phylum Firmicutes, have been shown to exhibit immunomodulatory properties in vitro and in vivo, but they have not yet been characterized in the context of human disease. This study addresses the community composition and immune function of this bacterial fraction in MS. We identify MS-associated spore-forming taxa (primarily in the class Clostridia) and show that their presence correlates with impaired differentiation of IL-10-secreting, regulatory T lymphocytes in vitro. Colonization of antibiotic-treated mice with spore-forming bacteria allowed us to identify some bacterial taxa favoring IL-10+ lymphocyte differentiation and others inducing differentiation of proinflammatory, IFN-γ+ T lymphocytes. However, when fed into antibiotic-treated mice, both MS and control-derived spore-forming bacteria were able to induce similar IL-10-expressing Treg immunoregulatory responses, thus ameliorating symptoms of experimental allergic encephalomyelitis (EAE). Our analysis also identified Akkermansia muciniphila as a key organism that may interact either directly or indirectly with spore-forming bacteria to exacerbate the inflammatory effects of MS-associated gut microbiota. Thus, changes in the spore-forming fraction may influence T lymphocyte-mediated inflammation in MS. This experimental approach of isolating a subset of microbiota based on its functional characteristics may be useful to investigate other microbial fractions at greater depth. IMPORTANCE To address the impact of microbiome on disease development, it is essential to go beyond a descriptive study and evaluate the physiological importance of microbiome changes. Our study integrates computational analysis with in vitro and in vivo exploration of inflammatory properties of spore-forming microbial communities, revealing novel functional correlations. We specifically show that while small differences exist between the microbiomes of MS patients and healthy subjects, these differences are exacerbated in the chloroform-resistant fraction. We further demonstrate that, when purified from MS patients, this fraction is correlated with impaired immunomodulatory responses in vitro.},
}
@article {pmid30417112,
year = {2018},
author = {Boesmans, L and Valles-Colomer, M and Wang, J and Eeckhaut, V and Falony, G and Ducatelle, R and Van Immerseel, F and Raes, J and Verbeke, K},
title = {Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of Butyricicoccus pullicaecorum to Healthy Volunteers.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00094-18},
pmid = {30417112},
issn = {2379-5077},
abstract = {Advances in gut microbiota research have triggered interest in developing colon butyrate producers as niche-specific next-generation probiotics, targeted at increasing colon butyrate production and countering disease-associated microbiota alterations. Crucial steps in the development of next-generation probiotics are the design of formulations with a reasonable shelf life as well as the safety demonstration of an intervention in healthy volunteers. One such potential next-generation butyrate-producing probiotic is Butyricicoccus pullicaecorum 25-3T, with demonstrated safety in in vitro as well as animal models. Here, we examined the strain's safety, tolerability, and impact on microbiota composition and metabolic activity in healthy volunteers in a randomized, double-blind, placebo-controlled crossover study in 30 healthy volunteers. The study design consisted of two 4-week intervention periods (108 CFU B. pullicaecorum [treatment] or maltodextrin [placebo] per day) with a 3-week washout in between. We assessed adverse events, blood parameters (primary endpoints), and fecal microbiota composition and metabolite profiles (secondary endpoints). The number of reported adverse events during the B. pullicaecorum treatment was similar to that of placebo intervention, as were observed changes in blood chemistry parameters, bowel habits, and fecal calprotectin concentrations. Administration of the strain did not induce any disruptive effect in microbiota composition or metabolic activity. In this first human intervention trial with a butyrate-producing Clostridium cluster IV isolate, we demonstrated B. pullicaecorum 25-3T administration to be both safe and well tolerated by healthy participants. This safety study paves the way for the further development of the strain as a next-generation probiotic. IMPORTANCE This study is the first to determine the safety and tolerance in humans of a butyrate-producing Clostridium cluster IV next-generation probiotic. Advances in gut microbiota research have triggered interest in developing colon butyrate producers as next-generation probiotics. Butyricicoccus pullicaecorum 25-3T is one such potential probiotic, with demonstrated safety in vitro as well as in animal models. Here, we produced an encapsulated B. pullicaecorum formulation that largely preserved its viability over an 8-month storage period at 4°C. Administration of this formulation to healthy volunteers allowed us to establish the intervention as safe and well tolerated. The probiotic intervention did not cause disruptive alterations in the composition or metabolic activity of health-associated microbiota. The results presented pave the way for the exploration of the impact of the strain on microbiota alterations in a clinical setting.},
}
@article {pmid30417111,
year = {2018},
author = {Minich, JJ and Humphrey, G and Benitez, RAS and Sanders, J and Swafford, A and Allen, EE and Knight, R},
title = {High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00166-18},
pmid = {30417111},
issn = {2379-5077},
abstract = {Next-generation sequencing technologies have enabled many advances across biology, with microbial ecology benefiting primarily through expanded sample sizes. Although the cost of running sequencing instruments has decreased substantially over time, the price of library preparation methods has largely remained unchanged. In this study, we developed a low-cost miniaturized (5-µl volume) high-throughput (384-sample) amplicon library preparation method with the Echo 550 acoustic liquid handler. Our method reduces costs of library preparation to $1.42 per sample, a 58% reduction compared to existing automated methods and a 21-fold reduction from commercial kits, without compromising sequencing success or distorting the microbial community composition analysis. We further validated the optimized method by sampling five body sites from 46 Pacific chub mackerel fish caught across 16 sampling events over seven months from the Scripps Institution of Oceanography pier in La Jolla, CA. Fish microbiome samples were processed with the miniaturized 5-µl reaction volume with 0.2 µl of genomic DNA (gDNA) and the standard 25-µl reaction volume with 1 µl of gDNA. Between the two methods, alpha diversity was highly correlated (R2 > 0.95), while distances of technical replicates were much lower than within-body-site variation (P < 0.0001), further validating the method. The cost savings of implementing the miniaturized library preparation (going from triplicate 25-µl reactions to triplicate 5-µl reactions) are large enough to cover a MiSeq sequencing run for 768 samples while preserving accurate microbiome measurements. IMPORTANCE Reduced costs of sequencing have tremendously impacted the field of microbial ecology, allowing scientists to design more studies with larger sample sizes that often exceed 10,000 samples. Library preparation costs have not kept pace with sequencing prices, although automated liquid handling robots provide a unique opportunity to bridge this gap while also decreasing human error. Here, we take advantage of an acoustic liquid handling robot to develop a high-throughput miniaturized library preparation method of a highly cited and broadly used 16S rRNA gene amplicon reaction. We evaluate the potential negative effects of reducing the PCR volume along with varying the amount of gDNA going into the reaction. Our optimized method reduces sample-processing costs while continuing to generate a high-quality microbiome readout that is indistinguishable from the original method.},
}
@article {pmid30417109,
year = {2018},
author = {Mazel, F and Davis, KM and Loudon, A and Kwong, WK and Groussin, M and Parfrey, LW},
title = {Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?.},
journal = {mSystems},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSystems.00097-18},
pmid = {30417109},
issn = {2379-5077},
abstract = {Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as &quot;phylosymbiosis.&quot; Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.},
}
@article {pmid30417108,
year = {2018},
author = {Ren, L and Zhang, R and Rao, J and Xiao, Y and Zhang, Z and Yang, B and Cao, D and Zhong, H and Ning, P and Shang, Y and Li, M and Gao, Z and Wang, J},
title = {Transcriptionally Active Lung Microbiome and Its Association with Bacterial Biomass and Host Inflammatory Status.},
journal = {mSystems},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSystems.00199-18},
pmid = {30417108},
issn = {2379-5077},
abstract = {Alteration of the lung microbiome has been observed in several respiratory tract diseases. However, most previous studies were based on 16S ribosomal RNA and shotgun metagenome sequencing; the viability and functional activity of the microbiome, as well as its interaction with host immune systems, have not been well studied. To characterize the active lung microbiome and its associations with host immune response and clinical features, we applied metatranscriptome sequencing to bronchoalveolar lavage fluid (BALF) samples from 25 patients with chronic obstructive pulmonary disease (COPD) and from nine control cases without known pulmonary disease. Community structure analyses revealed three distinct microbial compositions, which were significantly correlated with bacterial biomass, human Th17 immune response, and COPD exacerbation frequency. Specifically, samples with transcriptionally active Streptococcus, Rothia, or Pseudomonas had bacterial loads 16 times higher than samples enriched for Escherichia and Ralstonia. These high-bacterial-load samples also tended to undergo a stronger Th17 immune response. Furthermore, an increased proportion of lymphocytes was found in samples with active Pseudomonas. In addition, COPD patients with active Streptococcus or Rothia infections tended to have lower rates of exacerbations than patients with active Pseudomonas and patients with lower bacterial biomass. Our results support the idea of a stratified structure of the active lung microbiome and a significant host-microbe interaction. We speculate that diverse lung microbiomes exist in the population and that their presence and activities could either influence or reflect different aspects of lung health. IMPORTANCE Recent studies of the microbiome proposed that resident microbes play a beneficial role in maintaining human health. Although lower respiratory tract disease is a leading cause of sickness and mortality, how the lung microbiome interacts with human health remains largely unknown. Here we assessed the association between the lung microbiome and host gene expression, cytokine concentration, and over 20 clinical features. Intriguingly, we found a stratified structure of the active lung microbiome which was significantly associated with bacterial biomass, lymphocyte proportion, human Th17 immune response, and COPD exacerbation frequency. These observations suggest that the microbiome plays a significant role in lung homeostasis. Not only microbial composition but also active functional elements and host immunity characteristics differed among different individuals. Such diversity may partially account for the variation in susceptibility to particular diseases.},
}
@article {pmid30417106,
year = {2018},
author = {DiMucci, D and Kon, M and Segrè, D},
title = {Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks.},
journal = {mSystems},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSystems.00181-18},
pmid = {30417106},
issn = {2379-5077},
abstract = {Microbes affect each other's growth in multiple, often elusive, ways. The ensuing interdependencies form complex networks, believed to reflect taxonomic composition as well as community-level functional properties and dynamics. The elucidation of these networks is often pursued by measuring pairwise interactions in coculture experiments. However, the combinatorial complexity precludes an exhaustive experimental analysis of pairwise interactions, even for moderately sized microbial communities. Here, we used a machine learning random forest approach to address this challenge. In particular, we show how partial knowledge of a microbial interaction network, combined with trait-level representations of individual microbial species, can provide accurate inference of missing edges in the network and putative mechanisms underlying the interactions. We applied our algorithm to three case studies: an experimentally mapped network of interactions between auxotrophic Escherichia coli strains, a community of soil microbes, and a large in silico network of metabolic interdependencies between 100 human gut-associated bacteria. For this last case, 5% of the network was sufficient to predict the remaining 95% with 80% accuracy, and the mechanistic hypotheses produced by the algorithm accurately reflected known metabolic exchanges. Our approach, broadly applicable to any microbial or other ecological network, may drive the discovery of new interactions and new molecular mechanisms, both for therapeutic interventions involving natural communities and for the rational design of synthetic consortia. IMPORTANCE Different organisms in a microbial community may drastically affect each other's growth phenotypes, significantly affecting the community dynamics, with important implications for human and environmental health. Novel culturing methods and the decreasing costs of sequencing will gradually enable high-throughput measurements of pairwise interactions in systematic coculturing studies. However, a thorough characterization of all interactions that occur within a microbial community is greatly limited both by the combinatorial complexity of possible assortments and by the limited biological insight that interaction measurements typically provide without laborious specific follow-ups. Here, we show how a simple and flexible formal representation of microbial pairs can be used for the classification of interactions via machine learning. The approach we propose predicts with high accuracy the outcome of yet-to-be performed experiments and generates testable hypotheses about the mechanisms of specific interactions.},
}
@article {pmid30417001,
year = {2018},
author = {Patil, NP and Le, V and Sligar, AD and Mei, L and Chavarria, D and Yang, EY and Baker, AB},
title = {Algal Polysaccharides as Therapeutic Agents for Atherosclerosis.},
journal = {Frontiers in cardiovascular medicine},
volume = {5},
number = {},
pages = {153},
doi = {10.3389/fcvm.2018.00153},
pmid = {30417001},
issn = {2297-055X},
abstract = {Seaweed-derived polysaccharides including agar and alginate, have found widespread applications in biomedical research and medical therapeutic applications including wound healing, drug delivery, and tissue engineering. Given the recent increases in the incidence of diabetes, obesity and hyperlipidemia, there is a pressing need for low cost therapeutics that can economically and effectively slow the progression of atherosclerosis. Marine polysaccharides have been consumed by humans for millennia and are available in large quantities at low cost. Polysaccharides such as fucoidan, laminarin sulfate and ulvan have shown promise in reducing atherosclerosis and its accompanying risk factors in animal models. However, others have been tested in very limited context in scientific studies. In this review, we explore the current state of knowledge for these promising therapeutics and discuss the potential and challenges of using seaweed derived polysaccharides as therapies for atherosclerosis.},
}
@article {pmid30416839,
year = {2018},
author = {Chu, H and Williams, B and Schnabl, B},
title = {Gut microbiota, fatty liver disease, and hepatocellular carcinoma.},
journal = {Liver research},
volume = {2},
number = {1},
pages = {43-51},
doi = {10.1016/j.livres.2017.11.005},
pmid = {30416839},
issn = {2096-2878},
abstract = {Intestinal bacteria contribute to the pathogenesis of non-alcoholic fatty liver disease (NAFLD). Recently developed microbial profiling techniques are beginning to shed light on the nature of the changes in the gut microbiota that accompany NAFLD and non-alcoholic steatohepatitis (NASH). In this review, we summarize the role of gut microbiota in the development of NAFLD, NASH, and hepatocellular carcinoma (HCC). We highlight the mechanisms by which gut microbiota contribute to NAFLD/NASH, including through alterations in gut epithelial permeability, choline metabolism, endogenous alcohol production, release of inflammatory cytokines, regulation of hepatic Toll-like receptor (TLR), and bile acid metabolism. In addition, we analyze possible mechanisms for enhanced hepatic carcinogenesis, including alterations in bile acid metabolism, release of inflammatory cytokines, and expression of TLR-4. Finally, we describe therapeutic approaches for NAFLD/NASH and preventive strategies for HCC involving modulation of the intestinal microbiota or affected host pathways. Although recent studies have provided useful information, large-scale prospective studies are required to better characterize the intestinal microbiota and metabolome, in order to demonstrate a causative role for changes in the gut microbiota in the etiology of NAFLD/NASH, to identify new therapeutic strategies for NAFLD/NASH, and to develop more effective methods of preventing HCC.},
}
@article {pmid30416739,
year = {2018},
author = {Wang, Z and Lou, H and Wang, Y and Shamir, R and Jiang, R and Chen, T},
title = {Erratum: Author Correction: GePMI: a statistical model for personal intestinal microbiome identification.},
journal = {NPJ biofilms and microbiomes},
volume = {4},
number = {},
pages = {28},
doi = {10.1038/s41522-018-0071-4},
pmid = {30416739},
issn = {2055-5008},
abstract = {[This corrects the article DOI: 10.1038/s41522-018-0065-2.].},
}
@article {pmid30416659,
year = {2018},
author = {Zhang, WQ and Zhao, SK and Luo, JW and Dong, XP and Hao, YT and Li, H and Shan, L and Zhou, Y and Shi, HB and Zhang, ZY and Peng, CL and Zhao, XG},
title = {Alterations of fecal bacterial communities in patients with lung cancer.},
journal = {American journal of translational research},
volume = {10},
number = {10},
pages = {3171-3185},
pmid = {30416659},
issn = {1943-8141},
abstract = {Emerging evidence suggests the microbiome may affect a number of diseases, including lung cancer. However, the direct relationship between gut bacteria and lung cancer remains uncharacterized. In this study, we directly sequenced the hypervariable V1-V2 regions of the 16S rRNA gene in fecal samples from patients with lung cancer and healthy volunteers. Unweighted principal coordinate analysis (PCoA) revealed a clear difference in the bacterial community membership between the lung cancer group and the healthy control group. The lung cancer group had remarkably higher levels of Bacteroidetes, Fusobacteria, Cyanobacteria, Spirochaetes, and Lentisphaerae but dramatically lower levels of Firmicutes and Verrucomicrobia than the healthy control group (P < 0.05). Despite significant interindividual variation, eight predominant genera were significantly different between the two groups. The lung cancer group had higher levels of Bacteroides, Veillonella, and Fusobacterium but lower levels of Escherichia-Shigella, Kluyvera, Fecalibacterium, Enterobacter, and Dialister than the healthy control group (P < 0.05). Most notably, correlations between certain specific bacteria and serum inflammatory biomarkers were identified. Our findings demonstrated an altered bacterial community in patients with lung cancer, providing a significant step in understanding the relationship between gut bacteria and lung cancer. To our knowledge, this is the first study to evaluate the correlations between certain specific bacteria and inflammatory indicators. To better understand this relationship, further studies should investigate the underlying mechanisms of gut bacteria in lung cancer animal models.},
}
@article {pmid30416540,
year = {2018},
author = {Graf, BL and Zhang, L and Corradini, MG and Kuhn, P and Newman, SS and Salbaum, JM and Raskin, I},
title = {Physicochemical differences between malanga (Xanthosoma sagittifolium) and potato (Solanum tuberosum) tubers are associated with differential effects on the gut microbiome.},
journal = {Journal of functional foods},
volume = {45},
number = {},
pages = {268-276},
doi = {10.1016/j.jff.2018.04.032},
pmid = {30416540},
issn = {1756-4646},
abstract = {Malanga (Xanthosoma sagittifolium) is used as a medicinal food for infant development and gastritis. We compared the physicochemical properties and gut microbial effects of malanga versus potato (Solanum tuberosum) using nutritional analysis, rheometry, in vitro TNO Intestinal Model, and C57Bl/6J mouse models. Malanga was characterized by higher starch (70.7% v. 66.3%), lower amylose:amylopectin (0.33 v. 0.59), higher free sugar (5.44% v. 3.23%), lower viscosity (271.0 v. 863.0 mPa.s), and higher bioaccessible and bioavailable sugar (0.89 v. 0.11 g bioaccessible sucrose per 20 g load in vitro; blood glucose levels of 129.1 v. 95.2 and 133.8 v. 104.3 mg/dL after 20 and 60 min in vivo). Gut microbiota of mice fed a high fat diet containing 20% malanga for 14 d exhibited significantly higher α diversity than those fed 20% potato, indicating that minor physicochemical differences between similar tuber crops are associated with significantly different effects on the gut microbiome.},
}
@article {pmid30416489,
year = {2018},
author = {Stamps, BW and Leddy, MB and Plumlee, MH and Hasan, NA and Colwell, RR and Spear, JR},
title = {Characterization of the Microbiome at the World's Largest Potable Water Reuse Facility.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2435},
doi = {10.3389/fmicb.2018.02435},
pmid = {30416489},
issn = {1664-302X},
abstract = {Conventional water resources are not sufficient in many regions to meet the needs of growing populations. Due to cyclical weather cycles, drought, and climate change, water stress has increased worldwide including in Southern California, which serves as a model for regions that integrate reuse of wastewater for both potable and non-potable use. The Orange County Water District (OCWD) Advanced Water Purification Facility (AWPF) is a highly engineered system designed to treat and produce up to 100 million gallons per day (MGD) of purified water from a municipal wastewater source for potable reuse. Routine facility microbial water quality analysis is limited to standard indicators at this and similar facilities. Given recent advances in high throughput DNA sequencing techniques, complete microbial profiling of communities in water samples is now possible. By using 16S/18S rRNA gene sequencing, metagenomic and metatranscriptomic sequencing coupled to a highly accurate identification method along with 16S rRNA gene qPCR, we describe a detailed view of the total microbial community throughout the facility. The total bacterial load of the water at stages of the treatment train ranged from 3.02 × 106 copies in source, unchlorinated wastewater feed to 5.49 × 101 copies of 16S rRNA gene/mL after treatment (consisting of microfiltration, reverse osmosis, and ultraviolet/advanced oxidation). Microbial diversity and load decreased by several orders of magnitude after microfiltration and reverse osmosis treatment, falling to almost non-detectable levels that more closely resembled controls of molecular grade laboratory water than the biomass detected in the source water. The presence of antibiotic resistance genes and viruses was also greatly reduced. Overall, system design performance was achieved, and comprehensive microbial community analysis was found to enable a more complete characterization of the water/wastewater microbial signature.},
}
@article {pmid30415891,
year = {2018},
author = {Gosalbes, MJ and Compte, J and Moriano-Gutierrez, S and Vallès, Y and Jiménez-Hernández, N and Pons, X and Artacho, A and Francino, MP},
title = {Metabolic adaptation in the human gut microbiota during pregnancy and the first year of life.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ebiom.2018.10.071},
pmid = {30415891},
issn = {2352-3964},
abstract = {BACKGROUND: The relationship between the gut microbiome and the human host is dynamic and we may expect adjustments in microbiome function if host physiology changes. Metatranscriptomic approaches should be key in unraveling how such adjustments occur.<br><br>METHODS: We employ metatranscriptomic sequencing analyses to study gene expression in the gut microbiota of infants through their first year of life, and of their mothers days before delivery and one year afterwards.<br><br>FINDINGS: In infants, hallmarks of aerobic metabolism disappear from the microbial metatranscriptome as development proceeds, while the expression of functions related to carbohydrate transport and metabolism increases and diversifies, approaching that observed in non-pregnant women. Butyrate synthesis enzymes are overexpressed at three months of age, even though most butyrate-producing organisms are still rare. In late pregnancy, the microbiota readjusts the expression of carbohydrate-related functions in a manner consistent with a high availability of glucose.<br><br>INTERPRETATION: Our findings suggest that butyrate production may be ensured in the gut of young infants before the typical butyrate synthesizers of the adult gut become abundant. The late pregnancy gut microbiota may be able to access the high levels of blood glucose characteristic of this period. Moreover, late pregnancy gut bacteria may reach stationary phase, which may affect their likelihood of translocating across the intestinal epithelium.<br><br>FUNDS: This work was supported by grants CSD2009-00006 (CONSOLIDER Program) and SAF2009-13032-C02-02 from MICINN (Ministry of Science and Innovation, Spain), and by grant SAF2012-31187 from MINECO (Ministry of Economics and Competitiveness, Spain).},
}
@article {pmid30415609,
year = {2018},
author = {Aslam, H and Green, J and Jacka, FN and Collier, F and Berk, M and Pasco, J and Dawson, SL},
title = {Fermented foods, the gut and mental health: a mechanistic overview with implications for depression and anxiety.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/1028415X.2018.1544332},
pmid = {30415609},
issn = {1476-8305},
abstract = {Mental disorders including depression and anxiety are often comorbid with gut problems, suggesting a bidirectional relationship between mental health and gut function. Several mechanisms might explain this comorbidity, such as inflammation and immune activation; intestinal permeability; perturbations in the hypothalamic-pituitary-adrenal axis; neurotransmitter/neuropeptide dysregulation; dietary deficiencies; and disturbed gut microbiome composition. The potential of modulating the microbiome-gut-brain axis, and subsequently mental health, through the use of functional foods, is an emerging and novel topic of interest. Fermented foods are considered functional foods due to their putative health benefits. The process of microbial fermentation converts food substrates into more nutritionally and functionally rich products, resulting in functional microorganisms (probiotics), substrates that enhance proliferation of beneficial bacteria in the gut (prebiotics), and bioactive components (biogenics). These functional ingredients act biologically in the gastrointestinal tract and have the ability to modify the gut microbiota, influence translocation of endotoxins and subsequent immune activation, and promote host nutrition. This narrative review explores the theoretical potential of the functional components present in fermented foods to alter gut physiology and to impact the biological mechanisms thought to underpin depression and anxiety. Pre-clinical studies indicate the benefits of fermented foods in relieving perturbed gut function and for animal models of depression and anxiety. However, in humans, the literature relating to the relevance of fermented food for treating or preventing depression and anxiety is sparse, heterogeneous and has significant limitations. This review identifies a critical research gap for further evaluation of fermented foods in the management of depression anxiety in humans.},
}
@article {pmid30415449,
year = {2018},
author = {Wang, F and Men, X and Zhang, G and Liang, K and Xin, Y and Wang, J and Li, A and Zhang, H and Liu, H and Wu, L},
title = {Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos.},
journal = {AMB Express},
volume = {8},
number = {1},
pages = {182},
doi = {10.1186/s13568-018-0713-1},
pmid = {30415449},
issn = {2191-0855},
support = {2017CP01//Yunnan Academy of Tobacco Sciences Project/ ; ZDYF2017155//Hainan's Key Project of Research and Development Plan/ ; 2017252//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; },
abstract = {Selection of optimal primer pairs in 16S rRNA gene sequencing is a pivotal issue in microorganism diversity analysis. However, limited effort has been put into investigation of specific primer sets for analysis of the bacterial diversity of aging flue-cured tobaccos (AFTs), as well as prediction of the function of the bacterial community. In this study, the performance of four primer pairs in determining bacterial community structure based on 16S rRNA gene sequences in AFTs was assessed, and the functions of genes were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Results revealed that the primer set 799F-1193R covering the amplification region V5V6V7 gave a more accurate picture of the bacterial community structure of AFTs, with lower co-amplification levels of chloroplast and mitochondrial genes, and more genera covered than when using the other primers. In addition, functional gene prediction suggested that the microbiome of AFTs was involved in kinds of interested pathways. A high abundance of functional genes involved in nitrogen metabolism was detected in AFTs, reflecting a high level of bacteria involved in degrading harmful nitrogen compounds and generating nitrogenous nutrients for others. Additionally, the functional genes involved in biosynthesis of valuable metabolites and degradation of toxic compounds provided information that the AFTs possess a huge library of microorganisms and genes that could be applied to further studies. All of these findings provide a significance reference for researchers working on the bacterial diversity assessment of tobacco-related samples.},
}
@article {pmid30415359,
year = {2018},
author = {Malfertheiner, P and Venerito, M and Schulz, C},
title = {Helicobacter pylori Infection: New Facts in Clinical Management.},
journal = {Current treatment options in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11938-018-0209-8},
pmid = {30415359},
issn = {1092-8472},
abstract = {PURPOSE: The global prevalence of Helicobacter pylori remains high in spite of its significant downwards trajectory in many regions. The clinical management of H. pylori infection merits guidance to meet ongoing challenges on whom and how to test, prevent, and cure related diseases.<br><br>RECENT FINDINGS: Several international guidelines and consensus reports have updated the management strategies for cure of the H. pylori infection. The definition of H. pylori gastritis as an infectious disease independent of whether or not presenting with clinical manifestations and symptoms has broadened the use of the test and treat strategy. Patients on selected long-term medications, such as aspirin, other anti-platelet agents, NSAIDs, and PPIs should be considered for H. pylori test and treat. Important progress is made with initiatives in primary and secondary gastric cancer prevention. Uncertainties persist in the interpretation of the role of H. pylori in association with extragastric diseases. Selection of therapies needs to address individual antibiotic resistance and regional surveillance of resistance for the adoption of an effective treatment algorithm.<br><br>CONCLUSION: Clinical aspects of H. pylori infection have evolved over time and the therapeutic management requires continuous adaptation. A vaccine is still a non-fulfilled promise. The future will tell us more about the role of H. pylori in interactions with the gut microbiome.},
}
@article {pmid30415167,
year = {2018},
author = {Singh, JP and Ojinnaka, EU and Krumins, JA and Goodey, NM},
title = {Abiotic factors determine functional outcomes of microbial inoculation of soils from a metal contaminated brownfield.},
journal = {Ecotoxicology and environmental safety},
volume = {168},
number = {},
pages = {450-456},
doi = {10.1016/j.ecoenv.2018.10.114},
pmid = {30415167},
issn = {1090-2414},
abstract = {Whole community microbial inoculation can improve soil function in contaminated environments. Here we conducted a case study to investigate whether biotic factors (inoculum) or abiotic factors (soil base) have more impact on the extracellular enzymatic activities in a whole community microbial inoculation. To this end, we cross-inoculated microbial communities between two heavy metal-contaminated soils, with high and low extracellular enzyme activities, respectively. We measured extracellular phosphatase activity, a proxy for soil function, after self- and cross-inoculation of microbial communities into sterilized soils, and all activities were normalized to non-inoculated controls. We found that inoculation increased phosphatase activity in the soils. For soils treated with different inocula, we found significant differences in the microbial community compositions but no significant differences in the extracellular phosphatase activities normalized to their respective sterilized, non-inoculated controls (4.7 ± 1.8 and 3.3 ± 0.5 for soils inoculated with microbial communities from 146 to 43, respectively). On the other hand, normalized phosphatase activities between the two soil bases were significantly different (4.1 ± 0.12 and 1.9 ± 0.12 for soil bases 146 and 43, respectively) regardless of the source of the inoculum that did not vary between soil bases. The results indicate that the abiotic properties of the soils were a significant predictor for phosphatase activity but not for the end-point composition of the microbial community. The findings suggest that targeted microbial inocula from metal contaminated soils can increase phosphatase activity, and likely soil functioning in general, but the degree to which this happens depends on the abiotic environment, in this case, metal contamination.},
}
@article {pmid30415160,
year = {2018},
author = {Davison, JM and Wischmeyer, PE},
title = {Probiotic and synbiotic therapy in the critically ill: State of the art.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {59},
number = {},
pages = {29-36},
doi = {10.1016/j.nut.2018.07.017},
pmid = {30415160},
issn = {1873-1244},
abstract = {Recent medical history has largely viewed our bacterial symbionts as pathogens to be eradicated rather than as essential partners in optimal health. However, one of the most exciting scientific advances in recent years has been the realization that commensal microorganisms (our microbiome) play vital roles in human physiology in nutrition, vitamin synthesis, drug metabolism, protection against infection, and recovery from illness. Recent data show that loss of &quot;health-promoting&quot; microbes and overgrowth of pathogenic bacteria (dysbiosis) in patients in the intensive care unit (ICU) appears to contribute to nosocomial infections, sepsis, and poor outcomes. Dysbiosis results from many factors, including ubiquitous antibiotic use and altered nutrition delivery in illness. Despite modern antibiotic therapy, infections and mortality from often multidrug-resistant organisms are increasing. This raises the question of whether restoration of a healthy microbiome via probiotics or synbiotics (probiotic and prebiotic combinations) to intervene on ubiquitous ICU dysbiosis would be an optimal intervention in critical illness to prevent infection and to improve recovery. This review will discuss recent innovative experimental data illuminating mechanistic pathways by which probiotics and synbiotics may provide clinical benefit. Furthermore, a review of recent clinical data demonstrating that probiotics and synbiotics can reduce complications in ICU and other populations will be undertaken. Overall, growing data for probiotic and symbiotic therapy reveal a need for definitive clinical trials of these therapies, as recently performed in healthy neonates. Future studies should target administration of probiotics and synbiotics with known mechanistic benefits to improve patient outcomes. Optimally, future probiotic and symbiotic studies will be conducted using microbiome signatures to characterize actual ICU dysbiosis and determine, and perhaps even personalize, ideal probiotic and symbiotic therapies.},
}
@article {pmid30414595,
year = {2018},
author = {Valdes, AM and Menni, C},
title = {Inflammatory markers and mediators in heart disease.},
journal = {Aging},
volume = {},
number = {},
pages = {},
doi = {10.18632/aging.101640},
pmid = {30414595},
issn = {1945-4589},
}
@article {pmid30414380,
year = {2018},
author = {Cześnikiewicz-Guzik, M and Nosalski, R and Mikolajczyk, TP and Vidler, F and Dohnal, T and Dembowska, E and Graham, D and Harrison, DG and Guzik, TJ},
title = {Th1 type immune responses to Porphyromonas gingivalis antigens exacerbate Angiotensin II dependent hypertension and vascular dysfunction.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.14536},
pmid = {30414380},
issn = {1476-5381},
abstract = {BACKGROUND AND PURPOSE: Emerging evidence indicates that hypertension is mediated by immune mechanisms. We hypothesized that exposure to Porphyromonas gingivalis antigens, commonly encountered in periodontal disease, can enhance immune activation in hypertension and exacerbate blood pressure elevation, vascular inflammation and vascular dysfunction.<br><br>EXPERIMENTAL APPROACH: Th1 immune response were elicited through immunizations using Porphyromonas gingivalis lysate antigens (10ug) conjugated with aluminium oxide (50ug) and IL-12 (1ug). The hypertension and vascular endothelial dysfunction evoked by sub-pressor doses of Angiotensin II (0.25mg/kg/day) were studied and vascular inflammation was quantified by flow cytometry and real time polymerase chain reaction.<br><br>KEY RESULTS: Systemic T cell activation, characteristic for hypertension, was exacerbated by P. gingivalis antigen stimulations. This translated into increased aortic vascular inflammation with enhanced leukocytes, in particular, T cell and macrophage infiltration. Expression of the Th1 cytokines, Interferon-γ and Tumour Necrosis Factor-α and the transcription factor TBX21 was increased in aortas of P. gingivalis/Interleukin-12/aluminium oxide immunized mice, while IL-4 and TGF-β were unchanged. These immune changes in mice with induced T helper type 1 immune responses were associated with enhanced blood pressure elevation and endothelial dysfunction compared to control mice in response to two weeks infusion of a sub-pressor dose of Angiotensin II.<br><br>CONCLUSION AND IMPLICATIONS: These studies support the concept that Th1 immune responses induced by bacterial antigens such as P. gingivalis can increase sensitivity to sub-pressor pro-hypertensive insults such as low dose Angiotensin II, therefore providing a mechanistic link between chronic infection such as periodontitis and hypertension.},
}
@article {pmid30414225,
year = {2018},
author = {Mullaney, TG and Lam, D and Kluger, R and D'Souza, B},
title = {Randomized controlled trial of probiotic use for post-colonoscopy symptoms.},
journal = {ANZ journal of surgery},
volume = {},
number = {},
pages = {},
doi = {10.1111/ans.14883},
pmid = {30414225},
issn = {1445-2197},
abstract = {BACKGROUND: Symptoms of bloating, discomfort and altered bowel function persist post-colonoscopy in up to 20% of patients. A previous randomized controlled trial of probiotics for post-colonoscopy symptoms has demonstrated a reduction in duration of pain with the use of probiotics. This was performed with air insufflation and the question was asked whether the effect would persist with the use of carbon dioxide to insufflate the colon.<br><br>METHODS: Eligible patients were recruited and randomized to receive either probiotic or placebo capsules post colonoscopy. A questionnaire was completed documenting the presence of pre-procedural and post-procedural symptoms for the following 2 weeks. The results were entered into a database and processed by an independent statistician. The primary outcome was mean pain score and incidence of bloating over the first 7 days and at 14 days post procedure. The secondary outcome was the time to return of normal bowel function.<br><br>RESULTS: Two hundred and forty participants were recruited and randomized (120 probiotic and 120 placebo). Data were available for 75 patients in the probiotic and 75 in the placebo group. There was no significant difference between groups in post-procedural discomfort, bloating nor time to return of normal bowel function. Subgroup analysis of the patients with preexisting symptoms showed a reduction in incidence of bloating with the use of probiotics.<br><br>CONCLUSION: There may be a role for the use of probiotics in the subgroup of patients with preexisting symptoms; however, routine use of probiotics to ameliorate post-procedural symptoms of carbon dioxide insufflation colonoscopy cannot be advocated.},
}
@article {pmid30414158,
year = {2019},
author = {Bosch, TCG},
title = {Hydra as Model to Determine the Role of FOXO in Longevity.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1890},
number = {},
pages = {231-238},
doi = {10.1007/978-1-4939-8900-3_19},
pmid = {30414158},
issn = {1940-6029},
abstract = {In non-senescent Hydra, continuously high activity of transcription factor FOXO contributes to continuous stem cell proliferation. Here, we describe how genetic manipulation of Hydra polyps using embryo-microinjection allows uncovering the role of FOXO in coordinating both stem cell proliferation and antimicrobial peptide0073 , effector molecules of the innate immune system, and regulators of the microbiome.},
}
@article {pmid30413754,
year = {2018},
author = {Tuncil, YE and Thakkar, RD and Marcia, ADR and Hamaker, BR and Lindemann, SR},
title = {Divergent short-chain fatty acid production and succession of colonic microbiota arise in fermentation of variously-sized wheat bran fractions.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16655},
doi = {10.1038/s41598-018-34912-8},
pmid = {30413754},
issn = {2045-2322},
abstract = {Though the physical structuring of insoluble dietary fiber sources may strongly impact their processing by microbiota in the colon, relatively little mechanistic information exists to explain how these aspects affect microbial fiber fermentation. Here, we hypothesized that wheat bran fractions varying in size would be fermented differently by gut microbiota, which would lead to size-dependent differences in metabolic fate (as short-chain fatty acids; SCFAs) and community structure. To test this hypothesis, we performed an in vitro fermentation assay in which wheat bran particles from a single source were separated by sieving into five size fractions and inoculated with fecal microbiota from three healthy donors. SCFA production, measured by gas chromatography, uncovered size fraction-dependent relationships between total SCFAs produced as well as the molar ratios of acetate, propionate, and butyrate. 16S rRNA sequencing revealed that these size-dependent metabolic outcomes were accompanied by the development of divergent microbial community structures. We further linked these distinct results to subtle, size-dependent differences in chemical composition. These results suggest that physical context can drive differences in microbiota composition and function, that fiber-microbiota interaction studies should consider size as a variable, and that manipulating the size of insoluble fiber-containing particles might be used to control gut microbiome composition and metabolic output.},
}
@article {pmid30413478,
year = {2018},
author = {Poudel, R and Jumpponen, A and Kennelly, MM and Rivard, CL and Gomez-Montano, L and Garrett, KA},
title = {Rootstocks shape the rhizobiome: Rhizosphere and endosphere bacterial communities in the grafted tomato system.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.01765-18},
pmid = {30413478},
issn = {1098-5336},
abstract = {Root-associated microbes are critical to plant health and performance, although understanding of the factors that structure these microbial communities and theory to predict microbial assemblages are still limited. Here we use a grafted tomato system to study the effects of rootstock genotypes and grafting in endosphere and rhizosphere microbiomes that were evaluated by sequencing 16S rRNA. We compared the microbiomes of nongrafted tomato cultivar BHN589, selfgrafted BHN589, and BHN589 grafted to Maxifort or RST-04-106 hybrid rootstocks. OTU-based bacterial diversity was greater in Maxifort compared to nongraft controls, whereas bacterial diversity in the controls (selfgraft and nongraft) and the other rootstock (RST-04-106) was similar. Grafting itself did not affect bacterial diversity; diversity in the selfgraft was similar to the nongraft. Bacterial diversity was higher in the rhizosphere than in the endosphere for all treatments. However, despite the lower overall diversity, there was a greater number of differentially abundant OTUs (DAOTUs) in the endosphere, with the greatest number of DAOTUs associated with Maxifort. In a PERMANOVA analysis, there was evidence for an effect of rootstock genotype on bacterial communities. The endosphere-rhizosphere compartment and study site explained a high percentage of the differences among bacterial communities. Further analyses identified OTUs responsive to rootstock genotypes in both the endosphere and the rhizosphere. Our findings highlight the effects of rootstocks on bacterial diversity and composition. The influence of rootstock and plant compartment on microbial communities indicates opportunities for the development of designer communities and microbiome-based breeding to improve future crop production.IMPORTANCE Understanding factors that control microbial communities is essential for designing and supporting microbiome-based agriculture. In this study, we used a grafted tomato system to study the effect of rootstock genotypes and grafting on bacterial communities colonizing the endosphere and the rhizosphere. Comparing the bacterial communities in control treatments (nongraft and selfgraft plants) with the hybrid rootstocks used by farmers, we evaluated the effect of rootstocks on overall bacterial diversity and composition. These findings indicate the potential for using plant genotype to indirectly select bacterial taxa. In addition, we identify taxa responsive to each rootstock treatments, which may represent candidate taxa useful for biocontrol and in biofertilizers.},
}
@article {pmid30412889,
year = {2018},
author = {Nathani, NM and Mootapally, C and Dave, BP},
title = {Antibiotic resistance genes allied to the pelagic sediment microbiome in the Gulf of Khambhat and Arabian Sea.},
journal = {The Science of the total environment},
volume = {653},
number = {},
pages = {446-454},
doi = {10.1016/j.scitotenv.2018.10.409},
pmid = {30412889},
issn = {1879-1026},
abstract = {Antibiotics have been widely spread in the environments, imposing profound stress on the resistome of the residing microbes. Marine microbiomes are well established large reservoirs of novel antibiotics and corresponding resistance genes. The Gulf of Khambhat is known for its extreme tides and complex sedimentation process. We performed high throughput sequencing and applied bioinformatics techniques on pelagic sediment microbiome across four coordinates of the Gulf of Khambhat to assess the marine resistome, its corresponding bacterial community and compared with the open Arabian Sea sample. We identified a total of 2354 unique types of resistance genes, with most abundant and diverse gene profile in the area that had anthropogenic activities being carried out on-shore. The genes with >1% abundance in all samples included carA, macB, sav1866, tlrC, srmB, taeA, tetA, oleC and bcrA which belonged to the macrolides, glycopeptides and peptide drug classes. ARG enriched phyla distribution was quite varying between all the sites, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes among the dominant phyla. Based on the outcomes, we also propose potential biomarker candidates Desulfovibrio, Thermotaga and Pelobacter for antibiotic monitoring in the two of the Gulf samples probable contamination prone environments, and genera Nitrosocccus, Marinobacter and Streptomyces in the rest of the three studied samples. Outcomes support the concept that ARGs naturally originate in environments and human activities contribute to the dissemination of antibiotic resistance.},
}
@article {pmid30412640,
year = {2018},
author = {Lin, C and Culver, J and Weston, B and Underhill, E and Gorky, J and Dhurjati, P},
title = {GutLogo: Agent-based modeling framework to investigate spatial and temporal dynamics in the gut microbiome.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0207072},
doi = {10.1371/journal.pone.0207072},
pmid = {30412640},
issn = {1932-6203},
abstract = {Knowledge of the spatial and temporal dynamics of the gut microbiome is essential to understanding the state of human health, as over a hundred diseases have been correlated with changes in microbial populations. Unfortunately, due to the complexity of the microbiome and the limitations of in vivo and in vitro experiments, studying spatial and temporal dynamics of gut bacteria in a biological setting is extremely challenging. Thus, in silico experiments present an excellent alternative for studying such systems. In consideration of these issues, we have developed a user-friendly agent-based model, GutLogo, that captures the spatial and temporal development of four representative bacterial genera populations in the ileum. We demonstrate the utility of this model by simulating population responses to perturbations in flow rate, nutrition, and probiotics. While our model predicts distinct changes in population levels due to these perturbations, most of the simulations suggest that the gut populations will return to their original steady states once the disturbance is removed. We hope that, in the future, the GutLogo model is utilized and customized by interested parties, as GutLogo can serve as a basic modeling framework for simulating a variety of physiological scenarios and can be extended to capture additional complexities of interest.},
}
@article {pmid30412600,
year = {2018},
author = {Shah, MS and DeSantis, T and Yamal, JM and Weir, T and Ryan, EP and Cope, JL and Hollister, EB},
title = {Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0207002},
doi = {10.1371/journal.pone.0207002},
pmid = {30412600},
issn = {1932-6203},
abstract = {Microbes colonizing colorectal cancer (CRC) tumors have the potential to affect disease, and vice-versa. The manner in which they differ from microbes in physically adjacent tissue or stool within the case in terms of both, taxonomy and biological activity remains unclear. In this study, we systematically analyzed previously published 16S rRNA sequence data from CRC patients with matched tumor:tumor-adjacent biopsies (n = 294 pairs, n = 588 biospecimens) and matched tumor biopsy:fecal pairs (n = 42 pairs, n = 84 biospecimens). Procrustes analyses, random effects regression, random forest (RF) modeling, and inferred functional pathway analyses were conducted to assess community similarity and microbial diversity across heterogeneous patient groups and studies. Our results corroborate previously reported association of increased Fusobacterium with tumor biopsies. Parvimonas and Streptococcus abundances were also elevated while Faecalibacterium and Ruminococcaceae abundances decreased in tumors relative to tumor-adjacent biopsies and stool samples from the same case. With the exception of these limited taxa, the majority of findings from individual studies were not confirmed by other 16S rRNA gene-based datasets. RF models comparing tumor and tumor-adjacent specimens yielded an area under curve (AUC) of 64.3%, and models of tumor biopsies versus fecal specimens exhibited an AUC of 82.5%. Although some taxa were shared between fecal and tumor samples, their relative abundances varied substantially. Inferred functional analysis identified potential differences in branched amino acid and lipid metabolism. Microbial markers that reliably occur in tumor tissue can have implications for microbiome based and microbiome targeting therapeutics for CRC.},
}
@article {pmid30412201,
year = {2018},
author = {Taroncher-Oldenburg, G and Jones, S and Blaser, M and Bonneau, R and Christey, P and Clemente, JC and Elinav, E and Ghedin, E and Huttenhower, C and Kelly, D and Kyle, D and Littman, D and Maiti, A and Maue, A and Olle, B and Segal, L and van Hylckama Vlieg, JET and Wang, J},
title = {Translating microbiome futures.},
journal = {Nature biotechnology},
volume = {36},
number = {11},
pages = {1037-1042},
doi = {10.1038/nbt.4287},
pmid = {30412201},
issn = {1546-1696},
}
@article {pmid30412196,
year = {2018},
author = {Kwak, MJ and Kong, HG and Choi, K and Kwon, SK and Song, JY and Lee, J and Lee, PA and Choi, SY and Seo, M and Lee, HJ and Jung, EJ and Park, H and Roy, N and Kim, H and Lee, MM and Rubin, EM and Lee, SW and Kim, JF},
title = {Author Correction: Rhizosphere microbiome structure alters to enable wilt resistance in tomato.},
journal = {Nature biotechnology},
volume = {36},
number = {11},
pages = {1117},
doi = {10.1038/nbt1118-1117},
pmid = {30412196},
issn = {1546-1696},
}
@article {pmid30411820,
year = {2018},
author = {Sapountzis, P and Nash, DR and Schiøtt, M and Boomsma, JJ},
title = {The evolution of abdominal microbiomes in fungus-growing ants.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.14931},
pmid = {30411820},
issn = {1365-294X},
abstract = {The attine ants are a monophyletic lineage that switched to fungus-farming ca. 55-60 MYA. They have become a model for the study of complex symbioses after additional fungal and bacterial symbionts were discovered, but their abdominal endosymbiotic bacteria remain largely unknown. Here we present a comparative microbiome analysis of endosymbiotic bacteria spanning the entire phylogenetic tree. We show that, across 17 representative sympatric species from eight genera sampled in Panama, abdominal microbiomes are dominated by Mollicutes, α- and γ-Proteobacteria, and Actinobacteria. Bacterial abundances increase from basal to crown branches in the phylogeny reflecting a shift towards putative specialized and abundant abdominal microbiota after the ants domesticated gongylidia-bearing cultivars, but before the origin of industrial-scale farming based on leaf-cutting herbivory. This transition coincided with the ancestral single colonization event of Central/North America ca. 20 MYA, documented in a recent phylogenomic study showing that the entire crown-group of the higher attine ants, including the leaf-cutting ants, evolved there and not in South America. Several bacterial species are located in gut tissues or abdominal organs of the evolutionarily derived, but not the basal attine ants. The composition of abdominal microbiomes appears to be affected by the presence/absence of defensive antibiotic-producing actinobacterial biofilms on the worker ants' cuticle, but the significance of this association remains unclear. The patterns of diversity, abundance, and sensitivity of the abdominal microbiomes that we obtained explore novel territory in the comparative analysis of attine fungus-farming symbioses and raise new questions for further in-depth research. This article is protected by copyright. All rights reserved.},
}
@article {pmid30411189,
year = {2018},
author = {Dror, H and Novak, L and Evans, JS and López-Legentil, S and Shenkar, N},
title = {Core and Dynamic Microbial Communities of Two Invasive Ascidians: Can Host-Symbiont Dynamics Plasticity Affect Invasion Capacity?.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1276-z},
pmid = {30411189},
issn = {1432-184X},
support = {2014025//United States - Israel Binational Science Foundation/ ; 2014025//United States - Israel Binational Science Foundation/ ; },
abstract = {Ascidians (Chordata, Ascidiacea) are considered to be prominent marine invaders, able to tolerate highly polluted environments and fluctuations in salinity and temperature. Here, we examined the seasonal and spatial dynamics of the microbial communities in the inner-tunic of two invasive ascidians, Styela plicata (Lesueur 1823) and Herdmania momus (Savigny 1816), in order to investigate the changes that occur in the microbiome of non-indigenous ascidians in different environments. Microbial communities were characterized using next-generation sequencing of partial (V4) 16S rRNA gene sequences. A clear differentiation between the ascidian-associated microbiome and bacterioplankton was observed, and two distinct sets of operational taxonomic units (OTUs), one core and the other dynamic, were recovered from both species. The relative abundance of the dynamic OTUs in H. momus was higher than in S. plicata, for which core OTU structure was maintained independently of location. Ten and seventeen core OTUs were identified in S. plicata and H. momus, respectively, including taxa with reported capabilities of carbon fixing, ammonia oxidization, denitrification, and heavy-metal processing. The ascidian-sourced dynamic OTUs clustered in response to site and season but significantly differed from the bacterioplankton community structure. These findings suggest that the associations between invasive ascidians and their symbionts may enhance host functionality while maintaining host adaptability to changing environmental conditions.},
}
@article {pmid30411009,
year = {2018},
author = {Van den Abbeele, P and Kamil, A and Fleige, L and Chung, Y and De Chavez, P and Marzorati, M},
title = {Different Oat Ingredients Stimulate Specific Microbial Metabolites in the Gut Microbiome of Three Human Individuals in Vitro.},
journal = {ACS omega},
volume = {3},
number = {10},
pages = {12446-12456},
doi = {10.1021/acsomega.8b01360},
pmid = {30411009},
issn = {2470-1343},
abstract = {We used a standardized in vitro simulation of the intestinal environment of three human donors to investigate the effect of six oat ingredients, which were produced by the application of different processing techniques, on the gut microbial community. Fructooligosaccharide was used as the positive control. Consistent changes in pH and gas production, on average -0.4 pH units and +32 kPa, indicated the high fermentability of the oat ingredients, and the resulting increased production of metabolites that are considered as beneficial for human health. These metabolites included acetate and lactate, but mostly propionate (+13.6 mM on average). All oat ingredients resulted in increased bifidobacteria levels with an average increase of 0.73 log. Moreover, a decreased production of proteolytic markers was observed, including branched short-chain fatty acids and ammonium. The results were donor-specific and product-specific. The results suggested an association between the total amounts of dietary fiber and the prebiotic potentials of different ingredients. Furthermore, as mechanical processing of oat products has previously been linked to increased extractability of dietary fibers, the obtained results suggest that different processing techniques might have impacted the potential functional properties of the final ingredients.},
}
@article {pmid30410727,
year = {2018},
author = {Morris, JJ},
title = {What is the hologenome concept of evolution?.},
journal = {F1000Research},
volume = {7},
number = {},
pages = {},
doi = {10.12688/f1000research.14385.1},
pmid = {30410727},
issn = {2046-1402},
abstract = {All multicellular organisms are colonized by microbes, but a gestalt study of the composition of microbiome communities and their influence on the ecology and evolution of their macroscopic hosts has only recently become possible. One approach to thinking about the topic is to view the host-microbiome ecosystem as a &quot;holobiont&quot;. Because natural selection acts on an organism's realized phenotype, and the phenotype of a holobiont is the result of the integrated activities of both the host and all of its microbiome inhabitants, it is reasonable to think that evolution can act at the level of the holobiont and cause changes in the &quot;hologenome&quot;, or the collective genomic content of all the individual bionts within the holobiont. This relatively simple assertion has nevertheless been controversial within the microbiome community. Here, I provide a review of recent work on the hologenome concept of evolution. I attempt to provide a clear definition of the concept and its implications and to clarify common points of disagreement.},
}
@article {pmid30410609,
year = {2018},
author = {Wu, J and Xu, S and Xiang, C and Cao, Q and Li, Q and Huang, J and Shi, L and Zhang, J and Zhan, Z},
title = {Tongue Coating Microbiota Community and Risk Effect on Gastric Cancer.},
journal = {Journal of Cancer},
volume = {9},
number = {21},
pages = {4039-4048},
doi = {10.7150/jca.25280},
pmid = {30410609},
issn = {1837-9664},
abstract = {Background: Although oral hygiene and health have long been reported to be associated with increased risk of gastric cancer (GC), the direct relationship of oral microbes with the risk of GC have not been evaluated fully. We aimed to test whether tongue coating microbiome was associated with GC risk. Methods: Pyrosequencing of 16S rRNA gene of tongue coating microbiome was used in 57 newly diagnosed gastric adenocarcinomas and 80 healthy controls. Benjamini-Hochberg (BH) was applied for multiple comparison correction. Co-abundance group (CAGs) analysis was adopted. Results: We found that higher relative abundance of Firmicutes, and lower of Bacteroidetes were associated with increased risk of GC. In genus level, Streptococcus trended with a higher risk of GC, the four other genera (Neisseria, Prevotella, Prevotella7, and Porphyromonas) were found to have a decreased risk of GC. Different from overall GC and non-cardia cancer, Alloprevotella and Veillonella trended with the higher risk of cardia cancer. Finally, we analyzed the microbiota by determining CAGs and six clusters were identified. Except the Cluster 2 (mainly Streptococcus and Abiotrophia), the other clusters had an inverse association with GC. Of them, the Cluster 6 (mainly Prevotella and Prevotella7 etc) had a relatively good classification power with 0.76 of AUC. Conclusion: Microbiome in tongue coating may have potential guiding value for early detection and prevention of GC.},
}
@article {pmid30410285,
year = {2018},
author = {Alexander, W},
title = {2018 European Association for the Study of Diabetes.},
journal = {P &amp; T : a peer-reviewed journal for formulary management},
volume = {43},
number = {11},
pages = {689-693},
pmid = {30410285},
issn = {1052-1372},
abstract = {We review sessions on the association of diuretic use and amputations, albiglutide and cardiovascular outcomes with diabetes and cardiovascular disease, how lorcaserin affects diabetes in overweight patients, how testosterone therapy improves diabetes in hypogonadal men, the pros and cons of gastric bypass surgery, how low-calorie sweeteners affect the gut microbiome, and more.},
}
@article {pmid30410105,
year = {2018},
author = {Tang, WHW and Li, DY and Hazen, SL},
title = {Dietary metabolism, the gut microbiome, and heart failure.},
journal = {Nature reviews. Cardiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41569-018-0108-7},
pmid = {30410105},
issn = {1759-5010},
abstract = {Advances in our understanding of how the gut microbiota contributes to human health and diseases have expanded our insight into how microbial composition and function affect the human host. Heart failure is associated with splanchnic circulation congestion, leading to bowel wall oedema and impaired intestinal barrier function. This situation is thought to heighten the overall inflammatory state via increased bacterial translocation and the presence of bacterial products in the systemic blood circulation. Several metabolites produced by gut microorganisms from dietary metabolism have been linked to pathologies such as atherosclerosis, hypertension, heart failure, chronic kidney disease, obesity, and type 2 diabetes mellitus. These findings suggest that the gut microbiome functions like an endocrine organ by generating bioactive metabolites that can directly or indirectly affect host physiology. In this Review, we discuss several newly discovered gut microbial metabolic pathways, including the production of trimethylamine and trimethylamine N-oxide, short-chain fatty acids, and secondary bile acids, that seem to participate in the development and progression of cardiovascular diseases, including heart failure. We also discuss the gut microbiome as a novel therapeutic target for the treatment of cardiovascular disease, and potential strategies for targeting intestinal microbial processes.},
}
@article {pmid30409838,
year = {2018},
author = {Tian, Y and Cai, J and Gui, W and Nichols, RG and Koo, I and Zhang, J and Anitha, M and Patterson, AD},
title = {Berberine Directly Impacts the Gut Microbiota to Promote Intestinal Farnesoid X Receptor Activation.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {},
number = {},
pages = {},
doi = {10.1124/dmd.118.083691},
pmid = {30409838},
issn = {1521-009X},
abstract = {Intestinal bacteria play an important role in bile acid metabolism and in the regulation of multiple host metabolic pathways (e.g., lipid and glucose homeostasis) through modulation of intestinal farnesoid X receptor (FXR) activity. Here, we examined the effect of berberine (BBR), a natural plant alkaloid, on intestinal bacteria using in vitro and in vivo models. In vivo, the metabolomic response and changes in mouse intestinal bacterial communities treated with BBR (100 mg/kg) for 5 days were assessed using NMR- and mass spectrometry-based metabolomics coupled with multivariate data analysis. Short-term BBR exposure altered intestinal bacteria by reducing the Clostridium cluster XIVa and IV and their bile salt hydrolase (BSH) activity, which resulted in the accumulation of taurocholic acid (TCA). The accumulation of TCA was associated with activation of intestinal FXR, which can mediate bile acid, lipid, and glucose metabolism. In vitro, isolated mouse cecal bacteria were incubated with three doses of BBR (0.1, 1, and 10 mg/ml) for 4 h in an anaerobic chamber. NMR-based metabolomics combined with flow cytometry was used to evaluate the direct physiologic and metabolic impact of BBR on the bacteria. In vitro, BBR exposure not only altered bacterial physiology, but also changed the bacterial community composition and function, especially reducing BSH expressing bacteria like Clostridium spp. These data suggest that BBR directly impacts bacteria to alter bile acid metabolism and activate FXR signaling. These data provide new insights into the link between intestinal bacteria, nuclear receptor signaling, and xenobiotics.},
}
@article {pmid30409598,
year = {2019},
author = {Wang, H and Shou, Y and Zhu, X and Xu, Y and Shi, L and Xiang, S and Feng, X and Han, J},
title = {Stability of vitamin B12 with the protection of whey proteins and their effects on the gut microbiome.},
journal = {Food chemistry},
volume = {276},
number = {},
pages = {298-306},
doi = {10.1016/j.foodchem.2018.10.033},
pmid = {30409598},
issn = {1873-7072},
abstract = {Cobalamin degrades in the presence of light and heat, which causes spectral changes and loss of coenzyme activity. In the presence of beta-lactoglobulin or alpha-lactalbumin, the thermal- and photostabilities of adenosylcobalamin (ADCBL) and cyanocobalamin (CNCBL) are increased by 10-30%. Similarly, the stabilities of ADCBL and CNCBL are increased in the presence of whey proteins by 19.7% and 2.2%, respectively, when tested in gastric juice for 2 h. Due to the limited absorption of cobalamin during digestion, excess cobalamin can enter the colon and modulate the gut microbiome. In a colonic model in vitro, supplementation with cobalamin and whey enhanced the proportions of Firmicutes and Bacteroidetes spp. and reduced those of Proteobacteria spp., which includes pathogens such as Escherichia and Shigella spp., and Pseudomonas spp. Thus, while complex formation could improve the stability and bioavailability of cobalamin, these complexes might also mediate gut microecology to influence human nutrition and health.},
}
@article {pmid30409559,
year = {2018},
author = {Shinde, R and McGaha, TL},
title = {The Aryl Hydrocarbon Receptor: Connecting Immunity to the Microenvironment.},
journal = {Trends in immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.it.2018.10.010},
pmid = {30409559},
issn = {1471-4981},
abstract = {The aryl hydrocarbon receptor (AhR) is a cytoplasmic receptor and transcription factor activated through cognate ligand binding. It is an important factor in immunity and tissue homeostasis, and structurally diverse compounds from the environment, diet, microbiome, and host metabolism can induce AhR activity. Emerging evidence suggests that AhR is a key sensor allowing immune cells to adapt to environmental conditions and changes in AhR activity have been associated with autoimmune disorders and cancer. Furthermore, AhR agonists or antagonists can impact immune disease outcomes identifying AhR as a potentially actionable target for immunotherapy. In this review, we describe known ligands stimulating AhR activity, downstream proinflammatory and suppressive mechanisms potentiated by AhR, and how this understanding is being applied to immunopathology to help control disease outcomes.},
}
@article {pmid30409169,
year = {2018},
author = {Ma, C and Sun, Z and Zeng, B and Huang, S and Zhao, J and Zhang, Y and Su, X and Xu, J and Wei, H and Zhang, H},
title = {Cow-to-mouse fecal transplantations suggest intestinal microbiome as one cause of mastitis.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {200},
doi = {10.1186/s40168-018-0578-1},
pmid = {30409169},
issn = {2049-2618},
support = {ID0E61AE8001//National Natural Science Foundation of China/ ; ID0EO2AE8002//Postdoctoral Science Foundation of Jiangsu Province/ ; },
abstract = {BACKGROUND: Mastitis, which affects nearly all lactating mammals including human, is generally thought to be caused by local infection of the mammary glands. For treatment, antibiotics are commonly prescribed, which however are of concern in both treatment efficacy and neonate safety. Here, using bovine mastitis which is the most costly disease in the dairy industry as a model, we showed that intestinal microbiota alone can lead to mastitis.<br><br>RESULTS: Fecal microbiota transplantation (FMT) from mastitis, but not healthy cows, to germ-free (GF) mice resulted in mastitis symptoms in mammary gland and inflammations in serum, spleen, and colon. Probiotic intake in parallel with FMT from diseased cows led to relieved mastitis symptoms in mice, by shifting the murine intestinal microbiota to a state that is functionally distinct from either healthy or diseased microbiota yet structurally similar to the latter. Despite conservation in mastitis symptoms, diseased cows and mice shared few mastitis-associated bacterial organismal or functional markers, suggesting striking divergence in mastitis-associated intestinal microbiota among lactating mammals. Moreover, an &quot;amplification effect&quot; of disease-health distinction in both microbiota structure and function was apparent during the cow-to-mouse FMT.<br><br>CONCLUSIONS: Hence, dysbiosis of intestinal microbiota may be one cause of mastitis, and probiotics that restore intestinal microbiota function are an effective and safe strategy to treat mastitis.},
}
@article {pmid30409123,
year = {2018},
author = {Rounge, TB and Meisal, R and Nordby, JI and Ambur, OH and de Lange, T and Hoff, G},
title = {Evaluating gut microbiota profiles from archived fecal samples.},
journal = {BMC gastroenterology},
volume = {18},
number = {1},
pages = {171},
doi = {10.1186/s12876-018-0896-6},
pmid = {30409123},
issn = {1471-230X},
support = {-//Cancer Registry of Norway Funds/ ; },
abstract = {BACKGROUND: Associations between colorectal cancer and microbiota have been identified. Archived fecal samples might be valuable sample sources for investigating causality in carcinogenesis and biomarkers discovery due to the potential of performing longitudinal studies. However, the quality, quantity and stability of the gut microbiota in these fecal samples must be assessed prior to such studies. We evaluated i) cross-contamination during analysis for fecal blood and ii) evaporation in stored perforated fecal immunochemical tests (iFOBT) samples, iii) temperature stability as well as iv) comparison of the gut microbiota diversity and composition in archived, iFOBT and fresh fecal samples in order to assess feasibility of large scale microbiota studies.<br><br>METHODS: The microbiota profiles were obtained by sequencing the V3-V4 region of 16S rDNA gene.<br><br>RESULTS: The iFOBT does not introduce any cross-sample contamination detectable by qPCR. Neither could we detect evaporation during freeze-thaw cycle of perforated iFOBT samples. Our results confirm room temperature stability of the gut microbiome. Diverse microbial profiles were achieved in 100% of fresh, 81% of long-term archived and 96% of iFOBT samples. Microbial diversity and composition were comparable between fresh and iFOBT samples, however, diversity differed significantly between long-term archived, fresh and iFOBT samples.<br><br>CONCLUSION: Our data showed that it is feasible to exploit archived fecal sample sets originally collected for testing of fecal blood. The advantages of using these sample sets for microbial biomarker discovery and longitudinal observational studies are the availability of high-quality diagnostic and follow-up data. However, care must be taken when microbiota are profiled in long-term archived fecal samples.},
}
@article {pmid30409105,
year = {2018},
author = {Heeney, DD and Zhai, Z and Bendiks, Z and Barouei, J and Martinic, A and Slupsky, C and Marco, ML},
title = {Lactobacillus plantarum bacteriocin is associated with intestinal and systemic improvements in diet-induced obese mice and maintains epithelial barrier integrity in vitro.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/19490976.2018.1534513},
pmid = {30409105},
issn = {1949-0984},
abstract = {We investigated the Lactobacillus plantarum bacteriocin plantaricin EF (PlnEF) system for its contributions to L. plantarum mediated benefits in a mouse model of diet-induced obesity. C57BL/6J mice on a high-fat diet (HFD) were administered a rifampicin resistant mutant of L. plantarum NCMIB8826 (NICMB8826-R) or an isogenic ΔplnEFI mutant strain, LM0419, every 48 h for nine weeks. Mice fed wild-type L. plantarum, but not LM0419, reduced their consumption of the HFD starting three weeks into the study and exhibited an overall 10% reduction in weight gain. The responses were independent of glucose homeostasis, as both NCMIB8826-R and LM0419 fed mice had improved oral glucose tolerance compared to sham controls. Although bacteriocins have antibacterial properties, the ileal, cecal, and fecal microbiota and cecocolic metabolomes were unchanged between mice fed either wild-type L. plantarum or the ΔplnEFI mutant. Instead, only mice fed NCMIB8826-R showed an increased production of ZO-1 in ileal tissues. To verify a potential role for the plantaricin EF system in supporting intestinal epithelial function, synthesized PlnEF peptides were applied to Caco-2 cell monolayers challenged with TNF-α and IFN-γ. The combination of PlnE and PlnF were required to prevent sustained cytokine-induced losses to Caco-2 cell para- and transcellular permeability and elevated IL-8 levels. In conclusion, this study shows that probiotic L. plantarum ameliorates the effects of obesogenic diets through a mechanism that involves the plantaricin EF system and likely includes L. plantarum - induced fortification of the intestinal epithelium.},
}
@article {pmid30409024,
year = {2018},
author = {Maki, KA and Diallo, AF and Lockwood, MB and Franks, AT and Green, SJ and Joseph, PV},
title = {Considerations When Designing a Microbiome Study: Implications for Nursing Science.},
journal = {Biological research for nursing},
volume = {},
number = {},
pages = {1099800418811639},
doi = {10.1177/1099800418811639},
pmid = {30409024},
issn = {1552-4175},
abstract = {Nurse scientists play an important role in studying complex relationships among human genetics, environmental factors, and the microbiome, all of which can contribute to human health and disease. Therefore, it is essential that they have the tools necessary to execute a successful microbiome research study. The purpose of this article is to highlight important methodological factors for nurse scientists to consider when designing a microbiome study. In addition to considering factors that influence host-associated microbiomes (i.e., microorganisms associated with organisms such as humans, mice, and rats), this manuscript highlights study designs and methods for microbiome analysis. Exemplars are presented from nurse scientists who have incorporated microbiome methods into their program of research. This review is intended to be a resource to guide nursing-focused microbiome research and highlights how study of the microbiome can be incorporated to answer research questions.},
}
@article {pmid30404281,
year = {2016},
author = {Kang, TH and Kim, HJ},
title = {Farewell to Animal Testing: Innovations on Human Intestinal Microphysiological Systems.},
journal = {Micromachines},
volume = {7},
number = {7},
pages = {},
doi = {10.3390/mi7070107},
pmid = {30404281},
issn = {2072-666X},
abstract = {The human intestine is a dynamic organ where the complex host-microbe interactions that orchestrate intestinal homeostasis occur. Major contributing factors associated with intestinal health and diseases include metabolically-active gut microbiota, intestinal epithelium, immune components, and rhythmical bowel movement known as peristalsis. Human intestinal disease models have been developed; however, a considerable number of existing models often fail to reproducibly predict human intestinal pathophysiology in response to biological and chemical perturbations or clinical interventions. Intestinal organoid models have provided promising cytodifferentiation and regeneration, but the lack of luminal flow and physical bowel movements seriously hamper mimicking complex host-microbe crosstalk. Here, we discuss recent advances of human intestinal microphysiological systems, such as the biomimetic human &quot;Gut-on-a-Chip&quot; that can employ key intestinal components, such as villus epithelium, gut microbiota, and immune components under peristalsis-like motions and flow, to reconstitute the transmural 3D lumen-capillary tissue interface. By encompassing cutting-edge tools in microfluidics, tissue engineering, and clinical microbiology, gut-on-a-chip has been leveraged not only to recapitulate organ-level intestinal functions, but also emulate the pathophysiology of intestinal disorders, such as chronic inflammation. Finally, we provide potential perspectives of the next generation microphysiological systems as a personalized platform to validate the efficacy, safety, metabolism, and therapeutic responses of new drug compounds in the preclinical stage.},
}
@article {pmid30408565,
year = {2018},
author = {DeFilipp, Z and Hohmann, E and Jenq, RR and Chen, YB},
title = {Fecal microbiota transplantation: restoring the injured microbiome after allogeneic hematopoietic cell transplantation.},
journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbmt.2018.10.022},
pmid = {30408565},
issn = {1523-6536},
abstract = {Disruption of the intestinal microbiome early after allogeneic hematopoietic cell transplantation (allo-HCT) has been linked to adverse outcomes in transplant recipients. To date, it remains unknown as to whether microbiome-directed interventions will be able to impact important clinical endpoints. Fecal microbiota transplantation (FMT) is a compelling intervention to restore healthy diversity to the intestinal microenvironment after allo-HCT, but currently has no established role in transplant recipients. In this review, we examine the utilization of FMT as treatment for Clostridium difficile infections and acute graft-versus-host disease, as well as a restorative intervention early after allo-HCT. Ongoing and planned studies will help determine the ultimate role of FMT in recipients of allo-HCT.},
}
@article {pmid30408471,
year = {2018},
author = {Wah, DTO and Ossenkopp, KP and Bishnoi, I and Kavaliers, M},
title = {Predator odor exposure in early adolescence influences the effects of the bacterial product, propionic acid, on anxiety, sensorimotor gating, and acoustic startle response in male rats in later adolescence and adulthood.},
journal = {Physiology &amp; behavior},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.physbeh.2018.11.003},
pmid = {30408471},
issn = {1873-507X},
abstract = {It is becoming evident than the adolescent period is a sensitive period in stress response programming. Stressors during this time may alter signaling from the gut microbiome, which has been shown to increase the risk for psychiatric disorders. It was hypothesized that adolescent stressors may potentiate the symptoms of anxiety and sensory abnormalities induced by a gut bacterial product, the short-chain fatty acid, propionic acid (PPA). The present study investigated the effects of repeated predator odor exposure during early adolescence on male rats administered PPA in late adolescence and adulthood on a behavioral test battery. Male adolescent Long-Evans rats were repeatedly exposed to a worn or unworn cat collar stimulus in early adolescence on postnatal days (P) 28, P30, P32, and P34. They were administered either PPA (500 mg/kg i.p.), or its vehicle in late adolescence on P40 and P43, and were subsequently tested on the light-dark anxiety task and acoustic startle task, respectively. In adulthood, the rats were again injected with PPA or its vehicle on P74 and P77, and subsequently tested on the light-dark apparatus and acoustic startle task, respectively. The repeated predator odor exposure was aversive and produced long-term anxiogenic effects as measured by the light-dark apparatus. PPA decreased activity and percent prepulse inhibition of the acoustic startle response, with its effects on vertical activity, a putative measure of escape behavior, being potentiated by prior predator stress. PPA's effects in adulthood were diminished in comparison to adolescence. These results suggest the importance of evaluating the effects of early adolescent stress on subsequent environmental insults on the development of behavioral abnormalities.},
}
@article {pmid30408195,
year = {2018},
author = {Kodama, WA and Xu, Z and Metcalf, JL and Song, SJ and Harrison, N and Knight, R and Carter, DO and Happy, CB},
title = {Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.13949},
pmid = {30408195},
issn = {1556-4029},
support = {2014-R2-CX-K011//National Institute of Justice/ ; //Office of Justice Programs/ ; //US Department of Justice/ ; },
abstract = {Microbes can be used effectively as trace evidence, at least in research settings. However, it is unknown whether skin microbiomes change prior to autopsy and, if so, whether these changes interfere with linking objects to decedents. The current study included microbiomes from 16 scenes of death in the City and County of Honolulu and tested whether objects at the scenes can be linked to individual decedents. Postmortem skin microbiomes were stable during repeated sampling up to 60 h postmortem and were similar to microbiomes of an antemortem population. Objects could be traced to decedents approximately 75% of the time, with smoking pipes and medical devices being especially accurate (100% match), house and car keys being poor (0%), and other objects like phones intermediate (~80%). These results show that microbes from objects at death scenes can be matched to individual decedents, opening up a new method of establishing associations and identifications.},
}
@article {pmid30408037,
year = {2018},
author = {Wu, HX and Chen, X and Chen, H and Lu, Q and Yang, Z and Ren, W and Liu, J and Shao, S and Wang, C and King-Jones, K and Chen, MS},
title = {Variation and diversification of the microbiome of Schlechtendalia chinensis on two alternate host plants.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0200049},
doi = {10.1371/journal.pone.0200049},
pmid = {30408037},
issn = {1932-6203},
abstract = {Schlechtendalia chinensis, a gall-inducing aphid, has two host plants in its life cycle. Its wintering host is a moss (typically Plagiomnium maximoviczii) and its main host is Rhus chinensis (Sumac), on which it forms galls during the summer. This study investigated bacteria associated with S. chinensis living on the two different host plants by sequencing 16S rRNAs. A total of 183 Operational Taxonomic Units (OTUs) from 50 genera were identified from aphids living on moss, whereas 182 OTUs from 49 genera were found from aphids living in Sumac galls. The most abundant bacterial genus among identified OTUs from aphids feeding on both hosts was Buchnera. Despite similar numbers of OTUs, the composition of bacterial taxa showed significant differences between aphids living on moss and those living on R. chinensis. Specifically, there were 12 OTUs from 5 genera (family) unique to aphids living on moss, and 11 OTUs from 4 genera (family) unique to aphids feeding in galls on R. chinensis. Principal Coordinate Analysis (PCoA) also revealed that bacteria from moss-residing aphids clustered differently from aphids collected from galls. Our results provide a foundation for future analyses on the roles of symbiotic bacteria in plant-aphid interactions in general, and how gall-specific symbionts differ in this respect.},
}
@article {pmid30407581,
year = {2018},
author = {Dempsey, JL and Wang, D and Siginir, G and Fei, Q and Raftery, D and Gu, H and Cui, JY},
title = {Pharmacological Activation of PXR and CAR Down-regulates Distinct Bile Acid-metabolizing Intestinal Bacteria and Alters Bile Acid Homeostasis.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1093/toxsci/kfy271},
pmid = {30407581},
issn = {1096-0929},
abstract = {The gut microbiome regulates important host metabolic pathways including xenobiotic metabolism and intermediary metabolism, such as the conversion of primary bile acids (BAs) into secondary BAs. The nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are well-known regulators for xenobiotic biotransformation in liver. However, little is known regarding the potential effects of PXR and CAR on the composition and function of the gut microbiome. To test our hypothesis that activation of PXR and CAR regulates gut microbiota and secondary BA synthesis, nine-week-old male conventional (CV) and germ-free (GF) mice were orally gavaged with corn oil, PXR agonist PCN (75 mg/kg), or CAR agonist TCPOBOP (3 mg/kg) once daily for four days. PCN and TCPOBOP decreased two taxa in the Bifidobacterium genus, which corresponded with decreased gene abundance of the BA-deconjugating enzyme bile salt hydrolase. In liver and small intestinal content (SIC) of GF mice, there was a TCPOBOP-mediated increase in total, primary, and conjugated BAs corresponding with increased Cyp7a1 mRNA. Bifidobacterium, Dorea, Peptociccaceae, Anaeroplasma, and Ruminococcus positively correlated with T-UDCA in LIC, but negatively correlated with T-CDCA in serum. In conclusion, PXR and CAR activation down-regulates BA-metabolizing bacteria in the intestine and modulates BA homeostasis in a gut microbiota-dependent manner.},
}
@article {pmid30407218,
year = {2018},
author = {Zhang, X and Guo, R and Kambara, H and Ma, F and Luo, HR},
title = {The role of CXCR2 in acute inflammatory responses and its antagonists as anti-inflammatory therapeutics.},
journal = {Current opinion in hematology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOH.0000000000000476},
pmid = {30407218},
issn = {1531-7048},
abstract = {PURPOSE OF REVIEW: CXCR2 is key stimulant of immune cell migration and recruitment, especially of neutrophils. Alleviating excessive neutrophil accumulation and infiltration could prevent prolonged tissue damage in inflammatory disorders. This review focuses on recent advances in our understanding of the role of CXCR2 in regulating neutrophil migration and the use of CXCR2 antagonists for therapeutic benefit in inflammatory disorders.<br><br>RECENT FINDINGS: Recent studies have provided new insights into how CXCR2 signaling regulates hematopoietic cell mobilization and function in both health and disease. We also summarize several CXCR2 regulatory mechanisms during infection and inflammation such as via Wip1, T-bet, P-selectin glycoprotein ligand-1, granulocyte-colony-stimulating factor, and microbiome. Moreover, we provide an update of studies investigating CXCR2 blockade in the laboratory and in clinical trials.<br><br>SUMMARY: Neutrophil homeostasis, migration, and recruitment must be precisely regulated. The CXCR2 signaling pathway is a potential target for modifying neutrophil dynamics in inflammatory disorders. We discuss the recent clinical use of CXCR2 antagonists for controlling inflammation.},
}
@article {pmid30406866,
year = {2018},
author = {Whidbey, C and Wright, AT},
title = {Activity-Based Protein Profiling-Enabling Multimodal Functional Studies of Microbial Communities.},
journal = {Current topics in microbiology and immunology},
volume = {},
number = {},
pages = {},
doi = {10.1007/82_2018_128},
pmid = {30406866},
issn = {0070-217X},
abstract = {Microorganisms living in community are critical to life on Earth, playing numerous and profound roles in the environment and human and animal health. Though their essentiality to life is clear, the mechanistic underpinnings of community structure, interactions, and functions are largely unexplored and in need of function-dependent technologies to unravel the mysteries. Activity-based protein profiling offers unprecedented molecular-level characterization of functions within microbial communities and provides an avenue to determine how external exposures result in functional alterations to microbiomes. Herein, we illuminate the current state and prospective contributions of ABPP as it relates to microbial communities. We provide details on the design, development, and validation of probes, challenges associated with probing in complex microbial communities, provide some specific examples of the biological applications of ABPP in microbes and microbial communities, and highlight potential areas for development. The future of ABPP holds real promise for understanding and considerable impact in microbiome studies associated with personalized medicine, precision agriculture, veterinary health, environmental studies, and beyond.},
}
@article {pmid30406643,
year = {2018},
author = {Gao, B and Chi, L and Tu, P and Gao, N and Lu, K},
title = {The carbamate aldicarb altered the gut microbiome, metabolome and lipidome of C57BL/6J mice.},
journal = {Chemical research in toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.chemrestox.8b00179},
pmid = {30406643},
issn = {1520-5010},
abstract = {The gut microbiome is highly involved in numerous aspects of host physiology, from energy harvest to stress response, and can confer many benefits to the host. The gut microbiome development could be affected by genetic and environmental factors, including the pesticides. The carbamate insecticide aldicarb has been extensively used in agriculture, which raises serious public health concern. However, the impact of aldicarb on the gut microbiome, host metabolome and lipidome has not been well studied yet. Herein, we use multi-omics approaches, including16S rRNA sequencing, shotgun metagenomics sequencing, metabolomics and lipidomics, to elucidate aldicarb-induced toxicity in the gut microbiome and the host metabolic homeostasis. We demonstrated that aldicarb perturbed the gut microbiome development trajectory, enhanced gut bacterial pathogenicity, altered complex lipid profile, induced oxidative stress, protein degradation and DNA damage. The brain metabolism was also disturbed by the aldicarb exposure. These findings may provide a novel understanding of the toxicity of carbamate insecticides.},
}
@article {pmid30406186,
year = {2018},
author = {Li, Y and Dugyala, SR and Ptacek, TS and Gilmore, JH and Frohlich, F},
title = {Maternal Immune Activation Alters Adult Behavior, Gut Microbiome and Juvenile Brain Oscillations in Ferrets.},
journal = {eNeuro},
volume = {5},
number = {5},
pages = {},
doi = {10.1523/ENEURO.0313-18.2018},
pmid = {30406186},
issn = {2373-2822},
abstract = {Maternal immune activation (MIA) has been identified as a causal factor in psychiatric disorders by epidemiological studies in humans and mechanistic studies in rodent models. Addressing this gap in species between mice and human will accelerate the understanding of the role of MIA in the etiology of psychiatric disorders. Here, we provide the first study of MIA in the ferret (Mustela putorius furo), an animal model with a rich history of developmental investigations due to the similarities in developmental programs and cortical organization with primates. We found that after MIA by injection of PolyIC in the pregnant mother animal, the adult offspring exhibited reduced social behavior, less eye contact with humans, decreased recognition memory, a sex-specific increase in amphetamine-induced hyperlocomotion, and altered gut microbiome. We also studied the neurophysiological properties of the MIA ferrets in development by in-vivo recordings of the local field potential (LFP) from visual cortex in five- to six-week-old animals, and found that the spontaneous and sensory-evoked LFP had decreased power, especially in the gamma frequency band. Overall, our results provide the first evidence for the detrimental effect of MIA in ferrets and support the use of the ferret as an intermediate model species for the study of disorders with neurodevelopmental origin.},
}
@article {pmid30406117,
year = {2018},
author = {Shang, Y and Kumar, S and Oakley, B and Kim, WK},
title = {Chicken Gut Microbiota: Importance and Detection Technology.},
journal = {Frontiers in veterinary science},
volume = {5},
number = {},
pages = {254},
doi = {10.3389/fvets.2018.00254},
pmid = {30406117},
issn = {2297-1769},
abstract = {Sustainable poultry meat and egg production is important to provide safe and quality protein sources in human nutrition worldwide. The gastrointestinal (GI) tract of chickens harbor a diverse and complex microbiota that plays a vital role in digestion and absorption of nutrients, immune system development and pathogen exclusion. However, the integrity, functionality, and health of the chicken gut depends on many factors including the environment, feed, and the GI microbiota. The symbiotic interactions between host and microbe is fundamental to poultry health and production. The diversity of the chicken GI microbiota is largely influenced by the age of the birds, location in the digestive tract and diet. Until recently, research on the poultry GI microbiota relied on conventional microbiological techniques that can only culture a small proportion of the complex community comprising the GI microbiota. 16S rRNA based next generation sequencing is a powerful tool to investigate the biological and ecological roles of the GI microbiota in chicken. Although several challenges remain in understanding the chicken GI microbiome, optimizing the taxonomic composition and biochemical functions of the GI microbiome is an attainable goal in the post-genomic era. This article reviews the current knowledge on the chicken GI function and factors that influence the diversity of gut microbiota. Further, this review compares past and current approaches that are used in chicken GI microbiota research. A better understanding of the chicken gut function and microbiology will provide us new opportunities for the improvement of poultry health and production.},
}
@article {pmid30406045,
year = {2018},
author = {Tsaousis, AD and Hamblin, KA and Elliott, CR and Young, L and Rosell-Hidalgo, A and Gourlay, CW and Moore, AL and van der Giezen, M},
title = {The Human Gut Colonizer Blastocystis Respires Using Complex II and Alternative Oxidase to Buffer Transient Oxygen Fluctuations in the Gut.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {371},
doi = {10.3389/fcimb.2018.00371},
pmid = {30406045},
issn = {2235-2988},
abstract = {Blastocystis is the most common eukaryotic microbe in the human gut. It is linked to irritable bowel syndrome (IBS), but its role in disease has been contested considering its widespread nature. This organism is well-adapted to its anoxic niche and lacks typical eukaryotic features, such as a cytochrome-driven mitochondrial electron transport. Although generally considered a strict or obligate anaerobe, its genome encodes an alternative oxidase. Alternative oxidases are energetically wasteful enzymes as they are non-protonmotive and energy is liberated in heat, but they are considered to be involved in oxidative stress protective mechanisms. Our results demonstrate that the Blastocystis cells themselves respire oxygen via this alternative oxidase thereby casting doubt on its strict anaerobic nature. Inhibition experiments using alternative oxidase and Complex II specific inhibitors clearly demonstrate their role in cellular respiration. We postulate that the alternative oxidase in Blastocystis is used to buffer transient oxygen fluctuations in the gut and that it likely is a common colonizer of the human gut and not causally involved in IBS. Additionally the alternative oxidase could act as a protective mechanism in a dysbiotic gut and thereby explain the absence of Blastocystis in established IBS environments.},
}
@article {pmid30405968,
year = {2018},
author = {Cicala, F and Cisterna-Céliz, JA and Moore, JD and Rocha-Olivares, A},
title = {Structure, dynamics and predicted functional role of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5830},
doi = {10.7717/peerj.5830},
pmid = {30405968},
issn = {2167-8359},
abstract = {The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities of abalone species characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their abalone host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA gene pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed that Mycoplasma dominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intraspecific variation. This resulted from changes in predominant species composition in each GI microbiota, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found between species for the explored metabolic pathways despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a significant taxonomic split and functional overlap between the microbiota of HF and HC abalone.},
}
@article {pmid30405931,
year = {2018},
author = {Singer, G and Kashofer, K and Castellani, C and Till, H},
title = {Hirschsprung's Associated Enterocolitis (HAEC) Personalized Treatment with Probiotics Based on Gene Sequencing Analysis of the Fecal Microbiome.},
journal = {Case reports in pediatrics},
volume = {2018},
number = {},
pages = {3292309},
doi = {10.1155/2018/3292309},
pmid = {30405931},
issn = {2090-6803},
abstract = {Approximately 40% of children with Hirschsprung's disease (HD) suffer from Hirschsprung's associated enterocolitis (HAEC) despite correct surgery. Disturbances of the intestinal microbiome may play a role. Treatment with probiotics based on individual analyses of the fecal microbiome has not been published for HD patients with recurrent HAEC yet. A boy with trisomy 21 received transanal pull-through at the age of 6 months for rectosigmoid HD. With four years, he suffered from recurrent episodes of HAEC. The fecal microbiome was measured during three healthy and three HAEC episodes by next-generation sequencing. The patient was started on daily probiotics for 3 months; the fecal microbiome was measured weekly. The fecal microbiome differed significantly between healthy and HAEC episodes. HAEC episodes were associated with significant decreases of Actinobacteria and significant increases of Bacteroidetes and Proteobacteria. Probiotic treatment led to a significant increase of alpha diversity and a significant increase of Bifidobacterium and Streptococcus as well as decreases of Rikenellaceae, Pseudobutyrivibrio, Blautia, and Lachnospiraceae. A longitudinal observation of the microbiome has never been performed following correction of Hirschsprung's disease. Probiotic treatment significantly changed the fecal microbiome; the alterations were not limited to strains contained in the administered probiotics.},
}
@article {pmid30405664,
year = {2018},
author = {Syranidou, E and Thijs, S and Avramidou, M and Weyens, N and Venieri, D and Pintelon, I and Vangronsveld, J and Kalogerakis, N},
title = {Responses of the Endophytic Bacterial Communities of Juncus acutus to Pollution With Metals, Emerging Organic Pollutants and to Bioaugmentation With Indigenous Strains.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1526},
doi = {10.3389/fpls.2018.01526},
pmid = {30405664},
issn = {1664-462X},
abstract = {Plants and their associated bacteria play a crucial role in constructed wetlands. In this study, the impact of different levels of pollution and bioaugmentation with indigenous strains individually or in consortia was investigated on the composition of the endophytic microbial communities of Juncus acutus. Five treatments were examined and compared in where the wetland plant was exposed to increasing levels of metal pollution (Zn, Ni, Cd) and emerging pollutants (BPA, SMX, CIP), enriched with different combinations of single or mixed endophytic strains. High levels of mixed pollution had a negative effect on alpha diversity indices of the root communities; moreover, the diversity indices were negatively correlated with the increasing metal concentrations. It was demonstrated that the root communities were separated depending on the level of mixed pollution, while the family Sphingomonadaceae exhibited the higher relative abundance within the root endophytic communities from high and low polluted treatments. This study highlights the effects of pollution and inoculation on phytoremediation efficiency based on a better understanding of the plant microbiome community composition.},
}
@article {pmid30405651,
year = {2018},
author = {Dita, M and Barquero, M and Heck, D and Mizubuti, ESG and Staver, CP},
title = {Fusarium Wilt of Banana: Current Knowledge on Epidemiology and Research Needs Toward Sustainable Disease Management.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1468},
doi = {10.3389/fpls.2018.01468},
pmid = {30405651},
issn = {1664-462X},
abstract = {Banana production is seriously threatened by Fusarium wilt (FW), a disease caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc). In the mid-twentieth century FW, also known as &quot;Panama disease&quot;, wiped out the Gros Michel banana industry in Central America. The devastation caused by Foc race 1 was mitigated by a shift to resistant Cavendish cultivars, which are currently the source of 99% of banana exports. However, a new strain of Foc, the tropical race 4 (TR4), attacks Cavendish clones and a diverse range of other banana varieties. Foc TR4 has been restricted to East and parts of Southeast Asia for more than 20 years, but since 2010 the disease has spread westward into five additional countries in Southeast and South Asia (Vietnam, Laos, Myanmar, India, and Pakistan) and at the transcontinental level into the Middle East (Oman, Jordan, Lebanon, and Israel) and Africa (Mozambique). The spread of Foc TR4 is of great concern due to the limited knowledge about key aspects of disease epidemiology and the lack of effective management models, including resistant varieties and soil management approaches. In this review we summarize the current knowledge on the epidemiology of FW of banana, highlighting knowledge gaps in pathogen survival and dispersal, factors driving disease intensity, soil and plant microbiome and the dynamics of the disease. Comparisons with FW in other crops were also made to indicate possible differences and commonalities. Our current understanding of the role of main biotic and abiotic factors on disease intensity is reviewed, highlighting research needs and futures directions. Finally, a set of practices and their impact on disease intensity are discussed and proposed as an integrative management approach that could eventually be used by a range of users, including plant protection organizations, researchers, extension workers and growers.},
}
@article {pmid30405595,
year = {2018},
author = {Lai, KP and Ng, AH and Wan, HT and Wong, AY and Leung, CC and Li, R and Wong, CK},
title = {Dietary Exposure to the Environmental Chemical, PFOS on the Diversity of Gut Microbiota, Associated With the Development of Metabolic Syndrome.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2552},
doi = {10.3389/fmicb.2018.02552},
pmid = {30405595},
issn = {1664-302X},
abstract = {The gut microbiome is a dynamic ecosystem formed by thousands of diverse bacterial species. This bacterial diversity is acquired early in life and shaped over time by a combination of multiple factors, including dietary exposure to distinct nutrients and xenobiotics. Alterations of the gut microbiota composition and associated metabolic activities in the gut are linked to various immune and metabolic diseases. The microbiota could potentially interact with xenobiotics in the gut environment as a result of their board enzymatic capacities and thereby affect the bioavailability and toxicity of the xenobiotics in enterohepatic circulation. Consequently, microbiome-xenobiotic interactions might affect host health. Here, we aimed to investigate the effects of dietary perfluorooctane sulfonic acid (PFOS) exposure on gut microbiota in adult mice and examine the induced changes in animal metabolic functions. In mice exposed to dietary PFOS for 7 weeks, body PFOS and lipid contents were measured, and to elucidate the effects of PFOS exposure, the metabolic functions of the animals were assessed using oral glucose-tolerance test and intraperitoneal insulin-tolerance and pyruvate-tolerance tests; moreover, on Day 50, cecal bacterial DNA was isolated and subject to 16S rDNA sequencing. Our results demonstrated that PFOS exposure caused metabolic disturbances in the animals, particularly in lipid and glucose metabolism, but did not substantially affect the diversity of gut bacterial species. However, marked modulations were detected in the abundance of metabolism-associated bacteria belonging to the phyla Firmicutes, Bacteroidetes, Proteobacteria, and Cyanobacteria, including, at different taxonomic levels, Turicibacteraceae, Turicibacterales, Turicibacter, Dehalobacteriaceae, Dehalobacterium, Allobaculum, Bacteroides acidifaciens, Alphaproteobacteria, and 4Cod-2/YS2. The results of PICRUSt analysis further indicated that PFOS exposure perturbed gut metabolism, inducing notable changes in the metabolism of amino acids (arginine, proline, lysine), methane, and a short-chain fatty acid (butanoate), all of which are metabolites widely recognized to be associated with inflammation and metabolic functions. Collectively, our study findings provide key information regarding the biological relevance of microbiome-xenobiotic interactions associated with the ecology of gut microbiota and animal energy metabolism.},
}
@article {pmid30405589,
year = {2018},
author = {Jarvis, KG and Daquigan, N and White, JR and Morin, PM and Howard, LM and Manetas, JE and Ottesen, A and Ramachandran, P and Grim, CJ},
title = {Microbiomes Associated With Foods From Plant and Animal Sources.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2540},
doi = {10.3389/fmicb.2018.02540},
pmid = {30405589},
issn = {1664-302X},
abstract = {Food microbiome composition impacts food safety and quality. The resident microbiota of many food products is influenced throughout the farm to fork continuum by farming practices, environmental factors, and food manufacturing and processing procedures. Currently, most food microbiology studies rely on culture-dependent methods to identify bacteria. However, advances in high-throughput DNA sequencing technologies have enabled the use of targeted 16S rRNA gene sequencing to profile complex microbial communities including non-culturable members. In this study we used 16S rRNA gene sequencing to assess the microbiome profiles of plant and animal derived foods collected at two points in the manufacturing process; post-harvest/pre-retail (cilantro) and retail (cilantro, masala spice mixes, cucumbers, mung bean sprouts, and smoked salmon). Our findings revealed microbiome profiles, unique to each food, that were influenced by the moisture content (dry spices, fresh produce), packaging methods, such as modified atmospheric packaging (mung bean sprouts and smoked salmon), and manufacturing stage (cilantro prior to retail and at retail). The masala spice mixes and cucumbers were comprised mainly of Proteobacteria, Firmicutes, and Actinobacteria. Cilantro microbiome profiles consisted mainly of Proteobacteria, followed by Bacteroidetes, and low levels of Firmicutes and Actinobacteria. The two brands of mung bean sprouts and the three smoked salmon samples differed from one another in their microbiome composition, each predominated by either by Firmicutes or Proteobacteria. These data demonstrate diverse and highly variable resident microbial communities across food products, which is informative in the context of food safety, and spoilage where indigenous bacteria could hamper pathogen detection, and limit shelf life.},
}
@article {pmid30405577,
year = {2018},
author = {Bertelli, C and Courtois, S and Rosikiewicz, M and Piriou, P and Aeby, S and Robert, S and Loret, JF and Greub, G},
title = {Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2520},
doi = {10.3389/fmicb.2018.02520},
pmid = {30405577},
issn = {1664-302X},
abstract = {In drinking water distribution systems (DWDS), a disinfectant residual is usually applied to limit bacterial regrowth. However, delivering water with no or reduced chlorine residual could potentially decrease the selection for antimicrobial resistant microorganisms, favor bacterial regrowth and result in changes in bacterial populations. To evaluate the feasibility of water reduction in local DWDS while ensuring water safety, water quality was measured over 2 months in two different networks, each of them harboring sub-areas with normal and reduced chlorine. Water quality remained good in chlorine reduced samples, with limited development of total flora and absence of coliforms. Furthermore, 16S rRNA amplicon-based metagenomics was used to investigate the diversity and the composition of microbial communities in the sub-networks. Taxonomic classification of sequence reads showed a reduced bacterial diversity in sampling points with higher chlorine residuals. Chlorine disinfection created more homogeneous bacterial population, dominated by Pseudomonas, a genus that contains some major opportunistic pathogens such as P. aeruginosa. In the absence of chlorine, a larger and unknown biodiversity was unveiled, also highlighted by a decreased rate of taxonomic classification to the genus and species level. Overall, this experiment in a functional DWDS will facilitate the move toward potable water delivery systems without residual disinfectants and will improve water taste for consumers.},
}
@article {pmid30405571,
year = {2018},
author = {Biagi, E and Aceti, A and Quercia, S and Beghetti, I and Rampelli, S and Turroni, S and Soverini, M and Zambrini, AV and Faldella, G and Candela, M and Corvaglia, L and Brigidi, P},
title = {Microbial Community Dynamics in Mother's Milk and Infant's Mouth and Gut in Moderately Preterm Infants.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2512},
doi = {10.3389/fmicb.2018.02512},
pmid = {30405571},
issn = {1664-302X},
abstract = {Mother's own milk represents the optimal source for preterm infant nutrition, as it promotes immune defenses and gastrointestinal function, protects against necrotizing enterocolitis, improves long-term clinical outcome and is hypothesized to drive gut microbiota assembly. Preterm infants at birth usually do not receive their mother's milk directly from the breast, because active suckling and coordination between suckling, swallowing and breathing do not develop until 32-34 weeks gestational age, but actual breastfeeding is usually possible as they grow older. Here, we enrolled moderately preterm infants (gestational age 32-34 weeks) to longitudinally characterize mothers' milk and infants' gut and oral microbiomes, up to more than 200 days after birth, through 16S rRNA sequencing. This peculiar population offers the chance to disentangle the differential contribution of human milk feeding per se vs. actual breastfeeding in the development of infant microbiomes, that have both been acknowledged as crucial contributors to short and long-term infant health status. In this cohort, the milk microbiome composition seemed to change following the infant's latching to the mother's breast, shifting toward a more diverse microbial community dominated by typical oral microbes, i.e., Streptococcus and Rothia. Even if all infants in the present study were fed human milk, features typical of healthy, full term, exclusively breastfed infants, i.e., high percentages of Bifidobacterium and low abundances of Pseudomonas in fecal and oral samples, respectively, were detected in samples taken after actual breastfeeding started. These findings underline the importance of encouraging not only human milk feeding, but also an early start of actual breastfeeding in preterm infants, since the infant's latching to the mother's breast might constitute an independent factor helping the health-promoting assembly of the infant gut microbiome.},
}
@article {pmid30405455,
year = {2018},
author = {Horne, R and Foster, JA},
title = {Metabolic and Microbiota Measures as Peripheral Biomarkers in Major Depressive Disorder.},
journal = {Frontiers in psychiatry},
volume = {9},
number = {},
pages = {513},
doi = {10.3389/fpsyt.2018.00513},
pmid = {30405455},
issn = {1664-0640},
abstract = {Advances in understanding the role of the microbiome in physical and mental health are at the forefront of medical research and hold potential to have a direct impact on precision medicine approaches. In the past 7 years, we have studied the role of microbiota-brain communication on behavior in mouse models using germ-free mice, mice exposed to antibiotics, and healthy specific pathogen free mice. Through our work and that of others, we have seen an amazing increase in our knowledge of how bacteria signal to the brain and the implications this has for psychiatry. Gut microbiota composition and function are influenced both by genetics, age, sex, diet, life experiences, and many other factors of psychiatric and bodily disorders and thus may act as potential biomarkers of the gut-brain axis that could be used in psychiatry and co-morbid conditions. There is a particular need in major depressive disorder and other mental illness to identify biomarkers that can stratify patients into more homogeneous groups to provide better treatment and for development of new therapeutic approaches. Peripheral outcome measures of host-microbe bidirectional communication have significant translational value as biomarkers. Enabling stratification of clinical populations, based on individual biological differences, to predict treatment response to pharmacological and non-pharmacological interventions. Here we consider the links between co-morbid metabolic syndrome and depression, focusing on biomarkers including leptin and ghrelin in combination with assessing gut microbiota composition, as a potential tool to help identify individual differences in depressed population.},
}
@article {pmid30405366,
year = {2018},
author = {Russo, EB},
title = {Cannabis Therapeutics and the Future of Neurology.},
journal = {Frontiers in integrative neuroscience},
volume = {12},
number = {},
pages = {51},
doi = {10.3389/fnint.2018.00051},
pmid = {30405366},
issn = {1662-5145},
abstract = {Neurological therapeutics have been hampered by its inability to advance beyond symptomatic treatment of neurodegenerative disorders into the realm of actual palliation, arrest or reversal of the attendant pathological processes. While cannabis-based medicines have demonstrated safety, efficacy and consistency sufficient for regulatory approval in spasticity in multiple sclerosis (MS), and in Dravet and Lennox-Gastaut Syndromes (LGS), many therapeutic challenges remain. This review will examine the intriguing promise that recent discoveries regarding cannabis-based medicines offer to neurological therapeutics by incorporating the neutral phytocannabinoids tetrahydrocannabinol (THC), cannabidiol (CBD), their acidic precursors, tetrahydrocannabinolic acid (THCA) and cannabidiolic acid (CBDA), and cannabis terpenoids in the putative treatment of five syndromes, currently labeled recalcitrant to therapeutic success, and wherein improved pharmacological intervention is required: intractable epilepsy, brain tumors, Parkinson disease (PD), Alzheimer disease (AD) and traumatic brain injury (TBI)/chronic traumatic encephalopathy (CTE). Current basic science and clinical investigations support the safety and efficacy of such interventions in treatment of these currently intractable conditions, that in some cases share pathological processes, and the plausibility of interventions that harness endocannabinoid mechanisms, whether mediated via direct activity on CB1 and CB2 (tetrahydrocannabinol, THC, caryophyllene), peroxisome proliferator-activated receptor-gamma (PPARγ; THCA), 5-HT1A (CBD, CBDA) or even nutritional approaches utilizing prebiotics and probiotics. The inherent polypharmaceutical properties of cannabis botanicals offer distinct advantages over the current single-target pharmaceutical model and portend to revolutionize neurological treatment into a new reality of effective interventional and even preventative treatment.},
}
@article {pmid30405234,
year = {2018},
author = {Eisenstein, M},
title = {Ulcerative colitis: towards remission.},
journal = {Nature},
volume = {563},
number = {7730},
pages = {S33},
doi = {10.1038/d41586-018-07276-2},
pmid = {30405234},
issn = {1476-4687},
}
@article {pmid30405233,
year = {2018},
author = {Eisenstein, M},
title = {Gut reaction.},
journal = {Nature},
volume = {563},
number = {7730},
pages = {S34-S35},
doi = {10.1038/d41586-018-07277-1},
pmid = {30405233},
issn = {1476-4687},
}
@article {pmid30405201,
year = {2018},
author = {Wankhade, UD and Zhong, Y and Kang, P and Alfaro, M and Chintapalli, SV and Piccolo, BD and Mercer, KE and Andres, A and Thakali, KM and Shankar, K},
title = {Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16502},
doi = {10.1038/s41598-018-34453-0},
pmid = {30405201},
issn = {2045-2322},
support = {6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; },
abstract = {The contributions of maternal diet and obesity in shaping offspring microbiome remain unclear. Here we employed a mouse model of maternal diet-induced obesity via high-fat diet feeding (HFD, 45% fat calories) for 12 wk prior to conception on offspring gut microbial ecology. Male and female offspring were provided access to control or HFD from weaning until 17 wk of age. Maternal HFD-associated programming was sexually dimorphic, with male offspring from HFD dams showing hyper-responsive weight gain to postnatal HFD. Likewise, microbiome analysis of offspring cecal contents showed differences in α-diversity, β-diversity and higher Firmicutes in male compared to female mice. Weight gain in offspring was significantly associated with abundance of Lachnospiraceae and Clostridiaceae families and Adlercreutzia, Coprococcus and Lactococcus genera. Sex differences in metagenomic pathways relating to lipid metabolism, bile acid biosynthesis and immune response were also observed. HFD-fed male offspring from HFD dams also showed worse hepatic pathology, increased pro-inflammatory cytokines, altered expression of bile acid regulators (Cyp7a1, Cyp8b1 and Cyp39a1) and serum bile acid concentrations. These findings suggest that maternal HFD alters gut microbiota composition and weight gain of offspring in a sexually dimorphic manner, coincident with fatty liver and a pro-inflammatory state in male offspring.},
}
@article {pmid30405146,
year = {2018},
author = {Lloyd, MM and Pespeni, MH},
title = {Microbiome shifts with onset and progression of Sea Star Wasting Disease revealed through time course sampling.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16476},
doi = {10.1038/s41598-018-34697-w},
pmid = {30405146},
issn = {2045-2322},
support = {IOS-1555058//National Science Foundation (NSF)/ ; IOS-1555058//National Science Foundation (NSF)/ ; },
abstract = {The recent outbreak of Sea Star Wasting Disease (SSWD) is one of the largest marine epizootics in history, but the host-associated microbial community changes specific to disease progression have not been characterized. Here, we sampled the microbiomes of ochre sea stars, Pisaster ochraceus, through time as animals stayed healthy or became sick and died with SSWD. We found community-wide differences in the microbiomes of sick and healthy sea stars, changes in microbial community composition through disease progression, and a decrease in species richness of the microbiome in late stages of SSWD. Known beneficial taxa (Pseudoalteromonas spp.) decreased in abundance at symptom onset and through disease progression, while known pathogenic (Tenacibaculum spp.) and putatively opportunistic bacteria (Polaribacter spp. and Phaeobacter spp.) increased in abundance in early and late disease stages. Functional profiling revealed microbes more abundant in healthy animals performed functions that inhibit growth of other microbes, including pathogen detection, biosynthesis of secondary metabolites, and degradation of xenobiotics. Changes in microbial composition with disease onset and progression suggest that a microbial imbalance of the host could lead to SSWD or be a consequence of infection by another pathogen. This work highlights the importance of the microbiome in SSWD and also suggests that a healthy microbiome may help confer resistance to SSWD.},
}
@article {pmid30405010,
year = {2018},
author = {Rodríguez-Rabassa, M and López, P and Rodríguez-Santiago, RE and Cases, A and Felici, M and Sánchez, R and Yamamura, Y and Rivera-Amill, V},
title = {Cigarette Smoking Modulation of Saliva Microbial Composition and Cytokine Levels.},
journal = {International journal of environmental research and public health},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/ijerph15112479},
pmid = {30405010},
issn = {1660-4601},
support = {NIMHD-G12-MD007579//National Institutes of Health/ ; 5 NU58DP005055-05-00//Centers for Disease Control and Prevention/ ; },
abstract = {Tobacco use has been implicated as an immunomodulator in the oral cavity and contributes to the development of oral cancer. In the present study, we investigated the effects of cigarette smoking on bacterial diversity and host responses compared to healthy nonsmoking controls. Saliva samples were collected from eighteen smokers and sixteen nonsmoking individuals by passive drool. The 16S rRNA gene was used to characterize the salivary microbiome by using the Illumina MiSeq platform. Cytokine and chemokine expression analyses were performed to evaluate the host response. Significant differences in cytokine and chemokine expression levels of MDC, IL-10, IL-5, IL-2, IL-4, IL-7, adrenocorticotropic hormone (ACTH), insulin, and leptin were observed between smokers and nonsmokers. Taxonomic analyses revealed differences between the two groups, and some bacterial genera associated with the smokers group had correlations with hormones and cytokines identified as statistically different between smokers and nonsmokers. These factors have been associated with inflammation and carcinogenesis in the oral cavity. The data obtained may aid in the identification of the interactions between the salivary microbiome, host inflammatory responses, and metabolism in smokers.},
}
@article {pmid30404810,
year = {2018},
author = {Harvey, E and Rose, K and Eden, JS and Lo, N and Abeyasuriya, T and Shi, M and Doggett, SL and Holmes, EC},
title = {Extensive Diversity of RNA Viruses in Australian Ticks.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JVI.01358-18},
pmid = {30404810},
issn = {1098-5514},
abstract = {Understanding the microbiome of ticks in Australia is of considerable interest given the ongoing debate over whether Lyme disease, and its causative agent the bacterium Borrelia burgdorferi sensu lato, are present in Australia. The diversity of bacteria infecting Australian ticks has been studied using both culture and metagenomics based techniques. However, little is known about the virome of Australian ticks, including whether this includes viruses with the potential to infect mammals. We used a meta-transcriptomics approach to reveal the diversity and evolution of viruses from Australian ticks collected from two locations on the central-east coast of Australia, including metropolitan Sydney. From this we identified 19 novel RNA viruses belonging to 12 families, as well as one previously described RNA virus. The majority of these viruses were related to arthropod-associated viruses suggesting that they do not utilize mammalian hosts. However, two novel viruses discovered in ticks feeding on bandicoot marsupials clustered closely within the mammalian-associated hepacivirus and pestivirus groups (family Flaviviridae). Another bandicoot tick yielded a novel coltivirus (family Reoviridae) - a group of largely tick-associated viruses containing the known human pathogen Colorado tick fever virus and its relative Eyach virus. Importantly, our transcriptomic data provided no evidence for the presence of B. burgdorferi s.l. in any tick sample, providing further evidence against the presence of Lyme Disease in Australia. In sum, this study reveals that Australian ticks harbor a diverse virome, including some viruses that merit additional screening in the context of emerging infectious disease.IMPORTANCE Each year a growing number of individuals along the east coast of Australia experience debilitating disease following tick bites. As there is no evidence for the presence of the causative agent of Lyme disease, Borrelia Burgdorferi sensu lato, in Australian ticks, the etiological basis of this disease syndrome remains controversial. To characterize the viruses associated with Australian ticks, particularly those that might be associated with mammalian infection, we performed unbiased RNA sequencing on 146 ticks collected across two locations along the coast of New South Wales, Australia. This revealed 19 novel RNA viruses from a diverse set of families. Notably, three of these viruses clustered with known mammalian viruses, including a novel coltivirus that was related to the human pathogen Colorado tick fever virus.},
}
@article {pmid30404570,
year = {2018},
author = {Alam, A and Neish, A},
title = {Role of gut microbiota in intestinal wound healing and barrier function.},
journal = {Tissue barriers},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/21688370.2018.1539595},
pmid = {30404570},
issn = {2168-8370},
abstract = {The mammalian intestine harbors a highly complex and abundant ensemble of bacteria that flourish in a nutrient-rich environment while profoundly influencing many aspects of host biology. The intestine coevolved with its resident microbes in a manner where the mucosa developed a barrier function to segregate the resident microbes from the rest of the body, and yet paradoxically, allowing integration of microbial signals for the host benefit. In this review, we provided a comprehensive overview of why the gut microbiota is key to the efficient development and maintenance of the intestinal barrier. We also highlighted how a destabilized equilibrium between gut microbiota and the host may eventuate in a wide range of intestinal diseases characterized by the disrupted intestinal barrier. Finally, the review delineated how microenvironmental changes in the injured mucosa result in an enrichment of a pro-regenerating consortium of bacteria, which augments mucosal wound repair and restoration of barrier functions.},
}
@article {pmid30404568,
year = {2018},
author = {Bajorek, S and Parker, L and Li, N and Winglee, K and Weaver, M and Johnson, J and Sioda, M and Gauthier, J and Lemas, DJ and Jobin, C and Lorca, G and Neu, J and Fodor, AA},
title = {Initial microbial community of the neonatal stomach immediately after birth.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/19490976.2018.1520578},
pmid = {30404568},
issn = {1949-0984},
abstract = {The purpose of this prospective cross-sectional cohort pilot study is to explore the initial microbial community of gastric aspirate fluid as collected immediately after birth and its relationships with mode of delivery and preterm birth. Twenty-nine gastric aspirate samples collected immediately after birth from infants born between 24-40 weeks gestation were analyzed for microbial composition. Total microbial content was low in many samples, with a substantial number sharing taxonomic composition with negative controls. qPCR targeting the 16S rRNA gene showed that infants delivered vaginally had a higher microbial load than infants delivered by C-section. Some pre-term samples showed high relative abundance of genus Ureaplasma, consistent with previous literature that has implicated infections with this taxon as a potential cause of pre-term birth. Vaginally born term infant samples, by contrast, had significantly higher levels of genus Lactobacillus with Lactobacillus crispatus the most dominant species. Microbial evaluation showed that vaginally born term infant gastric aspirate samples had higher levels of lactobacilli than pre-terms. Samples from many infants had low microbial load near the edge of the detection limit.},
}
@article {pmid30403635,
year = {2018},
author = {Zheng, H and Wang, H and Dewhurst, R and Roehe, R},
title = {Improving the Inference of Co-occurrence Networks in the Bovine Rumen Microbiome.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1109/TCBB.2018.2879342},
pmid = {30403635},
issn = {1557-9964},
abstract = {The importance of the composition and signature of rumen microbial communities has gained increasing attention. One of the key techniques was to infer co-abundance networks through correlation analysis based on relative abundances. In this study, we proposed the use of a framework including a compendium of two correlation measures and three dissimilarity metrics to mitigate the compositional effect in the inference of significant associations in the bovine rumen microbiome. We tested the framework on rumen microbiome data including both 16S rRNA and KEGG genes associated with methane production in cattle. Based on the identification of significant positive and negative associations supported by multiple metrics, two co-occurrence networks, e.g. co-presence and mutual-exclusion networks, were constructed. Significant modules associated with methane emissions were identified. In comparison to previous studies, our analysis demonstrates that deriving microbial associations based on the correlations between relative abundances may not only lead to missing information but also produce spurious associations. To bridge together different co-presence and mutual-exclusion relations, a multiplex network model has been proposed for integrative analysis of co-occurrence networks which has great potential to support the prediction of animal phytotypes and to provide additional insights into biological mechanisms of the microbiome associated with the traits.},
}
@article {pmid30402924,
year = {2018},
author = {Ketchesin, KD and Becker-Krail, D and McClung, CA},
title = {Mood-Related Central and Peripheral Clocks.},
journal = {The European journal of neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1111/ejn.14253},
pmid = {30402924},
issn = {1460-9568},
abstract = {Mood disorders, including major depression, bipolar disorder, and seasonal affective disorder, are debilitating disorders that affect a significant portion of the global population. Individuals suffering from mood disorders often show significant disturbances in circadian rhythms and sleep. Moreover, environmental disruptions to circadian rhythms can precipitate or exacerbate mood symptoms in vulnerable individuals. Circadian clocks exist throughout the central nervous system and periphery, where they regulate a wide variety of physiological processes implicated in mood regulation. These processes include monoaminergic and glutamatergic transmission, HPA axis function, metabolism, and immune function. While there seems to be a clear link between circadian rhythm disruption and mood regulation, the mechanisms that underlie this association remain unclear. This review will touch on the interactions between the circadian system and each of these processes and discuss their potential role in the development of mood disorders. While clinical studies are presented, much of the review will focus on studies in animal models, which are attempting to elucidate the molecular cellular mechanisms in which circadian genes regulate mood. This article is protected by copyright. All rights reserved.},
}
@article {pmid30402873,
year = {2018},
author = {Ceresola, ER and Ferrarese, R and Preti, A and Canducci, F},
title = {Targeting patients' microbiota with probiotics and natural fibers in adults and children with constipation.},
journal = {European review for medical and pharmacological sciences},
volume = {22},
number = {20},
pages = {7045-7057},
pmid = {30402873},
issn = {2284-0729},
abstract = {OBJECTIVE: Functional constipation (FC) is a common condition in which the gut microbiota composition plays a fundamental role. The increasing knowledge on the role of gut microbes in the regulation of gut motility and stool consistency has allowed reconsidering, with a new scientific-based approach, the possibility to target the composition of intestinal bacterial populations for FC treatment. In this review, we evaluate recent attempts that used prebiotics, natural fibers or probiotics to treat FC, with a deep microbiome-based focus.<br><br>MATERIALS AND METHODS: This is a literature review of articles published in Medline, Web of Science, and the Cochrane Library. Studies on FC in adults and children were identified using the following terms: constipation AND probiotics OR prebiotics OR synbiotics PR fibers OR microbiome OR microbiota. Selected animal studies were also considered if showing mechanistic observations.<br><br>RESULTS: FC is associated with alteration in microbiome composition. Motility and fecal consistency are affected with different efficacy by the type of fiber, prebiotic or probiotic strain used in patients.<br><br>CONCLUSIONS: Selected bacterial strains, mainly belonging to the Bifidobacterium genus, and some poorly or non-fermented natural fibers, such as Psyllium, may significantly improve FC and may represent the basis for an effective supplementation.},
}
@article {pmid30402680,
year = {2018},
author = {Shah, A and Morrison, M and Holtmann, G},
title = {A novel treatment for patients with constipation: Dawn of a new age for translational microbiome research?.},
journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12664-018-0912-3},
pmid = {30402680},
issn = {0975-0711},
}
@article {pmid30402335,
year = {2018},
author = {Hwang, JS and Im, CR and Im, SH},
title = {Erratum: Immune Disorders and Its Correlation with Gut Microbiome.},
journal = {Immune network},
volume = {18},
number = {5},
pages = {e40},
doi = {10.4110/in.2018.18.e40},
pmid = {30402335},
issn = {1598-2629},
abstract = {[This corrects the article on p. 129 in vol. 12, PMID: 23091436.].},
}
@article {pmid30402068,
year = {2018},
author = {Al Rubaiee, Z and Al-Murayati, H and Møller, AP},
title = {Recapture probability, flight morphology, and microorganisms.},
journal = {Current zoology},
volume = {64},
number = {3},
pages = {277-283},
doi = {10.1093/cz/zox030},
pmid = {30402068},
issn = {1674-5507},
abstract = {Microorganisms on and within organisms are ubiquitous and interactions with their hosts range from mutualistic over commensal, to pathogenic. We hypothesized that microorganisms might affect the ability of barn swallows Hirundo rustica to escape from potential predators, with positive associations between the abundance of microorganisms and escape ability implying mutualistic effects, while negative associations would imply antagonistic effects. We quantified escape behavior as the ability to avoid capture in a mist net and hence as a small number of recaptures. Because recapture probability may also depend on timing of reproduction and reproductive success, we also tested whether the association between recapture and microorganisms was mediated by an association between recapture and life history. We found intermediate to strong positive relationships between recapture probability and abundance of Bacillus megaterium, but not abundance of other bacteria or fungi. The abundance of B. megaterium was associated with an advance in laying date and an increase in reproductive success. However, these effects were independent of the number of recaptures. This interpretation is supported by the fact that there was no direct correlation between laying date and reproductive success on one hand and the number of recaptures on the other. These findings have implications not only for predator-prey interactions, but also for capture-mark-recapture analyses of vital rates such as survival and dispersal.},
}
@article {pmid30401869,
year = {2018},
author = {Rackaityte, E and Lynch, SV},
title = {Rules of engagement in the gut microbiome.},
journal = {Nature medicine},
volume = {24},
number = {11},
pages = {1642-1644},
doi = {10.1038/s41591-018-0242-0},
pmid = {30401869},
issn = {1546-170X},
}
@article {pmid30401779,
year = {2018},
author = {Bratburd, JR and Keller, C and Vivas, E and Gemperline, E and Li, L and Rey, FE and Currie, CR},
title = {Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans.},
journal = {mBio},
volume = {9},
number = {6},
pages = {},
doi = {10.1128/mBio.02032-18},
pmid = {30401779},
issn = {2150-7511},
abstract = {The gut microbiota confers resistance to pathogens of the intestinal ecosystem, yet the dynamics of pathogen-microbiome interactions and the metabolites involved in this process remain largely unknown. Here, we use gnotobiotic mice infected with the virulent pathogen Salmonella enterica serovar Typhimurium or the opportunistic pathogen Candida albicans in combination with metagenomics and discovery metabolomics to identify changes in the community and metabolome during infection. To isolate the role of the microbiota in response to pathogens, we compared mice monocolonized with the pathogen, uninfected mice &quot;humanized&quot; with a synthetic human microbiome, or infected humanized mice. In Salmonella-infected mice, by 3 days into infection, microbiome community structure and function changed substantially, with a rise in Enterobacteriaceae strains and a reduction in biosynthetic gene cluster potential. In contrast, Candida-infected mice had few microbiome changes. The LC-MS metabolomic fingerprint of the cecum differed between mice monocolonized with either pathogen and humanized infected mice. Specifically, we identified an increase in glutathione disulfide, glutathione cysteine disulfide, inosine 5'-monophosphate, and hydroxybutyrylcarnitine in mice infected with Salmonella in contrast to uninfected mice and mice monocolonized with Salmonella These metabolites potentially play a role in pathogen-induced oxidative stress. These results provide insight into how the microbiota community members interact with each other and with pathogens on a metabolic level.IMPORTANCE The gut microbiota is increasingly recognized for playing a critical role in human health and disease, especially in conferring resistance to both virulent pathogens such as Salmonella, which infects 1.2 million people in the United States every year (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, et al., Emerg Infect Dis 17:7-15, 2011, https://doi.org/10.3201/eid1701.P11101), and opportunistic pathogens like Candida, which causes an estimated 46,000 cases of invasive candidiasis each year in the United States (Centers for Disease Control and Prevention, Antibiotic Resistance Threats in the United States, 2013, 2013). Using a gnotobiotic mouse model, we investigate potential changes in gut microbial community structure and function during infection using metagenomics and metabolomics. We observe that changes in the community and in biosynthetic gene cluster potential occur within 3 days for the virulent Salmonella enterica serovar Typhimurium, but there are minimal changes with a poorly colonizing Candida albicans In addition, the metabolome shifts depending on infection status, including changes in glutathione metabolites in response to Salmonella infection, potentially in response to host oxidative stress.},
}
@article {pmid30401772,
year = {2018},
author = {Blau, K and Bettermann, A and Jechalke, S and Fornefeld, E and Vanrobaeys, Y and Stalder, T and Top, EM and Smalla, K},
title = {The Transferable Resistome of Produce.},
journal = {mBio},
volume = {9},
number = {6},
pages = {},
doi = {10.1128/mBio.01300-18},
pmid = {30401772},
issn = {2150-7511},
abstract = {Produce is increasingly recognized as a reservoir of human pathogens and transferable antibiotic resistance genes. This study aimed to explore methods to characterize the transferable resistome of bacteria associated with produce. Mixed salad, arugula, and cilantro purchased from supermarkets in Germany were analyzed by means of cultivation- and DNA-based methods. Before and after a nonselective enrichment step, tetracycline (TET)-resistant Escherichia coli were isolated and plasmids conferring TET resistance were captured by exogenous plasmid isolation. TET-resistant E. coli isolates, transconjugants, and total community DNA (TC-DNA) from the microbial fraction detached from leaves or after enrichment were analyzed for the presence of resistance genes, class 1 integrons, and various plasmids by real-time PCR and PCR-Southern blot hybridization. Real-time PCR primers were developed for IncI and IncF plasmids. TET-resistant E. coli isolated from arugula and cilantro carried IncF, IncI1, IncN, IncHI1, IncU, and IncX1 plasmids. Three isolates from cilantro were positive for IncN plasmids and blaCTX-M-1 From mixed salad and cilantro, IncF, IncI1, and IncP-1β plasmids were captured exogenously. Importantly, whereas direct detection of IncI and IncF plasmids in TC-DNA failed, these plasmids became detectable in DNA extracted from enrichment cultures. This confirms that cultivation-independent DNA-based methods are not always sufficiently sensitive to detect the transferable resistome in the rare microbiome. In summary, this study showed that an impressive diversity of self-transmissible multiple resistance plasmids was detected in bacteria associated with produce that is consumed raw, and exogenous capturing into E. coli suggests that they could transfer to gut bacteria as well.IMPORTANCE Produce is one of the most popular food commodities. Unfortunately, leafy greens can be a reservoir of transferable antibiotic resistance genes. We found that IncF and IncI plasmids were the most prevalent plasmid types in E. coli isolates from produce. This study highlights the importance of the rare microbiome associated with produce as a source of antibiotic resistance genes that might escape cultivation-independent detection, yet may be transferred to human pathogens or commensals.},
}
@article {pmid30401457,
year = {2018},
author = {Santos-Cortez, RLP and Chiong, CM and Frank, DN and Ryan, AF and Giese, APJ and Bootpetch Roberts, T and Daly, KA and Steritz, MJ and Szeremeta, W and Pedro, M and Pine, H and Yarza, TKL and Scholes, MA and Llanes, EGDV and Yousaf, S and Friedman, N and Tantoco, MLC and Wine, TM and Labra, PJ and Benoit, J and Ruiz, AG and de la Cruz, RAR and Greenlee, C and Yousaf, A and Cardwell, J and Nonato, RMA and Ray, D and Ong, KMC and So, E and Robertson, CE and Dinwiddie, J and Lagrana-Villagracia, SM and , and Gubbels, SP and Shaikh, RS and Cass, SP and Einarsdottir, E and Lee, NR and Schwartz, DA and Gloria-Cruz, TLI and Bamshad, MJ and Yang, IV and Kere, J and Abes, GT and Prager, JD and Riazuddin, S and Chan, AL and Yoon, PJ and Nickerson, DA and Cutiongco-de la Paz, EM and Streubel, SO and Reyes-Quintos, MRT and Jenkins, HA and Mattila, P and Chan, KH and Mohlke, KL and Leal, SM and Hafrén, L and Chonmaitree, T and Sale, MM and Ahmed, ZM},
title = {FUT2 Variants Confer Susceptibility to Familial Otitis Media.},
journal = {American journal of human genetics},
volume = {103},
number = {5},
pages = {679-690},
doi = {10.1016/j.ajhg.2018.09.010},
pmid = {30401457},
issn = {1537-6605},
abstract = {Non-secretor status due to homozygosity for the common FUT2 variant c.461G>A (p.Trp154∗) is associated with either risk for autoimmune diseases or protection against viral diarrhea and HIV. We determined the role of FUT2 in otitis media susceptibility by obtaining DNA samples from 609 multi-ethnic families and simplex case subjects with otitis media. Exome and Sanger sequencing, linkage analysis, and Fisher exact and transmission disequilibrium tests (TDT) were performed. The common FUT2 c.604C>T (p.Arg202∗) variant co-segregates with otitis media in a Filipino pedigree (LOD = 4.0). Additionally, a rare variant, c.412C>T (p.Arg138Cys), is associated with recurrent/chronic otitis media in European-American children (p = 1.2 × 10-5) and US trios (TDT p = 0.01). The c.461G>A (p.Trp154∗) variant was also over-transmitted in US trios (TDT p = 0.01) and was associated with shifts in middle ear microbiota composition (PERMANOVA p < 10-7) and increased biodiversity. When all missense and nonsense variants identified in multi-ethnic US trios with CADD > 20 were combined, FUT2 variants were over-transmitted in trios (TDT p = 0.001). Fut2 is transiently upregulated in mouse middle ear after inoculation with non-typeable Haemophilus influenzae. Four FUT2 variants-namely p.Ala104Val, p.Arg138Cys, p.Trp154∗, and p.Arg202∗-reduced A antigen in mutant-transfected COS-7 cells, while the nonsense variants also reduced FUT2 protein levels. Common and rare FUT2 variants confer susceptibility to otitis media, likely by modifying the middle ear microbiome through regulation of A antigen levels in epithelial cells. Our families demonstrate marked intra-familial genetic heterogeneity, suggesting that multiple combinations of common and rare variants plus environmental factors influence the individual otitis media phenotype as a complex trait.},
}
@article {pmid30401435,
year = {2018},
author = {Koh, A and Molinaro, A and Ståhlman, M and Khan, MT and Schmidt, C and Mannerås-Holm, L and Wu, H and Carreras, A and Jeong, H and Olofsson, LE and Bergh, PO and Gerdes, V and Hartstra, A and de Brauw, M and Perkins, R and Nieuwdorp, M and Bergström, G and Bäckhed, F},
title = {Microbially Produced Imidazole Propionate Impairs Insulin Signaling through mTORC1.},
journal = {Cell},
volume = {175},
number = {4},
pages = {947-961.e17},
doi = {10.1016/j.cell.2018.09.055},
pmid = {30401435},
issn = {1097-4172},
abstract = {Interactions between the gut microbiota, diet, and the host potentially contribute to the development of metabolic diseases. Here, we identify imidazole propionate as a microbially produced histidine-derived metabolite that is present at higher concentrations in subjects with versus without type 2 diabetes. We show that imidazole propionate is produced from histidine in a gut simulator at higher concentrations when using fecal microbiota from subjects with versus without type 2 diabetes and that it impairs glucose tolerance when administered to mice. We further show that imidazole propionate impairs insulin signaling at the level of insulin receptor substrate through the activation of p38γ MAPK, which promotes p62 phosphorylation and, subsequently, activation of mechanistic target of rapamycin complex 1 (mTORC1). We also demonstrate increased activation of p62 and mTORC1 in liver from subjects with type 2 diabetes. Our findings indicate that the microbial metabolite imidazole propionate may contribute to the pathogenesis of type 2 diabetes.},
}
@article {pmid30400268,
year = {2018},
author = {Ojo-Okunola, A and Nicol, M and du Toit, E},
title = {Human Breast Milk Bacteriome in Health and Disease.},
journal = {Nutrients},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/nu10111643},
pmid = {30400268},
issn = {2072-6643},
support = {U54HG009824//NIH Office of the Director/ ; 1U01AI110466-01A1//H3Africa U01 AWARD FROM THE NATIONAL INSTITUTES OF HEALTH OF THE USA/ ; OPP1017641; OPP1017579//Bill and Melinda Gates Foundation/ ; },
abstract = {It is well-known that, beyond nutritional components, human breast milk (HBM) contains a wide variety of non-nutritive bio-factors perfectly suited for the growing infant. In the pre-2000 era, HBM was considered sterile and devoid of micro-organisms. Though HBM was not included as part of the human microbiome project launched in 2007, great strides have been made in studying the bacterial diversity of HBM in both a healthy state and diseased state, and in understanding their role in infant health. HBM provides a vast array of beneficial micro-organisms that play a key role in colonizing the infant's mucosal system, including that of the gut. They also have a role in priming the infant's immune system and supporting its maturation. In this review, we provide an in-depth and updated insight into the immunomodulatory, metabolic, and anti-infective role of HBM bacteriome (bacterial community) and its effect on infant health. We also provide key information from the literature by exploring the possible origin of microbial communities in HBM, the bacterial diversity in this niche and the determinants influencing the HBM bacteriome. Lastly, we investigate the role of the HBM bacteriome in maternal infectious disease (human immunodeficiency virus (HIV) and mastitis)), and cancer. Key gaps in HBM bacterial research are also identified.},
}
@article {pmid30399554,
year = {2018},
author = {Liang, B and Ma, J and Cai, W and Li, Z and Liu, W and Qi, M and Zhao, Y and Ma, X and Deng, Y and Wang, A and Zhou, J},
title = {Response of chloramphenicol-reducing biocathode resistome to continuous electrical stimulation.},
journal = {Water research},
volume = {148},
number = {},
pages = {398-406},
doi = {10.1016/j.watres.2018.10.073},
pmid = {30399554},
issn = {1879-2448},
abstract = {Understanding the fate of overall antibiotic resistance genes (ARGs) during the biological treatment of antibiotic containing wastewater is a central issue for the water ecological safety assessment. Although the microbial electrode-respiration based biotransformation process could significantly detoxify some antibiotic contaminants, e.g. chloramphenicol (CAP), the response of CAP-reducing biocathode microbiome and resistome to continuous electrical stimulation, especially ARGs network interactions, are poorly understood. Here, using highthroughput functional gene array (GeoChip v4.6) and Illumina 16S rRNA gene MiSeq sequencing, the structure, composition, diversity and network interactions of CAP-reducing biocathode microbiome and resistome in response to continuous electrical stimulation were investigated. Our results indicate that the CAP bioelectroreduction process could significantly accelerate the elimination of antibacterial activity of CAP during CAP-containing wastewater treatment compared to the pure bioreduction process. Continuous electrical stimulation could obviously alter both the microbiome and resistome structures and consistently decrease the phylogenetic, functional and overall ARGs diversity and network complexity within the CAP-reducing biofilms. The relative abundances of overall ARGs and specific CAP resistance related major facilitator superfamily (MFS) transporter genes were significantly negatively correlated with the reduction efficiency of CAP to inactive antibacterial product AMCl (partially dechlorinated aromatic amine), which may reduce the ecological risk associated with the evolution of multidrug-resistant bacteria and ARGs during antibiotic-containing wastewater treatment process. This study offers new insights into the response of an antibiotic reducing biocathode resistome to continuous electrical stimulation and provides useful information on the assessment of overall ARGs risk for the bioelectrochemical treatment of antibiotic contaminants.},
}
@article {pmid30399404,
year = {2018},
author = {Hantsoo, L and Jašarević, E and Criniti, S and McGeehan, B and Tanes, C and Sammel, MD and Elovitz, MA and Compher, C and Wu, G and Epperson, CN},
title = {Childhood Adversity Impact on Gut Microbiota and Inflammatory Response to Stress During Pregnancy.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2018.11.005},
pmid = {30399404},
issn = {1090-2139},
abstract = {BACKGROUND: Adverse childhood experiences (ACEs), such as abuse or chronic stress, program an exaggerated adult inflammatory response to stress. Emerging rodent research suggests that the gut microbiome may be a key mediator in the association between early life stress and dysregulated glucocorticoid-immune response. However, ACE impact on inflammatory response to stress, or on the gut microbiome, have not been studied in human pregnancy, when inflammation increases risk of poor outcomes. The aim of this study was to assess the relationships among ACE, the gut microbiome, and cytokine response to stress in pregnant women.<br><br>METHODS: Physically and psychiatrically healthy adult pregnant women completed the Adverse Childhood Experiences Questionnaire (ACE-Q) and gave a single stool sample between 20 and 26 weeks gestation. Stool DNA was isolated and 16S sequencing was performed. Three 24-hour food recalls were administered to assess dietary nutrient intake. A subset of women completed the Trier Social Stress Test (TSST) at 22-34 weeks gestation; plasma interleukin-6 (IL-6), interleukin-1β (IL-1β), high sensitivity C-reactive protein (hsCRP), tumor necrosis factor α (TNF-α), and cortisol were measured at four timepoints pre and post stressor, and area under the curve (AUC) was calculated.<br><br>RESULTS: Forty-eight women completed the ACE-Q and provided stool; 19 women completed the TSST. Women reporting 2 or more ACEs (high ACE) had greater differential abundance of gut Prevotella than low ACE participants (q=5.7x10^-13). Abundance of several gut taxa were significantly associated with cortisol, IL-6, TNF-α and CRP AUCs regardless of ACE status. IL-6 response to stress was buffered among high ACE women with high intake of docosahexaenoic acid (DHA) (p=0.03) and eicosapentaenoic acid (EPA) (p=0.05).<br><br>DISCUSSION: Our findings suggest that multiple childhood adversities are associated with changes in gut microbiota composition during pregnancy, and such changes may contribute to altered inflammatory and glucocorticoid response to stress. While preliminary, this is the first study to demonstrate an association between gut microbiota and acute glucocorticoid-immune response to stress in a clinical sample. Finally, exploratory analyses suggested that high ACE women with high dietary intake of ω-3 polyunsaturated fatty acids (PUFAs) had a dampened inflammatory response to acute stress, suggesting potentially protective effects of ω-3s in this high-risk population. Given the adverse effects of inflammation on pregnancy and the developing fetus, mechanisms by which childhood adversity influence the gut-brain axis and potential protective factors such as diet should be further explored.},
}
@article {pmid30399327,
year = {2018},
author = {O'Connor, H and MacSharry, J and Bueso, YF and Lindsay, S and Kavanagh, EL and Tangney, M and Clyne, M and Saldova, R and McCann, A},
title = {Resident bacteria in breast cancer tissue: pathogenic agents or harmless commensals?.},
journal = {Discovery medicine},
volume = {26},
number = {142},
pages = {93-102},
pmid = {30399327},
issn = {1944-7930},
abstract = {Breast cancer is the second most common cancer in women. Recent evidence identifies a unique microbiome in breast tissue; a site previously thought to be sterile. The identification that this microbiome varies considerably from healthy subjects to cancer patients has prompted investigations into the role of specific bacterial species in oncogenesis. Indeed, certain bacteria have been shown to aid cancer development in vitro by promoting genomic instability, invasion, and chemotherapy resistance. However, the in vivo role of the breast microbiome in cancer appears to be more complex, involving numerous interactions between its constituent species and host cells. As such, reduced abundances of species which exert a protective effect against oncogenesis have come into focus and there is an emerging consensus that states of microbial dysbiosis, in which the normal balance of bacterial species is altered, can contribute to the development of cancer. This review summarizes the findings to date from the available literature pertaining to the microbiome in breast cancer and outlines areas worthy of further investigation.},
}
@article {pmid30399141,
year = {2018},
author = {Aw, WC and Towarnicki, SG and Melvin, RG and Youngson, NA and Garvin, MR and Hu, Y and Nielsen, S and Thomas, T and Pickford, R and Bustamante, S and Vila-Sanjurjo, A and Smyth, GK and Ballard, JWO},
title = {Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness.},
journal = {PLoS genetics},
volume = {14},
number = {11},
pages = {e1007735},
doi = {10.1371/journal.pgen.1007735},
pmid = {30399141},
issn = {1553-7404},
abstract = {Diet may be modified seasonally or by biogeographic, demographic or cultural shifts. It can differentially influence mitochondrial bioenergetics, retrograde signalling to the nuclear genome, and anterograde signalling to mitochondria. All these interactions have the potential to alter the frequencies of mtDNA haplotypes (mitotypes) in nature and may impact human health. In a model laboratory system, we fed four diets varying in Protein: Carbohydrate (P:C) ratio (1:2, 1:4, 1:8 and 1:16 P:C) to four homoplasmic Drosophila melanogaster mitotypes (nuclear genome standardised) and assayed their frequency in population cages. When fed a high protein 1:2 P:C diet, the frequency of flies harbouring Alstonville mtDNA increased. In contrast, when fed the high carbohydrate 1:16 P:C food the incidence of flies harbouring Dahomey mtDNA increased. This result, driven by differences in larval development, was generalisable to the replacement of the laboratory diet with fruits having high and low P:C ratios, perturbation of the nuclear genome and changes to the microbiome. Structural modelling and cellular assays suggested a V161L mutation in the ND4 subunit of complex I of Dahomey mtDNA was mildly deleterious, reduced mitochondrial functions, increased oxidative stress and resulted in an increase in larval development time on the 1:2 P:C diet. The 1:16 P:C diet triggered a cascade of changes in both mitotypes. In Dahomey larvae, increased feeding fuelled increased β-oxidation and the partial bypass of the complex I mutation. Conversely, Alstonville larvae upregulated genes involved with oxidative phosphorylation, increased glycogen metabolism and they were more physically active. We hypothesise that the increased physical activity diverted energy from growth and cell division and thereby slowed development. These data further question the use of mtDNA as an assumed neutral marker in evolutionary and population genetic studies. Moreover, if humans respond similarly, we posit that individuals with specific mtDNA variations may differentially metabolise carbohydrates, which has implications for a variety of diseases including cardiovascular disease, obesity, and perhaps Parkinson's Disease.},
}
@article {pmid30398470,
year = {2018},
author = {Sirota, M and Thomas, CG and Liu, R and Zuhl, M and Banerjee, P and Wong, RJ and Quaintance, CC and Leite, R and Chubiz, J and Anderson, R and Chappell, J and Kim, M and Grobman, W and Zhang, G and Rokas, A and England, SK and Parry, S and Shaw, GM and Simpson, JL and Thomson, E and Butte, AJ and , },
title = {Enabling precision medicine in neonatology, an integrated repository for preterm birth research.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180219},
doi = {10.1038/sdata.2018.219},
pmid = {30398470},
issn = {2052-4463},
abstract = {Preterm birth, or the delivery of an infant prior to 37 weeks of gestation, is a significant cause of infant morbidity and mortality. In the last decade, the advent and continued development of molecular profiling technologies has enabled researchers to generate vast amount of 'omics' data, which together with integrative computational approaches, can help refine the current knowledge about disease mechanisms, diagnostics, and therapeutics. Here we describe the March of Dimes' Database for Preterm Birth Research (http://www.immport.org/resources/mod), a unique resource that contains a variety of 'omics' datasets related to preterm birth. The database is open publicly, and as of January 2018, links 13 molecular studies with data across tens of thousands of patients from 6 measurement modalities. The data in the repository are highly diverse and include genomic, transcriptomic, immunological, and microbiome data. Relevant datasets are augmented with additional molecular characterizations of almost 25,000 biological samples from public databases. We believe our data-sharing efforts will lead to enhanced research collaborations and coordination accelerating the overall pace of discovery in preterm birth research.},
}
@article {pmid30398150,
year = {2018},
author = {Matos, RC and Leulier, F},
title = {Everyone wins.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
doi = {10.7554/eLife.42676},
pmid = {30398150},
issn = {2050-084X},
abstract = {Aeromonas bacteria living in the gut of zebrafish produce a specific molecule to pacify the immune system of their host.},
}
@article {pmid30397546,
year = {2018},
author = {Md Zoqratt, MZH and Eng, WWH and Thai, BT and Austin, CM and Gan, HM},
title = {Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5826},
doi = {10.7717/peerj.5826},
pmid = {30397546},
issn = {2167-8359},
abstract = {Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3-V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.},
}
@article {pmid30397444,
year = {2018},
author = {Ma, ZS},
title = {DAR (diversity-area relationship): Extending classic SAR (species-area relationship) for biodiversity and biogeography analyses.},
journal = {Ecology and evolution},
volume = {8},
number = {20},
pages = {10023-10038},
doi = {10.1002/ece3.4425},
pmid = {30397444},
issn = {2045-7758},
abstract = {I extend the classic SAR, which has achieved status of ecological law and plays a critical role in global biodiversity and biogeography analyses, to general DAR (diversity-area relationship). The extension was aimed to remedy a serious application limitation of the traditional SAR that only addressed one aspect of biodiversity scaling-species richness scaling over space, but ignoring species abundance information. The extension was further inspired by a recent consensus that Hill numbers offer the most appropriate measures for alpha-diversity and multiplicative beta-diversity. In particular, Hill numbers are essentially a series of Renyi's entropy values weighted differently along the rare-common-dominant spectrum of species abundance distribution and are in the units of effective number of species (or species equivalents such as OTUs). I therefore postulate that Hill numbers should follow the same or similar law of the traditional SAR. I test the postulation with the American gut microbiome project (AGP) dataset of 1,473 healthy North American individuals. I further propose three new concepts and develop their statistical estimation formulae based on the new DAR extension, including: (i) DAR profile-z-q relationship (DAR scaling parameter z at different diversity order q), (ii) PDO (pair-wise diversity overlap) profile-g-q relationship (PDO parameter g at order q, and (iii) MAD (maximal accrual diversity: Dmax) profile-Dmax-q. While the classic SAR is a special case of our new DAR profile, the PDO and MAD profiles offer novel tools for analyzing biodiversity (including alpha-diversity and beta-diversity) and biogeography over space.},
}
@article {pmid30397357,
year = {2018},
author = {Tirosh, O and Conlan, S and Deming, C and Lee-Lin, SQ and Huang, X and , and Su, HC and Freeman, AF and Segre, JA and Kong, HH},
title = {Expanded skin virome in DOCK8-deficient patients.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-018-0211-7},
pmid = {30397357},
issn = {1546-170X},
abstract = {Human microbiome studies have revealed the intricate interplay of host immunity and bacterial communities to achieve homeostatic balance. Healthy skin microbial communities are dominated by bacteria with low viral representation1-3, mainly bacteriophage. Specific eukaryotic viruses have been implicated in both common and rare skin diseases, but cataloging skin viral communities has been limited. Alterations in host immunity provide an opportunity to expand our understanding of microbial-host interactions. Primary immunodeficient patients manifest with various viral, bacterial, fungal, and parasitic infections, including skin infections4. Dedicator of cytokinesis 8 (DOCK8) deficiency is a rare primary human immunodeficiency characterized by recurrent cutaneous and systemic infections, as well as atopy and cancer susceptibility5. DOCK8, encoding a guanine nucleotide exchange factor highly expressed in lymphocytes, regulates actin cytoskeleton, which is critical for migration through collagen-dense tissues such as skin6. Analyzing deep metagenomic sequencing data from DOCK8-deficient skin samples demonstrated a notable increase in eukaryotic viral representation and diversity compared with healthy volunteers. De novo assembly approaches identified hundreds of novel human papillomavirus genomes, illuminating microbial dark matter. Expansion of the skin virome in DOCK8-deficient patients underscores the importance of immune surveillance in controlling eukaryotic viral colonization and infection.},
}
@article {pmid30397052,
year = {2018},
author = {Zhanel, G and Critchley, I and Lin, LY and Alvandi, N},
title = {Microbiological Profile of Sarecycline: A Novel Targeted Spectrum Tetracycline for the Treatment of Acne Vulgaris.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1128/AAC.01297-18},
pmid = {30397052},
issn = {1098-6596},
abstract = {Sarecycline is the first narrow spectrum tetracycline-class antibiotic being developed for acne treatment. In addition to exhibiting activity against important skin/soft tissue pathogens, sarecycline exhibits targeted antibacterial activity against clinical isolates of Cutibacterium acnes In the current study, sarecycline was 16 to 32-fold less active than broad spectrum tetracyclines-such as minocycline and doxycycline-against aerobic Gram-negative bacilli associated with normal human intestinal microbiome. Also, reduced activity against Escherichia coli was observed in vivo in a murine septicemia model with PD50 values at >40 mg/kg and 5.72 mg/kg for sarecycline and doxycycline, respectively. Sarecycline was also 4 to 8-fold less active against representative anaerobic bacteria that also comprise normal human intestinal microbiome. Additionally, sarecycline displayed a low propensity for resistance development in C. acnes strains, with spontaneous mutation frequencies of 10-10 at 4 to 8-times the MIC, similar to minocycline and vancomycin. When tested against Gram-positive pathogens with defined tetracycline resistance mechanisms, sarecycline was more active than tetracycline against the tet(K) and tet(M) strains, with MIC ranging from 0.125 to 1.0 ug/mL and 8 ug/mL, respectively, compared with 16 to 64 ug/mL and 64 ug/mL for tetracycline, respectively. However, sarecycline activity in the tet(K) and tet(M) strains were decreased compared to wildtype, which demonstrated MIC ranging from 0.06 to 0.25 ug/mL, though not as pronounced as tetracycline. These findings support sarecycline as a narrow spectrum tetracycline-class antibiotic that is an effective agent for the treatment of acne and further warrants investigation into the potential reduced effects on the gut microbiome.},
}
@article {pmid30396567,
year = {2018},
author = {Christianson, MS and Bellver, J},
title = {Innovations in assisted reproductive technologies: impact on contemporary donor egg practice and future advances.},
journal = {Fertility and sterility},
volume = {110},
number = {6},
pages = {994-1002},
doi = {10.1016/j.fertnstert.2018.09.020},
pmid = {30396567},
issn = {1556-5653},
abstract = {Innovations in assisted reproductive technologies (ART) have driven progress in the donor egg field since the birth of the first baby derived from a donor egg in 1983. Over time, donor oocytes have become an increasingly used option for patients unable to conceive with autologous oocytes. In donor egg, the unique separation of the oocyte source and recipient uterus has created a model that has propelled advances in ART. Progressive ART innovations that have optimized the oocyte donor and resulting embryo include the following: evaluation of ovarian reserve, controlled ovarian hyperstimulation regimens that reduce the risk of ovarian hyperstimulation syndrome, blastocyst culture, oocyte cryopreservation, and preimplantation genetic testing. For donor egg recipients, methods to optimize the endometrium to maximize implantation include endometrial receptivity testing, immunologic donor-recipient matching, and increased understanding of the uterine microbiome.},
}
@article {pmid30396371,
year = {2018},
author = {Meisel, JS and Nasko, DJ and Brubach, B and Cepeda-Espinoza, V and Chopyk, J and Corrada-Bravo, H and Fedarko, M and Ghurye, J and Javkar, K and Olson, ND and Shah, N and Allard, SM and Bazinet, AL and Bergman, NH and Brown, A and Caporaso, JG and Conlan, S and DiRuggiero, J and Forry, SP and Hasan, NA and Kralj, J and Luethy, PM and Milton, DK and Ondov, BD and Preheim, S and Ratnayake, S and Rogers, SM and Rosovitz, MJ and Sakowski, EG and Schliebs, NO and Sommer, DD and Ternus, KL and Uritskiy, G and Zhang, SX and Pop, M and Treangen, TJ},
title = {Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {197},
doi = {10.1186/s40168-018-0582-5},
pmid = {30396371},
issn = {2049-2618},
support = {R01-AI-100947//National Institutes of Health/ ; U54CA143924//National Institutes of Health/ ; U54CA143925//National Institutes of Health/ ; IIS-1513615//National Science Foundation (US)/ ; 1565100//National Science Foundation (US)/ ; DEB1556574//National Science Foundation (US)/ ; W911NF-17-2-0089//Intelligence Advanced Research Projects Activity (US)/ ; R01 GM114267//National Institutes of Health (US)/ ; HSHQDC-15-C-00064//Science and Technology Directorate/ ; },
abstract = {The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.},
}
@article {pmid30396369,
year = {2018},
author = {Armstrong, AJS and Shaffer, M and Nusbacher, NM and Griesmer, C and Fiorillo, S and Schneider, JM and Preston Neff, C and Li, SX and Fontenot, AP and Campbell, T and Palmer, BE and Lozupone, CA},
title = {An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {198},
doi = {10.1186/s40168-018-0580-7},
pmid = {30396369},
issn = {2049-2618},
support = {R01 DK108366//National Institute of Diabetes and Digestive and Kidney Diseases/ ; R01 DK104047//National Institute of Diabetes and Digestive and Kidney Diseases/ ; U01 HL098996//National Heart, Lung, and Blood Institute/ ; U01 HL121816//National Heart, Lung, and Blood Institute/ ; T32 AI052066//National Institute of Allergy and Infectious Diseases/ ; 2 T15 LM009451-06//U.S. National Library of Medicine/ ; },
abstract = {BACKGROUND: Gut microbiome characteristics associated with HIV infection are of intense research interest but a deep understanding has been challenged by confounding factors across studied populations. Notably, a Prevotella-rich microbiome described in HIV-infected populations is now understood to be common in men who have sex with men (MSM) regardless of HIV status, but driving factors and potential health implications are unknown.<br><br>RESULTS: Here, we further define the MSM-associated gut microbiome and describe compositional differences between the fecal microbiomes of Prevotella-rich MSM and non-MSM that may underlie observed pro-inflammatory properties. Furthermore, we show relatively subtle gut microbiome changes in HIV infection in MSM and women that include an increase in potential pathogens that is ameliorated with antiretroviral therapy (ART). Lastly, using a longitudinal cohort, we describe microbiome changes that happen after ART initiation.<br><br>CONCLUSIONS: This study provides an in-depth characterization of microbiome differences that occur in a US population infected with HIV and demonstrates the degree to which these differences may be driven by lifestyle factors, ART, and HIV infection itself. Understanding microbiome compositions that occur with sexual behaviors that are high risk for acquiring HIV and untreated and ART-treated HIV infection will guide the investigation of immune and metabolic functional implications to ultimately target the microbiome therapeutically.},
}
@article {pmid30396009,
year = {2018},
author = {Woerner, AE and Novroski, NMM and Wendt, FR and Ambers, A and Wiley, R and Schmedes, SE and Budowle, B},
title = {Forensic human identification with targeted microbiome markers using nearest neighbor classification.},
journal = {Forensic science international. Genetics},
volume = {38},
number = {},
pages = {130-139},
doi = {10.1016/j.fsigen.2018.10.003},
pmid = {30396009},
issn = {1878-0326},
abstract = {From the perspective of forensics genetics, the human microbiome is a rich, relatively untapped resource for human identity testing. Since it varies within and among people, and perhaps temporally, the potential forensic applications of the use of the microbiome can exceed that of human identification. However, the same inherent variability in microbial distributions may pose a substantial barrier to forming predictions on an individual as the source of the microbial sample unless stable signatures of the microbiome are identified and targeted. One of the more commonly adopted strategies for microbial human identification relies on quantifying which taxa are present and their respective abundance levels. It remains an open question if such microbial signatures are more individualizing than estimates of the degree of genetic relatedness between microbial samples. This study attempts to address this question by contrasting two prediction strategies. The first approach uses phylogenetic distance to predict the host individual; thus it operates under the premise that microbes within individuals are more closely related than microbes between/among individuals. The second approach uses population genetic measures of diversity at clade-specific markers, serving as a fine-grained assessment of microbial composition and quantification. Both assessments were performed using targeted sequencing of 286 markers from 22 microbial taxa sampled in 51 individuals across three body sites measured in triplicate. Nearest neighbor and reverse nearest neighbor classifiers were constructed based on the pooled data and yielded 71% and 78% accuracy, respectively, when diversity was considered, and performed significantly worse when a phylogenetic distance was used (54% and 63% accuracy, respectively). However, empirical estimates of classification accuracy were 100% when conditioned on a maximum nearest neighbor distance when diversity was used, while identification based on a phylogenetic distance failed to reach saturation. These findings suggest that microbial strain composition is more individualizing than that of a phylogeny, perhaps indicating that microbial composition may be more individualizing than recent common ancestry. One inference that may be drawn from these findings is that host-environment interactions may maintain the targeted microbial profile and that this maintenance may not necessarily be repopulated by intra-individual microbial strains.},
}
@article {pmid30396006,
year = {2018},
author = {Velikonja, A and Lipoglavšek, L and Zorec, M and Orel, R and Avguštin, G},
title = {Alterations in gut microbiota composition and metabolic parameters after dietary intervention with barley beta glucans in patients with high risk for metabolic syndrome development.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anaerobe.2018.11.002},
pmid = {30396006},
issn = {1095-8274},
abstract = {Metabolic syndrome is a complex disease that is exponentially increasing in the western world, and diet is one of the possible ways to improve the metabolic status of patients. Barley beta glucans are dietary fibres that show promise for improvement cholesterol levels and postprandial glucose response, but they have been rarely investigated in human trials with concurrent focus on gut microbiota. A double-blind, placebo-controlled, randomised clinical trial was conducted with 43 volunteers with high risk for metabolic syndrome development or with diagnosed metabolic syndrome. During a four-week intervention study, participants consumed experimental bread containing 6 g of barley beta glucans or equal bread but without beta glucans. After dietary intervention, total plasma cholesterol decreased in the test group (-0.26 ± 0.54, p = 0.019), but not in the control group. Short chain fatty acids (SCFA) composition in faeces significantly changed with increase of propionic acid in test group (43.2%, p = 0.045) and with decrease of acetic acid in control group (41.8%, p = 0.011). The microbiome analysis based on Illumina paired end sequencing of 16S rRNA genes showed a decrease in microbial diversity and richness in the test group. The pre-intervention gut microbiota composition showed higher abundance of health associated Bifidobacterium spp. and Akkermansia municiphila within cholesterol-responsive group, showing that diet-induced metabolic response is possibly dependent on individual gut microbiota composition.},
}
@article {pmid30394894,
year = {2018},
author = {Dent, E and Hoogendijk, EO and Wright, ORL},
title = {New insights into the anorexia of ageing: from prevention to treatment.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCO.0000000000000525},
pmid = {30394894},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: Undernutrition in older adults is associated with frailty, functional decline, and mortality. The 'anorexia of ageing' is the age-related appetite and weight loss underpinning such undernutrition. This review examines the latest evidence for its prevention and treatment.<br><br>RECENT FINDINGS: Existing nutritional therapies for the anorexia of ageing include supporting nutritional intake with fortified food or supplements, including omega-3 fatty acids, multivitamins, and vitamin D. The Mediterranean diet provides high fat intake and nutrient density in a moderate volume of colourful and flavoursome food and is strengthening in evidence for healthy ageing. Studies of the gut microbiome, which potentially regulates normal appetite by acting on the brain-gut communication axis, are pertinent. Utilization of the genetic profile of individuals to determine nutritional needs is an exciting advancement of the past decade and may become common practice.<br><br>SUMMARY: Prevention or early treatment of the anorexia of ageing in older adults is critical. Latest evidence suggests that once significant weight loss has occurred, aggressive nutritional support may not result in improved outcomes.},
}
@article {pmid30394861,
year = {2018},
author = {Siddharthan, R and Chapek, M and Warren, M and Martindale, R},
title = {Probiotics in Prevention of Surgical Site Infections.},
journal = {Surgical infections},
volume = {},
number = {},
pages = {},
doi = {10.1089/sur.2018.231},
pmid = {30394861},
issn = {1557-8674},
abstract = {Despite significant improvements in peri-operative care, surgical site infections (SSIs) remain an important contributor to morbidity, cost, and death. The human gastrointestinal tract is a complex microenvironment linking host cells and the indigenous microflora or &quot;microbiome,&quot; creating a &quot;super-organism&quot; that engages in macro-nutrient and micro-nutrient extraction for the host while serving as a barrier to toxins and other detrimental bacterial end-products. Maintaining a healthy microbiome in the peri-operative period may enable control of multi-drug resistance (MDR) organisms, whereas use of antibiotics simply resets the dysbiotic relation by eliminating multiple strains of bacteria. Such loss of microbial diversity or abundance can slow wound healing. Use of pro-biotics to prevent infection has been evaluated in several studies, but their utility is not yet clear. There is a clear need for randomized trials to draw firm conclusions about their efficacy and to make clinical recommendations.},
}
@article {pmid30394587,
year = {2018},
author = {Bettoli, V and Manfredini, M and Massoli, L and Carillo, C and Barozzi, A and Amendolagine, G and Ruina, G and Musmeci, D and Libanore, M and Curtolo, A and Mantovani, L and Contini, C and Pellacani, G and Corazza, M},
title = {Rates of Antibiotic Resistance / Sensitivity in Bacterial Cultures of Hidradenitis Suppurativa Patients.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.15332},
pmid = {30394587},
issn = {1468-3083},
abstract = {BACKGROUND: Antibiotic (AB) treatment is one of the first steps in the management of Hidradenitis Suppurativa (HS). Bacteria, in HS patients, may play a double role, as triggering factors of inflammatory reactions and/or agents of infection.<br><br>OBJECTIVES: The aims of this study are: 1) to assess prevalence and AB resistance of bacterial growths in HS patients 2) assessment of the clinical relevance of obtained data in guiding the selection of the most effective AB therapy.<br><br>METHODS: Purulent material from 137 skin lesions of HS patients was collected with swabs. Bacterial flora and AB sensitivity were determined using microbiological cultures for aerobic and anaerobic bacteria.<br><br>RESULTS: A total of 114 samples resulted positive for bacteria. Sample were collected from the axillae, groin and perianal areas. A total of 163 single bacterial growths were observed; 55% were gram-positive and 44% were gram-negative. Among them, 18.4% were anaerobic. The most frequent bacterial families included enterobacteriacee (30.7%), staphylococcus (25.2%), and streptococcus (14.1%). The most frequent genus or species were proteus spp. (13.5%) and e.coli (9.8%). The prevalence of AB resistance observed was clindamycin 65.7%, rifampicin 69.3%, penicillin 70.0%, ciprofloxacin 74%, tetracycline 84.7% and erythromycin 89.0%. A limitation of the study is represented the short culture period adopted which may have impaired the isolation of anaerobes.<br><br>CONCLUSIONS: Bacterial growth in HS patients has shown a high level of resistance to ABs, including rifampicin, clindamycin and tetracyclines, cited as an empiric choice in HS therapeutic guidelines. A targeted and specific AB therapy, driven by microbiological evaluations with prolonged culture periods, seems more appropriate than empiric, generic, non-specific, therapeutic approaches. Current knowledge regarding HS bacterial AB resistance should be considered in the update of current therapeutic guidelines for HS. This article is protected by copyright. All rights reserved.},
}
@article {pmid30394174,
year = {2018},
author = {Dinan, TG and Cryan, JF},
title = {Schizophrenia and the Microbiome: Time to Focus on the Impact of Antipsychotic Treatment on the Gut Microbiota.},
journal = {The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/15622975.2018.1540793},
pmid = {30394174},
issn = {1814-1412},
}
@article {pmid30393777,
year = {2018},
author = {Zhang, F and Zhao, S and Ren, C and Zhu, Y and Zhou, H and Lai, Y and Zhou, F and Jia, Y and Zheng, K and Huang, Z},
title = {CRISPRminer is a knowledge base for exploring CRISPR-Cas systems in microbe and phage interactions.},
journal = {Communications biology},
volume = {1},
number = {},
pages = {180},
doi = {10.1038/s42003-018-0184-6},
pmid = {30393777},
issn = {2399-3642},
abstract = {CRISPR-Cas systems not only play key roles in prokaryotic acquired immunity, but can also be adapted as powerful genome editing tools. Understanding the native role of CRISPR-Cas systems in providing adaptive immunity can lead to new CRISPR-based technologies. Here, we develop CRISPRminer, a knowledge base and web server to comprehensively collect and investigate the knowledge of CRISPR-Cas systems and generate instructive annotations, including CRISPR arrays and Cas protein annotation, CRISPR-Cas system classification, self-targeting events detection, microbe-phage interaction inference, and anti-CRISPR annotation. CRISPRminer is user-friendly and freely available at http://www.microbiome-bigdata.com/CRISPRminer.},
}
@article {pmid30393044,
year = {2018},
author = {De Santis, F and Del Vecchio, M and Castagnoli, L and De Braud, F and Franceschini, D and Fucà, G and Hiscott, J and Malmberg, KJ and McGranahan, N and Pietrantonio, F and Rivoltini, L and Sangaletti, S and Tagliabue, E and Tripodo, C and Vernieri, C and Zitvogel, L and Pupa, SM and Di Nicola, M},
title = {Innovative therapy, monoclonal antibodies, and beyond: Highlights from the eighth annual meeting.},
journal = {Cytokine &amp; growth factor reviews},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cytogfr.2018.10.005},
pmid = {30393044},
issn = {1879-0305},
abstract = {The eighth annual conference of &quot;Innovative therapy, monoclonal antibodies, and beyond&quot; was held in Milan on Jan. 26, 2018, and hosted by Fondazione IRCCS-Istituto Nazionale dei Tumori (Fondazione IRCCS INT). The conference was divided into two main scientific sessions, of i) pre-clinical assays and novel biotargets, and ii) clinical translation, as well as a third session of presentations from young investigators, which focused on recent achievements within Fondazione IRCCS INT on immunotherapy and targeted therapies. Presentations in the first session addressed the issue of cancer immunotherapy activity with respect to tumor heterogeneity, with key topics addressing: 1) tumor heterogeneity and targeted therapy, with the definition of the evolutionary Index as an indicator of tumor heterogeneity in both space and time; 2) the analysis of cancer evolution, with the introduction of the TRACERx Consortium-a multi-million pound UK research project focused on non-small cell lung cancer (NSCLC); 3) the use of anti-estrogen agents to boost immune recognition of breast cancer cells; and 4) the high degree of functional plasticity within the NK cell repertoire, including the expansion of adaptive NK cells following viral challenges. The second session addressed: 1) the effectiveness of radiotherapy to enhance the proportion of patients responsive to immune-checkpoint blockers (ICBs); 2) the use of MDSC scores in selecting melanoma patients with high probability to be responsive to ICBs; and 3) the relevance of the gut microbiome as a predictive factor, and the potential of its perturbation in increasing the immune response rate to ICBs. Overall, a picture emerged of tumor heterogeneity as the main limitation that impairs the effectiveness of anti-cancer therapies. Thus, the choice of a specific therapy based on reproducible and selective predictive biomarkers is an urgent unmet clinical need that should be addressed in order to increase the proportion of long-term responding patients and to improve the sustainability of novel drugs.},
}
@article {pmid30392721,
year = {2018},
author = {Cogdill, AP and Gaudreau, PO and Arora, R and Gopalakrishnan, V and Wargo, JA},
title = {The Impact of Intratumoral and Gastrointestinal Microbiota on Systemic Cancer Therapy.},
journal = {Trends in immunology},
volume = {39},
number = {11},
pages = {900-920},
doi = {10.1016/j.it.2018.09.007},
pmid = {30392721},
issn = {1471-4981},
abstract = {The human microbiome is a complex aggregate of microorganisms, and their genomes exert a number of influences crucial to the metabolic, immunologic, hormonal, and homeostatic function of the host. Recent work, both in preclinical mouse models and human studies, has shed light on the impact of gut and tumor microbiota on responses to systemic anticancer therapeutics. In light of this, strategies to target the microbiome to improve therapeutic responses are underway, including efforts to target gut and intratumoral microbes. Here, we discuss mechanisms by which microbiota may impact systemic and antitumor immunity, in addition to outstanding questions in the field. A deeper understanding of these is critical as we devise putative strategies to target the microbiome.},
}
@article {pmid30392534,
year = {2018},
author = {Yatera, K and Noguchi, S and Mukae, H},
title = {The microbiome in the lower respiratory tract.},
journal = {Respiratory investigation},
volume = {56},
number = {6},
pages = {432-439},
doi = {10.1016/j.resinv.2018.08.003},
pmid = {30392534},
issn = {2212-5353},
abstract = {With the advent of new technologies evaluating the microbiome in the sample such as next-generation sequencer (NGS), current increase of an interest in understanding of the lung microbiome and its roles in lung diseases are marked. Gathering the data of bacterial flora in the lung and their changes during disease courses is unraveling the pathogenesis and the mechanism of disease progression particularly in patients with bronchial asthma, chronic obstructive pulmonary disease and infectious lung diseases. To clarify the relationship between the lung microbiome and pulmonary diseases, new information may help us to create new treatment and prevention strategies of some pulmonary diseases by controlling the lung microbiome. Using bacterial 16S ribosomal RNA gene sequence, NGS can rapidly estimate large amount of bacterial sequences in the phylum and genus levels, and some of them in species levels in a very short period of time. In addition to new information of the microbiome using NGS in the respiratory tract, other techniques using basically Sanger method in combination with the clone library construction can also be useful to identify pathogenic bacterial species with their ratio in the respiratory samples such as bacterial pneumonia, lung abscess and nontuberculous mycobacteriosis. These modalities to identify and semi-quantify bacterial burden in the respiratory tract have revealed new bacterial information in each infectious lung disease. This review describes current understanding of the lung microbiome in several representative lung diseases.},
}
@article {pmid30392417,
year = {2018},
author = {Choy, ATF and Carnevale, I and Coppola, S and Meijer, LL and Kazemier, G and Zaura, E and Deng, D and Giovannetti, E},
title = {The microbiome of pancreatic cancer: from molecular diagnostics to new therapeutic approaches to overcome chemoresistance caused by metabolic inactivation of gemcitabine.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2018.1544495},
pmid = {30392417},
issn = {1744-8352},
abstract = {INTRODUCTION: Pancreatic cancer is a complex disease, with an extremely poor response to chemotherapy. Emerging evidence indicates that the tumor microenvironment (TME) might play an important role in mediating chemoresistance. Areas covered: The evaluated study by Geller and collaborators describes several bacterial species within pancreatic tumor tissues and TME and investigated their roles in gemcitabine chemoresistance. Intratumor bacteria express the enzyme cytidine deaminase (CDD), whose long form (CDDL) was shown to metabolize gemcitabine into its inactive metabolite. CDDL is mostly expressed by Gammaproteobacteria and this was among the most common species in pancreatic cancer tissues. Interestingly, mouse models of colorectal cancer injected with bacterial CDDL displayed a reduced response to gemcitabine, but this resistance was neutralized by the antibiotic ciprofloxacin. Expert Commentary: The increased knowledge on the microbiome in pancreatic tissues, as well as its role in chemoresistance, will provide innovative prognostic and therapeutic strategies.},
}
@article {pmid30392013,
year = {2018},
author = {Hendrikx, T and Schnabl, B},
title = {Antimicrobial proteins: intestinal guards to protect against liver disease.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00535-018-1521-8},
pmid = {30392013},
issn = {1435-5922},
abstract = {Alterations of gut microbes play a role in the pathogenesis and progression of many disorders including liver and gastrointestinal diseases. Both qualitative and quantitative changes in gut microbiota have been associated with liver disease. Intestinal dysbiosis can disrupt the integrity of the intestinal barrier leading to pathological bacterial translocation and the initiation of an inflammatory response in the liver. In order to sustain symbiosis and protect from pathological bacterial translocation, antimicrobial proteins (AMPs) such as a-defensins and C-type lectins are expressed in the gastrointestinal tract. In this review, we provide an overview of the role of AMPs in different chronic liver disease such as alcoholic steatohepatitis, non-alcoholic fatty liver disease, and cirrhosis. In addition, potential approaches to modulate the function of AMPs and prevent bacterial translocation are discussed.},
}
@article {pmid30391469,
year = {2018},
author = {Frost, F and Kacprowski, T and Rühlemann, M and Bülow, R and Kühn, JP and Franke, A and Heinsen, FA and Pietzner, M and Nauck, M and Völker, U and Völzke, H and Aghdassi, AA and Sendler, M and Mayerle, J and Weiss, FU and Homuth, G and Lerch, MM},
title = {Impaired Exocrine Pancreatic Function Associates With Changes in Intestinal Microbiota Composition and Diversity.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2018.10.047},
pmid = {30391469},
issn = {1528-0012},
abstract = {BACKGROUND &amp; AIMS: Changes in intestinal microbiome composition are associated with inflammatory, metabolic, and malignant disorders. We studied how exocrine pancreatic function affects intestinal microbiota.<br><br>METHODS: We performed 16S rRNA gene sequencing analysis of stool samples from 1795 volunteers from the population-based study of health in Pomerania who had no history of pancreatic disease. We also measured fecal pancreatic elastase by ELISA and performed quantitative imaging of secretin-stimulated pancreatic fluid secretion. Associations of exocrine pancreatic function with microbial diversity or individual genera were calculated by permutational analysis of variance or linear regression, respectively.<br><br>RESULTS: Differences in pancreatic elastase levels associated with significantly (P<.0001) greater changes in microbiota diversity than with participant age, body mass index, sex, smoking, alcohol consumption, or dietary factors. Significant changes in the abundance of thirty taxa, such as an increase in Prevotella (q<.0001) and a decrease of Bacteroides (q<.0001), indicated a shift from a type-1 to a type-2 enterotype. Changes in pancreatic fluid secretion alone were also associated with changes in microbial diversity (P=.0002), although to a lesser degree.<br><br>CONCLUSIONS: In an analysis of fecal samples from 1795 volunteers, pancreatic acinar cell, rather than duct cell, function is presently the single most significant host factor to be associated with changes in intestinal microbiota composition.},
}
@article {pmid30390805,
year = {2018},
author = {Wang, Q and Yang, F and Jia, H},
title = {Mining the Microbiome for Drug Targets.},
journal = {Methods in enzymology},
volume = {610},
number = {},
pages = {59-72},
doi = {10.1016/bs.mie.2018.09.014},
pmid = {30390805},
issn = {1557-7988},
abstract = {The human microbiome is our &quot;other genome.&quot; Implicated in a growing list of complex diseases, for which genomic studies typically explain a portion of the disease susceptibility, the human gut microbiome has been at the spotlight for our understanding of human diseases. As the microbiome is intrinsically more variable than the human genome, it is important to take careful considerations at each step of a study. Here, we put forward our recommendations, which we envision would facilitate identification of true drug targets in the human microbiome in the colon as well as at other body sites.},
}
@article {pmid30390741,
year = {2018},
author = {Wu, BG and Segal, LN},
title = {The Lung Microbiome and Its Role in Pneumonia.},
journal = {Clinics in chest medicine},
volume = {39},
number = {4},
pages = {677-689},
doi = {10.1016/j.ccm.2018.07.003},
pmid = {30390741},
issn = {1557-8216},
abstract = {The use of next-generation sequencing and multiomic analysis reveals new insights on the identity of microbes in the lower airways blurring the lines between commensals and pathogens. Microbes are not found in isolation; rather they form complex metacommunities where microbe-host and microbe-microbe interactions play important roles on the host susceptibility to pathogens. In addition, the lower airway microbiota exert significant effects on host immune tone. Thus, this review highlights the roles that microbes in the respiratory tract play in the development of pneumonia.},
}
@article {pmid30390509,
year = {2018},
author = {Leng, L and Nobu, MK and Narihiro, T and Yang, P and Amy Tan, GY and Lee, PH},
title = {Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: Pathways and mechanisms.},
journal = {Water research},
volume = {148},
number = {},
pages = {281-291},
doi = {10.1016/j.watres.2018.10.063},
pmid = {30390509},
issn = {1879-2448},
abstract = {Glycerol is presently being generated in surplus with the rapid growth of the biodiesel industry and seeks ways to be upcycled, rather than to be treated with costs. Glycerol for the co-production of 1,3-propanediol (1,3-PDO) and caproate has a great prospect. Yet, its technical difficulty lies in the enhancement of caproate productivity, which requires the presence of ethanol as a co-substrate and necessitates the co-existence of functional microbes for glycerol fermentation and chain elongation. This study successfully achieved 6.38 mM C 1,3-PDO d-1 and 2.95 mM C caproate d-1 in a 2-L mixed-cultured semi-continuous fermenter with a glycerol-ethanol-acetate stoichiometric ratio of 4:3:1. Such conversions were mainly facilitated by a microbial community of Eubacterium limosum, Clostridium kluyveri and Massilibacterium senegalense. With such a synergistic microbiome, the co-production of 1,3-PDO and caproate was achieved from glycerol without ethanol addition. Based on metagenomics, E. limosum is capable of converting glycerol to 1,3-PDO, ethanol and H2, and also redirecting the electron potential of H2 into acetate via the Wood-Ljungdahl pathway, which is then used for chain elongation. C. kluyveri worked synergistically with E. limosum by consuming ethanol and acetate for caproate production. M. senegalense encodes for ethanol oxidation to acetate and butyrate, facilitating the generation of these intermediates for C. kluyveri elongation to caproate. During the transition between fermentation and elongation, an unexpected observation of poly-β-hydroxybutyrate (PHB) formation and reutilization by M. senegalense may be associated with butyrate formation for further caproate generation. The knowledge gleaned from the substrate constitute, microbial consortium and their synergetic metabolism demonstrates a resource upgrade potential for crude glycerol or glycerol-containing wastewater generated from the biodiesel industry.},
}
@article {pmid30390412,
year = {2018},
author = {Han, B and Lin, CJ and Hu, G and Wang, MC},
title = {'Inside Out': a dialogue between mitochondria and bacteria.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.14692},
pmid = {30390412},
issn = {1742-4658},
abstract = {Mitochondria play crucial roles in regulating metabolism and longevity. A body of recent evidences reveals that the gut microbiome can also exert significant effects on these activities in the host. Here, by summarizing the currently known mechanisms underlying these regulations, and by comparing mitochondrial fission-fusion dynamics with bacterial interactions such as quorum sensing, we hypothesize that the microbiome impacts the host by communicating with their intracellular relatives, mitochondria. We highlight recent discoveries supporting this model, and these new findings reveal that metabolite molecules derived from bacteria can fine-tune mitochondrial dynamics in intestinal cells and hence influence host metabolic fitness and longevity. This perspective mode of chemical communication between bacteria and mitochondria may help us understand complex and dynamic environment-microbiome-host interactions regarding their vital impacts on health and diseases. This article is protected by copyright. All rights reserved.},
}
@article {pmid30390235,
year = {2018},
author = {Vitetta, L},
title = {Probiotics Can Break the Toxic Relationship Between the Intestinal Microbiome and the Kidney.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-018-5355-2},
pmid = {30390235},
issn = {1573-2568},
}
@article {pmid30389765,
year = {2018},
author = {Junges, R and Sturød, K and Salvadori, G and Åmdal, HA and Chen, T and Petersen, FC},
title = {Characterization of a signaling system in the oral commensal Streptococcus mitis that mediates interspecies communication with the pathogen Streptococcus pneumoniae.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02297-18},
pmid = {30389765},
issn = {1098-5336},
abstract = {Streptococcus mitis is found in the oral cavity and nasopharynx and forms a significant portion of the human microbiome. In this study, in silico analyses indicated the presence of an Rgg/SHP cell-to-cell communication system in S. mitis Although Rgg presented higher similarity to a repressor in Streptococcus pyogenes, auto-inducing assays and an rgg deletion mutant revealed that in S. mitis Rgg acts as an activator. Transcriptome analysis showed that in addition to shp, the system regulates two other downstream genes, comprising a segment of a putative lantibiotic gene cluster that is in a conjugative element locus in different members of the mitis group. Close comparison to a similar lantibiotic gene cluster in Streptococcus pneumoniae indicated that S. mitis lacked the full set of genes. Despite the potential of SHP to trigger a futile cycle of auto-induction, growth was not significantly affected for the rgg mutant under normal or antibiotic stress conditions. The S. mitis SHP was, however, fully functional in promoting cross-species communication and increasing S. pneumoniae surface polysaccharide production, which in this species is regulated by Rgg/SHP. The activity of SHPs produced by both species was detected in co-cultures using a S. mitis reporter strain. In competitive assays, a slight advantage was observed for the rgg mutants. We conclude that the Rgg/SHP system in S. mitis regulates the expression of its own shp, and activates an Rgg/SHP system in S. pneumoniae that regulates surface polysaccharide synthesis. Fundamentally, cross-communication of such systems may have a role during multi-species interactions.IMPORTANCEBacteria secrete signal molecules into the environment which are sensed by other cells when the density reaches a certain threshold. In this study, we describe a communication system in Streptococcus mitis, a commensal species from the oral cavity, which we also found in several species and strains of streptococci from the mitis group. Further, we show that this system can promote cross-communication with S. pneumoniae, a closely-related major human pathogen. Importantly, we show that this cross-communication can take place during co-culture. While the genes regulated in S. mitis are likely part of a futile cycle of activation, the target genes in S. pneumoniae are potentially involved in virulence. The understanding of such complex communication networks can provide important insights into the dynamics of bacterial communities.},
}
@article {pmid30389589,
year = {2018},
author = {Axelrad, JE and Olén, O and Askling, J and Lebwohl, B and Khalili, H and Sachs, MC and Ludvigsson, JF},
title = {Gastrointestinal Infection Increases Odds of Inflammatory Bowel Disease in a Nationwide Case-Control Study.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2018.09.034},
pmid = {30389589},
issn = {1542-7714},
abstract = {BACKGROUND &amp; AIMS: Gastrointestinal infections have been associated with later development of inflammatory bowel diseases (IBD). However, studies have produced conflicting results. We performed a nationwide case-control study in Sweden to determine whether gastroenteritis is associated with the development of Crohn's disease (CD) or ulcerative colitis (UC).<br><br>METHODS: Using the Swedish National Patient Register, we identified 44,214 patients with IBD (26,450 with UC; 13,387 with CD; and 4,377 with IBD-unclassified) from 2002 to 2014 and matched them with 436,507 individuals in the general population (controls). We then identified patients and controls with reported episodes of gastroenteritis (from 1964 to 2014) and type of pathogen associated. We collected medical and demographic data and used logistic regression to estimate odds ratios (ORs) for IBD associated with enteric infection.<br><br>RESULTS: Of the patients with IBD, 3105 (7.0%) (1672 with UC, 1050 with CD, and 383 with IBD-unclassified) had a record of previous gastroenteritis compared with 17,685 controls (4.1%). IBD cases had higher odds for an antecedent episode of gastrointestinal infection (aOR, 1.64; 1.57-1.71), bacterial gastrointestinal infection (aOR, 2.02; 1.82-2.24), parasitic gastrointestinal infection (aOR, 1.55; 1.03-2.33), and viral gastrointestinal infection (aOR, 1.55; 1.34-1.79). Patients with UC had higher odds of previous infection with Salmonella, Escherichia coli, Campylobacter, or Clostridium difficile compared to controls. Patients with CD had higher odds of previous infection with Salmonella, Campylobacter, Yersinia enterocolitica, Clostridium difficile, amoeba, or norovirus compared to controls. Increasing numbers of gastroenteritis episodes were associated with increased odds of IBD, and a previous episode of gastroenteritis was significant associated with odds for IBD more than 10 years later (aOR, 1.26; 1.19-1.33).<br><br>CONCLUSION: In an analysis of the Swedish National Patient Register, we found previous episodes of gastroenteritis to increase odds of later development of IBD. Although we cannot formally exclude misclassification bias, enteric infections might induce microbial dysbiosis that contributes to the development of IBD in susceptible individuals.},
}
@article {pmid30388453,
year = {2018},
author = {Vangay, P and Johnson, AJ and Ward, TL and Al-Ghalith, GA and Shields-Cutler, RR and Hillmann, BM and Lucas, SK and Beura, LK and Thompson, EA and Till, LM and Batres, R and Paw, B and Pergament, SL and Saenyakul, P and Xiong, M and Kim, AD and Kim, G and Masopust, D and Martens, EC and Angkurawaranon, C and McGready, R and Kashyap, PC and Culhane-Pera, KA and Knights, D},
title = {US Immigration Westernizes the Human Gut Microbiome.},
journal = {Cell},
volume = {175},
number = {4},
pages = {962-972.e10},
doi = {10.1016/j.cell.2018.10.029},
pmid = {30388453},
issn = {1097-4172},
abstract = {Many US immigrant populations develop metabolic diseases post immigration, but the causes are not well understood. Although the microbiome plays a role in metabolic disease, there have been no studies measuring the effects of US immigration on the gut microbiome. We collected stool, dietary recalls, and anthropometrics from 514 Hmong and Karen individuals living in Thailand and the United States, including first- and second-generation immigrants and 19 Karen individuals sampled before and after immigration, as well as from 36 US-born European American individuals. Using 16S and deep shotgun metagenomic DNA sequencing, we found that migration from a non-Western country to the United States is associated with immediate loss of gut microbiome diversity and function in which US-associated strains and functions displace native strains and functions. These effects increase with duration of US residence and are compounded by obesity and across generations.},
}
@article {pmid30388249,
year = {2018},
author = {Moreira, RTF and Lallo, MA and Alvares-Saraiva, AM and Hurtado, ECP and Konno, FT and Spadacci-Morena, D and Coutinho, SDA},
title = {Dichotomous response of Malassezia-infected macrophages to Malassezia pachydermatis and Malassezia furfur.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myy104},
pmid = {30388249},
issn = {1460-2709},
abstract = {Malassezia pachydermatis and Malassezia furfur are lipophilic yeasts of the cutaneous microbiome, although these organisms are occasionally responsible for serious invasive infections in neonates. Since phagocytosis is an important mechanism mediating the adaptive immune response, here we evaluated the phagocytosis capacity and production of nitric oxide and cytokine by macrophages after challenged with M. furfur CBS-1878 and M. pachydermatis CBS-1696. The phagocytic indexes was determined using RAW 264.7 cultivated or not with M. furfur or M. pachydermatis in the concentrations of 5:1 or 2:1 (yeasts:macrophages ratio) for 6 h, 24 h, and 48 h following the challenges. Evaluation of nitric oxide and pro- and anti-inflammatory cytokines (interleukin [IL]-2, IL-4, IL-6, IL-10, IL-17A, interferon (IFN)-γ and tumor necrosis factor [TNF]-α) by Griess method and flow cytometry, respectively, were performed in the different intervals by collecting the cell culture supernatant. Results showed a higher phagocytic index in the 5:1 ratio in 24 h for both species. Malassezia pachydermatis-infected macrophages had superior phagocytic indexes than M. furfur-infected macrophages. Phagocytosis evaluation at 48 h showed significant microorganisms proliferation and macrophages death, particularly in macrophages infected with M. pachydermatis, suggesting yeast evasion mechanism. Significant variations in the nitric oxide production were observed in macrophages infected with both species. Levels of TNF-α and IL-4 cytokines have increased in M. furfur and M. pachydermatis macrophage-infected cultures, respectively. The low microbicidal activity and the presence of pro- and anti-inflammatory cytokines reinforce the dichotomous character of the relation of these yeasts with the host, acting as a commensal in the cutaneous microbiome or causing infection.},
}
@article {pmid30388197,
year = {2018},
author = {Dai, Z and Wong, SH and Yu, J and Wei, Y},
title = {Batch effects correction for microbiome data with Dirichlet-multinomial regression.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/bty874},
pmid = {30388197},
issn = {1367-4811},
}
@article {pmid30388112,
year = {2018},
author = {Jiang, ZD and Jenq, RR and Ajami, NJ and Petrosino, JF and Alexander, AA and Ke, S and Iqbal, T and DuPont, AW and Muldrew, K and Shi, Y and Peterson, C and Do, KA and DuPont, HL},
title = {Safety and preliminary efficacy of orally administered lyophilized fecal microbiota product compared with frozen product given by enema for recurrent Clostridium difficile infection: A randomized clinical trial.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0205064},
doi = {10.1371/journal.pone.0205064},
pmid = {30388112},
issn = {1932-6203},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) via colonoscopy or enema has become a commonly used treatment of recurrent C. difficile infection (CDI).<br><br>AIMS: To compare the safety and preliminary efficacy of orally administered lyophilized microbiota product compared with frozen product by enema.<br><br>METHODS: In a single center, adults with ≥ 3 episodes of recurrent CDI were randomized to receive encapsulated lyophilized fecal microbiota from 100-200 g of donor feces (n = 31) or frozen FMT from 100 g of donor feces (n = 34) by enema. Safety during the three months post FMT was the primary study objective. Prevention of CDI recurrence during the 60 days after FMT was a secondary objective. Fecal microbiome changes were examined in first 39 subjects studied.<br><br>RESULTS: Adverse experiences were commonly seen in equal frequency in both groups and did not appear to relate to the route of delivery of FMT. CDI recurrence was prevented in 26 of 31 (84%) subjects randomized to capsules and in 30 of 34 (88%) receiving FMT by enema (p = 0.76). Both products normalized fecal microbiota diversity while the lyophilized orally administered product was less effective in repleting Bacteroidia and Verrucomicrobia classes compared to frozen product via enema.<br><br>CONCLUSIONS: The route of delivery, oral or rectal, did not influence adverse experiences in FMT. In preliminary evaluation, both routes appeared to show equivalent efficacy, although the dose may need to be higher for lyophilized product. Spore-forming bacteria appear to be the most important engrafting organisms in FMT by the oral route using lyophilized product.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT02449174.},
}
@article {pmid30387240,
year = {2018},
author = {Xie, J and Li, S and Zhang, W and Xia, Y},
title = {RNAi-knockdown of the Locusta migratoria nuclear export factor protein results in insect mortality and alterations in gut microbiome.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.5258},
pmid = {30387240},
issn = {1526-4998},
abstract = {BACKGROUND: The migratory locust Locusta migratoria is one of the most important agricultural pests worldwide. The nuclear export factor 1 (NXF1) protein plays a crucial role in mediating mRNAs transport from the nucleus to the cytoplasm. This study was to evaluate whether NXF1 could be a potential target for RNAi-mediated pest control of L. migratoria.<br><br>RESULTS: We cloned and characterized the nuclear export factor, lm-nxf1 of L. migratoria. Lm-nxf1 was expressed in all tissues examined, including head, fat body, hemolymph, trunk, leg and midgut, with high expression observed in the hemolymph and fat body. Injection of lm-nxf1 dsRNA into hemolymph resulted in inhibition of mRNA export in hemocytes, which were used as a target for observing mRNA export. Total hemocyte levels were reduced by ca. 97% in lm-nxf1-dsRNA-treated locusts, and high insect mortality occurred with LT50 = 7.75 d as compared with 18.15 d for gfp-dsRNA-treated controls. Further, the locust intestine became atrophy, and the opportunistic pathogens Enterobacter aerogenes, Klebsiella pneumoniae and Enterobacter asburiae were specifically detected in midgut after lm-nxf1 dsRNA treatment.<br><br>CONCLUSIONS: The results reveal that knockdown of the lm-nxf1 gene affects the survival of L. migratoria, indicating that lm-nxf1 is a potential target for RNAi-mediated pest control. This article is protected by copyright. All rights reserved.},
}
@article {pmid30387230,
year = {2018},
author = {Song, W and Tiruthani, K and Wang, Y and Shen, L and Hu, M and Dorosheva, O and Qiu, K and Kinghorn, KA and Liu, R and Huang, L},
title = {Trapping of Lipopolysaccharide to Promote Immunotherapy against Colorectal Cancer and Attenuate Liver Metastasis.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e1805007},
doi = {10.1002/adma.201805007},
pmid = {30387230},
issn = {1521-4095},
support = {CA198999/GF/NIH HHS/United States ; CA157738/GF/NIH HHS/United States ; //Eshelman Institute for Innovation/ ; 51673185//National Natural Science Foundation of China/ ; //China Scholarship Council/ ; },
abstract = {The development and progression of colorectal cancer (CRC) is closely related to gut microbiome. Here, the impact of lipopolysaccharide (LPS), one of the most prevalent products in the gut microbiome, on CRC immunotherapy is investigated. It is found that LPS is abundant in orthotopic CRC tissue and is associated with low responses to anti-PD-L1 mAb therapy, and clearance of Gram-negative bacteria from the gut using polymyxin B (PmB) or blockade of Toll-like receptor 4 using TAK-242 will both relieve the immunosuppressive microenvironment and boost T-cell infiltration into the CRC tumor. Further, an engineered LPS-targeting fusion protein is designed and its coding sequence is loaded into a lipid-protamine-DNA (LPD) nanoparticle system for selective expression of LPS trap protein and blocking LPS inside the tumor, and this nanotrapping system significantly relieves the immunosuppressive microenvironment and boosts anti-PD-L1 mAb therapy against CRC tumors. This LPS trap system even attenuates CRC liver metastasis when applied, suggesting the importance of blocking LPS in the gut-liver axis. The strategy applied here may provide a useful new way for treating CRC as well as other epithelial cancers that interact with mucosa microbiome.},
}
@article {pmid30387176,
year = {2018},
author = {Zhang, R and Huang, Z and Yu, G and Zhang, Z},
title = {Characterization of microbiota diversity of field-collected Haemaphysalis longicornis (Acari: Ixodidae) with regard to sex and blood meals.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jobm.201800372},
pmid = {30387176},
issn = {1521-4028},
support = {2017GSF221017//Key Research and Development project of Shandong Province/ ; },
abstract = {Haemaphysalis longicornis is a prominent tick species in China, and the major vector of an emerging tick-borne disease: severe fever with thrombocytopenia syndrome (SFTS). Microbiome diversity of ticks is influenced by several factors. In this study, we investigated microbiome diversity in field-collected female and male H. longicornis ticks and compared the microbial composition of fed and unfed ticks and of those feeding on different hosts using barcode sequencing of V3-V4 region of 16S RNA gene. Regardless of sex, host, and feeding status; the highest abundance among all samples was found for the genus Coxiella. The relative numbers of Coxiella sequences decreased with the length of the blood feeding, whereas the numbers of Staphylococcus and Corynebacterium increased gradually. The dominance of Coxiella across all samples indicates that it is an obligate symbiont of H. longicornis. Overall, higher microbiome richness was detected in male ticks than in female ticks. Fed ticks showed a more diverse microbe composition than unfed ticks, and ticks fed on goats exhibited the highest diversity. These findings of this study can serve as a basis for future studies of microbiota biology and interactions between the microbes and pathogens of H. longicornis.},
}
@article {pmid30386791,
year = {2018},
author = {Sewell, AK and Han, M and Qi, B},
title = {An unexpected benefit from E. coli: how enterobactin benefits host health.},
journal = {Microbial cell (Graz, Austria)},
volume = {5},
number = {10},
pages = {469-471},
doi = {10.15698/mic2018.10.653},
pmid = {30386791},
issn = {2311-2638},
abstract = {Iron plays many critical roles in human biology, such as aiding the transport of oxygen and mediating redox reactions. Iron is essential for life, yet little is known about how iron is taken up into mitochondria to impact the labile iron pool. Iron deficiency is one of the most prevalent human nutrient-deficiency diseases in the world and is a major cause of anemia that affects >25% of the world's population, but unfortunately the current treatment (oral iron supplementation) is inefficient and has many side effects. A greater understanding of iron uptake, and discovery of molecules that aid in this process, may lead to more effective treatments for iron deficiency. In this study, we uncovered a unique and surprising role for an Escherichia coli-produced siderophore enterobactin (Ent) that facilitates iron uptake by the host, observed in both C. elegans and mammalian cells. Although siderophores are well-known Fe+3 scavengers, this activity has previously been described to only benefit iron acquisition by bacteria, not the host. This unexpected function is dependent on the binding of Ent to the host's ATP synthase α-subunit but is independent of other subunits of the ATP synthase. This finding marks a major shift regarding the role of this siderophore in the &quot;iron tug-of-war&quot; paradigm, which is often used to describe the fight between the bacteria and the host for this essential micronutrient. Instead, this study presents E. coli as a commensal &quot;friend&quot; that provides a molecule that supports the host's iron homeostasis. This work reveals a novel, beneficial role of a bacteria-generated molecule in aiding the host's iron homeostasis, and points to surprising new benefits from commensal bacteria.},
}
@article {pmid30386575,
year = {2018},
author = {Kreisinger, J and Schmiedová, L and Petrželková, A and Tomášek, O and Adámková, M and Michálková, R and Martin, JF and Albrecht, T},
title = {Fecal microbiota associated with phytohaemagglutinin-induced immune response in nestlings of a passerine bird.},
journal = {Ecology and evolution},
volume = {8},
number = {19},
pages = {9793-9802},
doi = {10.1002/ece3.4454},
pmid = {30386575},
issn = {2045-7758},
abstract = {The vertebrate gastrointestinal tract is inhabited by a diverse community of bacteria, the so-called gut microbiota (GM). Research on captive mammalian models has revealed tight mutual interactions between immune functions and GM. However, our knowledge of GM versus immune system interactions in wild populations and nonmammalian species remains poor. Here, we focus on the association between GM community structure and immune response measured via the phytohaemagglutinin (PHA) skin swelling test in 12-day-old nestlings of a passerine bird, the barn swallow (Hirundo rustica). The PHA test, a widely used method in field ecoimmunology, assesses cell-mediated immunity. GM structure was inferred based on high-throughput 16S rRNA sequencing of microbial communities in fecal samples. We did not find any association between PHA response and GM diversity; however, our data revealed that the intensity of PHA response was correlated with differences in GM composition at the whole-community level. Ten bacterial operational taxonomic units corresponding to both putative commensal and pathogens were identified as drivers of the compositional variation. In conclusion, our study suggests existence of GM versus immune system interactions in a free-living nonmammalian species, which corresponds with previous research on captive vertebrates.},
}
@article {pmid30386532,
year = {2018},
author = {Moludi, J and Alizadeh, M and Lotfi Yagin, N and Pasdar, Y and Nachvak, SM and Abdollahzad, H and Sadeghpour Tabaei, A},
title = {New insights on atherosclerosis: A cross-talk between endocannabinoid systems with gut microbiota.},
journal = {Journal of cardiovascular and thoracic research},
volume = {10},
number = {3},
pages = {129-137},
doi = {10.15171/jcvtr.2018.21},
pmid = {30386532},
issn = {2008-5117},
abstract = {The incidence of atherosclerosis is increasing rapidly all over the world. Inflammatory processes have outstanding role in coronary artery disease (CAD) etiology and other atherosclerosis manifestations. Recently attentions have been increased about gut microbiota in many fields of medicine especially in inflammatory diseases like atherosclerosis. Ineffectiveness in gut barrier functions and subsequent metabolic endotoxemia (caused by rise in plasma lipopolysaccharide levels) is associated with low-grade chronic inflammation i.e. a recognized feature of atherosclerosis. Furthermore, the role of trimethylamine-N-oxide (TMAO), a gut bacterial metabolite has been suggested in atherosclerosis development. On the other hand, the effectiveness of gut microbiota modulation that results in TMAO reduction has been investigated. Moreover, considerable evidence supports a role for the endocannabinoid system (ECS) in atherosclerosis pathology which affects gut microbiota, but their effects on atherosclerosis are controversial. Therefore, we presented some evidence about the relationship between gut microbiota and ECS in atherosclerosis. We also presented evidences that gut microbiota modulation by pre/probiotics can have significant influence on the ECS.},
}
@article {pmid30386323,
year = {2018},
author = {Méndez-Salazar, EO and Ortiz-López, MG and Granados-Silvestre, MLÁ and Palacios-González, B and Menjivar, M},
title = {Altered Gut Microbiota and Compositional Changes in Firmicutes and Proteobacteria in Mexican Undernourished and Obese Children.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2494},
doi = {10.3389/fmicb.2018.02494},
pmid = {30386323},
issn = {1664-302X},
abstract = {Mexico is experiencing an epidemiological and nutritional transition period, and Mexican children are often affected by the double burden of malnutrition, which includes undernutrition (15.3% of children) and obesity (13.6%). The gut microbiome is a complex and metabolically active community of organisms that influences the host phenotype. Although previous studies have shown alterations in the gut microbiota in undernourished children, the affected bacterial communities remain unknown. The present study investigated and compared the bacterial richness and diversity of the fecal microbiota in groups of undernourished (n = 12), obese (n = 12), and normal-weight (control) (n = 12) Mexican school-age children. We used next-generation sequencing to analyze the V3-V4 region of the bacterial 16S rRNA gene, and we also investigated whether there were correlations between diet and relevant bacteria. The undernourished and obese groups showed lower bacterial richness and diversity than the normal-weight group. Enterotype 1 correlated positively with dietary fat intake in the obese group and with carbohydrate intake in the undernourished group. The results showed that undernourished children had significantly higher levels of bacteria in the Firmicutes phylum and in the Lachnospiraceae family than obese children, while the Proteobacteria phylum was overrepresented in the obese group. The level of Lachnospiraceae correlated negatively with energy consumption and positively with leptin level. This is the first study to examine the gut microbial community structure in undernourished and obese Mexican children living in low-income neighborhoods. Our analysis revealed distinct taxonomic profiles for undernourished and obese children.},
}
@article {pmid30385796,
year = {2018},
author = {Nishitsuji, K and Watanabe, S and Xiao, J and Nagatomo, R and Ogawa, H and Tsunematsu, T and Umemoto, H and Morimoto, Y and Akatsu, H and Inoue, K and Tsuneyama, K},
title = {Effect of coffee or coffee components on gut microbiome and short-chain fatty acids in a mouse model of metabolic syndrome.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16173},
doi = {10.1038/s41598-018-34571-9},
pmid = {30385796},
issn = {2045-2322},
support = {24390181//Japan Society for the Promotion of Science (JSPS)/ ; 25340121//Japan Society for the Promotion of Science (JSPS)/ ; 15K15098//Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {We previously showed that male Tsumura Suzuki obese diabetes (TSOD) mice, a spontaneous mouse model of metabolic syndrome, manifested gut dysbiosis and subsequent disruption of the type and quantity of plasma short-chain fatty acids (SCFAs), and daily coffee intake prevented nonalcoholic steatohepatitis in this mouse model. Here, we present a preliminary study on whether coffee and its major components, caffeine and chlorogenic acid, would affect the gut dysbiosis and the disrupted plasma SCFA profile of TSOD mice, which could lead to improvement in the liver pathology of these mice. Three mice per group were used. Daily intake of coffee or its components for 16 wk prevented liver lobular inflammation without improving obesity in TSOD mice. Coffee and its components did not repair the altered levels of Gram-positive and Gram-negative bacteria and an increased abundance of Firmicutes in TSOD mice but rather caused additional changes in bacteria in six genera. However, caffeine and chlorogenic acid partially improved the disrupted plasma SCFA profile in TSOD mice, although coffee had no effects. Whether these alterations in the gut microbiome and the plasma SCFA profile might affect the liver pathology of TSOD mice may deserve further investigation.},
}
@article {pmid30385553,
year = {2018},
author = {Rabesandratana, T},
title = {Microbiome conservancy stores global fecal samples.},
journal = {Science (New York, N.Y.)},
volume = {362},
number = {6414},
pages = {510-511},
doi = {10.1126/science.362.6414.510},
pmid = {30385553},
issn = {1095-9203},
}
@article {pmid30385457,
year = {2018},
author = {Abdel-Haq, R and Schlachetzki, JCM and Glass, CK and Mazmanian, SK},
title = {Microbiome-microglia connections via the gut-brain axis.},
journal = {The Journal of experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1084/jem.20180794},
pmid = {30385457},
issn = {1540-9538},
abstract = {Microglia, the resident immune cells in the brain, are essential for modulating neurogenesis, influencing synaptic remodeling, and regulating neuroinflammation by surveying the brain microenvironment. Microglial dysfunction has been implicated in the onset and progression of several neurodevelopmental and neurodegenerative diseases; however, the multitude of factors and signals influencing microglial activity have not been fully elucidated. Microglia not only respond to local signals within the brain but also receive input from the periphery, including the gastrointestinal (GI) tract. Recent preclinical findings suggest that the gut microbiome plays a pivotal role in regulating microglial maturation and function, and altered microbial community composition has been reported in neurological disorders with known microglial involvement in humans. Collectively, these findings suggest that bidirectional crosstalk between the gut and the brain may influence disease pathogenesis. Herein, we discuss recent studies showing a role for the gut microbiome in modulating microglial development and function in homeostatic and disease conditions and highlight possible future research to develop novel microbial treatments for disorders of the brain.},
}
@article {pmid30385328,
year = {2018},
author = {Ananthakrishnan, AN and Singal, AG and Chang, L},
title = {The Gut Microbiome and Digestive Health - A New Frontier.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2018.10.040},
pmid = {30385328},
issn = {1542-7714},
}
@article {pmid30385304,
year = {2018},
author = {De Grandi, R and Capaccio, P and Bidossi, A and Bottagisio, M and Drago, L and Torretta, S and Pignataro, L and De Vecchi, E},
title = {Salivary calculi microbiota: new insights into microbial networks and pathogens reservoir.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.micinf.2018.10.002},
pmid = {30385304},
issn = {1769-714X},
abstract = {Sialolithiasis represents the most common disorders of salivary glands in middle-aged patients. It has been hypothesized that the retrograde migration of bacteria from the oral cavity to gland ducts may facilitate the formation of stones. Thus, in the present study, a microbiome characterization of salivary calculi was performed to evaluate the abundance and the potential correlations between microorganisms constituting the salivary calculi microbiota. Our data supported the presence of a core microbiota of sialoliths constituted principally by Streptococcus spp., Fusobacterium spp. and Eikenella spp., along with the presence of important pathogens commonly involved in infective sialoadenitis.},
}
@article {pmid30385177,
year = {2018},
author = {Peng, J and Xiao, X and Hu, M and Zhang, X},
title = {Interaction between gut microbiome and cardiovascular disease.},
journal = {Life sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.lfs.2018.10.063},
pmid = {30385177},
issn = {1879-0631},
abstract = {Traditional cardiovascular risk factors do not underlie all incidence of cardiovascular disease. In recent years, accumulating evidence has demonstrated that gut microbiota and its metabolites also play a pivotal role in the onset and development of cardiovascular disease, including atherosclerosis, hypertension, heart failure, atrial fibrillation and myocardial fibrosis. Trillions of bacteria indwell the gastrointestinal tract and metabolize nutrients into trimethylamine-N-oxide, short-chain fatty acids and so on. Targeting these microorganisms and relevant metabolic pathways has beneficial effects in cardiovascular disease. This review will summarize the role of gut microbiota and its metabolites, mainly trimethylamine-N-oxide, in the pathogenesis of cardiovascular diseases, and discuss the possible mechanisms that drive cardiovascular diseases and highlight potential therapies in this field.},
}
@article {pmid30385083,
year = {2018},
author = {Floreani, A and Restrepo-Jiménez, P and Secchi, MF and De Martin, S and Leung, PSC and Krawitt, E and Bowlus, CL and Gershwin, ME and Anaya, JM},
title = {Etiopathogenesis of autoimmune hepatitis.},
journal = {Journal of autoimmunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaut.2018.10.020},
pmid = {30385083},
issn = {1095-9157},
abstract = {Autoimmune hepatitis is a chronic inflammatory liver disease characterized by hypergammaglobulinemia, the presence of autoantibodies, and inflammation within the liver, including lymphocytic infiltrates and interface hepatitis. Autoimmune hepatitis shows a female predominance and can present at any age and in any ethnicity. The disease is thought to be a consequence of a break of immune tolerance leading to an autoimmune process that induces liver injury. The self-attack is triggered by T-helper cell-mediated liver autoantigen recognition and B-cell production of autoantibodies, and is sustained by impaired regulatory T cells number and function. Superimposed on a genetic predisposition, infections and environmental factors have been studied as triggering factors for the disease. Allelic variants in the HLA locus have been associated with susceptibility; associations with single nucleotide polymorphisms within non-HLA genes have also been assessed. Several factors have been described as triggers of autoimmune responses in predisposed individuals, including infections, alcohol, vitamin D deficiency, and an altered composition of the intestinal microbiome. Importantly, drugs and herbal agents may trigger classical autoimmune hepatitis, or may induce a liver disease with autoimmune features. Interactions between female hormones and genetic factors have been hypothesized to play a role in autoimmunity, although the exact role for these factors has not been fully established. Herein we present a review of the etiology of autoimmune hepatitis including de novo autoimmune hepatitis post-liver transplantation as well as animal models for its study.},
}
@article {pmid30384952,
year = {2018},
author = {Gopalsamy, SN and Woodworth, MH and Wang, T and Carpentieri, CT and Mehta, N and Friedman-Moraco, RJ and Mehta, AK and Larsen, CP and Kraft, CS},
title = {The Use of Microbiome Restoration Therapeutics to Eliminate Intestinal Colonization With Multidrug-Resistant Organisms.},
journal = {The American journal of the medical sciences},
volume = {356},
number = {5},
pages = {433-440},
doi = {10.1016/j.amjms.2018.08.015},
pmid = {30384952},
issn = {1538-2990},
abstract = {Antibiotic resistance (AR) has been described by the World Health Organization as an increasingly serious threat to global public health. Many mechanisms of AR have become widespread due to global selective pressures such as widespread antibiotic use. The intestinal tract is an important reservoir for many multidrug-resistant organisms (MDROs), and next-generation sequencing has expanded understanding of the resistome, defined as the comprehensive sum of genetic determinants of AR. Intestinal decolonization has been explored as a strategy to eradicate MDROs with selective digestive tract decontamination and probiotics being notable examples with mixed results. This review focuses on fecal microbiota transplantation and the early evidence supporting its efficacy in decolonizing MDROs and potential mechanisms of action to reduce AR genes. Current evidence suggests that fecal microbiota transplantation may have promise in restoring healthy microbial diversity and reducing AR, and clinical trials are underway to better characterize its safety and efficacy.},
}
@article {pmid30384950,
year = {2018},
author = {Ihekweazu, FD and Versalovic, J},
title = {Development of the Pediatric Gut Microbiome: Impact on Health and Disease.},
journal = {The American journal of the medical sciences},
volume = {356},
number = {5},
pages = {413-423},
doi = {10.1016/j.amjms.2018.08.005},
pmid = {30384950},
issn = {1538-2990},
abstract = {The intestinal microbiota are important in human growth and development. Microbial composition may yield insights into the temporal development of microbial communities and vulnerabilities to disorders of microbial ecology such as recurrent Clostridium difficile infection. Discoveries of key microbiome features of carbohydrate and amino acid metabolism are lending new insights into possible therapies or preventative strategies for inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). In this review, we summarize the current understanding of the development of the pediatric gastrointestinal microbiome, the influence of the microbiome on the developing brain through the gut-brain axis, and the impact of dysbiosis on disease development. Dysbiosis is explored in the context of pediatric allergy and asthma, recurrent C. difficile infection, IBD, IBS, and metabolic disorders. The central premise is that the human intestinal microbiome plays a vital role in health and disease, beginning in the prenatal period and extending throughout childhood.},
}
@article {pmid30384948,
year = {2018},
author = {Wilcox, CM},
title = {Study of the Microbiome Has Reached Prime Time.},
journal = {The American journal of the medical sciences},
volume = {356},
number = {5},
pages = {409-410},
doi = {10.1016/j.amjms.2018.08.006},
pmid = {30384948},
issn = {1538-2990},
}
@article {pmid30384488,
year = {2018},
author = {Yuan, XL and Cao, M and Liu, XM and Du, YM and Shen, GM and Zhang, ZF and Li, JH and Zhang, P},
title = {Composition and Genetic Diversity of the Nicotiana tabacum Microbiome in Different Topographic Areas and Growth Periods.},
journal = {International journal of molecular sciences},
volume = {19},
number = {11},
pages = {},
doi = {10.3390/ijms19113421},
pmid = {30384488},
issn = {1422-0067},
support = {31700295//Natural Science Foundation of China/ ; 2016A02//Science Foundation for Young Scholars of Institute of Tobacco Research of Chinese Academy of Agricultural Sciences/ ; },
abstract = {Fungal endophytes are the most ubiquitous plant symbionts on earth and are phylogenetically diverse. Studies on the fungal endophytes in tobacco have shown that they are widely distributed in the leaves, stems, and roots, and play important roles in the composition of the microbial ecosystem of tobacco. Herein, we analyzed and quantified the endophytic fungi of healthy tobacco leaves at the seedling stage (SS), resettling growth stage (RGS), fast-growing stage (FGS), and maturing stage (MS) at three altitudes (600, 1000, and 1300 m). We sequenced the internal transcribed spacer (ITS) region of fungal samples to delimit operational taxonomic units (OTUs) and phylogenetically characterize the communities. The results showed that the numbers of clustering OTUs at SS, RGS, FGS, and MS were 516, 709, 469, and 428, respectively. At the phylum level, species in Ascomycota and Basidiomycota had absolute predominance, representing 97.8% and 2.0% of the total number of species, respectively. We also found the number of fungi at the RGS and FGS stages was higher than those at the other two stages. Additionally, OTU richness was determined by calculating the Observed Species, Shannon, Simpson, Chao1, abundance-based coverage estimator (ACE), Good's coverage and phylogenetic distance (PD)_whole_tree indices based on the total number of species. Our results showed RGS samples had the highest diversity indices. Furthermore, we found that the diversity of fungal communities tended to decrease with increasing altitude. The results from this study indicated that tobacco harbors an abundant and diverse endophytic fungal community, which provides new opportunities for exploring their potential utilization.},
}
@article {pmid30384345,
year = {2018},
author = {Riepl, M},
title = {Compounding to Prevent and Treat Dysbiosis of the Human Vaginal Microbiome.},
journal = {International journal of pharmaceutical compounding},
volume = {22},
number = {6},
pages = {456-465},
pmid = {30384345},
issn = {1092-4221},
abstract = {Homeostasis of the human vaginal microbiome, which consists of the bacteriome (colonizing bacteria) and the mycobiome (resident fungi), is essential to the health of the female reproductive system. Dysbiosis of either microbial community can be caused by a variety of factors ranging from behavioral issues (personal-hygiene practices, the choice of contraceptives, smoking, etc.) to biological variables (the host-microbiome composition, menstruation, the robustness of the host's immune response). Clinicians often consult compounding pharmacistsbabout the formulation and use of customized preparations to treat vaginal diseases and re-establish a healthful vaginal microenvironment when commercially manufactured products have failed or are unavailable. In this article, the function of the human vaginal bacteriome and mycobiome are examined, a common microorganism identified in each of those microenvironments is discussed, factors that cause dysbiosis are reviewed, and the role of biofilm in the vaginal microbiota is explored. A question typical of those asked by prescribers committed to improving women's health and decreasing the incidence of recurring bacterial vaginosis or fungal infections is answered. Formulations for compounds that help ensure or reestablish the homeostasis of the human vaginal bacteriome and mycobiome are also provided.},
}
@article {pmid30384329,
year = {2018},
author = {Schooley, RT},
title = {The human microbiome: implications for health and disease, including HIV infection.},
journal = {Topics in antiviral medicine},
volume = {26},
number = {3},
pages = {75-78},
pmid = {30384329},
issn = {2161-5853},
abstract = {Our increased understanding of the human microbiome has brought insight into the role it plays in health and disease, including HIV infection. Studies have shown that the gut microbiome is less diverse in individuals with HIV infection than in noninfected control subjects. Efforts to modify the microbiome to bolster immune reconstitution in people with HIV infection have so far been unsuccessful. The vaginal microbiome affects risk of HIV acquisition, with Lactobacillus dominance being protective compared with vaginosis characterized by larger populations of Gardnerella. The vaginal microbiome might also affect efficacy of topical tenofovir disoproxil fumarate preexposure prophylaxis. This article summarizes a presentation by Robert T. Schooley, MD, at the IAS-USA continuing education program held in San Francisco in May 2018.},
}
@article {pmid30384071,
year = {2018},
author = {Wang, C and Yue, S and Hao, Z and Ren, G and Lu, D and Zhang, Q and Zhao, M},
title = {Pubertal exposure to the endocrine disruptor mono-2-ethylhexyl ester at body burden level caused cholesterol imbalance in mice.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {244},
number = {},
pages = {657-666},
doi = {10.1016/j.envpol.2018.08.091},
pmid = {30384071},
issn = {1873-6424},
abstract = {Metabolic disturbance is the prerequisite to developing metabolic disease. An increasing number of reports have shown that exposure to environmental endocrine-disrupting chemicals (EDCs) can cause metabolic syndrome and may be related to metabolic disease. However, the potential mechanism of EDC-related lipid metabolism disruption in the endocrine organs (especially gut microbiome) during pubertal exposure remains elusive at the body burden level. We observed that male mice fed with 0.05 mg/kg b.w. MEHP under a high-fat diet caused enhancement in the fat mass, total cholesterol, high- and low-density lipoprotein cholesterol. MEHP intake induced a significant shift in microbiota composition, including the relative abundance of Firmicutes and reduction of Verrucomicrobia. Statistical analysis showed a positive correlation between several bacterial taxa and cholesterol body burden. Also, MEHP intake induced adipocyte hypertrophy and cholesterol overloading, which sense cholesterol synthesis genes such as Srebp2 and Hmgcr. That caused adipocyte dysfunction. Finally, cholesterol deposition and transportation was imbalance in the mice liver. Conclusively, by targeting the endocrine organs, EDCs would increase the risk of cholesterol burden even at a low concentration when coupled with a high-fat diet during pubertal period in male mice.},
}
@article {pmid30383976,
year = {2018},
author = {Li, B and Yu, FZ and Minich, A and Hock, A and Lee, C and Pierro, A},
title = {Neonatal Intestinal Injury Induced by Maternal Separation: Pathogenesis and Pharmacological Targets.},
journal = {Canadian journal of physiology and pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjpp-2018-0370},
pmid = {30383976},
issn = {1205-7541},
abstract = {Maternal separation (MS) is a well-studied phenomenon thought to play a role in the pathogenesis of many diseases ranging from neuropsychiatric to early intestinal disorders such as necrotizing enterocolitis. The existing evidence suggests that MS initiates a variety of processes that in turn lead to early intestinal injury. Although there are many theories as to how MS alters normal physiological processes, the exact mechanism of action remains to be elucidated. This review aims to describe some of the pathological processes affecting the intestine that are caused by MS, including: (i) brain-gut axis, (ii) intestinal epithelial barrier function, (iii) microbiome, (iv) oxidative stress and endoplasmic reticulum stress, and (v) gut inflammation.},
}
@article {pmid30383890,
year = {2018},
author = {Stinson, LF and Keelan, JA and Payne, MS},
title = {Identification and removal of contaminating microbial DNA from PCR reagents: impact on low biomass microbiome analyses.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/lam.13091},
pmid = {30383890},
issn = {1472-765X},
abstract = {Reagent-derived contamination can compromise the integrity of microbiome data, particularly in low microbial biomass samples. This contamination has recently been attributed to the &quot;kitome&quot; (contamination introduced by the DNA extraction kit), prior to which attention was mostly paid to potential contamination introduced by PCR reagents. In this study, we assessed the proportion to which our DNA extraction kit and PCR master mix introduce contaminating microbial DNA to bacterial microbial profiles generated by 16S rRNA gene sequencing. Utilizing a commercial dsDNase treatment protocol to decontaminate the PCR master mix, we demonstrated that the vast majority of contaminating DNA was derived from the PCR master mix. Importantly, this contamination was almost completely eliminated using the simple dsDNase treatment, resulting in a 99% reduction in contaminating bacterial reads. We suggest that dsDNase treatment of PCR reagents should be explored as a simple and effective way of reducing contamination in low biomass microbiome studies and producing more robust and reliable data. This article is protected by copyright. All rights reserved.},
}
@article {pmid30382878,
year = {2018},
author = {Walker, AW},
title = {Studying the microbiome and its complexities: an interview with Alan Walker.},
journal = {BMC biology},
volume = {16},
number = {1},
pages = {134},
doi = {10.1186/s12915-018-0599-z},
pmid = {30382878},
issn = {1741-7007},
abstract = {Alan Walker is a Senior Lecturer at the University of Aberdeen, UK, studying the intestinal microbiota and its interactions with the host's diet. In this interview, Alan discusses his research interests, earlier studies of the ways contaminants can affect microbiome analyses, the excitement of experiments going well, and why science doesn't need to be combative.},
}
@article {pmid30382844,
year = {2018},
author = {Huang, KC},
title = {When a physicist wanders into biology…: an interview with KC Huang.},
journal = {BMC biology},
volume = {16},
number = {1},
pages = {130},
doi = {10.1186/s12915-018-0595-3},
pmid = {30382844},
issn = {1741-7007},
abstract = {Kerwyn Casey (&quot;KC&quot;) Huang is an Associate Professor at Stanford University, studying the physical nature of biological systems and the underpinnings of fundamental processes such as cell shape determination, cell division, and intracellular and microbial community organization. In this interview, KC discusses how the ability to pursue insights at scales from molecules to cellular communities can shed new light on longstanding questions, the necessity for new tools in exploring the microbiome, how to create an empowering lab environment, and why integrating chemistry with physics and biology can bring us closer to asking the right questions.},
}
@article {pmid30382834,
year = {2018},
author = {Hanage, WP},
title = {From bacterial genomics to clinical epidemiology: an interview with Bill Hanage.},
journal = {BMC biology},
volume = {16},
number = {1},
pages = {122},
doi = {10.1186/s12915-018-0588-2},
pmid = {30382834},
issn = {1741-7007},
abstract = {Bill Hanage is an Associate Professor of Epidemiology at Harvard School of Public Health, where he studies fundamental and applied epidemiology using genomic and evolutionary methods. Bill spoke to us about the different types of selection that determine pathogen populations, asking reviewers to highlight positives of papers, and whether we're closer to a causal framework for studying the microbiome.},
}
@article {pmid30382422,
year = {2018},
author = {Vázquez-Chimalhua, E and Ruíz-Herrera, LF and Barrera-Ortiz, S and Valencia-Cantero, E and López-Bucio, J},
title = {The bacterial volatile dimethyl-hexa-decylamine reveals an antagonistic interaction between jasmonic acid and cytokinin in controlling primary root growth of Arabidopsis seedlings.},
journal = {Protoplasma},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00709-018-1327-9},
pmid = {30382422},
issn = {1615-6102},
support = {2.26//Universidad Michoacana de San Nicolás de Hidalgo/ ; },
abstract = {Chemical communication underlies major adaptive traits in plants and shapes the root microbiome. An increasing number of diffusible and/or volatile organic compounds released by bacteria have been identified, which play phytostimulant or protective functions, including dimethyl-hexa-decylamine (DMHDA), a volatile biosynthesized by Arthrobacter agilis UMCV2 that induces jasmonic acid (JA) signaling in Arabidopsis. Here, he found that the growth repressing effects of both DMHDA and JA are antagonized by kinetin and correlated with an inhibition of cytokinin-related ARR5::GUS and TCS::GFP expression in Arabidopsis primary roots. Moreover, we demonstrate that shoot supplementation of JA triggers JAZ1 expression both locally and systemically and represses cytokinin-dependent promoter activity in roots. A similar effect was observed after cotyledon wounding, in which an increase of JA-inducible LOX2:GUS expression represses root growth, which correlates with the loss of TCS::GFP detection at the very root tip. Our data demonstrate that the bacterial volatile DMHDA crosstalks with cytokinin signaling and reveals the downstream antagonistic interaction between JA and cytokinin in controlling root growth.},
}
@article {pmid30382244,
year = {2018},
author = {Pedersen, HK and Forslund, SK and Gudmundsdottir, V and Petersen, AØ and Hildebrand, F and Hyötyläinen, T and Nielsen, T and Hansen, T and Bork, P and Ehrlich, SD and Brunak, S and Oresic, M and Pedersen, O and Nielsen, HB},
title = {A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41596-018-0064-z},
pmid = {30382244},
issn = {1750-2799},
abstract = {We recently presented a three-pronged association study that integrated human intestinal microbiome data derived from shotgun-based sequencing with untargeted serum metabolome data and measures of host physiology. Metabolome and microbiome data are high dimensional, posing a major challenge for data integration. Here, we present a step-by-step computational protocol that details and discusses the dimensionality-reduction techniques used and methods for subsequent integration and interpretation of such heterogeneous types of data. Dimensionality reduction was achieved through a combination of data normalization approaches, binning of co-abundant genes and metabolites, and integration of prior biological knowledge. The use of prior knowledge to overcome functional redundancy across microbiome species is one central advance of our method over available alternative approaches. Applying this framework, other investigators can integrate various '-omics' readouts with variables of host physiology or any other phenotype of interest (e.g., connecting host and microbiome readouts to disease severity or treatment outcome in a clinical cohort) in a three-pronged association analysis to identify potential mechanistic links to be tested in experimental settings. Although we originally developed the framework for a human metabolome-microbiome study, it is generalizable to other organisms and environmental metagenomes, as well as to studies including other -omics domains such as transcriptomics and proteomics. The provided R code runs in ~1 h on a standard PC.},
}
@article {pmid30381384,
year = {2018},
author = {Palmer-Young, EC and Raffel, TR and McFrederick, QS},
title = {Temperature-mediated inhibition of a bumblebee parasite by an intestinal symbiont.},
journal = {Proceedings. Biological sciences},
volume = {285},
number = {1890},
pages = {},
doi = {10.1098/rspb.2018.2041},
pmid = {30381384},
issn = {1471-2954},
abstract = {Competition between organisms is often mediated by environmental factors, including temperature. In animal intestines, nonpathogenic symbionts compete physically and chemically against pathogens, with consequences for host infection. We used metabolic theory-based models to characterize differential responses to temperature of a bacterial symbiont and a co-occurring trypanosomatid parasite of bumblebees, which regulate body temperature during flight and incubation. We hypothesized that inhibition of parasites by bacterial symbionts would increase with temperature, due to symbionts having higher optimal growth temperatures than parasites. We found that a temperature increase over the range measured in bumblebee colonies would favour symbionts over parasites. As predicted by our hypothesis, symbionts reduced the optimal growth temperature for parasites, both in direct competition and when parasites were exposed to symbiont spent medium. Inhibitory effects of the symbiont increased with temperature, reflecting accelerated growth and acid production by symbionts. Our results indicate that high temperatures, whether due to host endothermy or environmental factors, can enhance the inhibitory effects of symbionts on parasites. Temperature-modulated manipulation of microbiota could be one explanation for fever- and heat-induced reductions of infection in animals, with consequences for diseases of medical and conservation concern.},
}
@article {pmid30380474,
year = {2018},
author = {Cerqueira, F and Matamoros, V and Bayona, J and Piña, B},
title = {Antibiotic resistance genes distribution in microbiomes from the soil-plant-fruit continuum in commercial Lycopersicon esculentum fields under different agricultural practices.},
journal = {The Science of the total environment},
volume = {652},
number = {},
pages = {660-670},
doi = {10.1016/j.scitotenv.2018.10.268},
pmid = {30380474},
issn = {1879-1026},
abstract = {While the presence of antibiotic resistance genes (ARGs) in agricultural soils and products has been firmly established, their distribution among the different plant parts and the contribution of agricultural practices, including irrigation with reclaimed water, have not been adequately addressed yet. To this end, we analyzed the levels of seven ARGs (sul1, blaTEM, blaCTX-M-32, mecA, qnrS1, tetM, blaOXA-58), plus the integrase gene intl1, in soils, roots, leaves, and fruits from two commercial tomato fields irrigated with either unpolluted groundwater or from a channel impacted by treated wastewater, using culture-independent, quantitative real-time PCR methods. ARGs and intl1 sequences were found in leaves and fruits at levels representing from 1 to 10% of those found in roots or soil. The relative abundance of intl1 sequences correlated with tetM, blaTEM, and sul1 levels, suggesting a high horizontal mobility potential for these ARGs. High-throughput 16S rDNA sequencing revealed microbiome differences both between sample types (soil plus roots versus leaves plus fruits) and sampling zones, and a correlation between the prevalence of Pseudomonadaceae and the levels of different ARGs, particularly in fruits and leaves. We concluded that both microbiome composition and ARGs levels in plants parts, including fruits, were likely influenced by agricultural practices.},
}
@article {pmid30379400,
year = {2018},
author = {Van Hecke, T and De Vrieze, J and Boon, N and De Vos, WH and Vossen, E and De Smet, S},
title = {Combined Consumption of Beef-Based Cooked Mince and Sucrose Stimulates Oxidative Stress, Cardiac Hypertrophy, and Colonic Outgrowth of Desulfovibrionaceae in Rats.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e1800962},
doi = {10.1002/mnfr.201800962},
pmid = {30379400},
issn = {1613-4133},
abstract = {SCOPE: High consumption of red meat and sucrose increases the epidemiological risk for chronic diseases. Mechanistic hypotheses include alterations in oxidative status, gut microbial composition, fat deposition and low-grade inflammation.<br><br>METHODS AND RESULTS: For two weeks, 40 rats consumed a diet high in white or red meat (chicken-based or beef-based cooked mince respectively), and containing corn starch or sucrose in a 2 × 2 factorial design. Lard was mixed with lean chicken or beef to obtain comparable dietary fatty acid profiles. Beef (vs. chicken)-fed rats had higher lipid oxidation products (malondialdehyde, 4-hydroxy-2-nonenal and hexanal) in stomach content and blood, and lower blood glutathione. Sucrose (vs. corn starch)-fed rats showed increased blood lipid oxidation products and glutathione peroxidase activity, higher liver weight and malondialdehyde concentrations, and mesenterial and retroperitoneal fat accumulation. Beef-sucrose-fed rats had increased cardiac weight, suggesting pathophysiological effects on the cardiovascular system. The colonic microbiome of beef-sucrose-fed rats showed an outgrowth of the sulfate-reducing family of the Desulfovibrionaceae, partly in expense of the Lactobacillus genus, indicating intestinal dysbiosis. Blood C-reactive protein, a marker for inflammation, was not different among groups.<br><br>CONCLUSIONS: Consumption of a cooked beef-based meat product with sucrose increased oxidative stress parameters and promoted cardiac hypertrophy and intestinal dysbiosis. This article is protected by copyright. All rights reserved.},
}
@article {pmid30378274,
year = {2018},
author = {Haaland, RE and Fountain, J and Hu, Y and Holder, A and Dinh, C and Hall, L and Pescatore, NA and Heeke, S and Hart, CE and Xu, J and Hu, YJ and Kelley, CF},
title = {Repeated rectal application of a hyperosmolar lubricant is associated with microbiota shifts but does not affect PrEP drug concentrations: results from a randomized trial in men who have sex with men.},
journal = {Journal of the International AIDS Society},
volume = {21},
number = {10},
pages = {e25199},
doi = {10.1002/jia2.25199},
pmid = {30378274},
issn = {1758-2652},
support = {//United States Centers for Disease Control and Prevention/ ; },
abstract = {INTRODUCTION: Oral pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC) is highly effective in preventing HIV infection among men who have sex with men (MSM). The effects of consistent personal lubricant use in the rectum on tissue PrEP drug concentrations and the rectal microbiota are unknown. We investigated rectal PrEP drug concentrations and the microbiota in MSM before and after repeated rectal application of a hyperosmolar lubricant.<br><br>METHODS: We randomized 60 HIV-negative MSM to apply 4 mL of hyperosmolar rectal lubricant daily (n = 20), take daily oral TDF/FTC (n = 19), or both (n = 21) for seven days. Blood, rectal biopsies and rectal secretions were collected via rigid sigmoidoscopy before and on day 8 after product use. Tenofovir (TFV) and FTC as well as their intracellular metabolites tenofovir-diphosphate (TFV-DP), FTC-triphosphate (FTC-TP) were measured by HPLC-mass spectrometry. Rectal mucosal microbiota was sequenced with 16S rRNA sequencing using Illumina MiSeq.<br><br>RESULTS: Seven days of lubricant application was not associated with differences in PrEP drug concentrations in rectal tissue or secretions. Lubricant use was associated with a decrease in the relative abundance of the Bacteroides genus (p = 0.01) and a non-significant increase in the Prevotella genus (p = 0.09) in the rectum. PrEP drug concentrations in rectal tissue and secretions were not associated with microbiota composition or diversity either before or after lubricant use.<br><br>CONCLUSIONS: Repeated rectal application of a hyperosmolar lubricant does not affect mucosal PrEP drug concentrations but is associated with changes in the rectal microbiome.},
}
@article {pmid30378133,
year = {2018},
author = {Camarena-Pozos, DA and Flores-Núñez, VM and López, MG and López-Bucio, J and Partida-Martinez, LP},
title = {Smells from the desert: microbial volatiles that affect plant growth and development of native and non-native plant species.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.13476},
pmid = {30378133},
issn = {1365-3040},
abstract = {The plant microbiota can affect host fitness via the emission of microbial volatile organic compounds (mVOCs) that influence growth and development. However, evidence of these molecules and their effects in plants from arid ecosystems is limited. We screened the mVOCs produced by 40 core and representative members of the microbiome of agaves and cacti in their interaction with Arabidopsis thaliana and Nicotiana benthamiana. We used SPME-GC-MS to characterize the chemical diversity of mVOCs and tested the effects of selected compounds on growth and development of model and host plants. Our study revealed that ca. 90% of the bacterial strains promoted plant growth both in A. thaliana and N. benthamiana. Bacterial VOCs were mainly composed of esters, alcohols and S-containing compounds with 25% of them not previously characterized. Remarkably, ethyl isovalerate, isoamyl acetate, 3-methyl-1-butanol, benzyl alcohol, 2-phenylethyl alcohol and 3-(methylthio)-1-propanol, and some of their mixtures, displayed beneficial effects in A. thaliana and also improved growth and development of Agave tequilana and Agave salmiana in just 60 days. Volatiles produced by bacteria isolated from agaves and cacti are promising molecules for the sustainable production of crops in arid and semi-arid regions.},
}
@article {pmid30377993,
year = {2018},
author = {Cho, MS and Kim, SY and Suk, KT and Kim, BY},
title = {Modulation of gut microbiome in nonalcoholic fatty liver disease: pro-, pre-, syn-, and antibiotics.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12275-018-8346-2},
pmid = {30377993},
issn = {1976-3794},
abstract = {Nonalcoholic fatty liver disease (NAFLD) is one of the most common types of liver diseases worldwide and its incidence continues to increase. NAFLD occurs when the body can no longer effectively store excess energy in the adipose tissue. Despite the increasing prevalence of NAFLD, making lifestyle changes, including increased exercise, is often an elusive goal for patients with NAFLD. The liver directly connects to the gut-gastrointestinal milieu via the portal vein, which are all part of the gut-liver axis. Therefore, the gut-microbiome and microbial products have been actively studied as likely key factors in NAFLD pathophysiology. Hence, dysbiosis of the gut microbiome and therapeutic manipulation of the gut-liver axis are being investigated. Novel therapeutic approaches for modulating gut microbiota through the administration of probiotics, prebiotics, synbiotics, and antibiotics have been proposed with numerous promising initial reports on the effectiveness and clinical applications of these approaches. This review delves into the current evidence on novel therapies that modulate gut microbiota and discusses ongoing clinical trials targeting the gut-liver axis for the management and prevention of NAFLD.},
}
@article {pmid30377739,
year = {2018},
author = {Hansen, RL and Dueñas, ME and Looft, T and Lee, YJ},
title = {Nanoparticle microarray for high-throughput microbiome metabolomics using matrix-assisted laser desorption ionization mass spectrometry.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00216-018-1436-5},
pmid = {30377739},
issn = {1618-2650},
support = {2017-67007-25949//National Institute of Food and Agriculture/ ; },
abstract = {A high-throughput matrix-assisted laser desorption/ionization mass spectrometry (MALDI)-MS-based metabolomics platform was developed using a pre-fabricated microarray of nanoparticles and organic matrices. Selected organic matrices, inorganic nanoparticle (NP) suspensions, and sputter coated metal NPs, as well as various additives, were tested for metabolomics analysis of the turkey gut microbiome. Four NPs and one organic matrix were selected as the optimal matrix set: α-cyano-4-hydroycinnamic acid, Fe3O4 and Au NPs in positive ion mode with 10 mM sodium acetate, and Cu and Ag NPs in negative ion mode with no additive. Using this set of five matrices, over two thousand unique metabolite features were reproducibly detected across intestinal samples from turkeys fed a diet amended with therapeutic or sub-therapeutic antibiotics (200 g/ton or 50 g/ton bacitracin methylene disalicylate (BMD), respectively), or non-amended feed. Among the thousands of unique features, 56 of them were chemically identified using MALDI-MS/MS, with the help of in-parallel liquid chromatography (LC)-MS/MS analysis. Lastly, as a proof of concept application, this protocol was applied to 52 turkey cecal samples at three different time points from the antibiotic feed trial. Statistical analysis indicated variations in the metabolome of turkeys with different ages or treatments. Graphical abstract ᅟ.},
}
@article {pmid30377676,
year = {2018},
author = {Kuo, SM},
title = {Does Modification of the Large Intestinal Microbiome Contribute to the Anti-Inflammatory Activity of Fermentable Fiber?.},
journal = {Current developments in nutrition},
volume = {2},
number = {2},
pages = {nzx004},
doi = {10.3945/cdn.117.001180},
pmid = {30377676},
issn = {2475-2991},
abstract = {Fiber is an inadequately understood and insufficiently consumed nutrient. This review examines the possible causal relation between fiber-induced microbiome changes and the anti-inflammatory activity of fiber. To demonstrate the dominant role of fermentable plant fiber in shaping the intestinal microbiome, animal and human fiber-feeding studies are reviewed. Using culture-, PCR-, and sequencing-based microbial analyses, a higher prevalence of Bifidobacterium and Lactobacillus genera was observed from the feeding of different types of fermentable fiber. This finding was reported in studies performed on several host species including human. Health conditions and medications that are linked to intestinal microbial alterations likely also change the nutrient environment of the large intestine. The unique gene clusters of Bifidobacterium and Lactobacillus that enable the catabolism of plant glycans and the ability of Bifidobacterium and Lactobacillus to reduce the colonization of proteobacteria probably contribute to their prevalence in a fiber-rich intestinal environment. The fiber-induced microbiome changes could contribute to the anti-inflammatory activity of fiber. Although most studies did not measure fecal microbial density or total daily fecal microbial output (colon microbial load), limited evidence suggests that the increase in intestinal commensal microbial load plays an important role in the anti-inflammatory activity of fiber. Various probiotic supplements, including Bifidobacterium and Lactobacillus, showed anti-inflammatory activity only in the presence of fiber, which promoted microbial growth as indicated by increasing plasma short-chain fatty acids. Probiotics alone or pure fiber administered under sterile conditions showed no anti-inflammatory activity. The potential mechanisms that could mediate the anti-inflammatory effect of common microbial metabolites are reviewed, but more in vivo trials are needed. Future studies including simultaneous microbial composition and load measurements are also important.},
}
@article {pmid30377660,
year = {2018},
author = {Geldart, KG and Kommineni, S and Forbes, M and Hayward, M and Dunny, GM and Salzman, NH and Kaznessis, YN},
title = {Engineered E. coli Nissle 1917 for the reduction of vancomycin-resistant Enterococcus in the intestinal tract.},
journal = {Bioengineering &amp; translational medicine},
volume = {3},
number = {3},
pages = {197-208},
doi = {10.1002/btm2.10107},
pmid = {30377660},
issn = {2380-6761},
abstract = {Vancomycin-resistant Enterococcus (VRE) poses a serious threat in hospitals where they densely colonize the intestinal tracts of patients. In vulnerable hosts, these pathogens may translocate to the bloodstream and become lethal. The ability to selectively reduce VRE in the intestinal tracts of patients could potentially prevent many of these translocation events and reduce the spread of the pathogen. Herein, we have engineered Escherichia. coli Nissle 1917 to produce and secrete three antimicrobial peptides, Enterocin A, Enterocin B, and Hiracin JM79, to specifically target and kill Enterococcus. These peptides exhibited potent activity against both Enterococcus faecium and Enterococcus faecalis, the two most prominent species responsible for VRE infections. We first discuss the optimization of the system used to express and secrete the peptides. We then show that by simultaneously expressing these peptides, both E. faecium and E. faecalis were drastically inhibited. We then demonstrate a suppression of the development of resistance when supernatant from the E. coli producer strains was used to treat E. faecium. Finally, we tested the efficacy of the probiotic in a VRE colonization model in mice. These studies showed that administration of the engineered probiotic significantly reduced the levels of both E. faecium and E. faecalis in the feces of male Balb/cJ mice.},
}
@article {pmid30377376,
year = {2018},
author = {Franzosa, EA and McIver, LJ and Rahnavard, G and Thompson, LR and Schirmer, M and Weingart, G and Lipson, KS and Knight, R and Caporaso, JG and Segata, N and Huttenhower, C},
title = {Species-level functional profiling of metagenomes and metatranscriptomes.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41592-018-0176-y},
pmid = {30377376},
issn = {1548-7105},
abstract = {Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types.},
}
@article {pmid30377368,
year = {2018},
author = {McDonald, D and Vázquez-Baeza, Y and Koslicki, D and McClelland, J and Reeve, N and Xu, Z and Gonzalez, A and Knight, R},
title = {Striped UniFrac: enabling microbiome analysis at unprecedented scale.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41592-018-0187-8},
pmid = {30377368},
issn = {1548-7105},
}
@article {pmid30377191,
year = {2018},
author = {Wu, WK and Chen, CC and Liu, PY and Panyod, S and Liao, BY and Chen, PC and Kao, HL and Kuo, HC and Kuo, CH and Chiu, THT and Chen, RA and Chuang, HL and Huang, YT and Zou, HB and Hsu, CC and Chang, TY and Lin, CL and Ho, CT and Yu, HT and Sheen, LY and Wu, MS},
title = {Identification of TMAO-producer phenotype and host-diet-gut dysbiosis by carnitine challenge test in human and germ-free mice.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2018-317155},
pmid = {30377191},
issn = {1468-3288},
abstract = {OBJECTIVE: The gut microbiota-derived metabolite, trimethylamine N-oxide (TMAO) plays an important role in cardiovascular disease (CVD). The fasting plasma TMAO was shown as a prognostic indicator of CVD incident in patients and raised the interest of intervention targeting gut microbiota. Here we develop a clinically applicable method called oral carnitine challenge test (OCCT) for TMAO-related therapeutic drug efforts assessment and personalising dietary guidance.<br><br>DESIGN: A pharmacokinetic study was performed to verify the design of OCCT protocol. The OCCT was conducted in 23 vegetarians and 34 omnivores to validate gut microbiota TMAO production capacity. The OCCT survey was integrated with gut microbiome, host genotypes, dietary records and serum biochemistry. A humanised gnotobiotic mice study was performed for translational validation.<br><br>RESULTS: The OCCT showed better efficacy than fasting plasma TMAO to identify TMAO producer phenotype. The omnivores exhibited a 10-fold higher OR to be high TMAO producer than vegetarians. The TMAO-associated taxa found by OCCT in this study were consistent with previous animal studies. The TMAO producer phenotypes were also reproduced in humanised gnotobiotic mice model. Besides, we found the faecal CntA gene was not associated with TMAO production; therefore, other key relevant microbial genes might be involved. Finally, we demonstrated the urine TMAO exhibited a strong positive correlation with plasma TMAO (r=0.92, p<0.0001) and improved the feasibility of OCCT.<br><br>CONCLUSION: The OCCT can be used to identify TMAO-producer phenotype of gut microbiota and may serve as a personal guidance in CVD prevention and treatment.<br><br>TRIAL REGISTRATION NUMBER: NCT02838732; Results.},
}
@article {pmid30377189,
year = {2018},
author = {He, Z and Gharaibeh, RZ and Newsome, RC and Pope, JL and Dougherty, MW and Tomkovich, S and Pons, B and Mirey, G and Vignard, J and Hendrixson, DR and Jobin, C},
title = {Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2018-317200},
pmid = {30377189},
issn = {1468-3288},
abstract = {OBJECTIVE: Campylobacter jejuni produces a genotoxin, cytolethal distending toxin (CDT), which has DNAse activity and causes DNA double-strand breaks. Although C. jejuni infection has been shown to promote intestinal inflammation, the impact of this bacterium on carcinogenesis has never been examined.<br><br>DESIGN: Germ-free (GF) ApcMin/+ mice, fed with 1% dextran sulfate sodium, were used to test tumorigenesis potential of CDT-producing C. jejuni. Cells and enteroids were exposed to bacterial lysates to determine DNA damage capacity via γH2AX immunofluorescence, comet assay and cell cycle assay. To examine the interplay of CDT-producing C. jejuni, gut microbiome and host in tumorigenesis, colonic RNA-sequencing and faecal 16S rDNA sequencing were performed. Rapamycin was administrated to investigate the prevention of CDT-producing C. jejuni-induced tumorigenesis.<br><br>RESULTS: GF ApcMin/+ mice colonised with human clinical isolate C. jejuni81-176 developed significantly more and larger tumours when compared with uninfected mice. C. jejuni with a mutated cdtB subunit, mutcdtB, attenuated C. jejuni-induced tumorigenesis in vivo and decreased DNA damage response in cells and enteroids. C. jejuni infection induced expression of hundreds of colonic genes, with 22 genes dependent on the presence of cdtB. The C. jejuni-infected group had a significantly different microbial gene expression profile compared with the mutcdtB group as shown by metatranscriptomic data, and different microbial communities as measured by 16S rDNA sequencing. Finally, rapamycin could diminish the tumorigenic capability of C. jejuni.<br><br>CONCLUSION: Human clinical isolate C. jejuni 81-176 promotes colorectal cancer and induces changes in microbial composition and transcriptomic responses, a process dependent on CDT production.},
}
@article {pmid30377046,
year = {2018},
author = {Robertson, SJ and Goethel, A and Girardin, SE and Philpott, DJ},
title = {Innate Immune Influences on the Gut Microbiome: Lessons from Mouse Models.},
journal = {Trends in immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.it.2018.10.004},
pmid = {30377046},
issn = {1471-4981},
abstract = {The gut microbiota is important in health and disease. Whereas the intestinal immune system has evolved to protect the mucosal barrier against pathogens, there is much interest in understanding how it influences the composition and functions of resident microbial communities. Overall, host innate immunity exerts little influence on the microbiota at homeostasis, but increases upon immune activation and the onset of inflammation, as well as in the presence of certain members of the microbiota. However, many experiments have not adequately incorporated study design to detect such immune influences, including using proper control groups, precise sampling and timing, and measures beyond broad-scale descriptions of dysbiosis for microbial analysis. We discuss these and other challenges in the context of current understanding of chronic inflammatory disease.},
}
@article {pmid30376898,
year = {2018},
author = {Leiby, JS and McCormick, K and Sherrill-Mix, S and Clarke, EL and Kessler, LR and Taylor, LJ and Hofstaedter, CE and Roche, AM and Mattei, LM and Bittinger, K and Elovitz, MA and Leite, R and Parry, S and Bushman, FD},
title = {Lack of detection of a human placenta microbiome in samples from preterm and term deliveries.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {196},
doi = {10.1186/s40168-018-0575-4},
pmid = {30376898},
issn = {2049-2618},
support = {P30 AI045008//National Institute of Allergy and Infectious Diseases/ ; T32 AI007632//National Institute of Allergy and Infectious Diseases/ ; T32 AI007324//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND: Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is colonized with bacteria. For example, analysis of DNA from placenta samples yielded small proportions of microbial sequences which were proposed to represent normal bacterial colonization. However, an analysis by our group showed no distinction between background negative controls and placenta samples. Also supporting the idea that the womb is sterile is the observation that germ-free mammals can be generated by sterile delivery of neonates into a sterile isolator, after which neonates remain germ-free, which would seem to provide strong data in support of sterility of the womb.<br><br>RESULTS: To probe this further and to investigate possible placental colonization associated with spontaneous preterm birth, we carried out another study comparing microbiota in placenta samples from 20 term and 20 spontaneous preterm deliveries. Both 16S rRNA marker gene sequencing and shotgun metagenomic sequencing were used to characterize placenta and control samples. We first quantified absolute amounts of bacterial 16S rRNA gene sequences using 16S rRNA gene quantitative PCR (qPCR). As in our previous study, levels were found to be low in the placenta samples and indistinguishable from negative controls. Analysis by DNA sequencing did not yield a placenta microbiome distinct from negative controls, either using marker gene sequencing as in our previous work, or with shotgun metagenomic sequencing. Several types of artifacts, including erroneous read classifications and barcode misattribution, needed to be identified and removed from the data to clarify this point.<br><br>CONCLUSIONS: Our findings do not support the existence of a consistent placental microbiome, in either placenta from term deliveries or spontaneous preterm births.},
}
@article {pmid30376889,
year = {2018},
author = {Hale, VL and Jeraldo, P and Chen, J and Mundy, M and Yao, J and Priya, S and Keeney, G and Lyke, K and Ridlon, J and White, BA and French, AJ and Thibodeau, SN and Diener, C and Resendis-Antonio, O and Gransee, J and Dutta, T and Petterson, XM and Sung, J and Blekhman, R and Boardman, L and Larson, D and Nelson, H and Chia, N},
title = {Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers.},
journal = {Genome medicine},
volume = {10},
number = {1},
pages = {78},
doi = {10.1186/s13073-018-0586-6},
pmid = {30376889},
issn = {1756-994X},
support = {R01CA179243//National Institutes of Health/ ; R01CA170357//National Institutes of Health/ ; P30DK084567//National Institute of Diabetes and Digestive and Kidney Diseases/ ; U24DK100469//Mayo Clinic Metabolomics Resource Core/ ; },
abstract = {BACKGROUND: Links between colorectal cancer (CRC) and the gut microbiome have been established, but the specific microbial species and their role in carcinogenesis remain an active area of inquiry. Our understanding would be enhanced by better accounting for tumor subtype, microbial community interactions, metabolism, and ecology.<br><br>METHODS: We collected paired colon tumor and normal-adjacent tissue and mucosa samples from 83 individuals who underwent partial or total colectomies for CRC. Mismatch repair (MMR) status was determined in each tumor sample and classified as either deficient MMR (dMMR) or proficient MMR (pMMR) tumor subtypes. Samples underwent 16S rRNA gene sequencing and a subset of samples from 50 individuals were submitted for targeted metabolomic analysis to quantify amino acids and short-chain fatty acids. A PERMANOVA was used to identify the biological variables that explained variance within the microbial communities. dMMR and pMMR microbial communities were then analyzed separately using a generalized linear mixed effects model that accounted for MMR status, sample location, intra-subject variability, and read depth. Genome-scale metabolic models were then used to generate microbial interaction networks for dMMR and pMMR microbial communities. We assessed global network properties as well as the metabolic influence of each microbe within the dMMR and pMMR networks.<br><br>RESULTS: We demonstrate distinct roles for microbes in dMMR and pMMR CRC. Bacteroides fragilis and sulfidogenic Fusobacterium nucleatum were significantly enriched in dMMR CRC, but not pMMR CRC. These findings were further supported by metabolic modeling and metabolomics indicating suppression of B. fragilis in pMMR CRC and increased production of amino acid proxies for hydrogen sulfide in dMMR CRC.<br><br>CONCLUSIONS: Integrating tumor biology and microbial ecology highlighted distinct microbial, metabolic, and ecological properties unique to dMMR and pMMR CRC. This approach could critically improve our ability to define, predict, prevent, and treat colorectal cancers.},
}
@article {pmid30376869,
year = {2018},
author = {Khoruts, A},
title = {Targeting the microbiome: from probiotics to fecal microbiota transplantation.},
journal = {Genome medicine},
volume = {10},
number = {1},
pages = {80},
doi = {10.1186/s13073-018-0592-8},
pmid = {30376869},
issn = {1756-994X},
abstract = {The modern techniques of microbiome science can be applied to the development and evaluation of all microbiota-directed products, including probiotics and fecal microbiota transplantation.},
}
@article {pmid30376392,
year = {2018},
author = {Jackson, MI and Jewell, DE},
title = {Balance of saccharolysis and proteolysis underpins improvements in stool quality induced by adding a fiber bundle containing bound polyphenols to either hydrolyzed meat or grain-rich foods.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/19490976.2018.1526580},
pmid = {30376392},
issn = {1949-0984},
abstract = {Dietary fiber is a key component in gastrointestinal health maintenance partly due to its fermentation by the gut microbiome. The food-dependent effects of a novel fiber bundle added to hydrolyzed meat (HM) or grain-rich (GR) foods in healthy dogs (n = 16) or those with chronic enteritis/gastroenteritis (n = 16) were examined. Addition of fiber to either food improved stool quality in dogs regardless of health status; microbiome diversity of dogs with chronic enteritis/gastroenteritis became more similar to healthy dogs. The abundance of bacteria mediating beneficial saccharolytic processes (eg, Lachnospiraceae) significantly increased on addition of fiber to the GR food, while those mediating detrimental proteolytic catabolism (eg, Desulfovibrionaceae) significantly decreased. Fiber addition to the HM food led to significant changes in saccharolytic/proteolytic bacteria. Higher levels of free saccharides in feces upon fiber addition to either food indicated increased saccharolysis. Fiber addition to the GR food decreased levels of fecal free amino acids, indicating decreased proteolysis. Addition of fiber decreased fecal pH for both foods but likely by different mechanisms: addition of fiber to the HM food led to increased straight-chain short-chain fatty acids (SCFAs) and no significant change in proteolytic branched-chain SFCAs, while in the GR food, fiber mainly led to decreased proteolytic branched-chain SFCAs. Other postbiotics related to intestinal health were consistently altered when fiber was added to either food. Plant-derived bioactive molecules were enriched in feces from dogs fed either food with added fiber, which could account for the observed modulation of the canine gut microbiome and shifts in metabolic capacity.},
}
@article {pmid30376356,
year = {2018},
author = {Leitao Filho, FS and Alotaibi, NM and Ngan, D and Tam, S and Yang, J and Hollander, Z and Chen, V and FitzGerald, JM and Nislow, C and Leung, JM and Man, SFP and Sin, DD},
title = {Sputum Microbiome is Associated with 1-Year Mortality Following COPD Hospitalizations.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.201806-1135OC},
pmid = {30376356},
issn = {1535-4970},
abstract = {RATIONALE: Lung dysbiosis promotes airway inflammation and decreased local immunity, potentially playing a role in the pathogenesis of acute exacerbations of COPD (AECOPD). We determined the relationship between sputum microbiome at the time of AECOPD hospitalization and 1-year mortality in a COPD cohort.<br><br>METHODS: We used sputum samples from 102 patients hospitalized due to AECOPD. All subjects were followed for one year after discharge. The microbiome profile was assessed through sequencing of 16S rRNA gene. Microbiome analyses were performed according to 1-year mortality status. To investigate the effect of alpha diversity measures and taxa features on time to death, we applied Cox proportional-hazards regression models and obtained hazard ratios (HR) associated with these variables.<br><br>MEASUREMENTS AND MAIN RESULTS: We observed significantly lower values of alpha diversity (Richness, Shannon Index, Evenness, and Faith's Phylogenetic Diversity) among non-survivors (n=19, 18.6%) compared to survivors (n=83, 81.4%). Beta diversity analysis also demonstrated significant differences between both groups (adj. PERMANOVA, p=0.010). The survivors had a higher relative abundance of Veillonella; in contrast, non-survivors had a higher abundance of Staphylococcus. The adjusted HRs for 1-year mortality increased significantly with decreasing alpha diversity. We also observed lower survival among patients in whom sputum samples were negative for Veillonella (HR: 13.5, 95% CI: 4.2 - 43.9, p<0.001) or positive for Staphylococcus (HR: 7.3, 95% CI: 1.6 - 33.2, p=0.01).<br><br>CONCLUSION: The microbiome profile of sputum in AECOPD is associated with 1-year mortality and may be used to identify subjects with a poor prognosis at the time of hospitalization.},
}
@article {pmid30376063,
year = {2018},
author = {Alikina, OV and Glazunova, OA and Bykov, AA and Kiselev, SS and Tutukina, MN and Shavkunov, KS and Ozoline, ON},
title = {A cohabiting bacterium alters the spectrum of short RNAs secreted by Escherichia coli.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fny262},
pmid = {30376063},
issn = {1574-6968},
abstract = {Recently, it has been found that bacteria secrete short RNAs able to affect gene expression in eukaryotic cells, while certain mammalian microRNAs 'shape the gut microbiome' altering bacterial transcriptome. The involvement of bacterial RNAs in communication with other bacteria is also expected, but has not been documented yet. Here, we compared the fractions of extremely short (12-22 nucleotides) RNAs secreted by Escherichia coli grown in a pure culture and jointly with bacteria of the Paenibacillus genus. Besides fragments of rRNAs and tRNAs, abundant in all samples, secreted oligonucleotides (exoRNAs) predominantly contained GC-rich fragments of messenger and antisense RNAs processed from regions with stable secondary structures. They differed in composition from oligonucleotides of intracellular fraction, where fragments of small regulatory RNAs were prevalent. Both fractions contained RNAs capable to form complementary duplexes, while for exoRNA samples a higher percentage of 3'-end modified RNAs and different endonuclease cleavage were detected. The presence of a cohabiting bacterium altered the spectrum of E. coli exoRNAs indicating a population-dependent control over their composition. Possible mechanisms of this effect are discussed.},
}
@article {pmid30375992,
year = {2018},
author = {Dubey, AK and Uppadhyaya, N and Nilawe, P and Chauhan, N and Kumar, S and Gupta, UA and Bhaduri, A},
title = {LogMPIE, pan-India profiling of the human gut microbiome using 16S rRNA sequencing.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180232},
doi = {10.1038/sdata.2018.232},
pmid = {30375992},
issn = {2052-4463},
abstract = {The &quot;Landscape Of Gut Microbiome - Pan-India Exploration&quot;, or LogMPIE study, is the first large-scale, nationwide record of the Indian gut microbiome. The primary objective of the study was to identify and map the Indian gut microbiome baseline. This observational study was conducted across 14 geographical locations in India. Enrolled subjects were uniformly distributed across geographies (north, east, west and south) and body mass index (obese and non-obese). Furthermore, factors influencing the microbiome, such as age and physical activity, were also considered in the study design. The LogMPIE study recorded data from 1004 eligible subjects and reported 993 unique microorganisms across the Indian microbiome diaspora. The data not only map the Indian gut microbiome baseline but also function as a useful resource to study, analyse and identify signatures characterizing the physiological dispositions of the subjects. Furthermore, they provide insight into the unique features describing the Indian microbiome. The data are open and may be accessed from the European Nucleotide Archive (ENA) portal of the European Bioinformatics Institute (https://www.ebi.ac.uk/ena/data/view/PRJEB25642).},
}
@article {pmid30375712,
year = {2018},
author = {D'Ippolito, S and Di Nicuolo, F and Pontecorvi, A and Gratta, M and Scambia, G and Di Simone, N},
title = {Endometrial microbes and microbiome: Recent insights on the inflammatory and immune &quot;players&quot; of the human endometrium.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {},
number = {},
pages = {e13065},
doi = {10.1111/aji.13065},
pmid = {30375712},
issn = {1600-0897},
abstract = {In recent years, extended scientific works shed light on the important role played by the endometrium in early pregnancy. This review examines our current knowledge about the delicate balance between microbial and cellular immune agents at endometrial level: All of them might affect endometrial receptivity. In contrast to the classical thinking of human endometrium as a sterile tissue, several recent studies have drawn attention to a resident population of microorganisms, which reaches only a 30% of concordance with those of the cervical-vaginal flora. At present, the understanding of the microbiome in relation to human reproduction is in its infancy and further studies are needed to clarify the activity of endometrial microbiome and the possible effects of a &quot;reproductive tract dysbiosis&quot; on fertility. Moreover, in the human endometrium, there is a complex system works preventing the risk of infection as well as enabling, when pregnancy occurs, the acceptance of the blastocyst. In this way, the endometrium plays a central role in the uterine immune surveillance. A better understanding of the different agents that may affect endometrial receptivity would improve the diagnosis and treatment of obstetric complications related to defective implantation and placentation.},
}
@article {pmid30375646,
year = {2018},
author = {Philip, N and Walsh, L},
title = {The potential ecological effects of Casein Phosphopeptide-Amorphous Calcium Phosphate in dental caries prevention.},
journal = {Australian dental journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/adj.12661},
pmid = {30375646},
issn = {1834-7819},
abstract = {Contemporary caries prevention protocols recommend not only effective remineralizing agents but also ecological measures to reverse the dental plaque dysbiosis responsible for the disease pathogenesis. There is a high-level of evidence supporting the remineralizing efficacy of Casein Phosphopeptide-Amorphous Calcium Phosphate (CPP-ACP) from studies around the world. There is now emerging evidence that CPP-ACP may also have a beneficial influence on the dental plaque microbial ecology and homeostasis. The ecological cariostatic effects of CPP-ACP are believed to be mediated predominantly through its anti-adhesion, buffering, and biofilm disrupting actions. This review principally discusses the ecological mechanisms of CPP-ACP and presents the current evidence for its effects on the oral microbiome ecology. This article is protected by copyright. All rights reserved.},
}
@article {pmid30375452,
year = {2018},
author = {Yoon, HY and Kim, HN and Lee, SH and Kim, SJ and Chang, Y and Ryu, S and Shin, H and Kim, HL and Lee, JH},
title = {Association between Neutrophil-to-Lymphocyte Ratio and Gut Microbiota in a Large Population: a Retrospective Cross-Sectional Study.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16031},
doi = {10.1038/s41598-018-34398-4},
pmid = {30375452},
issn = {2045-2322},
support = {2010-0027945//Korea Health Industry Development Institute (KHIDI)/ ; 2010-0027945//Korea Health Industry Development Institute (KHIDI)/ ; NRF-2016R1A6A3A11932719//National Research Foundation of Korea (NRF)/ ; NRF-2016R1A6A3A11932719//National Research Foundation of Korea (NRF)/ ; NRF-2018R1D1A1B07050067//National Research Foundation of Korea (NRF)/ ; },
abstract = {Gut microbiota and blood neutrophil-to-lymphocyte ratio (NLR) are associated with systemic inflammation; however, data on the association between gut microbiota and NLR are lacking. We investigated the association between gut microbiota and NLR. A total of 1,309 subjects who had available data on NLR and 16 S rRNA sequencing of gut microbiota were included in this study. They were grouped according to NLR quartile (Q) as follows: lower Q (n = 328, <25% of NLR range), middle 2Q (n = 653, ≥25% to <75%) and upper Q (n = 328, ≥75%). The diversity and composition of the human gut microbiota in the groups were calculated. The phylogenetic diversity of gut microbiota in the lower group was significantly higher than in the middle 2Q group (P = 0.040). The beta-diversity was significantly different among the three groups (P = 0.043), between the lower and middle 2Q groups (P = 0.029), and between the lower and upper groups (P = 0.026). Bacteroides eggerthii showed a positive correlation with NLR (q = 0.015). The diversity and composition of the gut microbiome were different between the NLR groups. Particularly, patients with a lower NLR had a greater diversity of gut microbiota.},
}
@article {pmid30375445,
year = {2018},
author = {Shang, L and Deng, D and Buskermolen, JK and Janus, MM and Krom, BP and Roffel, S and Waaijman, T and van Loveren, C and Crielaard, W and Gibbs, S},
title = {Multi-species oral biofilm promotes reconstructed human gingiva epithelial barrier function.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16061},
doi = {10.1038/s41598-018-34390-y},
pmid = {30375445},
issn = {2045-2322},
abstract = {Since the oral mucosa is continuously exposed to abundant microbes, one of its most important defense features is a highly proliferative, thick, stratified epithelium. The cellular mechanisms responsible for this are still unknown. The aim of this study was to determine whether multi-species oral biofilm contribute to the extensive stratification and primed antimicrobial defense in epithelium. Two in vitro models were used: 3D reconstructed human gingiva (RHG) and oral bacteria representative of multi-species commensal biofilm. The organotypic RHG consists of a reconstructed stratified gingiva epithelium on a gingiva fibroblast populated hydrogel (lamina propria). Biofilm was cultured from healthy human saliva, and consists of typical commensal genera Granulicatella and major oral microbiota genera Veillonella and Streptococcus. Biofilm was applied topically to RHG and host-microbiome interactions were studied over 7 days. Compared to unexposed RHG, biofilm exposed RHG showed increased epithelial thickness, more organized stratification and increased keratinocyte proliferation. Furthermore biofilm exposure increased production of RHG anti-microbial proteins Elafin, HBD2 and HBD3 but not HBD1, adrenomedullin or cathelicidin LL-37. Inflammatory and antimicrobial cytokine secretion (IL-6, CXCL8, CXCL1, CCL20) showed an immediate and sustained increase. In conclusion, exposure of RHG to commensal oral biofilm actively contributes to RHG epithelial barrier function.},
}
@article {pmid30374951,
year = {2018},
author = {Vinberg, M and Ottesen, NM and Meluken, I and Sørensen, N and Pedersen, O and Kessing, LV and Miskowiak, KW},
title = {Remitted affective disorders and high familial risk of affective disorders associate with aberrant intestinal microbiota.},
journal = {Acta psychiatrica Scandinavica},
volume = {},
number = {},
pages = {},
doi = {10.1111/acps.12976},
pmid = {30374951},
issn = {1600-0447},
support = {//Hørslev Foundation/ ; //The Research fund of the Capital Region of Denmark/ ; //Axel Thomsens Foundation/ ; //Novo Nordisk Foundation/ ; R108-A10015//Lundbeck Foundation/ ; //(Laegevidenskabens fremme) Foundation/ ; //Augustinus Foundation/ ; },
abstract = {OBJECTIVE: Affective disorders seem associated with aberrant intestinal microbiota but whether this pattern also occurs in individuals at increased heritable risk is unknown. We investigated associations between gut microbiota profiles and affective disorders by comparing monozygotic (MZ) twins concordant (affected twins with unipolar or bipolar disorder in remission) and discordant to affective disorders (high-risk) with MZ twins without affective disorders (low-risk).<br><br>METHODS: Stool samples were collected from 128 MZ twins and the microbiome was profiled using 16S rDNA sequencing of the V3-V4 region.<br><br>RESULTS: Affected twins had a lower diversity and an absence of a specific operational taxonomical unit (OTU) in comparison with low-risk twins. The high-risk twins exhibited the same pattern although the lower diversity was only at a trend level. The OTU belonged to the family Christensenellaceae. The findings were not explained by lifestyle factors (smoking, alcohol consumption, body mass index, or psychotropic medication).<br><br>CONCLUSION: Affected twins in remission and high-risk twins presented aberrant gut microbiota with depletion of a specific OTU. If replicated, this reduced relative sequence absence may together with the globally altered microbiota composition act as a vulnerability marker by accentuating the effect of gene-environment interactions in individuals genetically disposed for an affective disorder.},
}
@article {pmid30374830,
year = {2018},
author = {Pretzl, B and Sälzer, S and Ehmke, B and Schlagenhauf, U and Dannewitz, B and Dommisch, H and Eickholz, P and Jockel-Schneider, Y},
title = {Administration of systemic antibiotics during non-surgical periodontal therapy-a consensus report.},
journal = {Clinical oral investigations},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00784-018-2727-0},
pmid = {30374830},
issn = {1436-3771},
support = {2.2-220.522-97/15_1//Commission for Young Scientists and Gender Equality, University of Wuerzburg/ ; 2.2-220.522-97/2015_1//IZKF/ ; },
abstract = {AIM: The aim of this meta-review was to evaluate whether there is a meaningful clinical benefit regarding the use of systemic adjunctive antibiotics in the treatment of patients with periodontitis. Additionally, a consensus regarding possible recommendations for future administration of antibiotics should be reached.<br><br>METHODS: A structured literature search was performed by two independent investigators focusing on systematic reviews (SR) covering adjunctive systemic antibiosis during non-surgical periodontal therapy. Additionally, recent randomized clinical trials (RCT, July 2015 to July 2017) were searched systematically to update the latest SR. Results were summarized and discussed in a plenary to reach a consensus.<br><br>RESULTS: Mostly, systematic reviews and RCTs showed a significant positive effect of adjunctive systematic antibiosis compared to controls. These positive effects gain clinical relevance in patients with severe periodontal disease aged 55 years and younger.<br><br>CONCLUSION: Systemic antibiotics as an adjunct to non-surgical periodontal therapy should be sensibly administered and restrictively used. Only certain groups of periodontitis patients show a significant and clinically relevant benefit after intake of systemic antibiosis during periodontal therapy.<br><br>CLINICAL RELEVANCE: Avoiding antibiotic resistance and possible side effects on the human microbiome should be a focus of dentists and physicians. Thus, a sensible administration of antibiotics is mandatory. This manuscript suggests guidelines for a reasonable use.},
}
@article {pmid30374457,
year = {2018},
author = {England, WE and Kim, T and Whitaker, RJ},
title = {Metapopulation Structure of CRISPR-Cas Immunity in Pseudomonas aeruginosa and Its Viruses.},
journal = {mSystems},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSystems.00075-18},
pmid = {30374457},
issn = {2379-5077},
abstract = {Viruses that infect the widespread opportunistic pathogen Pseudomonas aeruginosa have been shown to influence physiology and critical clinical outcomes in cystic fibrosis (CF) patients. To understand how CRISPR-Cas immune interactions may contribute to the distribution and coevolution of P. aeruginosa and its viruses, we reconstructed CRISPR arrays from a highly sampled longitudinal data set from CF patients attending the Copenhagen Cystic Fibrosis Clinic in Copenhagen, Denmark (R. L. Marvig, L. M. Sommer, S. Molin, and H. K. Johansen, Nat Genet 47:57-64, 2015, https://doi.org/10.1038/ng.3148). We show that new spacers are not added to or deleted from CRISPR arrays over time within a single patient but do vary among patients in this data set. We compared assembled CRISPR arrays from this data set to CRISPR arrays extracted from 726 additional publicly available P. aeruginosa sequences to show that local diversity in this population encompasses global diversity and that there is no evidence for population structure associated with location or environment sampled. We compare over 3,000 spacers from our global data set to 98 lytic and temperate viruses and proviruses and find a subset of related temperate virus clusters frequently targeted by CRISPR spacers. Highly targeted viruses are matched by different spacers in different arrays, resulting in a pattern of distributed immunity within the global population. Understanding the multiple immune contexts that P. aeruginosa viruses face can be applied to study of P. aeruginosa gene transfer, the spread of epidemic strains in cystic fibrosis patients, and viral control of P. aeruginosa infection. IMPORTANCE Pseudomonas aeruginosa is a widespread opportunistic pathogen and a major cause of morbidity and mortality in cystic fibrosis patients. Microbe-virus interactions play a critical role in shaping microbial populations, as viral infections can kill microbial populations or contribute to gene flow among microbes. Investigating how P. aeruginosa uses its CRISPR immune system to evade viral infection aids our understanding of how this organism spreads and evolves alongside its viruses in humans and the environment. Here, we identify patterns of CRISPR targeting and immunity that indicate P. aeruginosa and its viruses evolve in both a broad global population and in isolated human &quot;islands.&quot; These data set the stage for exploring metapopulation dynamics occurring within and between isolated &quot;island&quot; populations associated with CF patients, an essential step to inform future work predicting the specificity and efficacy of virus therapy and the spread of invasive viral elements and pathogenic epidemic bacterial strains.},
}
@article {pmid30374420,
year = {2018},
author = {Zhou, Z and Chen, J and Yao, H and Hu, H},
title = {Fusobacterium and Colorectal Cancer.},
journal = {Frontiers in oncology},
volume = {8},
number = {},
pages = {371},
doi = {10.3389/fonc.2018.00371},
pmid = {30374420},
issn = {2234-943X},
abstract = {Colorectal cancer (CRC) is the third most common cancer worldwide and its pathogenesis has been extensively explored over the past decades. Recently, microorganisms in the gastrointestinal tract have emerged as potential etiological agents. In particular, a direct proportional association between Fusobacterium and CRC has been described. Since then, the functional impact of Fusobacterium in CRC development has been studied using various mouse models. Although some epidemiologic studies did not establish an obvious relationship between Fusobacterium and CRC, numerous pathogenic mechanisms leading to the disease have been described. For instance, Fusobacterium can activate the E-cadherin/β-catenin signaling pathway and is associated with particular epigenetic phenotype, such as microsatellite instability (MSI) and hypermethylation, via its strong adhesive and invasive abilities resulting in malignant transformation of epithelial cells. Also, Fusobacterium could alter the tumor microenvironment (TME) significantly by myeloid-derived suppressor cells (MDSCs), tumor associated macrophages (TAMs), and tumor associated neutrophils (TANs) recruitment and local immune suppression. Herein, we provide an in-depth review of the relationship between Fusobacterium and colorectal cancer. In light of the emergence of microbiome-based therapeutics, potential therapies and preventive strategies for colorectal cancer related to Fusobacterium are also discussed.},
}
@article {pmid30374341,
year = {2018},
author = {Ijaz, UZ and Sivaloganathan, L and McKenna, A and Richmond, A and Kelly, C and Linton, M and Stratakos, AC and Lavery, U and Elmi, A and Wren, BW and Dorrell, N and Corcionivoschi, N and Gundogdu, O},
title = {Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2452},
doi = {10.3389/fmicb.2018.02452},
pmid = {30374341},
issn = {1664-302X},
abstract = {Chickens are a key food source for humans yet their microbiome contains bacteria that can be pathogenic to humans, and indeed potentially to chickens themselves. Campylobacter is present within the chicken gut and is the leading cause of bacterial foodborne gastroenteritis within humans worldwide. Infection can lead to secondary sequelae such as Guillain-Barré syndrome and stunted growth in children from low-resource areas. Despite the global health impact and economic burden of Campylobacter, how and when Campylobacter appears within chickens remains unclear. The lack of day to day microbiome data with replicates, relevant metadata, and a lack of natural infection studies have delayed our understanding of the chicken gut microbiome and Campylobacter. Here, we performed a comprehensive day to day microbiome analysis of the chicken cecum from day 3 to 35 (12 replicates each day; final n = 379). We combined metadata such as chicken weight and feed conversion rates to investigate what the driving forces are for the microbial changes within the chicken gut over time, and how this relates to Campylobacter appearance within a natural habitat setting. We found a rapidly increasing microbial diversity up to day 12 with variation observed both in terms of genera and abundance, before a stabilization of the microbial diversity after day 20. In particular, we identified a shift from competitive to environmental drivers of microbial community from days 12 to 20 creating a window of opportunity whereby Campylobacter can appear. Campylobacter was identified at day 16 which was 1 day after the most substantial changes in metabolic profiles observed. In addition, microbial variation over time is most likely influenced by the diet of the chickens whereby significant shifts in OTU abundances and beta dispersion of samples often corresponded with changes in feed. This study is unique in comparison to the most recent studies as neither sampling was sporadic nor Campylobacter was artificially introduced, thus the experiments were performed in a natural setting. We believe that our findings can be useful for future intervention strategies and help reduce the burden of Campylobacter within the food chain.},
}
@article {pmid30374329,
year = {2018},
author = {Takahashi, H and Kotani, K and Tanaka, K and Egucih, Y and Anzai, K},
title = {Therapeutic Approaches to Nonalcoholic Fatty Liver Disease: Exercise Intervention and Related Mechanisms.},
journal = {Frontiers in endocrinology},
volume = {9},
number = {},
pages = {588},
doi = {10.3389/fendo.2018.00588},
pmid = {30374329},
issn = {1664-2392},
abstract = {Exercise training ameliorates nonalcoholic fatty liver disease (NAFLD) as well as obesity and metabolic syndrome. Although it is difficult to eliminate the effects of body weight reduction and increased energy expenditure-some pleiotropic effects of exercise training-a number of studies involving either aerobic exercise training or resistance training programs showed ameliorations in NAFLD that are independent of the improvements in obesity and insulin resistance. In vivo studies have identified effects of exercise training on the liver, which may help to explain the &quot;direct&quot; or &quot;independent&quot; effect of exercise training on NAFLD. Exercise training increases peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α) expression, improves mitochondrial function and leads to reduced hepatic steatosis, inflammation, fibrosis, and tumor genesis. Crosstalk between the liver and adipose tissue, skeletal muscle and the microbiome is also a possible mechanism for the effect of exercise training on NAFLD. Although numerous studies have reported benefits of exercise training on NAFLD, the optimal duration and intensity of exercise for the prevention or treatment of NAFLD have not been established. Maintaining adherence of patients with NAFLD to exercise training regimes is another issue to be resolved. The use of comprehensive analytical approaches to identify biomarkers such as hepatokines that specifically reflect the effect of exercise training on liver functions might help to monitor the effect of exercise on NAFLD, and thereby improve adherence of these patients to exercise training. Exercise training is a robust approach for alleviating the pathogenesis of NAFLD, although further clinical and experimental studies are required.},
}
@article {pmid30374300,
year = {2018},
author = {Cuomo, A and Maina, G and Rosso, G and Beccarini Crescenzi, B and Bolognesi, S and Di Muro, A and Giordano, N and Goracci, A and Neal, SM and Nitti, M and Pieraccini, F and Fagiolini, A},
title = {The Microbiome: A New Target for Research and Treatment of Schizophrenia and its Resistant Presentations? A Systematic Literature Search and Review.},
journal = {Frontiers in pharmacology},
volume = {9},
number = {},
pages = {1040},
doi = {10.3389/fphar.2018.01040},
pmid = {30374300},
issn = {1663-9812},
abstract = {Background: The gastrointestinal system hosts roughly 1,800 distinct phyla and about 40,000 bacterial classes, which are known as microbiota, and which are able to influence the brain. For instance, microbiota can also influence the immune response through the activation of the immune system or through the release of mediators that are able to cross the brain blood barrier or that can interact with other substances that have free access to the brain, such as tryptophan and kynurenic acid, which is a metabolite of tryptophan and which has been involved in the pathogenesis of schizophrenia. Objectives: This paper reviews the possible relationships between microbiome, schizophrenia and treatment resistance. Given the possibility of a role of immune activation and alterations, we also describe the relationship between schizophrenia and immune inflammatory response. Finally, we report on the studies about the use of probiotic and prebiotics in schizophrenia. Methods: Cochrane library and PubMed were searched from the year 2000 to 2018 for publications about microbiome, immune-mediated pathology, schizophrenia and neurodevelopmental disorders. The following search string was used: (microbiome or immune mediated) AND (schizophrenia OR neurodevelopmental disorder). Associated publications were hand-searched from the list of references of the identified papers. A narrative review was also conducted about the use of probiotics and prebiotics in schizophrenia. Results: There exists a close relationship between the central nervous system and the gastrointestinal tract, which makes it likely that there is a relationship between schizophrenia, including its resistant forms, and microbiota. This paper provides a summary of the most important studies that we identified on the topic. Conclusions: Schizophrenia in particular, remain a challenge for researchers and practitioners and the possibility of a role of the microbiome and of immune-mediated pathology should be better explored, not only in animal models but also in clinical trials of agents that are able to alter gut microbiota and possibly influence the mechanisms of gastrointestinal inflammation. Microbiome targeted treatments have not been well-studied yet in patients with mental illness in general, and with schizophrenia in particular. Nonetheless, the field is well worth of being appropriately investigated.},
}
@article {pmid30374198,
year = {2018},
author = {Baumann-Dudenhoeffer, AM and D'Souza, AW and Tarr, PI and Warner, BB and Dantas, G},
title = {Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-018-0216-2},
pmid = {30374198},
issn = {1546-170X},
abstract = {Commensal gut bacterial communities (microbiomes) are predicted to influence human health and disease1,2. Neonatal gut microbiomes are colonized with maternal and environmental flora and mature toward a stable composition over 2-3 years3,4. To study pre- and postnatal determinants of infant microbiome development, we analyzed 402 fecal metagenomes from 60 infants aged 0-8 months, using longitudinal generalized linear mixed models (GLMMs). Distinct microbiome signatures correlated with breastfeeding, formula ingredients, and maternal gestational weight gain (GWG). Amino acid synthesis pathway accretion in breastfed microbiomes complemented normative breastmilk composition. Prebiotic oligosaccharides, designed to promote breastfed-like microflora5, predicted functional pathways distinct from breastfed infant microbiomes. Soy formula in six infants was positively associated with Lachnospiraceae and pathways suggesting a short-chain fatty acid (SCFA)-rich environment, including glycerol to 1-butanol fermentation, which is potentially dysbiotic. GWG correlated with altered carbohydrate degradation and enriched vitamin synthesis pathways. Maternal and postnatal antibiotics predicted microbiome alterations, while delivery route had no persistent effects. Domestic water source correlates suggest water may be an underappreciated determinant of microbiome acquisition. Clinically important microbial pathways with statistically significant dietary correlates included dysbiotic markers6,7, core enterotype features8, and synthesis pathways for enteroprotective9 and immunomodulatory10,11 metabolites, epigenetic mediators1, and developmentally critical vitamins12, warranting further investigation.},
}
@article {pmid30374168,
year = {2018},
author = {Reese, AT and Pereira, FC and Schintlmeister, A and Berry, D and Wagner, M and Hale, LP and Wu, A and Jiang, S and Durand, HK and Zhou, X and Premont, RT and Diehl, AM and O'Connell, TM and Alberts, SC and Kartzinel, TR and Pringle, RM and Dunn, RR and Wright, JP and David, LA},
title = {Microbial nitrogen limitation in the mammalian large intestine.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-018-0267-7},
pmid = {30374168},
issn = {2058-5276},
abstract = {Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.},
}
@article {pmid30373673,
year = {2018},
author = {Cannon, MV and Bogale, H and Rutt, L and Humphrys, M and Korpe, P and Duggal, P and Ravel, J and Serre, D},
title = {A high-throughput sequencing assay to comprehensively detect and characterize unicellular eukaryotes and helminths from biological and environmental samples.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {195},
doi = {10.1186/s40168-018-0581-6},
pmid = {30373673},
issn = {2049-2618},
abstract = {BACKGROUND: Several of the most devastating human diseases are caused by eukaryotic parasites transmitted by arthropod vectors or through food and water contamination. These pathogens only represent a fraction of all unicellular eukaryotes and helminths that are present in the environment and many uncharacterized organisms might have subtle but pervasive effects on health, including by modifying the microbiome where they reside. Unfortunately, while we have modern molecular tools to characterize bacterial and, to a lesser extent, fungal communities, we lack suitable methods to comprehensively investigate and characterize most unicellular eukaryotes and helminths: the detection of these organisms often relies on microscopy that cannot differentiate related organisms, while molecular assays can only detect the pathogens specifically tested.<br><br>RESULTS: Here, we describe a novel sequencing-based assay, akin to bacterial 16S rRNA sequencing, that enables high-throughput detection and characterization of a wide range of unicellular eukaryotes and helminths, including those from taxonomical groups containing all common human parasites. We designed and evaluated taxon-specific PCR primer pairs that selectively amplify all species from eight taxonomical groups (Apicomplexa, Amoeba, Diplomonadida, Kinetoplastida, Parabasalia, Nematoda, Platyhelminthes, and Microsporidia). We then used these primers to screen DNA extracted from clinical, biological, and environmental samples, and after next-generation sequencing, identified both known and previously undescribed organisms from most taxa targeted.<br><br>CONCLUSIONS: This novel high-throughput assay enables comprehensive detection and identification of eukaryotic parasites and related organisms, from a wide range of complex biological and environmental samples. This approach can be easily deployed to many settings and will efficiently complement existing methods and provide a holistic perspective on the microbiome.},
}
@article {pmid30373669,
year = {2018},
author = {Nasko, DJ and Koren, S and Phillippy, AM and Treangen, TJ},
title = {RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification.},
journal = {Genome biology},
volume = {19},
number = {1},
pages = {165},
doi = {10.1186/s13059-018-1554-6},
pmid = {30373669},
issn = {1474-760X},
support = {W911NF-17-2-0089//Army Research Office/ ; },
abstract = {In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes. These results suggest a need for new classification approaches specially adapted for large databases.},
}
@article {pmid30373468,
year = {2018},
author = {Sinha, T and Vich Vila, A and Garmaeva, S and Jankipersadsing, SA and Imhann, F and Collij, V and Bonder, MJ and Jiang, X and Gurry, T and Alm, EJ and D'Amato, M and Weersma, RK and Scherjon, S and Wijmenga, C and Fu, J and Kurilshikov, A and Zhernakova, A},
title = {Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/19490976.2018.1528822},
pmid = {30373468},
issn = {1949-0984},
abstract = {Several gastrointestinal diseases show a sex imbalance, although the underlying (patho)physiological mechanisms behind this are not well understood. The gut microbiome may be involved in this process, forming a complex interaction with host immune system, sex hormones, medication and other environmental factors. Here we performed sex-specific analyses of fecal microbiota composition in 1135 individuals from a population-based cohort. The overall gut microbiome composition of females and males was significantly different (p = 0.001), with females showing a greater microbial diversity (p = 0.009). After correcting for the effects of intrinsic factors, smoking, diet and medications, female hormonal factors such as the use of oral contraceptives and undergoing an ovariectomy were associated with microbial species and pathways. Females had a higher richness of antibiotic-resistance genes, with the most notable being resistance to the lincosamide nucleotidyltransferase (LNU) gene family. The higher abundance of resistance genes is consistent with the greater prescription of the Macrolide-Lincosamide-Streptogramin classes of antibiotics to females. Furthermore, we observed an increased resistance to aminoglycosides in females with self-reported irritable bowel syndrome. These results throw light upon the effects of common medications that are differentially prescribed between sexes and highlight the importance of sex-specific analysis when studying the gut microbiome and resistome.},
}
@article {pmid30372560,
year = {2018},
author = {Wu, JF and Muthusamy, A and Al-Ghalith, GA and Knights, D and Guo, B and Wu, B and Remmel, RP and Schladt, DP and Alegre, ML and Oetting, WS and Jacobson, PA and Israni, AK},
title = {Urinary Microbiome Associated with Chronic Allograft Dysfunction in Kidney Transplant Recipients.},
journal = {Clinical transplantation},
volume = {},
number = {},
pages = {e13436},
doi = {10.1111/ctr.13436},
pmid = {30372560},
issn = {1399-0012},
abstract = {BACKGROUND: We performed a study to identify differences in the urinary microbiome associated with chronic allograft dysfunction (CAD) and compared the urinary microbiome of male and female transplant recipients with CAD.<br><br>METHODS: This case-control study enrolled 67 patients within the Deterioration of Kidney Allograft Function (DeKAF) Genomics cohort at two transplant centers. CAD was defined as a greater than 25% rise in serum creatinine relative to a 3 month post-transplant baseline. Urine samples from patients with and without CAD were analyzed using 16S V4 bacterial ribosomal DNA sequences.<br><br>RESULTS: Corynebacterium was more prevalent in female and male patients with CAD compared to non-CAD female patients (p=0.0005). A total 21 distinct Operational Taxonomic Unit (OTUs) were identified as significantly different when comparing CAD and non-CAD patients using (Kruskal-Wallis, p<0.01). A subset analysis of female patients with CAD compared to non-CAD females identified similar differentially abundant OTUs, including the genera Corynebacterium and Staphylococcus (Kruskal-Wallis; p =0.01; p=0.004 respectively). Male CAD vs. female CAD analysis showed greater abundance of phylum Proteobacteria in males.<br><br>CONCLUSION: There were differences in the urinary microbiome when comparing female and male CAD patients with their female non-CAD counterparts and these differences persisted in the subset analysis limited to female patients only. This article is protected by copyright. All rights reserved.},
}
@article {pmid30372516,
year = {2018},
author = {Zare, A and Johansson, AM and Karlsson, E and Delhomme, N and Stenberg, P},
title = {The gut microbiome participates in transgenerational inheritance of low temperature responses in Drosophila melanogaster.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.13278},
pmid = {30372516},
issn = {1873-3468},
abstract = {Environmental perturbations induce transcriptional changes, some of which may be inherited even in the absence of the initial stimulus. Previous studies have focused on transfers through the germ-line although microbiota is also passed on to the offspring. Thus, we inspected the involvement of the gut microbiome in transgenerational inheritance of environmental exposures in Drosophila melanogaster. We grew flies in the cold versus control temperatures and compared their transcriptional patterns in both conditions as well as in their offspring. F2 flies grew in control temperature while we controlled their microbiota acquisition from either F1 sets. Transcriptional status of some genes was conserved transgenerationally, and a subset of these genes, mainly expressed in the gut, was transcriptionally dependent on the acquired microbiome. This article is protected by copyright. All rights reserved.},
}
@article {pmid30371894,
year = {2018},
author = {Noronha, A and Modamio, J and Jarosz, Y and Guerard, E and Sompairac, N and Preciat, G and Daníelsdóttir, AD and Krecke, M and Merten, D and Haraldsdóttir, HS and Heinken, A and Heirendt, L and Magnúsdóttir, S and Ravcheev, DA and Sahoo, S and Gawron, P and Friscioni, L and Garcia, B and Prendergast, M and Puente, A and Rodrigues, M and Roy, A and Rouquaya, M and Wiltgen, L and Žagare, A and John, E and Krueger, M and Kuperstein, I and Zinovyev, A and Schneider, R and Fleming, RMT and Thiele, I},
title = {The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gky992},
pmid = {30371894},
issn = {1362-4962},
abstract = {A multitude of factors contribute to complex diseases and can be measured with 'omics' methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the Virtual Metabolic Human (VMH, www.vmh.life) database encapsulating current knowledge of human metabolism within five interlinked resources 'Human metabolism', 'Gut microbiome', 'Disease', 'Nutrition', and 'ReconMaps'. The VMH captures 5180 unique metabolites, 17 730 unique reactions, 3695 human genes, 255 Mendelian diseases, 818 microbes, 632 685 microbial genes and 8790 food items. The VMH's unique features are (i) the hosting of the metabolic reconstructions of human and gut microbes amenable for metabolic modeling; (ii) seven human metabolic maps for data visualization; (iii) a nutrition designer; (iv) a user-friendly webpage and application-programming interface to access its content; (v) user feedback option for community engagement and (vi) the connection of its entities to 57 other web resources. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community.},
}
@article {pmid30370976,
year = {2018},
author = {Suzuki, T and Yazaki, Y and Voors, AA and Jones, DJL and Chan, DCS and Anker, SD and Cleland, JG and Dickstein, K and Filippatos, G and Hillege, HL and Lang, CC and Ponikowski, P and Samani, NJ and van Veldhuisen, DJ and Zannad, F and Zwinderman, AH and Metra, M and Ng, LL},
title = {Association with outcomes and response to treatment of trimethylamine N-oxide in heart failure (from BIOSTAT-CHF).},
journal = {European journal of heart failure},
volume = {},
number = {},
pages = {},
doi = {10.1002/ejhf.1338},
pmid = {30370976},
issn = {1879-0844},
support = {FP7-242209-BIOSTAT-CHF//European Commission/ ; EudraCT 2010- 020808-29//European Commission/ ; 17ek0210011h0005//Practical Research Project for Life-Style related Diseases including Cardiovascular Diseases and Diabetes Mellitus from Japan Agency for Medical Research and Development (AMED)/ ; //Japan Heart Foundation/ ; //University of Tokyo/ ; //John and Lucille van Geest Foundation/ ; //National Institute for Health Research/ ; //Leicester Biomedical Research Centre/ ; },
abstract = {AIMS: Association of elevated circulating levels of trimethylamine N-oxide (TMAO) with adverse outcomes in patients with heart failure (HF) has been described. However, response of TMAO levels to treatment and medications has not been investigated. Therefore, we investigated whether TMAO levels are responsive to guideline-recommended treatment and medications, and further reflect changes in outcomes.<br><br>METHODS AND RESULTS: TMAO levels were investigated in the systems BIOlogy Study to TAilored Treatment in Chronic Heart Failure (BIOSTAT-CHF), which addressed response to guideline-recommended pharmacological treatment. TMAO levels in 2234 patients with new-onset or progressively worsening HF showed strong associations with adverse events (mortality and/or rehospitalisation) at 1, 2 and 3 years [hazard ratio (HR) 1.37-1.51, P ≤ 0.019). Analysis of 972 patients with plasma available at both enrolment and follow-up visit showed reductions of B-type natriuretic peptide (BNP) levels with guideline-based treatment (P < 0.001), but not for TMAO levels. Moreover, patients with higher TMAO levels than median before and after treatment showed increased association with adverse outcomes [HR 2.21, 95% confidence interval (CI) 1.43-3.43, P < 0.001] compared to patients with lower than median levels either before or after treatment (HR 1.13, 95% CI 0.63-2.04, P = 0.684 and HR 1.14, 95% CI 0.64-2.03, P = 0.662, respectively).<br><br>CONCLUSION: TMAO levels were associated with adverse outcomes (mortality and/or rehospitalisation) in BIOSTAT-CHF, and did not respond to guideline-based pharmacological treatment in contrast to BNP levels which did as expected. Lower TMAO levels were associated with favourable outcome regardless of treatment.},
}
@article {pmid30370932,
year = {2018},
author = {Bourrat, P},
title = {Have Causal Claims About the Gut Microbiome Been Over-Hyped?.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e1800178},
doi = {10.1002/bies.201800178},
pmid = {30370932},
issn = {1521-1878},
support = {60811//John Templeton Foundation/ ; //Macquarie University/ ; },
abstract = {Microbiome research attributes to whole microbiomes a causal role in the occurrence of different health outcomes. I argue, following some distinctions about causal relationships and explanations made within a philosophical account of causation, the &quot;interventionist account,&quot; that such claims need more scrutiny.},
}
@article {pmid30370682,
year = {2018},
author = {Nogueira, T and David, PHC and Pothier, J},
title = {Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach.},
journal = {Drug development research},
volume = {},
number = {},
pages = {},
doi = {10.1002/ddr.21466},
pmid = {30370682},
issn = {1098-2299},
support = {//The authors received no specific funding for this work./ ; },
abstract = {The exposure of the human gut to antibiotics can have a great impact on human health. Antibiotics pertain to the preservation of human health and are useful tools for fighting bacterial infections. They can be used for curing infections and can play a critical role in immunocompromised or chronic patients, or in fighting childhood severe malnutrition. Yet, the genomic and phylogenetic diversity of the human gut changes under antibiotic exposure. Antibiotics can also have severe side effects on human gut health, due to the spreading of potential antibiotic resistance genetic traits and to their correlation with virulence of some bacterial pathogens. They can shape, and even disrupt, the composition and functioning diversity of the human gut microbiome. Traditional bacterial antibiotic resistances have been evaluated at clone or population level. However, the understanding of these two apparently disparate perspectives as both friends and foes may come from the study of microbiomes as a whole and from the evaluation of both positive and negative effects of antibiotics on microbial community dynamics and diversity. In this review we present some metagenomic tools and databases that enable the studying of antibiotic resistance in human gut metagenomes, enabling the development of personalized medicine strategies, new antimicrobial therapy protocols and patient follow-up.},
}
@article {pmid30370643,
year = {2018},
author = {Brandt, N and Kotowska, D and Kristensen, CM and Olesen, J and Lützhøft, DO and Halling, JF and Hansen, M and Al-Soud, WA and Hansen, L and Kiilerich, P and Pilegaard, H},
title = {The impact of exercise training and resveratrol supplementation on gut microbiota composition in high-fat diet fed mice.},
journal = {Physiological reports},
volume = {6},
number = {20},
pages = {e13881},
doi = {10.14814/phy2.13881},
pmid = {30370643},
issn = {2051-817X},
support = {//Danish Council for Strategic Research/ ; //Danish Medical research Council/ ; },
abstract = {The aim of this study was to examine the effect of exercise training and dietary supplementation of resveratrol on the composition of gut microbiota and to test the hypothesis that exercise training and resveratrol can prevent high-fat diet (HFD)-induced changes in the gut microbiota. Mice fed a HFD supplemented with resveratrol (4 g/kg food) were protected against diet-induced obesity, while exercise trained HFD-fed animals (running on average 50 km/week) were not. Dietary resveratrol supplementation induced changes predominantly in the low-abundant bacteria, while exercise training induced changes in the high-abundant bacteria in the gut as analyzed by ADONIS test with Weighted UniFrac distances. Interestingly, the two interventions affected the gut microbiome independently of the inflammatory state of the HFD-fed animals as assessed by the systemic serum amyloid A levels. These results suggest that both resveratrol supplementation and regular physical activity modulate the composition of murine microbiota independently of the systemic inflammatory state. Moreover, the effects of exercise training on the microbiota seem to occur without changes in adiposity, while resveratrol-mediated alterations may relate to adipose tissue mass.},
}
@article {pmid30370305,
year = {2018},
author = {Staude, B and Oehmke, F and Lauer, T and Behnke, J and Göpel, W and Schloter, M and Schulz, H and Krauss-Etschmann, S and Ehrhardt, H},
title = {The Microbiome and Preterm Birth: A Change in Paradigm with Profound Implications for Pathophysiologic Concepts and Novel Therapeutic Strategies.},
journal = {BioMed research international},
volume = {2018},
number = {},
pages = {7218187},
doi = {10.1155/2018/7218187},
pmid = {30370305},
issn = {2314-6141},
abstract = {Preterm birth poses a global challenge with a continuously increasing disease burden during the last decades. Advances in understanding the etiopathogenesis did not lead to a reduction of prematurely born infants so far. A balanced development of the host microbiome in early life is key for the maturation of the immune system and many other physiological functions. With the tremendous progress in new diagnostic possibilities, the contribution of microbiota changes to preterm birth and the acute and long-term sequelae of prematurity have come into the research focus. This review summarizes the latest advances in the understanding of microbiomes in the amniotic cavity and the female lower genital tract and how changes in microbiota structures contribute to preterm delivery. The exhibition of these highly vulnerable infants to the hostile environment in the neonatal intensive care unit necessarily entails the rapid colonization with a nonbalanced microbiome in a situation where the organism is still very prone and at an early stage of development. The global research efforts to decipher pathologic changes will pave the way to new pre- and postnatal therapeutic concepts.},
}
@article {pmid30369912,
year = {2018},
author = {Moisander, PH and Shoemaker, KM and Daley, MC and McCliment, E and Larkum, J and Altabet, MA},
title = {Copepod-Associated Gammaproteobacteria Respire Nitrate in the Open Ocean Surface Layers.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2390},
doi = {10.3389/fmicb.2018.02390},
pmid = {30369912},
issn = {1664-302X},
abstract = {Microbial dissimilatory nitrate reduction to nitrite, or nitrate respiration, was detected in association with copepods in the oxygenated water column of the North Atlantic subtropical waters. These unexpected rates correspond to up to 0.09 nmol N copepod-1 d-1 and demonstrate a previously unaccounted nitrogen transformation in the oceanic pelagic surface layers. Genes and transcripts for both the periplasmic and membrane associated dissimilatory nitrate reduction pathways (Nap and Nar, respectively) were detected. The napA genes and transcripts were closely related with sequences from several clades of Vibrio sp., while the closest relatives of the narG sequences were Pseudoalteromonas spp. and Alteromonas spp., many of them representing clades only distantly related to previously described cultivated bacteria. The discovered activity demonstrates a novel Gammaproteobacterial respiratory role in copepod association, presumably providing energy for these facultatively anaerobic bacteria, while supporting a reductive path of nitrogen in the oxygenated water column of the open ocean.},
}
@article {pmid30368579,
year = {2018},
author = {Zhu, L and Liao, R and Wu, N and Zhu, G and Yang, C},
title = {Heat stress mediates changes in fecal microbiome and functional pathways of laying hens.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-018-9465-8},
pmid = {30368579},
issn = {1432-0614},
support = {CARS-40-K03//Agriculture Research System of China/ ; },
abstract = {Chicken gastrointestinal microbiota plays important roles in health, productivity, and disease. However, knowledge of the relationship between heat stress and the gut microbial ecosystem of poultry, especially laying hens, is still limited. Here, we aimed to provide important knowledge for heat stress intervention in the egg industry. We performed high-throughput sequencing metagenomics on fecal contents to unravel the microbial taxa and functional capacity of the gut microbiome of caged laying hens under heat stress. Results showed that the fecal microbial communities of laying hens were dominated by Firmicutes, Bacteroidetes, and Proteobacteria phyla. The Firmicutes were significantly decreased, and Bacteroidetes were increased in the fecal microbiota under heat stress. Functional prediction of these changes in microbiota revealed that metabolism-related pathways, including cysteine and methionine metabolism and benzoate degradation, were more abundant. Conversely, retinol metabolism and phenylpropanoid biosynthesis were decreased by heat stress, suggesting differences in metabolism between layers in different temperature environments. Clear contributions were identified between active taxa (genus level) and metabolic pathways, which were associated with the liver and intestinal dysfunction in layers. These data revealed that heat stress induced a significant taxonomic perturbation in the gut microbiome of caged laying hens. This was related to the negative effects of heat stress in poultry and provided important basic knowledge for heat stress intervention.},
}
@article {pmid30368524,
year = {2018},
author = {Li, X and Jousset, A and de Boer, W and Carrión, VJ and Zhang, T and Wang, X and Kuramae, EE},
title = {Legacy of land use history determines reprogramming of plant physiology by soil microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0300-0},
pmid = {30368524},
issn = {1751-7370},
abstract = {Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.},
}
@article {pmid30368255,
year = {2018},
author = {Lowe, PP and Gyongyosi, B and Satishchandran, A and Iracheta-Vellve, A and Cho, Y and Ambade, A and Szabo, G},
title = {Reduced gut microbiome protects from alcohol-induced neuroinflammation and alters intestinal and brain inflammasome expression.},
journal = {Journal of neuroinflammation},
volume = {15},
number = {1},
pages = {298},
doi = {10.1186/s12974-018-1328-9},
pmid = {30368255},
issn = {1742-2094},
support = {R01AA017729//National Institute on Alcohol Abuse and Alcoholism/ ; F30AA024680//Foundation for the National Institutes of Health/ ; F30 AA022283//Foundation for the National Institutes of Health/ ; F31 AA025545//Foundation for the National Institutes of Health/ ; },
abstract = {BACKGROUND: The end-organ effects of alcohol span throughout the entire body, from the gastrointestinal tract to the central nervous system (CNS). In the intestine, alcohol use changes the microbiome composition and increases gut permeability allowing translocation of microbial components into the circulation. Gut-derived pathogen-associated signals initiate inflammatory responses in the liver and possibly elsewhere in the body. Because previous studies showed that the gut microbiome contributes to alcohol-induced liver disease, we hypothesized that antibiotic administration to reduce the gut microbiome would attenuate alcohol-induced inflammation in the brain and small intestine (SI).<br><br>METHODS: Six- to 8-week-old C57BL/6J female mice were fed alcohol in a liquid diet or a calorie-matched control diet for 10 days with an acute alcohol binge or sugar on the final day (acute-on-chronic alcohol administration). Some mice were treated with oral antibiotics daily to diminish the gut microbiome. We compared serum levels of TNFα, IL-6, and IL-1β by ELISA; expression of cytokines Tnfα, Mcp1, Hmgb1, Il-17, Il-23, Il-6, and Cox2; and inflammasome components Il-1β, Il-18, Casp1, Asc, and Nlrp3 in the CNS and SI by qRT-PCR. Microglial morphology was analyzed using immunohistochemical IBA1 staining in the cortex and hippocampus.<br><br>RESULTS: Antibiotics dramatically reduced the gut microbiome load in both alcohol- and pair-fed mice. Alcohol-induced neuroinflammation and increase in SI cytokine expression were attenuated in mice with antibiotic treatment. Acute-on-chronic alcohol did not induce serum TNFα, IL-6, and IL-1β. Alcohol feeding significantly increased the expression of proinflammatory cytokines such as Tnfα, Mcp1, Hmgb1, Il-17, and Il-23 in the brain and intestine. Reduction in the gut bacterial load, as a result of antibiotic treatment, attenuated the expression of all of these alcohol-induced proinflammatory cytokines in both the brain and SI. Alcohol feeding resulted in microglia activation and morphologic changes in the cortex and hippocampus characterized by a reactive phenotype. These alcohol-induced changes were abrogated following an antibiotic-induced reduction in the gut microbiome. Unexpectedly, antibiotic treatment increased the mRNA expression of some inflammasome components in both the brain and intestine.<br><br>CONCLUSIONS: Our data show for the first time that the acute-on-chronic alcohol administration in mice induces both neuroinflammation and intestinal inflammation and that reduction in the intestinal bacterial load can attenuate alcohol-associated CNS and gut inflammation. Gut microbiome-derived signals contribute to neuroinflammation in acute-on-chronic alcohol exposure.},
}
@article {pmid30367989,
year = {2018},
author = {Cota, D and Mishra, S and Shengule, S},
title = {Terminalia arjuna hydroalcoholic extract ameliorates trinitrobenzenesulphonic acid induced colitis mediated through inhibition of inflammation, oxidative stress and improvement in structure of gut microbiota.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jep.2018.10.020},
pmid = {30367989},
issn = {1872-7573},
abstract = {Terminalia arjuna Roxb. (Combretaceae) is traditionally used in Ayurveda medicine and holds ethnomedicinal importance for treatment of gastrointestinal disorders. In view of its anti-inflammatory, antidiarrheal and antioxidant potential, it could be beneficial for the treatment of inflammatory bowel disease (IBD), which is associated with interaction between genetic, environmental factors and intestinal microbiome leading to dysregulated immune responses. This study evaluates the effect of hydroalcoholic extract of Terminalia arjuna bark (TAHA) in trinitrobenzenesulfonic acid (TNBS) model of rat colitis which resembles human IBD.<br><br>MATERIALS AND METHODS: TAHA (500, 250, 125mg/kg) was administered orally for 28 days in TNBS induced rats. Response to treatment was assessed by comparing observations in diseased and treated groups using disease activity index (DAI); macroscopic/histological damage; determining oxidative stress indicators: myeloperoxidase, malondialdehyde, nitric oxide, catalase, superoxide dismutase, and reduced glutathione; gene expression of pro-inflammatory cytokines such as IL-6, IL-1β, TNF-α and chemokine: MCP-1. Furthermore, the role of TAHA in altering the gut microbiota profile in rat feces and plasma zinc was also studied.<br><br>RESULTS: TAHA treatment in colitic rats directed decreased DAI scores, macroscopic and histologic damage. It also reduced myeloperoxidase, malondialdehyde and nitric oxide level. Whereas, prevented depletion of plasma catalase, superoxide dismutase and glutathione level. In addition, TAHA treatment down-regulated the gene expression of pro-inflammatory mediators and displayed altered beneficial effect on fecal microbiota. Furthermore, enhanced plasma zinc level supported the beneficial effect of TAHA in colitic rats. The dose of TAHA that produced most significant beneficial effect was 500mg/kg.<br><br>CONCLUSION: TAHA administration relieved the disease activity in TNBS induced colitis by reducing expression of pro-inflammatory cytokines and chemokine, decreasing oxidative stress, and improving plasma zinc level and structure of gut microbiota.},
}
@article {pmid30367675,
year = {2018},
author = {Grier, A and McDavid, A and Wang, B and Qiu, X and Java, J and Bandyopadhyay, S and Yang, H and Holden-Wiltse, J and Kessler, HA and Gill, AL and Huyck, H and Falsey, AR and Topham, DJ and Scheible, KM and Caserta, MT and Pryhuber, GS and Gill, SR},
title = {Neonatal gut and respiratory microbiota: coordinated development through time and space.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {193},
doi = {10.1186/s40168-018-0566-5},
pmid = {30367675},
issn = {2049-2618},
support = {HHSN272201200005C//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND: Postnatal development of early life microbiota influences immunity, metabolism, neurodevelopment, and infant health. Microbiome development occurs at multiple body sites, with distinct community compositions and functions. Associations between microbiota at multiple sites represent an unexplored influence on the infant microbiome. Here, we examined co-occurrence patterns of gut and respiratory microbiota in pre- and full-term infants over the first year of life, a period critical to neonatal development.<br><br>RESULTS: Gut and respiratory microbiota collected as longitudinal rectal, throat, and nasal samples from 38 pre-term and 44 full-term infants were first clustered into community state types (CSTs) on the basis of their compositional profiles. Multiple methods were used to relate the occurrence of CSTs to temporal microbiota development and measures of infant maturity, including gestational age (GA) at birth, week of life (WOL), and post-menstrual age (PMA). Manifestation of CSTs followed one of three patterns with respect to infant maturity: (1) chronological, with CST occurrence frequency solely a function of post-natal age (WOL), (2) idiosyncratic to maturity at birth, with the interval of CST occurrence dependent on infant post-natal age but the frequency of occurrence dependent on GA at birth, and (3) convergent, in which CSTs appear first in infants of greater maturity at birth, with occurrence frequency in pre-terms converging after a post-natal interval proportional to pre-maturity. The composition of CSTs was highly dissimilar between different body sites, but the CST of any one body site was highly predictive of the CSTs at other body sites. There were significant associations between the abundance of individual taxa at each body site and the CSTs of the other body sites, which persisted after stringent control for the non-linear effects of infant maturity. Canonical correlations exist between the microbiota composition at each pair of body sites, with the strongest correlations between proximal locations.<br><br>CONCLUSION: These findings suggest that early microbiota is shaped by neonatal innate and adaptive developmental responses. Temporal progression of CST occurrence is influenced by infant maturity at birth and post-natal age. Significant associations of microbiota across body sites reveal distal connections and coordinated development of the infant microbial ecosystem.},
}
@article {pmid30367598,
year = {2018},
author = {Shi, JY and Huang, H and Zhang, YN and Cao, JB and Yiu, SM},
title = {BMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion.},
journal = {BMC bioinformatics},
volume = {19},
number = {Suppl 9},
pages = {281},
doi = {10.1186/s12859-018-2274-3},
pmid = {30367598},
issn = {1471-2105},
abstract = {BACKGROUND: Human Microbiome Project reveals the significant mutualistic influence between human body and microbes living in it. Such an influence lead to an interesting phenomenon that many noninfectious diseases are closely associated with diverse microbes. However, the identification of microbe-noninfectious disease associations (MDAs) is still a challenging task, because of both the high cost and the limitation of microbe cultivation. Thus, there is a need to develop fast approaches to screen potential MDAs. The growing number of validated MDAs enables us to meet the demand in a new insight. Computational approaches, especially machine learning, are promising to predict MDA candidates rapidly among a large number of microbe-disease pairs with the advantage of no limitation on microbe cultivation. Nevertheless, a few computational efforts at predicting MDAs are made so far.<br><br>RESULTS: In this paper, grouping a set of MDAs into a binary MDA matrix, we propose a novel predictive approach (BMCMDA) based on Binary Matrix Completion to predict potential MDAs. The proposed BMCMDA assumes that the incomplete observed MDA matrix is the summation of a latent parameterizing matrix and a noising matrix. It also assumes that the independently occurring subscripts of observed entries in the MDA matrix follows a binomial model. Adopting a standard mean-zero Gaussian distribution for the nosing matrix, we model the relationship between the parameterizing matrix and the MDA matrix under the observed microbe-disease pairs as a probit regression. With the recovered parameterizing matrix, BMCMDA deduces how likely a microbe would be associated with a particular disease. In the experiment under leave-one-out cross-validation, it exhibits the inspiring performance (AUC = 0.906, AUPR =0.526) and demonstrates its superiority by ~ 7% and ~ 5% improvements in terms of AUC and AUPR respectively in the comparison with the pioneering approach KATZHMDA.<br><br>CONCLUSIONS: Our BMCMDA provides an effective approach for predicting MDAs and can be also extended to other similar predicting tasks of binary relationship (e.g. protein-protein interaction, drug-target interaction).},
}
@article {pmid30367461,
year = {2018},
author = {Whitaker, BK and Reynolds, HL and Clay, K},
title = {Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switchgrass).},
journal = {Ecology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ecy.2543},
pmid = {30367461},
issn = {0012-9658},
abstract = {Experimental tests of community assembly mechanisms for host-associated microbiomes in nature are lacking. Asymptomatic foliar fungal endophytes are a major component of the plant microbiome and are increasingly recognized for their impacts on plant performance, including pathogen defense, hormonal manipulation, and drought tolerance. However, it remains unclear whether fungal endophytes preferentially colonize certain host ecotypes or genotypes, reflecting some degree of biotic adaptation in the symbioses, or whether colonization is simply a function of spore type and abundance within the local environment. Whether host ecotype, local environment, or some combination of both controls the pattern of microbiome formation across hosts represents a new dimension to the age-old debate of nature versus nurture. Here we used a reciprocal transplant design to explore the extent of host specificity and biotic adaptation in the plant microbiome, as evidenced by differential colonization of host genetic types by endophytes. Specifically, replicate plants from three locally-adapted ecotypes of the native grass Panicum virgatum (switchgrass) were transplanted at three geographically distinct field sites (one home and two away) in the Midwestern US. At the end of the growing season, plant leaves were harvested and the fungal microbiome characterized using culture-dependent sequencing techniques. Our results demonstrated that fungal endophyte community structure was determined by local environment (i.e., site), but not by host ecotype. Fungal richness and diversity also strongly differed by site, with lower fungal diversity at a riparian field site, whereas host ecotype had no effect. By contrast, there were significant differences in plant phenotypes across all ecotypes and sites, indicating ecotypic differentiation of host phenotype. Overall, our results indicate that environmental factors are the primary drivers of community structure in the switchgrass fungal microbiome. This article is protected by copyright. All rights reserved.},
}
@article {pmid30367438,
year = {2018},
author = {Konturek, PC and Harsch, IA and Konturek, K and Schink, M and Zopf, Y},
title = {[Gut-liver axis: How intestinal bacteria affect the liver].},
journal = {MMW Fortschritte der Medizin},
volume = {160},
number = {Suppl 5},
pages = {11-15},
doi = {10.1007/s15006-018-1051-6},
pmid = {30367438},
issn = {1613-3560},
abstract = {BACKGROUND: Liver and intestine are in close contact with each other. The risk of damage to the liver increases, when the intestinal barrier is damaged (&quot;leaky gut&quot;) .<br><br>METHOD: The review article describes how intestinal bacteria influence the pathogenesis of chronic liver diseases and what treatment options are available.<br><br>RESULTS AND CONCLUSIONS: Intestinal dysbiosis plays an important role in the development of chronic liver diseases such as alcoholic liver disease, nonalcoholic fatty liver disease, primary biliary cholangitis, primary sclerosing cholangitis, and cirrhosis. Intestinal microbial modulating therapy with probiotics, prebiotics or synbiotics shows positive effects. The more precise meaning of this therapeutic approach needs to be clarified in further studies.},
}
@article {pmid30367437,
year = {2018},
author = {Straube, A and Müller, H and Stiegelbauer, V and Frauwallner, A},
title = {[Migraine prophylaxis with a probiotic. Results of an uncontrolled observational study with 1,020 patients].},
journal = {MMW Fortschritte der Medizin},
volume = {160},
number = {Suppl 5},
pages = {16-21},
doi = {10.1007/s15006-018-1052-5},
pmid = {30367437},
issn = {1613-3560},
abstract = {BACKGROUND: Patients with migraine often also suffer from gastrointestinal disorders such as irritable bowel syndrome, inflammatory bowel disease or celiac disease. All these diseases share increased intestinal permeability (&quot;leaky gut&quot;) and thus increased inflammatory activity. There is an increase in proinflammatoric cytokines in the serum, which in turn can trigger migraine attacks. Probiotics can have a positive effect on the intestinal epithelium and reduce inflammatory activity. A first uncontrolled, small study of 39 migraineurs showed a decrease in the rate of attacks under the daily intake of a probiotic.<br><br>METHOD: In an uncontrolled observational study, the influence of a specially formulated multispecies probiotic on the frequency of migraine attacks and the intensity of migraine-associated complaints was recorded. The self-assessment of 1,020 patients was evaluated.<br><br>RESULTS: Over the treatment period of 8 weeks, the number of headache days was reduced from 2 to 1.4 days per week. The headache intensity decreased from 5.1 to 2.1 points (0 = not present to 6 = very intensive). The migraine-associated complaints were reduced and the use of painkillers halved. All results were statistically significant (p ≤ 0.001).<br><br>CONCLUSION: It can be suggested that this multispecies probiotic formulation has a positive influence on intensity and frequency of migraine attacks. However, randomized, placebo-controlled trials are required for further confirmation.},
}
@article {pmid30367140,
year = {2018},
author = {Hasegawa, Y and Curtis, B and Yutuc, V and Rulien, M and Morrisroe, K and Watkins, K and Ferrier, C and English, C and Hewitson, L and Slupsky, CM},
title = {Microbial structure and function in infant and juvenile rhesus macaques are primarily affected by age, not vaccination status.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15867},
doi = {10.1038/s41598-018-34019-0},
pmid = {30367140},
issn = {2045-2322},
abstract = {Although thimerosal, an ethylmercury-based preservative, has been removed from most pediatric vaccines in the United States, some multidose vaccines, such as influenza vaccines, still contain thimerosal. Considering that a growing number of studies indicate involvement of the gut microbiome in infant immune development and vaccine responses, it is important to elucidate the impact of pediatric vaccines, including thimerosal-containing vaccines, on gut microbial structure and function. Here, a non-human primate model was utilized to assess how two vaccine schedules affect the gut microbiome in infants (5-9 days old) and juveniles (77-88 weeks old) through 16S ribosomal RNA sequencing and metabolomics analyses of the fecal samples. Two treatment groups (n = 12/group) followed either the vaccine schedule that was in place during the 1990s (intensive exposure to thimerosal) or an expanded schedule administered in 2008 (prenatal and postnatal exposure to thimerosal mainly via influenza vaccines), and were compared with a control group (n = 16) that received saline injections. The primary impact on gut microbial structure and function was age. Although a few statistically significant impacts of the two common pediatric vaccine schedules were observed when confounding factors were considered, the magnitude of the differences was small, and appeared to be positive with vaccination.},
}
@article {pmid30367055,
year = {2018},
author = {Correa, MA and Matusovsky, B and Brackney, DE and Steven, B},
title = {Generation of axenic Aedes aegypti demonstrate live bacteria are not required for mosquito development.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {4464},
doi = {10.1038/s41467-018-07014-2},
pmid = {30367055},
issn = {2041-1723},
abstract = {The mosquito gut microbiome plays an important role in mosquito development and fitness, providing a promising avenue for novel mosquito control strategies. Here we present a method for rearing axenic (bacteria free) Aedes aegypti mosquitoes, consisting of feeding sterilized larvae on agar plugs containing a high concentration of liver and yeast extract. This approach allows for the complete development to adulthood while maintaining sterility; however, axenic mosquito's exhibit delayed development time and stunted growth in comparison to their bacterially colonized cohorts. These data challenge the notion that live microorganisms are required for mosquito development, and suggest that the microbiota's main role is nutritional. Furthermore, we colonize axenic mosquitoes with simplified microbial communities ranging from a single bacterial species to a three-member community, demonstrating the ability to control the composition of the microbiota. This axenic system will allow the systematic manipulation of the mosquito microbiome for a deeper understanding of microbiota-host interactions.},
}
@article {pmid30367006,
year = {2018},
author = {Lynch, A and Tammireddy, SR and Doherty, MK and Whitfield, PD and Clarke, DJ},
title = {The glycine lipids of Bacteroides thetaiotaomicron are important for fitness during growth in vivo and in vitro.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02157-18},
pmid = {30367006},
issn = {1098-5336},
abstract = {Acylated amino acids function as important components of the cellular membrane in some bacteria. Biosynthesis is initiated by the N-acylation of the amino acid and this is followed by subsequent O-acylation of the acylated molecule resulting in the production of the mature diacylated amino acid lipid. In this study we use both genetics and liquid chromatography-mass spectrometry (LC-MS) to characterize the biosynthesis and function of a diacylated glycine lipid (GL) species produced in Bacteroides thetaiotaomicron We, and others, have previously reported the identification of a gene, named glsB in this study, that encodes a N-acyltransferase activity responsible for the production of a monoacylated glycine called N-acyl-3-hydroxy-palmitoyl glycine (or commendamide). In all of the Bacteroidales genomes so far sequenced the glsB gene is located immediately downstream from a gene, named glsA, also predicted to encode a protein with acyltransferase activity. We use LC-MS to show that co-expression of glsB and glsA results in the production of GL in Escherichia coli We constructed a deletion mutant of the glsB gene in B. thetaiotaomicron and we confirm that glsB is required for the production of GL in B. thetaiotaomicron Moreover, we show that glsB is important for the ability of B. thetaiotaomicron to adapt to stress and colonize the mammalian gut. Therefore, this report describes the genetic requirements for the biosynthesis of GL, a diacylated amino acids species that contributes to fitness in the human gut bacterium, B. thetaiotaomicronIMPORTANCE The gut microbiome has an important role in both health and disease of the host. The mammalian gut microbiome is often dominated by bacteria from the Bacteroidales, an Order that includes Bacteroides and Prevotella In this study we have identified an acylated amino acid, called glycine lipid, produced by Bacteroides thetaiotaomicron, a beneficial bacterium originally isolated from the human gut. In addition to identifying the genes required for the production of glycine lipids we show that glycine lipids have an important role during the adaptation of B. thetaiotaomicron to a number of environmental stresses including exposure to either bile or air. We also show that glycine lipids are important for the normal colonization of the murine gut by B. thetaiotaomicron This work identifies glycine lipids as an important fitness determinant in B. thetaiotaomicron and therefore increases our understanding of the molecular mechanisms underpinning colonization of the mammalian gut by beneficial bacteria.},
}
@article {pmid30367004,
year = {2018},
author = {Dror, B and Savidor, A and Salam, BB and Sela, N and Lampert, Y and Teper-Bamnolker, P and Daus, A and Carmeli, S and Sela Saldinger, S and Eshel, D},
title = {High Levels of CO2 Induce Spoilage by Leuconostoc mesenteroides by Upregulating Dextran-Synthesis Genes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.00473-18},
pmid = {30367004},
issn = {1098-5336},
abstract = {During non-ventilated storage of carrots, CO2 gradually accumulates to high levels and causes modifications in the carrot's microbiome toward dominance of Lactobacillales and Enterobacteriales The lactic acid bacterium Leuconostoc mesenteroides secretes a slimy exudate over the surface of the carrots. The objective of this study was to characterize the slime components and the potential cause for its secretion under high CO2 levels. Proteomic analysis of the exudate revealed the presence of bacterial glucosyltranferases as the main proteins, specifically dextransucrase. Chemical analysis of the exudate revealed high levels of dextran and several simple sugars. Exudate volume and dextran amount were significantly higher when L. mesenteroides was incubated under high CO2 levels compared to an aerated environment. Treatment of carrot medium plates with commercial dextransucrase or exudate protein extract showed similar sugar profiles and dextran production. Transcriptome analysis demonstrated that dextran production is related to upregulation of the L. mesenteroides dextransucrase-encoding genes dsrD and dsrT during the first 4-8 h of exposure to high CO2 levels compared to aerated conditions. Phylogenetic analysis of L. mesenteroides YL48 dsrD revealed high similarity to other dsr genes harbored by different Leuconostoc species. The ecological benefit of dextran production under elevated CO2 requires further investigation. However, this study implies an overlooked role of CO2 in the physiology and fitness of L. mesenteroides in stored carrot, and perhaps in other food items, during storage under non-ventilated conditions.IMPORTANCE The bacterium L. mesenteroides is known to cause spoilage of different types of food by secreting a slimy fluid that damages the quality and appearance of the produce. Here we identified a potential mechanism by which high levels of CO2 can affect the spoilage caused by this bacterium by upregulating dextran-synthesis genes. These results have broader implications for the study of Leuconostoc physiology and degradation ability, and its potential biotechnological applications.},
}
@article {pmid30366683,
year = {2018},
author = {Lewiecki, EM and Bilezikian, JP and Giangregorio, L and Greenspan, SL and Khosla, S and Kostenuik, P and Krohn, K and McClung, MR and Miller, PD and Pacifici, R},
title = {Proceedings of the 2018 Santa Fe Bone Symposium: Advances in the Management of Osteoporosis.},
journal = {Journal of clinical densitometry : the official journal of the International Society for Clinical Densitometry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jocd.2018.09.010},
pmid = {30366683},
issn = {1094-6950},
abstract = {The Santa Fe Bone Symposium is an annual meeting devoted to clinical applications of recent advances in skeletal research. The 19th Santa Fe Bone Symposium convened August 3-4, 2018, in Santa Fe, New Mexico, USA. Attendees included physicians of many specialties, fellows in training, advanced practice providers, clinical researchers, and bone density technologists. The format consisted of lectures, case presentations by endocrinology fellows, and panel discussions, with all involving extensive interactive discussions. Topics were diverse, including an evolutionary history of calcium homeostasis, osteoporosis treatment in the very old, optimizing outcomes with orthopedic surgery, microbiome and bone, new strategies for combination and sequential therapy of osteoporosis, exercise as medicine, manifestations of parathyroid hormone excess and deficiency, parathyroid hormone as a therapeutic agent, cell senescence and bone health, and managing patients outside clinical practice guidelines. The National Bone Health Alliance conducted a premeeting on development of fracture liaison services. A workshop was devoted to Bone Health TeleECHO (Bone Health Extension for Community Healthcare Outcomes), a strategy of ongoing medical education for healthcare professions to expand capacity to deliver best practice skeletal healthcare in underserved communities and reduce the osteoporosis treatment gap.},
}
@article {pmid30366573,
year = {2018},
author = {Marietta, E and Horwath, I and Balakrishnan, B and Taneja, V},
title = {Role of the intestinal microbiome in autoimmune diseases and its use in treatments.},
journal = {Cellular immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cellimm.2018.10.005},
pmid = {30366573},
issn = {1090-2163},
abstract = {The role of the intestinal microbiome in the pathogenesis of autoimmune diseases such as rheumatoid arthritis, multiple sclerosis, and type 1 diabetes is being increasingly appreciated. Many studies have reported that the compositions of the intestinal microbiomes of patients with these autoimmune diseases are different from those of healthy individuals. Analyses of the intestinal microbiome of humans suggest that various factors affect the composition of the intestinal microbiome, including, but not limited to: geographical location, diet, sex, and age. However, patients with rheumatoid arthritis and type 1 diabetes show unique intestinal microbiome profile even after considering these confounding factors. This review will describe the known differences in the microbial composition for each of the aforementioned autoimmune diseases, how it impacts the immune system, and how these compositions may potentially be modulated by treatments with probiotics, prebiotics, and other microbiome altering therapies.},
}
@article {pmid30366260,
year = {2018},
author = {Sharma, S and Tripathi, P},
title = {Gut microbiome and type 2 diabetes: where we are and where to go?.},
journal = {The Journal of nutritional biochemistry},
volume = {63},
number = {},
pages = {101-108},
doi = {10.1016/j.jnutbio.2018.10.003},
pmid = {30366260},
issn = {1873-4847},
abstract = {Type 2 diabetes mellitus (T2D) is a highly prevalent metabolic disorder characterized by an imbalance in blood glucose level, altered lipid profile and high blood pressure. Genetic constituents, high-fat and high-energy dietary habits, and a sedentary lifestyle are three major factors that contribute to high risk of T2D. Several studies have reported gut microbiome dysbiosis as a factor in rapid progression of insulin resistance in T2D that accounts for about 90% of all diabetes cases worldwide. The gut microbiome dysbiosis may reshape intestinal barrier functions and host metabolic and signaling pathways, which are directly or indirectly related to the insulin resistance in T2D. Thousands of the metabolites derived from microbes interact with the epithelial, hepatic and cardiac cell receptors that modulate host physiology. Xenobiotics including dietary components, antibiotics and nonsteroidal anti-inflammatory drugs strongly affect the gut microbial composition and can promote dysbiosis. Any change in the gut microbiota can shift the host metabolism towards increased energy harvest during diabetes and obesity. However, the exact mechanisms behind the dynamics of gut microbes and their impact on host metabolism at the molecular level are yet to be deciphered. We reviewed the published literature for better understanding of the dynamics of gut microbiota, factors that potentially induce gut microbiome dysbiosis and their relation to the progression of T2D. Special emphasis was also given to understand the gut microbiome induced breaching of intestinal barriers and/or tight junctions and their relation to insulin resistance.},
}
@article {pmid30366123,
year = {2018},
author = {Steinhoff-Wagner, J and Hayer, JJ and Heinemann, C},
title = {Antibiotics as confounding factor in newborn calf studies investigating effects on the intestinal microbiome.},
journal = {Research in veterinary science},
volume = {121},
number = {},
pages = {104-105},
doi = {10.1016/j.rvsc.2018.10.006},
pmid = {30366123},
issn = {1532-2661},
}
@article {pmid30366118,
year = {2018},
author = {Maya-Lucas, O and Murugesan, S and Nirmalkar, K and Alcaraz, LD and Hoyo-Vadillo, C and Pizano-Zárate, ML and García-Mena, J},
title = {The gut microbiome of Mexican children affected by obesity.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anaerobe.2018.10.009},
pmid = {30366118},
issn = {1095-8274},
abstract = {Obesity is a metabolic disorder and global health issue. In Mexico 34.4% of children between 5 and 11 years-old are overweight or obese. Here we address this issue studying the gut microbiome in a sample of Mexican children affected by obesity. We performed metagenomic shotgun-sequencing of DNA isolated from fecal samples from a cohort of normal weight and obese Mexican children using Illumina platform with HiSeq 2500. We also examined their metabolic factors and fecal short-chain fatty acids concentration. The results show that a remarkable dysbiosis of bacteria, archaea and viruses was not observed in the obese children group compared to the normal weight group; however, the archaeal community exhibited an increase of unclassified Methanobrevibacter spp. in obese children. The bacterial communities of all participants were clustered into three different enterotypes. Most normal weight children have a gut bacterial community dominated by Ruminococcus spp. (Enterotype 3), while most obese children had a community dominated by Prevotella spp. (Enterotype 2). On the other hand, changes in the gut microbiome were correlated with clinical metadata and could be used to stratify individuals based on their phenotype. The species Megamonas spp. were over-represented in obese children, whereas members of the family Oscillospiraceae were depleted in the same individuals and negatively correlated with levels of serum cholesterol. A microbiome comparative metabolic pathway analysis showed that two KEGG pathway modules of glycolysis, Glycolysis I (from Glucose 6-Phosphate), and Glycolysis II (from Fructose 6-Phosphate) were significantly overrepresented in normal weight children. Our results establish specific alterations in the gut microbiome of Mexican children affected of obesity, along with clinical alterations, providing information on the microbiome composition that may be useful for prognosis, diagnosis, and treatment.},
}
@article {pmid30365870,
year = {2018},
author = {Yang, Y and Cai, Q and Shu, XO and Steinwandel, MD and Blot, WJ and Zheng, W and Long, J},
title = {Prospective Study of Oral Microbiome and Colorectal Cancer Risk in Low-income and African American Populations.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.31941},
pmid = {30365870},
issn = {1097-0215},
abstract = {Oral microbiome may play an important role in cancer pathogenesis. However, no study has prospectively investigated the association of the oral microbiome with subsequent risk of developing colorectal cancer (CRC). We conducted a nested case-control study including 231 incident CRC cases and 462 controls within the Southern Community Cohort Study with 75% of the subjects being African-Americans. The controls were individually matched to cases based on age, Ethnic group, smoking, season-of-study enrollment and recruitment method. Oral microbiota were assessed using 16S rRNA gene sequencing in pre-diagnostic mouth rinse samples. Multiple bacterial taxa showed an association with CRC risk at P < 0.05. Oral pathogens Treponema denticola and Prevotella intermedia were associated with an increased risk of CRC, with odds ratios (ORs) and 95% confidence intervals (CIs) of 1.76(1.19-2.60) and 1.55(1.08-2.22), respectively, for the individuals carrying these bacteria compared to non-carriers. In the phylum Actinobacteria, Bifidobacteriaceae was more abundant among CRC patients than among controls. In the phylum Bacteroidetes, Prevotella denticola and Prevotella sp. oral taxon 300 were associated with an increased CRC risk, while Prevotella melaninogenica was associated with a decreased risk of CRC. In the phylum Firmicutes, Carnobacteriaceae, Streptococcaceae, Erysipelotrichaceae, Streptococcus, Solobacterium, Streptococcus sp. oral taxon 058 and Solobacterium moorei showed associations with a decreased risk of CRC. Most of these associations were observed among both African- and European-Americans. Most of the associations were not significant after Bonferroni correction for multiple testing, which may be conservative. Our study suggests that the oral microbiome may play a significant role in CRC etiology. This article is protected by copyright. All rights reserved.},
}
@article {pmid30365587,
year = {2018},
author = {Del Rosso, JQ and Harper, J and Kircik, L and Albon, G and Berson, D and Hebert, A and Day, D},
title = {Consensus Recommendations on Adjunctive Topical Management of Atopic Dermatitis.},
journal = {Journal of drugs in dermatology : JDD},
volume = {17},
number = {10},
pages = {1070-1076},
pmid = {30365587},
issn = {1545-9616},
abstract = {Atopic dermatitis (AD) is well-recognized as a very common chronic and relapsing pruritic skin disorder affecting both children and adults worldwide. The adverse effects on the quality of life of affected individuals and their families is well-established. The pathophysiology of AD is complex, leading to interindividual variations in clinical presentation and severity. The chronicity of AD, characterized by periods of exacerbation and remission, supports a strong need to develop measures that can effectively and safely prolong remissions between flares of the disease. This article provides an overview of AD including prevalence, severity, and disease course/progression, succinct summaries of pathophysiology and medical management, and discussion of epidermal barrier dysfunction and skin microbiome shifting associated with AD. Additional emphasis is placed on adjunctive topical skin barrier approaches that may prolong disease-free remissions. Results from a panel of dermatologists queried about adjunctive approaches to AD, using a modified-Delphi approach, are also discussed. J Drugs Dermatol. 2018;17(10):1070-1076. THIS ARTICLE HAD BEEN MADE AVAILABLE FREE OF CHARGE. PLEASE SCROLL DOWN TO ACCESS THE FULL TEXT OF THIS ARTICLE WITHOUT LOGGING IN. NO PURCHASE NECESSARY. PLEASE CONTACT THE PUBLISHER WITH ANY QUESTIONS..},
}
@article {pmid30365583,
year = {2018},
author = {Chandra, J and Retuerto, M and Seité, S and Martin, R and Kus, M and Ghannoum, MA and Baron, E and Mukherjee, PK},
title = {Effect of an Emollient on the Mycobiome of Atopic Dermatitis Patients.},
journal = {Journal of drugs in dermatology : JDD},
volume = {17},
number = {10},
pages = {1039-1048},
pmid = {30365583},
issn = {1545-9616},
abstract = {INTRODUCTION: Atopic dermatitis (AD) is associated with changes in skin bacterial microbiome. Emollient treatment induces change in bacterial microbiome in AD, but its effect on fungal microbiome (&quot;mycobiome&quot;) and their inter-kingdom correlations is unknown. We used Ion-Torrent sequencing to characterize the mycobiome of AD patients in response to emollient treatment.<br><br>METHODS: Skin swabs were collected from lesional and non-lesional skin of AD patients suffering from moderate AD, after informed consent and according to GCP guidelines. Genomic DNA was extracted from each swab using the MoBio PowerSoil DNA Isolation kit and used for mycobiome sequencing analyses as described in our earlier publications. Principal coordinates analyses (PCoA), diversity, abundance, and correlations analyses were conducted in R and relevant packages using non-parametric tests (P less than .05 was significant).<br><br>RESULTS: Swab samples from 10 patients (7 females, 3 males; mean age, 10.5 years) were analyzed. Emollient treatment induced a significant reduction of Scoring Atopic Dermatitis (SCORAD) score (P less than .001). PCoA showed pre-treatment and post-treatment samples clustered differently at all taxa levels. Six genera were detected in only non-lesional samples, while four were detected in only lesional samples. In non-lesional samples, Shannon diversity index was significantly increased after emollient treatment (P less than equal to .04), while lesional skin exhibited non-significant decrease. Ascomycota was the most abundant phylum and Dothideomycetes was the most abundant Class in most samples. Eight fungal species were either significantly different (P less than .05) or showed a strong trend (P less than .1) between pre- and post-treatment samples of lesional and non-lesional skin. In lesional skin, Gram-negative Pseudomonas spp. correlated significantly with pathogenic fungal species (Aspergillus, Candida spp.) in pre-treatment samples; these correlations were not detected in post-treatment samples. Moreover, lesional skin exhibited significant correlations between Gram-positive bacteria (Corynebacterium kroppenstedtiian and Staphylococcus pettenkoferi) and pathogenic Candida species in pre-treatment samples, but not in post- treated samples.<br><br>DISCUSSION: Emollient treatment may induce beneficial microbial changes in the mycobiome and augment host-microbe balance on skin in AD. Clinical relevance of these results need to be investigated. J Drugs Dermatol. 2018;17(10):1039-1048.},
}
@article {pmid30365522,
year = {2018},
author = {Romano-Keeler, J and Shilts, MH and Tovchigrechko, A and Wang, C and Brucker, RM and Moore, DJ and Fonnesbeck, C and Meng, S and Correa, H and Lovvorn, HN and Tang, YW and Hooper, L and Bordenstein, SR and Das, SR and Weitkamp, JH},
title = {Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0206366},
doi = {10.1371/journal.pone.0206366},
pmid = {30365522},
issn = {1932-6203},
abstract = {OBJECTIVE: Necrotizing enterocolitis (NEC) is the most common surgical emergency in preterm infants, and pathogenesis associates with changes in the fecal microbiome. As fecal samples incompletely represent microbial communities in intestinal mucosa, we sought to determine the NEC tissue-specific microbiome and assess its contribution to pathogenesis.<br><br>DESIGN: We amplified and sequenced the V1-V3 hypervariable region of the bacterial 16S rRNA gene extracted from intestinal tissue and corresponding fecal samples from 12 surgical patients with NEC and 14 surgical patients without NEC. Low quality and non-bacterial sequences were removed, and taxonomic assignment was made with the Ribosomal Database Project. Operational taxonomic units were clustered at 97%. We tested for differences between NEC and non-NEC samples in microbiome alpha- and beta-diversity and differential abundance of specific taxa between NEC and non-NEC samples. Additional analyses were performed to assess the contribution of other demographic and environmental confounding factors on the infant tissue and fecal microbiome.<br><br>RESULTS: The fecal and tissue microbial communities were different. NEC was associated with a distinct microbiome, which was characterized by low diversity, higher abundances of Staphylococcus and Clostridium_sensu_stricto, and lower abundances of Actinomyces and Corynebacterium. Infant age and vancomycin exposure correlated with shifts in the tissue microbiome.<br><br>CONCLUSION: The observed low diversity in NEC tissues suggests that NEC is associated with a bacterial bloom and a distinct mucosal bacterial community. The exact bacterial species that constitute the bloom varied by infant and were strongly influenced by age and exposure to vancomycin.},
}
@article {pmid30365127,
year = {2018},
author = {Fan, Y and Zhang, C and Jin, S and Gao, Z and Cao, J and Wang, A and Li, D and Wang, Q and Sun, X and Bai, D},
title = {Progress of immune checkpoint therapy in the clinic (Review).},
journal = {Oncology reports},
volume = {},
number = {},
pages = {},
doi = {10.3892/or.2018.6819},
pmid = {30365127},
issn = {1791-2431},
abstract = {Cancer cells can escape antitumor immune responses by exploiting inhibitory immune checkpoints. Immune checkpoint therapy, mainly including anti‑CTLA‑4 therapy and anti‑PD‑1/PD‑L1 therapy, can enhance antitumor immune responses by blocking the inhibitory signals of the immune system. This therapy has produced clinical advances in a fraction of patients. Deeper insight into the tumor microenvironment and immune checkpoint inhibitors will improve this therapy. Here, we review immune checkpoint inhibitors that prevent tumor immune escape and recent clinical studies of immune checkpoint therapy. We also compare the efficacy of different combination immunotherapies, describe how the relationship between the gut microbiome and immune system can determine the therapeutic outcomes for immune checkpoint inhibitors and introduce several novel immune checkpoints that are potential targets for antitumor immunotherapy in the future.},
}
@article {pmid30365027,
year = {2018},
author = {Shi, W and Qi, H and Sun, Q and Fan, G and Liu, S and Wang, J and Zhu, B and Liu, H and Zhao, F and Wang, X and Hu, X and Li, W and Liu, J and Tian, Y and Wu, L and Ma, J},
title = {gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gky1008},
pmid = {30365027},
issn = {1362-4962},
abstract = {Meta-omics approaches have been increasingly used to study the structure and function of the microbial communities. A variety of large-scale collaborative projects are being conducted to encompass samples from diverse environments and habitats. This change has resulted in enormous demands for long-term data maintenance and capacity for data analysis. The Global Catalogue of Metagenomics (gcMeta) is a part of the 'Chinese Academy of Sciences Initiative of Microbiome (CAS-CMI)', which focuses on studying the human and environmental microbiome, establishing depositories of samples, strains and data, as well as promoting international collaboration. To accommodate and rationally organize massive datasets derived from several thousands of human and environmental microbiome samples, gcMeta features a database management system for archiving and publishing data in a standardized way. Another main feature is the integration of more than ninety web-based data analysis tools and workflows through a Docker platform which enables data analysis by using various operating systems. This platform has been rapidly expanding, and now hosts data from the CAS-CMI and a number of other ongoing research projects. In conclusion, this platform presents a powerful and user-friendly service to support worldwide collaborative efforts in the field of meta-omics research. This platform is freely accessible at https://gcmeta.wdcm.org/.},
}
@article {pmid30364728,
year = {2018},
author = {Htun, KS and Fong, Y and Kyaw, AA and Aung, ST and Oo, KZ and Zaw, T and Lockhart, PJ and Russell, B and Cook, GM and Aung, HL and Hlaing, TM},
title = {Microbiome dataset from the upper respiratory tract of patients living with HIV, HIV/TB and TB from Myanmar.},
journal = {Data in brief},
volume = {21},
number = {},
pages = {354-357},
doi = {10.1016/j.dib.2018.10.003},
pmid = {30364728},
issn = {2352-3409},
abstract = {This article contains microbiome data from the upper respiratory tract of patients living with HIV/TB, HIV and TB from Meiktila, a town in Myanmar where there is a high incidence of HIV and TB. Microbiomes were compared for HIV/TB infected and healthy adults from the same population. We collected nasopharyngeal and oropharyngeal swabs from a total of 33 participants (Healthy {5},
HIV/TB {8},
HIV {14},
and TB {6}
). DNA was extracted from the swabs and subjected to custom single step 16s rRNA sequencing on an Illumina MiSeq platform. The sequencing data is available via http://www.ncbi.nlm.nih.gov/bioproject/ PRJNA432583.},
}
@article {pmid30364192,
year = {2018},
author = {Paternoster, S and Falasca, M},
title = {Dissecting the Physiology and Pathophysiology of Glucagon-Like Peptide-1.},
journal = {Frontiers in endocrinology},
volume = {9},
number = {},
pages = {584},
doi = {10.3389/fendo.2018.00584},
pmid = {30364192},
issn = {1664-2392},
abstract = {An aging world population exposed to a sedentary life style is currently plagued by chronic metabolic diseases, such as type-2 diabetes, that are spreading worldwide at an unprecedented rate. One of the most promising pharmacological approaches for the management of type 2 diabetes takes advantage of the peptide hormone glucagon-like peptide-1 (GLP-1) under the form of protease resistant mimetics, and DPP-IV inhibitors. Despite the improved quality of life, long-term treatments with these new classes of drugs are riddled with serious and life-threatening side-effects, with no overall cure of the disease. New evidence is shedding more light over the complex physiology of GLP-1 in health and metabolic diseases. Herein, we discuss the most recent advancements in the biology of gut receptors known to induce the secretion of GLP-1, to bridge the multiple gaps into our understanding of its physiology and pathology.},
}
@article {pmid30364169,
year = {2018},
author = {Guo, Y and Xie, J and Li, X and Yuan, Y and Zhang, L and Hu, W and Luo, H and Yu, H and Zhang, R},
title = {Antidepressant Effects of Rosemary Extracts Associate With Anti-inflammatory Effect and Rebalance of Gut Microbiota.},
journal = {Frontiers in pharmacology},
volume = {9},
number = {},
pages = {1126},
doi = {10.3389/fphar.2018.01126},
pmid = {30364169},
issn = {1663-9812},
abstract = {It is currently believed that inflammation acts as a central part in the pathophysiology of depression. Rosemary extracts (RE), the crucial active constituents extracted from Rosmarinus officinalis Linn, have drawn wide concerns because of their potential for anti-inflammatory effects. However, no study has highlighted the antidepressant effects of RE on chronic restraint stress (CRS) mice, and the inflammatory mechanisms related to gut microbiome have not yet been elucidated. This study showed that depressive-like behaviors, gut microbiota dysbiosis, and activation of inflammatory reactions in the hippocampus and serum of CRS mice, as well as activation of inflammatory reactions in BV-2 microglia cells induced by lipopolysaccharide (LPS), could be attenuated by RE. We found that the pretreatment with RE increased the time in the center of open field test (OFT), and decreased immobility duration in tail suspension test (TST) as well as forced swimming test (FST). Furthermore, RE enhanced the sequences proportion of Lactobacillus and Firmicutes, and reduced the sequences proportion of Bacteroidetes and Proteobacteria in feces. Moreover, RE obviously suppressed protein expression of IL-1β, TNF-α, p-NF-κ B p65 and Iba1 in hippocampus, and elevated BDNF as well as p-AKT/AKT expression. Importantly, pre-incubation with RE protected microglia by alleviating protein expression of IL-1β, TNF-α and p-NF-κ B p65 induced by LPS. Additionally, RE downregulated the level of IL-1β and TNF-α in serum. In conclusion, this study showed the antidepressant effects of RE are mediated by anti-inflammatory effects in hippocampus, serum and BV-2 microglia as well as rebalancing gut microbiota.},
}
@article {pmid30361871,
year = {2018},
author = {Adalsteinsdottir, SA and Magnusdottir, OK and Halldorsson, TI and Birgisdottir, BE},
title = {Towards an Individualized Nutrition Treatment: Role of the Gastrointestinal Microbiome in the Interplay Between Diet and Obesity.},
journal = {Current obesity reports},
volume = {},
number = {},
pages = {},
doi = {10.1007/s13679-018-0321-z},
pmid = {30361871},
issn = {2162-4968},
abstract = {PURPOSE OF REVIEW: Dietary treatments for obesity have relatively low long-term success. Recent studies have identified the gastrointestinal microbiome as a factor of high relevance. The current knowledge on the interplay between diet, obesity, and the gastrointestinal microbiome and the potential for individualized dietary treatment will be discussed.<br><br>RECENT FINDINGS: Studies indicate that each individual digests and metabolizes identical food substances differently depending on their gastrointestinal microbiome composition. Factors related to this crosstalk may improve our understanding of weight homeostasis and treatment of obesity. Long-time dietary intake is the key in the composition of the gastrointestinal microbiome which seems to be an important factor for energy balance, resulting in emerging opportunities for increasingly varied obesity treatment. Compliance to dietary treatment is critical for long-term success as enduring changes in gastrointestinal microbiome seem to slow over time. More research is urgently needed to investigate this missing link in our understanding of obesity.},
}
@article {pmid30361800,
year = {2018},
author = {Gold, SM and Willing, A and Leypoldt, F and Paul, F and Friese, MA},
title = {Sex differences in autoimmune disorders of the central nervous system.},
journal = {Seminars in immunopathology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00281-018-0723-8},
pmid = {30361800},
issn = {1863-2300},
support = {LFF FV-45//Landesforschungsförderung Hamburg/ ; },
abstract = {Stronger adaptive immune responses in females can be observed in different mammals, resulting in better control of infections compared to males. However, this presumably evolutionary difference likely also drives higher incidence of autoimmune diseases observed in humans. Here, we summarize sex differences in the most common autoimmune diseases of the central nervous system (CNS) and discuss recent advances in the understanding of possible underlying immunological and CNS intrinsic mechanisms. In multiple sclerosis (MS), the most common inflammatory disease of the CNS, but also in rarer conditions, such as neuromyelitis optica spectrum disorders (NMOSD) or neuronal autoantibody-mediated autoimmune encephalitis (AE), sex is one of the top risk factors, with women being more often affected than men. Immunological mechanisms driving the sex bias in autoimmune CNS diseases are complex and include hormonal as well as genetic and epigenetic effects, which could also be exerted indirectly via modulation of the microbiome. Furthermore, CNS intrinsic differences could underlie the sex bias in autoimmunity by differential responses to injury. The strong effects of sex on incidence and possibly also activity and progression of autoimmune CNS disorders suggest that treatments need to be tailored to each sex to optimize efficacy. To date, however, due to a lack of systematic studies on treatment responses in males versus females, evidence in this area is still sparse. We argue that studies taking sex differences into account could pave the way for sex-specific and therefore personalized treatment.},
}
@article {pmid30361783,
year = {2018},
author = {Pfeiffer, RF},
title = {Gastrointestinal Dysfunction in Parkinson's Disease.},
journal = {Current treatment options in neurology},
volume = {20},
number = {12},
pages = {54},
doi = {10.1007/s11940-018-0539-9},
pmid = {30361783},
issn = {1092-8480},
abstract = {PURPOSE OF REVIEW: During the past 25 years, there has been an explosion of information regarding the occurrence of gastrointestinal dysfunction in Parkinson's disease. In this review, the clinical features of gastrointestinal dysfunction in Parkinson's disease will be described and information regarding the potential role of the enteric nervous system and the gut microbiome in the genesis of Parkinson's disease will be addressed.<br><br>RECENT FINDINGS: Recognition is growing regarding the role that gastroparesis and small intestinal dysfunction may play in Parkinson's disease, especially with regard to erratic responses to anti-Parkinson medication. The presence of enteric nervous system involvement in Parkinson's disease is now well established, but whether the enteric nervous system is the starting point for Parkinson's disease pathology remains a source of debate. The potential role of the gut microbiome also is beginning to emerge. Gastrointestinal dysfunction is a prominent nonmotor feature of Parkinson's disease and dysfunction can be found along the entire length of the gastrointestinal tract. The enteric nervous system is clearly involved in Parkinson's disease. Whether it is the initial source of pathology is still a source of controversy. There also is growing recognition of the role that the gut microbiome may play in Parkinson's disease, but much more research is needed to fully assess this aspect of the disorder.},
}
@article {pmid30361622,
year = {2018},
author = {Falk, GW},
title = {2017 David Sun Lecture: Screening and Surveillance of Barrett's Esophagus: Where Are We Now and What Does the Future Hold?.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41395-018-0374-3},
pmid = {30361622},
issn = {1572-0241},
abstract = {Barrett's esophagus and esophageal adenocarcinoma continue to present considerable management challenges in the Western world. Despite our best efforts to date, the prognosis of advanced esophageal adenocarcinoma remains poor and far too many individuals with esophageal adenocarcinoma have not had a prior endoscopy to detect Barrett's esophagus. As such, current strategies of screening for Barrett's esophagus and subsequent surveillance need to be further optimized. Screening today is limited to high definition white light endoscopy in high-risk patient populations and as such has multiple limitations. However, a variety of exciting new techniques including risk prediction tools, tethered capsule endomicroscopy, a cytology sponge, breath testing for exhaled volatile organic compounds, and assessment of the oral microbiome are now under study in an effort to develop less expensive population-based screening methods. Similarly, endoscopic surveillance, as currently practiced has a variety of limitations. Inexpensive readily available adjuncts are already available to optimize surveillance including increased inspection time in an effort to detect mucosal or vascular abnormalities, special attention to the right hemisphere of the esophagus, and utilization of narrow band imaging or other electronic chromoendoscopy techniques. To improve endoscopic surveillance, a variety of new paradigms are under study including wide area trans-epithelial sampling, advanced endoscopic imaging, molecular imaging, clinical risk stratification and utilization of biomarkers of increased risk. However, progress will be challenging due to the complexity of esophageal cancer biology and the rarity of progression to cancer among patients with nondysplastic Barrett's epithelium.},
}
@article {pmid30360360,
year = {2018},
author = {Ogawa, A and Takakura, K and Sano, K and Kanematsu, H and Yamano, T and Saishin, T and Terada, S},
title = {Microbiome Analysis of Biofilms of Silver Nanoparticle-Dispersed Silane-Based Coated Carbon Steel Using a Next-Generation Sequencing Technique.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {7},
number = {4},
pages = {},
doi = {10.3390/antibiotics7040091},
pmid = {30360360},
issn = {2079-6382},
abstract = {Previously, we demonstrated that silver nanoparticle-dispersed silane-based coating could inhibit biofilm formation in conditions where seawater was used as a bacterial source and circulated in a closed laboratory biofilm reactor. However, it is still unclear whether the microbiome of a biofilm of silver nanoparticle-dispersed silane-based coating samples (Ag) differs from that of a biofilm of non-dispersed silane-based coating samples (Non-Ag). This study aimed to perform a microbiome analysis of the biofilms grown on the aforementioned coatings using a next-generation sequencing (NGS) technique. For this, a biofilm formation test was conducted by allowing seawater to flow through a closed laboratory biofilm reactor; subsequently, DNAs extracted from the biofilms of Ag and Non-Ag were used to prepare 16S rRNA amplicon libraries to analyze the microbiomes by NGS. Results of the operational taxonomy unit indicated that the biofilms of Non-Ag and Ag comprised one and no phyla of archaea, respectively, whereas Proteobacteria was the dominant phylum for both biofilms. Additionally, in both biofilms, Non-Ag and Ag, Marinomonas was the primary bacterial group involved in early stage biofilm formation, whereas Anaerospora was primarily involved in late-stage biofilm formation. These results indicate that silver nanoparticles will be unrelated to the bacterial composition of biofilms on the surface of silane-based coatings, while they control biofilm formation there.},
}
@article {pmid30359969,
year = {2018},
author = {Aucoin, M and LaChance, L and Cooley, K and Kidd, S},
title = {Diet and Psychosis: A Scoping Review.},
journal = {Neuropsychobiology},
volume = {},
number = {},
pages = {1-23},
doi = {10.1159/000493399},
pmid = {30359969},
issn = {1423-0224},
abstract = {INTRODUCTION: Schizophrenia spectrum disorders (SSD) represent a cluster of severe mental illnesses. Diet has been identified as a modifiable risk factor and opportunity for intervention in many physical illnesses and more recently in mental illnesses such as unipolar depression; however, no dietary guidelines exist for patients with SSD.<br><br>OBJECTIVE: This review sought to systematically scope the existing literature in order to identify nutritional interventions for the prevention or treatment of mental health symptoms in SSD as well as gaps and opportunities for further research.<br><br>METHODS: This review followed established methodological approaches for scoping reviews including an extensive a priori search strategy and duplicate screening. Because of the large volume of results, an online program (Abstrackr) was used for screening and tagging. Data were extracted based on the dietary constituents and analyzed.<br><br>RESULTS: Of 55,330 results identified by the search, 822 studies met the criteria for inclusion. Observational evidence shows a connection between the presence of psychotic disorders and poorer quality dietary patterns, higher intake of refined carbohydrates and total fat, and lower intake or levels of fibre, ω-3 and ω-6 fatty acids, vegetables, fruit, and certain vitamins and minerals (vitamin B12 and B6, folate, vitamin C, zinc, and selenium). Evidence illustrates a role of food allergy and sensitivity as well as microbiome composition and specific phytonutrients (such as L-theanine, sulforaphane, and resveratrol). Experimental studies have demonstrated benefit using healthy diet patterns and specific vitamins and minerals (vitamin B12 and B6, folate, and zinc) and amino acids (serine, lysine, glycine, and tryptophan).<br><br>DISCUSSION: Overall, these findings were consistent with many other bodies of knowledge about healthy dietary patterns. Many limitations exist related to the design of the individual studies and the ability to extrapolate the results of studies using dietary supplements to dietary interventions (food). Dietary recommendations are presented as well as recommendations for further research including more prospective observational studies and intervention studies that modify diet constituents or entire dietary patterns with statistical power to detect mental health outcomes.},
}
@article {pmid30359695,
year = {2018},
author = {Neilands, J and Davies, JR and Bikker, FJ and Svensäter, G},
title = {Parvimonas micra stimulates expression of gingipains from Porphyromonas gingivalis in multi-species communities.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anaerobe.2018.10.007},
pmid = {30359695},
issn = {1095-8274},
abstract = {Dental biofilms are complex ecosystems containing many bacterial species that live in mutualistic relationships. These interactions can profoundly affect the virulence properties of the community. In this study we investigated how the production of gingipains, virulence factors from Porphyromonas gingivalis important in periodontal disease, was affected by other commonly found members of the sub-gingival microbiome. To mimic the subgingival microbiome, multispecies consortia (P. gingivalis, Fusobacterium nucleatum, Actinomyces naeslundii, Streptococus oralis, Streptococcus mitis, Streptococcus gordonii and Streptococcus cristatus, with or without Parvimonas micra) as well as dual species consortia (P. gingivalis with P. micra, S. oralis or F. nucleatum) were constructed and maintained anaerobically in 10% serum for up to seven days. The number of P. gingivalis was determined by plating on Brucella agar and the gingipain specific fluorogenic substrate BikKam-10 was used to investigate gingipain activity. The effect of secreted products from P. micra on gingipain activity was investigated by adding supernatants from P. micra to P. gingivalis cultures. The most prominent secreted proteins in the supernatant were identified using mass spectrometry. P. gingivalis was unable to grow in serum, either alone or in the presence of S. oralis or F. nucleatum. In contrast, with P. micra growth was significantly enhanced and this was associated with an increase in gingipain activity. In the multi-species consortia, the presence of P. micra caused a 13-fold increase in gingipain activity. Exposure of P. gingivalis to supernatants from P. micra for 24 hours caused a 3-fold increase in gingipain activity. This effect was reduced by 43% after heat-treatment of the supernatant. Two dimensional gel electrophoresis revealed that several of the most prominent proteins in the P. micra supernatant were glycolytic enzymes. The results from this study suggests that gingipains are produced in response to a P. micra derived signaling molecule that is most likely a protein. This is the first time it has been shown that P. micra can affect P. gingivalis virulence properties. This is likely to be of significance for the development of be of periodontitis since these two microorganisms are often found together in the subgingival biofilm.},
}
@article {pmid30359683,
year = {2018},
author = {Kennedy, K and Heimall, J and Spergel, JM},
title = {Advances in Atopic Dermatitis in 2017.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2018.10.012},
pmid = {30359683},
issn = {1097-6825},
abstract = {This review encompasses relevant scientific and clinical advances in atopic dermatitis published in 2017. These include articles from the Journal as well as other prominent publications that have contributed to the emerging field of the microenvironment of the skin and molecular patterns guiding biologic treatment strategies. The most commonly questioned and explored themes of the year included the impact of the microbiome on atopic dermatitis development as well as cell signaling and severity of symptoms. Topics also included the description of patient specific molecular endotypes within the larger atopic dermatitis population. All of these factors will create potential opportunities to guide personalized therapy with the broadening array of topical and systemic interventions currently available, as well as provide new insights to guide development of novel, molecularly targeted therapeutics. With recent FDA approval of the first wave of new, targeted therapies for atopic dermatitis (AD), additional information exploring the safety profiles and long-term effects of these medications was also at the forefront of 2017.},
}
@article {pmid30359185,
year = {2018},
author = {Skye, SM and Zhu, W and Romano, KA and Guo, CJ and Wang, Z and Jia, X and Kirsop, J and Haag, B and Lang, JM and DiDonato, JA and Tang, WHW and Lusis, AJ and Rey, FE and Fischbach, MA and Hazen, SL},
title = {Microbial Transplantation With Human Gut Commensals Containing CutC Is Sufficient to Transmit Enhanced Platelet Reactivity and Thrombosis Potential.},
journal = {Circulation research},
volume = {123},
number = {10},
pages = {1164-1176},
doi = {10.1161/CIRCRESAHA.118.313142},
pmid = {30359185},
issn = {1524-4571},
abstract = {RATIONALE: Gut microbes influence cardiovascular disease and thrombosis risks through the production of trimethylamine N-oxide (TMAO). Microbiota-dependent generation of trimethylamine (TMA)-the precursor to TMAO-is rate limiting in the metaorganismal TMAO pathway in most humans and is catalyzed by several distinct microbial choline TMA-lyases, including the proteins encoded by the cutC/D (choline utilization C/D) genes in multiple human commensals.<br><br>OBJECTIVE: Direct demonstration that the gut microbial cutC gene is sufficient to transmit enhanced platelet reactivity and thrombosis potential in a host via TMA/TMAO generation has not yet been reported.<br><br>METHODS AND RESULTS: Herein, we use gnotobiotic mice and a series of microbial colonization studies to show that microbial cutC-dependent TMA/TMAO production is sufficient to transmit heightened platelet reactivity and thrombosis potential in a host. Specifically, we examine in vivo thrombosis potential employing germ-free mice colonized with either high TMA-producing stable human fecal polymcrobial communities or a defined CutC-deficient background microbial community coupled with a CutC-expressing human commensal±genetic disruption of its cutC gene (ie, Clostridium sporogenes Δ cutC).<br><br>CONCLUSIONS: Collectively, these studies point to the microbial choline TMA-lyase pathway as a rational molecular target for the treatment of atherothrombotic heart disease.},
}
@article {pmid30359170,
year = {2018},
author = {Graves, DT and Corrêa, JD and Silva, TA},
title = {The Oral Microbiota Is Modified by Systemic Diseases.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {22034518805739},
doi = {10.1177/0022034518805739},
pmid = {30359170},
issn = {1544-0591},
abstract = {Periodontal diseases are initiated by bacteria that accumulate in a biofilm on the tooth surface and affect the adjacent periodontal tissue. Systemic diseases such as diabetes, rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE) increase susceptibility to destructive periodontal diseases. In human studies and in animal models, these diseases have been shown to enhance inflammation in the periodontium and increase the risk or severity of periodontitis. All 3 systemic diseases are linked to a decrease in bacterial taxa associated with health and an increase in taxa associated with disease. Although there is controversy regarding the specific oral bacterial changes associated with each disease, it has been reported that diabetes increases the levels of Capnocytophaga, Porphyromonas, and Pseudomonas, while Prevotella and Selenomonas are increased in RA and Selenomonas, Leptotrichia, and Prevotella in SLE. In an animal model, diabetes increased the pathogenicity of the oral microbiome, as shown by increased inflammation, osteoclastogenesis, and periodontal bone loss when transferred to normal germ-free hosts. Moreover, in diabetic animals, the increased pathogenicity could be substantially reversed by inhibition of IL-17, indicating that host inflammation altered the microbial pathogenicity. Increased IL-17 has also been shown in SLE, RA, and leukocyte adhesion deficiency and may contribute to oral microbial changes in these diseases. Successful RA treatment with anti-inflammatory drugs partially reverses the oral microbial dysbiosis. Together, these data demonstrate that systemic diseases characterized by enhanced inflammation disturb the oral microbiota and point to IL-17 as key mediator in this process.},
}
@article {pmid30358937,
year = {2018},
author = {Kim, AS and Willis, AL and Laubitz, D and Sharma, S and Song, BH and Chiu, AG and Le, CH and Chang, EH},
title = {The effect of maxillary sinus antrostomy size on the sinus microbiome.},
journal = {International forum of allergy &amp; rhinology},
volume = {},
number = {},
pages = {},
doi = {10.1002/alr.22224},
pmid = {30358937},
issn = {2042-6984},
support = {(ACCRFA16040002-1//Acclarent, Inc./ ; },
abstract = {BACKGROUND: The optimal maxillary antrostomy size to surgically treat sinusitis is not well known. In this study, we examined clinical metrics of disease severity and symptom scores, measured secreted inflammatory markers, and characterized the sinus microbiome to determine if there were significant differences in outcome between different maxillary ostial sizes.<br><br>METHODS: Prospective randomized, single-blinded clinical trial enrolling 12 individuals diagnosed with recurrent acute or chronic rhinosinusitis. Each patient was blinded and randomized to receive minimal maxillary ostial dilation via balloon sinuplasty on 1 side vs a mega-antrostomy on the contralateral side. Data collected included symptom scores (20-item Sino-Nasal Outcome Test [SNOT-20]), endoscopy, and radiologic Lund-Mackay scores. During surgery and at their postoperative visit swabs were obtained from each maxillary sinus, and 16S DNA and inflammatory cytokine levels analyzed. The use of each patient as their own control allowed us to minimize confounding variables.<br><br>RESULTS: There was statistically significant improvement in SNOT-20 symptom scores postoperatively in all patients. There were no significant differences between maxillary ostial size in postoperative endoscopy scores, cytokine profile, or bacterial burden. There were statistically significant differences in relative postoperative abundance of Staphylococcus, Lactococcus, and Cyanobacteria between the mega-antrostomy and mini-antrostomy.<br><br>CONCLUSIONS: The method used in surgical maxillary antrostomies had no effect on endoscopy scores or cytokine profiles. Microbiome analysis determined significant differences between the different antrostomy sizes in postoperative Staphylococcus, Lactococcus, and Cyanobacteria abundance. The clinical significance of these changes in the sinus microbiome are not known but may be a result of increased access to postoperative sinonasal irrigations.},
}
@article {pmid30358831,
year = {2018},
author = {Rodriguez-Mateos, A and Weber, T and Skene, SS and Ottaviani, JI and Crozier, A and Kelm, M and Schroeter, H and Heiss, C},
title = {Assessing the respective contributions of dietary flavanol monomers and procyanidins in mediating cardiovascular effects in humans: randomized, controlled, double-masked intervention trial.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajcn/nqy229},
pmid = {30358831},
issn = {1938-3207},
abstract = {Background: Flavanols are an important class of food bioactives that can improve vascular function even in healthy subjects. Cocoa flavanols (CFs) are composed principally of the monomer (-)-epicatechin (∼20%), with a degree of polymerisation (DP) of 1 (DP1), and oligomeric procyanidins (∼80%, DP2-10).<br><br>Objective: Our objective was to investigate the relative contribution of procyanidins and (-)-epicatechin to CF intake-related improvements in vascular function in healthy volunteers.<br><br>Design: In a randomized, controlled, double-masked, parallel-group dietary intervention trial, 45 healthy men (aged 18-35 y) consumed the following once daily for 1 mo: 1) a DP1-10 cocoa extract containing 130 mg (-)-epicatechin and 560 mg procyanidins, 2) a DP2-10 cocoa extract containing 20 mg (-)-epicatechin and 540 mg procyanidins, or 3) a control capsule, which was flavanol-free but had identical micro- and macronutrient composition.<br><br>Results: Consumption of DP1-10, but not of either DP2-10 or the control capsule, significantly increased flow-mediated vasodilation (primary endpoint) and the concentration of structurally related (-)-epicatechin metabolites (SREMs) in the circulatory system while decreasing pulse wave velocity and blood pressure. Total cholesterol significantly decreased after daily intake of both DP1-10 and DP2-10 as compared with the control.<br><br>Conclusions: CF-related improvements in vascular function are predominantly related to the intake of flavanol monomers and circulating SREMs in healthy humans but not to the more abundant procyanidins and gut microbiome-derived CF catabolites. Reduction in total cholesterol was linked to consumption of procyanidins but not necessarily to that of (-)-epicatechin. This trial was registered at clinicaltrials.gov as NCT02728466.},
}
@article {pmid30357573,
year = {2018},
author = {Hassell, JE and Nguyen, KT and Gates, CA and Lowry, CA},
title = {The Impact of Stressor Exposure and Glucocorticoids on Anxiety and Fear.},
journal = {Current topics in behavioral neurosciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/7854_2018_63},
pmid = {30357573},
issn = {1866-3370},
abstract = {Anxiety disorders and trauma- and stressor-related disorders, such as posttraumatic stress disorder (PTSD), are common and are associated with significant economic and social burdens. Although trauma and stressor exposure are recognized as a risk factors for development of anxiety disorders and trauma or stressor exposure is recognized as essential for diagnosis of PTSD, the mechanisms through which trauma and stressor exposure lead to these disorders are not well characterized. An improved understanding of the mechanisms through which trauma or stressor exposure leads to development and persistence of anxiety disorders or PTSD may result in novel therapeutic approaches for the treatment of these disorders. Here, we review the current state-of-the-art theories, with respect to mechanisms through which stressor exposure leads to acute or chronic exaggeration of avoidance or anxiety-like defensive behavioral responses and fear, endophenotypes in both anxiety disorders and trauma- and stressor-related psychiatric disorders. In this chapter, we will explore physiological responses and neural circuits involved in the development of acute and chronic exaggeration of anxiety-like defensive behavioral responses and fear states, focusing on the role of the hypothalamic-pituitary-adrenal (HPA) axis and glucocorticoid hormones.},
}
@article {pmid30357543,
year = {2018},
author = {Chi, L and Xue, J and Tu, P and Lai, Y and Ru, H and Lu, K},
title = {Gut microbiome disruption altered the biotransformation and liver toxicity of arsenic in mice.},
journal = {Archives of toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00204-018-2332-7},
pmid = {30357543},
issn = {1432-0738},
support = {R01ES024950//National Institutes of Health/ ; },
abstract = {The mammalian gut microbiome (GM) plays a critical role in xenobiotic biotransformation and can profoundly affect the toxic effects of xenobiotics. Previous in vitro studies have demonstrated that gut bacteria have the capability to metabolize arsenic (As); however, the specific roles of the gut microbiota in As metabolism in vivo and the toxic effects of As are largely unknown. Here, we administered sodium arsenite to conventionally raised mice (with normal microbiomes) and GM-disrupted mice with antibiotics to investigate the role of the gut microbiota in As biotransformation and its toxicity. We found that the urinary total As levels of GM-disrupted mice were much higher, but the fecal total As levels were lower, than the levels in the conventionally raised mice. In vitro experiments, in which the GM was incubated with As, also demonstrated that the gut bacteria could adsorb or take up As and thus reduce the free As levels in the culture medium. With the disruption of the gut microbiota, arsenic biotransformation was significantly perturbed. Of note, the urinary monomethylarsonic acid/dimethylarsinic acid ratio, a biomarker of arsenic metabolism and toxicity, was markedly increased. Meanwhile, the expression of genes of one-carbon metabolism, including folr2, bhmt, and mthfr, was downregulated, and the liver S-adenosylmethionine (SAM) levels were significantly decreased in the As-treated GM-disrupted mice only. Moreover, As exposure altered the expression of genes of the p53 signaling pathway, and the expression of multiple genes associated with hepatocellular carcinoma (HCC) was also changed in the As-treated GM-disrupted mice only. Collectively, disruption of the GM enhances the effect of As on one-carbon metabolism, which could in turn affect As biotransformation. GM disruption also increases the toxic effects of As and may increase the risk of As-induced HCC in mice.},
}
@article {pmid30356925,
year = {2018},
author = {Espinoza, JL and Wadasaki, Y and Takami, A},
title = {Infection Complications in Hematopoietic Stem Cells Transplant Recipients: Do Genetics Really Matter?.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2317},
doi = {10.3389/fmicb.2018.02317},
pmid = {30356925},
issn = {1664-302X},
abstract = {Hematopoietic stem cell transplantation (HSCT) is a highly advanced technique that offers a potential cure for an increasing number of life-threatening diseases. Enormous progress achieved in the last decade, including the refinement of donor selection and advancements in patient supportive care, had significantly improved transplant outcomes; however, invasive infections, graft-vs.-host disease (GVHD) and other serious complications still represent a major source of morbidity and mortality in HSCT recipients. The damage of anatomical barriers due to pre-transplant conditioning, a severely damaged immune function and a profound disruption in the composition of gut microbial commensals (gut microbiota) are alterations inherent to the transplant procedure that are directly implicated in the development of invasive infections and other HSCT complications. Although HLA-matching represents the most important genetic predictor of transplant outcomes, genetic variants in non-HLA genes, especially single nucleotide polymorphisms (SNPs) of genes encoding proteins associated with the immune response to tissue injury and pathogen infection have also been proposed as additional risk factors implicated in the occurrence of HSCT complications. Furthermore, although the microbiota composition is affected by several factors, recent evidence suggests that certain host genetic variants are associated with an altered composition of the gut microbiome and may, therefore, predispose some individuals to invasive infectious complications. This article summarizes the current understanding of the influence that genetic variants in non-HLA genes have on the development of infectious complications in HSCT recipients.},
}
@article {pmid30356893,
year = {2018},
author = {Lazuka, A and Auer, L and O'Donohue, M and Hernandez-Raquet, G},
title = {Anaerobic lignocellulolytic microbial consortium derived from termite gut: enrichment, lignocellulose degradation and community dynamics.},
journal = {Biotechnology for biofuels},
volume = {11},
number = {},
pages = {284},
doi = {10.1186/s13068-018-1282-x},
pmid = {30356893},
issn = {1754-6834},
abstract = {Background: Lignocellulose is the most abundant renewable carbon resource that can be used for biofuels and commodity chemicals production. The ability of complex microbial communities present in natural environments that are specialized in biomass deconstruction can be exploited to develop lignocellulose bioconversion processes. Termites are among the most abundant insects on earth and play an important role in lignocellulose decomposition. Although their digestive microbiome is recognized as a potential reservoir of microorganisms producing lignocellulolytic enzymes, the potential to enrich and maintain the lignocellulolytic activity of microbial consortia derived from termite gut useful for lignocellulose biorefinery has not been assessed. Here, we assessed the possibility of enriching a microbial consortium from termite gut and maintaining its lignocellulose degradation ability in controlled anaerobic bioreactors.<br><br>Results: We enriched a termite gut-derived consortium able to transform lignocellulose into carboxylates under anaerobic conditions. To assess the impact of substrate natural microbiome on the enrichment and the maintenance of termite gut microbiome, the enrichment process was performed using both sterilized and non-sterilized straw. The enrichment process was carried out in bioreactors operating under industrially relevant aseptic conditions. Two termite gut-derived microbial consortia were obtained from Nasutitermes ephratae by sequential batch culture on raw wheat straw as the sole carbon source. Analysis of substrate loss, carboxylate production and microbial diversity showed that regardless of the substrate sterility, the diversity of communities selected by the enrichment process strongly changed compared to that observed in the termite gut. Nevertheless, the community obtained on sterile straw displayed higher lignocellulose degradation capacity; it showed a high xylanase activity and an initial preference for hemicellulose.<br><br>Conclusions: This study demonstrates that it is possible to enrich and maintain a microbial consortium derived from termite gut microbiome in controlled anaerobic bioreactors, producing useful carboxylates from raw biomass. Our results suggest that the microbial community is shaped both by the substrate and the conditions that prevail during enrichment. However, when aseptic conditions are applied, it is also affected by the biotic pressure exerted by microorganisms naturally present in the substrate and in the surrounding environment. Besides the efficient lignocellulolytic consortium enriched in this study, our results revealed high levels of xylanase activity that can now be further explored for enzyme identification and overexpression for biorefinery purposes.},
}
@article {pmid30356851,
year = {2018},
author = {Galloway-Peña, J and Guindani, M},
title = {Editorial: Novel Approaches in Microbiome Analyses and Data Visualization.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2274},
doi = {10.3389/fmicb.2018.02274},
pmid = {30356851},
issn = {1664-302X},
}
@article {pmid30356788,
year = {2018},
author = {Prazeres, M},
title = {Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2404},
doi = {10.3389/fmicb.2018.02404},
pmid = {30356788},
issn = {1664-302X},
abstract = {Ocean warming is known to cause detrimental effects in coral reef fauna that rely on photo-symbiosis for survival. Microbial associations can facilitate the success of species across a range of environmental conditions, and play a role in the capacity of organisms to respond to climate change. In 2016, the Great Barrier Reef experienced its third mass bleaching event, with sea surface temperature rising to 1.3°C above long-term monthly summer averages. Here, I investigate the effects of ocean warming on the chlorophyll a (chl a) content and microbiome of the large benthic Foraminifera Amphistegina radiata. Samples were collected in January and April 2016, before and after the mass bleaching event. In total, 71 specimens were collected from two different depths (6- and 18-m) to investigate depth-dependant responses associated with changes in chl a and microbiome. Pigment analysis showed a significant reduction in chl a between time points in specimens collected at both depths. Reduction in pigmentation was accompanied by changes in the microbiome, and a significant interaction of depth and time was observed. Genus-level bacterial community associated with A. radiata was significantly different across depth and time. However, ocean warming affected populations at both depths to a similar extent, and resulted in change from a Betaproteobacteria-dominated assemblage in January to a more diverse bacterial community by April. Analysis of presence/absence and relative abundance of bacterial taxa revealed significant differences between time points at both depths analyzed. OTUs classified as Firmicutes, which were either absent, or present in very low relative abundances (<0.1%) across all sample groups in January, were identified in abundances as high as ∼20% in specimens collected from 18-m depth in April. Class-level shifts were observed in shallow-dwelling specimens, from high abundances of Betaproteobacteria to a high abundance and diversity of Actinobacteria. These results demonstrate the sensitivity of LBF to the effects of ocean warming, for which depth did not provide protection, and highlights the capacity of LBF to re-assemble bacterial communities after a disturbance. This study provides the first molecular-based demonstration of changes in foraminifera-associated bacterial assemblages during a bleaching event on a natural reef system.},
}
@article {pmid30356779,
year = {2018},
author = {Bouillaguet, S and Manoil, D and Girard, M and Louis, J and Gaïa, N and Leo, S and Schrenzel, J and Lazarevic, V},
title = {Root Microbiota in Primary and Secondary Apical Periodontitis.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2374},
doi = {10.3389/fmicb.2018.02374},
pmid = {30356779},
issn = {1664-302X},
abstract = {Apical periodontitis is an inflammatory disease of the dental periradicular tissues triggered by bacteria colonizing necrotic root canals. Primary apical periodontitis results from the microbial colonization of necrotic pulp tissues. Secondary apical periodontitis results from a persistent infection of incorrectly treated root canals. The aim of this study was to characterize the microbiota present in primary and secondary intraradicular infections associated with apical periodontitis using 16S rRNA gene amplicon sequencing. Teeth exhibiting apical periodontitis with or without root canal treatment were extracted after informed consent. From each tooth, the intraradicular content as well as a dentin sample (control) were collected and subjected to DNA extraction. PCR amplicons of the V3-V4 region of the bacterial 16S rRNA gene were pooled and sequenced (2 × 300) on an Illumina MiSeq instrument. The bioinformatics analysis pipeline included quality filtering, merging of forward and reverse reads, clustering of reads into operational taxonomic units (OTUs), removal of putative contaminant OTUs and assigning taxonomy. The most prevalent and abundant OTU in both dentin and root canal samples was assigned to anaerobic bacterium Fusobacterium nucleatum. Multivariate analysis showed clustering of microbiota by sample type (dentin vs. intraradicular content) and, in root canals, by pathology (primary vs. secondary infection). The proportions of Enterococcus faecalis and F. nucleatum were, respectively, higher and lower when comparing secondary to primary infected root canals. Co-occurrence network analysis provided evidence of microbial interactions specific to the infection type. The identification of bacterial taxa differentially abundant in primary and secondary intraradicular infections may provide the basis for targeted therapeutic approaches aimed at reducing the incidence of apical periodontitis.},
}
@article {pmid30356776,
year = {2018},
author = {Metzger, SA and Hernandez, LL and Skarlupka, JH and Walker, TM and Suen, G and Ruegg, PL},
title = {A Cohort Study of the Milk Microbiota of Healthy and Inflamed Bovine Mammary Glands From Dryoff Through 150 Days in Milk.},
journal = {Frontiers in veterinary science},
volume = {5},
number = {},
pages = {247},
doi = {10.3389/fvets.2018.00247},
pmid = {30356776},
issn = {2297-1769},
abstract = {The objective of this longitudinal cohort study was to describe the milk microbiota of dairy cow mammary glands based on inflammation status before and after the dry period. Individual mammary quarters were assigned to cohorts based on culture results and somatic cell count (SCC) at dryoff and twice in the first 2 weeks post-calving. Mammary glands that were microbiologically negative and had low SCC (< 100,000 cells/mL) at all 3 sampling periods were classified as Healthy (n = 80). Microbiologically negative mammary glands that had SCC ≥150,000 cells/mL at dryoff and the first post-calving sample were classified as Chronic Culture-Negative Inflammation (CHRON; n = 17). Quarters that did not have both culture-negative milk and SCC ≥ 150,000 cells/mL at dryoff but were culture-negative with SCC ≥ 150,000 at both post-calving sampling periods were classified as Culture-Negative New Inflammation (NEWINF; n = 6). Mammary glands with bacterial growth and SCC ≥ 150,000 cells/mL at all 3 periods were classified as Positive (POS; n = 3). Milk samples were collected from all enrolled quarters until 150 days in milk and subjected to microbiota analysis. Milk samples underwent total DNA extraction, a 40-cycle PCR to amplify the V4 region of the bacterial 16S rRNA gene, and next-generation sequencing. Healthy quarters had the lowest rate of PCR and sequencing success (53, 67, 83, and 67% for Healthy, CHRON, NEWINF, and POS, respectively). Chao richness was greatest in milk collected from Healthy quarters and Shannon diversity was greater in milk from Healthy and CHRON quarters than in milk collected from glands in the NEWINF or POS cohorts. Regardless of cohort, season was associated with both richness and diversity, but stage of lactation was not. The most prevalent OTUs included typical gut- and skin-associated bacteria such as those in the phylum Bacteroidetes and the genera Enhydrobacter and Corynebacterium. The increased sequencing success in quarters with worse health outcomes, combined with the lack of bacterial growth in most samples and the high PCR cycle number required for amplification of bacterial DNA, suggests that the milk microbiota of culture-negative, healthy mammary glands is less abundant than that of culture-negative glands with a history of inflammation.},
}
@article {pmid30356740,
year = {2018},
author = {Xu, Q and Gu, S and Chen, Y and Quan, J and Lv, L and Chen, D and Zheng, B and Xu, L and Li, L},
title = {Protective Effect of Pediococcus pentosaceus LI05 Against Clostridium difficile Infection in a Mouse Model.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2396},
doi = {10.3389/fmicb.2018.02396},
pmid = {30356740},
issn = {1664-302X},
abstract = {Clostridium difficile infection (CDI) is a major cause of infectious diarrhea among hospitalized patients. Probiotics could be instrumental in restoring the intestinal dysbiosis caused by CDI. Here, we examined the protective effect of Pediococcus pentosaceus LI05 in a mouse CDI model. C57BL/6 mice were administrated P. pentosaceus LI05 (LI05 group) or sterile anaerobic PBS (CDI group) everyday for 14 days. Mice were exposed to antibiotics cocktail for 5 days; then challenged with C. difficile strain VPI10463. Mice were monitored daily for survival and weight loss. Colonic tissue and serum samples were assessed for intestinal histopathology, intestinal barrier function and systemic inflammation. The oral administration of P. pentosaceus LI05 improved the survival rate and alleviated the histopathological impact of C. difficile. Compared to the CDI group, the levels of inflammatory mediators in the colon as well as inflammatory cytokines and chemokines in serum were substantially attenuated in the LI05 group. P. pentosaceus LI05 alleviated the CDI-induced of disruption of ZO-1, occludin and claudin-1. Additionally, fecal microbiome analysis showed an enrichment in the abundance of the Porphyromonadaceae and Rikenellaceae, while, the relative abundance of Enterobacteriaceae were decreased. Our results demonstrated that the preventive effect of P. pentosaceus LI05 against CDI was mediated via improving tight junction proteins and down-regulating the inflammatory response. Therefore, P. pentosaceus LI05 could be a promising probiotic in CDI.},
}
@article {pmid30356736,
year = {2018},
author = {Vitetta, L and Vitetta, G and Hall, S},
title = {Immunological Tolerance and Function: Associations Between Intestinal Bacteria, Probiotics, Prebiotics, and Phages.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2240},
doi = {10.3389/fimmu.2018.02240},
pmid = {30356736},
issn = {1664-3224},
abstract = {Post-birth there is a bacterial assault on all mucosal surfaces. The intestinal microbiome is an important participant in health and disease. The pattern of composition and concentration of the intestinal microbiome varies greatly. Therefore, achieving immunological tolerance in the first 3-4 years of life is critical for maintaining health throughout a lifetime. Probiotic bacteria are organisms that afford beneficial health effects to the host and in certain instances may protect against the development of disease. The potential benefits of modifying the composition of the intestinal microbial cohort for therapeutic benefit is evident in the use in high risks groups such as premature infants, children receiving antibiotics, rotavirus infections in non-vaccinated children and traveler's diarrhea in adults. Probiotics and prebiotics are postulated to have immunomodulating capabilities by influencing the intestinal microbial cohort and dampening the activity of pathobiont intestinal microbes, such as Klebsiella pneumonia and Clostridia perfringens. Lactobacilli and Bifidobacteria are examples of probiotics found in the large intestine and so far, the benefits afforded to probiotics have varied in efficacy. Most likely the efficacy of probiotic bacteria has a multifactorial dependency, namely on a number of factors that include agents used, the dose, the pattern of dosing, and the characteristics of the host and the underlying luminal microbial environment and the activity of bacteriophages. Bacteriophages, are small viruses that infect and lyse intestinal bacteria. As such it can be posited that these viruses display an effective local protective control mechanism for the intestinal barrier against commensal pathobionts that indirectly may assist the host in controlling bacterial concentrations in the gut. A co-operative activity may be envisaged between the intestinal epithelia, mucosal immunity and the activity of bacteriophages to eliminate pathobiots, highlighting the potential role of bacteriophages in assisting with maintaining intestinal homeostasis. Hence bacteriophage local control of inflammation and immune responses may be an additional immunological defense mechanism that exploits bacteriophage-mucin glycoprotein interactions that controls bacterial diversity and abundance in the mucin layers of the gut. Moreover, and importantly the efficacy of probiotics may be dependent on the symbiotic incorporation of prebiotics, and the abundance and diversity of the intestinal microbiome encountered. The virome may be an important factor that determines the efficacy of some probiotic formulations.},
}
@article {pmid30356690,
year = {2018},
author = {Abecia, L and Martínez-Fernandez, G and Waddams, K and Martín-García, AI and Pinloche, E and Creevey, CJ and Denman, SE and Newbold, CJ and Yáñez-Ruiz, DR},
title = {Analysis of the Rumen Microbiome and Metabolome to Study the Effect of an Antimethanogenic Treatment Applied in Early Life of Kid Goats.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2227},
doi = {10.3389/fmicb.2018.02227},
pmid = {30356690},
issn = {1664-302X},
abstract = {This work aimed to gain insight into the transition from milk to solid feeding at weaning combining genomics and metabolomics on rumen contents from goat kids treated with a methanogenic inhibitor (bromochloromethane, BCM). Sixteen goats giving birth to two kids were used. Eight does were treated (D+) with BCM after giving birth and over 2 months. One kid per doe in both groups was treated with BCM (k+) for 3 months while the other was untreated (k-). Rumen samples were collected from kids at weaning (W) and 1 (W + 1) and 4 (W + 4) months after and from does at weaning and subjected to 16S pyrosequencing and metabolomics analyses combining GC/LC-MS. Results from pyrosequencing showed a clear effect of age of kids, with more diverse bacterial community as solid feed becomes more important after weaning. A number of specific OTUs were significantly different as a result of BCM treatment of the kid at W while at W + 1 and W + 4 less OTUs were significantly changed. At W + 1, Prevotella was increased and Butyrivibrio decreased in BCM treated kids. At W + 4 only the effect of treating mothers resulted in significant changes in the abundance of some OTUs: Ruminococcus, Butyrivibrio and Prevotella. The analysis of the OTUs shared by different treatments revealed that kids at weaning had the largest number of unique OTUs compared with kids at W + 1 (137), W + 4 (238), and does (D) (23). D + k+ kids consistently shared more OTUs with mothers than the other three groups at the three sampling times. The metalobomic study identified 473 different metabolites. In does, lipid super pathway included the highest number of metabolites that were modified by BCM, while in kids all super-pathways were evenly affected. The metabolomic profile of samples from kids at W was different in composition as compared to W + 1 and W + 4, which may be directly ascribed to the process of rumen maturation and changes in the solid diet. This study shows the complexity of the bacterial community and metabolome in the rumen before weaning, which clearly differ from that after weaning and highlight the importance of the dam in transmitting the primary bacterial community after birth.},
}
@article {pmid30356676,
year = {2018},
author = {Balan, P and Chong, YS and Umashankar, S and Swarup, S and Loke, WM and Lopez, V and He, HG and Seneviratne, CJ},
title = {Keystone Species in Pregnancy Gingivitis: A Snapshot of Oral Microbiome During Pregnancy and Postpartum Period.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2360},
doi = {10.3389/fmicb.2018.02360},
pmid = {30356676},
issn = {1664-302X},
abstract = {It is well known that pregnancy is under the constant influence of hormonal, metabolic and immunological factors and this may impact the oral microbiota toward pregnancy gingivitis. However, it is still not clear how the oral microbial dysbiosis can modulate oral diseases as oral microbiome during pregnancy is very poorly characterized. In addition, the recent revelation that placental microbiome is akin to oral microbiome further potentiates the importance of oral dysbiosis in adverse pregnancy outcomes. Hence, leveraging on the 16S rRNA gene sequencing technology, we present a snapshot of the variations in the oral microbial composition with the progression of pregnancy and in the postpartum period and its association with pregnancy gingivitis. Despite the stability of oral microbial diversity during pregnancy and postpartum period, we observed that the microbiome makes a pathogenic shift during pregnancy and reverts back to a healthy microbiome during the postpartum period. Co-occurrence network analysis provided a mechanistic explanation of the pathogenicity of the microbiome during pregnancy and predicted taxa at hubs of interaction. Targeting the taxa which form the ecological guilds in the underlying microbiome would help to modulate the microbial pathogenicity during pregnancy, thereby alleviating risk for oral diseases and adverse pregnancy outcomes. Our study has also uncovered the possibility of novel species in subgingival plaque and saliva as the key players in the causation of pregnancy gingivitis. The keystone species hold the potential to open up avenues for designing microbiome modulation strategies to improve host health during pregnancy.},
}
@article {pmid30356313,
year = {2018},
author = {Huebinger, RM and Smith, AD and Zhang, Y and Monson, NL and Ireland, SJ and Barber, RC and Kubasiak, JC and Minshall, CT and Minei, JP and Wolf, SE and Allen, MS},
title = {Variations of the lung microbiome and immune response in mechanically ventilated surgical patients.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0205788},
doi = {10.1371/journal.pone.0205788},
pmid = {30356313},
issn = {1932-6203},
abstract = {Mechanically ventilated surgical patients have a variety of bacterial flora that are often undetectable by traditional culture methods. The source of infection in many of these patients remains unclear. To address this clinical problem, the microbiome profile and host inflammatory response in bronchoalveolar lavage samples from the surgical intensive care unit were examined relative to clinical pathology diagnoses. The hypothesis was tested that clinical diagnosis of respiratory tract flora were similar to culture positive lavage samples in both microbiome and inflammatory profile. Bronchoalveolar lavage samples were collected in the surgical intensive care unit as standard of care for intubated individuals with a clinical pulmonary infection score of >6 or who were expected to be intubated for >48 hours. Cytokine analysis was conducted with the Bioplex Pro Human Th17 cytokine panel. The microbiome of the samples was sequenced for the 16S rRNA region using the Ion Torrent. Microbiome diversity analysis showed the culture-positive samples had the lowest levels of diversity and culture negative with the highest based upon the Shannon-Wiener index (culture positive: 0.77 ± 0.36, respiratory tract flora: 2.06 ± 0.73, culture negative: 3.97 ± 0.65). Culture-negative samples were not dominated by a single bacterial genera. Lavages classified as respiratory tract flora were more similar to the culture-positive in the microbiome profile. A comparison of cytokine expression between groups showed increased levels of cytokines (IFN-g, IL-17F, IL-1B, IL-31, TNF-a) in culture-positive and respiratory tract flora groups. Culture-positive samples exhibited a more robust immune response and reduced diversity of bacterial genera. Lower cytokine levels in culture-negative samples, despite a greater number of bacterial species, suggest a resident nonpathogenic bacterial community may be indicative of a normal pulmonary environment. Respiratory tract flora samples were most similar to the culture-positive samples and may warrant classification as culture-positive when considering clinical treatment.},
}
@article {pmid30356246,
year = {2018},
author = {Cremonesi, P and Ceccarani, C and Curone, G and Severgnini, M and Pollera, C and Bronzo, V and Riva, F and Addis, MF and Filipe, J and Amadori, M and Trevisi, E and Vigo, D and Moroni, P and Castiglioni, B},
title = {Milk microbiome diversity and bacterial group prevalence in a comparison between healthy Holstein Friesian and Rendena cows.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0205054},
doi = {10.1371/journal.pone.0205054},
pmid = {30356246},
issn = {1932-6203},
abstract = {Dry and early lactation periods represent the most critical phases for udder health in cattle, especially in highly productive breeds, such as the Holstein Friesian (HF). On the other hand, some autochthonous cattle breeds, such as the Rendena (REN), have a lower prevalence of mastitis and other transition-related diseases. In this study, milk microbiota of 6 HF and 3 REN cows, all raised on the same farm under the same conditions, was compared. A special focus was placed on the transition period to define bacterial groups' prevalence with a plausible effect on mammary gland health. Four time points (dry-off, 1 d, 7-10 d and 30 d after calving) were considered. Through 16S rRNA sequencing, we characterized the microbiota composition for 117 out of the 144 milk samples initially collected, keeping only the healthy quarters, in order to focus on physiological microbiome changes and avoid shifts due to suspected diseases. Microbial populations were very different in the two breeds along all the time points, with REN milk showing a significantly lower microbial biodiversity. The taxonomic profiles of both cosmopolitan and local breeds were dominated by Firmicutes, mostly represented by the Streptococcus genus, although in very different proportions (HF 27.5%, REN 68.6%). Large differences in HF and REN cows were, also, evident from the metabolic predictive analysis from microbiome data. Finally, only HF milk displayed significant changes in the microbial composition along the transition period, while REN maintained a more stable microbiota. In conclusion, in addition to the influence on the final characteristics of dairy products obtained from milk of the two breeds, differences in the milk microbiome might, also, have an impact on their mammary gland health.},
}
@article {pmid30356215,
year = {2018},
author = {Schretter, CE and Vielmetter, J and Bartos, I and Marka, Z and Marka, S and Argade, S and Mazmanian, SK},
title = {A gut microbial factor modulates locomotor behaviour in Drosophila.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-018-0634-9},
pmid = {30356215},
issn = {1476-4687},
abstract = {While research into the biology of animal behaviour has primarily focused on the central nervous system, cues from peripheral tissues and the environment have been implicated in brain development and function1. There is emerging evidence that bidirectional communication between the gut and the brain affects behaviours including anxiety, cognition, nociception and social interaction1-9. Coordinated locomotor behaviour is critical for the survival and propagation of animals, and is regulated by internal and external sensory inputs10,11. However, little is known about how the gut microbiome influences host locomotion, or the molecular and cellular mechanisms involved. Here we report that germ-free status or antibiotic treatment results in hyperactive locomotor behaviour in the fruit fly Drosophila melanogaster. Increased walking speed and daily activity in the absence of a gut microbiome are rescued by mono-colonization with specific bacteria, including the fly commensal Lactobacillus brevis. The bacterial enzyme xylose isomerase from L. brevis recapitulates the locomotor effects of microbial colonization by modulating sugar metabolism in flies. Notably, thermogenetic activation of octopaminergic neurons or exogenous administration of octopamine, the invertebrate counterpart of noradrenaline, abrogates the effects of xylose isomerase on Drosophila locomotion. These findings reveal a previously unappreciated role for the gut microbiome in modulating locomotion, and identify octopaminergic neurons as mediators of peripheral microbial cues that regulate motor behaviour in animals.},
}
@article {pmid30356187,
year = {2018},
author = {Stewart, CJ and Ajami, NJ and O'Brien, JL and Hutchinson, DS and Smith, DP and Wong, MC and Ross, MC and Lloyd, RE and Doddapaneni, H and Metcalf, GA and Muzny, D and Gibbs, RA and Vatanen, T and Huttenhower, C and Xavier, RJ and Rewers, M and Hagopian, W and Toppari, J and Ziegler, AG and She, JX and Akolkar, B and Lernmark, A and Hyoty, H and Vehik, K and Krischer, JP and Petrosino, JF},
title = {Temporal development of the gut microbiome in early childhood from the TEDDY study.},
journal = {Nature},
volume = {562},
number = {7728},
pages = {583-588},
doi = {10.1038/s41586-018-0617-x},
pmid = {30356187},
issn = {1476-4687},
abstract = {The development of the microbiome from infancy to childhood is dependent on a range of factors, with microbial-immune crosstalk during this time thought to be involved in the pathobiology of later life diseases1-9 such as persistent islet autoimmunity and type 1 diabetes10-12. However, to our knowledge, no studies have performed extensive characterization of the microbiome in early life in a large, multi-centre population. Here we analyse longitudinal stool samples from 903 children between 3 and 46 months of age by 16S rRNA gene sequencing (n = 12,005) and metagenomic sequencing (n = 10,867), as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We show that the developing gut microbiome undergoes three distinct phases of microbiome progression: a developmental phase (months 3-14), a transitional phase (months 15-30), and a stable phase (months 31-46). Receipt of breast milk, either exclusive or partial, was the most significant factor associated with the microbiome structure. Breastfeeding was associated with higher levels of Bifidobacterium species (B. breve and B. bifidum), and the cessation of breast milk resulted in faster maturation of the gut microbiome, as marked by the phylum Firmicutes. Birth mode was also significantly associated with the microbiome during the developmental phase, driven by higher levels of Bacteroides species (particularly B. fragilis) in infants delivered vaginally. Bacteroides was also associated with increased gut diversity and faster maturation, regardless of the birth mode. Environmental factors including geographical location and household exposures (such as siblings and furry pets) also represented important covariates. A nested case-control analysis revealed subtle associations between microbial taxonomy and the development of islet autoimmunity or type 1 diabetes. These data determine the structural and functional assembly of the microbiome in early life and provide a foundation for targeted mechanistic investigation into the consequences of microbial-immune crosstalk for long-term health.},
}
@article {pmid30356183,
year = {2018},
author = {Vatanen, T and Franzosa, EA and Schwager, R and Tripathi, S and Arthur, TD and Vehik, K and Lernmark, Å and Hagopian, WA and Rewers, MJ and She, JX and Toppari, J and Ziegler, AG and Akolkar, B and Krischer, JP and Stewart, CJ and Ajami, NJ and Petrosino, JF and Gevers, D and Lähdesmäki, H and Vlamakis, H and Huttenhower, C and Xavier, RJ},
title = {The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.},
journal = {Nature},
volume = {562},
number = {7728},
pages = {589-594},
doi = {10.1038/s41586-018-0620-2},
pmid = {30356183},
issn = {1476-4687},
abstract = {Type 1 diabetes (T1D) is an autoimmune disease that targets pancreatic islet beta cells and incorporates genetic and environmental factors1, including complex genetic elements2, patient exposures3 and the gut microbiome4. Viral infections5 and broader gut dysbioses6 have been identified as potential causes or contributing factors; however, human studies have not yet identified microbial compositional or functional triggers that are predictive of islet autoimmunity or T1D. Here we analyse 10,913 metagenomes in stool samples from 783 mostly white, non-Hispanic children. The samples were collected monthly from three months of age until the clinical end point (islet autoimmunity or T1D) in the The Environmental Determinants of Diabetes in the Young (TEDDY) study, to characterize the natural history of the early gut microbiome in connection to islet autoimmunity, T1D diagnosis, and other common early life events such as antibiotic treatments and probiotics. The microbiomes of control children contained more genes that were related to fermentation and the biosynthesis of short-chain fatty acids, but these were not consistently associated with particular taxa across geographically diverse clinical centres, suggesting that microbial factors associated with T1D are taxonomically diffuse but functionally more coherent. When we investigated the broader establishment and development of the infant microbiome, both taxonomic and functional profiles were dynamic and highly individualized, and dominated in the first year of life by one of three largely exclusive Bifidobacterium species (B. bifidum, B. breve or B. longum) or by the phylum Proteobacteria. In particular, the strain-specific carriage of genes for the utilization of human milk oligosaccharide within a subset of B. longum was present specifically in breast-fed infants. These analyses of TEDDY gut metagenomes provide, to our knowledge, the largest and most detailed longitudinal functional profile of the developing gut microbiome in relation to islet autoimmunity, T1D and other early childhood events. Together with existing evidence from human cohorts7,8 and a T1D mouse model9, these data support the protective effects of short-chain fatty acids in early-onset human T1D.},
}
@article {pmid30356041,
year = {2018},
author = {Nobel, YR and Snider, EJ and Compres, G and Freedberg, DE and Khiabanian, H and Lightdale, CJ and Toussaint, NC and Abrams, JA},
title = {Increasing Dietary Fiber Intake Is Associated with a Distinct Esophageal Microbiome.},
journal = {Clinical and translational gastroenterology},
volume = {9},
number = {10},
pages = {199},
doi = {10.1038/s41424-018-0067-7},
pmid = {30356041},
issn = {2155-384X},
abstract = {INTRODUCTION: There is increasing evidence that the microbiome contributes to esophageal disease. Diet, especially fiber and fat intake, is a known potent modifier of the colonic microbiome, but its impact on the esophageal microbiome is not well described. We hypothesized that dietary fiber and fat intake would be associated with a distinct esophageal microbiome.<br><br>METHODS: We collected esophageal samples from 47 ambulatory patients scheduled to undergo endoscopy who completed a validated food frequency questionnaire quantifying dietary fiber and fat intake. Using 16S high-throughput sequencing, we determined composition of the esophageal microbiome and predicted functional capacity of microbiota based on fiber and fat intake.<br><br>RESULTS: Among all samples, the most abundant phyla were Firmicutes (54.0%), Proteobacteria (19.0%), Bacteroidetes (17.0%), Actinobacteria (5.2%), and Fusobacteria (4.3%). Increasing fiber intake was significantly associated with increasing relative abundance of Firmicutes (p = 0.04) and decreasing relative abundance of Gram-negative bacteria overall (p = 0.03). Low fiber intake was associated with increased relative abundance of several Gram-negative bacteria, including Prevotella, Neisseria, and Eikenella. Several predicted metabolic pathways differed between highest and lowest quartile of fiber intake. Fat intake was associated with altered relative abundance of few taxa, with no alterations at the phylum level and no changes in microbiome functional composition.<br><br>CONCLUSIONS: Dietary fiber, but not fat, intake was associated with a distinct esophageal microbiome. Diet should be considered an important modifier of the esophageal microbiome in future studies. Studies are also needed to elucidate how the effects of dietary fiber on the esophageal microbiome may contribute to esophageal disease.},
}
@article {pmid30355963,
year = {2018},
author = {Almendras, K and Leiva, D and Carú, M and Orlando, J},
title = {Carbon Consumption Patterns of Microbial Communities Associated with Peltigera Lichens from a Chilean Temperate Forest.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {11},
pages = {},
doi = {10.3390/molecules23112746},
pmid = {30355963},
issn = {1420-3049},
support = {11100381 and 1181510//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; },
abstract = {Lichens are a symbiotic association between a fungus and a green alga or a cyanobacterium, or both. They can grow in practically any terrestrial environment and play crucial roles in ecosystems, such as assisting in soil formation and degrading soil organic matter. In their thalli, they can host a wide diversity of non-photoautotrophic microorganisms, including bacteria, which play important functions and are considered key components of the lichens. In this work, using the BioLog® EcoPlate system, we studied the consumption kinetics of different carbon-sources by microbial communities associated with the thallus and the substrate of Peltigera lichens growing in a Chilean temperate rain forest dominated by Nothofagus pumilio. Based on the similarity of the consumption of 31 carbon-sources, three groups were formed. Among them, one group clustered the microbial metabolic profiles of almost all the substrates from one of the sampling sites, which exhibited the highest levels of consumption of the carbon-sources, and another group gathered the microbial metabolic profiles from the lichen thalli with the most abundant mycobiont haplotypes. These results suggest that the lichen thallus has a higher impact on the metabolism of its microbiome than on the microbial community of its substrate, with the latter being more diverse in terms of the metabolized sources and whose activity level is probably related to the availability of soil nutrients. However, although significant differences were detected in the microbial consumption of several carbon-sources when comparing the lichen thallus and the underlying substrate, d-mannitol, l-asparagine, and l-serine were intensively metabolized by both communities, suggesting that they share some microbial groups. Likewise, some communities showed high consumption of 2-hydroxybenzoic acid, d-galacturonic acid, and itaconic acid; these could serve as suitable sources of microorganisms as bioresources of novel bioactive compounds with biotechnological applications.},
}
@article {pmid30355737,
year = {2018},
author = {Gerner, EW and Bruckheimer, E and Cohen, A},
title = {Cancer pharmacoprevention: Targeting polyamine metabolism to manage risk factors for colon cancer.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.TM118.003343},
pmid = {30355737},
issn = {1083-351X},
abstract = {Cancer is a set of diseases characterized by uncontrolled cell growth. In certain cancers of the gastrointestinal tract, the adenomatous polyposis coli (APC) tumor suppressor gene is altered in either germline or somatic cells and causes formation of risk factors, such as benign colonic or intestinal neoplasia, which can progress to invasive cancer. APC is a key component of the WNT pathway, contributing to normal GI tract development, and APC alteration results in dysregulation of the pathway for production of polyamines, which are ubiquitous cations essential for cell growth. Studies with mice have identified non-steroidal anti-inflammatory drugs (NSAIDs) and difluoromethylornithine (DFMO), an inhibitor of polyamine synthesis, as potent inhibitors of colon carcinogenesis. Moreover, gene expression profiling has uncovered that NSAIDs activate polyamine catabolism and export. Several DFMO-NSAID combination strategies are effective and safe methods for reducing risk factors in clinical trials with patients having genetic or sporadic risk of colon cancer. These strategies affect cancer stem cells, inflammation, immune surveillance, and the microbiome. Pharmacotherapies consisting of drug combinations targeting the polyamine pathway provide a complementary approach to surgery and cytotoxic cancer treatments for treating patients with cancer risk factors. In this minireview, we discuss the role of polyamines in colon cancer and highlight the mechanisms of select pharmacoprevention agents to delay or prevent carcinogenesis in humans.},
}
@article {pmid30355671,
year = {2018},
author = {Tanca, A and Palomba, A and Fraumene, C and Manghina, V and Silverman, M and Uzzau, S},
title = {Clostridial Butyrate Biosynthesis Enzymes Are Significantly Depleted in the Gut Microbiota of Nonobese Diabetic Mice.},
journal = {mSphere},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSphere.00492-18},
pmid = {30355671},
issn = {2379-5042},
abstract = {Increasing evidence suggests that the intestinal microbiota is involved in the pathogenesis of type 1 diabetes (T1D). Here we sought to determine which gut microbial taxa and functions vary between nonobese diabetic (NOD) mice and genetically modified NOD mice protected from T1D (Eα16/NOD) at 10 weeks of age in the time window between insulitis development and T1D onset. The gut microbiota of NOD mice were investigated by analyzing stool samples with a metaproteogenomic approach, comprising both 16S rRNA gene sequencing and microbial proteome profiling through high-resolution mass spectrometry. A depletion of Firmicutes (particularly, several members of Lachnospiraceae) in the NOD gut microbiota was observed compared to the level in the Eα16/NOD mice microbiota. Moreover, the analysis of proteins actively produced by the gut microbiota revealed different profiles between NOD and Eα16/NOD mice, with the production of butyrate biosynthesis enzymes being significantly reduced in diabetic mice. Our results support a model for gut microbiota influence on T1D development involving bacterium-produced metabolites as butyrate.IMPORTANCE Alterations of the gut microbiota early in age have been hypothesized to impact T1D autoimmune pathogenesis. In the NOD mouse model, protection from T1D has been found to operate via modulation of the composition of the intestinal microbiota during a critical early window of ontogeny, although little is known about microbiota functions related to T1D development. Here, we show which gut microbial functions are specifically associated with protection from T1D in the time window between insulitis development and T1D onset. In particular, we describe that production of butyrate biosynthesis enzymes is significantly reduced in NOD mice, supporting the hypothesis that modulating the gut microbiota butyrate production may influence T1D development.},
}
@article {pmid30355662,
year = {2018},
author = {Hird, SM and Ganz, H and Eisen, JA and Boyce, WM},
title = {The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status.},
journal = {mSphere},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSphere.00382-18},
pmid = {30355662},
issn = {2379-5042},
abstract = {Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. Here, we analyze five Anas species to determine whether these duck species have similar IAV+ and IAV- cloacal microbiomes, or if the relationships among a host, influenza virus, and the microbiome are species specific. We assessed taxonomic composition of the microbiome, alpha diversity, and beta diversity and found very few patterns related to microbiome and infection status across species, while detecting strong differences within species. A host species-specific signal was stronger in IAV- ducks than IAV+ ducks, and the effect size of host species on the microbiome was three times higher in IAV- birds than IAV+ birds. The mallards and the northern shovelers, the species with highest sample sizes but also with differing feeding ecology, showed especially contrasting patterns in microbiome composition, alpha diversity, and beta diversity. Our results indicate that the microbiome may have a unique relationship with influenza virus infection at the species level.IMPORTANCE Waterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual's microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed microbiomes), including both IAV-negative and IAV-positive individuals. We demonstrate that there is not one consistent &quot;flu-like&quot; microbiome or response to flu across species. Individual duck species appear to have unique relationships between their microbiomes and IAV, and IAV-negative birds have a stronger tie to host species than the IAV-positive birds. In a broad context, understanding the role of the microbiome in IAV reservoir species may have future implications for avian disease management.},
}
@article {pmid30355562,
year = {2018},
author = {Trotter Ii, RT and Camplain, R and Eaves, ER and Fofanov, VY and Dmitrieva, NO and Hepp, CM and Warren, M and Barrios, BA and Pagel, N and Mayer, A and Baldwin, JA},
title = {Health Disparities and Converging Epidemics in Jail Populations: Protocol for a Mixed-Methods Study.},
journal = {JMIR research protocols},
volume = {7},
number = {10},
pages = {e10337},
doi = {10.2196/10337},
pmid = {30355562},
issn = {1929-0748},
abstract = {BACKGROUND: Incarcerated populations have increased in the last 20 years and >12 million individuals cycle in and out of jails each year. Previous research has predominately focused on the prison population. However, a substantial gap exists in understanding the health, well-being, and health care utilization patterns in jail populations.<br><br>OBJECTIVE: This pilot study has 5 main objectives: (1) define recidivists of the jail system, individuals characterized by high incarceration rates; (2) describe and compare the demographic and clinical characteristics of incarcerated individuals; (3) identify jail-associated health disparities; (4) estimate associations between incarceration and health; and (5) describe model patterns in health care and jail utilization.<br><br>METHODS: The project has two processes-a secondary data analysis and primary data collection-which includes a cross-sectional health survey and biological sample collection to investigate infectious disease characteristics of the jail population. This protocol contains pilot elements in four areas: (1) instrument validity and reliability; (2) individual item assessment; (3) proof of concept of content and database accessibility; and (4) pilot test of the &quot;honest broker&quot; system. Secondary data analysis includes the analysis of 6 distinct databases, each covered by a formal memorandum of agreement between Northern Arizona University and the designated institution: (1) the Superior Court of Arizona Public Case Finder database; (2) North Country Health Care; (3) Health Choice Integrated Care; (4) Criminal Justice Information Services; (5) Correctional Electronic Medical Records; and (6) iLEADS. We will perform data integration processes using an automated honest broker design. We will administer a cross-sectional health survey, which includes questions about health status, health history, health care utilization, substance use practices, physical activity, adverse childhood events, and behavioral health, among 200 Coconino County Detention Facility inmates. Concurrent with the survey administration, we will collect Methicillin-resistant and Methicillin-sensitive Staphylococcus aureus (samples from the nose) and dental microbiome (Streptococcus sobrinus and Streptococcus mutans samples from the mouth) from consenting participants.<br><br>RESULTS: To date, we have permission to link data across acquired databases. We have initiated data transfer, protection, and initial assessment of the 6 secondary databases. Of 199 inmates consented and enrolled, we have permission from 97.0% (193/199) to access and link electronic medical and incarceration records to their survey responses, and 95.0% (189/199) of interviewed inmates have given nasal and buccal swabs for analysis of S. aureus and the dental microbiome.<br><br>CONCLUSIONS: This study is designed to increase the understanding of health needs and health care utilization patterns among jail populations, with a special emphasis on frequently incarcerated individuals. Our findings will help identify intervention points throughout the criminal justice and health care systems to improve health and reduce health disparities among jail inmates.<br><br>RR1-10.2196/10337.},
}
@article {pmid30355393,
year = {2018},
author = {Lin, D and Peters, BA and Friedlander, C and Freiman, HJ and Goedert, JJ and Sinha, R and Miller, G and Bernstein, MA and Hayes, RB and Ahn, J},
title = {Association of dietary fibre intake and gut microbiota in adults.},
journal = {The British journal of nutrition},
volume = {120},
number = {9},
pages = {1014-1022},
doi = {10.1017/S0007114518002465},
pmid = {30355393},
issn = {1475-2662},
abstract = {Increasing evidence indicates that gut microbiota may influence colorectal cancer risk. Diet, particularly fibre intake, may modify gut microbiota composition, which may affect cancer risk. We investigated the relationship between dietary fibre intake and gut microbiota in adults. Using 16S rRNA gene sequencing, we assessed gut microbiota in faecal samples from 151 adults in two independent study populations: National Cancer Institute (NCI), n 75, and New York University (NYU), n 76. We calculated energy-adjusted fibre intake based on FFQ. For each study population with adjustment for age, sex, race, BMI and smoking, we evaluated the relationship between fibre intake and gut microbiota community composition and taxon abundance. Total fibre intake was significantly associated with overall microbial community composition in NYU (P=0·008) but not in NCI (P=0·81). In a meta-analysis of both study populations, higher fibre intake tended to be associated with genera of class Clostridia, including higher abundance of SMB53 (fold change (FC)=1·04, P=0·04), Lachnospira (FC=1·03, P=0·05) and Faecalibacterium (FC=1·03, P=0·06), and lower abundance of Actinomyces (FC=0·95, P=0·002), Odoribacter (FC=0·95, P=0·03) and Oscillospira (FC=0·96, P=0·06). A species-level meta-analysis showed that higher fibre intake was marginally associated with greater abundance of Faecalibacterium prausnitzii (FC=1·03, P=0·07) and lower abundance of Eubacterium dolichum (FC=0·96, P=0·04) and Bacteroides uniformis (FC=0·97, P=0·05). Thus, dietary fibre intake may impact gut microbiota composition, particularly class Clostridia, and may favour putatively beneficial bacteria such as F. prausnitzii. These findings warrant further understanding of diet-microbiota relationships for future development of colorectal cancer prevention strategies.},
}
@article {pmid30355348,
year = {2018},
author = {Tackmann, J and Arora, N and Schmidt, TSB and Rodrigues, JFM and von Mering, C},
title = {Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {192},
doi = {10.1186/s40168-018-0565-6},
pmid = {30355348},
issn = {2049-2618},
support = {31003A-160095//Swiss National Science Foundation/ ; },
abstract = {BACKGROUND: The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characterized site-specific microbiota and shown that sample origin can be accurately predicted by microbial content. However, these studies were usually restricted to single datasets with consistent experimental methods and conditions, as well as comparatively small sample numbers. The effects of study-specific biases and statistical power on classification performance and biomarker identification thus remain poorly understood. Furthermore, reliable detection in mixtures of different body sites or with noise from environmental contamination has rarely been investigated thus far. Finally, the impact of ecological associations between microbes on biomarker discovery was usually not considered in previous work.<br><br>RESULTS: Here we present the analysis of one of the largest cross-study sequencing datasets of microbial communities from human body sites (15,082 samples from 57 publicly available studies). We show that training a Random Forest Classifier on this aggregated dataset increases prediction performance for body sites by 35% compared to a single-study classifier. Using simulated datasets, we further demonstrate that the source of different microbial contributions in mixtures of different body sites or with soil can be detected starting at 1% of the total microbial community. We apply a biomarker selection method that excludes indirect environmental associations driven by microbe-microbe associations, yielding a parsimonious set of highly predictive taxa including novel biomarkers and excluding many previously reported taxa. We find a considerable fraction of unclassified biomarkers (&quot;microbial dark matter&quot;) and observe that negatively associated taxa have a surprisingly high impact on classification performance. We further detect a significant enrichment of rod-shaped, motile, and sporulating taxa for feces biomarkers, consistent with a highly competitive environment.<br><br>CONCLUSIONS: Our machine learning model shows strong body site classification performance, both in single-source samples and mixtures, making it promising for tasks requiring high accuracy, such as forensic applications. We report a core set of ecologically informed biomarkers, inferred across a wide range of experimental protocols and conditions, providing the most concise, general, and least biased overview of body site-associated microbes to date.},
}
@article {pmid30355167,
year = {2018},
author = {Leslie, JL and Annex, BH},
title = {The Microbiome and Endothelial Function.},
journal = {Circulation research},
volume = {123},
number = {9},
pages = {1015-1016},
doi = {10.1161/CIRCRESAHA.118.313813},
pmid = {30355167},
issn = {1524-4571},
}
@article {pmid30355158,
year = {2018},
author = {Malik, M and Suboc, TM and Tyagi, S and Salzman, N and Wang, J and Ying, R and Tanner, MJ and Kakarla, M and Baker, JE and Widlansky, ME},
title = {Lactobacillus plantarum 299v Supplementation Improves Vascular Endothelial Function and Reduces Inflammatory Biomarkers in Men With Stable Coronary Artery Disease.},
journal = {Circulation research},
volume = {123},
number = {9},
pages = {1091-1102},
doi = {10.1161/CIRCRESAHA.118.313565},
pmid = {30355158},
issn = {1524-4571},
abstract = {RATIONALE: A strong association has emerged between the gut microbiome and atherosclerotic disease. Our recent data suggest Lactobacillus plantarum 299v (Lp299v) supplementation reduces infarct size in male rats. Limited human data are available on the impact of Lp299v on the vasculature.<br><br>OBJECTIVE: To determine whether oral Lp299v supplementation improves vascular endothelial function and reduces systemic inflammation in humans with stable coronary artery disease (CAD).<br><br>METHODS AND RESULTS: Twenty men with stable CAD consumed a drink containing Lp299v (20 billion CFU) once daily for 6 weeks. After a 4-week washout, subjects were given an option of additionally participating in a 10-day study of oral liquid vancomycin (250 mg QID). Vascular endothelial function was measured by brachial artery flow-mediated dilation. Before and after Lp299v, plasma short-chain fatty acids, trimethylamine oxide, and adipokine levels were measured. Additional plasma samples underwent unbiased metabolomic analyses using liquid chromatography/mass spectroscopy. 16S rRNA sequencing was used to determine changes of the stool microbiome. Arterioles from patients with CAD were obtained, and endothelium-dependent vasodilation was measured by video microscopy after intraluminal incubation with plasma from Lp299v study subjects. Lp299v supplementation improved brachial flow-mediated dilation (P=0.008) without significant changes in plasma cholesterol profiles, fasting glucose, or body mass index. Vancomycin did not impact flow-mediated dilation. Lp299v supplementation decreased circulating levels of IL (interleukin)-8 (P=0.01), IL-12 (P=0.02), and leptin (P=0.0007) but did not significantly change plasma trimethylamine oxide concentrations (P=0.27). Plasma propionate (P=0.004) increased, whereas acetate levels decreased (P=0.03). Post-Lp299v plasma improved endothelium-dependent vasodilation in resistance arteries from patients with CAD (P=0.02).16S rRNA analysis showed the Lactobacillus genus was enriched in postprobiotic stool samples without other changes.<br><br>CONCLUSIONS: Lp299v improved vascular endothelial function and decreased systemic inflammation in men with CAD, independent of changes in traditional risk factors and trimethylamine oxide. Circulating gut-derived metabolites likely account for these improvements and merit further study.<br><br>CLINICAL TRIAL REGISTRATION: URL: http://www.clinicaltrials.gov . Unique identifier: NCT01952834.},
}
@article {pmid30354996,
year = {2018},
author = {Nie, J and Xie, L and Zhao, BX and Li, Y and Qiu, B and Zhu, F and Li, GF and He, M and Wang, Y and Wang, B and Liu, S and Zhang, H and Guo, H and Cai, Y and Huo, Y and Hou, FF and Xu, X and Qin, X},
title = {Serum Trimethylamine N-Oxide Concentration Is Positively Associated With First Stroke in Hypertensive Patients.},
journal = {Stroke},
volume = {49},
number = {9},
pages = {2021-2028},
doi = {10.1161/STROKEAHA.118.021997},
pmid = {30354996},
issn = {1524-4628},
abstract = {Background and Purpose- Trimethylamine N-oxide (TMAO)-a gut derived metabolite-has been shown to be atherogenic. It remains unknown whether TMAO is associated with the risk of first stroke. We aimed to determine the association between serum TMAO levels and first stroke in hypertensive patients without major cardiovascular diseases and examine any possible effect modifiers. Methods- We used a nested case-control design, using data from the CSPPT (China Stroke Primary Prevention Trial), including 622 patients with first stroke and 622 matched controls. The study was conducted from May 2008 to August 2013. The primary outcome was a first stroke. Results- After adjusting for choline, L-carnitine, and other important covariates, including baseline systolic blood pressure and time-averaged systolic blood pressure, during the treatment period, the risk of first stroke increased with each increment of TMAO level (per natural log [TMAO] increment: odds ratio, 1.22; 95% CI, 1.02-1.46). Consistently, compared with participants in the lowest tertile (<1.79 μmol/L) of serum TMAO levels, a significantly higher risk of first stroke was found in those in higher TMAO tertiles (≥1.79 μmol/L; odds ratio, 1.34; 95% CI, 1.00-1.81) or in TMAO tertile 3 (≥3.19 μmol/L; odds ratio, 1.43; 95% CI, 1.02-2.01). In the exploratory analysis, we observed an interaction between TMAO and folate levels (≥7.7 [median] versus <7.7 ng/mL) on first stroke (P for interaction, 0.030). Conclusions- Higher TMAO levels were associated with increased risk of first stroke in hypertensive patients. Our finding, if further confirmed, calls for a carefully designed clinical trial to further evaluate the role of higher TMAO levels on outcomes in hypertensive patients. Clinical Trial Registration- URL: https://www.clinicaltrials.gov . Unique identifier: NCT00794885.},
}
@article {pmid30354811,
year = {2018},
author = {Waghulde, H and Cheng, X and Galla, S and Mell, B and Cai, J and Pruett-Miller, SM and Vazquez, G and Patterson, A and Vijay Kumar, M and Joe, B},
title = {Attenuation of Microbiotal Dysbiosis and Hypertension in a CRISPR/Cas9 Gene Ablation Rat Model of GPER1.},
journal = {Hypertension (Dallas, Tex. : 1979)},
volume = {72},
number = {5},
pages = {1125-1132},
doi = {10.1161/HYPERTENSIONAHA.118.11175},
pmid = {30354811},
issn = {1524-4563},
abstract = {G-protein-coupled estrogen receptor, Gper1, has been implicated in cardiovascular disease, but its mechanistic role in blood pressure control is poorly understood. Here, we demonstrate that genetically salt-sensitive hypertensive rats with complete genomic excision of Gper1 by a multiplexed guide RNA CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 (CRISPR associated proteins) approach present with lower blood pressure, which was accompanied by altered microbiota, different levels of circulating short chain fatty acids, and improved vascular relaxation. Microbiotal transplantation from hypertensive Gper1+/+ rats reversed the cardiovascular protective effect exerted by the genomic deletion of Gper1. Thus, this study reveals a role for Gper1 in promoting microbiotal alterations that contribute to cardiovascular pathology. However, the exact mechanism by which Gper1 regulates blood pressure is still unknown. Our results indicate that the function of Gper1 is contextually dependent on the microbiome, whereby, contemplation of using Gper1 as a target for therapy of cardiovascular disease requires caution.},
}
@article {pmid30354349,
year = {2018},
author = {Marques, FZ},
title = {Missing Heritability of Hypertension and Our Microbiome.},
journal = {Circulation},
volume = {138},
number = {14},
pages = {1381-1383},
doi = {10.1161/CIRCULATIONAHA.118.036224},
pmid = {30354349},
issn = {1524-4539},
}
@article {pmid30353933,
year = {2018},
author = {Hirota, R and Ohya, Y and Yamamoto-Hanada, K and FukutomiI, Y and Muto, G and Ngatu-Nlandu, R and Nakamura, T and Nakamura, H},
title = {Triclosan-induced Alteration of Gut Microbiome and Aggravation of Asthmatic Airway Response in Aeroallergen-sensitized mice.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.13639},
pmid = {30353933},
issn = {1398-9995},
}
@article {pmid30353462,
year = {2018},
author = {Lee, ES and Song, EJ and Nam, YD and Lee, SY},
title = {Probiotics in human health and disease: from nutribiotics to pharmabiotics.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {56},
number = {11},
pages = {773-782},
doi = {10.1007/s12275-018-8293-y},
pmid = {30353462},
issn = {1976-3794},
abstract = {Probiotics are the most useful tools for balancing the gut microbiota and thereby influencing human health and disease. Probiotics have a range of effects, from those on nutritional status to medical conditions throughout the body from the gut to non-intestinal body sites such as the brain and skin. Research interest in probiotics with nutritive claims (categorized as nutribiotics) has evolved into interest in therapeutic and pharmacological probiotics with health claims (pharmabiotics). The concept of pharmabiotics emerged only two decades ago, and the new categorization of probiotics to nutribiotics and pharmabiotics was recently suggested, which are under the different regulation depending on that they are food or drug. Information of the gut microbiome has been continuously accumulating, which will make possible the gut microbiome-based healthcare in the future, when nutribiotics show potential for maintaining health while pharmabiotics are effective therapeutic tools for human diseases. This review describes the current understanding in the conceptualization and classification of probiotics. Here, we reviewed probiotics as nutribiotics with nutritional functions and pharmabiotics with pharmaceutic functions in different diseases.},
}
@article {pmid30353256,
year = {2018},
author = {Rewers, M and Hyöty, H and Lernmark, Å and Hagopian, W and She, JX and Schatz, D and Ziegler, AG and Toppari, J and Akolkar, B and Krischer, J and , },
title = {The Environmental Determinants of Diabetes in the Young (TEDDY) Study: 2018 Update.},
journal = {Current diabetes reports},
volume = {18},
number = {12},
pages = {136},
doi = {10.1007/s11892-018-1113-2},
pmid = {30353256},
issn = {1539-0829},
support = {U01 DK63829//National Institute of Diabetes and Digestive and Kidney Diseases/ ; U01 DK63861//National Institute of Diabetes and Digestive and Kidney Diseases/ ; U01 DK63821//National Institute of Diabetes and Digestive and Kidney Diseases/ ; U01 DK63865//National Institute of Diabetes and Digestive and Kidney Diseases/ ; U01 DK63863//National Institute of Diabetes and Digestive and Kidney Diseases/ ; U01 DK63836//National Institute of Diabetes and Digestive and Kidney Diseases/ ; U01 DK63790//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UC4 DK63829//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UC4 DK63861//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UC4 DK63821//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UC4 DK63865//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UC4 DK63863//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UC4 DK63836//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UC4 DK95300//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UC4 DK100238//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UC4 DK106955//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UC4 DK112243//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UC4 DK117483//National Institute of Diabetes and Digestive and Kidney Diseases/ ; HHSN267200700014C//National Institute of Diabetes and Digestive and Kidney Diseases/ ; UL1 TR000064//National Center for Advancing Translational Sciences/ ; UL1 TR001082//National Center for Advancing Translational Sciences/ ; },
abstract = {PURPOSE OF REVIEW: The environmental triggers of islet autoimmunity leading to type 1 diabetes (T1D) need to be elucidated to inform primary prevention. The Environmental Determinants of Diabetes in the Young (TEDDY) Study follows from birth 8676 children with T1D risk HLA-DR-DQ genotypes in the USA, Finland, Germany, and Sweden. Most study participants (89%) have no first-degree relative with T1D. The primary outcomes include the appearance of one or more persistent islet autoantibodies (islet autoimmunity, IA) and clinical T1D.<br><br>RECENT FINDINGS: As of February 28, 2018, 769 children had developed IA and 310 have progressed to T1D. Secondary outcomes include celiac disease and autoimmune thyroid disease. While the follow-up continues, TEDDY has already evaluated a number of candidate environmental triggers, including infections, probiotics, micronutrient, and microbiome. TEDDY results suggest that there are multiple pathways leading to the destruction of pancreatic beta-cells. Ongoing measurements of further specific exposures, gene variants, and gene-environment interactions and detailed &quot;omics&quot; studies will provide novel information on the pathogenesis of T1D.},
}
@article {pmid30353134,
year = {2018},
author = {Itcus, C and Pascu, MD and Lavin, P and Perşoiu, A and Iancu, L and Purcarea, C},
title = {Bacterial and archaeal community structures in perennial cave ice.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15671},
doi = {10.1038/s41598-018-34106-2},
pmid = {30353134},
issn = {2045-2322},
support = {PN-II-ID-PCE-2011-3-0742//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii (Executive Agency for Higher Education, Scientific Research, Development and Innovation Funding)/ ; EraNet-LAC ELAC2014/DCC0178//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii (Executive Agency for Higher Education, Scientific Research, Development and Innovation Funding)/ ; },
abstract = {Ice entrenched microcosm represents a vast reservoir of novel species and a proxy for past climate reconstitution. Among glacial ecosystems, ice caves represent one of the scarcely investigated frozen habitats. To characterize the microbial diversity of perennial ice from karst ecosystems, Roche 454 sequencing of 16S rRNA gene amplicons from the underground ice block of Scarisoara Ice Cave (Romania) was applied. The temporal distribution of bacterial and archaeal community structures from newly formed, 400, and 900 years old ice layers was surveyed and analyzed in relation with the age and geochemical composition of the ice substrate. The microbial content of cave ice layers varied from 3.3 104 up to 7.5 105 cells mL-1, with 59-78% viability. Pyrosequencing generated 273,102 reads for the five triplicate ice samples, which corresponded to 3,464 operational taxonomic units (OTUs). The distribution of the bacterial phyla in the perennial cave ice varied with age, organic content, and light exposure. Proteobacteria dominated the 1 and 900 years old organic rich ice deposits, while Actinobacteria was mostly found in 900 years old ice strata, and Firmicutes was best represented in 400 years old ice. Cyanobacteria and Chlorobi representatives were identified mainly from the ice block surface samples exposed to sunlight. Archaea was observed only in older ice strata, with a high incidence of Crenarchaeota and Thaumarchaeaota in the 400 years old ice, while Euryarchaeota dominated the 900 years old ice layers, with Methanomicrobia representing the predominant taxa. A large percentage (55.7%) of 16S rRNA gene amplicons corresponded to unidentified OTUs at genus or higher taxa levels, suggesting a greater undiscovered bacterial diversity in this glacial underground habitat. The prokaryotes distribution across the cave ice block revealed the presence of 99 phylotypes specific for different ice layers, in addition to the shared microbial community. Ice geochemistry represented an important factor that explained the microbial taxa distribution in the cave ice block, while the total organic carbon content had a direct impact on the cell density of the ice microcosm. Both bacterial and archaeal community structures appeared to be affected by climate variations during the ice formation, highlighting the cave ice microbiome as a source of putative paleoclimatic biomarkers. This report constitutes the first high-throughput sequencing study of the cave ice microbiome and its distribution across the perennial underground glacier of an alpine ice cave.},
}
@article {pmid30353125,
year = {2018},
author = {Combellick, JL and Shin, H and Shin, D and Cai, Y and Hagan, H and Lacher, C and Lin, DL and McCauley, K and Lynch, SV and Dominguez-Bello, MG},
title = {Differences in the fecal microbiota of neonates born at home or in the hospital.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15660},
doi = {10.1038/s41598-018-33995-7},
pmid = {30353125},
issn = {2045-2322},
abstract = {Research on the neonatal microbiome has been performed mostly on hospital-born infants, who often undergo multiple birth-related interventions. Both the hospital environment and interventions around the time of birth may affect the neonate microbiome. In this study, we determine the structure of the microbiota in feces from babies born in the hospital or at home, and from vaginal samples of their mothers. We included 35 vaginally-born, breast-fed neonates, 14 of whom delivered at home (4 in water), and 21 who delivered in the hospital. Feces from babies and mothers and maternal vaginal swab samples were collected at enrollment, the day of birth, followed by days 1, 2, 7, 14, 21, and 28. At the time of birth, the diversity of the vaginal microbiota of mothers delivering in the hospital was higher than in mothers delivering at home, and showed higher proportion of Lactobacillus. Among 20 infants not exposed to perinatal maternal antibiotics or water birth, fecal beta diversity differed significantly by birth site, with hospital-born infants having lower Bacteroides, Bifidobacterium, Streptococcus, and Lactobacillus, and higher Clostridium and Enterobacteriaceae family (LDA > 3.0), than babies born at home. At 1 month of age, feces from infants born in the hospital also induced greater pro-inflammatory gene expression (TLR4, IL-8, occludin and TGFβ) in human colon epithelial HT-29 cells. The results of this work suggest that hospitalization (perinatal interventions or the hospital environment) may affect the microbiota of the vaginal source and the initial colonization during labor and birth, with effects that could persist in the intestinal microbiota of infants 1 month after birth. More research is needed to determine specific factors that alter bacterial transmission between mother and baby and the long-term health implications of these differences for the developing infant.},
}
@article {pmid30353019,
year = {2018},
author = {Jenkins, TP and Formenti, F and Castro, C and Piubelli, C and Perandin, F and Buonfrate, D and Otranto, D and Griffin, JL and Krause, L and Bisoffi, Z and Cantacessi, C},
title = {A comprehensive analysis of the faecal microbiome and metabolome of Strongyloides stercoralis infected volunteers from a non-endemic area.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15651},
doi = {10.1038/s41598-018-33937-3},
pmid = {30353019},
issn = {2045-2322},
abstract = {Data from recent studies support the hypothesis that infections by human gastrointestinal (GI) helminths impact, directly and/or indirectly, on the composition of the host gut microbial flora. However, to the best of our knowledge, these studies have been conducted in helminth-endemic areas with multi-helminth infections and/or in volunteers with underlying gut disorders. Therefore, in this study, we explore the impact of natural mono-infections by the human parasite Strongyloides stercoralis on the faecal microbiota and metabolic profiles of a cohort of human volunteers from a non-endemic area of northern Italy (S+), pre- and post-anthelmintic treatment, and compare the findings with data obtained from a cohort of uninfected controls from the same geographical area (S-). Analyses of bacterial 16S rRNA high-throughput sequencing data revealed increased microbial alpha diversity and decreased beta diversity in the faecal microbial profiles of S+ subjects compared to S-. Furthermore, significant differences in the abundance of several bacterial taxa were observed between samples from S+ and S- subjects, and between S+ samples collected pre- and post-anthelmintic treatment. Faecal metabolite analysis detected marked increases in the abundance of selected amino acids in S+ subjects, and of short chain fatty acids in S- subjects. Overall, our work adds valuable knowledge to current understanding of parasite-microbiota associations and will assist future mechanistic studies aimed to unravel the causality of these relationships.},
}
@article {pmid30352962,
year = {2018},
author = {Ramírez, C and Coronado, J and Silva, A and Romero, J},
title = {Cetobacterium Is a Major Component of the Microbiome of Giant Amazonian Fish (Arapaima gigas) in Ecuador.},
journal = {Animals : an open access journal from MDPI},
volume = {8},
number = {11},
pages = {},
doi = {10.3390/ani8110189},
pmid = {30352962},
issn = {2076-2615},
support = {1140734//FONDECYT/ ; 1171129//FONDECYT/ ; 15PCTI-46284//CORFO/ ; },
abstract = {Arapaima gigas is a large air-breathing fish found in Amazonian rivers, a characteristic that gives this species an advantage in oxygen-deprived waters. It shows high potential for aquaculture in the Amazon region due to its fast growth rate that approaches 10⁻15 kg/year. The aim of this study was to explore the composition of the intestinal bacterial community of Arapaima gigas reared in Ecuador using 16S rRNA gene high-throughput sequencing. The analysis revealed significant differences in alpha diversity indices (p < 0.05) and differential distribution of minor components of the intestinal microbiome between small and large fish. However, components with greater relative abundance, such as Cetobacterium, are found in similar proportions.},
}
@article {pmid30352933,
year = {2018},
author = {Stanislawski, MA and Dabelea, D and Wagner, BD and Iszatt, N and Dahl, C and Sontag, MK and Knight, R and Lozupone, CA and Eggesbø, M},
title = {Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort.},
journal = {mBio},
volume = {9},
number = {5},
pages = {},
doi = {10.1128/mBio.01751-18},
pmid = {30352933},
issn = {2150-7511},
abstract = {Childhood obesity is a growing problem worldwide. Recent research suggests that the gut microbiota may play an important and potentially causal role in the development of obesity and may be one mechanism that explains the transgenerational transmission of obesity risk. Here we examine the early-life gut microbiota at days 4, 10, 30, 120, 365, and 730 and the association with body mass index (BMI) z-scores at age 12 in a Norwegian prospective cohort (n = 165), and evaluate how these BMI-associated taxa relate to maternal overweight/obesity (Ow/Ob) and excessive gestational weight gain (GWG). We performed 16S rRNA gene sequencing on the gut microbiota samples. Taxonomic phylogeny at days 10 and 730 was significantly associated with childhood BMI, and the gut microbiota taxa at two years of age explained over 50% of the variation in childhood BMI in this cohort. The subset of the early-life taxa within the gut microbiota that best predicted later childhood BMI showed substantial overlap with the maternal taxa most strongly associated with maternal Ow/Ob and excessive GWG. Our results show an association between the infant gut microbiota and later BMI, and they offer preliminary evidence that the infant gut microbiota, particularly at 2 years of age, may have potential to help identify children at risk for obesity.IMPORTANCE Understanding the role of the early-life gut microbiota in obesity is important because there may be opportunities for preventive strategies. We examined the relationships between infant gut microbiota at six times during the first two years of life and BMI at age 12 in a birth cohort of 165 children and their mothers. We found that the gut microbiota from early life to two years shows an increasingly strong association with childhood BMI. This study provides preliminary evidence that the gut microbiome at 2 years of age may offer useful information to help to identify youth who are at risk for obesity, which could facilitate more-targeted early prevention efforts.},
}
@article {pmid30352628,
year = {2018},
author = {Wilmoth, JL and Moran, MA and Thompson, A},
title = {Transient O2 pulses direct Fe crystallinity and Fe(III)-reducer gene expression within a soil microbiome.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {189},
doi = {10.1186/s40168-018-0574-5},
pmid = {30352628},
issn = {2049-2618},
support = {1331841//Division of Earth Sciences/ ; 1053470//Division of Earth Sciences/ ; 1451508//Division of Earth Sciences/ ; 1457761//Division of Environmental Biology/ ; 2009-65107-05830//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Many environments contain redox transition zones, where transient oxygenation events can modulate anaerobic reactions that influence the cycling of iron (Fe) and carbon (C) on a global scale. In predominantly anoxic soils, this biogeochemical cycling depends on Fe mineral composition and the activity of mixed Fe(III)-reducer populations that may be altered by periodic pulses of molecular oxygen (O2).<br><br>METHODS: We repeatedly exposed anoxic (4% H2:96% N2) suspensions of soil from the Luquillo Critical Zone Observatory to 1.05 × 102, 1.05 × 103, and 1.05 × 104 mmol O2 kg-1 soil h-1 during pulsed oxygenation treatments. Metatranscriptomic analysis and 57Fe Mössbauer spectroscopy were used to investigate changes in Fe(III)-reducer gene expression and Fe(III) crystallinity, respectively.<br><br>RESULTS: Slow oxygenation resulted in soil Fe-(oxyhydr)oxides of higher crystallinity (38.1 ± 1.1% of total Fe) compared to fast oxygenation (30.6 ± 1.5%, P < 0.001). Transcripts binning to the genomes of Fe(III)-reducers Anaeromyxobacter, Geobacter, and Pelosinus indicated significant differences in extracellular electron transport (e.g., multiheme cytochrome c, multicopper oxidase, and type-IV pilin gene expression), adhesion/contact (e.g., S-layer, adhesin, and flagellin gene expression), and selective microbial competition (e.g., bacteriocin gene expression) between the slow and fast oxygenation treatments during microbial Fe(III) reduction. These data also suggest that diverse Fe(III)-reducer functions, including cytochrome-dependent extracellular electron transport, are associated with type-III fibronectin domains. Additionally, the metatranscriptomic data indicate that Methanobacterium was significantly more active in the reduction of CO2 to CH4 and in the expression of class(III) signal peptide/type-IV pilin genes following repeated fast oxygenation compared to slow oxygenation.<br><br>CONCLUSIONS: This study demonstrates that specific Fe(III)-reduction mechanisms in mixed Fe(III)-reducer populations are uniquely sensitive to the rate of O2 influx, likely mediated by shifts in soil Fe(III)-(oxyhydr)oxide crystallinity. Overall, we provide evidence that transient oxygenation events play an important role in directing anaerobic pathways within soil microbiomes, which is expected to alter Fe and C cycling in redox-dynamic environments.},
}
@article {pmid30352623,
year = {2018},
author = {Benler, S and Cobián-Güemes, AG and McNair, K and Hung, SH and Levi, K and Edwards, R and Rohwer, F},
title = {A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {191},
doi = {10.1186/s40168-018-0573-6},
pmid = {30352623},
issn = {2049-2618},
support = {124351//National Science Foundation/ ; TG-MCB170036//xsede/ ; },
abstract = {BACKGROUND: Diversity-generating retroelements (DGRs) are genetic cassettes that selectively mutate target genes to produce hypervariable proteins. First characterized in Bordetella bacteriophage BPP-1, the DGR creates a hypervariable phage tail fiber that enables host tropism switching. Subsequent surveys for DGRs conclude that the majority identified to date are bacterial or archaeal in origin. This work examines bacteriophage and bacterial genomes for novel phage-encoded DGRs.<br><br>RESULTS: This survey discovered 92 DGRs that were only found in phages exhibiting a temperate lifestyle. The majority of phage-encoded DGRs were identified as prophages in bacterial hosts from the phyla Bacteroidetes, Proteobacteria, and Firmicutes. Sequence reads from these previously unidentified prophages were present in viral metagenomes (viromes), indicating these prophages can produce functional viruses. Five phages possessed hypervariable proteins with structural similarity to the tail fiber of BPP-1, whereas the functions of the remaining DGR target proteins were unknown. A novel temperate phage that harbors a DGR cassette targeting a protein of unknown function was induced from Bacteroides dorei. This phage, here named Bacteroides dorei Hankyphage, lysogenizes 13 different Bacteroides species and was present in 34% and 21% of whole-community metagenomes and human-associated viromes, respectively.<br><br>CONCLUSIONS: Here, the number of known DGR-containing phages is increased from four to 92. All of these phages exhibit a temperate lifestyle, including a cosmopolitan human-associated phage. Targeted hypervariation by temperate phages may be a ubiquitous mechanism underlying phage-bacteria interaction in the human microbiome.},
}
@article {pmid30352611,
year = {2018},
author = {Earl, JP and Adappa, ND and Krol, J and Bhat, AS and Balashov, S and Ehrlich, RL and Palmer, JN and Workman, AD and Blasetti, M and Sen, B and Hammond, J and Cohen, NA and Ehrlich, GD and Mell, JC},
title = {Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {190},
doi = {10.1186/s40168-018-0569-2},
pmid = {30352611},
issn = {2049-2618},
support = {R01DC013588//National Institutes of Health/ ; U01DK082316//National Institutes of Health/ ; R01DC02148//Foundation for the National Institutes of Health/ ; HHSN261201600383P//National Cancer Institute/ ; },
abstract = {BACKGROUND: Pan-bacterial 16S rRNA microbiome surveys performed with massively parallel DNA sequencing technologies have transformed community microbiological studies. Current 16S profiling methods, however, fail to provide sufficient taxonomic resolution and accuracy to adequately perform species-level associative studies for specific conditions. This is due to the amplification and sequencing of only short 16S rRNA gene regions, typically providing for only family- or genus-level taxonomy. Moreover, sequencing errors often inflate the number of taxa present. Pacific Biosciences' (PacBio's) long-read technology in particular suffers from high error rates per base. Herein, we present a microbiome analysis pipeline that takes advantage of PacBio circular consensus sequencing (CCS) technology to sequence and error correct full-length bacterial 16S rRNA genes, which provides high-fidelity species-level microbiome data.<br><br>RESULTS: Analysis of a mock community with 20 bacterial species demonstrated 100% specificity and sensitivity with regard to taxonomic classification. Examination of a 250-plus species mock community demonstrated correct species-level classification of > 90% of taxa, and relative abundances were accurately captured. The majority of the remaining taxa were demonstrated to be multiply, incorrectly, or incompletely classified. Using this methodology, we examined the microgeographic variation present among the microbiomes of six sinonasal sites, by both swab and biopsy, from the anterior nasal cavity to the sphenoid sinus from 12 subjects undergoing trans-sphenoidal hypophysectomy. We found greater variation among subjects than among sites within a subject, although significant within-individual differences were also observed. Propiniobacterium acnes (recently renamed Cutibacterium acnes) was the predominant species throughout, but was found at distinct relative abundances by site.<br><br>CONCLUSIONS: Our microbial composition analysis pipeline for single-molecule real-time 16S rRNA gene sequencing (MCSMRT, https://github.com/jpearl01/mcsmrt) overcomes deficits of standard marker gene-based microbiome analyses by using CCS of entire 16S rRNA genes to provide increased taxonomic and phylogenetic resolution. Extensions of this approach to other marker genes could help refine taxonomic assignments of microbial species and improve reference databases, as well as strengthen the specificity of associations between microbial communities and dysbiotic states.},
}
@article {pmid30352258,
year = {2018},
author = {Kreuter, R and Wankell, M and Ahlenstiel, G and Hebbard, L},
title = {The role of obesity in inflammatory bowel disease.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {1865},
number = {1},
pages = {63-72},
doi = {10.1016/j.bbadis.2018.10.020},
pmid = {30352258},
issn = {1879-260X},
abstract = {In just over a generation overweight and obesity has become a worldwide health concern. The ramifications for this on future health care costs and longevity are consequent, whilst increased adiposity is a harbinger for diabetes, kidney and bone failure, and cancer. An area of intense interest where the role of adiposity is avidly discussed is in inflammatory bowel disease (IBD), which presents mainly as Crohn's disease (CD) and ulcerative colitis (UC). Studies in patients associating IBD with a western diet are divergent. Nevertheless, elegant studies have found gene polymorphisms in humans that in murine models parallel the inflammatory and gut microbiome changes seen in IBD patients. However, an area not to be ignored are the alterations in adipocyte function with ensuing adiposity, in particular and a focus of this review, the dysregulation of the levels of adipocytokines such as leptin and adiponectin. Herein, we present and discuss the known influences of a western diet on IBD in patients and rodent models and how adipocytokines could influence the IBD disease process.},
}
@article {pmid30351381,
year = {2018},
author = {McClorry, S and Zavaleta, N and Llanos, A and Casapía, M and Lönnerdal, B and Slupsky, CM},
title = {Anemia in infancy is associated with alterations in systemic metabolism and microbial structure and function in a sex-specific manner: an observational study.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajcn/nqy249},
pmid = {30351381},
issn = {1938-3207},
abstract = {Background: Anemia is a term that describes low hemoglobin concentrations and can result from micronutrient deficiencies, infection, or low birth weight. Early-life anemia, particularly iron-deficiency anemia (IDA) is associated with several negative metabolic, developmental, and cognitive outcomes, some of which persist into adulthood.<br><br>Objective: The aim of this study was to investigate alterations in systemic metabolism and fecal microbial diversity and functionality associated with anemia and IDA in male and female infants from Iquitos, Peru.<br><br>Design: Cross-sectional stool and serum samples were collected from 95 infants (53 boys and 42 girls) at 12 mo of age. The fecal microbiome was assessed by using 16S ribosomal RNA gene sequencing, and the fecal and serum metabolomes were quantified using 1H-nuclear magnetic resonance.<br><br>Results: The prevalence of anemia was 64%, with a greater proportion of anemia in male infants attributed to iron deficiency. Metabolically, anemia was associated with decreased concentrations of tricarboxylic acid cycle metabolites in both sexes (males: succinate, P = 0.031; females: fumarate, P = 0.028). In addition, anemic male infants exhibited significantly lower serum concentrations of several amino acids compared with nonanemic male infants. Although no specific structural or functional differences in the microbiota were observed with anemia in general, likely due the heterogeneity of its etiology, IDA affected the microbiome both structurally and functionally. Specifically, the abundance of butyrate-producing bacteria was lower in IDA subjects of both sexes than in nonanemic, non-iron-deficient subjects of the same sex (females: Butyricicoccus, P = 0.041; males: Coprococcus, P = 0.010; Roseburia, P = 0.027). IDA male infants had higher concentrations of 4-hydroxyphenyllactate (P < 0.001) and putrescine (P = 0.042) than those without IDA, whereas IDA female infants exhibited higher concentrations of leucine (P = 0.011) and valine (P = 0.003).<br><br>Conclusions: Sexually dimorphic differences associated with anemia and IDA are suggestive of greater mitochondrial dysfunction and oxidative stress in male infants compared with female infants, and alterations in microbial structure and function may further contribute. Differences in metabolic pathways associated with anemia and IDA in each sex point to potential mechanisms for the associated lasting cognitive deficits. This trial is registered at clinicaltrials.gov as NCT03377777.},
}
@article {pmid30351160,
year = {2018},
author = {Redondo, N and Nova, E and Díaz-Prieto, LE and Marcos, A},
title = {Effects of moderate beer consumption on health.},
journal = {Nutricion hospitalaria},
volume = {35},
number = {Spec No6},
pages = {41-44},
pmid = {30351160},
issn = {1699-5198},
abstract = {According to the scientific literature, alcohol effects on health are dose-dependent, since beneficial effects have been observed when consumed at moderate level compared to abstinence or excessive consumption, in both observational and interventional studies. There are specifically two components in fermented beverages, mainly related to the beneficial effects on health when consumed in a moderate amount, namely polyphenolic compounds and ethanol. Indeed, a higher bone density has been reported in several studies, which has been associated to its polyphenolic compounds. Regarding cardiovascular and immunological effects, both polyphenols and ethanol seem to account for the anti-inflammatory andantioxidant functions.Promising research in the moderate consumption of alcoholic beverages have reported that the polyphenolic fraction of fermented drinks could benefit the gut microbiota composition and thus, host metabolism and health, suggesting that particularly, beer could be a new target for microbiome-based studies.However, it is very important to highlight that the moderate amount of beer must be consumed within an adequate lifestyle in order to avoid possible risks to develop non-communicable diseases, which are more and more frequent during the last three decades. And finally, the last message, albeit the possible benefits of the moderate consumption of fermented alcohol beverages, there are no recommendations to consume alcohol.},
}
@article {pmid30351033,
year = {2018},
author = {Aggarwal, S and Gomez-Smith, CK and Jeon, Y and LaPara, TM and Waak, M and Hozalski, RM},
title = {Effects of Chloramine and Coupon Material on Biofilm Abundance and Community Composition in Bench-Scale Simulated Water Distribution Systems and Comparison with Full-Scale Water Mains.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.8b02607},
pmid = {30351033},
issn = {1520-5851},
abstract = {The vast majority of bacteria in drinking water distribution systems (DWDSs) reside in biofilms on the interior walls of water mains. Little is known about how water quality conditions affect water-main biofilms because of the inherent limitations in experimenting with drinking water supplies and accessing the water mains for sampling. Bench-scale reactors permit experimentation and ease of biofilm sampling, yet questions remain as to how well biofilms in laboratory reactors represent those on water mains. In this study, the effects of DWDS pipe materials and chloramine residual on biofilms were investigated by cultivating biofilms on cement, polyvinyl chloride and high density polyethylene coupons in CDC reactors for up to 28 months in the presence of chloraminated or dechlorinated tap water. The bench-scale biofilm microbiomes were then compared with the microbiome on a water main from the full-scale system that supplied the water to the reactors. The presence of a chloramine residual (1.74 ± 0.21 mg/L) suppressed biofilm accumulation and selected for Mycobacteria-like and Sphingopyxis-like operational taxonomic units (OTUs) while the destruction of the chloramine residual resulted in a significant increase in biomass quantity and a shift toward a more diverse community dominated by Nitrospira-like OTUs, which, our results suggest, may be complete ammonia oxidizers (comammox). Coupon material, however, had a relatively minor effect on the abundance and community composition of the biofilm bacteria. Although biofilm communities from the chloraminated water reactor and the water mains shared some dominant populations (namely, Mycobacteria- and Nitrosomonas-like OTUs), the communities were significantly different. This manuscript provides novel insights into the effects of dechlorination and pipe material on biofilm community composition. Furthermore, to our knowledge, it is the first study to compare biofilm in a tap water-fed, bench-scale simulated distribution system to biofilm on water mains from the full-scale system supplying the tap water.},
}
@article {pmid30349856,
year = {2018},
author = {Nourbakhsh, B and Bhargava, P and Tremlett, H and Hart, J and Graves, J and Waubant, E},
title = {Altered tryptophan metabolism is associated with pediatric multiple sclerosis risk and course.},
journal = {Annals of clinical and translational neurology},
volume = {5},
number = {10},
pages = {1211-1221},
doi = {10.1002/acn3.637},
pmid = {30349856},
issn = {2328-9503},
support = {R01 NS071463/NS/NINDS NIH HHS/United States ; },
abstract = {Objective: To determine if altered tryptophan (Trp) metabolism is associated with MS risk or disease severity in children.<br><br>Methods: Participants with pediatric-onset MS and clinically isolated syndrome (CIS) within 4 years of disease onset and healthy controls underwent collection of serum. Longitudinal disability and processing speed measures and relapse data were collected in cases. Global metabolomics were conducted in 69/67 cases/controls. Targeted Trp measurement was performed in a discovery group (82 cases, 50 controls) and a validation group (92 cases, 50 controls), while functional gut microbiome analysis was done in 17 cases. Adjusted logistic, linear and negative binomial regression and Cox-proportional hazard models were used.<br><br>Results: Using global metabolomics data, higher relative abundances of Trp and indole lactate, a known gut microbiota-derived Trp metabolite, were associated with lower risk of MS. In cases, higher relative abundances of gut microbiota-derived Trp metabolites were associated with lower disability and higher processing speed scores and higher relative abundance of kynurenine was associated with higher relapse rate. Using targeted tryptophan measures, in the discovery and validation groups, each 1 mcg/mL increase in serum Trp level was associated with 20% (95% CI: 4-34%) and 32% (95% CI: 16-44%) decrease in adjusted odds of having MS, respectively. A lower relative abundance of gut microbial genes involved in Trp catabolism was associated with higher relapse risk.<br><br>Interpretation: Trp metabolism by the gut microbiota and the kynurenine pathway may be relevant to the risk of MS in children as well as MS activity and severity.},
}
@article {pmid30349532,
year = {2018},
author = {Rausch, S and Midha, A and Kuhring, M and Affinass, N and Radonic, A and Kühl, AA and Bleich, A and Renard, BY and Hartmann, S},
title = {Parasitic Nematodes Exert Antimicrobial Activity and Benefit From Microbiota-Driven Support for Host Immune Regulation.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2282},
doi = {10.3389/fimmu.2018.02282},
pmid = {30349532},
issn = {1664-3224},
abstract = {Intestinal parasitic nematodes live in intimate contact with the host microbiota. Changes in the microbiome composition during nematode infection affect immune control of the parasites and shifts in the abundance of bacterial groups have been linked to the immunoregulatory potential of nematodes. Here we asked if the small intestinal parasite Heligmosomoides polygyrus produces factors with antimicrobial activity, senses its microbial environment and if the anti-nematode immune and regulatory responses are altered in mice devoid of gut microbes. We found that H. polygyrus excretory/secretory products exhibited antimicrobial activity against gram+/- bacteria. Parasites from germ-free mice displayed alterations in gene expression, comprising factors with putative antimicrobial functions such as chitinase and lysozyme. Infected germ-free mice developed increased small intestinal Th2 responses coinciding with a reduction in local Foxp3+RORγt+ regulatory T cells and decreased parasite fecundity. Our data suggest that nematodes sense their microbial surrounding and have evolved factors that limit the outgrowth of certain microbes. Moreover, the parasites benefit from microbiota-driven immune regulatory circuits, as an increased ratio of intestinal Th2 effector to regulatory T cells coincides with reduced parasite fitness in germ-free mice.},
}
@article {pmid30349514,
year = {2018},
author = {Chen, M and Liao, Z and Lu, B and Wang, M and Lin, L and Zhang, S and Li, Y and Liu, D and Liao, Q and Xie, Z},
title = {Huang-Lian-Jie-Du-Decoction Ameliorates Hyperglycemia and Insulin Resistant in Association With Gut Microbiota Modulation.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2380},
doi = {10.3389/fmicb.2018.02380},
pmid = {30349514},
issn = {1664-302X},
abstract = {Background: Huang-Lian-Jie-Du-Decoction (HLJDD), a prescription of traditional Chinese medicine, has been clinically used to treat diabetes for thousands of years and its mechanism was reported to be related to gut microbiota. However, no study has explored the effect of HLJDD on the gut microbiota in type 2 diabetes mellitus (T2DM) yet. Therefore, in this study, we investigated the modulation of gut microbiota induced by HLJDD treatment in T2DM in order to unveil the underlying mechanism. Methods: A combination of high-fat diet (HFD) and streptozotocin (STZ) was used to induce T2DM in rats. Bacterial communities in the fecal samples from the control group, the T2DM model group, and the HLJDD-treated T2DM group were analyzed by 16S gene sequencing, followed with a subset sample analyzed by shotgun sequencing. Results: The HLJDD treatment significantly ameliorated hyperglycemia and inflammation in T2DM rats. Additionally, our results indicated that HLJDD treatment could not only restore the gut dysbiosis in T2DM rats, which was proved by an increasing amount of short chain fatty acids (SCFAs)-producing and anti-inflammatory bacteria such as Parabacteroides, Blautia, and Akkermansia as well as a decreasing amount of conditioned pathogenic bacteria (e.g., Aerococcus, Staphylococcus, and Corynebacterium), but also modulate the dysregulated function of gut microbiome in T2DM rats, including an up-regulation in bile acid biosynthesis as well as a reduction in glycolysis/gluconeogenesis and nucleotide metabolism. Conclusion: HLJDD treatment could ameliorate hyperglycemia and restore the dysregulated microbiota structure and function to a normal condition mainly by increasing SCFAs-producing bacteria and reducing conditioned pathogenic bacteria in T2DM rats, which provides insights into the mechanism of HLJDD treatment for T2DM from the view of gut microbiota.},
}
@article {pmid30349512,
year = {2018},
author = {Skriba, A and Pluhacek, T and Palyzova, A and Novy, Z and Lemr, K and Hajduch, M and Petrik, M and Havlicek, V},
title = {Early and Non-invasive Diagnosis of Aspergillosis Revealed by Infection Kinetics Monitored in a Rat Model.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2356},
doi = {10.3389/fmicb.2018.02356},
pmid = {30349512},
issn = {1664-302X},
abstract = {Background:Aspergillus fumigatus is a ubiquitous saprophytic airborne fungus responsible for more than one million deaths every year. The siderophores of A. fumigatus represent important virulence factors that contribute to the microbiome-metabolome dialog in a host. From a diagnostic point of view, the monitoring of Aspergillus secondary metabolites in urine of a host is promising due to the non-invasiveness, rapidity, sensitivity, and potential for standardization. Methods: Using a model of experimental aspergillosis in immunocompromised Lewis rats, the fungal siderophores ferricrocin (FC) and triacetylfusarinine C (TAFC) were monitored in rat urine before and after lung inoculation with A. fumigatus conidia. Molecular biomarkers in high-dose (HD) and low-dose (LD) infection models were separated using high performance liquid chromatography (HPLC) and were detected by mass spectrometry (MS). In the current work, we corroborated the in vivo MS infection kinetics data with micro-positron emission tomography/computed tomography (μPET/CT) kinetics utilizing 68Ga-labeled TAFC. Results: In the HD model, the initial FC signal reflecting aspergillosis appeared as early as 4 h post-infection. The results from seven biological replicates showed exponentially increasing metabolite profiles over time. In A. fumigatus, TAFC was found to be a less produced biomarker that exhibited a kinetic profile identical to that of FC. The amount of siderophores contributed by the inoculating conidia was negligible and undetectable in the HD and LD models, respectively. In the μPET/CT scans, the first detectable signal in HD model was recorded 48 h post-infection. Regarding the MS assay, among nine biological replicates in the LD model, three animals did not develop any infection, while one animal experienced an exponential increase of metabolites and died on day 6 post-infection. All remaining animals had constant or random FC levels and exhibited few or no symptoms to the experiment termination. In the LD model, the TAFC concentration was not statistically significant, while the μPET/CT scan was positive as early as 6 days post-infection. Conclusion: Siderophore detection in rat urine by MS represents an early and non-invasive tool for diagnosing aspergillosis caused by A. fumigatus. μPET/CT imaging further determines the infection location in vivo and allows the visualization of the infection progression over time.},
}
@article {pmid30349509,
year = {2018},
author = {Chaudhari, NM and Gautam, A and Gupta, VK and Kaur, G and Dutta, C and Paul, S},
title = {PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2322},
doi = {10.3389/fmicb.2018.02322},
pmid = {30349509},
issn = {1664-302X},
abstract = {The conglomerate of microorganisms inhabiting various body-sites of human, known as the human microbiome, is one of the key determinants of human health and disease. Comprehensive pan-genomic and functional analysis approach for human microbiome components can enrich our understanding about impact of microbiome on human health. By utilizing this approach we developed PanGFR-HM (http://www.bioinfo.iicb.res.in/pangfr-hm/) - a novel dynamic web-resource that integrates genomic and functional characteristics of 1293 complete microbial genomes available from Human Microbiome Project. The resource allows users to explore genomic/functional diversity and genome-based phylogenetic relationships between human associated microbial genomes, not provided by any other resource. The key features implemented here include pan-genome and functional analysis of organisms based on taxonomy or body-site, and comparative analysis between groups of organisms. The first feature can also identify probable gene-loss events and significantly over/under represented KEGG/COG categories within pan-genome. The unique second feature can perform comparative genomic, functional and pathways analysis between 4 groups of microbes. The dynamic nature of this resource enables users to define parameters for orthologous clustering and to select any set of organisms for analysis. As an application for comparative feature of PanGFR-HM, we performed a comparative analysis with 67 Lactobacillus genomes isolated from human gut, oral cavity and urogenital tract, and therefore characterized the body-site specific genes, enzymes and pathways. Altogether, PanGFR-HM, being unique in its content and functionality, is expected to provide a platform for microbiome-based comparative functional and evolutionary genomics.},
}
@article {pmid30349330,
year = {2018},
author = {Jiang, X and Deng, A and Yang, J and Bai, H and Yang, Z and Wu, J and Lv, H and Li, X and Wen, T},
title = {Pathogens in the Meibomian gland and conjunctival sac: microbiome of normal subjects and patients with Meibomian gland dysfunction.},
journal = {Infection and drug resistance},
volume = {11},
number = {},
pages = {1729-1740},
doi = {10.2147/IDR.S162135},
pmid = {30349330},
issn = {1178-6973},
abstract = {Objective: To explore the composition of the ocular microbiome in normal subjects and patients with Meibomian gland dysfunction (MGD).<br><br>Subjects and methods: Seventy subjects (140 eyes) were enrolled in our study. Signs of dry eye were evaluated and bacterial species in the conjunctival sac (CS) and Meibomian gland (MG) secretions were then identified by 16S rRNA gene sequencing. Additionally, 17 subjects (34 eyes) were further evaluated to determine differences in the microbiomes in the surface and deep layers of MG using a segmental secretion analysis.<br><br>Results: The positive bacterial isolation rate was markedly higher in MG secretions than in the CS. The bacterial composition of the control and mild group was simple, whereas the composition of bacteria was more complex as the severity of MGD increased. The positive bacterial isolation rate and number of bacterial types were significantly higher in the severe MGD group than those in the control, mild and moderate MGD groups. Corynebacterium macginleyi was only detected in the severe MGD group, with an isolation rate of up to 26.3%. Furthermore, a new grading system for bacterial severity of MGD was proposed and the severity of MGD appeared to be positively correlated with a higher grade of bacterial severity. The segmental secretion analysis showed severe MGD had a significantly higher incidence of bacterial discordance rate.<br><br>Conclusion: The severity of MGD was positively correlated with a higher isolation rate, a greater number of bacterial species, and a higher grade of bacterial severity, which implied that MGD might be correlated with bacterial changes. This study provided some basis for the indications of antibiotic in clinical practice.},
}
@article {pmid30349024,
year = {2018},
author = {Chen, Z and Yeoh, YK and Hui, M and Wong, PY and Chan, MCW and Ip, M and Yu, J and Burk, RD and Chan, FKL and Chan, PKS},
title = {Diversity of macaque microbiota compared to the human counterparts.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15573},
doi = {10.1038/s41598-018-33950-6},
pmid = {30349024},
issn = {2045-2322},
abstract = {Studies on the microbial communities in non-human primate hosts provide unique insights in both evolution and function of microbes related to human health and diseases. Using 16S rRNA gene amplicon profiling, we examined the oral, anal and vaginal microbiota in a group of non-captive rhesus macaques (N = 116) and compared the compositions with the healthy communities from Human Microbiome Project. The macaque microbiota was dominated by Bacteroidetes, Firmicutes and Proteobacteria; however, there were marked differences in phylotypes enriched across body sites indicative of strong niche specialization. Compared to human gut microbiota where Bacteroides predominately enriched, the surveyed macaque anal community exhibited increased abundance of Prevotella. In contrast to the conserved human vaginal microbiota extremely dominated by Lactobacillus, the macaque vaginal microbial composition was highly diverse while lactobacilli were rare. A constant decrease of the vaginal microbiota diversity was observed among macaque samples from juvenile, adult without tubectomy, and adult with tubectomy, with the most notable distinction being the enrichment of Halomonas in juvenile and Saccharofermentans in contracepted adults. Both macaque and human oral microbiota were colonized with three most common oral bacterial genera: Streptococcus, Haemophilus and Veillonella, and shared relatively conserved communities to each other. A number of bacteria related to human pathogens were consistently detected in macaques. The findings delineate the range of structure and diversity of microbial communities in a wild macaque population, and enable the application of macaque as an animal model for future characterization of microbes in transmission, genomics and function.},
}
@article {pmid30348820,
year = {2018},
author = {Friedman, JE},
title = {Developmental Programming of Obesity and Diabetes in Mouse, Monkey, and Man in 2018: Where Are We Headed?.},
journal = {Diabetes},
volume = {67},
number = {11},
pages = {2137-2151},
doi = {10.2337/dbi17-0011},
pmid = {30348820},
issn = {1939-327X},
abstract = {Childhood obesity and its comorbidities continue to accelerate across the globe. Two-thirds of pregnant women are obese/overweight, as are 20% of preschoolers. Gestational diabetes mellitus (GDM) is escalating, affecting up to 1 in 5 pregnant women. The field of developmental origins of health and disease has begun to move beyond associations to potential causal mechanisms for developmental programming. Evidence across species compellingly demonstrates that maternal obesity, diabetes, and Western-style diets create a long-lasting signature on multiple systems, including infant stem cells, the early immune system, and gut microbiota. Such exposures accelerate adipogenesis, disrupt mitochondrial metabolism, and impair energy sensing, affecting neurodevelopment, liver, pancreas, and skeletal muscle. Attempts to prevent developmental programming have met with very limited success. A challenging level of complexity is involved in how the host genome, metabolome, and microbiome throughout pregnancy and lactation increase the offspring's risk of metabolic diseases across the life span. Considerable gaps in knowledge include the timing of exposure(s) and permanence or plasticity of the response, encompassing effects from both maternal and paternal dysmetabolism. Basic, translational, and human intervention studies targeting pathways that connect diet, microbiota, and metabolism in mothers with obesity/GDM and their infants are a critical unmet need and present new challenges for disease prevention in the next generation.},
}
@article {pmid30348765,
year = {2018},
author = {Shin, W and Kim, HJ},
title = {Intestinal barrier dysfunction orchestrates the onset of inflammatory host-microbiome cross-talk in a human gut inflammation-on-a-chip.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1810819115},
pmid = {30348765},
issn = {1091-6490},
abstract = {The initiation of intestinal inflammation involves complex intercellular cross-talk of inflammatory cells, including the epithelial and immune cells, and the gut microbiome. This multicellular complexity has hampered the identification of the trigger that orchestrates the onset of intestinal inflammation. To identify the initiator of inflammatory host-microbiome cross-talk, we leveraged a pathomimetic &quot;gut inflammation-on-a-chip&quot; undergoing physiological flow and motions that recapitulates the pathophysiology of dextran sodium sulfate (DSS)-induced inflammation in murine models. DSS treatment significantly impaired, without cytotoxic damage, epithelial barrier integrity, villous microarchitecture, and mucus production, which were rapidly recovered after cessation of DSS treatment. We found that the direct contact of DSS-sensitized epithelium and immune cells elevates oxidative stress, in which the luminal microbial stimulation elicited the production of inflammatory cytokines and immune cell recruitment. In contrast, an intact intestinal barrier successfully suppressed oxidative stress and inflammatory cytokine production against the physiological level of lipopolysaccharide or nonpathogenic Escherichia coli in the presence of immune elements. Probiotic treatment effectively reduced the oxidative stress, but it failed to ameliorate the epithelial barrier dysfunction and proinflammatory response when the probiotic administration happened after the DSS-induced barrier disruption. Maintenance of epithelial barrier function was necessary and sufficient to control the physiological oxidative stress and proinflammatory cascades, suggesting that &quot;good fences make good neighbors.&quot; Thus, the modular gut inflammation-on-a-chip identifies the mechanistic contribution of barrier dysfunction mediated by intercellular host-microbiome cross-talk to the onset of intestinal inflammation.},
}
@article {pmid30348560,
year = {2018},
author = {Bargon, R and Bruenke, J and Carli, A and Fabritius, M and Goel, R and Goswami, K and Graf, P and Groff, H and Grupp, T and Malchau, H and Mohaddes, M and Novaes de Santana, C and Phillips, KS and Rohde, H and Rolfson, O and Rondon, A and Schaer, T and Sculco, P and Svensson, K},
title = {General Assembly, Research Caveats: Proceedings of International Consensus on Orthopedic Infections.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2018.09.076},
pmid = {30348560},
issn = {1532-8406},
}
@article {pmid30348449,
year = {2018},
author = {Rayner, F and Isaacs, JD},
title = {Therapeutic tolerance in autoimmune disease.},
journal = {Seminars in arthritis and rheumatism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semarthrit.2018.09.008},
pmid = {30348449},
issn = {1532-866X},
abstract = {Experimental immune tolerance induction, enabling tissues to be transplanted across animal strains, was first demonstrated in the 1950s. Therapeutic tolerance induction, whereby immune tolerance is used to treat or prevent transplant rejection, and as a treatment for autoimmunity, followed in the 1980s. Clinical translation has been slow but the pace of change is accelerating. Numerous strategies are now being tested clinically, ranging from monoclonal antibodies against T-cells, to peptide therapies, cellular therapies and microbiome manipulation. Furthermore, technology has advanced to the stage where we can start to monitor serological and cellular autoreactivity as biomarkers of response. In terms of autoimmunity, recognition of the prolonged phase of preclinical autoimmunity in several conditions, is leading to debate around treatment of at risk individuals, and trials in patients with prodromal clinical symptoms, such as seropositive arthralgia. Additionally, potent immunomodulatory drugs are achieving a substantial track record of safety. Putting these various factors together suggests that we can soon expect to see more trials of tolerogenic strategies in pre-clinical disease, with intensive immune monitoring to guide therapy.},
}
@article {pmid30347640,
year = {2018},
author = {LaMonte, MJ and Genco, RJ and Zheng, W and McSkimming, DI and Andrews, CA and Hovey, KM and Li, L and Sun, Y and Buck, MJ and Millen, AE and Falkner, KL and Wactawski-Wende, J},
title = {Substantial Differences in the Subgingival Microbiome Measured by 16S Metagenomics According to Periodontitis Status in Older Women.},
journal = {Dentistry journal},
volume = {6},
number = {4},
pages = {},
doi = {10.3390/dj6040058},
pmid = {30347640},
issn = {2304-6767},
support = {DE13505, DE4898, DE022654, and DE024523//National Institute of Dental and Craniofacial Research/ ; N01WH32122//National Heart, Lung, and Blood Institute/ ; },
abstract = {Aging invokes physiological changes, such as immunosenescence and inflammation, that could increase host susceptibility to oral microbiome shifts that enable periodontitis progression in later life. At present, there is a dearth of studies specifically evaluating the oral microbiome and periodontitis in older adults. We used high-throughput untargeted sequencing methods and functional metagenomic analyses to assess and compare the subgingival biofilm of postmenopausal women (mean age 71 years) according to periodontitis status. Subgingival plaque samples were obtained from 15 postmenopausal women with no periodontitis, and from 15 women with severe periodontitis, determined by probing measures. The 16S rRNA gene (V1⁻V3 region) was sequenced on the 454 FLX platform. The PICRUSt technique was used to provide information on what the potential functional characteristics of microbiota might be in healthy, compared with diseased, periodontium. The subgingival microbiome associated with periodontitis showed clear differences to that associated with health. Of the 464 species identified, 22.8% had elevated abundance in disease, while only 6.3% had elevated abundance in health. Among the 12 most prevalent organisms in periodontitis, one-half have previously been recognized as periodontal pathogens by other investigators. The subgingival microbiome in periodontitis contained genes that could code for specific activities, including microbial mobility, synthesis of endotoxin, and proteolytic degradation. The healthy microbiome included genes that could code for sustaining microbial life, including encoding for transporters, glycolysis, gluconeogenesis, the Krebs cycle, and protein kinases. In the present study on postmenopausal women, aged 60 and older, the subgingival microbiome differed in composition and potential function between those with and without periodontitis. Studies of functional gene expression, such as transcriptomics, are needed to definitively identify the molecules carrying out functions associated with pathogenic subgingival complexes. This, in turn, could lead to identification of targets for enhanced management of periodontitis and, possibly, other diseases, in later life.},
}
@article {pmid30346536,
year = {2018},
author = {Dovrolis, N and Drygiannakis, I and Filidou, E and Kandilogiannakis, L and Arvanitidis, K and Tentes, I and Kolios, G and Valatas, V},
title = {Gut Microbial Signatures Underline Complicated Crohn's Disease but Vary Between Cohorts; An In Silico Approach.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izy328},
pmid = {30346536},
issn = {1536-4844},
abstract = {Microflora dysbiosis is implicated in the pathophysiology of Crohn's disease. This work analyzes differences in microbial communities and relevant metabolic pathways among the nonstricturing nonpenetrating (B1), stricturing (B2), and penetrating (B3) subphenotypes of Crohn's disease vs healthy controls. We conducted a bioinformatics analysis using the QIIME pipeline and the Calypso, linear discriminant analysis effect size, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, and STAMP tools on publicly available 16S bacterial rRNA sequencing data from terminal ileum mucosal biopsies of healthy controls and the 3 subphenotypes of Crohn's disease. We analyzed differences in microbial diversity and taxonomy, inferred active metabolic pathways via relevant genes' abundance, and detected bacterial families that could serve as biomarkers. Microbiota α-diversity was decreased within all 3 Crohn's disease subphenotypes vs control samples, with more significant reductions in B2 and B3 compared with B1. β-diversity analysis identified similar microbial patterns in B2 and B3 samples, different from those of B1 and from those of healthy controls. Abundance analysis of microbial families in cohorts, beyond altered abundances compared with healthy controls, highlighted significant differences between the B2 and B3 subphenotypes and the B1 subphenotype. A similar pattern was observed in the inference of microbial metabolomics: the B2 and B3 cohorts had different predicted metabolotypes from the B1 cohort, in addition to differences observed in Crohn's disease vs healthy controls. Our findings indicate distinct microbiome signatures in complicated Crohn's disease subphenotypes and provide the basis for further investigation into the role of gut microflora in the natural course of Crohn's disease.},
}
@article {pmid30346157,
year = {2018},
author = {Sun, W and Xiao, E and Häggblom, M and Krumins, V and Dong, Y and Sun, X and Li, F and Wang, Q and Li, B and Yan, B},
title = {Bacterial survival strategies in an alkaline tailing site and the physiological mechanisms of dominant phylotypes as revealed by metagenomic analyses.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.8b03853},
pmid = {30346157},
issn = {1520-5851},
abstract = {Microorganism inhabiting mine tailings require specific metabolic strategies to survive, which may hold the potential to clean up the pollution. Effective in situ bioremediation will rely on in-depth understanding of the function of the bacterial communities, especially the abundant and metabolically active phylotypes. In this study, the microbial communities collected from a tailing pond were profiled by 16S rRNA gene amplicon sequencing as well as shotgun metagenomic analysis. Our results indicated that carbon and nitrogen fixation as well as metal resistance and transformation were widespread among the bacterial community members, especially in highly enriched phylotypes, such as members of Thiobacillus and Meiothermus. Important functional microbial guilds such as carbon and nitrogen fixers may contribute to phytoremediation by providing nutrients for hyperaccumulator plants. In addition, metal-metabolizing bacteria may influence metal speciation and solubility. This discovery provides an understanding for microbial survival strategies in the tailings and provides future potential for the manipulation of the tailing microbiome for in situ bioremediation.},
}
@article {pmid30346023,
year = {2018},
author = {Baqui, AH and Lee, AC and Koffi, AK and Khanam, R and Mitra, DK and Dasgupta, SK and Uddin, J and Ahmed, P and Rafiqullah, I and Rahman, M and Quaiyum, A and Koumans, EH and Christian, P and Saha, SK and Mullany, LC and Labrique, A and , },
title = {Prevalence of and risk factors for abnormal vaginal flora and its association with adverse pregnancy outcomes in a rural district in north-east Bangladesh.},
journal = {Acta obstetricia et gynecologica Scandinavica},
volume = {},
number = {},
pages = {},
doi = {10.1111/aogs.13492},
pmid = {30346023},
issn = {1600-0412},
abstract = {INTRODUCTION: The role of screening and treatment for abnormal vaginal flora (AVF) on adverse pregnancy outcomes remains unclear. Using data from women who participated in a population-based cluster randomized trial who were screened and treated for AVF, we report risk factors for AVF and association of persistent AVF with adverse perinatal outcomes.<br><br>MATERIAL AND METHODS: Pregnant women (n=4,221) <19 weeks of gestation provided self-administered mid-vaginal swabs; smears were Nugent scored. AVF was treated with oral clindamycin; if AVF was present 3 weeks after treatment, persistent AVF was re-treated. We examined risk factors for AVF and the association of persistent AVF with adverse pregnancy outcomes.<br><br>RESULTS: The prevalence of AVF was 16.5%; 9.8% of women had bacterial vaginosis and 6.8% had intermediate flora. Lower economic and educational status of women were associated with increased risk of AVF. One-third of women with AVF had persistent abnormal flora; these women had higher risk of a composite measure of adverse pregnancy outcomes from 20 to < 37 weeks (preterm live birth, preterm still birth, late miscarriage) [RR 1.33, 95% CI; 1.07 to 1.65)], and of late miscarriage alone [RR 4.15, 95% CI; 2.12 to 8.12)] compared to women without AVF.<br><br>CONCLUSIONS: In this study in Sylhet District, Bangladesh, rates of AVF and persistent AVF were high and persistent AVF was associated with adverse pregnancy outcomes, with an especially high associated risk for late miscarriage. Further characterization of the microbiome and relative bacterial species density associated with persistent AVF is needed. This article is protected by copyright. All rights reserved.},
}
@article {pmid30345822,
year = {2018},
author = {Kucuksezer, UC and Ozdemir, C and Akdis, M and Akdis, CA},
title = {Chronic rhinosinusitis: pathogenesis, therapy options, and more.},
journal = {Expert opinion on pharmacotherapy},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/14656566.2018.1527904},
pmid = {30345822},
issn = {1744-7666},
abstract = {INTRODUCTION: When rhinosinusitis - the inflammation of the nasal cavity and paranasal sinuses - persists for over 12 weeks, it is termed 'chronic rhinosinusitis' (CRS). Both innate and adaptive immunity contribute to the heterogeneous inflammatory pathogenesis of CRS, which is driven by genetic and environmental factors and the microbiome. CRS is classified by the presence of polyps. Molecular mechanisms in CRS with nasal polyps are similar to those in atopic diseases. Areas covered: This review focuses on the immune pathogenesis of CRS, differences between the two CRS subtypes, and latest treatments that may aid in the provision of personalized medicine. Expert opinion: Basic research in the last decade has helped significantly in enhancing our knowledge of the pathophysiologic processes of CRS, due to which there is now a better understanding of the associated natural history, physiopathology, novel treatments, and prevention strategies. Treatment success depends on the clarification of the underlying pathogenesis and disease-contributing factors. The exploration of disease endotypes and introduction of novel agents are important advancements. Prior studies performed without disease-endotyping resulted in the inefficiency of certain drugs and insignificant results. The identification of biomarkers, development of personalized approaches, and utilization of disease algorithms are required for CRS therapy success.},
}
@article {pmid30345379,
year = {2018},
author = {Alexander, S and John, GT and Korula, A and Vijayakumar, TS and David, VG and Mohapatra, A and Valson, AT and Jacob, S and Koshy, PM and Rajan, G and John, EE and Matthai, SM and Jeyaseelan, L and Ponnusamy, B and Cook, T and Pusey, C and Daha, MR and Feehally, J and Barratt, J and Varughese, S},
title = {Protocol and rationale for the first South Asian 5-year prospective longitudinal observational cohort study and biomarker evaluation investigating the clinical course and risk profile of IgA nephropathy: GRACE IgANI cohort.},
journal = {Wellcome open research},
volume = {3},
number = {},
pages = {91},
doi = {10.12688/wellcomeopenres.14644.1},
pmid = {30345379},
issn = {2398-502X},
abstract = {Background: IgA nephropathy (IgAN) is the most common primary glomerulonephritis and an important cause of end-stage kidney disease. Unlike the slowly progressive course seen among Caucasian and East Asian subjects (actuarial survival 80-85% over 10 years), in India about 30-40% of patients have nephrotic syndrome and renal dysfunction at presentation and a 10-year renal survival of 35%, as reported from a retrospective registry. These observations cannot be entirely attributed to a lack of uniform screening protocols or late referral and attest to the probability that IgAN may not be the same disease in different parts of the world. Methods: We will prospectively recruit 200 patients with IgAN (the GRACE IgANI- Glomerular Research And Clinical Experiments- Ig ANephropathy in Indians-cohort) and stratify them into low and high risk of progression based on published absolute renal risk scores. We will test the validity of this risk score in an unselected Indian IgAN population over a 5-year follow-up period. In parallel, we will undertake extensive exploratory serum, urine, renal and microbiome biomarker studies, firstly, to determine if the underlying pathogenic pathways are the same in Indian IgAN compared to those reported in Caucasian and East Asian IgAN. Secondly, we will systematically assess the value of measuring selected biomarkers and adding this data to traditional measures of risk in IgAN to predict kidney failure. We ultimately hope to generate a composite IgAN risk score specific for the Indian population. Ethics and data dissemination: Approval was obtained from the Institutional Review Board (Silver, Research and Ethics Committee) of the Christian Medical College, Vellore, India (Ref. No. IRB Min. No. 8962 [Other] dated 23.07.2014 and IRB Min. No. 9481 [Other] dated 24.06.2015). It is anticipated that results of this study will be presented at national and international meetings, with reports being published from late 2018.},
}
@article {pmid30345284,
year = {2018},
author = {Trebicka, J and Reiberger, T and Laleman, W},
title = {Gut-Liver Axis Links Portal Hypertension to Acute-on-Chronic Liver Failure.},
journal = {Visceral medicine},
volume = {34},
number = {4},
pages = {270-275},
doi = {10.1159/000490262},
pmid = {30345284},
issn = {2297-4725},
abstract = {Acute-on-chronic liver failure (ACLF) is considered a distinct syndrome in patients with liver disease, with systemic inflammation playing a central role. Portal hypertension (PHT) is also aggravated by inflammation and may subsequently impact the course of ACLF. PHT is more than just an increase in portal pressure in the portal venous system; it aggravates the course of liver disease and, thus, also facilitates the development of acute decompensation and ACLF. A critical mechanistic link between PHT and ACLF might be the gut-liver axis, which is discussed in this review.},
}
@article {pmid30345252,
year = {2018},
author = {Yodoshi, T and Hurt, TL},
title = {Fecal Microbiota Transplantation to Patients with Refractory Very Early Onset Ulcerative Colitis.},
journal = {Pediatric gastroenterology, hepatology &amp; nutrition},
volume = {21},
number = {4},
pages = {355-360},
doi = {10.5223/pghn.2018.21.4.355},
pmid = {30345252},
issn = {2234-8646},
abstract = {Recently, fecal microbiota transplantation (FMT) has been attracting attention as a possible medical treatment of ulcerative colitis (UC). A randomized controlled trial of FMT for children with UC is currently underway. Therapeutic effects of FMT for adults with UC remain controversial. We report two cases of early-onset UC in children. A patient was diagnosed with UC at age 1-year 9-month and underwent FMT at age 2-year 3-month. He attained clinical remission for three weeks after FMT, but then relapsed at four weeks, ultimately undergoing a total colectomy. Another child was diagnosed with UC at 2-year 10-month and she underwent FMT at age 5 years. She has remained in clinical remission following FMT for 24 months and her UC has been maintained without complications with tacrolimus and azathioprine. We report that FMT for early-onset UC appears to be safe and potentially effective.},
}
@article {pmid30345066,
year = {2018},
author = {Duran-Pinedo, AE and Solbiati, J and Frias-Lopez, J},
title = {The effect of the stress hormone cortisol on the metatranscriptome of the oral microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {4},
number = {},
pages = {25},
doi = {10.1038/s41522-018-0068-z},
pmid = {30345066},
issn = {2055-5008},
support = {R01 DE021553/DE/NIDCR NIH HHS/United States ; },
abstract = {Imbalances of the microbiome, also referred to as microbial dysbiosis, could lead to a series of different diseases. One factor that has been shown to lead to dysbiosis of the microbiome is exposure to psychological stressors. Throughout evolution microorganisms of the human microbiome have developed systems for sensing host-associated signals such as hormones associated with those stressors, enabling them to recognize essential changes in their environment, thus changing their expression gene profile to fit the needs of the new environment. The most widely accepted theory explaining the ability of hormones to affect the outcome of an infection involves the suppression of the immune system. Commensal microbiota is involved in stressor-induced immunomodulation, but other biological effects are not yet known. Here we present the impact that cortisol had on the community-wide transcriptome of the oral community. We used a metatranscriptomic approach to obtain first insights into the metabolic changes induced by this stress hormone as well as which members of the oral microbiome respond to the presence of cortisol in the environment. Our findings show that the stress hormone cortisol directly induces shifts in the gene expression profiles of the oral microbiome that reproduce results found in the profiles of expression of periodontal disease and its progression.},
}
@article {pmid30344635,
year = {2018},
author = {Lavoie, C and Courcelle, M and Redivo, B and Derome, N},
title = {Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs' gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.},
journal = {Evolutionary applications},
volume = {11},
number = {9},
pages = {1671-1685},
doi = {10.1111/eva.12658},
pmid = {30344635},
issn = {1752-4571},
abstract = {Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery-raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild-born parrs' gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, because the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs' gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs' microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery-reared parrs.},
}
@article {pmid30344525,
year = {2018},
author = {Wang, Y and Wang, Z and Wang, Y and Li, F and Jia, J and Song, X and Qin, S and Wang, R and Jin, F and Kitazato, K and Wang, Y},
title = {The Gut-Microglia Connection: Implications for Central Nervous System Diseases.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2325},
doi = {10.3389/fimmu.2018.02325},
pmid = {30344525},
issn = {1664-3224},
abstract = {The importance of the gut microbiome in central nervous system (CNS) diseases has long been recognized; however, research into this connection is limited, in part, owing to a lack of convincing mechanisms because the brain is a distant target of the gut. Previous studies on the brain revealed that most of the CNS diseases affected by the gut microbiome are closely associated with microglial dysfunction. Microglia, the major CNS-resident macrophages, are crucial for the immune response of the CNS against infection and injury, as well as for brain development and function. However, the current understanding of the mechanisms controlling the maturation and function of microglia is obscure, especially regarding the extrinsic factors affecting microglial function during the developmental process. The gut microflora has been shown to significantly influence microglia from before birth until adulthood, and the metabolites generated by the microbiota regulate the inflammation response mediated by microglia in the CNS; this inspired our hypothesis that microglia act as a critical mediator between the gut microbiome and CNS diseases. Herein, we highlight and discuss current findings that show the influence of host microbiome, as a crucial extrinsic factor, on microglia within the CNS. In addition, we summarize the CNS diseases associated with both the host microbiome and microglia and explore the potential pathways by which the gut bacteria influence the pathogenesis of CNS diseases. Our work is thus a comprehensive theoretical foundation for studies on the gut-microglia connection in the development of CNS diseases; and provides great potential for researchers to target pathways associated with the gut-microglia connection and overcome CNS diseases.},
}
@article {pmid30344514,
year = {2018},
author = {McManus, R and Ravenscraft, A and Moore, W},
title = {Bacterial Associates of a Gregarious Riparian Beetle With Explosive Defensive Chemistry.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2361},
doi = {10.3389/fmicb.2018.02361},
pmid = {30344514},
issn = {1664-302X},
support = {K12 GM000708/GM/NIGMS NIH HHS/United States ; },
abstract = {Bombardier beetles (Carabidae: Brachininae) are well known for their unique explosive defensive chemistry. These beetles are found in riparian corridors throughout the American Southwest, where they commonly form large diurnal multispecies aggregations in moist areas under rocks, in crevices, and in leaf litter. Using high throughput 16S amplicon sequencing, we provide the first microbiome survey of a bombardier beetle, Brachinus elongatulus, collected from two sites in Arizona. Two bacterial taxa were present in all individuals sampled: Enterococcus and Dysgonomonas. Enterococcus has been implicated in the production of fecal aggregation pheromone components, which have been shown to regulate aggregation in the German cockroach; it is possible that Enterococcus plays a similar role in Brachinus. Dysgonomonas was found in all the secretory cells of the defensive system and gut samples. Additional studies are needed to determine if these microbes play a role in these beetles' unique chemical defense. Results also show that the majority of B. elongatulus individuals collected from both sites were infected with Spiroplasma. Many Spiroplasma are intracellular, vertically transmitted insect symbionts that may manipulate host reproduction (e.g., cause male-killing) or provide resistance to nematodes and/or parasitoid wasps. Defensive protection could be especially beneficial to B. elongatulus, which are frequently parasitized by horsehair worms (Nematomorpha). In sum, findings suggest several testable hypotheses on the effects bacteria may have on bombardier beetle behavior and physiology.},
}
@article {pmid30344303,
year = {2018},
author = {Jankauskaitė, L and Misevičienė, V and Vaidelienė, L and Kėvalas, R},
title = {Lower Airway Virology in Health and Disease-From Invaders to Symbionts.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {54},
number = {5},
pages = {},
doi = {10.3390/medicina54050072},
pmid = {30344303},
issn = {1648-9144},
abstract = {Studies of human airway virome are relatively recent and still very limited. Culture-independent microbial techniques showed growing evidence of numerous viral communities in the respiratory microbial ecosystem. The significance of different acute respiratory viruses is already known in the pathogenesis of chronic conditions, such as asthma, cystic fibrosis (CF), or chronic obstructive lung disease (COPD), and their exacerbations. Viral pathogens, such as influenza, metapneumovirus, parainfluenza, respiratory syncytial virus, or rhinovirus, have been associated with impaired immune response, acute exacerbations, and decrease in lung function in chronic lung diseases. However, more data have attributed a role to Herpes family viruses or the newly identified Anelloviridae family of viruses in chronic diseases, such as asthma, idiopathic pulmonary fibrosis (IPF), or CF. Impaired antiviral immunity, bacterial colonization, or used medication, such as glucocorticoids or antibiotics, contribute to the imbalance of airway microbiome and may shape the local viral ecosystem. A specific part of virome, bacteriophages, frames lung microbial communities through direct contact with its host, the specific bacteria known as Pseudomonas aeruginosa or their biofilm formation. Moreover, antibiotic resistance is induced through phages via horizontal transfer and leads to more severe exacerbations of chronic airway conditions. Morbidity and mortality of asthma, COPD, CF, and IPF remains high, despite an increased understanding and knowledge about the impact of respiratory virome in the pathogenesis of these conditions. Thus, more studies focus on new prophylactic methods or therapeutic agents directed toward viral⁻host interaction, microbial metabolic function, or lung microbial composition rearrangement.},
}
@article {pmid30344015,
year = {2018},
author = {Weger, BD and Gobet, C and Yeung, J and Martin, E and Jimenez, S and Betrisey, B and Foata, F and Berger, B and Balvay, A and Foussier, A and Charpagne, A and Boizet-Bonhoure, B and Chou, CJ and Naef, F and Gachon, F},
title = {The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2018.09.023},
pmid = {30344015},
issn = {1932-7420},
abstract = {The circadian clock and associated feeding rhythms have a profound impact on metabolism and the gut microbiome. To what extent microbiota reciprocally affect daily rhythms of physiology in the host remains elusive. Here, we analyzed transcriptome and metabolome profiles of male and female germ-free mice. While mRNA expression of circadian clock genes revealed subtle changes in liver, intestine, and white adipose tissue, germ-free mice showed considerably altered expression of genes associated with rhythmic physiology. Strikingly, the absence of the microbiome attenuated liver sexual dimorphism and sex-specific rhythmicity. The resulting feminization of male and masculinization of female germ-free animals is likely caused by altered sexual development and growth hormone secretion, associated with differential activation of xenobiotic receptors. This defines a novel mechanism by which the microbiome regulates host metabolism.},
}
@article {pmid30343668,
year = {2018},
author = {Abelson, B and Sun, D and Que, L and Nebel, RA and Baker, D and Popiel, P and Amundsen, CL and Chai, T and Close, C and DiSanto, M and Fraser, MO and Kielb, SJ and Kuchel, G and Mueller, ER and Palmer, MH and Parker-Autry, C and Wolfe, AJ and Damaser, MS},
title = {Sex differences in lower urinary tract biology and physiology.},
journal = {Biology of sex differences},
volume = {9},
number = {1},
pages = {45},
doi = {10.1186/s13293-018-0204-8},
pmid = {30343668},
issn = {2042-6410},
abstract = {Females and males differ significantly in gross anatomy and physiology of the lower urinary tract, and these differences are commonly discussed in the medical and scientific literature. However, less attention is dedicated to investigating the varied development, function, and biology between females and males on a cellular level. Recognizing that cell biology is not uniform, especially in the lower urinary tract of females and males, is crucial for providing context and relevance for diverse fields of biomedical investigation. This review serves to characterize the current understanding of biological sex differences between female and male lower urinary tracts, while identifying areas for future research. First, the differences in overall cell populations are discussed in the detrusor smooth muscle, urothelium, and trigone. Second, the urethra is discussed, including anatomic discussions of the female and male urethra followed by discussions of cellular differences in the urothelial and muscular layers. The pelvic floor is then reviewed, followed by an examination of the sex differences in hormonal regulation, the urinary tract microbiome, and the reticuloendothelial system. Understanding the complex and dynamic development, anatomy, and physiology of the lower urinary tract should be contextualized by the sex differences described in this review.},
}
@article {pmid30343487,
year = {2018},
author = {Graf, FE and Palm, M and Warringer, J and Farewell, A},
title = {Inhibiting conjugation as a tool in the fight against antibiotic resistance.},
journal = {Drug development research},
volume = {},
number = {},
pages = {},
doi = {10.1002/ddr.21457},
pmid = {30343487},
issn = {1098-2299},
support = {//Centre for Antibiotic Resistance Research, CARe at University of Gothenburg/ ; 2016-06503_3//Vetenskapsrådet (JPIAMR, Transpred)/ ; },
abstract = {Hit, Lead &amp; Candidate Discovery Antibiotic resistance, especially in gram-negative bacteria, is spreading globally and rapidly. Development of new antibiotics lags behind; therefore, novel approaches to the problem of antibiotic resistance are sorely needed and this commentary highlights one relatively unexplored target for drug development: conjugation. Conjugation is a common mechanism of horizontal gene transfer in bacteria that is instrumental in the spread of antibiotic resistance among bacteria. Most resistance genes are found on mobile genetic elements and primarily spread by conjugation. Furthermore, conjugative elements can act as a reservoir to maintain antibiotic resistance in the bacterial population even in the absence of antibiotic selection. Thus, conjugation can spread antibiotic resistance quickly between bacteria of the microbiome and pathogens when selective pressure (antibiotics) is introduced. Potential drug targets include the plasmid-encoded conjugation system and the host-encoded proteins important for conjugation. Ideally, a conjugation inhibitor will be used alongside antibiotics to prevent the spread of resistance to or within pathogens while not acting as a growth inhibitor itself. Inhibiting conjugation will be an important addition to our arsenal of strategies to combat the antibiotic resistance crisis, allowing us to extend the usefulness of antibiotics.},
}
@article {pmid30343431,
year = {2018},
author = {Carbonero, F and Mayta-Apaza, AC and Yu, JZ and Lindeblad, M and Lyubimov, A and Neri, F and Szilagyi, E and Bartholomew, A},
title = {A comparative analysis of gut microbiota disturbances in the Gottingen minipig and rhesus macaque models of acute radiation syndrome following bioequivalent radiation exposures.},
journal = {Radiation and environmental biophysics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00411-018-0759-0},
pmid = {30343431},
issn = {1432-2099},
support = {NIH-NIAID-DAIT-05-037//National Institute of Allergy and Infectious Diseases/ ; HHS0100201100014I//U.S. Department of Health and Human Services/ ; },
abstract = {In rodent studies, the gut microbiota has been implicated in facilitating both radioresistance, by protecting the epithelium from apoptotic responses and radiosensitivity, inducing endothelial apoptotic responses. Despite the observation that large animal models, such as the Chinese Rhesus macaque and the Gottingen Minipig, demonstrate similarity to human physiologic responses to radiation, little is known about radiation-induced changes of the gut microbiome in these models. To compare the two models, we used bioequivalent radiation doses which resulted in an LD50 for Gottingen Minipigs and Chinese Rhesus macaques, 1.9 Gy and 6.8 Gy, respectively. Fecal samples taken prior and 3 days post-radiation were used for 16S rRNA gene sequence amplicon high throughput sequencing (Illumina MiSeq). Baseline gut microbiota profiles were dissimilar between minipigs and rhesus macaques. Irradiation profoundly impacted gut microbiota profiles in both animals. Significant increases of intracellular symbionts were common to both models and to reported changes in rodents suggesting universality of these findings post-radiation. Remarkably, opposite dynamics were observed for the main phyla, with increase of Firmicutes and decrease of Bacteroidetes and Proteobacteria in minipigs but with enrichment of Bacteroidetes in rhesus macaques. Minipig changes in magnitude and in variety of species affected were more extensive than those observed in rhesus macaques. This pilot study provides an important first step in comparing the radiosensitive pig model to the comparatively more radioresistant macaque model, for the identification of microbial elements which may influence radiosensitivity.},
}
@article {pmid30343291,
year = {2018},
author = {Reininghaus, EZ and Wetzlmair, LC and Fellendorf, FT and Platzer, M and Queissner, R and Birner, A and Pilz, R and Hamm, C and Maget, A and Rieger, A and Prettenhofer, A and Wurm, W and Mörkl, S and Dalkner, N},
title = {Probiotic Treatment in Individuals with Euthymic Bipolar Disorder: A Pilot-Study on Clinical Changes and Compliance.},
journal = {Neuropsychobiology},
volume = {},
number = {},
pages = {1-9},
doi = {10.1159/000493867},
pmid = {30343291},
issn = {1423-0224},
abstract = {The importance of the microbiome for psychological well-being has gained rising interest in the last decade. A strategy to examine the role of the microbiome in different diseases is the intake of supplements that modulate the gut microbiome. Despite promising results in animal studies, research in humans is sparse to date and especially in individuals with psychiatric disorders almost missing. The current report of the ProbioBIP-one pilot study aims at describing general effects of the intake of the probiotic OMNi-BiOTiC Stress repair® on psychological parameters as well as gastrointestinal symptoms and general compliance in a cohort of euthymic individuals with bipolar disorder (BD), receiving daily probiotic treatment over a time period of 3 months. Twenty-seven individuals with BD took part in the present study (mean age = 50.7 years, SD = 12.2; females 40.7%). In sum, there was a high compliance rate with 81.5% of the study participants completing all 3 study visits and 85% of planned probiotic ingestions taken. Gastrointestinal problems were prevalent in more than half of the patients at the time of inclusion (t1). Expectedly, in the whole cohort, a high proportion of study participants experienced changes concerning digestion during probiotic treatment, around one third reported positive changes (reduced flatulence and easier and more frequent bowel movements) after 1 month (t2) and further after 3 months (t3). In contrast, a smaller part of study participants reported gastrointestinal discomfort after 1 and after 3 months (mainly flatulence and obstipation). We found a significantly reduced cognitive reactivity to sad mood between t2 and t3 indicating that participants under probiotic supplementation perceived themselves to be less distracted by ruminative thoughts. Further changes in psychiatric symptoms were small due to the euthymic state and already low scoring at the time of inclusion. Nevertheless, we found a significant symptom reduction in the rating scales measuring manic symptoms. From a clinical point of view, probiotic supplementation might provide a well-tolerated tool to positively influence gastrointestinal quality of life as well as mental and somatic health, cognition and immune response and potentially have effects on psychiatric symptoms.},
}
@article {pmid30342588,
year = {2018},
author = {Workman, AD and Kohanski, MA and Cohen, NA},
title = {Biomarkers in Chronic Rhinosinusitis with Nasal Polyps.},
journal = {Immunology and allergy clinics of North America},
volume = {38},
number = {4},
pages = {679-692},
doi = {10.1016/j.iac.2018.06.006},
pmid = {30342588},
issn = {1557-8607},
support = {I01 CX001617/CX/CSRD VA/United States ; R01 DC013588/DC/NIDCD NIH HHS/United States ; },
abstract = {Chronic rhinosinusitis is a complex disease that exists along the inflammatory spectrum between types 1 and 2 inflammation. The classic phenotypic differentiation of chronic rhinosinusitis based on the presence or absence of inflammatory polyps remains one of the best differentiators of response to therapy. Development of biologics for the treatment of atopic disease and asthma and topical therapies for sinusitis have placed renewed emphasis on understanding the pathophysiology of polyp disease. Identification of key markers of polyposis will allow for better stratification of inflammatory polyp disease endotypes to objectively identify medical therapies and track response to treatment.},
}
@article {pmid30342360,
year = {2018},
author = {Wang, L and Cheng, H and Wang, D and Zhao, B and Zhang, J and Cheng, L and Yao, P and Di Narzo, A and Shen, Y and Yu, J and Li, Y and Xu, S and Chen, J and Fan, L and Lu, J and Jiang, J and Zhou, Y and Wang, C and Zhang, Z and Hao, K},
title = {Airway microbiome is associated with respiratory functions and responses to ambient particulate matter exposure.},
journal = {Ecotoxicology and environmental safety},
volume = {167},
number = {},
pages = {269-277},
doi = {10.1016/j.ecoenv.2018.09.079},
pmid = {30342360},
issn = {1090-2414},
abstract = {BACKGROUND: Ambient particulate matter (PM) exposure has been associated with respiratory function decline in epidemiological studies. We hypothesize that a possible underlying mechanism is the perturbation of airway microbiome by PM exposure.<br><br>METHODS: During October 2016-October 2017, on two human cohorts (n = 115 in total) in Shanghai China, we systematically collected three categories of data: (1) respiratory functions, (2) airway microbiome from sputum, and (3) PM2.5 (PM of ≤ 2.5 µm in diameter) level in ambient air. We investigated the impact of PM2.5 on airway microbiome as well as the link between airway microbiome and respiratory functions using linear mixed regression models.<br><br>RESULTS: The respiratory function of our primary interest includes forced vital capacity (FVC) and forced expiratory volume in 1st second (FEV1). FEV1/FVC, an important respiratory function trait and key diagnosis criterion of COPD, was significantly associated with airway bacteria load (p = 0.0038); and FEV1 was associated with airway microbiome profile (p = 0.013). Further, airway microbiome was significantly influenced by PM2.5 exposure (p = 4.48E-11).<br><br>CONCLUSIONS: To our knowledge, for the first time, we demonstrated the impact of PM2.5 on airway microbiome, and reported the link between airway microbiome and respiratory functions. The results expand our understanding on the scope of PM2.5 exposure's influence on human respiratory system, and point to novel etiological mechanism of PM2.5 exposure induced diseases.},
}
@article {pmid30342053,
year = {2018},
author = {Vallianou, NG and Stratigou, T and Tsagarakis, S},
title = {Microbiome and diabetes: Where are we now?.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.diabres.2018.10.008},
pmid = {30342053},
issn = {1872-8227},
abstract = {Alterations in the diversity or structure of gut microbiota known as dysbiosis, may affect metabolic activities, resulting in metabolic disorders, such as obesity and diabetes. The development of more sophisticated methods, such as metagenomics sequencing, PCR-denaturing gradient gel electrophoresis, microarrays and fluorescence in situ hybridization, has expanded our knowledge on gut microbiome. Dysbiosis has been related to increased plasma concentrations of gut microbiota-derived lipopolysaccharide (LPS), which triggers the production of a variety of cytokines and the recruitment of inflammatory cells. Metabolomics have demonstrated that butyrate and propionate suppress weight gain in mice with high fat diet-induced obesity, and acetate has been proven to reduce food intake in healthy mice. The role of prebiotics, probiotics, genetically modified bacteria and fecal microbiota transplantation, as potential therapeutic challenges for type 2 diabetes will be discussed in this review.},
}
@article {pmid30341964,
year = {2018},
author = {Kröger, A and Hülsmann, C and Fickl, S and Spinell, T and Hüttig, F and Kaufmann, F and Heimbach, A and Hoffmann, P and Enkling, N and Renvert, S and Schwarz, F and Demmer, RT and Papapanou, PN and Jepsen, S and Kebschull, M},
title = {The Severity of Human Peri-Implantitis Lesions Correlates with the Level of Submucosal Microbial Dysbiosis.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.13023},
pmid = {30341964},
issn = {1600-051X},
abstract = {AIM: To cross-sectionally analyze the submucosal microbiome of peri-implantitis (PI) lesions at different severity levels.<br><br>MATERIALS AND METHODS: Microbial signatures of 45 submucosal plaque samples from untreated peri-implantitis lesions obtained from 30 non-smoking, systemically healthy subjects were assessed by 16s sequencing. Linear mixed models were used to identify taxa with differential abundance by probing depth, after correction for age, gender, and multiple samples per subject. Network analyses were performed to identify groups of taxa with mutual occurrence or exclusion. Subsequently, the effects of peri-implant probing depth on submucosal microbial dysbiosis was calculated using the microbial dysbiosis index.<br><br>RESULTS: In total, we identified 337 different taxa in the submucosal microbiome of peri-implantitis. Total abundance of 12 taxa correlated significantly with increasing probing depth; a significant relationship with lower probing depth was found for 16 taxa. Network analysis identified two mutually exclusive complexes associated with shallow pockets and deeper pockets, respectively. Deeper peri-implant pockets were associated with significantly increased dysbiosis.<br><br>CONCLUSION: Increases in peri-implant pocket depth are associated with substantial changes in the submucosal microbiome and increasing levels of dysbiosis. This article is protected by copyright. All rights reserved.},
}
@article {pmid30341500,
year = {2018},
author = {Deja-Sikora, E and Gołębiewski, M and Kalwasińska, A and Krawiec, A and Kosobucki, P and Walczak, M},
title = {Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1270-5},
pmid = {30341500},
issn = {1432-184X},
support = {1919-B//Uniwersytet Mikolaja Kopernika w Toruniu/ ; },
abstract = {Intraterrestrial waters harbor microbial communities being extensively studied to understand microbial processes underlying subsurface ecosystem functioning. This paper provides the results of an investigation on the microbiomes of unique, subsurface sulfidic waters associated with Upper Jurassic, Cretaceous, and Miocene sediments. We used high-throughput 16S rDNA amplicon sequencing to reveal the structure of bacterial and archaeal communities in water samples differing in sulfide content (20-960 mg/dm3), salinity (1.3-3.2%), and depth of extraction (60-660 m below ground level). Composition of the bacterial communities strongly varied across the samples; however, the bacteria participating in the sulfur cycle were common in all sulfidic waters. The shallowest borehole water (60 m bgl) was dominated by sulfur-oxidizing Epsilonproteobacteria (Sulfurimonas, Sulfurovum). In the waters collected from greater depths (148-300 m bgl), the prevalence of Betaproteobacteria (Comamonadaceae) and sulfate/sulfur-reducing Deltaproteobacteria (Desulfopila, Desulfomicrobium, MSBL7) was observed. Sulfate reducers (members of Clostridia: Candidatus Desulforudis) were the most abundant bacteria in the deepest borehole water (660 m bgl). Out of 850 bacterial OTUs, only one, affiliated with the Comamonadaceae family, was found abundant (> 1% of total bacterial sequences) in all samples. Contribution of Archaea to the whole microbial communities was lower than 0.5%. Archaeal communities did not differ across the samples and they consisted of Halobacteriaceae. Out of 372 archaeal OTUs, five, belonging to the four genera Natronomonas, Halorubrum, Halobellus, and Halorhabdus, were the most numerous.},
}
@article {pmid30341443,
year = {2018},
author = {Zhernakova, DV and Le, TH and Kurilshikov, A and Atanasovska, B and Bonder, MJ and Sanna, S and Claringbould, A and Võsa, U and Deelen, P and Franke, L and de Boer, RA and Kuipers, F and Netea, MG and Hofker, MH and Wijmenga, C and Zhernakova, A and Fu, J and , and , },
title = {Author Correction: Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41588-018-0275-9},
pmid = {30341443},
issn = {1546-1718},
abstract = {In the version of this paper originally published, there was a typographical error. In the Discussion, the sentence &quot;In line with this, Ep-CAM-deficient mice exhibited increased intestinal permeability and decreased ion transport60, which may contribute to CVD susceptibility risk59&quot; originally read iron instead of ion transport. This error has been corrected in the HTML, PDF and print versions of the article.},
}
@article {pmid30341410,
year = {2018},
author = {Cryan, JF and Dinan, TG},
title = {Decoding the role of the microbiome on amygdala function and social behaviour.},
journal = {Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41386-018-0233-3},
pmid = {30341410},
issn = {1740-634X},
support = {SFI/12/RC/2273//Science Foundation Ireland (SFI)/ ; SFI/12/RC/2273//Science Foundation Ireland (SFI)/ ; },
}
@article {pmid30341386,
year = {2018},
author = {Arokiyaraj, S and Seo, SS and Kwon, M and Lee, JK and Kim, MK},
title = {Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15479},
doi = {10.1038/s41598-018-33750-y},
pmid = {30341386},
issn = {2045-2322},
support = {1610210//National Cancer Center (NCC)/ ; 1610210//National Cancer Center (NCC)/ ; 1610210//National Cancer Center (NCC)/ ; 1610210//National Cancer Center (NCC)/ ; 1610210//National Cancer Center (NCC)/ ; },
abstract = {The present study aimed to identify the cervical microbes that are associated with HPV negativity, HPV clearance and HPV persistence and to assess the microbes' longitudinal associations as related to HPV infection dynamics among Korean women. We enrolled 41 women with 107 samples, and classified them according to the HPV infection dynamics: HPV negativity (21 samples, 10 subjects), HPV clearance (42 samples, 15 subjects), and HPV persistence (44 samples, 16 subjects). Cervical swabs were collected at the baseline and six-month-interval follow-up visits. HPV positivity was determined by HPV DNA HC2 assay, and the microbiome was analyzed using 16SrRNA pyrosequencing, linear discriminant analysis effect size and multivariate logistic analysis. In the multivariate logistic analysis results, Lactobacillus crispatus (multivariate OR (mOR) = 8.25, 95% CI 2.13~32.0) was predominant in the HPV-negative group. We observed that Eubacterium eligens (mOR = 11.5, 95% CI 1.31~101.4), Gardnerella vaginalis (mOR = 17.0, 95% CI 2.18-131.8), and Ureaplasma urealyticum (mOR = 7.42, 95% CI 1.3-42.46) had the strongest associations with HPV clearance, and Lactobacillus johnsonii (mOR = 16.4, 95% CI 1.77-152.2) with HPV persistence. Overall, greater diversity was observed in HPV-persistence than in HPV-negative women. Our findings suggest that the presence and prevalence of a specific cervical microbiome are factors involved in HPV dynamics.},
}
@article {pmid30341117,
year = {2018},
author = {Jitsumura, M and Cunningham, AL and Hitchings, MD and Islam, S and Davies, AP and Row, PE and Riddell, AD and Kinross, J and Wilkinson, TS and Jenkins, GJ and Williams, JG and Harris, DA},
title = {Protocol for faecal microbiota transplantation in ulcerative colitis (FMTUC): a randomised feasibility study.},
journal = {BMJ open},
volume = {8},
number = {10},
pages = {e021987},
doi = {10.1136/bmjopen-2018-021987},
pmid = {30341117},
issn = {2044-6055},
abstract = {BACKGROUND: The interaction of the gut microbiota with the human host is implicated in the pathogenesis of inflammatory and immunological diseases including ulcerative colitis (UC). Faecal microbiota transplantation (FMT) as a method of restoring gut microbial diversity is of increasing interest as a therapeutic approach in the management of UC. The current literature lacks consensus about the dose of FMT, route of administration and duration of response.<br><br>METHODS AND ANALYSIS: This single-blinded randomised trial will explore the feasibility of FMT in 30 treatment-naïve patients with histologically confirmed distal UC limited to the recto-sigmoid region (up to 40 cm from the anal verge). This study aims to estimate the magnitude of treatment response to FMT under controlled conditions. The intervention (FMT) will be administered by rectal retention enema. It will test the feasibility of randomising patients to: (i) single FMT dose, (ii) five daily FMT doses or (iii) control (no FMT dose). All groups will receive standard antibiotic gut decontamination and bowel preparation before FMT. Recruitment will take place over a 24-month period with a 12-week patient follow-up. Trial objectives include evaluation of the magnitude of treatment response to FMT, investigation of the clinical value of metabolic phenotyping for predicting the clinical response to FMT and testing the recruitment rate of donors and patients for a study in FMT. This feasibility trial will enable an estimate of number of patients needed, help determine optimal study conditions and inform the choice of endpoints for a future definitive phase III study.<br><br>ETHICS AND DISSEMINATION: The trial is approved by the regional ethics committee and is sponsored by Abertawe Bro Morgannwg University's Health Board. Written informed consent from all patients will be obtained. Serious adverse events will be reported to the sponsor. Trial results will be disseminated via peer review publication and shared with trial participants.<br><br>TRIAL REGISTRATION NUMBER: ISRCTN 58082603; Pre-results.},
}
@article {pmid30340631,
year = {2018},
author = {Li, HY and Wang, H and Wang, HT and Xin, PY and Xu, XH and Ma, Y and Liu, WP and Teng, CY and Jiang, CL and Lou, LP and Arnold, W and Cralle, L and Zhu, YG and Chu, JF and Gilbert, JA and Zhang, ZJ},
title = {The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {187},
doi = {10.1186/s40168-018-0561-x},
pmid = {30340631},
issn = {2049-2618},
support = {41673081//National Natural Science Foundation of China/ ; 41373074//National Natural Science Foundation of China/ ; 31500409//National Natural Science Foundation of China/ ; 41877346//National Natural Science Foundation of China/ ; 2013C33001//Zhejiang Science and Technology Innovation Program/ ; DE-AC02-06CH11357//U.S. Department of Energy/ ; },
abstract = {BACKGROUND: Paddy soil dissolved organic matter (DOM) represents a major hotspot for soil biogeochemistry, yet we know little about its chemodiversity let alone the microbial community that shapes it. Here, we leveraged ultrahigh-resolution mass spectrometry, amplicon, and metagenomic sequencing to characterize the molecular distribution of DOM and the taxonomic and functional microbial diversity in paddy soils across China. We hypothesized that variances in microbial community significantly associate with changes in soil DOM molecular composition.<br><br>RESULTS: We report that both microbial and DOM profiles revealed geographic patterns that were associated with variation in mean monthly precipitation, mean annual temperature, and pH. DOM molecular diversity was significantly correlated with microbial taxonomic diversity. An increase in DOM molecules categorized as peptides, carbohydrates, and unsaturated aliphatics, and a decrease in those belonging to polyphenolics and polycyclic aromatics, significantly correlated with proportional changes in some of the microbial taxa, such as Syntrophobacterales, Thermoleophilia, Geobacter, Spirochaeta, Gaiella, and Defluviicoccus. DOM composition was also associated with the relative abundances of the microbial metabolic pathways, such as anaerobic carbon fixation, glycolysis, lignolysis, fermentation, and methanogenesis.<br><br>CONCLUSIONS: Our study demonstrates the continental-scale distribution of DOM is significantly correlated with the taxonomic profile and metabolic potential of the rice paddy microbiome. Abiotic factors that have a distinct effect on community structure can also influence the chemodiversity of DOM and vice versa. Deciphering these associations and the underlying mechanisms can precipitate understanding of the complex ecology of paddy soils, as well as help assess the effects of human activities on biogeochemistry and greenhouse gas emissions in paddy soils.},
}
@article {pmid30340536,
year = {2018},
author = {Verster, AJ and Borenstein, E},
title = {Competitive lottery-based assembly of selected clades in the human gut microbiome.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {186},
doi = {10.1186/s40168-018-0571-8},
pmid = {30340536},
issn = {2049-2618},
support = {DP2AT00780201//National Institutes of Health/ ; PGS//Natural Sciences and Engineering Research Council of Canada/ ; 1R01GM124312-01//National Institute of General Medical Sciences/ ; },
abstract = {BACKGROUND: While the composition of the gut microbiome has now been well described by several large-scale studies, models that can account for the range of microbiome compositions that have been observed are still lacking. One model that has been well studied in macro communities and that could be useful for understanding microbiome assembly is the competitive lottery model. This model posits that groups of organisms from a regional pool of species are able to colonize the same niche and that the first species to arrive will take over the entire niche, excluding other group members.<br><br>RESULTS: Here, we examined whether this model also plays a role in the assembly of the human gut microbiome, defining measures to identify groups of organisms whose distribution across samples conforms to the competitive lottery schema. Applying this model to multiple datasets with thousands of human gut microbiome samples, we identified several taxonomic groups that exhibit a lottery-like distribution, including the Akkermansia, Dialister, and Phascolarctobacterium genera. We validated that these groups exhibit lottery-like assembly in multiple independent microbiome datasets confirming that this assembly schema is universal and not cohort specific. Examining the distribution of species from these groups in the gut microbiome of developing infants, we found that the initial lottery winner can be replaced by a different member of the group. We further found that species from lottery-like groups tend to have fewer genes in their genomes, suggesting more specialized species that are less able to engage in niche differentiation.<br><br>CONCLUSIONS: Combined, our findings highlight the complex and dynamic process through which microbial communities assemble and suggest that different phylogenetic groups may follow different models during this process.},
}
@article {pmid30340395,
year = {2018},
author = {Zopf, Y and Reljic, D and Dieterich, W},
title = {Dietary Effects on Microbiota-New Trends with Gluten-Free or Paleo Diet.},
journal = {Medical sciences (Basel, Switzerland)},
volume = {6},
number = {4},
pages = {},
doi = {10.3390/medsci6040092},
pmid = {30340395},
issn = {2076-3271},
abstract = {A well-balanced diet is the basis for a healthy life. Both the western diet and special diets can have a relevant impact on the microbiome and promote the development of various diseases. There has been an increase in food-related disorders in recent years, largely associated with dramatic changes in food consumption trends and main nutrients. A major response to food intolerances has been the adoption of new dietary trends involving the reduction or exclusion of specific food ingredients. Especially gluten-containing, but also gluten-free cereals are in the cross-fire. Supporters of the gluten-free diet argue that gluten triggers inflammation and related diseases, while followers of the Paleo diet drastically impeach all cereals as dangerous for human health. To date, no controlled studies support or reject a positive health effect of a gluten-free or cereal-free diet. Future large-scale studies need to evaluate the effect of gluten-containing and gluten-free cereals and the various diets on human health, inflammatory parameters, clinical symptoms, and the gut microbiota (including the bacteria, fungi, and viruses). Dietary-associated changes in compositional and functional microbiota traits should be correlated with the health status for the future development of dietary recommendations and potential clinical interventions.},
}
@article {pmid30340391,
year = {2018},
author = {Cukrowska, B},
title = {Microbial and Nutritional Programming-The Importance of the Microbiome and Early Exposure to Potential Food Allergens in the Development of Allergies.},
journal = {Nutrients},
volume = {10},
number = {10},
pages = {},
doi = {10.3390/nu10101541},
pmid = {30340391},
issn = {2072-6643},
abstract = {The &quot;microbiota hypothesis&quot; ties the increase in allergy rates observed in highly developed countries over the last decades to disturbances in the gut microbiota. Gut microbiota formation depends on a number of factors and occurs over approximately 1000 days of life, including the prenatal period. During this period the microbiota helps establish the functional immune phenotype, including immune tolerance. The development of immune tolerance depends also on early exposure to potential food allergens, a process referred to as nutritional programming. This article elaborates on the concepts of microbial and nutritional programming and their role in the primary prevention of allergy.},
}
@article {pmid30340384,
year = {2018},
author = {Obrenovich, MEM},
title = {Leaky Gut, Leaky Brain?.},
journal = {Microorganisms},
volume = {6},
number = {4},
pages = {},
doi = {10.3390/microorganisms6040107},
pmid = {30340384},
issn = {2076-2607},
abstract = {'Leaky gut' syndrome, long-associated with celiac disease, has attracted much attention in recent years and for decades, was widely known in complementary/alternative medicine circles. It is often described as an increase in the permeability of the intestinal mucosa, which could allow bacteria, toxic digestive metabolites, bacterial toxins, and small molecules to 'leak' into the bloodstream. Nervous system involvement with celiac disease is know to occur even at subclinical levels. Gluten and gluten sensitivity are considered to trigger this syndrome in individuals genetically predisposed to celiac disease. However, the incidence of celiac disease in the general population is quite low. Nevertheless, increased public interest in gluten sensitivity has contributed to expanded food labels stating 'gluten-free' and the proliferation of gluten-free products, which further drives gluten-free lifestyle changes by individuals without frank celiac disease. Moreover, systemic inflammation is associated with celiac disease, depression, and psychiatric comorbidities. This mini-review focuses on the possible neurophysiological basis of leaky gut; leaky brain disease; and the microbiota's contribution to inflammation, gastrointestinal, and blood-brain barrier integrity, in order to build a case for possible mechanisms that could foster further 'leaky' syndromes. We ask whether a gluten-free diet is important for anyone or only those with celiac disease.},
}
@article {pmid30340338,
year = {2018},
author = {Liu, Y and Alookaran, JJ and Rhoads, JM},
title = {Probiotics in Autoimmune and Inflammatory Disorders.},
journal = {Nutrients},
volume = {10},
number = {10},
pages = {},
doi = {10.3390/nu10101537},
pmid = {30340338},
issn = {2072-6643},
support = {R01AT007083//National Institutes of Health/ ; R03AI117442//National Institutes of Health/ ; },
abstract = {Probiotics have been used to ameliorate gastrointestinal symptoms since ancient times. Over the past 40 years, probiotics have been shown to impact the immune system, both in vivo and in vitro. This interaction is linked to gut microbes, their polysaccharide antigens, and key metabolites produced by these bacteria. At least four metabolic pathways have been implicated in mechanistic studies of probiotics, based on mechanistic studies in animal models. Microbial⁻immune system crosstalk has been linked to: short-chain fatty acid production and signaling, tryptophan metabolism and the activation of aryl hydrocarbon receptors, nucleoside signaling in the gut, and activation of the intestinal histamine-2 receptor. Several randomized controlled trials have now shown that microbial modification by probiotics may improve gastrointestinal symptoms and multiorgan inflammation in rheumatoid arthritis, ulcerative colitis, and multiple sclerosis. Future work will need to carefully assess safety issues, selection of optimal strains and combinations, and attempts to prolong the duration of colonization of beneficial microbes.},
}
@article {pmid30340031,
year = {2018},
author = {Deguine, J},
title = {First Encounters.},
journal = {Cell},
volume = {175},
number = {3},
pages = {601-603},
doi = {10.1016/j.cell.2018.10.002},
pmid = {30340031},
issn = {1097-4172},
abstract = {The role of the microbiome across a range of physiological process is undebatable, but how this complex community is assembled and regulated remains only partially understood. Recent studies focused on a single sensor show that the neonatal period may represent a critical window and that immune interactions at this time could durably influence the members of the microbiome.},
}
@article {pmid30339501,
year = {2018},
author = {Elkrief, A and Derosa, L and Zitvogel, L and Kroemer, G and Routy, B},
title = {The intimate relationship between gut microbiota and cancer immunotherapy.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-5},
doi = {10.1080/19490976.2018.1527167},
pmid = {30339501},
issn = {1949-0984},
abstract = {Immunotherapy is widely used to treat a large variety of malignancies and has revolutionized the therapeutic approach to cancer. Major efforts are ongoing to identify biomarkers that predict response to immunotherapy as well as new strategies to improve ICI efficacy and clinical outcomes. Studies have shown that the gut microbiome determines the extent to which ICIs may invigorate the anticancer immune response. Here, the authors review recent studies that have described the effects of the gut microbiota on the efficacy of CTLA-4 and PD-1 inhibitors and outline potential future clinical directions of these findings.},
}
@article {pmid30338410,
year = {2018},
author = {Chen, X and Devaraj, S},
title = {Gut Microbiome in Obesity, Metabolic Syndrome, and Diabetes.},
journal = {Current diabetes reports},
volume = {18},
number = {12},
pages = {129},
doi = {10.1007/s11892-018-1104-3},
pmid = {30338410},
issn = {1539-0829},
abstract = {PURPOSE OF REVIEW: Obesity and diabetes are worldwide epidemics. There is also a growing body of evidence relating the gut microbiome composition to insulin resistance. The purpose of this review is to delineate the studies linking gut microbiota to obesity, metabolic syndrome, and diabetes.<br><br>RECENT FINDINGS: Animal studies as well as proof of concept studies using fecal transplantation demonstrate the pivotal role of the gut microbiota in regulating insulin resistance states and inflammation. While we still need to standardize methodologies to study the microbiome, there is an abundance of evidence pointing to the link between gut microbiome, inflammation, and insulin resistance, and future studies should be aimed at identifying unifying mechanisms.},
}
@article {pmid30338244,
year = {2018},
author = {Saxena, R and Mittal, P and Clavaud, C and Dhakan, DB and Hegde, P and Veeranagaiah, MM and Saha, S and Souverain, L and Roy, N and Breton, L and Misra, N and Sharma, VK},
title = {Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {346},
doi = {10.3389/fcimb.2018.00346},
pmid = {30338244},
issn = {2235-2988},
abstract = {Several scalp microbiome studies from different populations have revealed the association of dandruff with bacterial and fungal dysbiosis. However, the functional role of scalp microbiota in scalp disorders and health remains scarcely explored. Here, we examined the bacterial and fungal diversity of the scalp microbiome and their potential functional role in the healthy and dandruff scalp of 140 Indian women. Propionibacterium acnes and Staphylococcus epidermidis emerged as the core bacterial species, where the former was associated with a healthy scalp and the latter with dandruff scalp. Along with the commonly occurring Malassezia species (M. restricta and M. globosa) on the scalp, a strikingly high association of dandruff with yet uncharacterized Malassezia species was observed in the core mycobiome. Functional analysis showed that the fungal microbiome was enriched in pathways majorly implicated in cell-host adhesion in the dandruff scalp, while the bacterial microbiome showed a conspicuous enrichment of pathways related to the synthesis and metabolism of amino acids, biotin, and other B-vitamins, which are reported as essential nutrients for hair growth. A systematic measurement of scalp clinical and physiological parameters was also carried out, which showed significant correlations with the microbiome and their associated functional pathways. The results point toward a new potential role of bacterial commensals in maintaining the scalp nutrient homoeostasis and highlights an important and yet unknown role of the scalp microbiome, similar to the gut microbiome. This study, therefore, provides new perspectives on the better understanding of the pathophysiology of dandruff.},
}
@article {pmid30338216,
year = {2018},
author = {Karav, S and Casaburi, G and Frese, SA},
title = {Reduced colonic mucin degradation in breastfed infants colonized by Bifidobacterium longum subsp. infantis EVC001.},
journal = {FEBS open bio},
volume = {8},
number = {10},
pages = {1649-1657},
doi = {10.1002/2211-5463.12516},
pmid = {30338216},
issn = {2211-5463},
abstract = {Mucin glycoproteins play an important role in protecting the gut epithelium by keeping gut microbes from direct contact with the gut epithelium while allowing for diffusion of small molecules from the lumen to the epithelium. The mucin glycocalyx can be degraded by gut bacteria such as Bacteroides and Akkermansia, but other bacteria, such as Bifidobacterium longum subsp. Infantis, cannot consume mucin glycans. Untargeted mass spectrometry profiles were compared to microbiome profiles to assess how different gut microbiomes affect colonic mucin degradation. Samples obtained from nine infants colonized by Bifidobacterium infantis EVC001 and from 10 infants colonized by higher levels of mucolytic taxa (controls), including Bacteroides, were compared. Previously performed untargeted nano-high-performance liquid chromatography-chip/time-of-flight mass spectrometry was used to detect and quantify glycans originating from colonic mucin. Colonic mucin-derived O-glycans from control infants composed 37.68% (± 3.14% SD) of the total glycan structure pool, whereas colonic mucin-derived O-glycans made up of only 1.78% (± 0.038% SD) of the total in B. infantis EVC001 samples. The relative abundance of these colonic mucin-derived O-glycans in the total glycan pool was higher among control, 26.98% (± 8.48% SD), relative to B. infantis-colonized infants, 1.68% (± 1.12% SD). Key taxa, such as Bacteroidaceae, were significantly and positively correlated with the abundance of these structures, while Bifidobacteriaceae were significantly and negatively associated with these structures. These results suggest that colonization of infants by B. infantis may diminish colonic glycan degradation and help maintain barrier function in the gastrointestinal tract of infants.},
}
@article {pmid30337963,
year = {2018},
author = {O'Brien, CL and Kiely, CJ and Pavli, P},
title = {The microbiome of Crohn's disease aphthous ulcers.},
journal = {Gut pathogens},
volume = {10},
number = {},
pages = {44},
doi = {10.1186/s13099-018-0265-6},
pmid = {30337963},
issn = {1757-4749},
abstract = {Background: Reduced intestinal microbial diversity and bacterial imbalance (dysbiosis) are seen in studies of Crohn's disease. As it is difficult to obtain biopsy samples before disease presentation, the earliest mucosal lesions in Crohn's disease, aphthous ulcers, present the best chance at assessing microbial communities at the onset of disease or a new flare. The aim of our study was to compare the microbial communities of aphthous ulcers and adjacent normal mucosa from patients with Crohn's disease with normal mucosa from controls.<br><br>Results: We did not observe bacterial imbalance or reduced alpha diversity in Crohn's disease aphthous ulcers and adjacent mucosa, relative to control biopsies. Bacteroides were common to all Crohn's disease and control samples, and there were no bacterial taxa unique to aphthous ulcers. The relative abundance of Faecalibacterium was not reduced in aphthous ulcers relative to control mucosa, and was not more likely to be detected in control samples.<br><br>Conclusions: In contrast to well-documented changes seen in late-stage Crohn's disease, microbial communities of aphthous ulcers do not display evidence of bacterial imbalance or reduced diversity. Our data suggest that dysbiosis occurs during active disease, and improves when patients are in remission.},
}
@article {pmid30337914,
year = {2018},
author = {Munukka, E and Ahtiainen, JP and Puigbó, P and Jalkanen, S and Pahkala, K and Keskitalo, A and Kujala, UM and Pietilä, S and Hollmén, M and Elo, L and Huovinen, P and D'Auria, G and Pekkala, S},
title = {Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2323},
doi = {10.3389/fmicb.2018.02323},
pmid = {30337914},
issn = {1664-302X},
abstract = {Recent studies suggest that exercise alters the gut microbiome. We determined whether six-weeks endurance exercise, without changing diet, affected the gut metagenome and systemic metabolites of overweight women. Previously sedentary overweight women (n = 19) underwent a six-weeks endurance exercise intervention, but two were excluded due to antibiotic therapy. The gut microbiota composition and functions were analyzed by 16S rRNA gene amplicon sequencing and metagenomics. Body composition was analyzed with DXA X-ray densitometer and serum metabolomics with NMR metabolomics. Total energy and energy-yielding nutrient intakes were analyzed from food records using Micro-Nutrica software. Serum clinical variables were determined with KONELAB instrument. Soluble Vascular Adhesion Protein 1 (VAP-1) was measured with ELISA and its' enzymatic activity as produced hydrogen peroxide. The exercise intervention was effective, as maximal power and maximum rate of oxygen consumption increased while android fat mass decreased. No changes in diet were observed. Metagenomic analysis revealed taxonomic shifts including an increase in Akkermansia and a decrease in Proteobacteria. These changes were independent of age, weight, fat % as well as energy and fiber intake. Training slightly increased Jaccard distance of genus level β-diversity. Training did not alter the enriched metagenomic pathways, which, according to Bray Curtis dissimilarity analysis, may have been due to that only half of the subjects' microbiomes responded considerably to exercise. Nevertheless, tranining decreased the abundance of several genes including those related to fructose and amino acid metabolism. These metagenomic changes, however, were not translated into major systemic metabolic changes as only two metabolites, phospholipids and cholesterol in large VLDL particles, decreased after exercise. Training also decreased the amine oxidase activity of pro-inflammatory VAP-1, whereas no changes in CRP were detected. All clinical blood variables were within normal range, yet exercise slightly increased glucose and decreased LDL and HDL. In conclusion, exercise training modified the gut microbiome without greatly affecting systemic metabolites or body composition. Based on our data and existing literature, we propose that especially Akkermansia and Proteobacteria are exercise-responsive taxa. Our results warrant the need for further studies in larger cohorts to determine whether exercise types other than endurance exercise also modify the gut metagenome.},
}
@article {pmid30337906,
year = {2018},
author = {Meirelles, PM and Soares, AC and Oliveira, L and Leomil, L and Appolinario, LR and Francini-Filho, RB and de Moura, RL and de Barros Almeida, RT and Salomon, PS and Amado-Filho, GM and Kruger, R and Siegle, E and Tschoeke, DA and Kudo, I and Mino, S and Sawabe, T and Thompson, CC and Thompson, FL},
title = {Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2203},
doi = {10.3389/fmicb.2018.02203},
pmid = {30337906},
issn = {1664-302X},
abstract = {Local and global stressors have affected coral reef ecosystems worldwide. Switches from coral to algal dominance states and microbialization are the major processes underlying the global decline of coral reefs. However, most of the knowledge concerning microbialization has not considered physical disturbances (e.g., typhoons, waves, and currents). Southern Japan reef systems have developed under extreme physical disturbances. Here, we present analyses of a three-year investigation on the coral reefs of Ishigaki Island that comprised benthic and fish surveys, water quality analyses, metagenomics and microbial abundance data. At the four studied sites, inorganic nutrient concentrations were high and exceeded eutrophication thresholds. The dissolved organic carbon (DOC) concentration (up to 233.3 μM) and microbial abundance (up to 2.5 × 105 cell/mL) values were relatively high. The highest vibrio counts coincided with the highest turf cover (∼55-85%) and the lowest coral cover (∼4.4-10.2%) and fish biomass (0.06 individuals/m2). Microbiome compositions were similar among all sites and were dominated by heterotrophs. Our data suggest that a synergic effect among several regional stressors are driving coral decline. In a high hydrodynamics reef environment, high algal/turf cover, stimulated by eutrophication and low fish abundance due to overfishing, promote microbialization. Together with crown-of-thorns starfish (COTS) outbreaks and possible of climate changes impacts, theses coral reefs are likely to collapse.},
}
@article {pmid30337152,
year = {2018},
author = {Nho, K and Kueider-Paisley, A and MahmoudianDehkordi, S and Arnold, M and Risacher, SL and Louie, G and Blach, C and Baillie, R and Han, X and Kastenmüller, G and Jia, W and Xie, G and Ahmad, S and Hankemeier, T and van Duijn, CM and Trojanowski, JQ and Shaw, LM and Weiner, MW and Doraiswamy, PM and Saykin, AJ and Kaddurah-Daouk, R and , },
title = {Altered bile acid profile in mild cognitive impairment and Alzheimer's disease: Relationship to neuroimaging and CSF biomarkers.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jalz.2018.08.012},
pmid = {30337152},
issn = {1552-5279},
abstract = {INTRODUCTION: Bile acids (BAs) are the end products of cholesterol metabolism produced by human and gut microbiome co-metabolism. Recent evidence suggests gut microbiota influence pathological features of Alzheimer's disease (AD) including neuroinflammation and amyloid-β deposition.<br><br>METHOD: Serum levels of 20 primary and secondary BA metabolites from the AD Neuroimaging Initiative (n = 1562) were measured using targeted metabolomic profiling. We assessed the association of BAs with the &quot;A/T/N&quot; (amyloid, tau, and neurodegeneration) biomarkers for AD: cerebrospinal fluid (CSF) biomarkers, atrophy (magnetic resonance imaging), and brain glucose metabolism ([18F]FDG PET).<br><br>RESULTS: Of 23 BAs and relevant calculated ratios after quality control procedures, three BA signatures were associated with CSF Aβ1-42 (&quot;A&quot;) and three with CSF p-tau181 (&quot;T&quot;) (corrected P < .05). Furthermore, three, twelve, and fourteen BA signatures were associated with CSF t-tau, glucose metabolism, and atrophy (&quot;N&quot;), respectively (corrected P < .05).<br><br>DISCUSSION: This is the first study to show serum-based BA metabolites are associated with &quot;A/T/N&quot; AD biomarkers, providing further support for a role of BA pathways in AD pathophysiology. Prospective clinical observations and validation in model systems are needed to assess causality and specific mechanisms underlying this association.},
}
@article {pmid30337151,
year = {2018},
author = {MahmoudianDehkordi, S and Arnold, M and Nho, K and Ahmad, S and Jia, W and Xie, G and Louie, G and Kueider-Paisley, A and Moseley, MA and Thompson, JW and St John Williams, L and Tenenbaum, JD and Blach, C and Baillie, R and Han, X and Bhattacharyya, S and Toledo, JB and Schafferer, S and Klein, S and Koal, T and Risacher, SL and Kling, MA and Motsinger-Reif, A and Rotroff, DM and Jack, J and Hankemeier, T and Bennett, DA and De Jager, PL and Trojanowski, JQ and Shaw, LM and Weiner, MW and Doraiswamy, PM and van Duijn, CM and Saykin, AJ and Kastenmüller, G and Kaddurah-Daouk, R and , },
title = {Altered bile acid profile associates with cognitive impairment in Alzheimer's disease-An emerging role for gut microbiome.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jalz.2018.07.217},
pmid = {30337151},
issn = {1552-5279},
abstract = {INTRODUCTION: Increasing evidence suggests a role for the gut microbiome in central nervous system disorders and a specific role for the gut-brain axis in neurodegeneration. Bile acids (BAs), products of cholesterol metabolism and clearance, are produced in the liver and are further metabolized by gut bacteria. They have major regulatory and signaling functions and seem dysregulated in Alzheimer's disease (AD).<br><br>METHODS: Serum levels of 15 primary and secondary BAs and their conjugated forms were measured in 1464 subjects including 370 cognitively normal older adults, 284 with early mild cognitive impairment, 505 with late mild cognitive impairment, and 305 AD cases enrolled in the AD Neuroimaging Initiative. We assessed associations of BA profiles including selected ratios with diagnosis, cognition, and AD-related genetic variants, adjusting for confounders and multiple testing.<br><br>RESULTS: In AD compared to cognitively normal older adults, we observed significantly lower serum concentrations of a primary BA (cholic acid [CA]) and increased levels of the bacterially produced, secondary BA, deoxycholic acid, and its glycine and taurine conjugated forms. An increased ratio of deoxycholic acid:CA, which reflects 7α-dehydroxylation of CA by gut bacteria, strongly associated with cognitive decline, a finding replicated in serum and brain samples in the Rush Religious Orders and Memory and Aging Project. Several genetic variants in immune response-related genes implicated in AD showed associations with BA profiles.<br><br>DISCUSSION: We report for the first time an association between altered BA profile, genetic variants implicated in AD, and cognitive changes in disease using a large multicenter study. These findings warrant further investigation of gut dysbiosis and possible role of gut-liver-brain axis in the pathogenesis of AD.},
}
@article {pmid30337150,
year = {2018},
author = {Yonts, AB and Kronman, MP and Hamdy, RF},
title = {The Burden and Impact of Antibiotic Prescribing in Ambulatory Pediatrics.},
journal = {Current problems in pediatric and adolescent health care},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cppeds.2018.09.002},
pmid = {30337150},
issn = {1538-3199},
abstract = {Antibiotics are one of the most commonly prescribed classes of medication for children and adolescents. While they are arguably the most powerful tool we possess against bacterial infections, they are frequently given to children whose illnesses are due to viruses or other non-infectious etiologies. When antibiotics are not used judiciously, the consequences can be serious and accumulate over time. This review article quantifies the burden of antimicrobial use in the pediatric outpatient setting in the United States, reviews recommended first line antibiotic regimens for common outpatient pediatric and adolescent conditions, investigates the reasons for inappropriate prescribing of antibiotics in outpatient healthcare settings, and explores the range of consequences of overuse and inappropriate use of antibiotics, from adverse drug reactions to impact on the microbiome to rising rates of antimicrobial resistance in common ambulatory conditions.},
}
@article {pmid30337035,
year = {2018},
author = {Mai, T and Fatheree, NY and Gleason, W and Liu, Y and Rhoads, JM},
title = {Infantile Colic: New Insights into an Old Problem.},
journal = {Gastroenterology clinics of North America},
volume = {47},
number = {4},
pages = {829-844},
doi = {10.1016/j.gtc.2018.07.008},
pmid = {30337035},
issn = {1558-1942},
abstract = {Infant colic is a characteristic group of behaviors seen in young infants. The most prominent feature is prolonged crying. Additional characteristics, including clenching of the fists and flexion of the hips, have led to the suggestion that these behaviors are related to abdominal discomfort. In this article, we show emerging evidence to support the concept that infant colic could represent gut inflammation and microbial dysbiosis that impacts brain function and even brain development.},
}
@article {pmid30337034,
year = {2018},
author = {Thaxton, GE and Melby, PC and Manary, MJ and Preidis, GA},
title = {New Insights into the Pathogenesis and Treatment of Malnutrition.},
journal = {Gastroenterology clinics of North America},
volume = {47},
number = {4},
pages = {813-827},
doi = {10.1016/j.gtc.2018.07.007},
pmid = {30337034},
issn = {1558-1942},
abstract = {The volume of research into the pathogenesis and treatment of malnutrition has increased markedly over the past ten years, providing mechanistic insights that can be leveraged into more effective treatment options. These discoveries have been driven by several landmark studies employing metabolomics, metagenomics, and new preclinical models. This review highlights some of the most important recent findings, focusing in particular on the emerging roles of prenatal and perinatal factors, protein deficiency, impaired gut barrier function, immune deficiency, and the intestinal microbiome.},
}
@article {pmid30337032,
year = {2018},
author = {Lenfestey, MW and Neu, J},
title = {Gastrointestinal Development: Implications for Management of Preterm and Term Infants.},
journal = {Gastroenterology clinics of North America},
volume = {47},
number = {4},
pages = {773-791},
doi = {10.1016/j.gtc.2018.07.005},
pmid = {30337032},
issn = {1558-1942},
abstract = {The gastrointestinal (GI) system provides digestive, absorptive, neuroendocrine, and immunologic functions to support overall health. If normal development is interrupted, a variety of complications and disease can arise. This article explores normal development of the GI tract and specific clinical challenges pertinent to preterm and term infants. Specific topics include abnormal motility, gastroesophageal reflux, current feeding recommendations for preterm infants, effects of parenteral nutrition, and the relationship between the GI tract and the immune system.},
}
@article {pmid30337029,
year = {2018},
author = {Khlevner, J and Park, Y and Margolis, KG},
title = {Brain-Gut Axis: Clinical Implications.},
journal = {Gastroenterology clinics of North America},
volume = {47},
number = {4},
pages = {727-739},
doi = {10.1016/j.gtc.2018.07.002},
pmid = {30337029},
issn = {1558-1942},
abstract = {This article provides an overarching view of what is currently known about the physiology of the brain-gut axis in both health and disease and how these concepts apply to irritable bowel syndrome, the most common functional gastrointestinal disorder in pediatrics.},
}
@article {pmid30337028,
year = {2018},
author = {Chumpitazi, BP},
title = {Update on Dietary Management of Childhood Functional Abdominal Pain Disorders.},
journal = {Gastroenterology clinics of North America},
volume = {47},
number = {4},
pages = {715-726},
doi = {10.1016/j.gtc.2018.07.001},
pmid = {30337028},
issn = {1558-1942},
abstract = {Diet plays a significant role for children with functional abdominal pain disorders. A large majority of these children identify at least 1 food that exacerbates their symptoms. Malabsorbed carbohydrates may have both direct and microbiome-mediated physiologic effects. There are several factors associated with carbohydrate symptom generation, including (1) the amount ingested, (2) ingestion with a meal, (3) small intestinal enzymatic activity, (4) consuming the carbohydrate with microorganisms capable of breaking down the carbohydrate, (5) the gut microbiome, and (6) host factors. Therapies include carbohydrate (single and/or comprehensive) restriction, selective prebiotic and/or enzyme supplementation. Fiber supplementation may also be beneficial.},
}
@article {pmid30336831,
year = {2018},
author = {Libby, P and Loscalzo, J and Ridker, PM and Farkouh, ME and Hsue, PY and Fuster, V and Hasan, AA and Amar, S},
title = {Inflammation, Immunity, and Infection in Atherothrombosis: JACC Review Topic of the Week.},
journal = {Journal of the American College of Cardiology},
volume = {72},
number = {17},
pages = {2071-2081},
doi = {10.1016/j.jacc.2018.08.1043},
pmid = {30336831},
issn = {1558-3597},
support = {U01 HG007690/HG/NHGRI NIH HHS/United States ; R01 HL061795/HL/NHLBI NIH HHS/United States ; R01 DE014079/DE/NIDCR NIH HHS/United States ; P50 GM107618/GM/NIGMS NIH HHS/United States ; R01 HL076801/HL/NHLBI NIH HHS/United States ; U54 HL119145/HL/NHLBI NIH HHS/United States ; R01 HL080472/HL/NHLBI NIH HHS/United States ; R37 HL061795/HL/NHLBI NIH HHS/United States ; K24 AI112393/AI/NIAID NIH HHS/United States ; R01 HL125034/HL/NHLBI NIH HHS/United States ; },
abstract = {Observations on human and experimental atherosclerosis, biomarker studies, and now a large-scale clinical trial support the operation of immune and inflammatory pathways in this disease. The factors that incite innate and adaptive immune responses implicated in atherogenesis and in lesion complication include traditional risk factors such as protein and lipid components of native and modified low-density lipoprotein, angiotensin II, smoking, visceral adipose tissue, and dysmetabolism. Infectious processes and products of the endogenous microbiome might also modulate atherosclerosis and its complications either directly, or indirectly by eliciting local and systemic responses that potentiate disease expression. Trials with antibiotics have not reduced recurrent cardiovascular events, nor have vaccination strategies yet achieved clinical translation. However, anti-inflammatory interventions such as anticytokine therapy and colchicine have begun to show efficacy in this regard. Thus, inflammatory and immune mechanisms can link traditional and emerging risk factors to atherosclerosis, and offer novel avenues for therapeutic intervention.},
}
@article {pmid30336775,
year = {2018},
author = {Roguet, A and Eren, AM and Newton, RJ and McLellan, SL},
title = {Fecal source identification using random forest.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {185},
doi = {10.1186/s40168-018-0568-3},
pmid = {30336775},
issn = {2049-2618},
support = {R01AI091829//National Institutes of Health/ ; },
abstract = {BACKGROUND: Clostridiales and Bacteroidales are uniquely adapted to the gut environment and have co-evolved with their hosts resulting in convergent microbiome patterns within mammalian species. As a result, members of Clostridiales and Bacteroidales are particularly suitable for identifying sources of fecal contamination in environmental samples. However, a comprehensive evaluation of their predictive power and development of computational approaches is lacking. Given the global public health concern for waterborne disease, accurate identification of fecal pollution sources is essential for effective risk assessment and management. Here, we use random forest algorithm and 16S rRNA gene amplicon sequences assigned to Clostridiales and Bacteroidales to identify common fecal pollution sources. We benchmarked the accuracy, consistency, and sensitivity of our classification approach using fecal, environmental, and artificial in silico generated samples.<br><br>RESULTS: Clostridiales and Bacteroidales classifiers were composed mainly of sequences that displayed differential distributions (host-preferred) among sewage, cow, deer, pig, cat, and dog sources. Each classifier correctly identified human and individual animal sources in approximately 90% of the fecal and environmental samples tested. Misclassifications resulted mostly from false-positive identification of cat and dog fecal signatures in host animals not used to build the classifiers, suggesting characterization of additional animals would improve accuracy. Random forest predictions were highly reproducible, reflecting the consistency of the bacterial signatures within each of the animal and sewage sources. Using in silico generated samples, we could detect fecal bacterial signatures when the source dataset accounted for as little as ~ 0.5% of the assemblage, with ~ 0.04% of the sequences matching the classifiers. Finally, we developed a proxy to estimate proportions among sources, which allowed us to determine which sources contribute the most to observed fecal pollution.<br><br>CONCLUSION: Random forest classification with 16S rRNA gene amplicons offers a rapid, sensitive, and accurate solution for identifying host microbial signatures to detect human and animal fecal contamination in environmental samples.},
}
@article {pmid30336272,
year = {2018},
author = {Prattichizzo, F and Giuliani, A and Mensà, E and Sabbatinelli, J and De Nigris, V and Rippo, MR and La Sala, L and Procopio, AD and Olivieri, F and Ceriello, A},
title = {Pleiotropic effects of metformin: Shaping the microbiome to manage type 2 diabetes and postpone ageing.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arr.2018.10.003},
pmid = {30336272},
issn = {1872-9649},
abstract = {Metformin is the first-choice therapy to lower glycaemia and manage type 2 diabetes. Continuously emerging epidemiological data and experimental models are showing additional protective effects of metformin against a number of age-related diseases (ARDs), e.g., cardiovascular diseases and cancer. This evidence has prompted the design of a specific trial, i.e., the Targeting Aging with Metformin (TAME) trial, to test metformin as an anti-ageing molecule. However, a unifying or prevailing mechanism of action of metformin is still debated. Here, we summarize the epidemiological data linking metformin to ARD prevention. Then, we dissect the deeply studied mechanisms of action explaining its antihyperglycemic effect and the putative mechanisms supporting its anti-ageing properties, focusing on studies using clinically pertinent doses. We hypothesize that the molecular observations obtained in different models with metformin could be indirectly mediated by its effect on gut flora. Novel evidence suggests that metformin reshapes the human microbiota, promoting the growth of beneficial bacterial species and counteracting the expansion of detrimental bacterial species. In turn, this action would influence the balance between pro- and anti-inflammatory circulating factors, thereby promoting glycaemic control and healthy ageing. This framework may reconcile diverse observations, providing information for designing further studies to elucidate the complex interplay between metformin and the metabiome harboured in mammalian body compartments, thereby paving the way for innovative, bacterial-based therapeutics to manage type 2 diabetes and foster a longer healthspan.},
}
@article {pmid30335763,
year = {2018},
author = {Orantes, LC and Monroy, C and Dorn, PL and Stevens, L and Rizzo, DM and Morrissey, L and Hanley, JP and Rodas, AG and Richards, B and Wallin, KF and Helms Cahan, S},
title = {Uncovering vector, parasite, blood meal and microbiome patterns from mixed-DNA specimens of the Chagas disease vector Triatoma dimidiata.},
journal = {PLoS neglected tropical diseases},
volume = {12},
number = {10},
pages = {e0006730},
doi = {10.1371/journal.pntd.0006730},
pmid = {30335763},
issn = {1935-2735},
abstract = {Chagas disease, considered a neglected disease by the World Health Organization, is caused by the protozoan parasite Trypanosoma cruzi, and transmitted by >140 triatomine species across the Americas. In Central America, the main vector is Triatoma dimidiata, an opportunistic blood meal feeder inhabiting both domestic and sylvatic ecotopes. Given the diversity of interacting biological agents involved in the epidemiology of Chagas disease, having simultaneous information on the dynamics of the parasite, vector, the gut microbiome of the vector, and the blood meal source would facilitate identifying key biotic factors associated with the risk of T. cruzi transmission. In this study, we developed a RADseq-based analysis pipeline to study mixed-species DNA extracted from T. dimidiata abdomens. To evaluate the efficacy of the method across spatial scales, we used a nested spatial sampling design that spanned from individual villages within Guatemala to major biogeographic regions of Central America. Information from each biotic source was distinguished with bioinformatics tools and used to evaluate the prevalence of T. cruzi infection and predominant Discrete Typing Units (DTUs) in the region, the population genetic structure of T. dimidiata, gut microbial diversity, and the blood meal history. An average of 3.25 million reads per specimen were obtained, with approximately 1% assigned to the parasite, 20% to the vector, 11% to bacteria, and 4% to putative blood meals. Using a total of 6,405 T. cruzi SNPs, we detected nine infected vectors harboring two distinct DTUs: TcI and a second unidentified strain, possibly TcIV. Vector specimens were sufficiently variable for population genomic analyses, with a total of 25,710 T. dimidiata SNPs across all samples that were sufficient to detect geographic genetic structure at both local and regional scales. We observed a diverse microbiotic community, with significantly higher bacterial species richness in infected T. dimidiata abdomens than those that were not infected. Unifrac analysis suggests a common assemblage of bacteria associated with infection, which co-occurs with the typical gut microbial community derived from the local environment. We identified vertebrate blood meals from five T. dimidiata abdomens, including chicken, dog, duck and human; however, additional detection methods would be necessary to confidently identify blood meal sources from most specimens. Overall, our study shows this method is effective for simultaneously generating genetic data on vectors and their associated parasites, along with ecological information on feeding patterns and microbial interactions that may be followed up with complementary approaches such as PCR-based parasite detection, 18S eukaryotic and 16S bacterial barcoding.},
}
@article {pmid30335629,
year = {2018},
author = {Dayananda, P and Wilcox, MH},
title = {Irritable bowel syndrome following Clostridium difficile infection.},
journal = {Current opinion in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOG.0000000000000490},
pmid = {30335629},
issn = {1531-7056},
abstract = {PURPOSE OF REVIEW: The aim of this review was to provide an overview of the current understanding of the diagnosis, pathophysiology, and the role of the gut microbiome in Clostridium difficile infection (CDI)-related postinfectious irritable bowel syndrome (PI-IBS).<br><br>RECENT FINDINGS: PI-IBS is a recognized pathological entity and was estimated to affect 1 in 10 patients with infectious enteritis. CDI remains a major healthcare burden worldwide with a one in four chance of recurrence of symptoms following treatment. While there is growing interest in functional gastrointestinal disorders including PI-IBS, studies examining the prevalence and risk factors of CDI-related PI-IBS remain scarce. One of many proposed mechanisms for PI-IBS is related to dysbiosis of the gut microbiota, which is the hallmark of CDI pathogenesis. Therefore, restoration of the gut microbiota, which is associated with successful outcomes in CDI, may be a potential treatment option for PI-IBS. However, two randomized controlled trails exploring the restoration of the gut microbiota using faecal microbiota transplant came to differing conclusions.<br><br>SUMMARY: PI-IBS, particularly CDI-related PI-IBS, remains an understudied area. A better understanding of the pathophysiology of PI-IBS is essential to developing more specific and effective management strategies.},
}
@article {pmid30335369,
year = {2018},
author = {Spirito, C and Marzilli, A and Angenent, LT},
title = {Higher Substrate Ratios of Ethanol to Acetate Steered Chain Elongation Toward n-Caprylate in a Bioreactor with Product Extraction.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.8b03856},
pmid = {30335369},
issn = {1520-5851},
abstract = {Syngas fermentation to ethanol and acetate has recently been coupled to microbial chain elongation to produce medium-chain carboxylates (MCCs), including n-caproate and n-caprylate. These medium chain carboxylates are relatively hydrophobic, and thus easier to extract from solution than miscible ethanol. Here, we examined the effect of eleven different ethanol-to-acetate substrate ratios (ranging from 1.8 to 275 g COD g COD-1 [1.2 to 183 mole mole-1]) on directing chain elongation toward n-caprylate in a 0.7-L upflow anaerobic filter with product extraction. During an eight-month operating period, we monitored the performance and characterized the microbiome composition of this chain-elongating bioreactor. We also developed a thermodynamic model to predict the favorability of n-caprylate production at different substrate ratios. As predicted by our model, higher ethanol-to-acetate substrate ratios fed to our bioreactor led to higher specificities for n-caprylate production. We observed that feeding primarily ethanol to the bioreactor (i.e., ethanol-to-acetate substrate ratio of 275 g COD g COD-1) resulted in the highest specificity for n-caprylate, but the n-caprylate production rate decreased at this high ratio, resulting in lower conversion efficiencies. Thus, care should be taken not to overload the system with primarily ethanol as the substrate and to lower the organic loading rate.},
}
@article {pmid30333965,
year = {2018},
author = {Wise, A and Robertson, B and Choudhury, B and Rautava, S and Isolauri, E and Salminen, S and Bode, L},
title = {Infants Are Exposed to Human Milk Oligosaccharides Already in utero.},
journal = {Frontiers in pediatrics},
volume = {6},
number = {},
pages = {270},
doi = {10.3389/fped.2018.00270},
pmid = {30333965},
issn = {2296-2360},
abstract = {Human milk oligosaccharides (HMOs) are complex carbohydrates that are highly abundant in and, in their complexity, unique to human milk. Accumulating evidence indicates that exposure to HMOs in the postnatal period affects immediate as well as long-term infant health and development. However, studies reported in the 1970s showed that HMOs already appear in maternal urine and blood during pregnancy and as early as the first trimester. In this pilot study we aimed to determine whether or not HMOs also appear in amniotic fluid. We enrolled women during pregnancy and collected their urine and amniotic fluid at birth as well as their milk 4 days postpartum. We analyzed the samples by high-performance liquid chromatography (HPLC) and mass spectrometry and identified several HMOs including 2'-fucosyllactose, 3-fucosyllactose, difucosyllactose, and 6'-sialyllactose to be present in different relative abundancies in all three tissues. This is the first report that HMOs appear in amniotic fluid and that the fetus is already exposed to HMOs in utero, warranting future research to investigate the immediate and long-term implications on fetal and infant health and development.},
}
@article {pmid30333815,
year = {2018},
author = {Ogai, K and Nagase, S and Mukai, K and Iuchi, T and Mori, Y and Matsue, M and Sugitani, K and Sugama, J and Okamoto, S},
title = {A Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2362},
doi = {10.3389/fmicb.2018.02362},
pmid = {30333815},
issn = {1664-302X},
abstract = {The swabbing and tape-stripping methods have traditionally been used for collecting skin microbiome samples for skin bacterial analysis, although no reports have compared the outcome of these methods for collecting skin bacteria. Our purpose was to show the differences in microbial composition between samples collected using the swabbing and tape-stripping methods, by both the next generation sequencing and culture studies. The skin microbiome was collected by both methods, and the samples were processed for a sequence-based microbiome analysis and culture study. The next-generation sequencing results showed that skin bacteria collected using the tape-stripping method were comparable to those collected using the swabbing method. In the culture study, the tape-stripping method collected a greater number and wider variety of viable skin bacteria than the swabbing method. These results suggest that the tape-stripping method is comparable to the swabbing method for collecting viable skin bacteria, without losing fidelity to the composition of skin microbiome.},
}
@article {pmid30333810,
year = {2018},
author = {Lane, B and Sharma, S and Niu, C and Maina, AW and Wagacha, JM and Bluhm, BH and Woloshuk, CP},
title = {Changes in the Fungal Microbiome of Maize During Hermetic Storage in the United States and Kenya.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2336},
doi = {10.3389/fmicb.2018.02336},
pmid = {30333810},
issn = {1664-302X},
abstract = {Prior to harvest, maize kernels are invaded by a diverse population of fungal organisms that comprise the microbiome of the grain mass. Poor post-harvest practices and improper drying can lead to the growth of mycotoxigenic storage fungi and deterioration of grain quality. Hermetic storage bags are a low-cost technology for the preservation of grain during storage, which has seen significant adoption in many regions of Sub-Saharan Africa. This study explored the use of high-throughput DNA sequencing of the fungal Internal Transcribed Spacer 2 (ITS2) region for characterization of the fungal microbiome before and after 3 months of storage in hermetic and non-hermetic (woven) bags in the United States and Kenya. Analysis of 1,377,221 and 3,633,944 ITS2 sequences from the United States and Kenya, respectively, resulted in 251 and 164 operational taxonomic units (OTUs). Taxonomic assignment of these OTUs revealed 63 and 34 fungal genera in the US and Kenya samples, respectively, many of which were not detected by traditional plating methods. The most abundant genus was Fusarium, which was identified in all samples. Storage fungi were detected in the grain mass prior to the storage experiments and increased in relative abundance within the woven bags. The results also indicate that storage location had no effect on the fungal microbiome of grain stored in the United States, while storage bag type led to significant changes in fungal composition. The fungal microbiome of the Kenya grain also underwent significant changes in composition during storage and fungal diversity increased during storage regardless of bag type. Our results indicated that extraction of DNA from ground kernels is sufficient for identifying the fungi associated with the maize. The results also indicated that bag type was the most important factor influencing changes in fungal microbiome during storage. The results also support the recommended use of hermetic storage for reducing food safety risks, especially from mycotoxigenic fungi.},
}
@article {pmid30333238,
year = {2018},
author = {Dutzan, N and Kajikawa, T and Abusleme, L and Greenwell-Wild, T and Zuazo, CE and Ikeuchi, T and Brenchley, L and Abe, T and Hurabielle, C and Martin, D and Morell, RJ and Freeman, AF and Lazarevic, V and Trinchieri, G and Diaz, PI and Holland, SM and Belkaid, Y and Hajishengallis, G and Moutsopoulos, NM},
title = {A dysbiotic microbiome triggers TH17 cells to mediate oral mucosal immunopathology in mice and humans.},
journal = {Science translational medicine},
volume = {10},
number = {463},
pages = {},
doi = {10.1126/scitranslmed.aat0797},
pmid = {30333238},
issn = {1946-6242},
abstract = {Periodontitis is one of the most common human inflammatory diseases, yet the mechanisms that drive immunopathology and could be therapeutically targeted are not well defined. Here, we demonstrate an expansion of resident memory T helper 17 (TH17) cells in human periodontitis. Phenocopying humans, TH17 cells expanded in murine experimental periodontitis through local proliferation. Unlike homeostatic oral TH17 cells, which accumulate in a commensal-independent and interleukin-6 (IL-6)-dependent manner, periodontitis-associated expansion of TH17 cells was dependent on the local dysbiotic microbiome and required both IL-6 and IL-23. TH17 cells and associated neutrophil accumulation were necessary for inflammatory tissue destruction in experimental periodontitis. Genetic or pharmacological inhibition of TH17 cell differentiation conferred protection from immunopathology. Studies in a unique patient population with a genetic defect in TH17 cell differentiation established human relevance for our murine experimental studies. In the oral cavity, human TH17 cell defects were associated with diminished periodontal inflammation and bone loss, despite increased prevalence of recurrent oral fungal infections. Our study highlights distinct functions of TH17 cells in oral immunity and inflammation and paves the way to a new targeted therapeutic approach for the treatment of periodontitis.},
}
@article {pmid30333180,
year = {2018},
author = {Kato, T and Yamazaki, K and Nakajima, M and Date, Y and Kikuchi, J and Hase, K and Ohno, H and Yamazaki, K},
title = {Oral Administration of Porphyromonas gingivalis Alters the Gut Microbiome and Serum Metabolome.},
journal = {mSphere},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSphere.00460-18},
pmid = {30333180},
issn = {2379-5042},
abstract = {Periodontal disease induced by periodontopathic bacteria like Porphyromonas gingivalis is demonstrated to increase the risk of metabolic, inflammatory, and autoimmune disorders. Although precise mechanisms for this connection have not been elucidated, we have proposed mechanisms by which orally administered periodontopathic bacteria might induce changes in gut microbiota composition, barrier function, and immune system, resulting in an increased risk of diseases characterized by low-grade systemic inflammation. Accumulating evidence suggests a profound effect of altered gut metabolite profiles on overall host health. Therefore, it is possible that P. gingivalis can affect these metabolites. To test this, C57BL/6 mice were administered with P. gingivalis W83 orally twice a week for 5 weeks and compared with sham-inoculated mice. The gut microbial communities were analyzed by pyrosequencing the 16S rRNA genes. Inferred metagenomic analysis was used to determine the relative abundance of KEGG pathways encoded in the gut microbiota. Serum metabolites were analyzed using nuclear magnetic resonance (NMR)-based metabolomics coupled with multivariate statistical analyses. Oral administration of P. gingivalis induced a change in gut microbiota composition. The distributions of metabolic pathways differed between the two groups, including those related to amino acid metabolism and, in particular, the genes for phenylalanine, tyrosine, and tryptophan biosynthesis. Also, alanine, glutamine, histidine, tyrosine, and phenylalanine were significantly increased in the serum of P. gingivalis-administered mice. In addition to altering immune modulation and gut barrier function, oral administration of P. gingivalis affects the host's metabolic profile. This supports our hypothesis regarding a gut-mediated systemic pathology resulting from periodontal disease.IMPORTANCE Increasing evidence suggest that alterations of the gut microbiome underlie metabolic disease pathology by modulating gut metabolite profiles. We have shown that orally administered Porphyromonas gingivalis, a representative periodontopathic bacterium, alters the gut microbiome; that may be a novel mechanism by which periodontitis increases the risk of various diseases. Given the association between periodontal disease and metabolic diseases, it is possible that P. gingivalis can affect the metabolites. Metabolite profiling analysis demonstrated that several amino acids related to a risk of developing diabetes and obesity were elevated in P. gingivalis-administered mice. Our results revealed that the increased risk of various diseases by P. gingivalis might be mediated at least in part by alteration of metabolic profiles. The findings should add new insights into potential links between periodontal disease and systemic disease for investigators in periodontal disease and also for investigators in the field of other diseases, such as metabolic diseases.},
}
@article {pmid30333179,
year = {2018},
author = {Xue, Z and Kable, ME and Marco, ML},
title = {Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products.},
journal = {mSphere},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSphere.00410-18},
pmid = {30333179},
issn = {2379-5042},
abstract = {DNA sequencing and analysis methods were compared for 16S rRNA V4 PCR amplicon and genomic DNA (gDNA) mock communities encompassing nine bacterial species commonly found in milk and dairy products. The two communities comprised strain-specific DNA that was pooled before (gDNA) or after (PCR amplicon) the PCR step. The communities were sequenced on the Illumina MiSeq and Ion Torrent PGM platforms and then analyzed using the QIIME 1 (UCLUST) and Divisive Amplicon Denoising Algorithm 2 (DADA2) analysis pipelines with taxonomic comparisons to the Greengenes and Ribosomal Database Project (RDP) databases. Examination of the PCR amplicon mock community with these methods resulted in operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) that ranged from 13 to 118 and were dependent on the DNA sequencing method and read assembly steps. The additional 4 to 109 OTUs/ASVs (from 9 OTUs/ASVs) included assignments to spurious taxa and sequence variants of the 9 species included in the mock community. Comparisons between the gDNA and PCR amplicon mock communities showed that combining gDNAs from the different strains prior to PCR resulted in up to 8.9-fold greater numbers of spurious OTUs/ASVs. However, the DNA sequencing method and paired-end read assembly steps conferred the largest effects on predictions of bacterial diversity, with effect sizes of 0.88 (Bray-Curtis) and 0.32 (weighted Unifrac), independent of the mock community type. Overall, DNA sequencing performed with the Ion Torrent PGM and analyzed with DADA2 and the Greengenes database resulted in the most accurate predictions of the mock community phylogeny, taxonomy, and diversity.IMPORTANCE Validated methods are urgently needed to improve DNA sequence-based assessments of complex bacterial communities. In this study, we used 16S rRNA PCR amplicon and gDNA mock community standards, consisting of nine, dairy-associated bacterial species, to evaluate the most commonly applied 16S rRNA marker gene DNA sequencing and analysis platforms used in evaluating dairy and other bacterial habitats. Our results show that bacterial metataxonomic assessments are largely dependent on the DNA sequencing platform and read curation method used. DADA2 improved sequence annotation compared with QIIME 1, and when combined with the Ion Torrent PGM DNA sequencing platform and the Greengenes database for taxonomic assignment, the most accurate representation of the dairy mock community standards was reached. This approach will be useful for validating sample collection and DNA extraction methods and ultimately investigating bacterial population dynamics in milk- and dairy-associated environments.},
}
@article {pmid30333051,
year = {2018},
author = {Fahimipour, AK and Hartmann, EM and Siemens, A and Kline, J and Levin, DA and Wilson, H and Betancourt-Román, CM and Brown, GZ and Fretz, M and Northcutt, D and Siemens, KN and Huttenhower, C and Green, JL and Van Den Wymelenberg, K},
title = {Daylight exposure modulates bacterial communities associated with household dust.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {175},
doi = {10.1186/s40168-018-0559-4},
pmid = {30333051},
issn = {2049-2618},
support = {P50 GM098911/GM/NIGMS NIH HHS/United States ; P50 GM098911//National Institutes of Health/ ; },
abstract = {BACKGROUND: Microbial communities associated with indoor dust abound in the built environment. The transmission of sunlight through windows is a key building design consideration, but the effects of light exposure on dust communities remain unclear. We report results of an experiment and computational models designed to assess the effects of light exposure and wavelengths on the structure of the dust microbiome. Specifically, we placed household dust in replicate model &quot;rooms&quot; with windows that transmitted visible, ultraviolet, or no light and measured taxonomic compositions, absolute abundances, and viabilities of the resulting bacterial communities.<br><br>RESULTS: Light exposure per se led to lower abundances of viable bacteria and communities that were compositionally distinct from dark rooms, suggesting preferential inactivation of some microbes over others under daylighting conditions. Differences between communities experiencing visible and ultraviolet light wavelengths were relatively minor, manifesting primarily in abundances of dead human-derived taxa. Daylighting was associated with the loss of a few numerically dominant groups of related microorganisms and apparent increases in the abundances of some rare groups, suggesting that a small number of microorganisms may have exhibited modest population growth under lighting conditions. Although biological processes like population growth on dust could have generated these patterns, we also present an alternate statistical explanation using sampling models from ecology; simulations indicate that artefactual, apparent increases in the abundances of very rare taxa may be a null expectation following the selective inactivation of dominant microorganisms in a community.<br><br>CONCLUSIONS: Our experimental and simulation-based results indicate that dust contains living bacterial taxa that can be inactivated following changes in local abiotic conditions and suggest that the bactericidal potential of ordinary window-filtered sunlight may be similar to ultraviolet wavelengths across dosages that are relevant to real buildings.},
}
@article {pmid30332487,
year = {2018},
author = {Wyman, SK and Avila-Herrera, A and Nayfach, S and Pollard, KS},
title = {A most wanted list of conserved microbial protein families with no known domains.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0205749},
doi = {10.1371/journal.pone.0205749},
pmid = {30332487},
issn = {1932-6203},
abstract = {The number and proportion of genes with no known function are growing rapidly. To quantify this phenomenon and provide criteria for prioritizing genes for functional characterization, we developed a bioinformatics pipeline that identifies robustly defined protein families with no annotated domains, ranks these with respect to phylogenetic breadth, and identifies them in metagenomics data. We applied this approach to 271 965 protein families from the SFams database and discovered many with no functional annotation, including >118 000 families lacking any known protein domain. From these, we prioritized 6 668 conserved protein families with at least three sequences from organisms in at least two distinct classes. These Function Unknown Families (FUnkFams) are present in Tara Oceans Expedition and Human Microbiome Project metagenomes, with distributions associated with sampling environment. Our findings highlight the extent of functional novelty in sequence databases and establish an approach for creating a &quot;most wanted&quot; list of genes to prioritize for further characterization.},
}
@article {pmid30332459,
year = {2018},
author = {Su, M and Nie, Y and Shao, R and Duan, S and Jiang, Y and Wang, M and Xing, Z and Sun, Q and Liu, X and Xu, W},
title = {Diversified gut microbiota in newborns of mothers with gestational diabetes mellitus.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0205695},
doi = {10.1371/journal.pone.0205695},
pmid = {30332459},
issn = {1932-6203},
abstract = {Gestational diabetes mellitus (GDM), a high-risk pregnancy complication of great effect on the perinatal health of women and newborns, may cause changes of gut microbiota in mothers and further affect gut microbiota in newborns. This study aimed to investigate the potential effect of mother GDM on newborns' gut microbiota. Meconium DNA was extracted from a total of 34 full-term and C-sectioned newborns, in which 20 newborns had mothers diagnosed with GDM, while 14 had unaffected mothers. Sequencing and bioinformatics analysis of 16S rRNA indicated that the gut microbiota of GDM newborns showed differences compared to control newborns. The taxonomy analyses suggested that the overall bacterial content significantly differed by maternal diabetes status, with the microbiome of the GDM group showing lower alpha-diversity than that of control group. The phyla of Proteobacteria and Actinobacteria in GDM newborns increased, while that of Bacteroidetes significantly reduced (P<0.05). Moreover, several unique gut microbiota in phylum of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Planctomycetes found in control newborns were absent in GDM ones. At genus level, the relative abundance of Prevotella and Lactobacillus significantly decreased (P<0.05) in GDM newborns. Correlation analysis indicated that maternal fasting glucose levels were positively correlated with the relative abundance of phylum Actinobacteria and genus Acinetobacter, while negatively correlated with that of phylum Bacteroidetes and genus Prevotella. However, bacteria in GDM grade A2 (GDM_A2) newborns did not show any statistical variation compared to those from control newborns, which might be attributed to the additional intervention by insulin. The results of this study have important implications for understanding the potential effects of GDM on the gut microbiota of newborns and thus possibly their metabolism at later stages in their lives.},
}
@article {pmid30332379,
year = {2018},
author = {Martins, A and Castro, L},
title = {[The Role of Microbiome in Fibromyalgia... A New Therapeutic Target].},
journal = {Acta medica portuguesa},
volume = {31},
number = {9},
pages = {516},
doi = {10.20344/amp.11073},
pmid = {30332379},
issn = {1646-0758},
}
@article {pmid30332350,
year = {2018},
author = {Baranzini, SE},
title = {Insights into microbiome research 3: Who's there versus what are they doing?.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {24},
number = {12},
pages = {1541-1542},
doi = {10.1177/1352458518788974},
pmid = {30332350},
issn = {1477-0970},
abstract = {The main two questions that large microbiome studies typically address are &quot;who's there?&quot; and &quot;what are they doing?&quot; The first question aims at screening what kind of organisms are present, and it provides a low-resolution, relative composition of the microbiome. The second question focuses on precisely characterizing microbial communities by sequencing their entire genome on and providing insights into their metabolic capabilities. While DNA sequencing has become relatively affordable, differences in cost still exist between targeted and shotgun approaches, thus making these strategies quite complementary and commonly used.},
}
@article {pmid30329017,
year = {2018},
author = {Graspeuntner, S and Waschina, S and Künzel, S and Twisselmann, N and Rausch, TK and Cloppenborg-Schmidt, K and Zimmermann, J and Viemann, D and Herting, E and Göpel, W and Baines, JF and Kaleta, C and Rupp, J and Härtel, C and Pagel, J},
title = {Gut dysbiosis with Bacilli dominance and accumulation of fermentation products precedes late-onset sepsis in preterm infants.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciy882},
pmid = {30329017},
issn = {1537-6591},
abstract = {Background: Gut dysbiosis has been suggested as a major risk factor for the development of late-onset sepsis (LOS), a main cause of mortality and morbidity in preterm infants. We aimed to assess specific signatures of the gut microbiome including metabolic profiles in preterm infants <34 weeks of gestation preceding LOS.<br><br>Methods: In a single center cohort fecal samples of preterm infants were prospectively collected during the period of highest vulnerability for LOS (day 7, 14, 21 of life). Following 16S rRNA gene profiling, we assessed microbial community function using microbial metabolic network modeling. Data were adjusted for gestational age and use of probiotics.<br><br>Results: We studied stool samples of 71 preterm infants with LOS and 164 unaffected controls (no LOS/necrotizing enterocolitis). The bacteria isolated in diagnostic blood culture in most cases corresponded to the genera in the gut microbiome. LOS cases had a decelerated development of microbial diversity. Before onset of disease, LOS cases had specific gut microbiome signatures with higher abundance of Bacilli (specifically coagulase-negative Staphylococci, CoNS) and a lack of anaerobic bacteria. In-silico modeling of bacterial community metabolism suggested accumulation of the fermentation products ethanol and formic acid in LOS cases before the onset of disease.<br><br>Conclusions: Intestinal dysbiosis preceding LOS is characterized by an accumulation of Bacilli and their fermentation products and a paucity of anaerobic bacteria. Early microbiome and metabolic patterns may become a valuable biomarker to guide individualized prevention strategies of LOS in highly vulnerable populations.},
}
@article {pmid30328245,
year = {2018},
author = {Lee, P and Yacyshyn, BR and Yacyshyn, MB},
title = {Gut microbiota and obesity: An opportunity to alter obesity through Fecal Microbiota Transplant (FMT).},
journal = {Diabetes, obesity &amp; metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.13561},
pmid = {30328245},
issn = {1463-1326},
abstract = {Obesity is a global pandemic with immense health consequences for individuals and societies. Multiple factors including environmental influences and genetic predispositions are known to influence the development of obesity. Despite an increasing understanding of the factors driving the obesity episdemic, therapeutic interventions to prevent or reverse obesity are limited in their impact. Manipulation of the human gut microbiome provides a new potential therapeutic approach in the fight against obesity. Specific gut bacteria and their metabolites are known to affect host metabolism and feeding behavior, and dysbiosis of this biosystem may lead to metabolic syndrome. Potential therapies to alter the gut microbiota to treat obesity include dietary changes, supplementation of the diet with probiotic organisms and prebiotic compounds that influence bacterial growth, and the use of fecal microbiota transplant, in which gut microbiota from healthy indiviudals are introduced into the gut. In this review, we will examine the growing scientific evidence supporting the mechanisms by which the human gut microbiota may influence carbohydrate metabolism and obesity and the various possible therapies that may utilize the gut microbiota to help correct metabolic dysfunction. This article is protected by copyright. All rights reserved.},
}
@article {pmid30327643,
year = {2018},
author = {Xu, H and Wei, Y and Ma, H and Liu, Y and Zhang, Y and Hu, L and Li, J},
title = {Alterations of Gut Microbiome in the Patients With Severe Fever With Thrombocytopenia Syndrome.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2315},
doi = {10.3389/fmicb.2018.02315},
pmid = {30327643},
issn = {1664-302X},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne infectious disease caused by SFTS virus, and the number of SFTS cases increased year by year in China. Previous studies had indicated that gut microbiome closely associated with human health and diseases, including infection diseases, liver diseases, gastrointestinal diseases and metabolic diseases. The aim of this study is to investigate the alterations and involvements of gut microbial in SFTS patients. We compared the gut microbiome of 26 SFTS patients between 20 health controls using the Illumina MiSeq sequencing platform. Reduced gut microbiota diversity and dramatic shifts of fecal microbial composition in SFTS patients were observed compared with health controls. In the intestinal microbial of SFTS patients, the Lachnospiraceae and Ruminococcaceae which could produce short-chain fatty acids were clearly dropped compared with health people, meanwhile, Sutterella which have anti-inflammation properties were reduced too. On the contrary, some common opportunistic pathogens like Enterococcus and Streptococcus and endotoxin-producing bacteria Escherichia which could rise the risk of infections were increased in SFTS patients than healthy people, in addition lactate-producing bacteria Lactobacillaceae also significantly increased in SFTS patients. In addition, research findings on the correlation between gut microbiota and biochemical data found that the changes of gut microbiota of SFTS patients were closely associated with clinical symptoms, key serum enzymes, infection and mortality. These alterations of gut microbiome in SFTS patients suggest the potential contributions of gut microbial to the pathogenesis of SFTS.},
}
@article {pmid30327098,
year = {2018},
author = {de Souza, JRB and Dias, FFG and Caliman, JD and Augusto, F and Hantao, LW},
title = {Opportunities for green microextractions in comprehensive two-dimensional gas chromatography / mass spectrometry-based metabolomics - A review.},
journal = {Analytica chimica acta},
volume = {1040},
number = {},
pages = {1-18},
doi = {10.1016/j.aca.2018.08.034},
pmid = {30327098},
issn = {1873-4324},
abstract = {Microextractions have become an attractive class of techniques for metabolomics. The most popular technique is solid-phase microextraction that revolutionized the field of modern sample preparation in the early nineties. Ever since this milestone, microextractions have taken on many principles and formats comprising droplets, fibers, membranes, needles, and blades. Sampling devices may be customized to impart exhaustive or equilibrium-based characteristics to the extraction method. Equilibrium-based approaches may rely on additional methods for calibration, such as diffusion-based or on-fiber kinetic calibration to improve bioanalysis. In addition, microextraction-based methods may enable minimally invasive sampling protocols and measure the average free concentration of analytes in heterogeneous multiphasic biological systems. On-fiber derivatization has evidenced new opportunities for targeted and untargeted analysis in metabolomics. All these advantages have highlighted the potential of microextraction techniques for in vivo and on-site sampling and sample preparation, while many opportunities are still available for laboratory protocols. In this review, we outline and discuss some of the most recent applications using microextractions techniques for comprehensive two-dimensional gas chromatography-based metabolomics, including potential research opportunities.},
}
@article {pmid30326981,
year = {2018},
author = {Humer, E and Kröger, I and Neubauer, V and Reisinger, N and Zebeli, Q},
title = {Supplementation of a clay mineral-based product modulates plasma metabolomic profile and liver enzymes in cattle fed grain-rich diets.},
journal = {Animal : an international journal of animal bioscience},
volume = {},
number = {},
pages = {1-10},
doi = {10.1017/S1751731118002665},
pmid = {30326981},
issn = {1751-732X},
abstract = {Grain-rich diets often lead to subacute ruminal acidosis (SARA) impairing rumen and systemic cattle health. Recent data suggest beneficial effects of a clay mineral (CM)- based product on the rumen microbiome of cattle during SARA. This study sought to investigate whether the CM supplementation can counteract SARA-induced perturbations of the bovine systemic health. The study used an intermittent diet-induced SARA-model with eight dry Holstein cows receiving either no additive as control or CM via concentrates (n=8 per treatment). Cows received first a forage diet (Baseline) for 1 week, followed by a 1-week SARA-challenge (SARA 1), a 1-week recovery phase (Recovery) and finally a second SARA-challenge for 2 weeks (SARA 2). Cows were monitored for feed intake, reticular pH and chewing behavior. Blood samples were taken and analyzed for metabolites related to glucose and lipid metabolism as well as liver health biomarkers. In addition, a targeted electrospray ionization-liquid chromatography-MS-based metabolomics approach was carried out on the plasma samples obtained at the end of the Baseline and SARA 1 phase. Data showed that supplementing the cows' diet with CM improved ruminating chews per regurgitated bolus by 16% in SARA 1 (P=0.01) and enhanced the dry matter intake during the Recovery phase (P=0.05). Moreover, the SARA-induced decreases in several amino acids and phosphatidylcholines were less pronounced in cows receiving CM (P≤0.10). The CM-supplemented cows also had lower concentrations of lactate (P=0.03) and biogenic amines such as histamine and spermine (P<0.01) in the blood. In contrast, the concentration of acylcarnitines with key metabolic functions was increased in the blood of treated cows (P≤0.05). In SARA 2, the CM-cows had lower concentrations of the liver enzymes aspartate aminotransferase and γ-glutamyltransferase (P<0.05). In conclusion, the data suggest that supplementation of CM holds the potential to alleviate the negative effects of high-grain feeding in cattle by counteracting multiple SARA-induced perturbations in the systemic metabolism and liver health.},
}
@article {pmid30326425,
year = {2018},
author = {Luis, AS and Martens, EC},
title = {Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes.},
journal = {Current opinion in chemical biology},
volume = {47},
number = {},
pages = {126-133},
doi = {10.1016/j.cbpa.2018.09.012},
pmid = {30326425},
issn = {1879-0402},
abstract = {Individual human gut bacteria often encode hundreds of enzymes for degrading different polysaccharides. Identification of co-localized and co-regulated genes in these bacteria has been a successful approach to identify enzymes that participate in full or partial saccharification of complex carbohydrates, often unmasking novel catalytic activities. Here, we review recent studies that have led to the discovery of new activities from gut bacteria and summarize a general scheme for identifying gut bacteria with novel catalytic abilities, locating the enzymes involved and investigating their activities in detail. The strength of this approach is amplified by the availability of abundant genomic and metagenomic data for the human gut microbiome, which facilitates comparative approaches to mine existing data for new or orthologous enzymes.},
}
@article {pmid30325537,
year = {2018},
author = {Lunjani, N and Satitsuksanoa, P and Lukasik, Z and Sokolowska, M and Eiwegger, T and O'Mahony, L},
title = {Recent Developments and Highlights in Mechanisms of Allergic Diseases: Microbiome.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.13634},
pmid = {30325537},
issn = {1398-9995},
abstract = {All body surfaces are exposed to a wide variety of microbes, which significantly influence immune reactivity within the host. This review provides an update on some of the critical novel findings that have been published on the influence of the microbiome on atopic dermatitis, food allergy and asthma. Microbial dysbiosis has consistently been observed in the skin, gut and lungs of patients with atopic dermatitis, food allergy and asthma respectively and the role of specific microbes in allergic disorders is being intensively investigated. However, many of these discoveries have yet to be translated into routine clinical practice. This article is protected by copyright. All rights reserved.},
}
@article {pmid30325408,
year = {2018},
author = {Pedersen, KB and Pulliam, CF and Patel, A and Del Piero, F and Watanabe, TTN and Wankhade, UD and Shankar, K and Hicks, C and Ronis, MJ},
title = {Liver tumorigenesis is promoted by a high saturated-fat diet specifically in male mice and is associated with hepatic expression of the proto-oncogene Agap2 and enrichment of the intestinal microbiome with Coprococcus.},
journal = {Carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1093/carcin/bgy141},
pmid = {30325408},
issn = {1460-2180},
abstract = {Liver cancer results in a high degree of mortality, especially among men. Since fatty liver disease is a risk factor for development of hepatocellular carcinoma, we investigated the role of dietary fat type in tumor promotion by high fat diets in mice after initiation with the chemical carcinogen diethyl nitrosamine. Tumor incidence and multiplicity was significantly greater in males than in females. In males, fat type had complex effects on tumorigenesis. Preneoplastic foci were most prevalent in mice fed a polyunsaturated fat diet enriched in docosahexaenoic acid (DHA), while carcinomas and large visible liver tumors were significantly greater in mice fed a saturated fat diet made with cocoa butter relative to mice fed mono- or polyunsaturated fats. Different mechanisms thus seemed involved in early and late tumor promotion. The hepatic transcriptome and gut microbiome were assessed for traits associated with tumorigenesis. Hepatic expression of more than 20% of all genes was affected by sex, whereas fat type affected fewer genes. In males, the saturated fat diet induced expression of the proto-oncogene Agap2 and affected the expression of several cytochrome P450 genes, and genes involved in lipid, bile acid and fatty acid metabolism. The gut microbiome had a higher level of genus Akkermansia and a lower level of Firmicutes in females than in males. Males fed saturated fat had an altered microbiome, including an enrichment of the genus Coprococcus. In conclusion, sex and the dietary fat type affect the gut microbiome, the hepatic transcriptome and ultimately hepatic tumor growth.},
}
@article {pmid30325092,
year = {2018},
author = {Zhang, SY and Tsementzi, D and Hatt, JK and Bivins, A and Khelurkar, N and Brown, J and Tripathi, SN and Konstantinidis, KT},
title = {Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14439},
pmid = {30325092},
issn = {1462-2920},
abstract = {Little is known about microbial communities in the Ganges River, India and how they respond to intensive anthropogenic inputs. Here we applied shotgun metagenomics sequencing to study microbial community dynamics and function in planktonic samples collected along a ~700 km river transect, including urban cities and rural settings in upstream waters, before and after the monsoon rainy season. Our results showed that 11-32% of the microbes represented terrestrial, sewage and human inputs (allochthonous). Sewage inputs significantly contributed to the higher abundance, by 13-fold of human gut microbiome (HG) associated sequences and 2-fold of antibiotic resistance genes (ARGs) in the Ganges relative to other riverine ecosystems in Europe, North and South America. Metagenome-assembled genome sequences (MAGs) representing allochthonous populations were detectable and tractable across the river after 1-2 days of (downstream) transport (>200 km apart). Only ~8% of these MAGs were abundant in U.S. freshwater ecosystems, revealing distinct biodiversity for the Ganges. Microbial communities in the rainy season exhibited increased alpha-diversity and spatial heterogeneity and showed significantly weaker distance-decay patterns compared to the dry season. These results advance our understanding of the Ganges microbial communities and how they respond to anthropogenic pollution. This article is protected by copyright. All rights reserved.},
}
@article {pmid30324843,
year = {2018},
author = {Stalder, JF and Fluhr, JW and Foster, T and Glatz, M and Proksch, E},
title = {The emerging role of skin microbiome in atopic dermatitis and its clinical implication.},
journal = {The Journal of dermatological treatment},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/09546634.2018.1516030},
pmid = {30324843},
issn = {1471-1753},
abstract = {In recent years, the importance of the microbiome in maintaining healthy skin has become apparent. Both the classic microbiology cultivation techniques used since the early 1970s and the next-generation sequencing procedures refined in the past decade reveal the importance of skin microbiome in healthy and diseased skin. To strengthen and eventually restore a healthy microbiome in patients with dermatological conditions like atopic dermatitis (AD), it is important to consider the factors that influence the composition of the microbiome, such as skin pH and skin barrier integrity. Moreover, targeting the microbiome may support established treatment regimens in years to come. Initial studies have generated promising results, suggesting that AD treatments, including select emollients and topical corticosteroids, have a positive impact on the microbiome. This paper reviews different aspects of microbiome in AD and their implications in clinical practice.},
}
@article {pmid30324555,
year = {2018},
author = {Millien, V and Rosen, D and Hou, J and Shah, R},
title = {Proinflammatory Sulfur-Reducing Bacteria Are More Abundant in Colonic Biopsies of Patients with Microscopic Colitis Compared to Healthy Controls.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-018-5313-z},
pmid = {30324555},
issn = {1573-2568},
support = {CIN 13-413//VA HSR&amp;D Center for Innovations in Quality, Effectiveness and Safety/ ; },
abstract = {BACKGROUND: Microscopic colitis (MC), a subtype of inflammatory bowel disease, is a chronic condition of unknown etiology. Recent evidence has linked MC with intriguing changes in the stool microbiota, which may be linked to disease pathogenesis. The composition of the mucosal microbiome in patients with MC remains unclear.<br><br>METHODS: We performed a cross-sectional study comparing colonic tissue samples from patients with MC to those of healthy controls at the Michael E. DeBakey VA Medical Center. We included adults older than 18 who underwent a colonoscopy with biopsies to evaluate chronic diarrhea. Cases were defined by histology consistent with MC and controls by the absence of histologic disease. We conducted structured chart review to exclude other gastrointestinal diseases and obtain demographic (age, sex, race) and clinical (duration of symptoms and concurrent medications) information for cases and controls. We extracted bacterial DNA from formalin-fixed paraffin-embedded tissue samples and sequenced the v4 region of the 16S rRNA gene. Operational taxonomic unit (OTU) clustering was performed using UPARSE, and OTUs were assigned using the SILVA database. Statistical analysis was performed in QIIME and LEfSe. Comparisons with FDR-adjusted p values of less than 0.05 were considered statistically significant.<br><br>RESULTS: We included 20 MC patients and 20 controls with mean ages of 62 and 54, respectively. Most cases were White (95%), 60% had symptoms for greater than 12 months, and 50% were taking PPIs and NSAIDs at the time of their diagnosis. Compared to controls, MC patients had a significant increase in the proinflammatory sulfur-reducing bacterial family Desulfovibrionales. The Coriobacteriaceae family, abundant in the healthy gut, was significantly decreased in MC cases. There was also an increase in the genus Actinomyces in MC patients on PPI and an increase in the class Bacilli among those taking NSAIDs.<br><br>DISCUSSION: Patients with MC have an increase in the proinflammatory family Desulfovibrionales. Actinomyces and Bacilli were associated with medications (PPI and NSAID) known to increase the risk of MC. Our findings may have important implications for understanding the pathogenesis of MC.},
}
@article {pmid30324425,
year = {2018},
author = {Campbell-Tofte, J and Vrahatis, A and Josefsen, K and Mehlsen, J and Winther, K},
title = {Investigating the aetiology of adverse events following HPV vaccination with systems vaccinology.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-018-2925-6},
pmid = {30324425},
issn = {1420-9071},
abstract = {In contrast to the insidious and poorly immunogenic human papillomavirus (HPV) infections, vaccination with the HPV virus-like particles (vlps) is non-infectious and stimulates a strong neutralizing-antibody response that protects HPV-naïve vaccinees from viral infection and associated cancers. However, controversy about alleged adverse events following immunization (AEFI) with the vlps have led to extensive reductions in vaccine acceptance, with countries like Japan dropping it altogether. The AEFIs are grouped into chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME). In this review, we present a hypothesis that the AEFIs might arise from malfunctions within the immune system when confronted with the unusual antigen. In addition, we outline how the pathophysiology of the AEFIs can be cost-effectively investigated with the holistic principles of systems vaccinology in a two-step process. First, comprehensive immunological profiles of HPV vaccinees exhibiting the AEFIs are generated by integrating the data derived from serological profiling for prominent HPV antibodies and serum cytokines, with data from serum metabolomics, peripheral white blood cells transcriptomics and gut microbiome profiling. Next, the immunological profiles are compared with corresponding profiles generated for matched (a) HPV vaccinees without AEFIs; (b) non-HPV-vaccinated individuals with CFS/ME-like symptoms; and (c) non-HPV-vaccinated individuals without CFS/ME. In these comparisons, any causal links between HPV vaccine and the AEFIs, as well as the underlying molecular basis for the links will be revealed. Such a study should provide an objective basis for evaluating HPV vaccine safety and for identifying biomarkers for individuals at risk of developing AEFI with HPV vaccination.},
}
@article {pmid30324342,
year = {2018},
author = {Waterhouse, M and Hope, B and Krause, L and Morrison, M and Protani, MM and Zakrzewski, M and Neale, RE},
title = {Vitamin D and the gut microbiome: a systematic review of in vivo studies.},
journal = {European journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00394-018-1842-7},
pmid = {30324342},
issn = {1436-6215},
abstract = {PURPOSE: Variation in the human microbiome has been linked with a variety of physiological functions, including immune regulation and metabolism and biosynthesis of vitamins, hormones, and neurotransmitters. Evidence for extraskeletal effects of vitamin D has been accruing and it has been suggested that the effect of vitamin D on health is partially mediated through the microbiome. We aimed to critically evaluate the evidence linking vitamin D and the gastrointestinal microbiome.<br><br>METHODS: We systematically searched the Embase, Web of Science, PubMed and CINAHL databases, including peer-reviewed publications that reported an association between a measure of vitamin D and the gastrointestinal microbiome in humans or experimental animals.<br><br>RESULTS: We included 10 mouse and 14 human studies. Mouse studies compared mice fed diets containing different levels of vitamin D (usually high versus low), or vitamin D receptor knockout or Cyp27B1 knockout with wild-type mice. Five mouse studies reported an increase in Bacteroidetes (or taxa within that phylum) in the low vitamin D diet or gene knockout group. Human studies were predominantly observational; all but two of the included studies found some association between vitamin D and the gut microbiome, but the nature of differences observed varied across studies.<br><br>CONCLUSIONS: Despite substantial heterogeneity, we found evidence to support the hypothesis that vitamin D influences the composition of the gastrointestinal microbiome. However, the research is limited, having been conducted either in mice or in mostly small, selected human populations. Future research in larger population-based studies is needed to fully understand the extent to which vitamin D modulates the microbiome.},
}
@article {pmid30323970,
year = {2018},
author = {Liu, Y and O'Brien, JL and Ajami, NJ and Scheurer, ME and Amirian, ES and Armstrong, G and Tsavachidis, S and Thrift, AP and Jiao, L and Wong, MC and Smith, DP and Spitz, MR and Bondy, ML and Petrosino, JF and Kheradmand, F},
title = {Lung tissue microbial profile in lung cancer is distinct from emphysema.},
journal = {American journal of cancer research},
volume = {8},
number = {9},
pages = {1775-1787},
pmid = {30323970},
issn = {2156-6976},
support = {R01 HL082487/HL/NHLBI NIH HHS/United States ; R01 HL110883/HL/NHLBI NIH HHS/United States ; K07 CA181480/CA/NCI NIH HHS/United States ; R01 CA127219/CA/NCI NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 ES023512/ES/NIEHS NIH HHS/United States ; },
abstract = {OBJECTIVES: The composition and structure of site-specific microbiota have been investigated as potential biomarkers for a variety of chronic inflammatory diseases and cancers. While many studies have focused on the changes in the airway microbiota using respiratory specimens from patients with various respiratory diseases, more research is needed to explore the microbial profiles within the distal lung parenchyma in smokers with lung cancer and/or emphysema.<br><br>MATERIALS AND METHODS: To describe and contrast lung tissue-associated microbial signatures in smokers with lung cancer and/or emphysema, we employed culture-independent pyrosequencing of 16S rRNA gene hypervariable V4 region and compositional analysis in non-malignant lung tissue samples obtained from 40 heavy smokers, including 10 emphysema-only, 11 lung cancer-only, and 19 with both lung cancer and emphysema.<br><br>RESULTS AND CONCLUSION: The emphysema-only group presented a lower bacterial community evenness defined by a significantly lower Shannon diversity index compared to the lung cancer patients with or without emphysema (P = 0.006). Furthermore, community compositions of lung cancer patients with or without emphysema were characterized by a significantly lower abundance of Proteobacteria (primary the genera Acinetobacter and Acidovorax) and higher prevalence of Firmicutes (Streptococcus) and Bacteroidetes (Prevotella), compared to emphysema-only patients. In conclusion, the lung microbial composition and communities structures of smokers with lung cancer are distinct from the emphysema-only patients. Although preliminary, our findings suggest that lung microbiome changes could be a biomarker of lung cancer that could eventually be used to help screening for the disease.},
}
@article {pmid30323887,
year = {2018},
author = {López-Leal, G and Cornejo-Granados, F and Hurtado-Ramírez, JM and Mendoza-Vargas, A and Ochoa-Leyva, A},
title = {Functional and taxonomic classification of a greenhouse water drain metagenome.},
journal = {Standards in genomic sciences},
volume = {13},
number = {},
pages = {20},
doi = {10.1186/s40793-018-0326-y},
pmid = {30323887},
issn = {1944-3277},
abstract = {Microbiome sequencing has become the standard procedure in the study of new ecological and human-constructed niches. To our knowledge, this is the first report of a metagenome from the water of a greenhouse drain. We found that the greenhouse is not a diverse niche, mainly dominated by Rhizobiales and Rodobacterales. The analysis of the functions encoded in the metagenome showed enrichment of characteristic features of soil and root-associated bacteria such as ABC-transporters and hydrolase enzymes. Additionally, we found antibiotic resistances genes principally for spectinomycin, tetracycline, and aminoglycosides. This study aimed to identify the bacteria and functional gene composition of a greenhouse water drain sample and also provide a genomic resource to search novel proteins from a previously unexplored niche. All the metagenome proteins and their annotations are available to the scientific community via http://microbiomics.ibt.unam.mx/tools/metagreenhouse/.},
}
@article {pmid30323800,
year = {2018},
author = {Bai, X and Lu, S and Yang, J and Jin, D and Pu, J and Díaz Moyá, S and Xiong, Y and Rossello-Mora, R and Xu, J},
title = {Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2321},
doi = {10.3389/fmicb.2018.02321},
pmid = {30323800},
issn = {1664-302X},
abstract = {The metataxonomic approach combining 16S rRNA gene amplicon sequencing using the PacBio Technology with the application of the operational phylogenetic unit (OPU) approach, has been used to analyze the fecal microbial composition of the high-altitude and herbivorous Tibetan antelopes. The fecal samples of the antelope were collected in Hoh Xil National Nature Reserve, at an altitude over 4500 m, the largest depopulated zone in Qinghai-Tibetan Plateau, China, where non-native animals or humans may experience life-threatening acute mountain sickness. In total, 104 antelope fecal samples were enrolled in this study, and were clustered into 61,258 operational taxonomic units (OTUs) at an identity of 98.7% and affiliated with 757 OPUs, including 144 known species, 256 potentially new species, 103 potentially higher taxa within known lineages. In addition, 254 comprised sequences not affiliating with any known family, and the closest relatives were unclassified lineages of existing orders or classes. A total of 42 out of 757 OPUs conformed to the core fecal microbiome, of which four major lineages, namely, un-cultured Ruminococcaceae, Lachnospiraceae, Akkermansia, and Christensenellaceae were associated with human health or longevity. The current study reveals that the fecal core microbiome of antelope is mainly composited of uncultured bacteria. The most abundant core taxa, namely, uncultured Ruminococcaceae, uncultured Akkermansia, uncultured Bacteroides, uncultured Christensenellaceae, uncultured Mollicutes, and uncultured Lachnospiraceae, may represent new bacterial candidates at high taxa levels, and several may have beneficial roles in health promotion or anti-intestinal dysbiosis. These organisms should be further isolated and evaluated for potential effect on human health and longevity.},
}
@article {pmid30323795,
year = {2018},
author = {Xu, M and Jiang, Z and Huang, W and Yin, J and Ou, S and Jiang, Y and Meng, L and Cao, S and Yu, A and Cao, J and Shen, Y},
title = {Altered Gut Microbiota Composition in Subjects Infected With Clonorchis sinensis.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2292},
doi = {10.3389/fmicb.2018.02292},
pmid = {30323795},
issn = {1664-302X},
abstract = {Clonorchiasis is an infectious disease caused by helminths of Clonorchis sinensis (C. sinensis). The adult parasite mainly inhabits the bile duct and gall bladder, and results in various complications to the hepatobiliary system. The amount of bile secreted into the intestine is reduced in cases of C. sinensis infection, which may alter the pH of the gut and decrease the amount of surfactant protein D released from the gallbladder. However, the impact of parasitic infection on the human gut microbiome remains unclear. To this end, we examined the gut microbiota composition in 47 modified Kato-Katz thick smear-positive (egg-positive) volunteers and 42 healthy controls from five rural communities. Subjects were grouped into four sub-populations based on age and infection status. High-throughput 16S rRNA gene sequencing revealed significant changes in alpha diversity between EP1 and EN1. The beta diversity showed alterations between C. sinensis-infected subjects and healthy controls. In C. sinensis infected patients, we found the significant reduction of certain taxa, such as Bacteroides and anti-inflammatory Bifidobacterium (P < 0.05). Bacteroides, a predominant gut bacteria in healthy populations, was negatively correlated with the number of C. sinensis eggs per gram (EPG, r = -0.37, P adjust < 0.01 in 20-60 years old group; r = -0.64, P adjust = 0.04 in the 60+ years old group). What's more, the reduction in the abundance of Bifidobacterium, a common probiotic, was decreased particularly in the 60 + years old group (r = -0.50, P = 0.04). The abundance of Dorea, a potentially pro-inflammatory microbe, was higher in infected subjects than in healthy individuals (P < 0.05). Variovorax was a unique bacteria that was only detected in infected subjects. These results clearly demonstrate the significant influence of C. sinensis infection on the human gut microbiota and provided new insights into the control, prevention, diagnosis, and clinical study of clonorchiasis through the human gut microbiota.},
}
@article {pmid30323331,
year = {2018},
author = {Tamburini, FB and Andermann, TM and Tkachenko, E and Senchyna, F and Banaei, N and Bhatt, AS},
title = {Precision identification of diverse bloodstream pathogens in the gut microbiome.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-018-0202-8},
pmid = {30323331},
issn = {1546-170X},
support = {K08 CA184420/CA/NCI NIH HHS/United States ; },
abstract = {A comprehensive evaluation of every patient with a bloodstream infection includes an attempt to identify the infectious source. Pathogens can originate from various places, such as the gut microbiota, skin and the external environment. Identifying the definitive origin of an infection would enable precise interventions focused on management of the source1,2. Unfortunately, hospital infection control practices are often informed by assumptions about the source of various specific pathogens; if these assumptions are incorrect, they lead to interventions that do not decrease pathogen exposure3. Here, we develop and apply a streamlined bioinformatic tool, named StrainSifter, to match bloodstream pathogens precisely to a candidate source. We then leverage this approach to interrogate the gut microbiota as a potential reservoir of bloodstream pathogens in a cohort of hematopoietic cell transplantation recipients. We find that patients with Escherichia coli and Klebsiella pneumoniae bloodstream infections have concomitant gut colonization with these organisms, suggesting that the gut may be a source of these infections. We also find cases where typically nonenteric pathogens, such as Pseudomonas aeruginosa and Staphylococcus epidermidis, are found in the gut microbiota, thereby challenging the existing informal dogma of these infections originating from environmental or skin sources. Thus, we present an approach to distinguish the source of various bloodstream infections, which may facilitate more accurate tracking and prevention of hospital-acquired infections.},
}
@article {pmid30323265,
year = {2018},
author = {Beckmann, S and Luk, AWS and Gutierrez-Zamora, ML and Chong, NHH and Thomas, T and Lee, M and Manefield, M},
title = {Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0296-5},
pmid = {30323265},
issn = {1751-7370},
support = {LP100100128//Australian Research Council (ARC)/ ; },
abstract = {Despite the significance of biogenic methane generation in coal beds, there has never been a systematic long-term evaluation of the ecological response to biostimulation for enhanced methanogenesis in situ. Biostimulation tests in a gas-free coal seam were analysed over 1.5 years encompassing methane production, cell abundance, planktonic and surface associated community composition and chemical parameters of the coal formation water. Evidence is presented that sulfate reducing bacteria are energy limited whilst methanogenic archaea are nutrient limited. Methane production was highest in a nutrient amended well after an oxic preincubation phase to enhance coal biofragmentation (calcium peroxide amendment). Compound-specific isotope analyses indicated the predominance of acetoclastic methanogenesis. Acetoclastic methanogenic archaea of the Methanosaeta and Methanosarcina genera increased with methane concentration. Acetate was the main precursor for methanogenesis, however more acetate was consumed than methane produced in an acetate amended well. DNA stable isotope probing showed incorporation of 13C-labelled acetate into methanogenic archaea, Geobacter species and sulfate reducing bacteria. Community characterisation of coal surfaces confirmed that methanogenic archaea make up a substantial proportion of coal associated biofilm communities. Ultimately, methane production from a gas-free subbituminous coal seam was stimulated despite high concentrations of sulfate and sulfate-reducing bacteria in the coal formation water. These findings provide a new conceptual framework for understanding the coal reservoir biosphere.},
}
@article {pmid30323120,
year = {2018},
author = {Filosa, S and Di Meo, F and Crispi, S},
title = {Polyphenols-gut microbiota interplay and brain neuromodulation.},
journal = {Neural regeneration research},
volume = {13},
number = {12},
pages = {2055-2059},
doi = {10.4103/1673-5374.241429},
pmid = {30323120},
issn = {1673-5374},
abstract = {Increasing evidence suggests that food ingested polyphenols can have beneficial effects in neuronal protection acting against oxidative stress and inflammatory injury. Moreover, polyphenols have been reported to promote cognitive functions. Biotransformation of polyphenols is needed to obtain metabolites active in brain and it occurs through their processing by gut microbiota. Polyphenols metabolites could directly act as neurotransmitters crossing the blood-brain barrier or indirectly by modulating the cerebrovascular system. The microbiota-gut-brain axis is considered a neuroendocrine system that acts bidirectionally and plays an important role in stress responses. The metabolites produced by microbiota metabolism can modulate gut bacterial composition and brain biochemistry acting as neurotransmitters in the central nervous system. Gut microbiota composition can be influenced by dietary ingestion of natural bioactive molecules such as probiotics, prebiotics and polyphenol. Microbiota composition can be altered by dietary changes and gastrointestinal dysfunctions are observed in neurodegenerative diseases. In addition, several pieces of evidence support the idea that alterations in gut microbiota and enteric neuroimmune system could contribute to onset and progression of these age-related disorders. The impact of polyphenols on microbiota composition strengthens the idea that maintaining a healthy microbiome by modulating diet is essential for having a healthy brain across the lifespan. Moreover, it is emerging that they could be used as novel therapeutics to prevent brain from neurodegeneration.},
}
@article {pmid30322931,
year = {2018},
author = {Shukla, SP and Plata, C and Reichelt, M and Steiger, S and Heckel, DG and Kaltenpoth, M and Vilcinskas, A and Vogel, H},
title = {Microbiome-assisted carrion preservation aids larval development in a burying beetle.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1812808115},
pmid = {30322931},
issn = {1091-6490},
abstract = {The ability to feed on a wide range of diets has enabled insects to diversify and colonize specialized niches. Carrion, for example, is highly susceptible to microbial decomposers, but is kept palatable several days after an animal's death by carrion-feeding insects. Here we show that the burying beetle Nicrophorus vespilloides preserves carrion by preventing the microbial succession associated with carrion decomposition, thus ensuring a high-quality resource for their developing larvae. Beetle-tended carcasses showed no signs of degradation and hosted a microbial community containing the beetles' gut microbiota, including the yeast Yarrowia In contrast, untended carcasses showed visual and olfactory signs of putrefaction, and their microbial community consisted of endogenous and soil-originating microbial decomposers. This regulation of the carcass' bacterial and fungal community and transcriptomic profile was associated with lower concentrations of putrescine and cadaverine (toxic polyamines associated with carcass putrefaction) and altered levels of proteases, lipases, and free amino acids. Beetle-tended carcasses develop a biofilm-like matrix housing the yeast, which, when experimentally removed, leads to reduced larval growth. Thus, tended carcasses hosted a mutualistic microbial community that promotes optimal larval development, likely through symbiont-mediated extraintestinal digestion and detoxification of carrion nutrients. The adaptive preservation of carrion coordinated by the beetles and their symbionts demonstrates a specialized resource-management strategy through which insects modify their habitats to enhance fitness.},
}
@article {pmid30322864,
year = {2018},
author = {Durack, J and Lynch, SV},
title = {The gut microbiome: Relationships with disease and opportunities for therapy.},
journal = {The Journal of experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1084/jem.20180448},
pmid = {30322864},
issn = {1540-9538},
abstract = {Over the past decade, our view of human-associated microbes has expanded beyond that of a few species toward an appreciation of the diverse and niche-specialized microbial communities that develop in the human host with chronological age. The largest reservoir of microbes exists in the distal gastrointestinal tract, both in the lumen, where microbes facilitate primary and secondary metabolism, and on mucosal surfaces, where they interact with host immune cell populations. While local microbial-driven immunomodulation in the gut is well described, more recent studies have demonstrated a role for the gut microbiome in influencing remote organs and mucosal and hematopoietic immune function. Unsurprisingly, therefore, perturbation to the composition and function of the gut microbiota has been associated with chronic diseases ranging from gastrointestinal inflammatory and metabolic conditions to neurological, cardiovascular, and respiratory illnesses. Considerable effort is currently focused on understanding the natural history of microbiome development in humans in the context of health outcomes, in parallel with improving our knowledge of microbiome-host molecular interactions. These efforts ultimately aim to develop effective approaches to rehabilitate perturbed human microbial ecosystems as a means to restore health or prevent disease. This review details the role of the gut microbiome in modulating host health with a focus on immunomodulation and discusses strategies for manipulating the gut microbiome for the management or prevention of chronic inflammatory conditions.},
}
@article {pmid30322585,
year = {2018},
author = {Sandall, J and Tribe, RM and Avery, L and Mola, G and Visser, GH and Homer, CS and Gibbons, D and Kelly, NM and Kennedy, HP and Kidanto, H and Taylor, P and Temmerman, M},
title = {Short-term and long-term effects of caesarean section on the health of women and children.},
journal = {Lancet (London, England)},
volume = {392},
number = {10155},
pages = {1349-1357},
doi = {10.1016/S0140-6736(18)31930-5},
pmid = {30322585},
issn = {1474-547X},
abstract = {A caesarean section (CS) can be a life-saving intervention when medically indicated, but this procedure can also lead to short-term and long-term health effects for women and children. Given the increasing use of CS, particularly without medical indication, an increased understanding of its health effects on women and children has become crucial, which we discuss in this Series paper. The prevalence of maternal mortality and maternal morbidity is higher after CS than after vaginal birth. CS is associated with an increased risk of uterine rupture, abnormal placentation, ectopic pregnancy, stillbirth, and preterm birth, and these risks increase in a dose-response manner. There is emerging evidence that babies born by CS have different hormonal, physical, bacterial, and medical exposures, and that these exposures can subtly alter neonatal physiology. Short-term risks of CS include altered immune development, an increased likelihood of allergy, atopy, and asthma, and reduced intestinal gut microbiome diversity. The persistence of these risks into later life is less well investigated, although an association between CS use and greater incidence of late childhood obesity and asthma are frequently reported. There are few studies that focus on the effects of CS on cognitive and educational outcomes. Understanding potential mechanisms that link CS with childhood outcomes, such as the role of the developing neonatal microbiome, has potential to inform novel strategies and research for optimising CS use and promote optimal physiological processes and development.},
}
@article {pmid30322526,
year = {2018},
author = {McMullen, C and Orsel, K and Alexander, TW and van der Meer, F and Plastow, G and Timsit, E},
title = {Evolution of the nasopharyngeal bacterial microbiota of beef calves from spring processing to 40 days after feedlot arrival.},
journal = {Veterinary microbiology},
volume = {225},
number = {},
pages = {139-148},
doi = {10.1016/j.vetmic.2018.09.019},
pmid = {30322526},
issn = {1873-2542},
abstract = {The composition of the nasopharyngeal bacterial microbiota has been shown to play a role in cattle respiratory health. However, previous studies are narrow in scope regarding longitudinal observations, limiting our understanding of how respiratory bacteria evolve over time. The objective was therefore to characterize this microbiota and its evolution over time in beef calves. A total of 120 crossbred beef-breed steer calves were enrolled in a study in southern Alberta at the time of first vaccination (spring processing), comprising three groups (40 calves/group) that originated from different ranches and were placed in different feedlots. Deep nasopharyngeal swab samples were collected from the calves at the time of spring processing, arrival at the feedlot, and a targeted 40 days after feedlot arrival. The swabs were processed for DNA extraction and the V4 region of the 16S rRNA gene was sequenced to evaluate the microbiota. The composition of the microbiota differed among groups of calves, with each group showing different relative abundances of 963 observed sequence variants. Mycoplasma was the most abundant genus and M. dispar the most abundant species across all groups. There was a distinct shift in the composition of the microbiota over time for all calf groups; however, changes in sequence variants differed by group. Variations in both microbiota composition and temporal changes of sequence variants according to calf group indicates that the respiratory microbiota of beef cattle may lack a common pattern of evolution from ranch to feedlot, and that future studies should account for potential group effects.},
}
@article {pmid30322445,
year = {2018},
author = {D'hoe, K and Vet, S and Faust, K and Moens, F and Falony, G and Gonze, D and Lloréns-Rico, V and Gelens, L and Danckaert, J and De Vuyst, L and Raes, J},
title = {Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
doi = {10.7554/eLife.37090},
pmid = {30322445},
issn = {2050-084X},
abstract = {Whereas the composition of the human gut microbiome is well resolved, predictive understanding is still lacking. Here, we followed a bottom-up strategy to explore human gut community dynamics: we established a synthetic community composed of three representative human gut isolates (Roseburia intestinalis L1-82, Faecalibacterium prausnitzii A2-165 and Blautia hydrogenotrophica S5a33) and explored their interactions under well-controlled conditions in vitro. Systematic mono- and pair-wise fermentation experiments confirmed competition for fructose and cross-feeding of formate. We quantified with a mechanistic model how well tri-culture dynamics was predicted from mono-culture data. With the model as reference, we demonstrated that strains grown in co-culture behaved differently than in mono-culture and confirmed their altered behavior at the transcriptional level. In addition, we showed with replicate tri-cultures and simulations that dominance in tri-culture sensitively depended on initial conditions. Our work has important implications for gut microbial community modeling as well as ecological interaction detection from batch cultures.},
}
@article {pmid30321601,
year = {2018},
author = {Fournier, CN and Houser, M and Tansey, MG and Glass, JD and Hertzberg, VS},
title = {The gut microbiome and neuroinflammation in amyotrophic lateral sclerosis? Emerging clinical evidence.},
journal = {Neurobiology of disease},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbd.2018.10.007},
pmid = {30321601},
issn = {1095-953X},
}
@article {pmid30321529,
year = {2018},
author = {Bayigga, L and Kateete, DP and Anderson, DJ and Sekikubo, M and Nakanjako, D},
title = {Diversity of vaginal microbiota in sub-Saharan Africa and its effects on HIV transmission and prevention.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2018.10.014},
pmid = {30321529},
issn = {1097-6868},
abstract = {The vaginal microbial community (&quot;microbiota&quot;) is a key component of the reproductive health of women, providing protection against urogenital infections. In Sub-Saharan Africa, there is a high prevalence of bacterial vaginosis (BV), a condition defined by bacterial overgrowth and a shift away from a lactobacillus-dominated profile towards increased percentages of strict anaerobic species. BV is associated with an increased risk of HIV acquisition and transmission, as well as an increased risk of acquiring other sexually transmitted infections , pre-term births and pelvic inflammatory disease. Vaginal microbiota, rich in taxa of strict anaerobic species, disrupts the mucosal epithelial barrier through secretion of metabolites and enzymes that mediate inflammation. Advancements in next-generation sequencing technologies such as whole genome sequencing have led to deeper profiling of the vaginal microbiome and further study of its potential role in HIV pathogenesis and treatment. Until recently data on the composition of the vaginal microbiome in sub-Saharan Africa has been limited, however a number of studies have been published that highlight the critical role of vaginal microbiota in disease and health in African women. This article reviews these recent findings and identifies gaps in knowledge about variations in female genital commensal bacteria that could provide vital information to improve the effectiveness of interventions to prevent HIV and other sexually transmitted infections. In addition, we review the effects of pregnancy, contraception and sexual practices on vaginal microbiome and the potential of vaginal microbiota on HIV transmission and prevention. A better understanding of the role of vaginal microbiota in host susceptibility to HIV infection and its prevention among African women, could inform the development of novel local and systemic interventions to minimize new HIV infections among high risk women.},
}
@article {pmid30320765,
year = {2018},
author = {Bishara, A and Moss, EL and Kolmogorov, M and Parada, AE and Weng, Z and Sidow, A and Dekas, AE and Batzoglou, S and Bhatt, AS},
title = {High-quality genome sequences of uncultured microbes by assembly of read clouds.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1038/nbt.4266},
pmid = {30320765},
issn = {1546-1696},
support = {K08 CA184420/CA/NCI NIH HHS/United States ; },
abstract = {Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. Here, we present an application of read clouds, short-read sequences tagged with long-range information, to microbiome samples. We present Athena, a de novo assembler that uses read clouds to improve metagenomic assemblies. We applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques. Read-cloud metagenomic sequencing and Athena assembly produced the most comprehensive individual genome drafts with high contiguity (>200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20×) raw short-read-sequence coverage. We also sequenced a complex marine-sediment sample and generated 24 intermediate-quality genome drafts (>70% complete, <10% contaminated), nine of which were complete (>90% complete, <5% contaminated). Our approach allows for culture-free generation of high-quality microbial genome drafts by using a single shotgun experiment.},
}
@article {pmid30320619,
year = {2018},
author = {Divers, J and Langefeld, CD and Lyles, DS and Ma, L and Freedman, BI},
title = {Protective association between JC polyoma viruria and kidney disease.},
journal = {Current opinion in nephrology and hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/MNH.0000000000000464},
pmid = {30320619},
issn = {1473-6543},
abstract = {PURPOSE OF REVIEW: The presence of viruses in urine (urine virome) typically reflects infection in the kidneys and urinary tract. The urinary virome is associated with HIV-associated nephropathy and chronic glomerulosclerosis. There are many associations of this microbiome with human diseases that remain to be described. This manuscript reviews emerging data on relationships between kidney disease and urinary tract infection/colonization with JC polyomavirus (JCPyV).<br><br>RECENT FINDINGS: Approximately 30% of the adult population sheds JCPyV in the urine. Further, urinary tract infection with one polyomavirus strain appears to inhibit secondary infections. The presence of urinary JCPyV and BK polyomavirus (BKPyV) replication were measured with polymerase chain reaction in African Americans to assess relationships with apolipoprotein L1 gene (APOL1)-associated nephropathy. Urinary JCPyV was associated with paradoxically lower rates of nephropathy in those with APOL1 high-risk genotypes. Subsequent studies revealed African Americans with JCPyV viruria had lower rates of nondiabetic nephropathy independent from APOL1.<br><br>SUMMARY: Urinary tract JCPyV replication is common and associates with lower rates of nephropathy. This relationship is observed in diverse settings. Results support a host immune system that fails to eradicate nonnephropathic viruses and is also less likely to manifest renal parenchymal inflammation resulting in glomerulosclerosis.},
}
@article {pmid30320222,
year = {2018},
author = {Cheng, S and Ma, X and Geng, S and Jiang, X and Li, Y and Hu, L and Li, J and Wang, Y and Han, X},
title = {Fecal Microbiota Transplantation Beneficially Regulates Intestinal Mucosal Autophagy and Alleviates Gut Barrier Injury.},
journal = {mSystems},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSystems.00137-18},
pmid = {30320222},
issn = {2379-5077},
abstract = {Fecal microbiota transplantation (FMT) is one of the most effective ways to regulate the gut microbiota. Here, we investigated the effect of exogenous fecal microbiota on gut function from the perspective of analysis of the mucosal proteomes in a piglet model. A total of 289 differentially expressed proteins were annotated with 4,068 gene ontology (GO) function entries in the intestinal mucosa, and the levels of autophagy-related proteins in the forkhead box O (FoxO) signaling pathway were increased whereas the levels of proteins related to inflammation response were decreased in the recipient. Then, to assess the alleviation of epithelial injury in the Escherichia coli K88-infected piglets following FMT, intestinal microbiome-metabolome responses were determined. 16S rRNA gene sequencing showed that the abundances of beneficial bacteria, such as Lactobacillus and Succinivibrio, were increased whereas those of Enterobacteriaceae and Proteobacteria bacteria were decreased in the infected piglets following FMT. Metabolomic analysis revealed that levels of 58 metabolites, such as lactic acid and succinic acid, were enhanced in the intestinal lumen and that seven metabolic pathways, such as branched-chain amino acid metabolism pathways, were upregulated in the infected piglets following FMT. In concordance with the metabolome data, results of metagenomics prediction analysis also demonstrated that FMT modulated the metabolic functions of gut microbiota associated with linoleic acid metabolism. In addition, intestinal morphology was improved, a result that coincided with the decrease of intestinal permeability and the enhancement of mucins and mucosal expression of tight junction proteins in the recipient. Taken together, the results showed that FMT triggered intestinal mucosal protective autophagy and alleviated gut barrier injury through alteration of the gut microbial structure. IMPORTANCE The gut microbiota plays a crucial role in human and animal health, and its disorder causes multiple diseases. Over the past decade, FMT has gained increasing attention due to the success in treating Clostridium difficile infection (CDI) and inflammatory bowel disease (IBD). Although FMT appears to be effective, how FMT functions in the recipient remains unknown. Whether FMT exerts this beneficial effect through a series of changes in the host organism caused by alteration of gut microbial structure is also not known. In the present study, newborn piglets and E. coli K88-infected piglets were selected as models to explore the interplay between host and gut microbiota following FMT. Our results showed that FMT triggered intestinal mucosal autophagy and alleviated gut barrier injury caused by E. coli K88. This report provides a theoretical basis for the use of FMT as a viable therapeutic method for gut microbial regulation.},
}
@article {pmid30320216,
year = {2018},
author = {Blair, PM and Land, ML and Piatek, MJ and Jacobson, DA and Lu, TS and Doktycz, MJ and Pelletier, DA},
title = {Exploration of the Biosynthetic Potential of the Populus Microbiome.},
journal = {mSystems},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSystems.00045-18},
pmid = {30320216},
issn = {2379-5077},
abstract = {Natural products (NPs) isolated from bacteria have dramatically advanced human society, especially in medicine and agriculture. The rapidity and ease of genome sequencing have enabled bioinformatics-guided NP discovery and characterization. As a result, NP potential and diversity within a complex community, such as the microbiome of a plant, are rapidly expanding areas of scientific exploration. Here, we assess biosynthetic diversity in the Populus microbiome by analyzing both bacterial isolate genomes and metagenome samples. We utilize the fully sequenced genomes of isolates from the Populus root microbiome to characterize a subset of organisms for NP potential. The more than 3,400 individual gene clusters identified in 339 bacterial isolates, including 173 newly sequenced organisms, were diverse across NP types and distinct from known NP clusters. The ribosomally synthesized and posttranslationally modified peptides were both widespread and divergent from previously characterized molecules. Lactones and siderophores were prevalent in the genomes, suggesting a high level of communication and pressure to compete for resources. We then consider the overall bacterial diversity and NP variety of metagenome samples compared to the sequenced isolate collection and other plant microbiomes. The sequenced collection, curated to reflect the phylogenetic diversity of the Populus microbiome, also reflects the overall NP diversity trends seen in the metagenomic samples. In our study, only about 1% of all clusters from sequenced isolates were positively matched to a previously characterized gene cluster, suggesting a great opportunity for the discovery of novel NPs involved in communication and control in the Populus root microbiome. IMPORTANCE The plant root microbiome is one of the most diverse and abundant biological communities known. Plant-associated bacteria can have a profound effect on plant growth and development, and especially on protection from disease and environmental stress. These organisms are also known to be a rich source of antibiotic and antifungal drugs. In order to better understand the ways bacterial communities influence plant health, we evaluated the diversity and uniqueness of the natural product gene clusters in bacteria isolated from poplar trees. The complex molecule clusters are abundant, and the majority are unique, suggesting a great potential to discover new molecules that could not only affect plant health but also could have applications as antibiotic agents.},
}
@article {pmid30320049,
year = {2018},
author = {Hsu, PS and Nanan, R},
title = {Does Breast Milk Nurture T Lymphocytes in Their Cradle?.},
journal = {Frontiers in pediatrics},
volume = {6},
number = {},
pages = {268},
doi = {10.3389/fped.2018.00268},
pmid = {30320049},
issn = {2296-2360},
abstract = {Breast feeding has been associated with improved infant outcomes in multiple aspects, including immune outcomes such as infections and potentially atopy and autoimmunity. However associations do not necessarily implicate cause and effect and at this point, exactly how breast feeding and components of breast milk may modulate the infant's immune compartment remains unclear, especially in humans. Some lines of evidence suggest that breastfeeding affects the development of the infant's thymus, a critical organ for T cell development. This may be a direct effect mediated by breast milk components or alternatively, a secondary effect from the impact of breast feeding on the infant's gut microbiome. Here we discuss the potential mechanisms and impact of this association between breast feeding and thymic development.},
}
@article {pmid30319618,
year = {2018},
author = {Erdei, L and Bolla, BS and Bozó, R and Tax, G and Urbán, E and Kemény, L and Szabó, K},
title = {TNIP1 Regulates Cutibacterium acnes-Induced Innate Immune Functions in Epidermal Keratinocytes.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2155},
doi = {10.3389/fimmu.2018.02155},
pmid = {30319618},
issn = {1664-3224},
abstract = {Human skin cells recognize the presence of the skin microbiome through pathogen recognition receptors. Epidermal keratinocytes are known to activate toll-like receptors (TLRs) 2 and 4 in response to the commensal Cutibacterium acnes (C. acnes, formerly known as Propionibacterium acnes) bacterium and subsequently to induce innate immune and inflammatory events. These events may lead to the appearance of macroscopic inflammatory acne lesions in puberty: comedos, papules and, pustules. Healthy skin does not exhibit inflammation or skin lesions, even in the continuous presence of the same microbes. As the molecular mechanism for this duality is still unclear, we aimed to identify factors and mechanisms that control the innate immune response to C. acnes in keratinocytes using a human immortalized keratinocyte cell line, HPV-KER, normal human keratinocytes (NHEK) and an organotypic skin model (OSM). TNIP1, a negative regulator of the NF-κB signaling pathway, was found to be expressed in HPV-KER cells, and its expression was rapidly induced in response to C. acnes treatment, which was confirmed in NHEK cells and OSMs. Expression changes were not dependent on the C. acnes strain. However, we found that the extent of expression was dependent on C. acnes dose. Bacterial-induced changes in TNIP1 expression were regulated by signaling pathways involving NF-κB, p38, MAPKK and JNK. Experimental modification of TNIP1 levels affected constitutive and C. acnes-induced NF-κB promoter activities and subsequent inflammatory cytokine and chemokine mRNA and protein levels. These results suggest an important role for this negative regulator in the control of bacterially induced TLR signaling pathways in keratinocytes. We showed that all-trans retinoic acid (ATRA) induced elevated TNIP1 expression in HPV-KER cells and also in OSMs, where TNIP1 levels increased throughout the epidermis. ATRA also reduced constitutive and bacterium-induced levels of TNFα, CCL5 and TLR2, while simultaneously increasing CXCL8 and TLR4 expression. Based on these findings, we propose that ATRA may exhibit dual effects in acne therapy by both affecting the expression of the negative regulator TNIP1 and attenuating TLR2-induced inflammation. Overall, TNIP1, as a possible regulator of C. acnes-induced innate immune and inflammatory events in keratinocytes, may play important roles in the maintenance of epidermal homeostasis.},
}
@article {pmid30319615,
year = {2018},
author = {Lin, GL and McGinley, JP and Drysdale, SB and Pollard, AJ},
title = {Epidemiology and Immune Pathogenesis of Viral Sepsis.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2147},
doi = {10.3389/fimmu.2018.02147},
pmid = {30319615},
issn = {1664-3224},
abstract = {Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. Sepsis can be caused by a broad range of pathogens; however, bacterial infections represent the majority of sepsis cases. Up to 42% of sepsis presentations are culture negative, suggesting a non-bacterial cause. Despite this, diagnosis of viral sepsis remains very rare. Almost any virus can cause sepsis in vulnerable patients (e.g., neonates, infants, and other immunosuppressed groups). The prevalence of viral sepsis is not known, nor is there enough information to make an accurate estimate. The initial standard of care for all cases of sepsis, even those that are subsequently proven to be culture negative, is the immediate use of broad-spectrum antibiotics. In the absence of definite diagnostic criteria for viral sepsis, or at least to exclude bacterial sepsis, this inevitably leads to unnecessary antimicrobial use, with associated consequences for antimicrobial resistance, effects on the host microbiome and excess healthcare costs. It is important to understand non-bacterial causes of sepsis so that inappropriate treatment can be minimised, and appropriate treatments can be developed to improve outcomes. In this review, we summarise what is known about viral sepsis, its most common causes, and how the immune responses to severe viral infections can contribute to sepsis. We also discuss strategies to improve our understanding of viral sepsis, and ways we can integrate this new information into effective treatment.},
}
@article {pmid30319585,
year = {2018},
author = {Wirth, R and Kádár, G and Kakuk, B and Maróti, G and Bagi, Z and Szilágyi, Á and Rákhely, G and Horváth, J and Kovács, KL},
title = {The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2285},
doi = {10.3389/fmicb.2018.02285},
pmid = {30319585},
issn = {1664-302X},
abstract = {The cow rumen harbors a great variety of diverse microbes, which form a complex, organized community. Understanding the behavior of this multifarious network is crucial in improving ruminant nutrient use efficiency. The aim of this study was to expand our knowledge by examining 10 Holstein dairy cow rumen fluid fraction whole metagenome and transcriptome datasets. DNA and mRNA sequence data, generated by Ion Torrent, was subjected to quality control and filtering before analysis for core elements. The taxonomic core microbiome consisted of 48 genera belonging to Bacteria (47) and Archaea (1). The genus Prevotella predominated the planktonic core community. Core functional groups were identified using co-occurrence analysis and resulted in 587 genes, from which 62 could be assigned to metabolic functions. Although this was a minimal functional core, it revealed key enzymes participating in various metabolic processes. A diverse and rich collection of enzymes involved in carbohydrate metabolism and other functions were identified. Transcripts coding for enzymes active in methanogenesis made up 1% of the core functions. The genera associated with the core enzyme functions were also identified. Linking genera to functions showed that the main metabolic pathways are primarily provided by Bacteria and several genera may serve as a &quot;back-up&quot; team for the central functions. The key actors in most essential metabolic routes belong to the genus Prevotella. Confirming earlier studies, the genus Methanobrevibacter carries out the overwhelming majority of rumen methanogenesis and therefore methane emission mitigation seems conceivable via targeting the hydrogenotrophic methanogenesis.},
}
@article {pmid30319571,
year = {2018},
author = {Zuo, T and Ng, SC},
title = {The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2247},
doi = {10.3389/fmicb.2018.02247},
pmid = {30319571},
issn = {1664-302X},
abstract = {In the twenty first century, the changing epidemiology of inflammatory bowel disease (IBD) globally with increasing disease incidence across many countries relates to the altered gut microbiota, due to a combinatorial effect of environmental factors, human immune responses and genetics. IBD is a gastrointestinal disease associated with a gut microbial dysbiosis, including an expansion of facultative anaerobic bacteria of the family Enterobacteriaceae. Advances in high-throughput sequencing enable us to entangle the gut microbiota in human health and IBD beyond the gut bacterial microbiota, expanding insights into the mycobiota, virobiota and helminthes. Caudovirales (viruses) and Basidiomycota, Ascomycota, and Candida albicans (fungi) are revealed to be increased in IBD. The deconvolution of the gut microbiota in IBD lays the basis for unveiling the roles of these various gut microbiota components in IBD pathogenesis and being conductive to instructing on future IBD diagnosis and therapeutics. Here we comprehensively elucidate the alterations in the gut microbiota in IBD, discuss the effect of diets in the gut microbiota in relation to IBD, and illustrate the potential of manipulation of gut microbiota for IBD therapeutics. The therapeutic strategy of antibiotics, prebiotics, probiotics and fecal microbiota transplantation will benefit the effective application of precision microbiome manipulation in IBD.},
}
@article {pmid30319569,
year = {2018},
author = {D'Amico, F and Candela, M and Turroni, S and Biagi, E and Brigidi, P and Bega, A and Vancini, D and Rampelli, S},
title = {The Rootstock Regulates Microbiome Diversity in Root and Rhizosphere Compartments of Vitis vinifera Cultivar Lambrusco.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2240},
doi = {10.3389/fmicb.2018.02240},
pmid = {30319569},
issn = {1664-302X},
abstract = {Plants belonging to Vitis vinifera varieties are usually grafted on different rootstocks to enhance the plant defenses against pathogens and increase productivity under harsh environmental conditions. Particularly, in Emilia-Romagna region (Italy), Vitis vinifera cultivar Lambrusco can be grafted on a hybrid of V. berlandieri × V. riparia (5BB) or V. berlandieri × V. rupestris (1103P). However, the latter shows potassium absorption problems, with a consequent reduction in grapevine production. Since it has recently been demonstrated that the rootstock has the potential to select for different microorganisms at the root-soil interface, here we hypothesized that the potassium deficiency of 1103P could be partially accounted for by the peculiarities of the rootstock microbiome. We thus employed 16S rRNA sequencing to compare root and rhizosphere microbiomes in plants of V. vinifera cultivar Lambrusco grafted on the two aforementioned rootstocks. According to our findings, 1103P shows a reduced diversity in root and rhizosphere microbiomes, including members of potassium-solubilizing microorganisms, possibly explaining the inadequate potassium absorption of this hybrid. Besides confirming the importance of the rootstock as a determinant of the composition of plant microbiomes, our data indicate the relevance of rootstock-selected microbiomes as possible regulators of potassium absorption by V. vinifera.},
}
@article {pmid30319557,
year = {2018},
author = {Huws, SA and Creevey, CJ and Oyama, LB and Mizrahi, I and Denman, SE and Popova, M and Muñoz-Tamayo, R and Forano, E and Waters, SM and Hess, M and Tapio, I and Smidt, H and Krizsan, SJ and Yáñez-Ruiz, DR and Belanche, A and Guan, L and Gruninger, RJ and McAllister, TA and Newbold, CJ and Roehe, R and Dewhurst, RJ and Snelling, TJ and Watson, M and Suen, G and Hart, EH and Kingston-Smith, AH and Scollan, ND and do Prado, RM and Pilau, EJ and Mantovani, HC and Attwood, GT and Edwards, JE and McEwan, NR and Morrisson, S and Mayorga, OL and Elliott, C and Morgavi, DP},
title = {Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2161},
doi = {10.3389/fmicb.2018.02161},
pmid = {30319557},
issn = {1664-302X},
abstract = {The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in &quot;omic&quot; data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent &quot;omics&quot; approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.},
}
@article {pmid30319555,
year = {2018},
author = {Bedree, JK and Bor, B and Cen, L and Edlund, A and Lux, R and McLean, JS and Shi, W and He, X},
title = {Quorum Sensing Modulates the Epibiotic-Parasitic Relationship Between Actinomyces odontolyticus and Its Saccharibacteria epibiont, a Nanosynbacter lyticus Strain, TM7x.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2049},
doi = {10.3389/fmicb.2018.02049},
pmid = {30319555},
issn = {1664-302X},
support = {F31 DE026057/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE026186/DE/NIDCR NIH HHS/United States ; },
abstract = {The ultra-small, obligate parasitic epibiont, TM7x, the first and only current member of the long-elusive Saccharibacteria (formerly the TM7 phylum) phylum to be cultivated, was isolated in co-culture with its bacterial host, Actinomyces odontolyticus subspecies actinosynbacter, XH001. Initial phenotypic characterization of the TM7x-associated XH001 co-culture revealed enhanced biofilm formation in the presence of TM7x compared to XH001 as monoculture. Genomic analysis and previously published transcriptomic profiling of XH001 also revealed the presence of a putative AI-2 quorum sensing (QS) operon, which was highly upregulated upon association of TM7x with XH001. This analysis revealed that the most highly induced gene in XH001 was an lsrB ortholog, which encodes a putative periplasmic binding protein for the auto inducer (AI)-2 QS signaling molecule. Further genomic analyses suggested the lsrB operon in XH001 is a putative hybrid AI-2/ribose transport operon as well as the existence of a luxS ortholog, which encodes the AI-2 synthase. In this study, the potential role of AI-2 QS in the epibiotic-parasitic relationship between XH001 and TM7x in the context of biofilm formation was investigated. A genetic system for XH001 was developed to generate lsrB and luxS gene deletion mutants in XH001. Phenotypic characterization demonstrated that deletion mutations in either lsrB or luxS did not affect XH001's growth dynamic, mono-species biofilm formation capability, nor its ability to associate with TM7x. TM7x association with XH001 induced lsrB gene expression in a luxS-dependent manner. Intriguingly, unlike wild type XH001, which displayed significantly increased biofilm formation upon establishing the epibiotic-parasitic relationship with TM7x, XH001ΔlsrB, and XH001ΔluxS mutants failed to achieve enhanced biofilm formation when associated with TM7x. In conclusion, we demonstrated a significant role for AI-2 QS in modulating dual-species biofilm formation when XH001 and TM7x establish their epibiotic-parasitic relationship.},
}
@article {pmid30319548,
year = {2018},
author = {Amabebe, E and Anumba, DOC},
title = {Psychosocial Stress, Cortisol Levels, and Maintenance of Vaginal Health.},
journal = {Frontiers in endocrinology},
volume = {9},
number = {},
pages = {568},
doi = {10.3389/fendo.2018.00568},
pmid = {30319548},
issn = {1664-2392},
abstract = {Stress stimuli are ubiquitous and women do not enjoy any exemptions. The physiologic &quot;fight-or-flight&quot; response may be deleterious to the female lower genital tract microbiome if the stress stimuli persist for longer than necessary. Persistent exposure to psychosocial stress and stimulation of the hypothalamic-pituitary-adrenal (HPA) and sympathetic-adrenal-medullary (SAM) axes, and associated hormones are risk factors for several infections including genitourinary tract infections. Though this could be due to a dysregulated immune response, a cortisol-induced inhibition of vaginal glycogen deposition may be involved especially in the instance of vaginal infection. The estrogen-related increased vaginal glycogen and epithelial maturation are required for the maintenance of a healthy vaginal ecosystem (eubiosis). The ability of cortisol to disrupt this process as indicated in animal models is important in the pathogenesis of vaginal dysbiosis and the subsequent development of infection and inflammation. This phenomenon may be more crucial in pregnancy where a healthy Lactobacillus-dominated vaginal microbiota is sacrosanct, and there is local production of more corticotropin-releasing hormone (CRH) from the decidua, fetal membranes and placenta. To highlight the relationship between the stress hormone cortisol and the vaginal microbiomial architecture and function, the potential role of cortisol in the maintenance of vaginal health is examined.},
}
@article {pmid30318873,
year = {2018},
author = {Witkin, SS and Nasioudis, D and Leizer, J and Minis, E and Boester, A and Forney, LJ},
title = {Epigenetics and the vaginal microbiome: influence of the microbiota on the histone deacetylase level in vaginal epithelial cells from pregnant women.},
journal = {Minerva ginecologica},
volume = {},
number = {},
pages = {},
doi = {10.23736/S0026-4784.18.04322-8},
pmid = {30318873},
issn = {1827-1650},
abstract = {Histone deacetylase (HDAC) influences the acetylation status of histones at gene promotor loci, providing an epigenetic mechanism that regulates gene expression. We determined if variations in the composition of the vaginal microbiome in pregnant women were associated with alterations in the level of HDAC1 in vaginal epithelial cells and whether this influenced the concentration of compounds present in vaginal fluid. Vaginal epithelial cells were obtained from 150 women in their first trimester of pregnancy, lysed and assayed for HDAC1 by ELISA. Composition of the vaginal microbiome was determined by classification of sequences amplified from the V1-V3 region of bacterial ribosomal 16S rRNA genes. Vaginal secretions were assayed for total protein, matrix metalloproteinase (MMP)-8, the 70kDa heat shock protein (hsp70) and the D- and L-lactic acid isomers. Lactobacilli were numerically dominant in 119 (79.3%) of the women, with Lactobacillus crispatus being the most prevalent (45.3% of women). Gardnerella was the most prevalent non-Lactobacillus species (10.7% of women). The median HDAC1 level in epithelial cells was 6.1 ng/ml when lactobacilli predominated vs. 20.5 ng/ml when non-lactobacilli were dominant (p = 0.0039). Levels were lowest when L. crispatus was dominant (3.8 ng/ml) and highest with Streptococcus dominance (38.1 ng/ml). The concentration of HDAC1 was negatively correlated with the D-lactic acid level (p = 0.0183) and positively correlated with concentrations of MMP-8 and hsp70 (p<0.0001) in the vaginal fluid. We propose that the composition of the vaginal microbiome and level of D-lactic acid, by influencing the HDAC1 level in vaginal epithelial cells, may epigenetically contribute to variations in the concentration of compounds in vaginal fluid.},
}
@article {pmid30317668,
year = {2018},
author = {Manuelidis, L},
title = {Prokaryotic SPHINX 1.8 REP protein is tissue-specific and expressed in human germline cells.},
journal = {Journal of cellular biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/jcb.27907},
pmid = {30317668},
issn = {1097-4644},
abstract = {Small circular DNAs of 1.8 and 2.4 kb were initially discovered in highly infectious Creutzfeldt-Jakob Disease (CJD) and scrapie particles from mammalian brain and cultured cells. Surprisingly, these protected cytoplasmic &quot;SPHINX&quot; DNAs contained replication (REP) initiation sequences resembling those of Acinetobacter phage viruses. An antibody was generated against a REP peptide encoded by the SPHINX 1.8 open reading frame (ORF) that was not present in mammals. It bound to a 41kd &quot;spx1&quot; protein on Western blots. Cytologically, spx1 concentrated in spinal cord synapses and pancreatic islet, but not exocrine cells. We hypothesized that circular SPHINX DNAs are ancient symbiotic elements that can participate in functional differentiation and neurodegeneration. Cell and tissue-specific patterns of spx1 expression shown below implicate somatic cell-to-cell communication and differentiation functions that would favor conservation of SPHINX 1.8 in evolution. Remarkably, primary human oocytes and spermatogonia, but not mature sperm, displayed intense cytoplasmic spx1 signals that underscore the maternal inheritance of SPHINX 1.8. These findings should encourage investigations of unexplored networks of incorporated environmental infectious agents that can be key actors in progressive neurodegeneration, immunity, and cancer.},
}
@article {pmid30317641,
year = {2018},
author = {Fabiańska, I and Gerlach, N and Almario, J and Bucher, M},
title = {Plant-mediated effects of soil phosphorus on the root-associated fungal microbiota in Arabidopsis thaliana.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.15538},
pmid = {30317641},
issn = {1469-8137},
abstract = {Plants respond to phosphorus (P)-limitation through an array of morphological, physiological and metabolic changes which are part of the phosphate (Pi)-starvation response (PSR). This response influences the establishment of the arbuscular mycorrhizal (AM) symbiosis in most land plants. It is, however, unknown to what extent available P and the PSR redefine plant interactions with the fungal microbiota in soil. Using amplicon sequencing of the fungal taxonomical marker ITS2 we examined the changes in root-associated fungal communities in the AM non-host species Arabidopsis thaliana in response to soil amendment with P and to genetic perturbations in the plant PSR. We observed robust shifts in root-associated fungal communities of P-replete plants in comparison to their P-deprived counterparts, while bulk-soil communities remained unaltered. Moreover, plants carrying mutations in phosphate signaling network genes, phr1, phl1 and pho2, exhibited similarly altered root fungal communities characterized by the depletion of the chytridiomycete taxon Olpidium brassicae specifically under P-replete conditions. This study highlights the nutritional status and the underlying nutrient signaling network of an AM non-host plant, as previously unrecognized factors influencing the assembly of the plant fungal microbiota in response to P in nonsterile soil. This article is protected by copyright. All rights reserved.},
}
@article {pmid30317146,
year = {2018},
author = {Kaczmarek, JL and Liu, X and Charron, CS and Novotny, JA and Jeffery, EH and Seifried, HE and Ross, SA and Miller, MJ and Swanson, KS and Holscher, HD},
title = {Broccoli consumption affects the human gastrointestinal microbiota.},
journal = {The Journal of nutritional biochemistry},
volume = {63},
number = {},
pages = {27-34},
doi = {10.1016/j.jnutbio.2018.09.015},
pmid = {30317146},
issn = {1873-4847},
abstract = {The human gastrointestinal microbiota is increasingly linked to health outcomes; however, our understanding of how specific foods alter the microbiota is limited. Cruciferous vegetables such as broccoli are a good source of dietary fiber and phytonutrients, including glucosinolates, which can be metabolized by gastrointestinal microbes. This study aimed to determine the impact of broccoli consumption on the gastrointestinal microbiota of healthy adults. A controlled feeding, randomized, crossover study consisting of two 18-day treatment periods separated by a 24-day washout was conducted in healthy adults (n=18). Participants were fed at weight maintenance with the intervention period diet including 200 g of cooked broccoli and 20 g of raw daikon radish per day. Fecal samples were collected at baseline and at the end of each treatment period for microbial analysis. Beta diversity analysis indicated that bacterial communities were impacted by treatment (P=.03). Broccoli consumption decreased the relative abundance of Firmicutes by 9% compared to control (P=.05), increased the relative abundance of Bacteroidetes by 10% compared to control (P=.03) and increased Bacteroides by 8% relative to control (P=.02). Furthermore, the effects were strongest among participants with body mass index <26 kg/m2, and within this group, there were associations between bacterial relative abundance and glucosinolate metabolites. Functional prediction revealed that broccoli consumption increased the pathways involved in the functions of the endocrine system (P=.05), transport and catabolism (P=.04), and energy metabolism (P=.01). These results reveal that broccoli consumption affects the composition and function of the human gastrointestinal microbiota.},
}
@article {pmid30316910,
year = {2018},
author = {Liu, Y and Wei, M and Yue, K and Hu, M and Li, S and Men, L and Pi, Z and Liu, Z and Liu, Z},
title = {Study on Urine Metabolic Profile of Aβ25-35-Induced Alzheimer's Disease Using UHPLC-Q-TOF-MS.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2018.10.001},
pmid = {30316910},
issn = {1873-7544},
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder, with no effective method for its treatment so far. The pathogenesis of AD has been reported, but the endogenous metabolic profile and disease-related biomarkers are still not clear. To better understand AD, an AD model induced by injecting β-amyloid 25-35 (Aβ 25-35) solution into bilateral hippocampus was developed on Sprague-Dawley rats. After 8 weeks of modeling, the impairment of spatial learning and memory ability in AD rats were assessed by Morris water maze task. Hematoxylin and eosin staining and immunohistochemistry were used to investigate the pathological changes of hippocampus. The neurotransmitter concentrations in the hippocampus were measured using UHPLC-TQ-MS. Urinary metabolomics based on UHPLC-Q-TOF-MS was established to delineate the alterations of endogenous metabolites in AD rats. The results showed that compared with healthy control rats, AD rats suffered from cognitive dysfunction, hippocampus damage, Aβ formation and tau phosphorylation at 8 weeks after surgery, suggesting that the Aβ25-35-induced AD model was successfully established. In addition, the levels of γ-aminobutyric acid, acetylcholine, glycine, norepinephrine, serotonin, taurine and dopamine decreased and glutamate and aspartic acid increased in hippocampal tissue of AD rats. 45 altered metabolites mainly involved in 8 metabolic pathways were identified as the endogenous biomarkers of AD. According to the analysis of the biological significance of metabolic profiles, the pathogenesis of AD was mainly due to gut microbiome dysbiosis, inhibition of energy metabolism, oxidative stress injury and loss of neuronal protective substances.},
}
@article {pmid30316687,
year = {2018},
author = {Prescott, SL and Logan, AC},
title = {Planetary Health: From the Wellspring of Holistic Medicine to Personal and Public Health Imperative.},
journal = {Explore (New York, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.explore.2018.09.002},
pmid = {30316687},
issn = {1878-7541},
abstract = {The term planetary health - denoting the interconnections between the health of person and place at all scales - emerged from the environmental and holistic health movements of the 1970-80s; in 1980, Friends of the Earth expanded the World Health Organization definition of health, stating: &quot;health is a state of complete physical, mental, social and ecological well-being and not merely the absence of disease - personal health involves planetary health&quot;. By the 1990s, the concept of planetary health was part of the fabric of integrative medicine; more recently, after the 2015 Lancet Commission on Planetary Health report, the concept has penetrated mainstream academic and medical discourse. Here, we explore this history and describe its relevance to contemporary healthcare; integrative medicine is uniquely positioned to educate and advocate on behalf of patients and communities (current and future generations), helping to safeguard health of person, place and planet. We use the emerging microbiome science as a way to illustrate the interconnectivity and health implications of ecosystems (including social/political/economic systems) at all scales. As highlighted in the Canmore Declaration, mainstream planetary health discourse will be strengthened by inter-professional healthcare perspectives, and a more sophisticated understanding of the ways in which social dominance orientation and medical authoritarianism compromise the World Health Organization's broad vision of global health. Planetary health isn't a &quot;new discipline&quot;; it is merely an extension of a concept that was understood by our ancestors, and remains the vocation of all healthcare providers. Discourse on the topic requires cultural competency, critical consciousness and a greater appreciation of marginalized voices.},
}
@article {pmid30316501,
year = {2018},
author = {Metzger, SA and Hernandez, LL and Suen, G and Ruegg, PL},
title = {Understanding the Milk Microbiota.},
journal = {The Veterinary clinics of North America. Food animal practice},
volume = {34},
number = {3},
pages = {427-438},
doi = {10.1016/j.cvfa.2018.06.003},
pmid = {30316501},
issn = {1558-4240},
abstract = {The milk microbiota is an intriguing area of research because milk with no bacterial growth in culture was long thought to be sterile. Recent DNA sequencing techniques have been developed that do not require bacteria to be culturable, and DNA from new bacteria have been reported in milk from dairy cow mammary glands with or without mastitis. Methodologies and results vary among research groups, and not enough is known about the milk microbiota for the results to be used for diagnosis or prognosis of mastitis.},
}
@article {pmid30316308,
year = {2018},
author = {Storm, DW and Braga, LH and Cooper, CS},
title = {Continuous Antibiotic Prophylaxis in Pediatric Urology.},
journal = {The Urologic clinics of North America},
volume = {45},
number = {4},
pages = {525-538},
doi = {10.1016/j.ucl.2018.06.001},
pmid = {30316308},
issn = {1558-318X},
mesh = {Antibiotic Prophylaxis/*methods ; Child ; Humans ; Urinary Tract Infections/*prevention &amp; control ; *Urology ; },
abstract = {Continuous antibiotic prophylaxis (CAP) for urinary tract infection prevention in children with vesicoureteral reflux, hydronephrosis, and hydroureteronephrosis is reviewed. A more selective use of CAP is advocated based on a review of known individual risk factors in each of these conditions that subsequently helps identify the children most likely to benefit from CAP. Both short-term and potential long-term side effects of CAP are reviewed, including the impact of prophylactic antibiotics on bacterial resistance and the microbiome. Alternatives to continuous antibiotic prophylaxis including Vaccinium macrocarpon (Cranberry), probiotics, and vaccines are reviewed.},
}
@article {pmid30315828,
year = {2018},
author = {Skevaki, C and Renz, H},
title = {Advances in mechanisms of allergic disease 2017.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2018.09.027},
pmid = {30315828},
issn = {1097-6825},
abstract = {This review highlights advances in mechanisms of allergic disease, particularly type 2 innate lymphoid cells; TH2 lymphocytes; B cells; dendritic cells: microbiome and barrier function; eosinophils, mast cells. During the last year, considerable progress has been made in the further characterization of type 2 inflammation controlled by both adaptive (TH2) as well as innate (ILC2) effector cells. New pathways of lymphocyte activation, trafficking and recruitment, and effector cell mechanisms have been discovered. The plasticity of lymphocyte effector cell responses is another area where major progress has been achieved. Accumulating evidence will influence both our understanding of allergic disease but also our efforts for allergy prevention and treatment.},
}
@article {pmid30315762,
year = {2018},
author = {Greiman, SE and Cook, JA and Tkach, VV and Hoberg, EP and Menning, DM and Hope, AG and Sonsthagen, SA and Talbot, SL},
title = {Museum metabarcoding: A novel method revealing gut helminth communities of small mammals across space and time.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2018.08.001},
pmid = {30315762},
issn = {1879-0135},
abstract = {Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host and parasite/pathogen dynamics. We developed a new technique to identify intestinal helminth parasites and applied it to shrews (Eulipotyphla: Soricidae) because they are ubiquitous, occupy diverse habitats, and host a diverse and abundant parasite fauna. Notably, we included museum specimens preserved in various ways to explore the efficacy of using metabarcoding analyses that may enable identification of helminth symbiont communities from historical archives. We successfully sequenced the parasite communities (using 12S mtDNA, 16S mtDNA, 28S rDNA) of 23 whole gastrointestinal tracts. All gastrointestinal tracts were obtained from the Museum of Southwestern Biology, USA, and from recent field collections, varying both in time since fixation (ranging from 4 months to 16 years) and preservation method (70% or 95% ethanol stored at room temperature, or flash frozen in liquid nitrogen and stored at -80 °C). Our proof of concept demonstrates the feasibility of applying next generation DNA sequencing techniques to authoritatively identify the parasite/pathogen communities within whole gastrointestinal tracts from museum specimens of varying age and fixation, and the value of future preservation of host-associated whole gastrointestinal tracts in public research archives. This powerful approach facilitates future comparative examinations of the distributions and interactions among multiple associated groups of organisms through time and space.},
}
@article {pmid30315569,
year = {2018},
author = {Kelsey, C and Dreisbach, C and Alhusen, J and Grossmann, T},
title = {A primer on investigating the role of the microbiome in brain and cognitive development.},
journal = {Developmental psychobiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/dev.21778},
pmid = {30315569},
issn = {1098-2302},
support = {1F31NR01782101A1//National Institute for Nursing Research/ ; },
abstract = {Incorporating information regarding the gut microbiota into psychobiological research promises to shed new light on how individual differences in brain and cognitive development emerge. However, the investigation of the gut-brain axis in development is still in its infancy and poses several challenges, including data analysis. Considering that the gut microbiome is an eco-system containing millions of bacteria, one needs to utilize a breadth of methodologies and data analytic techniques. The present review serves two purposes. First, this review will inform developmental psychobiology researchers about the emerging study of the gut-brain axis in development and second, this review will propose methodologies and data analytic strategies for integrating microbiome data in developmental research.},
}
@article {pmid30315206,
year = {2018},
author = {Dubé, MP and Park, SY and Ross, H and Love, TMT and Morris, SR and Lee, HY},
title = {Daily HIV pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate-emtricitabine reduced Streptococcus and increased Erysipelotrichaceae in rectal microbiota.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15212},
doi = {10.1038/s41598-018-33524-6},
pmid = {30315206},
issn = {2045-2322},
support = {EI-11-SD-005//California HIV/AIDS Research Program (CHRP)/ ; R01-AI083115//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01-AI095066//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
abstract = {Daily PrEP is highly effective at preventing HIV-1 acquisition, but risks of long-term tenofovir disoproxil fumarate plus emtricitabine (TDF-FTC) include renal decline and bone mineral density decrease in addition to initial gastrointestinal side effects. We investigated the impact of TDF-FTC on the enteric microbiome using rectal swabs collected from healthy MSM before PrEP initiation and after 48 to 72 weeks of adherent PrEP use. The V4 region of the 16S ribosomal RNA gene sequencing showed that Streptococcus was significantly reduced from 12.0% to 1.2% (p = 0.036) and Erysipelotrichaceae family was significantly increased from 0.79% to 3.3% (p = 0.028) after 48-72 weeks of daily PrEP. Catenibacterium mitsuokai, Holdemanella biformis and Turicibacter sanguinis were increased within the Erysipelotrichaceae family and Streptococcus agalactiae, Streptococcus oralis, Streptococcus mitis were reduced. These changes were not associated with host factors including PrEP duration, age, race, tenofovir diphosphate blood level, any drug use and drug abuse, suggesting that the observed microbiome shifts were likely induced by daily PrEP use. Long-term PrEP resulted in increases of Catenibacterium mitsuokai and Holdemanella biformis, which have been associated with gut microbiome dysbiosis. Our observations can aid in characterizing PrEP's side effects, which is likely to improve PrEP adherence, and thus HIV-1 prevention.},
}
@article {pmid30315194,
year = {2018},
author = {Turon, M and Cáliz, J and Garate, L and Casamayor, EO and Uriz, MJ},
title = {Showcasing the role of seawater in bacteria recruitment and microbiome stability in sponges.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15201},
doi = {10.1038/s41598-018-33545-1},
pmid = {30315194},
issn = {2045-2322},
support = {CTM2013-43287-P//Ministerio de Econom&amp;#x00ED;a y Competitividad (Ministry of Economy and Competitiveness)/ ; CTM2017-88080-C2-2-R//Ministerio de Econom&amp;#x00ED;a y Competitividad (Ministry of Economy and Competitiveness)/ ; CTM2013-43287-P//Ministerio de Econom&amp;#x00ED;a y Competitividad (Ministry of Economy and Competitiveness)/ ; CGL2015-69043-P//Ministerio de Econom&amp;#x00ED;a y Competitividad (Ministry of Economy and Competitiveness)/ ; CTM2013-43287-P//Ministerio de Econom&amp;#x00ED;a y Competitividad (Ministry of Economy and Competitiveness)/ ; CTM2017-88080-C2-2-R//Ministerio de Econom&amp;#x00ED;a y Competitividad (Ministry of Economy and Competitiveness)/ ; },
abstract = {We studied the core bacterial communities of 19 sponge species from Nha Trang Bay (Central Vietnam), with particular emphasis on the contribution of planktonic seawater bacteria to the sponge core microbiomes. To ensure consistent sponge-microbe associations and accurate identification of planktonic bacteria transmitted from seawater, we were very restrictive with the definition of the sponge core microbiomes (present in all the replicates), and with the identification of valid biological 16S rRNA gene sequences (100% sequence identity) that belonged to potentially different bacterial taxa. We found a high overlap (>50% relative abundance) between the sponge species core microbiome and the seawater bacterial core in ca. a half of the studied species, including representatives of both, HMA and LMA sponges. From our restrictive analysis, we point to horizontal transmission as a relevant way of symbiont acquisition in sponges. Some species-specific recognition mechanisms may act in sponges to enrich specific seawater bacteria in their tissues. These mechanisms would allow the maintenance of bacterial communities in a species across geographical ranges. Moreover, besides contrasting preferences in bacteria selection from seawater, divergent physiological traits may also account for the different microbiomes in species of HMA and LMA sponges.},
}
@article {pmid30312415,
year = {2018},
author = {Fan, TJ and Tchaptchet, SY and Arsene, D and Mishima, Y and Liu, B and Sartor, RB and Carroll, IM and Miao, EA and Fodor, AA and Hansen, JJ},
title = {Environmental Factors Modify the Severity of Acute DSS Colitis in Caspase-11-Deficient Mice.},
journal = {Inflammatory bowel diseases},
volume = {24},
number = {11},
pages = {2394-2403},
doi = {10.1093/ibd/izy244},
pmid = {30312415},
issn = {1536-4844},
abstract = {Background: Human and mouse studies implicate the inflammasome in the pathogenesis of inflammatory bowel diseases, though the effects in mice are variable. The noncanonical inflammasome activator caspase-11 (Casp11) reportedly attenuates acute dextran sodium sulfate (DSS) colitis in mice. However, the effects of Casp11 on chronic experimental colitis and factors that influence the impact of Casp11 on acute DSS colitis are unknown.<br><br>Methods: We studied the role of Casp11 in Il10-/- mice and acute and chronic DSS colitis mouse models. We quantified colonic Casp11 mRNA using quantative polymerase chain reaction and colitis using weight loss, blinded histological scoring, IL-12/23p40 secretion by colonic explants, and fecal lipocalin-2. We determined fecal microbial composition using 16S amplicon sequencing.<br><br>Results: We detected increased colonic Casp11 mRNA in Il10-/- mice with chronic colitis, but not in mice with DSS colitis. The presence of Casp11 did not alter the severity of chronic colitis in DSS-treated or Il10-/- mice. Contrary to prior reports, we initially observed that Casp11 exacerbates acute DSS colitis. Subsequent experiments in the same animal facility revealed no effect of Casp11 on acute DSS colitis. There were pronounced stochastic changes in the fecal microbiome over this time. The majority of bacterial taxa that changed over time in wild-type vs Casp11-/- mice belong to the Clostridiales.<br><br>Conclusions: Casp11 does not impact chronic experimental colitis, and its effects on acute DSS colitis vary with environmental factors including the microbiota, particularly Clostridiales. Stochastic drifts in intestinal microbiota composition, even in mice in the same housing facility, should be considered when interpreting studies of acute DSS colitis models.},
}
@article {pmid30312395,
year = {2018},
author = {Navrátilová, D and Tláskalová, P and Kohout, P and Drevojan, P and Fajmon, K and Chytrý, M and Baldrian, P},
title = {Diversity of fungi and bacteria in species-rich grasslands increases with plant diversity in shoots but not in roots and soil.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiy208},
pmid = {30312395},
issn = {1574-6941},
abstract = {Microbial communities in roots and shoots of plants and in soil are important for plant growth and health and take part in important ecosystem processes. Therefore, understanding the factors that affect their diversity is important. We have analysed fungal and bacterial communities associated with plant shoots, roots and soil over a 1 km2 area in a semi-natural temperate grassland with 1-43 plant species per 0.1 m2, to describe the relationships between plant and microbial diversity and to identify the drivers of bacterial and fungal community composition. Microbial community composition differed between shoots, roots and soil. While both fungal and bacterial species richness in shoots increased with plant species richness, no correlation was found between plant and microbial diversity in roots and soil. Chemistry was a significant predictor of bacterial and fungal community composition in soil as was also the spatial location of the sampled site. In this species rich grassland, t