@article {pmid31306822,
year = {2019},
author = {Han, L and Cai, L and Zhang, H and Long, Z and Yu, Y and Fang, H},
title = {Development of antibiotic resistance genes in soils with ten successive treatments of chlortetracycline and ciprofloxacin.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {253},
number = {},
pages = {152-160},
doi = {10.1016/j.envpol.2019.07.031},
pmid = {31306822},
issn = {1873-6424},
abstract = {Antibiotic contamination caused by the long-term use of organic manure (OM) in greenhouse agricultural soils poses potential detrimental effects to the soil environment. By applying OM containing chlortetracycline (CTC) and/or ciprofloxacin (CIP) ten times in soil under laboratory conditions, we investigated the dissipation and accumulation characteristics of CTC and CIP in the soil, the changes in the microbial pollution-induced community tolerance (PICT), and the diversity and abundance of antibiotic resistance genes (ARGs) in the soil microbiome. The dissipation of CTC was rapid while CIP was accumulated in repeatedly treated soils; further, CIP could inhibit the dissipation of CTC. Meanwhile, the PICT to CTC and/or CIP significantly increased up to 15.0-fold after ten successive treatments compared to that in the first treatment. As the treatment frequency increased, significant upward trends in the abundances of tetracycline resistance genes tetA(G), tetX2, tetX, tetG, tetA(33), tetA, tetW, and tetA(P), fluoroquinolone resistance gene qnrA6, and multiple resistance gene mexF were revealed by both metagenomic and qPCR analyses. The findings demonstrated that repeated treatments with CTC and/or CIP can alter the dissipation rate, promote an increase in PICT to CTC and/or CIP, and increase the ARGs abundance in steps.},
}

@article {pmid31306584,
year = {2019},
author = {Fay, KT and Klingensmith, NJ and Chen, CW and Zhang, W and Sun, Y and Morrow, KN and Liang, Z and Burd, EM and Ford, ML and Coopersmith, CM},
title = {The gut microbiome alters immunophenotype and survival from sepsis.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {},
number = {},
pages = {fj201802188R},
doi = {10.1096/fj.201802188R},
pmid = {31306584},
issn = {1530-6860},
abstract = {The microbiome is increasingly implicated in immune regulation and mortality from sepsis. Mice with identical genetic backgrounds but distinct microbiomes were obtained from different vendors and analyzed following cecal ligation and puncture (CLP). β diversity of the microbiome measured from feces demonstrated significant differences between The Jackson Laboratory (Jax; Bar Harbor, ME, USA) and Charles River Laboratories (CR; Wilmington, MA, USA) C57/B6 mice. Jax mice had 7-d mortality of 90% following CLP, whereas CR mice had a mortality of 53%. Differences in vendor were associated with altered immunophenotype with increased splenic IFN-γ+CD4+ T cells, effector memory CD4+ T cells, and central memory CD4+ T cells and increased Peyer's patch effector memory CD4+ T cells in septic CR mice. To determine whether differences in the microbiome were responsible for these differences, Jax and CR mice were cohoused for 3 wk, after which they assumed a similar microbiota composition. Cohoused mice had improved survival following CLP compared to Jax mice and had similar survival regardless of their vendor of origin. All differences in immunophenotype between septic Jax and CR mice disappeared following cohousing. These findings suggest that the microbiome plays a crucial role in survival and the host immune response from sepsis and represents a potential target for therapeutic intervention.-Fay, K. T., Klingensmith, N. J., Chen, C.-W., Zhang, W., Sun, Y., Morrow, K. N., Liang, Z., Burd, E. M., Ford, M. L., Coopersmith, C. M. The gut microbiome alters immunophenotype and survival from sepsis.},
}

@article {pmid31306512,
year = {2019},
author = {Xu, Q and Biancalana, M and Grant, JC and Chiu, HJ and Jaroszewski, L and Knuth, MW and Lesley, SA and Godzik, A and Elsliger, MA and Deacon, AM and Wilson, IA},
title = {Structures of single-layer β-sheet proteins evolved from β-hairpin repeats.},
journal = {Protein science : a publication of the Protein Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/pro.3683},
pmid = {31306512},
issn = {1469-896X},
abstract = {Free-standing single β-sheets are extremely rare in naturally occurring proteins, even though β-sheet motifs are ubiquitous. Here we report on crystal structures of three homologous, single-layer, anti-parallel β-sheet proteins, comprised of three or four twisted β-hairpin repeats. The structures reveal that, in addition to the hydrogen bond network characteristic of β-sheets, additional hydrophobic interactions mediated by small clusters of residues adjacent to the turns likely play a significant role in the structural stability and compensate for the lack of a compact hydrophobic core. These structures enabled identification of a family of secreted proteins that are broadly distributed in bacteria from the human gut microbiome and involved in the metabolism of complex carbohydrates. A conserved surface patch, rich in solvent-exposed tyrosine residues, was also identified on the concave surface of the β-sheet. These new modular single-layer β-sheet proteins may serve as a new model system for studying folding and design of β-rich proteins. This article is protected by copyright. All rights reserved.},
}

@article {pmid31306499,
year = {2019},
author = {Seabloom, EW and Condon, B and Kinkel, L and Komatsu, KJ and Lumibao, CY and May, G and McCulley, RL and Borer, ET},
title = {Effects of nutrient supply, herbivory, and host community on fungal endophyte diversity.},
journal = {Ecology},
volume = {},
number = {},
pages = {e02758},
doi = {10.1002/ecy.2758},
pmid = {31306499},
issn = {1939-9170},
support = {//National Science Foundation/ ; //University of Minnesota/ ; },
abstract = {The microbes contained within free-living organisms can alter host growth, reproduction, and interactions with the environment. In turn, processes occurring at larger scales determine the local biotic and abiotic environment of each host that may affect the diversity and composition of the microbiome community. Here, we examine variation in the diversity and composition of the foliar fungal microbiome in the grass host, Andropogon gerardii, across four mesic prairies in the central United States. Composition of fungal endophyte communities differed among sites and among individuals within a site, but was not consistently affected by experimental manipulation of nutrient supply to hosts (A. gerardii) or herbivore reduction via fencing. In contrast, mean fungal diversity was similar among sites but was limited by total plant biomass at the plot scale. Our work demonstrates that distributed experiments motivated by ecological theory are a powerful tool to unravel the multiscale processes governing microbial community composition and diversity.},
}

@article {pmid31305265,
year = {2019},
author = {Zaiss, MM and Jones, RM and Schett, G and Pacifici, R},
title = {The gut-bone axis: how bacterial metabolites bridge the distance.},
journal = {The Journal of clinical investigation},
volume = {130},
number = {},
pages = {},
doi = {10.1172/JCI128521},
pmid = {31305265},
issn = {1558-8238},
abstract = {The gut microbiome is a key regulator of bone health that affects postnatal skeletal development and skeletal involution. Alterations in microbiota composition and host responses to the microbiota contribute to pathological bone loss, while changes in microbiota composition that prevent, or reverse, bone loss may be achieved by nutritional supplements with prebiotics and probiotics. One mechanism whereby microbes influence organs of the body is through the production of metabolites that diffuse from the gut into the systemic circulation. Recently, short-chain fatty acids (SCFAs), which are generated by fermentation of complex carbohydrates, have emerged as key regulatory metabolites produced by the gut microbiota. This Review will focus on the effects of SCFAs on the musculoskeletal system and discuss the mechanisms whereby SCFAs regulate bone cells.},
}

@article {pmid31304222,
year = {2019},
author = {Nafarin, AR and Hegar, B and Sjakti, HA and Vandenplas, Y},
title = {Gut microbiome pattern in adolescents with functional gastrointestinal disease.},
journal = {International journal of pediatrics & adolescent medicine},
volume = {6},
number = {1},
pages = {12-15},
doi = {10.1016/j.ijpam.2019.01.005},
pmid = {31304222},
issn = {2352-6467},
abstract = {Background: Functional gastrointestinal disease (FGID) has a worldwide prevalence of 10-45%, and is one of the most common causes of recurrent abdominal pain in children. FGID is characterized with abdominal discomfort and changes in bowel movement. Alteration in gut microbiota is associated with FGID, but data are limited, and there are no data from Indonesia.

Methods: A case-control study was conducted in 22 FGID children and 28 healthy subjects aged 13-18 years at the junior high school and senior high school in Central Jakarta. FGID was diagnosed using Rome IV criteria. Age, sex, and level of education were recorded. Stool samples were collected and investigated for Bifidobacterium spp. and Enterobacteriaceae.

Results: Most of the FGID subjects were females (17/22), with a median age of 16 years. The median values of Bifidobacterium spp. were 138.95 (range: 0.2-22,735.8) CFU/gram for the FGID subjects and 232.5 (range: 1.9-38,985.6) CFU/gram in healthy subjects, which showed no statistically significant difference (P = .49). The median values of Enterobacteriaceae were 58.9 (range: 2.5-9577.8) CFU/gram in FGID subjects and 85 (range: 12.1-3139.4) CFU/gram in healthy subjects, which showed no statistically significant difference (P = .94). Our findings indicate that the gut microbiome of adolescents with FGIDs is characterized by a huge variability in levels of Bifidobacterium spp. and Enterobacteriaceae.

Conclusion: Because of the wide range detected in the number of Bifidobacterium spp. and Enterobacteriaceae in FGID and healthy subjects, no statistically significant difference was observed. More studies in larger groups of selected patients may be needed.},
}

@article {pmid31304220,
year = {2019},
author = {Almana, Y and Mohammed, R},
title = {Current concepts in pediatric inflammatory bowel disease; IL10/IL10R colitis as a model disease.},
journal = {International journal of pediatrics & adolescent medicine},
volume = {6},
number = {1},
pages = {1-5},
doi = {10.1016/j.ijpam.2019.02.002},
pmid = {31304220},
issn = {2352-6467},
abstract = {Inflammatory bowel disease (IBD) is a heterogeneous group of disorders composed mainly of ulcerative colitis (UC) and Crohn's disease (CD) and undetermined IBD. The peak incidence of occurrence is mainly beyond the pediatric age group. Recent knowledge about genetic factors had been strongly linked to pediatric IBD (PIBD). Recent advances in genomic technologies have prompted the identification of genetic defects underlying rare, very early-onset IBD (VEO-IBD) as a disease subgroup noted especially in populations with higher consanguinity rates. A better understanding of key players in the complex homeostasis of the immune system in the gut and illustrating the relationships between intestinal microbiome, systemic immune dysregulation and primary immunodeficiency have received growing recognition over the years. In this article, we provide a review of the key players of the immunity of the gut, compare between adult and pediatric IBD as an interesting module to investigate the relationship between monogenic and multifactorial/polygenic diseases, list genetic mutations confirmed to be linked to VEO IBD and summarize the scientific work that led to the discovery of one of the monogenic mutations related to infantile colitis, namely IL10 and IL10 receptor defects.},
}

@article {pmid31304012,
year = {2019},
author = {Canibe, N and O'Dea, M and Abraham, S},
title = {Potential relevance of pig gut content transplantation for production and research.},
journal = {Journal of animal science and biotechnology},
volume = {10},
number = {},
pages = {55},
doi = {10.1186/s40104-019-0363-4},
pmid = {31304012},
issn = {1674-9782},
abstract = {It is becoming increasingly evident that the gastrointestinal microbiota has a significant impact on the overall health and production of the pig. This has led to intensified research on the composition of the gastrointestinal microbiota, factors affecting it, and the impact of the microbiota on health, growth performance, and more recently, behavior of the host. Swine production research has been heavily focused on assessing the effects of feed additives and dietary modifications to alter or take advantage of select characteristics of gastrointestinal microbes to improve health and feed conversion efficiency. Research on faecal microbiota transplantation (FMT) as a possible tool to improve outcomes in pigs through manipulation of the gastrointestinal microbiome is very recent and limited data is available. Results on FMT in humans demonstrating the transfer of phenotypic traits from donors to recipients and the high efficacy of FMT to treat Clostridium difficile infections in humans, together with data from pigs relating GI-tract microbiota composition with growth performance has likely played an important role in the interest towards this strategy in pig production. However, several factors can influence the impact of FMT on the recipient, and these need to be identified and optimized before this tool can be applied to pig production. There are obvious inherent biosecurity and regulatory issues in this strategy, since the donor's microbiome can never be completely screened for all possible non-desirable microorganisms. However, considering the success observed in humans, it seems worth investigating this strategy for certain applications in pig production. Further, FMT research may lead to the identification of specific bacterial group(s) essential for a particular outcome, resulting in the development of banks of clones which can be used as targeted therapeutics, rather than the broader approach applied in FMT. This review examines the factors associated with the use of FMT, and its potential application to swine production, and includes research on using the pig as model for human medical purposes.},
}

@article {pmid31303990,
year = {2019},
author = {Thamban Chandrika, N and Fosso, MY and Alimova, Y and May, A and Gonzalez, OA and Garneau-Tsodikova, S},
title = {Novel zafirlukast derivatives exhibit selective antibacterial activity against Porphyromonas gingivalis.},
journal = {MedChemComm},
volume = {10},
number = {6},
pages = {926-933},
doi = {10.1039/c9md00074g},
pmid = {31303990},
issn = {2040-2511},
abstract = {Periodontal disease is an oral chronic immune-inflammatory disease highly prevalent worldwide that is initiated by specific oral bacterial species leading to local and systemic effects. The development of new preventive/therapeutic strategies to specifically target oral periodontopathogens without perturbing oral microbiome species normally colonizing the oral cavity is needed. The fast and affordable strategy of repositioning of already FDA-approved drugs can be an answer to the development of novel treatments against periodontal pathogens such as Porphyromonas gingivalis. Herein, we report the synthesis and antibacterial activity of novel zafirlukast derivatives, their bactericidal effect, and their cytotoxicity against oral epithelial cell lines. Many of these derivatives exhibited superior antibacterial activity against P. gingivalis compared to the parent drug zafirlukast. The most promising compounds were found to be selective against P. gingivalis and they were bactericidal in their activity. Finally, we demonstrated that these potent derivatives of zafirlukast provided a better safety profile against oral epithelial cells compared to zafirlukast.},
}

@article {pmid31303969,
year = {2019},
author = {Chen, T and Olsen, I},
title = {Porphyromonas gingivalis and its CRISPR-Cas system.},
journal = {Journal of oral microbiology},
volume = {11},
number = {1},
pages = {1638196},
doi = {10.1080/20002297.2019.1638196},
pmid = {31303969},
issn = {2000-2297},
abstract = {The clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated proteins (Cas) are immune systems in prokaryotes present in most Bacteria and Archaea. They provide adaptive immunity against foreign elements such as bacteriophages/viruses, plasmids and transposons. During immunization a small sequence of foreign DNA, a so-called spacer is integrated into the CRISPR locus in the host cell. Spacers are then transcribed into small RNA guides that direct cleavage of foreign DNA by Cas nucleases. Immunization through spacer acquisition is transferred vertically to the progeny. It is possible that this genetic immune system of bacteria participates in modulating the microbiome of 'chronic' periodontitis, in which Porphyromonas gingivalis has been identified as a keystone pathogen causing microbial dysbiosis. An in-depth review of our current knowledge on the CRISPR-Cas systems in P. gingivalis is given in this paper with the attempt to understand how this anaerobic bacterium may protect itself in the periodontal pocket where bacteriophages are abundant and even out-number bacteria.},
}

@article {pmid31303186,
year = {2019},
author = {Garcia-Mazcorro, JF and Ishaq, SL and Rodriguez-Herrera, MV and Garcia-Hernandez, CA and Kawas, JR and Nagaraja, TG},
title = {Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits.},
journal = {Animal : an international journal of animal bioscience},
volume = {},
number = {},
pages = {1-9},
doi = {10.1017/S1751731119001599},
pmid = {31303186},
issn = {1751-732X},
abstract = {All livestock animal species harbour complex microbial communities throughout their digestive tract that support vital biochemical processes, thus sustaining health and productivity. In part as a consequence of the strong and ancient alliance between the host and its associated microbes, the gut microbiota is also closely related to productivity traits such as feed efficiency. This phenomenon can help researchers and producers develop new and more effective microbiome-based interventions using probiotics, also known as direct-fed microbials (DFMs), in Animal Science. Here, we focus on one type of such beneficial microorganisms, the yeast Saccharomyces. Saccharomyces is one of the most widely used microorganisms as a DFM in livestock operations. Numerous studies have investigated the effects of dietary supplementation with different species, strains and doses of Saccharomyces (mostly Saccharomyces cerevisiae) on gut microbial ecology, health, nutrition and productivity traits of several livestock species. However, the possible existence of Saccharomyces which are indigenous to the animals' digestive tract has received little attention and has never been the subject of a review. We for the first time provide a comprehensive review, with the objective of shedding light into the possible existence of indigenous Saccharomyces of the digestive tract of livestock. Saccharomyces cerevisiae is a nomadic yeast able to survive in a broad range of environments including soil, grass and silages. Therefore, it is very likely that cattle and other animals have been in direct contact with this and other types of Saccharomyces throughout their entire existence. However, to date, the majority of animal scientists seem to agree that the presence of Saccharomyces in any section of the gut only reflects dietary contamination; in other words, these are foreign organisms that are only transiently present in the gut. Importantly, this belief (i.e. that Saccharomyces come solely from the diet) is often not well grounded and does not necessarily hold for all the many other groups of microbes in the gut. In addition to summarizing the current body of literature involving Saccharomyces in the digestive tract, we discuss whether the beneficial effects associated with the consumption of Saccharomyces may be related to its foreign origin, though this concept may not necessarily satisfy the theories that have been proposed to explain probiotic efficacy in vivo. This novel review may prove useful for biomedical scientists and others wishing to improve health and productivity using Saccharomyces and other beneficial microorganisms.},
}

@article {pmid31302808,
year = {2019},
author = {Selvig, D and Piceno, Y and Terdiman, J and Zydek, M and Umetsu, SE and Balitzer, D and Fadrosh, D and Lynch, K and Lamere, B and Leith, T and Kassam, Z and Beck, K and Lewin, S and Ma, A and Somsouk, M and Lynch, SV and El-Nachef, N},
title = {Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-019-05715-2},
pmid = {31302808},
issn = {1573-2568},
abstract = {AIMS: This pilot study assessed the efficacy, safety, and microbiome dynamics of fecal microbiota transplantation (FMT) for patients with chronic pouchitis.

METHODS: A prospective open-label pilot study was performed at an academic center among pouchitis patients undergoing FMT. Patients received a minimum of a single FMT by pouchoscopy from healthy, screened donors. The primary outcome was clinical improvement in pouchitis assessed by patient survey at week 4. Secondary outcomes included decrease in total Pouchitis Disease Activity Index (PDAI) Score ≥ 3 at week 4, bowel movement frequency, ESR, CRP, fecal calprotectin, abdominal pain, and PDAI subscores including endoscopic and histologic changes. Stool samples were collected at baseline and 4 weeks post-FMT to assess bacterial microbiota using V4 16S rRNA sequencing.

RESULTS: Nineteen patients were enrolled; however, 1 patient was lost to follow-up. No patients had a major adverse event or escalation of therapy related to FMT. Total PDAI scores, endoscopic scores, and histologic scores did not decrease significantly post-FMT. However, there was a statistically significant improvement in bowel movement (BM) frequency (9.25-7.25 BM/day, p = 0.03) and trend for improvement in abdominal pain to improve post-FMT (p = 0.05). Bacterial microbiota profiling revealed no distinct community-level changes post-FMT, though a small number of specific bacterial taxa significantly differed in relative abundance.

CONCLUSIONS: A single FMT has a tolerable short-term safety profile and may be associated with a decrease in bowel movements in patients with chronic pouchitis; however, no robust endoscopic or histologic changes were observed.},
}

@article {pmid31302571,
year = {2019},
author = {Sacco, KA and Milner, JD},
title = {Gene-environment interactions in primary atopic disorders.},
journal = {Current opinion in immunology},
volume = {60},
number = {},
pages = {148-155},
doi = {10.1016/j.coi.2019.06.002},
pmid = {31302571},
issn = {1879-0372},
abstract = {Environmental factors modify disease presentation and severity in allergic disorders. Primary atopic disorders (PADs) are a heterogenous group of single gene disorders that lead to significant atopic and allergic disease manifestations. However, a number of these monogenic diseases have variable penetrance suggesting that gene-gene and/or gene-environment interactions could modulate the clinical phenotype. Environmental factors such as diet, the microbiome at the epithelial-environment interface, the presence and/or extent of infection, and psychologic stress can alter disease phenotypic expression of allergic diseases, and PADs provide discrete contexts in which to understand these influences. We outline how gene-environment interactions likely contribute to a variable penetrance and expressivity in PADs. Dietary modifications of both macronutrients and/or micronutrients alter T-cell metabolism and may influence effector T-cell function. The mucosal microbiome may affect local inflammation and may remotely influence regulatory elements, while psychologic stress can affect mast cell and other allergic effector cell function. Understanding gene-environment interactions in PADs can hopefully provide a foundation for interrogating gene-environment interactions to common allergic disorders, and also present opportunities for personalized interventions based on the altered pathways and environmental influences in affected individuals.},
}

@article {pmid31302570,
year = {2019},
author = {Stephen-Victor, E and Chatila, TA},
title = {Regulation of oral immune tolerance by the microbiome in food allergy.},
journal = {Current opinion in immunology},
volume = {60},
number = {},
pages = {141-147},
doi = {10.1016/j.coi.2019.06.001},
pmid = {31302570},
issn = {1879-0372},
abstract = {The steep rise in the incidence and prevalence of food allergy (FA) in the last few decades have focused attention of environmental mechanisms which act to promote disease, chief among which is the microbiome. Recent studies have now established the presence of pathogenic dysbiosis in FA that could be precipitated by a variety of environmental insults, including among others antibiotic usage and mode of delivery, that act to subvert the immune regulatory response that enforce tolerance to dietary antigens. A key attribute of this dysbiosis is the loss of Clostridial bacterial species that act to promote the formation of food allergen-specific nascent regulatory T cells in the gut. Significantly, different immunoprotective commensal bacteria, including members of the Clostridiales and Bacteroidales orders act to induce the transcription factor RORγt in nascent Treg cells via an upstream MyD88-dependent mechanism to promote tolerance to dietary antigens. Activation of this axis is disrupted by the dysbiosis, and can be restored by treatment with therapeutic microbiota. These findings highlight the potential for novel microbiota-based approaches to the prevention and treatment of the FA epidemic.},
}

@article {pmid31302555,
year = {2019},
author = {Li, PD and Jeewon, R and Aruna, B and Li, HY and Lin, FC and Wang, HK},
title = {Metabarcoding reveals differences in fungal communities between unflooded versus tidal flat soil in coastal saline ecosystem.},
journal = {The Science of the total environment},
volume = {690},
number = {},
pages = {911-922},
doi = {10.1016/j.scitotenv.2019.06.473},
pmid = {31302555},
issn = {1879-1026},
abstract = {In the saline-affected ecosystem, fungi have huge potential to promote growth, induce disease resistance and enhance tolerance against salt-stress of host plants. Since areas of plowland are gradually decreasing, the reclamation of coastal saline lands could play a crucial role in maintaining agricultural productivity and crop security globally. Therefore, it is of great significance to explore the fungal diversity in the coastal saline ecosystem. Here, we collected saline soil samples from unflooded areas and tidal flat areas, the two typical distinct landforms in coastal saline ecosystems, and used ITS metabarcoding to depict the diversity of fungal communities. We found that fungal species evenness had a remarkably higher variation from the tidal flat compared to unflooded soil samples. Furthermore, we also confirmed that the fungal niches differentiation reports in the coastal saline ecosystem. Our ITS based DNA sequencing revealed that both unflooded and tidal flat soil were mainly composed of amplicon sequence variants (ASVs) belonging to Ascomycota (93.43% and 86.91% respectively). Based on our findings, understanding the associations and distinctions of fungal microbiome between unflooded soil and tidal flat could provide the basis for the development of reclamation in coastal saline lands.},
}

@article {pmid31302481,
year = {2019},
author = {Keerthisinghe, TP and Wang, M and Zhang, Y and Dong, W and Fang, M},
title = {Low-dose tetracycline exposure alters gut bacterial metabolism and host-immune response: "Personalized" effect?.},
journal = {Environment international},
volume = {131},
number = {},
pages = {104989},
doi = {10.1016/j.envint.2019.104989},
pmid = {31302481},
issn = {1873-6750},
abstract = {The human gut microbiome (GM) in healthy people is chronically exposed to tetracycline (TET) via environmental exposure and dietary uptake. However, limited information is available on its effect on the GM metabolome and effect on the host, especially at the dietary exposure level. Here, we investigated how TET at both sub-pharmaceutical and dietary exposure levels affects the metabolome and the secretome-induced host immune response by studying several representative gut bacteria. Interestingly, the metabolome showed a highly species-specific pattern with a distinct dose-response relationship. B. fragilis was highly sensitive to TET and vitamin, nucleotide, and amino acid metabolism pathways were the most vulnerable metabolic pathways at dietary exposure level. For key metabolite short chain fatty acids, TET significantly induced the synthesis of butyrate in B. fragilis, rather than C. sporogenes and E. coli. Furthermore, TET induced the release of lipopolysaccharides (LPS) in E. coli and enhanced the immune response; however, there was no obvious effect on B. fragilis. Interestingly, the overall immune response modulation with TET exposure relied on the ratio between E. coli and B. fragilis, possibly due to the neutralization of active LPS from E. coli by the LPS from B. fragilis. Overall, our results showed that the effect of TET from environmental exposure on the host health would be highly dependent on the GM composition, especially for the gut bacterial metabolome and secretome induced immune response.},
}

@article {pmid31302340,
year = {2019},
author = {Santamaria, F and Montella, S and Stocchero, M and Pirillo, P and Bozzetto, S and Giordano, G and Poeta, M and Baraldi, E},
title = {Effects of pidotimod and bifidobacteria mixture on clinical symptoms and urinary metabolomic profile of children with recurrent respiratory infections: A randomized placebo-controlled trial.},
journal = {Pulmonary pharmacology & therapeutics},
volume = {},
number = {},
pages = {101818},
doi = {10.1016/j.pupt.2019.101818},
pmid = {31302340},
issn = {1522-9629},
abstract = {BACKGROUND: Many preschool children develop recurrent respiratory tract infections (RRI). Strategies to prevent RRI include the use of immunomodulators as pidotimod or probiotics, but there is limited evidence of their efficacy on clinical features or on urine metabolic profile.

OBJECTIVE: To evaluate whether pidotimod and/or bifidobacteria can reduce RRI morbidity and influence the urine metabolic profile in preschool children.

MATERIALS AND METHODS: Children aged 3-6 years with RRI were enrolled in a four-arm, exploratory, prospective, randomized, double-blinded, placebo-controlled trial. Patients were randomly assigned to receive pidotimod plus bifidobacteria, pidotimod plus placebo, bifidobacteria plus placebo or double placebo for the first 10 days of each month over 4 consecutive months. Respiratory symptoms and infections were recorded with a daily diary by parents during the study. Metabolomic analyses on urine samples collected before and after treatment were performed.

RESULTS: Compared to placebo, children receiving pidotimod, alone or with bifidobacteria, had more symptom-free days (69 versus 44, p = 0.003; and 65 versus 44, p = 0.02, respectively) and a lower percentage of days with common cold (17% versus 37%, p = 0.005; and 15% versus 37%, p = 0.004, respectively). The metabolomic analysis showed that children treated with Pidotimod (alone or in combination with bifidobacteria) present, respect to children treated with placebo, a biochemical profile characterized by compounds related to the pathway of steroids hormones, hippuric acid and tryptophan. No significant difference in the metabolic profile was found between children receiving bifidobacteria alone and controls.

CONCLUSIONS: Preschool children with RRI treated with pidotimod have better clinical outcomes and a different urine metabolomic profile than subjects receiving placebo. Further investigations are needed to clarify the connection between pidotimod and gut microbiome.},
}

@article {pmid31302235,
year = {2019},
author = {Wallace, IJ and Bendele, AM and Riew, G and Frank, EH and Hung, HH and Holowka, NB and Bolze, AS and Venable, EM and Yegian, A and Dingwall, HL and Carmody, RN and Grodzinsky, AJ and Lieberman, DE},
title = {Physical inactivity and knee osteoarthritis in guinea pigs.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2019.07.005},
pmid = {31302235},
issn = {1522-9653},
abstract = {OBJECTIVE: To investigate whether and how a sedentary lifestyle contributes to knee osteoarthritis (OA) incidence and severity.

DESIGN: An experiment was conducted using Hartley guinea pigs, an established idiopathic knee OA model. To simulate a sedentary lifestyle, growing animals (n=18) were housed for 22 weeks in small cages that restricted their mobility, while another group of animals (n=17) received daily treadmill exercise to simulate moderate physical activity. After the experiment, histological assessments, biochemical assays, and mechanical testing were conducted to compare tibial articular cartilage structure, strength, and degree of OA degeneration between sedentary and physically active animals. Groups were also compared based on body weight and composition, as well as gut microbial communities assessed using fecal 16S rRNA gene sequencing.

RESULTS: Prevalence of knee OA was similar between sedentary and physically active animals, but severity of the disease (cartilage lesion depth) was substantially greater in the sedentary group (p=0.02). In addition, during the experiment, sedentary animals developed cartilage with lower aggrecan quantity (p=0.03) and accumulated more body weight (p=0.005) and visceral adiposity (p=0.007). Groups did not differ greatly, however, in terms of cartilage thickness, collagen quantity, or stiffness, nor in terms of muscle weight, subcutaneous adiposity, or gut microbiome composition.

CONCLUSIONS: Our findings indicate that a sedentary lifestyle promotes the development of knee OA, particularly by enhancing disease severity rather than risk of onset, and this potentially occurs through multiple pathways including by engendering growth of functionally deficient joint tissues and the accumulation of excess body weight and adiposity.},
}

@article {pmid31302202,
year = {2019},
author = {Ezzy, AC and Hagstrom, AD and George, C and Hamlin, AS and Pereg, L and Murphy, AJ and Winter, G},
title = {Storage and handling of human faecal samples affect the gut microbiome composition: A feasibility study.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {105668},
doi = {10.1016/j.mimet.2019.105668},
pmid = {31302202},
issn = {1872-8359},
abstract = {Human gut microbiome analysis through faecal sampling typically involves five stages: sample collection, storage, DNA extraction, next generation sequencing and bioinformatics analysis. Of these, the first three are considered irreversible. This feasibility study describes an assessment of methodologies used for faecal DNA extraction and sample handling, using the parameters DNA yield, purity and resultant microbial profile. Six DNA extraction techniques, including commercially available kits and manual protocols were compared on human faecal samples (n = 3). Different extraction techniques produced significant variance in DNA yield (range 2.7-164 ng/mg faeces) and microbial diversity profiles, with considerable variation in phyla dominance (Firmicutes (P < 0.001), Bacteroidetes (P = 0.003), Actinobacteria (P = 0.003), One-way ANOVA). The most effective method, with the highest DNA yield, was a simple and inexpensive extraction technique named MetaHIT. Using this method, DNA was extracted from separate faecal samples (n = 3) and had been aliquoted to seven storage conditions including three stabilizing buffers and three temperature conditions, for a period of 120-h, with storage at -80 °C as a control treatment. DNA yield and purity was not statistically different between the control and remaining treatments. 16S rDNA-based diversity profile was largely comparable across the treatments with only minor differences in genera between samples stored at room temperature in air and - 80 °C control. Overall these results suggest that the choice of DNA extraction method has a greater influence on the resultant microbial diversity profile than the short-term storage method.},
}

@article {pmid31301989,
year = {2019},
author = {Becker, F and Gavins, FNE and Fontenot, J and Jordan, P and Yun, JY and Scott, R and Polk, PR and Friday, RE and Boktor, M and Musso, M and Romero, E and Boudreaux, S and Simmons, J and Hasselschwert, DL and Goetzmann, JE and Vanchiere, J and Cvek, U and Trutschl, M and Kilgore, P and Alexander, JS},
title = {Dynamic gut microbiome changes following regional intestinal lymphatic obstruction in primates.},
journal = {Pathophysiology : the official journal of the International Society for Pathophysiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pathophys.2019.06.004},
pmid = {31301989},
issn = {0928-4680},
abstract = {The pathogenesis of inflammatory bowel disease (IBD) has been linked with lymphostasis, but whether and how lymphatic obstruction might disturb the intestinal microbiome in the setting of Crohn's Disease (CD) is currently unknown. We employed a new model of CD in African Green monkeys, termed 'ATLAS' (African green monkey truncation of lymphatics with obstruction and sclerosis), to evaluate how gut lymphatic obstruction alters the intestinal microbiome at 7, 21 and 61 days. Remarkable changes in several microbial sub- groupings within the gut microbiome were observed at 7 days post-ATLAS compared to controls including increased abundance of Prevotellaceae and Bacteroidetes-Prevotella-Porphyromonas (BPP), which may contribute to disease activity in this model of gut injury. To the best of our knowledge, these findings represent the first report linking lymphatic structural/gut functional changes with alterations in the gut microbiome as they may relate to the pathophysiology of CD.},
}

@article {pmid31301692,
year = {2019},
author = {Stanton, DE and Batterman, SA and Von Fischer, J and Hedin, LO},
title = {Rapid nitrogen fixation by canopy microbiome in tropical forest determined by both phosphorus and molybdenum.},
journal = {Ecology},
volume = {},
number = {},
pages = {e02795},
doi = {10.1002/ecy.2795},
pmid = {31301692},
issn = {1939-9170},
abstract = {Biological nitrogen fixation is critical for the nitrogen cycle of tropical forests, yet we know little about the factors that control the microbial nitrogen-fixers that colonize the microbiome of leaves and branches that make up a forest canopy. Forest canopies are especially prone to nutrient limitation because they are (1) disconnected from soil nutrient pools, and (2) often subject to leaching. Earlier studies have suggested a role of phosphorus and molybdenum in controlling biological N-fixation rates, but experimental confirmation has hitherto been unavailable. We here present the results of a manipulation of canopy nutrient availability. Our findings demonstrate a primary role of phosphorus in constraining overall N-fixation by canopy cyanobacteria, but also a secondary role of molybdenum in determining per-cell fixation rates. A conservative evaluation suggests that canopy fixation can contribute to significant N fluxes at the ecosystem level, especially as bursts following atmospheric inputs of nutrient-rich dust. This article is protected by copyright. All rights reserved.},
}

@article {pmid31301494,
year = {2019},
author = {Taboada-Santos, A and Braz, GHR and Fernandez-Gonzalez, N and Carballa, M and Lema, JM},
title = {Thermal hydrolysis of sewage sludge partially removes organic micropollutants but does not enhance their anaerobic biotransformation.},
journal = {The Science of the total environment},
volume = {690},
number = {},
pages = {534-542},
doi = {10.1016/j.scitotenv.2019.06.492},
pmid = {31301494},
issn = {1879-1026},
abstract = {Pretreatment technologies prior to anaerobic digestion (AD) have been developed with the aim of enhancing biogas productivity and reducing the presence of pathogens in digested sludge. Among them, thermal hydrolysis (TH) appears as the most promising one. In wastewater treatment plants (WWTPs) sludge is the end point of many organic micropollutants (OMPs), which was proved to lead to important environmental and human risks since sludge is commonly used in agriculture. The objective of this work is to determine the fate OMPs in TH and subsequent AD. Sewage sludge was pretreated in a TH pilot plant at 170 °C for 20 min. Afterwards, two anaerobic digesters with a working volume of 14 L fed with fresh and pretreated sludge were operated in parallel in mesophilic conditions. TH proved to be an effective technology to partially or totally remove the dissolved fraction of OMPs as well as the fraction sorbed into those suspended solids that are solubilised after this pretreatment. However, it did not affect the OMPs sorbed concentration into solids that are not solubilised. Globally, the OMPs removal efficiency during TH appears to be linked to the solids solubilisation during this process. Afterwards, the OMPs biotransformation efficiency in AD of fresh and pretreated sludge was determined. Noticeable differences between the microbiome of both reactors was determined, but the anaerobic biotransformation was not substantially different for most of the OMPs. However, it affected musk fragrances, which presented considerably lower biotransformation efficiency in the reactor fed with pretreated sludge. Therefore, TH was proved effective in partially removing OMPs but not in enhancing their bioavailability and subsequent anaerobic biotransformation.},
}

@article {pmid31301451,
year = {2019},
author = {Allegretti, JR and Kassam, Z and Mullish, BH and Chiang, A and Carrellas, M and Hurtado, J and Marchesi, JR and McDonald, JAK and Pechlivanis, A and Barker, GF and Blanco, JM and Garcia-Perez, I and Wong, WF and Gerardin, Y and Silverstein, M and Kennedy, K and Thompson, C},
title = {Effects of Fecal Microbiota Transplantation With Oral Capsules in Obese Patients.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2019.07.006},
pmid = {31301451},
issn = {1542-7714},
abstract = {BACKGROUND & AIMS: Studies in mice have shown that the intestinal microbiota can contribute to obesity via the anorexigenic gut hormone glucagon-like peptide 1 (GLP1) and bile acids, which affect lipid metabolism. We performed a randomized, placebo-controlled pilot study of the effects of fecal microbiota transplantation (FMT) in obese, metabolically uncompromised patients.

METHODS: We performed a double-blind study of 22 obese patients (body mass index [BMI] ≥ 35kg/m2) without a diagnosis of diabetes, non-alcoholic steatohepatitis, or metabolic syndrome. Participants were randomly assigned (1:1) to groups that received FMT by capsules (induction dose of 30 capsules at week 4 and maintenance dose of 12 capsules at week 8) or placebo capsules. FMT capsules were derived from a single, lean donor (BMI, 17.5 kg/m2). Patients were followed through week 26; the primary outcome was safety. Stool and serum samples were collected from patients at baseline and at weeks 1, 4, 6, 8 and 12 after administration of the first dose of FMT or placebo and analyzed by 16S RNA gene sequencing. Stool and serum samples were analyzed for metabolomics by liquid chromatography-mass spectrometry. Additional outcomes were change in area under the curve for GLP1 at week 12.

RESULTS: We observed no significant differences in adverse events between patients who received FMT vs placebo. There was no increase in the area under the curve of GLP1 in either group. Patients who received FMT had sustained shifts in microbiomes associated with obesity toward those of the donor (P<.001). Patients who received FMT had a sustained decrease in stool levels of taurocholic acid (P<.05), compared with baseline; bile acid profiles began to more closely resemble those of the donor. We did not observe significant changes in mean BMI at week 12 in either group.

CONCLUSIONS: In a placebo-controlled pilot study, we found that FMT capsules (derived from a lean donor) were safe but did not reduce BMI in obese metabolically uncompromised patients. The FMT capsules were well tolerated and led to sustained changes in the intestinal microbiome and bile acid profiles that were similar to those of the lean donor.},
}

@article {pmid31301372,
year = {2019},
author = {Lowe, AJ and Wang, X and Mueller, JF and Abramson, MJ and Yeh, RY and Erbas, B and Dharmage, SC and Lodge, CJ},
title = {Exposure to breast-milk triclosan and parabens and eczema phenotypes at 12-months: a nested case-control study.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2019.07.001},
pmid = {31301372},
issn = {1097-6825},
abstract = {Levels of butyl-paraben in breastmilk at three months were associated with increased risk of atopic-eczema at 12 months of age, potentially due to altered gut microbiome.},
}

@article {pmid31301059,
year = {2019},
author = {Lew, LC and Hor, YY and Jaafar, MH and Lau, AS and Khoo, BY and Sasidharan, S and Choi, SB and Ong, KL and Kato, T and Nakanishi, Y and Ohno, H and Liong, MT},
title = {Effects of Potential Probiotic Strains on the Fecal Microbiota and Metabolites of D-Galactose-Induced Aging Rats Fed with High-Fat Diet.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12602-019-09545-6},
pmid = {31301059},
issn = {1867-1314},
support = {URICAS grant (1001/ PTEKIND/870030)//Universiti Sains Malaysia/ ; },
abstract = {Both aging and diet play an important role in influencing the gut ecosystem. Using premature senescent rats induced by D-galactose and fed with high-fat diet, this study aims to investigate the effects of different potential probiotic strains on the dynamic changes of fecal microbiome and metabolites. In this study, male Sprague-Dawley rats were fed with high-fat diet and injected with D-galactose for 12 weeks to induce aging. The effect of Lactobacillus plantarum DR7, L. fermentum DR9, and L. reuteri 8513d administration on the fecal microbiota profile, short-chain fatty acids, and water-soluble compounds were analyzed. It was found that the administration of the selected strains altered the gut microbiota diversity and composition, even at the phylum level. The fecal short-chain fatty acid content was also higher in groups that were administered with the potential probiotic strains. Analysis of the fecal water-soluble metabolites revealed that administration of L. plantarum DR7 and L. reuteri 8513d led to higher fecal content of compounds related to amino acid metabolism such as tryptophan, leucine, tyrosine, cysteine, methionine, valine, and lysine; while administration of L. fermentum DR9 led to higher prevalence of compounds related to carbohydrate metabolism such as erythritol, xylitol, and arabitol. In conclusion, it was observed that different strains of lactobacilli can cause difference alteration in the gut microbiota and the metabolites, suggesting the urgency to explore the specific metabolic impact of specific strains on the host.},
}

@article {pmid31301004,
year = {2019},
author = {Li, JKM and Chiu, PKF and Ng, CF},
title = {The impact of microbiome in urological diseases: a systematic review.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11255-019-02225-y},
pmid = {31301004},
issn = {1573-2584},
abstract = {OBJECTIVE: The term microbiome is used to signify the ecological community of commensal, symbiotic, and pathogenic microorganisms that share our body space, in which there were increasing evidences to suggest that they might have potential roles in various medical conditions. While the study of microbiome in the urinary system is not as robust as the systems included in the Human Microbiome Project, there are still evidences in the literature showing that microbiome may have a role in urological diseases. Therefore, we would like to perform a systematic review on the topic and summarize the available evidence on the impact of microbiome on urological diseases.

METHODOLOGY: This review was performed according to the Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) statement. After screening 589 abstracts and including additional studies (such as references from review papers), 76 studies were included for review and discussion.

RESULTS: Studies had suggested that there were correlations of microbiome of different body cavities (e.g., fecal, urinary and seminal fluid) with urological diseases. Also, different diseases would have different microbiome profile in different body cavities. Unfortunately, the studies on the association of microbiome and urological diseases were still either weak or inconsistent.

CONCLUSION: Studies suggested that there might be some relationship between microbiome and various urological diseases. However, further large-scale studies with control of confounding factors should be performed under a standardized methodology in order to have better understanding of the relationship. Also, more standardized reporting protocol for microbiome studies should be considered for better communications in future studies.},
}

@article {pmid31300992,
year = {2019},
author = {Sonthiphand, P and Ruangroengkulrith, S and Mhuantong, W and Charoensawan, V and Chotpantarat, S and Boonkaewwan, S},
title = {Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-019-05905-5},
pmid = {31300992},
issn = {1614-7499},
support = {New Researcher Grant//Mahidol University/ ; MRG6080235//Thailand Research Fund (TRF) Grant/ ; },
abstract = {Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.},
}

@article {pmid31300748,
year = {2019},
author = {Kong, LC and Wang, B and Wang, YM and Hu, RG and Atiewin, A and Gao, D and Gao, YH and Ma, HX},
title = {Characterization of bacterial community changes and antibiotic resistance genes in lamb manure of different incidence.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {10101},
doi = {10.1038/s41598-019-46604-y},
pmid = {31300748},
issn = {2045-2322},
support = {31702293//National Natural Science Foundation of China (National Science Foundation of China)/ ; 20190201294JC//Natural Science Foundation of Jilin Province (Natural Science Foundation of Jilin Province of China)/ ; },
abstract = {Bacterial enteritis is the most important disease in lamb for breeding greatly affects the growth of animals. Changes in the community of intestinal flora can cause the disorder of the colonic environment induced diarrhea. This study aimed to investigate the relationship between the incidence of bacterial enteritis and the number of intestinal microbiome, then the prevalence of drug-resistant genes was detected. Fecal samples were collected at five fattening sheep farms with different incidence of bacterial enteritis, pathogenic bacteria were isolated and identified, drug sensitivity tests were performed. Then, changes in number and structure of intestinal flora were compared by 16S rDNA V3-V4 region high-throughput sequencing, and the ARGs were detected using high-throughput real-time PCR. Our results revealed that the microbial communities were positively correlated with the incidence of bacterial enteritis in different farms. Bacterial communities were higher in YJ (with highest incidence of diarrhea) than any other farms. However, the ARGs seemed not to be more affected by the incidence of bacterial enteritis, but one of the significant findings to emerge from this study is that MCR-1 and NDM are detected in manure. This study has provided an insight of the changes occurring in intestinal flora and AGRs in fattening sheep farms with diverse incidence of bacterial enteritis.},
}

@article {pmid31300667,
year = {2019},
author = {Stevens, AJ and Purcell, RV and Darling, KA and Eggleston, MJF and Kennedy, MA and Rucklidge, JJ},
title = {Human gut microbiome changes during a 10 week Randomised Control Trial for micronutrient supplementation in children with attention deficit hyperactivity disorder.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {10128},
doi = {10.1038/s41598-019-46146-3},
pmid = {31300667},
issn = {2045-2322},
abstract = {It has been widely hypothesized that both diet and the microbiome play a role in the regulation of attention-deficit/hyperactivity disorder (ADHD) behaviour. However, there has been very limited scientific investigation into the potential biological connection. We performed a 10-week pilot study investigating the effects of a broad spectrum micronutrient administration on faecal microbiome content, using 16S rRNA gene sequencing. The study consisted of 17 children (seven in the placebo and ten in the treatment group) between the ages of seven and 12 years, who were diagnosed with ADHD. We found that micronutrient treatment did not drive large-scale changes in composition or structure of the microbiome. However, observed OTUs significantly increased in the treatment group, and showed no mean change in the placebo group. The differential abundance and relative frequency of Actinobacteria significantly decreased post- micronutrient treatment, and this was largely attributed to species from the genus Bifidobacterium. This was compensated by an increase in the relative frequency of species from the genus Collinsella. Further research is required to establish the role that Bifidobacterium contribute towards neuropsychiatric disorders; however, these findings suggest that micronutrient administration could be used as a safe, therapeutic method to modulate Bifidobacterium abundance, which could have potential implications for modulating and regulating ADHD behaviour. Our pilot study provides an initial observation into this area of research, and highlights an interesting avenue for further investigation in a larger cohort. Furthermore, these novel results provide a basis for future research on the biological connection between ADHD, diet and the microbiome.},
}

@article {pmid31300639,
year = {2019},
author = {Ziegler, M and Grupstra, CGB and Barreto, MM and Eaton, M and BaOmar, J and Zubier, K and Al-Sofyani, A and Turki, AJ and Ormond, R and Voolstra, CR},
title = {Coral bacterial community structure responds to environmental change in a host-specific manner.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3092},
doi = {10.1038/s41467-019-10969-5},
pmid = {31300639},
issn = {2041-1723},
support = {Baseline Funds//King Abdullah University of Science and Technology (KAUST)/ ; },
abstract = {The global decline of coral reefs heightens the need to understand how corals respond to changing environmental conditions. Corals are metaorganisms, so-called holobionts, and restructuring of the associated bacterial community has been suggested as a means of holobiont adaptation. However, the potential for restructuring of bacterial communities across coral species in different environments has not been systematically investigated. Here we show that bacterial community structure responds in a coral host-specific manner upon cross-transplantation between reef sites with differing levels of anthropogenic impact. The coral Acropora hemprichii harbors a highly flexible microbiome that differs between each level of anthropogenic impact to which the corals had been transplanted. In contrast, the microbiome of the coral Pocillopora verrucosa remains remarkably stable. Interestingly, upon cross-transplantation to unaffected sites, we find that microbiomes become indistinguishable from back-transplanted controls, suggesting the ability of microbiomes to recover. It remains unclear whether differences to associate with bacteria flexibly reflects different holobiont adaptation mechanisms to respond to environmental change.},
}

@article {pmid31300207,
year = {2019},
author = {Nené, NR and Reisel, D and Leimbach, A and Franchi, D and Jones, A and Evans, I and Knapp, S and Ryan, A and Ghazali, S and Timms, JF and Paprotka, T and Bjørge, L and Zikan, M and Cibula, D and Colombo, N and Widschwendter, M},
title = {Association between the cervicovaginal microbiome, BRCA1 mutation status, and risk of ovarian cancer: a case-control study.},
journal = {The Lancet. Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1470-2045(19)30340-7},
pmid = {31300207},
issn = {1474-5488},
abstract = {BACKGROUND: Various factors-including age, family history, inflammation, reproductive factors, and tubal ligation-modulate the risk of ovarian cancer. In this study, our aim was to establish whether women with, or at risk of developing, ovarian cancer have an imbalanced cervicovaginal microbiome.

METHODS: We did a case-control study in two sets of women aged 18-87 years in the Czech Republic, Germany, Italy, Norway, and the UK. The ovarian cancer set comprised women with epithelial ovarian cancer and controls (both healthy controls and those diagnosed with benign gynaecological conditions). The BRCA set comprised women with a BRCA1 mutation but without ovarian cancer and controls who were wild type for BRCA1 and BRCA2 (both healthy controls and those with benign gynaecological conditions). Cervicovaginal samples were gathered from all participants with the ThinPrep system and then underwent 16S rRNA gene sequencing. For each sample, we calculated the proportion of lactobacilli species (ie, Lactobacillus crispatus, Lactobacillus iners, Lactobacillus gasseri, and Lactobacillus jensenii), which are essential for the generation of a protective low vaginal pH, in the cervicovaginal microbiota. We grouped samples into those in which lactobacilli accounted for at least 50% of the species present (community type L) and those in which lactobacilli accounted for less than 50% of the species present (community type O). We assessed the adjusted association between BRCA1 status and ovarian cancer status and cervicovaginal microbiota community type, using a logistic regression model with a bias reduction method.

FINDINGS: Participants were recruited between Jan 2, 2016, and July 21, 2018. The ovarian cancer set (n=360) comprised 176 women with epithelial ovarian cancer, 115 healthy controls and 69 controls with benign gynaecological conditions. The BRCA set (n=220) included 109 women with BRCA1 mutations, 97 healthy controls wild type for BRCA1 and BRCA2 and 14 controls with a benign gynaecological condition wild type for BRCA1 and BRCA2. On the basis of two-dimensional density plots, receiver-operating characteristic curve analysis, and age thresholds used previously, we divided the cohort into those younger than 50 years and those aged 50 years or older. In the ovarian cancer set, women aged 50 years or older had a higher prevalence of community type O microbiota (81 [61%] of 133 ovarian cancer cases and 84 [59%] of 142 healthy controls) than those younger than 50 years (23 [53%] of 43 cases and 12 [29%] of 42 controls). In the ovarian cancer set, women younger than 50 years with ovarian cancer had a significantly higher prevalence of community type O microbiota than did age-matched controls under a logistic regression model with bias correction (odds ratio [OR] 2·80 [95% CI 1·17-6·94]; p=0·020). In the BRCA set, women with BRCA1 mutations younger than 50 years were also more likely to have community type O microbiota than age-matched controls (OR 2·79 [95% CI 1·25-6·68]; p=0·012), after adjustment for pregnancy (ever). This risk was increased further if more than one first-degree family member was affected by any cancer (OR 5·26 [95% CI 1·83-15·30]; p=0·0022). In both sets, we noted that the younger the participants, the stronger the association between community type O microbiota and ovarian cancer or BRCA1 mutation status (eg, OR for community type O for cases aged <40 years in the ovarian cancer set 7·00 [95% CI 1·27-51·44], p=0·025; OR for community type O for BRCA1 mutation carriers aged <35 years in the BRCA set 4·40 [1·14-24·36], p=0·031).

INTERPRETATION: The presence of ovarian cancer, or factors known to affect risk for the disease (ie, age and BRCA1 germline mutations), were significantly associated with having a community type O cervicovaginal microbiota. Whether re-instatement of a community type L microbiome by using, for example, vaginal suppositories containing live lactobacilli, would alter the microbiomial composition higher up in the female genital tract and in the fallopian tubes (the site of origin of high-grade serous ovarian cancer), and whether such changes could translate into a reduced incidence of ovarian cancer, needs to be investigated.

FUNDING: EU Horizon 2020 Research and Innovation Programme, EU Horizon 2020 European Research Council Programme, and The Eve Appeal.},
}

@article {pmid31299215,
year = {2019},
author = {Han, L and Zhang, H and Chen, S and Zhou, L and Li, Y and Zhao, K and Huang, F and Fan, Z and Xuan, L and Zhang, X and Dai, M and Lin, Q and Jiang, Z and Peng, J and Jin, H and Liu, Q},
title = {Intestinal microbiota can predict aGVHD following allogeneic hematopoietic stem 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.2019.07.006},
pmid = {31299215},
issn = {1523-6536},
abstract = {The intestinal microbiome plays an important role in the development of acute graft-versus-host disease (aGVHD). However, it has been rarely reported whether intestinal microbiota could predict the development of aGVHD. Here, we conducted a prospective study of microbiota in 141 patients post-transplantation. We found that the microbiota diversity was lower in the aGVHD group compared with non-aGVHD group at day 0 and day 15±1 (P = 0.018 and 0.009, respectively). Diversity was negatively associated with conditioning intensity (P = 0.017, day 0 and P = 0.045, day 15) and β-lactam antibiotics administration (P = 0.004, day 15). Intensified conditioning and β-lactam antibiotics were associated with a lower ratio of Treg/Th17 cells at day 15 (P = 0.030, 0.047, respectively). At day 15, the levels of the inflammatory factors (TNF-α, IL-6, IL-17A, IL-1β, and LPS) were higher in the intensified conditioning group compared with the standard group (P < 0.05). AIM score was defined as microbiota diversity and gradient of the four bacterials (Lachnospiraceae, Peptostreptococcaceae, Erysipelotrichaceae, and Enterobacteriaceae) at day 15 post-transplantation. AIM score was positively correlated with aGVHD grades (r = 0.481, P < 0.001), and the AIM score could be a predictor for the development of aGVHD (II-IV aGVHD: AUC = 0.75, P < 0.001; III-IV aGVHD: AUC = 0.84, P < 0.001). These findings suggest that intestinal microbiota and conditioning might induce aGVHD by inflammatory factors and the Treg/Th17 balance. The constitution of the intestinal microbiota at neutrophil engraftment may predict the development of aGVHD.},
}

@article {pmid31299175,
year = {2019},
author = {Gommers, LMM and Ederveen, THA and van der Wijst, J and Overmars-Bos, C and Kortman, GAM and Boekhorst, J and Bindels, RJM and de Baaij, JHF and Hoenderop, JGJ},
title = {Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {},
number = {},
pages = {fj201900839R},
doi = {10.1096/fj.201900839R},
pmid = {31299175},
issn = {1530-6860},
abstract = {Proton pump inhibitors (PPIs) are used by millions of patients for the treatment of stomach acid-reflux diseases. Although PPIs are generally considered safe, about 13% of the users develop hypomagnesemia. Despite rising attention for this issue, the underlying mechanism is still unknown. Here, we examine whether the gut microbiome is involved in the development of PPI-induced hypomagnesemia in wild-type C57BL/6J mice. After 4 wk of treatment under normal or low dietary Mg2+ availability, omeprazole significantly reduced serum Mg2+ levels only in mice on a low-Mg2+ diet without affecting the mRNA expression of colonic or renal Mg2+ transporters. Overall, 16S rRNA gene sequencing revealed a lower gut microbial diversity in omeprazole-treated mice. Omeprazole induced a shift in microbial composition, which was associated with a 3- and 2-fold increase in the abundance of Lactobacillus and Bifidobacterium, respectively. To examine the metabolic consequences of these microbial alterations, the colonic composition of organic acids was evaluated. Low dietary Mg2+ intake, independent of omeprazole treatment, resulted in a 10-fold increase in formate levels. Together, these results imply that both omeprazole treatment and low dietary Mg2+ intake disturb the gut internal milieu and may pose a risk for the malabsorption of Mg2+ in the colon.-Gommers, L. M. M., Ederveen, T. H. A., van der Wijst, J., Overmars-Bos, C., Kortman, G. A. M., Boekhorst, J., Bindels, R. J. M., de Baaij, J. H. F., Hoenderop, J. G. J. Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia.},
}

@article {pmid31299066,
year = {2019},
author = {Koedooder, R and Singer, M and Schoenmakers, S and Savelkoul, PHM and Morré, SA and de Jonge, JD and Poort, L and Cuypers, WJSS and Beckers, NGM and Broekmans, FJM and Cohlen, BJ and den Hartog, JE and Fleischer, K and Lambalk, CB and Smeenk, JMJS and Budding, AE and Laven, JSE},
title = {Corrigendum. The vaginal microbiome as a predictor for outcome of in vitro fertilization with or without intracytoplasmic sperm injection: a prospective study.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/dez127},
pmid = {31299066},
issn = {1460-2350},
}

@article {pmid31299021,
year = {2019},
author = {Brar, PC and Kohn, B},
title = {Use of the microbiome in the management of children with type 2 diabetes mellitus.},
journal = {Current opinion in pediatrics},
volume = {31},
number = {4},
pages = {524-530},
doi = {10.1097/MOP.0000000000000781},
pmid = {31299021},
issn = {1531-698X},
abstract = {PURPOSE OF REVIEW: The purpose of this review is to present recent data that defines our current understanding of the role of the gut microbiome in the development of T2DM.

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

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

@article {pmid31298622,
year = {2019},
author = {Windisch, O and Frossard, JL and Schiffer, E and Harbarth, S and Morel, P and Bühler, L},
title = {Microbiologic Changes Induced by Biliary Drainage Require Adapted Antibiotic Prophylaxis during Duodenopancreatectomy.},
journal = {Surgical infections},
volume = {},
number = {},
pages = {},
doi = {10.1089/sur.2019.088},
pmid = {31298622},
issn = {1557-8674},
abstract = {Background: Patients with periampullary tumors frequently undergo endoscopic biliary investigations and biliary drainage (BD) prior to surgery. Recent literature shows a shift of the biliary microbiome toward more resistant bacteria in patients having BD. This study aimed to evaluate the local microbiome and changes induced by BD and related antibiotic exposure and to consider the choice of antibiotic for peri-operative prophylaxis. Methods: A single-center retrospective cohort study included patients operated on for periampullary tumors between January 2013 and November 2017. All patients had intra-operative bile samples taken for culture and peri-operative antibiotic use as well as documentation of complications according to the Dindo-Clavien classification. Results: A total of 37 patients were included. All received pre-operative endoscopy, and 29 (78%) had BD preceded by administration of ceftriaxone or metronidazole. Intra-operative antibiotic prophylaxis consisted of cefuroxime (92%) or ceftriaxone (13%) combined with metronidazole (100%). Bacterial contamination of bile samples was more common in the BD group than in the no biliary drainage (NBD) group (93% vs 38%; p < 0.01). A shift was observed from bile containing mainly Escherichia coli and Streptococcus spp. toward Enterococcus faecalis (0 in the NBD group versus 44.8% in the BD group; p < 0.01), Enterococcus faecium (0 versus 23%; p = 0.3), and Candida albicans (0 versus 34.5%; p = 0.08). Post-operative antibiotic modifications were common. No difference was found regarding Dindo-Clavien complications, post-operative stay, or antibiotic use in the two groups, although one patient in the NBD group who had pre-operative biliary endoscopy with antibiotic prophylaxis developed a fatal septic clot caused by Escherichia coli resistant to cefuroxime. Conclusions: We observed a significant change toward colonization by enterococci and fungi in the microbiome of patients who had pre-operative biliary investigations or drainage with antibiotic prophylaxis. These findings indicate that bile samples should be obtained systematically during surgery for periampullary tumors to guide any post-operative antibiotic therapy and peri-operative antibiotic prophylaxis and might need adaptation to target the modified microbiome.},
}

@article {pmid31298298,
year = {2019},
author = {Wilson, KM and Rodrigues, DR and Briggs, WN and Duff, AF and Chasser, KM and Bielke, LR},
title = {Evaluation of the impact of in ovo administered bacteria on microbiome of chicks through 10 days of age.},
journal = {Poultry science},
volume = {},
number = {},
pages = {},
doi = {10.3382/ps/pez388},
pmid = {31298298},
issn = {1525-3171},
abstract = {Initial inoculation and colonization of the chicken gastrointestinal tract (GIT) by microbiota have been suggested to have a major influence on the growth performance and health of birds. Commercial practices in chicken production may alter or delay microbial colonization by pioneer colonizing bacteria that can have an impact on the development and maturation of the GIT and intestinal microflora. The objective of this study was to compare the impact of apathogenic Gram-negative isolates or lactic acid bacteria (LAB) as pioneer colonizers on the microbiome at the day of hatch (DOH) and evaluate the influence through 10 D of age on ceca. At 18 embryonic days (E), the amnion of embryos was inoculated with either saline (S), approximately 102 CFU of LAB (L), Citrobacter freundii (C), or Citrobacter species (C2). Once DNA was isolated from mucosal and digesta contents, samples underwent 2 × 300 paired-end Illumina MiSeq library preparation for microbiome analysis. An increased abundance of Lactobacillaceae family and Lactobacillus genus was observed in the L group at DOH (P < 0.05), whereas the abundance of Enterococcaceae and Enterococcus was numerically decreased. While Lactobacillus salivarius was one of the pioneer colonizers in the L group at 18E, the population decreased by 10 D (39.59 to 0.09%) and replaced with a population of undefined Lactobacillus (10.36%) and Lactobacillus reuteri (3.63%). Results suggest that L treatment may have accelerated a mature microbiota. Enterobacteriaceae was the dominant family (57.44%) in C group at DOH (P < 0.05). The C2 group only showed some abundance of the C2 species (7.92%) at DOH but had the highest overall abundance of undefined Lactobacillus in the ceca by 10 D (25.28%). Taken together, different isolates provided in ovo can have an impact on the initial microbiome of the GIT, and some of these differences in ceca remain notable at 10 D.},
}

@article {pmid31298267,
year = {2019},
author = {Ferreira, JA and Fuentes, S},
title = {Some comments on certain statistical aspects of the study of the microbiome.},
journal = {Briefings in bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bib/bbz077},
pmid = {31298267},
issn = {1477-4054},
abstract = {This note complements and clarifies part of the work of Hawinkel et al. recently published in the journal and suggests some more or less standard tools and methods for carrying out association studies of the microbiome.},
}

@article {pmid31298176,
year = {2019},
author = {Michels, N},
title = {Biological underpinnings from psychosocial stress towards appetite and obesity during youth: research implications towards metagenomics, epigenomics and metabolomics.},
journal = {Nutrition research reviews},
volume = {},
number = {},
pages = {1-12},
doi = {10.1017/S0954422419000143},
pmid = {31298176},
issn = {1475-2700},
abstract = {Psychosocial stress, uncontrolled eating and obesity are three interrelated epidemiological phenomena already present during youth. This broad narrative conceptual review summarises main biological underpinnings of the stress-diet-obesity pathway and how new techniques can further knowledge. Cortisol seems the main biological factor from stress towards central adiposity; and diet, physical activity and sleep are the main behavioural pathways. Within stress-diet, the concepts of comfort food and emotional eating are highlighted, as cortisol affects reward pathways and appetite brain centres with a role for insulin, leptin, neuropeptide Y (NPY), endocannabinoids, orexin and gastrointestinal hormones. More recently researched biological underpinnings are microbiota, epigenetic modifications and metabolites. First, the gut microbiota reaches the stress-regulating and appetite-regulating brain centres via the gut-brain axis. Second, epigenetic analyses are recommended as diet, obesity, stress and gut microbiota can change gene expression which then affects appetite, energy homeostasis and stress reactivity. Finally, metabolomics would be a good technique to disentangle stress-diet-obesity interactions as multiple biological pathways are involved. Saliva might be an ideal biological matrix as it allows metagenomic (oral microbiota), epigenomic and metabolomic analyses. In conclusion, stress and diet/obesity research should be combined in interdisciplinary collaborations with implementation of several -omics analyses.},
}

@article {pmid31298152,
year = {2019},
author = {Cӑtoi, AF and Vodnar, DC and Corina, A and Nikolic, D and Citarrella, R and Pérez-Martínez, P and Rizzo, M},
title = {Gut Microbiota, Obesity and Bariatric Surgery: Current Knowledge and Future Perspectives.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/1381612825666190708190437},
pmid = {31298152},
issn = {1873-4286},
abstract = {BACKGROUND: There is an urgent need for a better understanding and management of obesity and obesity-associated diseases. It is known that obesity is associated with structural and functional changes in the microbiome.

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

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

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

@article {pmid31298050,
year = {2019},
author = {Choi, Y and Lee, S and Kim, S and Lee, J and Ha, J and Oh, H and Lee, Y and Kim, Y and Yoon, Y},
title = {Vitamin E (α-tocopherol) consumption influences gut microbiota composition.},
journal = {International journal of food sciences and nutrition},
volume = {},
number = {},
pages = {1-5},
doi = {10.1080/09637486.2019.1639637},
pmid = {31298050},
issn = {1465-3478},
abstract = {This study evaluated if vitamin E consumption affects gut microbiota. Mice were grouped into control, low vitamin E (LV), and high vitamin E (HV). LV and HV were fed DL-α-tocopherol at 0.06 mg/20 g and 0.18 mg/20 g of body weight per day, respectively, for 34 days. Body weight of mice was measured before and after vitamin E treatment. Animals were sacrificed, liver, spleen, small intestine and large intestine collected, and weight and length were measured. Composition of gut microbiota was determined by microbiome analysis. Spleen weight index of LV was the highest. However, liver weight indices and intestinal lengths were not different. Body weights of LV group were higher than those of control. Ratio of Firmicutes to Bacteroidetes was different in LV compared to control and HV. These results indicate that low-level consumption of vitamin E increases spleen and body weight, and changes gut microbiota.},
}

@article {pmid31297792,
year = {2019},
author = {Zhang, Y and Zhang, Y and Kuang, Z and Xu, J and Li, C and Li, Y and Jiang, Y and Xie, J},
title = {Comparison of microbiomes and resistomes in two Karst groundwater sites in Chongqing, China.},
journal = {Ground water},
volume = {},
number = {},
pages = {},
doi = {10.1111/gwat.12924},
pmid = {31297792},
issn = {1745-6584},
abstract = {Karst groundwater is an important water resource as it accounts for about 15% of the total landscape of the earth and supplies 20% of potable water worldwide. The antibiotics resistance is an emerging global concern, and antibiotics residual and increase of antibiotic resistance genes represent serious global concerns and emerging pollutants. There is no report on the antibiotic resistance genes in groundwater. To survey resistome and microbiome in Karst groundwater, two Karst water samples were chosen for metagenome and metatranscriptome study, namely the 37th spring (C) and Dongcao spring (R) in Beibei, Chongqing, China. The two sites differ significantly in sulfur content, geochemical parameters, community structure, antibiotic resistance genes and mechanisms, and these results may be influenced by anthropogenic activities. Combining with the Antibiotic Resistance Genes Database (ARDB), three types of resistance genes baca, sul2, sul1 are present in R and C, and ant3ia, ermc, tetpa are also present in R. The number of all resistance genes in R was more than C, and Proteobacteria, Bacteroidetes, Nitrospirae are the main sources of antibiotic resistance genes. In addition, a large number of genes related to antibiotic gene transmission and drug resistance were found in both samples. Karst groundwater is an important source of drinking water and a possible venue for the transmission of microbial antibiotic resistance genes. However, few studies addressed this issue in Karst groundwater, despite its widespread and great importance to global ecosystem. Karst groundwater is a reservoir for antibiotic resistant genes, and measures to control these resistant genes are urgently needed. This article is protected by copyright. All rights reserved.},
}

@article {pmid31297343,
year = {2019},
author = {Mascitti, M and Togni, L and Troiano, G and Caponio, VCA and Gissi, DB and Montebugnoli, L and Procaccini, M and Lo Muzio, L and Santarelli, A},
title = {Beyond Head and Neck Cancer: The Relationship Between Oral Microbiota and Tumour Development in Distant Organs.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {232},
doi = {10.3389/fcimb.2019.00232},
pmid = {31297343},
issn = {2235-2988},
abstract = {An altered oral microbiota has been linked with the development of several oral diseases, such as dental caries, periodontal disease, and oral stomatitis. Moreover, poor oral health has been linked to head and neck cancer, particularly oral cancer. In recent years a growing number of studies indicate that oral microbiota could be involved in the development of primary tumours outside of head and neck region. The aim of this article is to review the recent studies based on high-throughput technology to present evidences of a relationship between oral microbiota and "non-head and neck tumours." Oral dysbiosis seem to be more pronounced in patients with tumours of gastrointestinal tract, in particular oesophageal, gastric, pancreatic, and colorectal cancers, paving the way for developing specific oral microbiota test to allow early cancer detection. Regarding other tumour types, the results are promising but highly preliminary and still debated. Currently, there are several factors that limit the generalization of the results, such as the small sample size, the lack of adequate clinical information about patients, the different sequencing techniques used, and biological sample heterogeneity. Although only at the beginning, the analysis of oral microbiota could be the next step in the evolution of cancer therapy and will help clinicians to develop individualised approaches to cancer prevention and treatment.},
}

@article {pmid31297154,
year = {2019},
author = {Li, H and Mei, X and Liu, B and Xie, G and Ren, N and Xing, D},
title = {Quantitative proteomic analysis reveals the ethanologenic metabolism regulation of Ethanoligenens harbinense by exogenous ethanol addition.},
journal = {Biotechnology for biofuels},
volume = {12},
number = {},
pages = {166},
doi = {10.1186/s13068-019-1511-y},
pmid = {31297154},
issn = {1754-6834},
abstract = {Background: H2-ethanol-coproducing bacteria, as primary fermenters, play important roles in the microbiome of bioreactors for bioenergy production from organic wastewater or solid wastes. Ethanoligenens harbinense YUAN-3 is an anaerobic ethanol-H2-fermenting bacterium. Ethanol is one of the main end-products of strain YUAN-3 that influence its fermentative process. Until recently, the molecular mechanism of metabolic regulation in strain YUAN-3 during ethanol accumulation has still been unclear. This study aims to elucidate the metabolic regulation mechanisms in strain YUAN-3, which contributes to effectively shape the microbiome for biofuel and bioenergy production from waste stream.

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

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

@article {pmid31297102,
year = {2019},
author = {Zhang, Z and Yang, J and Feng, Q and Chen, B and Li, M and Liang, C and Li, M and Li, Z and Xu, Q and Zhang, L and Chen, W},
title = {Compositional and Functional Analysis of the Microbiome in Tissue and Saliva of Oral Squamous Cell Carcinoma.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1439},
doi = {10.3389/fmicb.2019.01439},
pmid = {31297102},
issn = {1664-302X},
abstract = {Oral squamous cell carcinoma (OSCC) is affected by the interaction between oral pathogen and holobionts, or the combination of the host and its microbial communities. Studies have indicated the structure and feature of the microbiome in OSCC tissue and saliva, the relationships between microbiota and OSCC sites, stages remain unclear. In the present study, OSCC tissue (T), saliva (S) and mouthwash (W) samples were collected from the same subjects and carried out the microbiome study by 16S sequencing. The results showed the T group was significantly different from the S and W groups with the character of lower richness and diversity. Proteobacteria were most enriched in the T group at the phylum level, while Firmicutes were predominant in groups S and W. At the genus level, the predominant taxa of group T were Acinetobacter and Fusobacterium, and for group S and W, the predominant taxa were Streptococcus and Prevotella. The genera related to late stage tumors were Acinetobacter and Fusobacterium, suggesting microbiota may be implicated in OSCC developing. Both compositional and functional analyses indicated that microbes in tumor tissue were potential indicator for the initiation and development of OSCC.},
}

@article {pmid31297054,
year = {2019},
author = {Osorio, C and Kanukuntla, T and Diaz, E and Jafri, N and Cummings, M and Sfera, A},
title = {The Post-amyloid Era in Alzheimer's Disease: Trust Your Gut Feeling.},
journal = {Frontiers in aging neuroscience},
volume = {11},
number = {},
pages = {143},
doi = {10.3389/fnagi.2019.00143},
pmid = {31297054},
issn = {1663-4365},
abstract = {The amyloid hypothesis, the assumption that beta-amyloid toxicity is the primary cause of neuronal and synaptic loss, has been the mainstream research concept in Alzheimer's disease for the past two decades. Currently, this model is quietly being replaced by a more holistic, "systemic disease" paradigm which, like the aging process, affects multiple body tissues and organs, including the gut microbiota. It is well-established that inflammation is a hallmark of cellular senescence; however, the infection-senescence link has been less explored. Microbiota-induced senescence is a gradually emerging concept promoted by the discovery of pathogens and their products in Alzheimer's disease brains associated with senescent neurons, glia, and endothelial cells. Infectious agents have previously been associated with Alzheimer's disease, but the cause vs. effect issue could not be resolved. A recent study may have settled this debate as it shows that gingipain, a Porphyromonas gingivalis toxin, can be detected not only in Alzheimer's disease but also in the brains of older individuals deceased prior to developing the illness. In this review, we take the position that gut and other microbes from the body periphery reach the brain by triggering intestinal and blood-brain barrier senescence and disruption. We also surmise that novel Alzheimer's disease findings, including neuronal somatic mosaicism, iron dyshomeostasis, aggressive glial phenotypes, and loss of aerobic glycolysis, can be explained by the infection-senescence model. In addition, we discuss potential cellular senescence targets and therapeutic strategies, including iron chelators, inflammasome inhibitors, senolytic antibiotics, mitophagy inducers, and epigenetic metabolic reprograming.},
}

@article {pmid31296969,
year = {2019},
author = {Sanders, ME and Merenstein, DJ and Reid, G and Gibson, GR and Rastall, RA},
title = {Probiotics and prebiotics in intestinal health and disease: from biology to the clinic.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41575-019-0173-3},
pmid = {31296969},
issn = {1759-5053},
abstract = {Probiotics and prebiotics are microbiota-management tools for improving host health. They target gastrointestinal effects via the gut, although direct application to other sites such as the oral cavity, vaginal tract and skin is being explored. Here, we describe gut-derived effects in humans. In the past decade, research on the gut microbiome has rapidly accumulated and has been accompanied by increased interest in probiotics and prebiotics as a means to modulate the gut microbiota. Given the importance of these approaches for public health, it is timely to reiterate factual and supporting information on their clinical application and use. In this Review, we discuss scientific evidence on probiotics and prebiotics, including mechanistic insights into health effects. Strains of Lactobacillus, Bifidobacterium and Saccharomyces have a long history of safe and effective use as probiotics, but Roseburia spp., Akkermansia spp., Propionibacterium spp. and Faecalibacterium spp. show promise for the future. For prebiotics, glucans and fructans are well proven, and evidence is building on the prebiotic effects of other substances (for example, oligomers of mannose, glucose, xylose, pectin, starches, human milk and polyphenols).},
}

@article {pmid31296695,
year = {2019},
author = {Zimmermann, P and Curtis, N},
title = {Effect of intrapartum antibiotics on the intestinal microbiota of infants: a systematic review.},
journal = {Archives of disease in childhood. Fetal and neonatal edition},
volume = {},
number = {},
pages = {},
doi = {10.1136/archdischild-2018-316659},
pmid = {31296695},
issn = {1468-2052},
abstract = {INTRODUCTION: The use of intrapartum antibiotic prophylaxis (IAP) has become common practice in obstetric medicine and is used in up to 40% of deliveries. Despite its benefits, the risks associated with exposing large numbers of infants to antibiotics, especially long-term effects on health through changes in the microbiota, remain unclear. This systematic review summarises studies that have investigated the effect of IAP on the intestinal microbiota of infants.

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

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

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

@article {pmid31296531,
year = {2019},
author = {Tang, W and Putluri, V and Ambati, CR and Dorsey, TH and Putluri, N and Ambs, S},
title = {Liver- and Microbiome-derived Bile Acids Accumulate in Human Breast Tumors and Inhibit Growth and Improve Patient Survival.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-19-0094},
pmid = {31296531},
issn = {1078-0432},
abstract = {PURPOSE: Metabolomics is a discovery tool for novel associations of metabolites with disease. Here, we interrogated the metabolome of human breast tumors to describe metabolites whose accumulation affects tumor biology.

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

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

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

@article {pmid31296445,
year = {2019},
author = {Shen, N and Caixàs, A and Ahlers, M and Patel, K and Gao, Z and Dutia, R and Blaser, MJ and Clemente, JC and Laferrère, B},
title = {Longitudinal changes of microbiome composition and microbial metabolomics after surgical weight loss in individuals with obesity.},
journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.soard.2019.05.038},
pmid = {31296445},
issn = {1878-7533},
abstract = {BACKGROUND: Some of the metabolic effects of bariatric surgery may be mediated by the gut microbiome.

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

SETTINGS: University hospitals in the United States and Spain.

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

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

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

@article {pmid31294219,
year = {2018},
author = {Glassner, K and Quigley, EM and Franco, L and Victor, DW},
title = {Autoimmune liver disease and the enteric microbiome.},
journal = {AIMS microbiology},
volume = {4},
number = {2},
pages = {334-346},
doi = {10.3934/microbiol.2018.2.334},
pmid = {31294219},
issn = {2471-1888},
abstract = {The human enteric microbiome is highly complex and has more than 150 times more genes within it than its host. The host and the microbiome have a commensurate relationship that can evolve over time. The typically symbiotic relationship between the two can become pathogenic. The microbiome composition in adults reflects their history of exposure to bacteria and environmental factors during early life, their genetic background, age, interactions with the immune system, geographical location, and, most especially, their diet. Similarly, these factors are thought to contribute to the development of autoimmune disease. It is possible that alterations in the intestinal microbiome could lead to liver disease. There is emerging data for the contribution of the microbiome in development of primary sclerosing cholangitis, primary biliary cholangitis, and autoimmune hepatitis; liver disorders associated with aberrant immune function in genetically susceptible individuals.},
}

@article {pmid31294213,
year = {2018},
author = {Barros, I and Froufe, H and Marnellos, G and Egas, C and Delaney, J and Clamp, M and Santos, RS and Bettencourt, R},
title = {Metatranscriptomics profile of the gill microbial community during Bathymodiolus azoricus aquarium acclimatization at atmospheric pressure.},
journal = {AIMS microbiology},
volume = {4},
number = {2},
pages = {240-260},
doi = {10.3934/microbiol.2018.2.240},
pmid = {31294213},
issn = {2471-1888},
abstract = {Background: The deep-sea mussels Bathymodiolus azoricus (Bivalvia: Mytilidae) are the dominant macrofauna subsisting at the hydrothermal vents site Menez Gwen in the Mid-Atlantic Ridge (MAR). Their adaptive success in such challenging environments is largely due to their gill symbiotic association with chemosynthetic bacteria. We examined the response of vent mussels as they adapt to sea-level environmental conditions, through an assessment of the relative abundance of host-symbiont related RNA transcripts to better understand how the gill microbiome may drive host-symbiont interactions in vent mussels during hypothetical venting inactivity.

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

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

@article {pmid31294203,
year = {2018},
author = {Sharma, N and Bhatia, S and Sodhi, AS and Batra, N},
title = {Oral microbiome and health.},
journal = {AIMS microbiology},
volume = {4},
number = {1},
pages = {42-66},
doi = {10.3934/microbiol.2018.1.42},
pmid = {31294203},
issn = {2471-1888},
abstract = {The oral microbiome is diverse in its composition due to continuous contact of oral cavity with the external environment. Temperatures, diet, pH, feeding habits are important factors that contribute in the establishment of oral microbiome. Both culture dependent and culture independent approaches have been employed in the analysis of oral microbiome. Gene-based methods like PCR amplification techniques, random amplicon cloning, PCR-RELP, T-RELP, DGGE and DNA microarray analysis have been applied to increase oral microbiome related knowledge. Studies revealed that microbes from the phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria, Neisseria, TM7 predominately inhabits the oral cavity. Culture-independent molecular techniques revealed the presence of genera Megasphaera, Parvimonas and Desulfobulbus in periodontal disease. Bacteria, fungi and protozoa colonize themselves on various surfaces in oral cavity. Microbial biofilms are formed on the buccal mucosa, dorsum of the tongue, tooth surfaces and gingival sulcus. Various studies demonstrate relationship between unbalanced microflora and development of diseases like tooth caries, periodontal diseases, type 2 diabetes, circulatory system related diseases etc. Transcriptome-based remodelling of microbial metabolism in health and disease associated states has been well reported. Human diets and habitat can trigger virus activation and influence phage members of oral microbiome. As it is said, "Mouth, is the gateway to the total body wellness, thus oral microbiome influences overall health of an individual".},
}

@article {pmid31294181,
year = {2017},
author = {Abedon, ST},
title = {Active bacteriophage biocontrol and therapy on sub-millimeter scales towards removal of unwanted bacteria from foods and microbiomes.},
journal = {AIMS microbiology},
volume = {3},
number = {3},
pages = {649-688},
doi = {10.3934/microbiol.2017.3.649},
pmid = {31294181},
issn = {2471-1888},
abstract = {Bacteriophages can be used as antibacterial agents as a form of biological control, e.g., such as phage therapy. With active treatment, phages must "actively" produce new virions, in situ, to attain "inundative" densities, i.e., sufficient titers to eradicate bacteria over reasonable timeframes. Passive treatment, by contrast, can be accomplished using phages that are bactericidal but incapable of generating new phage virions in situ during their interaction with target bacteria. These ideas of active versus passive treatment come from theoretical considerations of phage therapy pharmacology, particularly as developed in terms of phage application to well-mixed cultures consisting of physically unassociated bacteria. Here I extend these concepts to bacteria which instead are physically associated. These are bacteria as found making up cellular arrangements or bacterial microcolonies-collectively, clonal bacterial "clumps". I consider circumstances where active phage replication would be required to effect desired levels of bacterial clearance, but populations of bacteria nevertheless are insufficiently prevalent to support phage replication to bacteria-inundative densities across environments. Clumped bacteria, however, may still support active treatment at more local, i.e., sub-millimeter, within-clump spatial scales, and potential consequences of this are explored mathematically. Application is to the post-harvest biocontrol of foodborne pathogens, and potentially also to precise microbiome editing. Adequate infection performance by phages in terms of timely burst sizes, that is, other than just adsorption rates and bactericidal activity, thus could be important for treatment effectiveness even if bacterial densities overall are insufficient to support active treatment across environments. Poor phage replication during treatment of even low bacterial numbers, such as given food refrigeration during treatment, consequently could be problematic to biocontrol success. In practical terms, this means that the characterization of phages for such purposes should include their potential to generate new virions under realistic in situ conditions across a diversity of potential bacterial targets.},
}

@article {pmid31294154,
year = {2017},
author = {Tang, J},
title = {Microbiome in the urinary system-a review.},
journal = {AIMS microbiology},
volume = {3},
number = {2},
pages = {143-154},
doi = {10.3934/microbiol.2017.2.143},
pmid = {31294154},
issn = {2471-1888},
abstract = {Urine was considered sterile in healthy individuals for many years, and the presence of bacteria signified urinary tract infection. With the development of Expanded Quantitative Urine Culture (EQUC) and utilization of molecular techniques, the previous clinical dogma is no longer valid. Instead, healthy people harbor a considerable microbial community, or microbiota, in their urinary systems. Similar to other physiological niches where microbiota contribute to the health status of their hosts, recent studies demonstrated different microbial populations also play a crucial role in urinary health of individuals. Understanding urinary microbiome thus allows a more holistic approach in the diagnosis, treatment, and prevention of diseases and disorders in urinary system. This review article provides an overview of current findings in urinary microbiome and discusses some of the gaps for future research.},
}

@article {pmid31295426,
year = {2019},
author = {Theuretzbacher, U and Piddock, LJV},
title = {Non-traditional Antibacterial Therapeutic Options and Challenges.},
journal = {Cell host & microbe},
volume = {26},
number = {1},
pages = {61-72},
doi = {10.1016/j.chom.2019.06.004},
pmid = {31295426},
issn = {1934-6069},
abstract = {The global challenges presented by drug-resistant bacterial infections have stimulated much activity in finding new treatments. This review summarizes the progress and setbacks of non-traditional approaches intent on circumventing bacterial drug resistance. These approaches include targeting virulence via toxin production and virulence factor secretion, impeding bacterial adhesion to host cells and biofilm formation, interrupting or inhibiting bacterial communication, and downregulating virulence. Other strategies include immune evasion, microbiome-modifying therapies, and the employment of phages as treatments or carriers. Finally, the prospects of nanoparticles, immunotherapy, antisense RNA, and drug-resistance-modulation approaches are discussed. The development of non-traditional treatments suffers similar challenges faced by developers of conventional antibiotics; however, most of these new strategies have additional and considerable hurdles before it can be shown that they are safe and efficacious for patient use. For the foreseeable future, it is likely that most of these treatments, if approved, will be used in combination with antibiotics.},
}

@article {pmid31295421,
year = {2019},
author = {Lam, KN and Alexander, M and Turnbaugh, PJ},
title = {Precision Medicine Goes Microscopic: Engineering the Microbiome to Improve Drug Outcomes.},
journal = {Cell host & microbe},
volume = {26},
number = {1},
pages = {22-34},
doi = {10.1016/j.chom.2019.06.011},
pmid = {31295421},
issn = {1934-6069},
abstract = {Despite the recognition, nearly a century ago, that the human microbiome plays a clinically relevant role in drug disposition, mechanistic insights, and translational applications are still limited. Here, we highlight the recent re-emergence of "pharmacomicrobiomics," which seeks to understand how inter-individual variations in the microbiome shape drug efficacy and side effect profiles. Multiple bacterial species, genes, and enzymes have already been implicated in the direct biotransformation of drugs, both from targeted case studies and from systematic computational and experimental analyses. Indirect mechanisms are also at play; for example, microbial interactions with the host immune system can have broad effects on immunomodulatory drugs. Finally, we discuss multiple emerging strategies for the precise manipulation of complex microbial communities to improve treatment outcomes. In the coming years, we anticipate a shift toward a more comprehensive view of precision medicine that encompasses our human and microbial genomes and their combined metabolic activities.},
}

@article {pmid31294712,
year = {2019},
author = {Orellana, E and Davies-Sala, C and Guerrero, LD and Vardé, I and Altina, M and Lorenzo, MC and Figuerola, EL and Pontiggia, RM and Erijman, L},
title = {Microbiome network analysis of co-occurrence patterns in anaerobic co-digestion of sewage sludge and food waste.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {79},
number = {10},
pages = {1956-1965},
doi = {10.2166/wst.2019.194},
pmid = {31294712},
issn = {0273-1223},
abstract = {Addition of food waste (FW) as a co-substrate in anaerobic digesters of wastewater treatment plants is a desirable strategy towards achievement of the potential of wastewater treatment plants to become energy-neutral, diverting at the same time organic waste from landfills. Because substrate type is a driver of variations in phylogenetic structure of digester microbiomes, it is critical to understand how microbial communities respond to changes in substrate composition and concentration. In this work, high throughput sequencing was used to monitor the dynamics of microbiome changes in four parallel laboratory-scale anaerobic digesters treating sewage sludge during acclimation to an increasing amount of food waste. A co-occurrence network was constructed using data from 49 metagenomes sampled over the 161 days of the digesters' operation. More than half of the nodes in the network were clustered in two major modules, i.e. groups of highly interconnected taxa that had much fewer connections with taxa outside the group. The dynamics of co-occurrence networks evidenced shifts that occurred within microbial communities due to the addition of food waste in the co-digestion process. A diverse and reproducible group of hydrolytic and fermentative bacteria, syntrophic bacteria and methanogenic archaea appeared to grow in a concerted fashion to allow stable performance of anaerobic co-digestion at high FW.},
}

@article {pmid31294385,
year = {2019},
author = {Carroll, MW and Kuenzig, ME and Mack, DR and Otley, AR and Griffiths, AM and Kaplan, GG and Bernstein, CN and Bitton, A and Murthy, SK and Nguyen, GC and Lee, K and Cooke-Lauder, J and Benchimol, EI},
title = {The Impact of Inflammatory Bowel Disease in Canada 2018: Children and Adolescents with IBD.},
journal = {Journal of the Canadian Association of Gastroenterology},
volume = {2},
number = {Suppl 1},
pages = {S49-S67},
doi = {10.1093/jcag/gwy056},
pmid = {31294385},
issn = {2515-2092},
abstract = {Canada has among the highest rates of childhood-onset IBD in the world. Over 7000 children and youth under 18 years old are living with IBD in Canada, and 600 to 650 children under 16 years old are diagnosed annually. While the peak age of onset of IBD is highest in the second and third decades of life, over the past two decades incidence has risen most rapidly in children under 5 years old. The treatment of children with IBD presents important challenges including therapeutic choices, risk of adverse events to medications, psychosocial impact on the child and family, increased cost of health care and the implications of the transition from pediatric to adult care. Despite the unique circumstances faced by children and their families, there is a lack of research to help understand the causes of the rising incidence and the best therapies for children with IBD. Scientific evidence-and specifically clinical trials of pharmaceuticals-are too often extrapolated from adult research. Health care providers must strive to understand the unique impact of childhood-onset IBD on patients and families, while researchers must expand work to address the important needs of this growing patient population.

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

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

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

@article {pmid31294381,
year = {2019},
author = {Kaplan, GG and Bernstein, CN and Coward, S and Bitton, A and Murthy, SK and Nguyen, GC and Lee, K and Cooke-Lauder, J and Benchimol, EI},
title = {The Impact of Inflammatory Bowel Disease in Canada 2018: Epidemiology.},
journal = {Journal of the Canadian Association of Gastroenterology},
volume = {2},
number = {Suppl 1},
pages = {S6-S16},
doi = {10.1093/jcag/gwy054},
pmid = {31294381},
issn = {2515-2092},
abstract = {Canada has among the highest incidence and prevalence of inflammatory bowel disease (IBD) in the world. After decades of rising incidence of IBD in Canada during the 20th Century, the prevalence of IBD in 2018 is 0.7% of the Canadian population. Forecasting models predict that prevalence of IBD will continue to rise to 1.0% of the population by 2030. In 2018, the number of Canadians living with IBD is approximately 270,000 and is predicted to rise to 403,000 Canadians in 2030. Inflammatory bowel disease affects all age groups with adolescents and young adults at highest risk of diagnosis. Canadians of all ethnicities are being diagnosed with IBD including known high-risk groups such as Ashkenazi Jews and offspring of South Asian immigrants who were previously thought to be low risk. Moreover, IBD has evolved into a global disease with rising incidence in newly industrialized countries in Asia and South America. The causes of IBD remain unsolved; however, the high rates of disease in Western countries and its emergence in newly industrialized countries suggest that environmental factors associated with urbanization, modernization, or Western diets may be pertinent to understanding the pathogenesis of the disease.

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

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

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

@article {pmid31294238,
year = {2018},
author = {Ritschard, JS and Amato, L and Kumar, Y and Müller, B and Meile, L and Schuppler, M},
title = {The role of the surface smear microbiome in the development of defective smear on surface-ripened red-smear cheese.},
journal = {AIMS microbiology},
volume = {4},
number = {4},
pages = {622-641},
doi = {10.3934/microbiol.2018.4.622},
pmid = {31294238},
issn = {2471-1888},
abstract = {The complex smear microbiota colonizing the surface of red-smear cheese fundamentally impacts the ripening process, appearance and shelf life of cheese. To decipher the prokaryotic composition of the cheese smear microbiome, the surface of a semi-hard surface ripened cheese was studied post-ripening by culture-based and culture-independent molecular approaches. The aim was to detect potential bacterial alterations in the composition of the cheese smear microbiota resulting from cheese storage in vacuum film-prepackaging, which is often accompanied by the development of a surface smear defect. Next-generation sequencing of amplified 16S rRNA gene fragments revealed an unexpected high diversity of a total of 132 different genera from the domains Bacteria and Archaea on the cheese surface. Beside typical smear organisms, our study revealed the presence of several microorganisms so far not associated with cheese, but related to milk, farm and cheese dairy environments. A 16S ribosomal RNA based analysis from total RNA identified the major metabolically active populations in the cheese surface smear as Actinobacteria of the genera Corynebacterium, Brevibacterium, Brachybacterium and Agrococcus. Comparison of data on a higher phylogenetic level revealed distinct differences in the composition of the cheese smear microbiome from the different samples. While the proportions of Proteobacteria and Bacteroidetes were increased in the smear of prepacked samples and in particular in defective smear, staphylococci showed an opposite trend and turned out to be strongly decreased in defective smear. In conclusion, next-generation sequencing of amplified 16S rRNA genes and 16S rRNA from total RNA extracts provided a much deeper insight into the bacterial composition of the cheese smear microbiota. The observed shifts in the microbial composition of samples from defect surface smear suggest that certain members of the Proteobacteria contribute to the observed negative organoleptic properties of the surface smear of cheese after prepacking in plastic foil.},
}

@article {pmid31294224,
year = {2018},
author = {Galbraith, H and Iwanowicz, D and Spooner, D and Iwanowicz, L and Keller, D and Zelanko, P and Adams, C},
title = {Exposure to synthetic hydraulic fracturing waste influences the mucosal bacterial community structure of the brook trout (Salvelinus fontinalis) epidermis.},
journal = {AIMS microbiology},
volume = {4},
number = {3},
pages = {413-427},
doi = {10.3934/microbiol.2018.3.413},
pmid = {31294224},
issn = {2471-1888},
abstract = {Production of natural gas using unconventional technologies has risen as demand for alternative fuels has increased. Impacts on the environment from waste generated from these processes are largely unexplored. In particular, the outcomes of organismal exposure to hydraulic fracturing waste have not been rigorously evaluated. We evaluated the effects of exposure to surrogate hydraulic fracturing waste (HF waste) on mucosal bacterial community structure of the brook trout (Salvelinus fontinalis) epidermis. Brook trout are fish native to streams at risk to HF waste exposure. Here, fish were exposed to four treatments (control, 0.00%; low, 0.01%; medium, 0.10%; and high, 1.0% concentrations) of surrogate HF waste synthesized to mimic concentrations documented in the field. Epidermal mucus samples were collected and assessed 15 days post-exposure to determine if the associated bacterial community varied among treatments. We observed differences in epidermal mucosal bacterial community composition at multiple taxonomic scales among treatments. These community changes reflected compositional differences in taxa dominance and community similarity rather than losses or gains in taxonomic richness. The dominant bacterial genus that explained the greatest variation in community structure between exposed and unexposed fish was Flavobacterium. Two genera associated with salmonid diseases, Flavobacterium and Pseudomonas, were statistically more abundant in high treatments than controls. These results suggest that exposure to low levels of HF waste influences bacterial colonization and may lead to a disruption that favors bacterial populations associated with fish disease.},
}

@article {pmid31293983,
year = {2019},
author = {Afrin, T and Murase, K and Kounosu, A and Hunt, VL and Bligh, M and Maeda, Y and Hino, A and Maruyama, H and Tsai, IJ and Kikuchi, T},
title = {Sequential Changes in the Host Gut Microbiota During Infection With the Intestinal Parasitic Nematode Strongyloides venezuelensis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {217},
doi = {10.3389/fcimb.2019.00217},
pmid = {31293983},
issn = {2235-2988},
abstract = {Soil-transmitted helminths (STHs) are medically important parasites that infect 1. 5 billion humans globally, causing a substantial disease burden. These parasites infect the gastrointestinal tract (GIT) of their host where they co-exist and interact with the host gut bacterial flora, leading to the coevolution of the parasites, microbiota, and host organisms. However, little is known about how these interactions change through time with the progression of infection. Strongyloidiasis is a human parasitic disease caused by the nematode Strongyloides stercoralis infecting 30-100 million people. In this study, we used a closely related rodent parasite Strongyloides venezuelensis and mice as a model of gastrointestinal parasite infection. We conducted a time-course experiment to examine changes in the fecal microbiota from the start of infection to parasite clearance. We found that bacterial taxa in the host intestinal microbiota changed significantly as the infection progressed, with an increase in the genera Bacteroides and Candidatus Arthromitus, and a decrease in Prevotella and Rikenellaceae. However, the microbiota recovered to the pre-infective state after parasite clearance from the host, suggesting that these perturbations are reversible. Microarray analysis revealed that this microbiota transition is likely to correspond with the host immune response. These findings give us an insight into the dynamics of parasite-microbiota interactions in the host gut during parasite infection.},
}

@article {pmid31293720,
year = {2019},
author = {Fasullo, M and Rau, P and Liu, DQ and Holzwanger, E and Mathew, JP and Guilarte-Walker, Y and Szabo, G},
title = {Proton pump inhibitors increase the severity of hepatic encephalopathy in cirrhotic patients.},
journal = {World journal of hepatology},
volume = {11},
number = {6},
pages = {522-530},
doi = {10.4254/wjh.v11.i6.522},
pmid = {31293720},
issn = {1948-5182},
abstract = {BACKGROUND: Liver cirrhosis is the late stage of hepatic fibrosis and is characterized by portal hypertension that can clinically lead to decompensation in the form of ascites, esophageal/gastric varices or encephalopathy. The most common sequelae associated with liver cirrhosis are neurologic and neuropsychiatric impairments labeled as hepatic encephalopathy (HE). Well established triggers for HE include infection, gastrointestinal bleeding, constipation, and medications. Alterations to the gut microbiome is one of the leading ammonia producers in the body, and therefore may make patients more susceptible to HE.

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

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

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

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

@article {pmid31293616,
year = {2019},
author = {Zhou, YH and Gallins, P},
title = {A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {579},
doi = {10.3389/fgene.2019.00579},
pmid = {31293616},
issn = {1664-8021},
abstract = {With the growing importance of microbiome research, there is increasing evidence that host variation in microbial communities is associated with overall host health. Advancement in genetic sequencing methods for microbiomes has coincided with improvements in machine learning, with important implications for disease risk prediction in humans. One aspect specific to microbiome prediction is the use of taxonomy-informed feature selection. In this review for non-experts, we explore the most commonly used machine learning methods, and evaluate their prediction accuracy as applied to microbiome host trait prediction. Methods are described at an introductory level, and R/Python code for the analyses is provided.},
}

@article {pmid31293535,
year = {2019},
author = {Ruiz, L and García-Carral, C and Rodriguez, JM},
title = {Unfolding the Human Milk Microbiome Landscape in the Omics Era.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1378},
doi = {10.3389/fmicb.2019.01378},
pmid = {31293535},
issn = {1664-302X},
abstract = {Studies conducted in the last years have demonstrated that human milk represents a continuous supply of beneficial bacteria to the infant gut, which contribute to the maturation of the digestive and immune functions in the developing infant. Nevertheless, the origin of bacterial populations in milk is not fully understood yet and they have been proposed to originate from maternal skin, infant's mouth, and (or) endogenously, from the maternal digestive tract through a mechanism involving immune cells. Understanding the composition, functions and assembly of the human milk microbiota has important implications not only for the infant gut microbiota establishment, but also for the mammary health since dysbiosis in the milk bacteria may lead to mastitis. Besides, host, microbial, medical and environmental factors may affect the composition of the human milk microbiome, with implications for the mother-infant health. Application of both culture-dependent and -independent techniques to assess the milk microbiome faces some practical limitations but, together, have allowed providing novel and complementary views on its origin, composition and functioning as summarized in this minireview. In the next future, the application of the ultimate advances in next-generation sequencing and omics approaches, including culturomics, will allow a detailed and comprehensive understanding of the composition and functions of these microbial communities, including their interactions with other milk components, expanding the opportunities to design novel microbiome-based modulation strategies for this ecosystem.},
}

@article {pmid31293524,
year = {2019},
author = {Lopes, DRG and La Reau, AJ and Duarte, MS and Detmann, E and Bento, CBP and Mercadante, MEZ and Bonilha, SFM and Suen, G and Mantovani, HC},
title = {The Bacterial and Fungal Microbiota of Nelore Steers Is Dynamic Across the Gastrointestinal Tract and Its Fecal-Associated Microbiota Is Correlated to Feed Efficiency.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1263},
doi = {10.3389/fmicb.2019.01263},
pmid = {31293524},
issn = {1664-302X},
abstract = {The ruminant gastrointestinal tract (GIT) microbiome plays a major role in the health, physiology and production traits of the host. In this work, we characterized the bacterial and fungal microbiota of the rumen, small intestine (SI), cecum and feces of 27 Nelore steers using next-generation sequencing and evaluated biochemical parameters within the GIT segments. We found that only the bacterial microbiota clustered according to each GIT segment. Bacterial diversity and richness as well as volatile fatty acid concentration was lowest in the SI. Taxonomic grouping of bacterial operational taxonomic units (OTUs) revealed that Lachnospiraceae (24.61 ± SD 6.58%) and Ruminococcaceae (20.87 ± SD 4.22%) were the two most abundant taxa across the GIT. For the fungi, the family Neocallismastigaceae dominated in all GIT segments, with the genus Orpinomyces being the most abundant. Twenty-eight bacterial and six fungal OTUs were shared across all GIT segments in at least 50% of the steers. We also evaluated if the fecal-associated microbiota of steers showing negative and positive residual feed intake (n-RFI and p-RFI, respectively) was associated with their feed efficiency phenotype. Diversity indices for both bacterial and fungal fecal microbiota did not vary between the two feed efficiency groups. Differences in the fecal bacterial composition between high and low feed efficiency steers were primarily assigned to OTUs belonging to the families Lachnospiraceae and Ruminococcaceae and to the genus Prevotella. The fungal OTUs shared across the GIT did not vary between feed efficiency groups, but 7 and 3 OTUs were found only in steers with positive and negative RFI, respectively. These results provide further insights into the composition of the Nelore GIT microbiota, which could have implications for improving animal health and productivity. Our findings also reveal differences in fecal-associated bacterial OTUs between steers from different feed efficiency groups, suggesting that fecal sampling may represent a non-invasive strategy to link the bovine microbiota with productivity phenotypes.},
}

@article {pmid31293523,
year = {2019},
author = {Ma, W and Mao, Q and Xia, W and Dong, G and Yu, C and Jiang, F},
title = {Gut Microbiota Shapes the Efficiency of Cancer Therapy.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1050},
doi = {10.3389/fmicb.2019.01050},
pmid = {31293523},
issn = {1664-302X},
abstract = {Systems biology provides an opportunity to discover the role that gut microbiota play in almost all aspects of human health. Existing evidence supports the hypothesis that gut microbiota is closely related to the pharmacological effects of chemical therapy and novel targeted immunotherapy. Gut microbiota shapes the efficiency of drugs through several key mechanisms: metabolism, immunomodulation, translocation, enzymatic degradation, reduction of diversity, and ecological variability. Therefore, gut microbiota have emerged as a novel target to enhance the efficacy and reduce the toxicity and adverse effects of cancer therapy. There is growing evidence to show that cancer therapy perturbs the host immune response and results in dysbiosis of the immune system, which then influences the efficiency of the therapy. Studies suggest that gut microbes play a significant role in cancer therapy by modulating drug efficacy, abolishing the anticancer effect, and mediating toxicity. In this review, we outline the role of gut microbiota in modulating cancer therapy and the implications for improving the efficacy of chemotherapy and immunotherapy in clinical practice. We also summarize the current limitations of the safety and effectiveness of probiotics in cancer therapies such as personalized cancer therapy.},
}

@article {pmid31293334,
year = {2019},
author = {Panacer, K and Whorwell, PJ},
title = {Dietary Lectin exclusion: The next big food trend?.},
journal = {World journal of gastroenterology},
volume = {25},
number = {24},
pages = {2973-2976},
doi = {10.3748/wjg.v25.i24.2973},
pmid = {31293334},
issn = {2219-2840},
abstract = {Until recently, with the exception of coeliac disease, gastroenterologists have not been particularly interested in the role of diet in the management of gastrointestinal disorders. However, patients have always felt that diet must play a part in their symptoms and, in the absence of any medical interest, have turned to alternative dietary practitioners for help, which can often have no evidence base. Fortunately, with the advent of the FODMAP diet (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) and the realisation that diet can have a profound effect on the microbiome, medical opinion is now changing. Nevertheless, research on the various diets that are now available is often completely lacking. Lectins are carbohydrate binding proteins which are widely distributed in nature and are found in a whole variety of commonly consumed foods. It seems likely that the exclusion of lectins from the diet could become the next "food fashion" for alternative practitioners to promote, especially as there is some evidence to suggest that certain lectins may be harmful to health. It is, therefore, the purpose of this viewpoint to try and stimulate research on the dietary effects of lectins, which is currently minimal, so that we can pre-empt a situation where we are unable to give patients or the public evidence based advice on this topic.},
}

@article {pmid31292752,
year = {2019},
author = {Pagliai, G and Russo, E and Niccolai, E and Dinu, M and Di Pilato, V and Magrini, A and Bartolucci, G and Baldi, S and Menicatti, M and Giusti, B and Marcucci, R and Rossolini, GM and Casini, A and Sofi, F and Amedei, A},
title = {Influence of a 3-month low-calorie Mediterranean diet compared to the vegetarian diet on human gut microbiota and SCFA: the CARDIVEG Study.},
journal = {European journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00394-019-02050-0},
pmid = {31292752},
issn = {1436-6215},
support = {4042.16092014.066000029//Regione Toscana/ ; },
abstract = {PURPOSE: We evaluated the effect of low-calorie mediterranean (MD) and vegetarian (VD) diets on gut microbiome (GM) composition and short-chain-fatty acids (SCFA) production.

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

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

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

@article {pmid31292342,
year = {2019},
author = {Okukawa, M and Watanabe, T and Miura, M and Konno, H and Yano, S and Nonomura, Y},
title = {Antibacterial Activity of 1,2-Alkanediol against Staphylococcus aureus and Staphylococcus epidermidis.},
journal = {Journal of oleo science},
volume = {},
number = {},
pages = {},
doi = {10.5650/jos.ess19074},
pmid = {31292342},
issn = {1347-3352},
abstract = {1,2-Alkanediol exhibits antibacterial activity against several bacteria and yeast. However, few studies have reported antimicrobial tests on skin microbiome. Bacterial microbiome on the skin surface include Staphylococcus aureus (S. aureus), which causes rough skin and inflammation in atopic dermatitis and Staphylococcus epidermidis (S. epidermidis), which enhances innate immunity. In this study, the minimal inhibitory concentration (MIC) was evaluated for 1,2-alkanediol comprising 4-12 carbon atoms against S. aureus and S. epidermidis. 1,2-Alkanediol comprising 6-12 carbon atoms exhibited antimicrobial activity against both species of Staphylococcus. The antibacterial activity depended on the alkyl chain length. In addition, the minimum bactericidal concentration (MBC) on agar was evaluated for 1,2-alkanediol comprising 6-12 carbon atoms. 1,2-Octanediol and 1,2-decanediol exhibited significant bactericidal activity.},
}

@article {pmid31292268,
year = {2019},
author = {Tinsley, N and Zhou, C and Tan, G and Rack, S and Lorigan, P and Blackhall, F and Krebs, M and Carter, L and Thistlethwaite, F and Graham, D and Cook, N},
title = {Cumulative Antibiotic Use Significantly Decreases Efficacy of Checkpoint Inhibitors in Patients with Advanced Cancer.},
journal = {The oncologist},
volume = {},
number = {},
pages = {},
doi = {10.1634/theoncologist.2019-0160},
pmid = {31292268},
issn = {1549-490X},
abstract = {BACKGROUND: With the advent of immunotherapy, substantial progress has been made in improving outcomes for patients with advanced cancer. However, not all patients benefit equally from treatment, and confounding immune-related issues may have an impact. Several studies suggest that antibiotic use (which alters the gut microbiome) may result in poorer outcomes for patients treated with immune checkpoint inhibitors (ICI).

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

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

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

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

@article {pmid31292231,
year = {2019},
author = {Mike, LA},
title = {mSphere of Influence: Systematically Decoding Microbial Chemical Communication.},
journal = {mSphere},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSphere.00319-19},
pmid = {31292231},
issn = {2379-5042},
abstract = {Laura A. Mike works in the field of bacterial pathogenesis. In this mSphere of Influence article, she reflects on how "Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters" by P. Cimermancic et al. (Cell 158:412-421, 2014, https://doi.org/10.1016/j.cell.2014.06.034) and "A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics" by M. S. Donia et al. (Cell 158:1402-1414, 2014, https://doi.org/10.1016/j.cell.2014.08.032) made an impact on her by systematically identifying microbiome-associated biosynthetic gene clusters predicted to synthesize secondary metabolites, which may facilitate interspecies interactions.},
}

@article {pmid31291502,
year = {2019},
author = {Ribeiro, ÂM and Puetz, L and Pattinson, NB and Dálen, L and Deng, Y and Zhang, G and da Fonseca, RR and Smit, B and Gilbert, MTP},
title = {31° South: The physiology of adaptation to arid conditions in a passerine bird.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.15176},
pmid = {31291502},
issn = {1365-294X},
abstract = {Arid environments provide ideal ground for investigating the mechanisms of adaptive evolution. High temperatures and low water availability are relentless stressors for many endotherms, including birds; yet birds persist in deserts. While physiological adaptation likely involves metabolic phenotypes, the underlying mechanisms (plasticity, genetics) are largely uncharacterized. To explore this, we took an intra-specific approach that focused on a species that is resident over a mesic to arid gradient, the Karoo scrub-robin (Cercotrichas coryphaeus). Specifically, we integrated environmental (climatic and primary productivity), physiological (metabolic rates: a measure of energy expenditure), genotypic (genetic variation underlying the machinery of energy production) and microbiome (involved in processing food from where energy is retrieved) data, to infer the mechanism of physiological adaptation. We that found the variation in energetic physiology phenotypes and gut microbiome composition are associated with environmental features as well as with variation in genes underlying energy metabolic pathways. Specifically, we identified a small list of candidate adaptive genes, some of them with known ties to relevant physiology phenotypes. Together our results suggest that selective pressures on energetic physiology mediated by genes related to energy homeostasis and possibly microbiota composition may facilitate adaptation to local conditions and provide an explanation to the high avian intra-specific divergence observed in harsh environments. This article is protected by copyright. All rights reserved.},
}

@article {pmid31291462,
year = {2019},
author = {Liu, Y and Ajami, NJ and El-Serag, HB and Hair, C and Graham, DY and White, DL and Chen, L and Wang, Z and Plew, S and Kramer, J and Cole, R and Hernaez, R and Hou, J and Husain, N and Jarbrink-Sehgal, ME and Kanwal, F and Ketwaroo, G and Natarajan, Y and Shah, R and Velez, M and Mallepally, N and Petrosino, JF and Jiao, L},
title = {Dietary quality and the colonic mucosa-associated gut microbiome in humans.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajcn/nqz139},
pmid = {31291462},
issn = {1938-3207},
abstract = {BACKGROUND: Despite tremendous interest in modulating the microbiome to improve health, the association between diet and the colonic mucosa-associated gut microbiome in healthy individuals has not been examined.

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

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

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

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

@article {pmid31291047,
year = {2019},
author = {Šoltys, K and Planý, M and Biocca, P and Vianello, V and Bučková, M and Puškárová, A and Sclocchi, MC and Colaizzi, P and Bicchieri, M and Pangallo, D and Pinzari, F},
title = {Lead soaps formation and biodiversity in a XVIII Century wax seal coloured with minium.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14735},
pmid = {31291047},
issn = {1462-2920},
abstract = {A multidisciplinary approach was carried out in order to study the biodeterioration and the associated microbiome of a XVIII Century wax seal coloured with minium. A small wax seal fragment was observed by scanning electron microscopy combined with energy dispersive spectroscopy (SEM-EDS) in non-destructive mode. The same object was analysed by RAMAN and Fourier-transform infrared (FTIR) spectroscopy. The identification of the microbiota growing on the seal was performed with both a culture-dependent strategy, combined with hydrolytic assays, and high throughput sequencing using the MinION platform. The whole bacterial 16S rRNA gene and the fungal markers ITS and 28S rRNA were targeted. It was observed that the carnauba wax coloured with lead tetroxide (minium) was covered by a biofilm consisting of a network of filaments and other structures of microbial origin. The culture-dependent and culture-independent investigations showed the presence of a complex microbiota composed mainly by fungal members which demonstrated interesting properties related to lipids and lead processing. The formation of lead soaps and secondary biogenic minerals were also described. This article is protected by copyright. All rights reserved.},
}

@article {pmid31290561,
year = {2019},
author = {Li, CX and You, ZX and Lin, YX and Liu, HY and Su, J},
title = {Skin microbiome differences relate to the grade of acne vulgaris.},
journal = {The Journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1346-8138.14952},
pmid = {31290561},
issn = {1346-8138},
support = {//Open Project of the State Key Laboratory of Respiratory Disease/ ; },
abstract = {The skin microbiome plays important roles in the pathogenesis and development of acne. We aimed to investigate the facial skin microbiome of acne and microbiome differences related to different grades of acne. Skin swabs from nine healthy controls and 67 acne patients were collected, and the skin microbiomes were analyzed using 16S rRNA gene sequencing. Compared with healthy controls, acne patients harbored significantly altered skin microbiomes. The skin microbiomes of patients with grade 1-3 acne were similar, but patients with grade 4 acne showed a significantly different skin microbiome compared with grade 1-3 acne, including increased alpha diversity and increased proportions of four Gram-negative bacteria (Faecalibacterium, Klebsiella, Odoribacter and Bacteroides). In conclusion, acne patients harbored an altered skin microbiome, and more significant dysbiosis was found in patients with grade 4 acne (severe acne). Our findings may provide evidence for the pathogenic mechanisms of acne and microbial-based strategies to avoid and treat acne, especially grade 4 acne.},
}

@article {pmid31290335,
year = {2019},
author = {Jensen, EA and Berryman, DE and Murphy, ER and Carroll, RK and Busken, J and List, EO and Broach, WH},
title = {Heterogeneity spacers in 16S rDNA primers improve analysis of mouse gut microbiomes via greater nucleotide diversity.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {},
doi = {10.2144/btn-2019-0025},
pmid = {31290335},
issn = {1940-9818},
abstract = {Illumina-based amplicon sequencing suffers from the deleterious effects of highly homogenous nucleotide composition, limiting the number of high-quality reads generated per run. We attempted to alleviate this limitation by comparing the results obtained from 16S ribosomal DNA (16S rDNA) sequencing of mouse gut microbiomes using Illumina V3-V4 primers (Run 1) and custom primers that incorporate a heterogeneity spacer (0-7 nucleotides) upstream of the 16S priming region (Run 2). Overall, Run 2 had higher quality sequences, a more diverse microbial profile, and higher precision within, and variation between, experimental groups than Run 1. Our primer design offers a simple way to increase the quality of 16S rDNA sequencing and increases the number of useable reads generated per Illumina run.},
}

@article {pmid31290060,
year = {2019},
author = {McLean, C and Jun, S and Kozyrskyj, A},
title = {Impact of maternal smoking on the infant gut microbiota and its association with child overweight: a scoping review.},
journal = {World journal of pediatrics : WJP},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12519-019-00278-8},
pmid = {31290060},
issn = {1867-0687},
support = {227312//Canadian Institutes of Health Research/Canada ; },
abstract = {BACKGROUND: Childhood obesity is a growing public health concern with evidence demonstrating that while infant exposure to maternal smoking is linked to low birth weight at birth, there is a rapid catch up in weight and increased risk of obesity in later life. This scoping review aims to synthesize up-to-date evidence on the impact of maternal smoking on the infant gut microbiota and its association with child overweight.

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

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

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

@article {pmid31289831,
year = {2019},
author = {Youens-Clark, K and Bomhoff, M and Ponsero, AJ and Wood-Charlson, EM and Lynch, J and Choi, I and Hartman, JH and Hurwitz, BL},
title = {iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences.},
journal = {GigaScience},
volume = {8},
number = {7},
pages = {},
doi = {10.1093/gigascience/giz083},
pmid = {31289831},
issn = {2047-217X},
abstract = {BACKGROUND: Scientists have amassed a wealth of microbiome datasets, making it possible to study microbes in biotic and abiotic systems on a population or planetary scale; however, this potential has not been fully realized given that the tools, datasets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community.

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

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

@article {pmid31289321,
year = {2019},
author = {Voorhies, AA and Mark Ott, C and Mehta, S and Pierson, DL and Crucian, BE and Feiveson, A and Oubre, CM and Torralba, M and Moncera, K and Zhang, Y and Zurek, E and Lorenzi, HA},
title = {Study of the impact of long-duration space missions at the International Space Station on the astronaut microbiome.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {9911},
doi = {10.1038/s41598-019-46303-8},
pmid = {31289321},
issn = {2045-2322},
support = {NNX12AB02G//National Aeronautics and Space Administration (NASA)/ ; },
abstract = {Over the course of a mission to the International Space Station (ISS) crew members are exposed to a number of stressors that can potentially alter the composition of their microbiomes and may have a negative impact on astronauts' health. Here we investigated the impact of long-term space exploration on the microbiome of nine astronauts that spent six to twelve months in the ISS. We present evidence showing that the microbial communities of the gastrointestinal tract, skin, nose and tongue change during the space mission. The composition of the intestinal microbiota became more similar across astronauts in space, mostly due to a drop in the abundance of a few bacterial taxa, some of which were also correlated with changes in the cytokine profile of crewmembers. Alterations in the skin microbiome that might contribute to the high frequency of skin rashes/hypersensitivity episodes experienced by astronauts in space were also observed. The results from this study demonstrate that the composition of the astronauts' microbiome is altered during space travel. The impact of those changes on crew health warrants further investigation before humans embark on long-duration voyages into outer space.},
}

@article {pmid31289141,
year = {2019},
author = {Wu, L and Zeng, T and Zinellu, A and Rubino, S and Kelvin, DJ and Carru, C},
title = {A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00325-19},
pmid = {31289141},
issn = {2379-5077},
abstract = {Sardinia, Italy, has a high prevalence of residents who live more than 100 years. The reasons for longevity in this isolated region are currently unknown. Gut microbiota may hold a clue. To explore the role gut microbiota may play in healthy aging and longevity, we used metagenomic sequencing to determine the compositional and functional differences in gut microbiota associated with populations of different ages in Sardinia. Our data revealed that the gut microbiota of both young and elderly Sardinians shared similar taxonomic and functional profiles. A different pattern was found in centenarians. Within the centenarian group, the gut microbiota was correlated with the functional independence measurement of the host. Centenarians had a higher diversity of core microbiota species and microbial genes than those in the young and elderly. We found that the gut microbiota in Sardinian centenarians displayed a rearranged taxonomic pattern compared with those of the young and elderly, featured by depletion of Faecalibacterium prausnitzii and Eubacterium rectale and enriched for Methanobrevibacter smithii and Bifidobacterium adolescentis Moreover, functional analysis revealed that the microbiota in centenarians had high capacity for central metabolism, especially glycolysis and fermentation to short-chain fatty acids (SCFAs), although the gut microbiota in centenarians was low in genes encoding enzymes involved in degradation of carbohydrates, including fibers and galactose.IMPORTANCE The gut microbiota has been proposed as a promising determinant for human health. Centenarians as a model for extreme aging may help us understand the correlation of gut microbiota with healthy aging and longevity. Here we confirmed that centenarians had microbiota elements usually associated with benefits to health. Our finding of a high capacity of glycolysis and related SCFA production represented a healthy microbiome and environment that is regarded as beneficial for host gut epithelium. The low abundance of genes encoding components of pathways involved in carbohydrate degradation was also found in the gut microbiota of Sardinian centenarians and is often associated with poor gut health. Overall, our study here represents an expansion of previous research investigating the age-related changes in gut microbiota. Furthermore, our study provides a new prospective for potential targets for gut microbiota intervention directed at limiting gut inflammation and pathology and enhancing a healthy gut barrier.},
}

@article {pmid31289068,
year = {2019},
author = {Keij, FM and Kornelisse, RF and Hartwig, NG and Mauff, K and Poley, MJ and Allegaert, K and Reiss, IKM and Tramper-Stranders, GA},
title = {RAIN study: a protocol for a randomised controlled trial evaluating efficacy, safety and cost-effectiveness of intravenous-to-oral antibiotic switch therapy in neonates with a probable bacterial infection.},
journal = {BMJ open},
volume = {9},
number = {7},
pages = {e026688},
doi = {10.1136/bmjopen-2018-026688},
pmid = {31289068},
issn = {2044-6055},
abstract = {INTRODUCTION: High morbidity and mortality rates of proven bacterial infection are the main reason for substantial use of intravenous antibiotics in neonates during the first week of life. In older children, intravenous-to-oral switch after 48 hours of intravenous therapy has been shown to have many advantages and is nowadays commonly practised. We, therefore, aim to evaluate the effectiveness, safety and cost-effectiveness of an early intravenous-to-oral switch in neonates with a probable bacterial infection.

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

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

TRIAL REGISTRATION NUMBER: NCT03247920.},
}

@article {pmid31288975,
year = {2019},
author = {Morley, VJ and Woods, RJ and Read, AF},
title = {Bystander Selection for Antimicrobial Resistance: Implications for Patient Health.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2019.06.004},
pmid = {31288975},
issn = {1878-4380},
abstract = {Antimicrobial therapy promotes resistance emergence in target infections and in off-target microbiota. Off-target resistance emergence threatens patient health when off-target populations are a source of future infections, as they are for many important drug-resistant pathogens. However, the health risks of antimicrobial exposure in off-target populations remain largely unquantified, making rational antibiotic stewardship challenging. Here, we discuss the contribution of bystander antimicrobial exposure to the resistance crisis, the implications for antimicrobial stewardship, and some novel opportunities to limit resistance evolution while treating target pathogens.},
}

@article {pmid31288964,
year = {2019},
author = {Uroz, S and Courty, PE and Oger, P},
title = {Plant Symbionts Are Engineers of the Plant-Associated Microbiome.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2019.06.008},
pmid = {31288964},
issn = {1878-4372},
abstract = {Plants interact throughout their lives with environmental microorganisms. These interactions determine plant development, nutrition, and fitness in a dynamic and stressful environment, forming the basis for the holobiont concept in which plants and plant-associated microbes are not considered as independent entities but as a single evolutionary unit. A primary open question concerns whether holobiont structure is shaped by its microbial members or solely by the plant. Current knowledge of plant-microbe interactions argues that the establishment of symbiosis directly and indirectly conditions the plant-associated microbiome. We propose to define the impact of the symbiont on the plant microbiome as the 'symbiosis cascade effect', in which the symbionts and their plant host jointly shape the plant microbiome.},
}

@article {pmid31288753,
year = {2019},
author = {Lam, TJ and Ye, Y},
title = {Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {567},
doi = {10.1186/s12864-019-5922-8},
pmid = {31288753},
issn = {1471-2164},
support = {1R01AI143254//National Institute of Allergy and Infectious Diseases/ ; 1R01AI108888//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND: Sequencing of microbiomes has accelerated the characterization of the diversity of CRISPR-Cas immune systems. However, the utilization of next generation short read sequences for the characterization of CRISPR-Cas dynamics remains limited due to the repetitive nature of CRISPR arrays. CRISPR arrays are comprised of short spacer segments (derived from invaders' genomes) interspaced between flanking repeat sequences. The repetitive structure of CRISPR arrays poses a computational challenge for the accurate assembly of CRISPR arrays from short reads. In this paper we evaluate the use of long read sequences for the analysis of CRISPR-Cas system dynamics in microbiomes.

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

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

@article {pmid31288283,
year = {2019},
author = {Wree, A and Geisler, LJ and Tacke, F},
title = {[Microbiome & NASH - partners in crime driving progression of fatty liver disease].},
journal = {Zeitschrift fur Gastroenterologie},
volume = {57},
number = {7},
pages = {871-882},
doi = {10.1055/a-0755-2595},
pmid = {31288283},
issn = {1439-7803},
abstract = {Along with the increasing prevalence of obesity, metabolic syndrome and type 2 diabetes, non-alcoholic fatty liver disease (NAFLD) is rapidly increasing and poses a major challenge for gastroenterologists. Many studies have demonstrated that the microbiome is closely associated with the progression of nutrition-related diseases, especially of fatty liver disease. Changes in the quantity and quality of the intestinal flora, commonly referred to as dysbiosis, result in altered food metabolism, increased permeability of the intestinal barrier ("leaky gut") and consecutive inflammatory processes in the liver. This favors both the progression of obesity and metabolic disorders as well as NAFLD towards non-alcoholic steatohepatitis (NASH), hepatic fibrosis, cirrhosis and hepatocellular carcinoma (HCC). Important molecular mechanisms include microbial metabolites, microbial and endogenous signaling substances (so-called PAMPs/DAMPs) as well as bile acids. Essential cellular mechanisms include immune cells in the gut and liver, especially macrophages and Kupffer cells, as well as intestinal epithelial cells and hepatocytes as central regulators of metabolism. In this review article, we briefly summarize the relevant species of the human microbiome, describe the microbial analytics, explain the most important molecular relationships between microbiome and NAFLD/NASH, and finally the opportunities and challenges of microbiome-modulating therapy for the treatment of fatty liver disease.},
}

@article {pmid31288247,
year = {2019},
author = {Lopez, SMC and Martin, JM and Johnson, M and Kurs-Lasky, M and Horne, WT and Marshall, CW and Cooper, VS and Williams, JV and Shaikh, N},
title = {A method of processing nasopharyngeal swabs to enable multiple testing.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41390-019-0498-1},
pmid = {31288247},
issn = {1530-0447},
abstract = {OBJECTIVE: To develop a method to perform multiple tests on single nasopharyngeal (NP) swab.

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

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

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

@article {pmid31287879,
year = {2019},
author = {Jarrett, OD and Srinivasan, S and Richardson, BA and Fiedler, T and Wallis, JM and Kinuthia, J and Jaoko, W and Mandaliya, K and Fredricks, DN and McClelland, RS},
title = {Specific vaginal bacteria are associated with increased risk of Trichomonas vaginalis acquisition in women.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiz354},
pmid = {31287879},
issn = {1537-6613},
abstract = {BACKGROUND: While bacterial vaginosis has been associated with an increased risk of Trichomonas vaginalis (TV) acquisition, it is unknown if other characteristics of the vaginal microbiota, including the presence of key bacterial species, impact a woman's risk of TV.

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

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

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

@article {pmid31287608,
year = {2019},
author = {Sun, L and Dicksved, J and Priyashantha, H and Lundh, Å and Johansson, M},
title = {Distribution of bacteria between different milk fractions, investigated using culture-dependent methods and molecular-based and fluorescent microscopy approaches.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jam.14377},
pmid = {31287608},
issn = {1365-2672},
abstract = {AIMS: To develop a protocol for DNA extraction using whole milk and further, to investigate how the use of whole instead of skimmed milk during DNA extraction affected the resulting microbial composition.

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

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

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

@article {pmid31287580,
year = {2019},
author = {McClanahan, D and Wong, A and Kezic, S and Samrao, A and Hajar, T and Hill, E and Simpson, EL},
title = {A randomized controlled trial of an emollient with ceramide and filaggrin-associated amino acids for the primary prevention of atopic dermatitis in high-risk infants.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.15786},
pmid = {31287580},
issn = {1468-3083},
abstract = {BACKGROUND: Skin barrier dysfunction may precede infantile development of clinical atopic dermatitis (AD). Early life emollient therapy to enhance barrier function may prevent or modify AD development in high-risk infants.

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

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

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

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

@article {pmid31286860,
year = {2019},
author = {Meola, M and Rifa, E and Shani, N and Delbès, C and Berthoud, H and Chassard, C},
title = {DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {560},
doi = {10.1186/s12864-019-5914-8},
pmid = {31286860},
issn = {1471-2164},
abstract = {BACKGROUND: Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation.

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

@article {pmid31286662,
year = {2019},
author = {Njoku, K and Crosbie, EJ},
title = {Does the vaginal microbiome drive cervical carcinogenesis?.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1471-0528.15867},
pmid = {31286662},
issn = {1471-0528},
abstract = {Since the discovery of lactic acid producing bacteria in the vagina by Albert Dodelein in 1892, multiple studies have explored the relationship between the vaginal microbiota and various physiological, infectious and malignant conditions (Łaniewski et al, Sci Rep. 2018;8(1):7593). Whether the vaginal microbiome influences the association between human papillomavirus (HPV) infection and cervical cancer is one example with several, albeit small studies assessing whether vaginal dysbiosis influences HPV acquisition, persistence and progression to cervical dysplasia and malignancy. Whilst findings from these studies have been consistent and highly suggestive of an altered vaginal microbiome (Brusselaers at al., Am J Obstet Gynaecol 2019: 221(1):9-18), compelling evidence for the specific bacterial community state type (CST) species linked with cervical disease is lacking. This article is protected by copyright. All rights reserved.},
}

@article {pmid31286231,
year = {2019},
author = {Bowen, J and Al-Dasooqi, N and Bossi, P and Wardill, H and Van Sebille, Y and Al-Azri, A and Bateman, E and Correa, ME and Raber-Durlacher, J and Kandwal, A and Mayo, B and Nair, RG and Stringer, A and Ten Bohmer, K and Thorpe, D and Lalla, RV and Sonis, S and Cheng, K and Elad, S and , },
title = {The pathogenesis of mucositis: updated perspectives and emerging targets.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00520-019-04893-z},
pmid = {31286231},
issn = {1433-7339},
abstract = {Mucositis research and treatment are a rapidly evolving field providing constant new avenues of research and potential therapies. The MASCC/ISOO Mucositis Study Group regularly assesses available literature relating to pathogenesis, mechanisms, and novel therapeutic approaches and distils this to summary perspectives and recommendations. Reviewers assessed 164 articles published between January 2011 and June 2016 to identify progress made since the last review and highlight new targets for further investigation. Findings were organized into sections including established and emerging mediators of toxicity, potential insights from technological advances in mucositis research, and perspective. Research momentum is accelerating for mucositis pathogenesis, and with this has come utilization of new models and interventions that target specific mechanisms of injury. Technological advances have the potential to revolutionize the field of mucositis research, although focused effort is needed to move rationally targeted interventions to the clinical setting.},
}

@article {pmid31285833,
year = {2019},
author = {Stanislawski, MA and Dabelea, D and Lange, LA and Wagner, BD and Lozupone, CA},
title = {Gut microbiota phenotypes of obesity.},
journal = {NPJ biofilms and microbiomes},
volume = {5},
number = {},
pages = {18},
doi = {10.1038/s41522-019-0091-8},
pmid = {31285833},
issn = {2055-5008},
abstract = {Obesity is a disease with a complex etiology and variable prevalence across different populations. While several studies have reported gut microbiota composition differences associated with obesity in humans, there has been a lack of consistency in the nature of the reported changes; it has been difficult to determine whether methodological differences between studies, underlying differences in the populations studied, or other factors are responsible for this discordance. Here we use 16 S rRNA data from previously published studies to explore how the gut microbiota-obesity relationship varies across heterogeneous Western populations, focusing mainly on the relationship between (1) alpha diversity and (2) Prevotella relative abundance with BMI. We provide evidence that the relationship between lower alpha diversity and higher BMI may be most consistent in non-Hispanic white (NHW) populations and/or those with high socioeconomic status, while the relationship between higher Prevotella relative abundance and BMI may be stronger among black and Hispanic populations. We further examine how diet may impact these relationships. This work suggests that gut microbiota phenotypes of obesity may differ with race/ethnicity or its correlates, such as dietary components or socioeconomic status. However, microbiome cohorts are often too small to study complex interaction effects and non-white individuals are greatly underrepresented, creating substantial challenges to understanding population-level patterns in the microbiome-obesity relationship. Further study of how population heterogeneity influences the relationship between the gut microbiota and obesity is warranted.},
}

@article {pmid31285584,
year = {2019},
author = {Edwards, RA and Vega, AA and Norman, HM and Ohaeri, M and Levi, K and Dinsdale, EA and Cinek, O and Aziz, RK and McNair, K and Barr, JJ and Bibby, K and Brouns, SJJ and Cazares, A and de Jonge, PA and Desnues, C and Díaz Muñoz, SL and Fineran, PC and Kurilshikov, A and Lavigne, R and Mazankova, K and McCarthy, DT and Nobrega, FL and Reyes Muñoz, A and Tapia, G and Trefault, N and Tyakht, AV and Vinuesa, P and Wagemans, J and Zhernakova, A and Aarestrup, FM and Ahmadov, G and Alassaf, A and Anton, J and Asangba, A and Billings, EK and Cantu, VA and Carlton, JM and Cazares, D and Cho, GS and Condeff, T and Cortés, P and Cranfield, M and Cuevas, DA and De la Iglesia, R and Decewicz, P and Doane, MP and Dominy, NJ and Dziewit, L and Elwasila, BM and Eren, AM and Franz, C and Fu, J and Garcia-Aljaro, C and Ghedin, E and Gulino, KM and Haggerty, JM and Head, SR and Hendriksen, RS and Hill, C and Hyöty, H and Ilina, EN and Irwin, MT and Jeffries, TC and Jofre, J and Junge, RE and Kelley, ST and Khan Mirzaei, M and Kowalewski, M and Kumaresan, D and Leigh, SR and Lipson, D and Lisitsyna, ES and Llagostera, M and Maritz, JM and Marr, LC and McCann, A and Molshanski-Mor, S and Monteiro, S and Moreira-Grez, B and Morris, M and Mugisha, L and Muniesa, M and Neve, H and Nguyen, NP and Nigro, OD and Nilsson, AS and O'Connell, T and Odeh, R and Oliver, A and Piuri, M and Prussin Ii, AJ and Qimron, U and Quan, ZX and Rainetova, P and Ramírez-Rojas, A and Raya, R and Reasor, K and Rice, GAO and Rossi, A and Santos, R and Shimashita, J and Stachler, EN and Stene, LC and Strain, R and Stumpf, R and Torres, PJ and Twaddle, A and Ugochi Ibekwe, M and Villagra, N and Wandro, S and White, B and Whiteley, A and Whiteson, KL and Wijmenga, C and Zambrano, MM and Zschach, H and Dutilh, BE},
title = {Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-019-0494-6},
pmid = {31285584},
issn = {2058-5276},
abstract = {Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.},
}

@article {pmid31285515,
year = {2019},
author = {Suenami, S and Konishi Nobu, M and Miyazaki, R},
title = {Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {9830},
doi = {10.1038/s41598-019-46388-1},
pmid = {31285515},
issn = {2045-2322},
support = {RGY0077/2016//Human Frontier Science Program (HFSP)/ ; },
abstract = {Gut microbiota are important for various aspects of host physiology, and its composition is generally influenced by both intrinsic and extrinsic contexts of the host. Social bee gut microbiota composition is simple and highly stable hypothesized to be due to their unique food habit and social interactions. Here, we focused on hornets, the largest of the eusocial wasps - Vespa mandarinia and V. simillima. Unlike the well-studied honey bees, adult hornets are generally herbivorous but also hunt insects for broods, a unique behavior which could influence their gut microbiota. Analysis of the gut microbiome using 16S rRNA gene sequencing revealed that the two species have simple gut microbiota, composed of seven or eight consistently maintained 'core' operational taxonomic units (OTUs). While the two Vespa species shared some OTUs, the structures of their gut communities differed. Phylogenetic analysis indicated association of core OTUs with host diet. Intriguingly, prey honey bee gut microbes were detected in the V. simillima gut (and to a lesser extent in V. mandarinia), suggesting migration of microorganisms from the prey gut. This is the first report uncovering gut microbiome in hornets, giving additional insight into how food habit affects gut microbiota of social insects.},
}

@article {pmid31285290,
year = {2019},
author = {Invernizzi, R and Molyneaux, PL},
title = {The contribution of infection and the respiratory microbiome in acute exacerbations of idiopathic pulmonary fibrosis.},
journal = {European respiratory review : an official journal of the European Respiratory Society},
volume = {28},
number = {152},
pages = {},
doi = {10.1183/16000617.0045-2019},
pmid = {31285290},
issn = {1600-0617},
abstract = {Idiopathic pulmonary fibrosis (IPF) arises in genetically susceptible individuals as a result of an aberrant wound-healing response following repetitive alveolar injury. The clinical course of the disease remains both variable and unpredictable with periods of more rapid decline, termed acute exacerbation of IPF (AE-IPF), often punctuating the disease trajectory. Exacerbations carry a significant morbidity and mortality, and their exact pathogenesis remains unclear. Given the emerging evidence that disruption and alteration in the lung microbiome plays a role in the pathogenesis and progression of IPF, this review discusses the current knowledge of the contribution of infection and the respiratory microbiome to AE-IPF.},
}

@article {pmid31285289,
year = {2019},
author = {Vandeplassche, E and Tavernier, S and Coenye, T and Crabbé, A},
title = {Influence of the lung microbiome on antibiotic susceptibility of cystic fibrosis pathogens.},
journal = {European respiratory review : an official journal of the European Respiratory Society},
volume = {28},
number = {152},
pages = {},
doi = {10.1183/16000617.0041-2019},
pmid = {31285289},
issn = {1600-0617},
abstract = {The lungs of patients with cystic fibrosis (CF) are colonised by a microbial community comprised of pathogenic species, such as Pseudomonas aeruginosa and Staphylococcus aureus, and microorganisms that are typically not associated with worse clinical outcomes (considered as commensals). Antibiotics directed at CF pathogens are often not effective and a discrepancy is observed between activity of these agents in vitro and in the patient. This review describes how interspecies interactions within the lung microbiome might influence the outcome of antibiotic treatment targeted at common CF pathogens. Protective mechanisms by members of the microbiome such as antibiotic degradation (indirect pathogenicity), alterations of the cell wall, production of matrix components decreasing antibiotic penetration, and changes in metabolism are discussed. Interspecies interactions that increase bacterial susceptibility are also addressed. Furthermore, we discuss how experimental conditions, such as culture media, oxygen levels, incorporation of host-pathogen interactions, and microbial community composition may influence the outcome of microbial interaction studies related to antibiotic activity. Hereby, the importance to create in vitro conditions reflective of the CF lung microenvironment is highlighted. Understanding the role of the CF lung microbiome in antibiotic efficacy may help find novel therapeutic and diagnostic approaches to better tackle chronic lung infections in this patient population.},
}

@article {pmid31284929,
year = {2019},
author = {Staudacher, AG and Stevens, WW},
title = {Sinus Infections, Inflammation, and Asthma.},
journal = {Immunology and allergy clinics of North America},
volume = {39},
number = {3},
pages = {403-415},
doi = {10.1016/j.iac.2019.03.008},
pmid = {31284929},
issn = {1557-8607},
abstract = {There is an important link between the upper and lower respiratory tracts whereby inflammation in one environment can influence the other. In acute rhinosinusitis, pathogen exposures are the primary driver for inflammation in the nose, which can exacerbate asthma. In chronic rhinosinusitis, a disease clinically associated with asthma, the inflammation observed is likely from a combination of an impaired epithelial barrier, dysregulated immune response, and potentially infection (or colonization) by specific pathogens. This review explores the associations between rhinosinusitis and asthma, with particular emphasis placed on the role of infections and inflammation.},
}