@article {pmid31430322,
year = {2019},
author = {Meyer, S and Thiel, V and Joergensen, RG and Sundrum, A},
title = {Relationships between feeding and microbial faeces indices in dairy cows at different milk yield levels.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0221266},
doi = {10.1371/journal.pone.0221266},
pmid = {31430322},
issn = {1932-6203},
abstract = {A study was carried out to gain quantitative information on the diet-dependent faecal microbial biomass of dairy cows, especially on the biomass fractions of fungi, Gram-positive (G+) and Gram-negative (G-) bacteria. Groups of high-yield, low-yield and non-lactating cows were investigated at four different farms. A mean faecal microbial biomass C (MBC) concentration of 33.5 mg g-1 DM was obtained by the chloroform fumigation extraction method. This is similar to a mean microbial C concentration of 31.8 mg g-1 DM, which is the sum of bacterial C and fungal C, estimated by cell-wall derived muramic acid (MurN) and fungal glucosamine (GlcN), respectively. However, the response of these two approaches to the feeding regime was contradictory, due to feeding effects on the conversion values. The higher neutral detergent fibre (NDF) and acid detergent fibre (ADF) concentrations in the non-lactating group led to higher (P < 0.05) concentrations of cellulose and lignin in their faeces in comparison with the lactating cows. This change in faecal chemical composition in the non-lactating group was accompanied by usually higher ratios of G+/G- phospholipid fatty acids (PLFA), ergosterol/MBC and fungal C/bacterial C. Although bacteria dominate the faecal microbial biomass, fungi contribute a considerable mean percentage of roughly 20% to the faecal microbiome, according to PLFA and amino sugar data, which requires more attention in the future. Near-infra red spectroscopic estimates of organic N and C fractions of cow faeces were able to model microbial biomarkers successfully, which might be useful in the future to predict its N2O emission potential and fertilizer value.},
}

@article {pmid31429989,
year = {2019},
author = {Velazquez, S and Griffiths, W and Dietz, L and Horve, P and Nunez, S and Hu, J and Shen, J and Fretz, M and Bi, C and Xu, Y and Van Den Wymelenberg, KG and Hartmann, EM and Ishaq, SL},
title = {From one species to another: A review on the interaction of chemistry and microbiology in relation to cleaning in the built environment.},
journal = {Indoor air},
volume = {},
number = {},
pages = {},
doi = {10.1111/ina.12596},
pmid = {31429989},
issn = {1600-0668},
abstract = {Since the advent of soap, personal hygiene practices have revolved around removal, sterilization, and disinfection - both of visible soil and microscopic organisms - for a myriad of cultural, aesthetic, or health-related reasons. Cleaning methods and products vary widely in their recommended use, effectiveness, risk to users or building occupants, environmental sustainability, and ecological impact. Advancements in science and technology have facilitated in-depth analyses of the indoor microbiome and studies in this field suggest that the traditional "scorched-earth cleaning" mentality - that surfaces must be completely sterilized and prevent microbial establishment - may contribute to long-term human health consequences. Moreover, the materials, products, activities, and microbial communities indoors all contribute to, or remove, chemical species to the indoor environment. This review examines the effects of cleaning with respect to the interaction of chemistry, indoor microbiology, and human health. PRACTICAL IMPLICATIONS: Simple interventions, such as hand washing, can dramatically improve health and reduce infectious disease. Chemical intervention, while effective, may encourage the development of microbial resistance over time if not implemented properly. Microbial communities adapt, reassemble, and persist, and recent theory in microbial ecology suggests that curating microbial communities may be more sustainable than perpetually attempting to remove them. This article is protected by copyright. All rights reserved.},
}

@article {pmid31429932,
year = {2019},
author = {Denu, L and Lubin, JB and Douglas, B and Tuluc, F and Silverman, MA},
title = {Diet-induced microbial autofluorescence confounds flow cytometry of ex vivo isolated fecal microbes.},
journal = {European journal of immunology},
volume = {},
number = {},
pages = {},
doi = {10.1002/eji.201948087},
pmid = {31429932},
issn = {1521-4141},
abstract = {Microbial flow cytometry is a powerful emerging technology with a broad range of applications including the study of complex microbial communities. Immunologists are increasingly using this technology to study antibody responses against pathogenic and commensal microbes. We employed microbial flow cytometry to quantify the proportion of fecal microbes bound by six different immunoglobulin isotypes: IgA, IgM, IgG1, IgG2b, IgG2c, and IgG3. In healthy mammals, secretory IgA (sIgA) binds to a subset of commensal microbes in the gut whereas IgG is not typically found in the intestinal tract of healthy mammals. Unexpectedly, fecal microbes isolated from SPF C57BL/6 mice housed in the Hill facility and imported from the vendors The Jackson Laboratory (JAX) and Taconic Biosciences (TAC) showed a strong signal in the Brilliant Violet 711 (BV711) channel. Unstained fecal samples from these mice demonstrated that the BV711 signal was due to bacterial autofluorescence. We found that murine diets containing alfalfa induce ex vivo microbial autofluorescence in the far red spectrum, likely due to chlorophyll. Analysis of unstained intestinal microbes is an important step in microbial flow cytometry to identify diet-induced autofluorescence. We recommend fluorophores with emission spectra below 650 nm (e.g. BV421, PE). This article is protected by copyright. All rights reserved.},
}

@article {pmid31429869,
year = {2019},
author = {Malard, LA and Anwar, MZ and Jacobsen, CS and Pearce, DA},
title = {Biogeographical patterns in soil bacterial communities across the Arctic region.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz128},
pmid = {31429869},
issn = {1574-6941},
abstract = {The considerable microbial diversity of soils, their variety and key role in biogeochemical cycling has led to growing interest in their global distribution and the impact that environmental change might have at the regional level. In the broadest study of Arctic soil bacterial communities to date, we used high-throughput DNA sequencing to investigate the bacterial diversity from 200 independent Arctic soil samples from 43 sites. We quantified the impact of spatial and environmental factors on bacterial community structure using variation partitioning analysis, illustrating a non-random distribution across the region. pH was confirmed as the key environmental driver structuring Arctic soil bacterial communities, while total organic carbon, moisture and conductivity were shown to have little effect. Specialist taxa were more abundant in acidic and alkaline soils while generalist taxa were more abundant in acidoneutral soils. Of 48,147 bacterial taxa, a core microbiome composed of only 13 taxa that were ubiquitously distributed and present within 95% of samples was identified, illustrating the high potential for endemism in the region. Overall, our results demonstrate the importance of spatial and edaphic factors on the structure of Arctic soil bacterial communities.},
}

@article {pmid31429791,
year = {2019},
author = {Casimiro-Soriguer, CS and Loucera, C and Perez Florido, J and López-López, D and Dopazo, J},
title = {Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples.},
journal = {Biology direct},
volume = {14},
number = {1},
pages = {15},
doi = {10.1186/s13062-019-0246-9},
pmid = {31429791},
issn = {1745-6150},
support = {SAF2017-88908-R//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; PT13/0001/0007//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; 676559//H2020 Societal Challenges/ ; 316861//H2020 Marie Skłodowska-Curie Actions/ ; },
abstract = {BACKGROUND: The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacterial abundance profiles.

RESULTS: Here we use a transformation of the conventional bacterial strain or gene abundance profiles to functional profiles that account for bacterial metabolism and other cell functionalities. These profiles are used as features for city classification in a machine learning algorithm that allows the extraction of the most relevant features for the classification.

CONCLUSIONS: We demonstrate here that the use of functional profiles not only predict accurately the most likely origin of a sample but also to provide an interesting functional point of view of the biogeography of the microbiota. Interestingly, we show how cities can be classified based on the observed profile of antibiotic resistances.

REVIEWERS: Open peer review: Reviewed by Jin Zhuang Dou, Jing Zhou, Torsten Semmler and Eran Elhaik.},
}

@article {pmid31429790,
year = {2019},
author = {Yue, S and He, T and Li, B and Qu, Y and Peng, H and Chen, J and Lei, M and Chen, C and Wu, W},
title = {Effectiveness of Yi-Zhi-An-Shen granules on cognition and sleep quality in older adults with amnestic mild cognitive impairment: protocol for a randomized, double-blind, placebo-controlled trial.},
journal = {Trials},
volume = {20},
number = {1},
pages = {518},
doi = {10.1186/s13063-019-3607-x},
pmid = {31429790},
issn = {1745-6215},
support = {JDZX2015298//State Administration of Traditional Chinese Medicine of the People's Republic of China/ ; JDZX2015298//Chengdu Science and Technology Bureau/ ; 2018-504//Cadres Health Care Research Program of Sichuan Province (CN)/ ; 2017-501//Cadres Health Care Research Program of Sichuan Province (CN)/ ; },
abstract = {BACKGROUND: Amnestic mild cognitive impairment (aMCI) is a syndrome characterized by significant forgetfulness that does not meet the criteria of dementia. Individuals with aMCI are at greater risk of progressing to dementia. Current studies suggest that good sleep quality is linked with preserved cognition in the elderly, and sleep complaints are common among the elderly with amnesia. Therefore, improving their sleep may be helpful for maintaining and improving their cognitive capacity. According to the theory of traditional Chinese medicine, Yi-Zhi-An-Shen is an herbal compound which may ameliorate forgetfulness and sleep disorders. As growing evidence indicates that the gut microbiome is associated with major mental symptoms, a hypothesis was proposed that Yi-Zhi-An-Shen granules (YZASG) might work by alternating microbial abundance and diversity. In this study, the investigators intend to assess the efficacy of YZASG on global cognition in the elderly suffering from aMCI and evaluate its safety as well as its potential mechanisms via sleep quality, fecal microbial 16S ribosomal DNA and metagenomics analyses, and serum markers.

METHODS/DESIGN: This study is a randomized, double-blind, placebo-controlled clinical trial. A total of 80 patients (aged 60-85 years) will be recruited and allocated randomly to a treatment group and a placebo group in a 1:1 ratio and will then be administered YZASG or isodose placebo three times a day. The intervention course is 16 weeks, with an 18 months follow-up. The primary outcome is the Alzheimer's Disease Assessment Scale-Cognitive Subscale. Secondary outcome measures are the Mini-Mental State Examination, Montreal Cognitive Assessment, Pittsburgh Sleep Quality Index, serum concentrations of immunological factors and inflammatory cytokines, and fecal microbiota. Fecal microbiota will only be collected at the baseline and endpoint of the intervention.

DISCUSSION: The results of this trial will be conducive to assessing the safety and effectiveness on cognition of YZASG in intervening aMCI among the elderly and determining if it takes effect via the improvement of sleep quality, regulation of gut microbiota, and concentration of certain serum markers.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT03601000 . Registered on 26 July 2018.},
}

@article {pmid31429723,
year = {2019},
author = {Siebert, JC and Neff, CP and Schneider, JM and Regner, EH and Ohri, N and Kuhn, KA and Palmer, BE and Lozupone, CA and Görg, C},
title = {VOLARE: visual analysis of disease-associated microbiome-immune system interplay.},
journal = {BMC bioinformatics},
volume = {20},
number = {1},
pages = {432},
doi = {10.1186/s12859-019-3021-0},
pmid = {31429723},
issn = {1471-2105},
support = {T32 AR007534/NH/NIH HHS/United States ; K08DK107905/NH/NIH HHS/United States ; DK108366/NH/NIH HHS/United States ; DK108366/NH/NIH HHS/United States ; LM008111/NH/NIH HHS/United States ; DK104047/NH/NIH HHS/United States ; DK104047/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Relationships between specific microbes and proper immune system development, composition, and function have been reported in a number of studies. However, researchers have discovered only a fraction of the likely relationships. "Omic" methodologies such as 16S ribosomal RNA (rRNA) sequencing and time-of-flight mass cytometry (CyTOF) immunophenotyping generate data that support generation of hypotheses, with the potential to identify additional relationships at a level of granularity ripe for further experimentation. Pairwise linear regressions between microbial and host immune features provide one approach for quantifying relationships between "omes", and the differences in these relationships across study cohorts or arms. This approach yields a top table of candidate results. However, the top table alone lacks the detail that domain experts such as microbiologists and immunologists need to vet candidate results for follow-up experiments.

RESULTS: To support this vetting, we developed VOLARE (Visualization Of LineAr Regression Elements), a web application that integrates a searchable top table, small in-line graphs illustrating the fitted models, a network summarizing the top table, and on-demand detailed regression plots showing full sample-level detail. We applied VOLARE to three case studies-microbiome:cytokine data from fecal samples in human immunodeficiency virus (HIV), microbiome:cytokine data in inflammatory bowel disease and spondyloarthritis, and microbiome:immune cell data from gut biopsies in HIV. We present both patient-specific phenomena and relationships that differ by disease state. We also analyzed interaction data from system logs to characterize usage scenarios. This log analysis revealed that users frequently generated detailed regression plots, suggesting that this detail aids the vetting of results.

CONCLUSIONS: Systematically integrating microbe:immune cell readouts through pairwise linear regressions and presenting the top table in an interactive environment supports the vetting of results for scientific relevance. VOLARE allows domain experts to control the analysis of their results, screening dozens of candidate relationships with ease. This interactive environment transcends the limitations of a static top table.},
}

@article {pmid31428718,
year = {2019},
author = {Finlin, BS and Zhu, B and Boyechko, T and Westgate, PM and Chia, CW and Egan, JM and Kern, PA},
title = {Effect of Rifaximin Treatment on Endotoxemia and Insulin Sensitivity in Humans.},
journal = {Journal of the Endocrine Society},
volume = {3},
number = {9},
pages = {1641-1651},
doi = {10.1210/js.2019-00148},
pmid = {31428718},
issn = {2472-1972},
abstract = {Context: The gut microbiome is a source of inflammatory factors such as lipopolysaccharide (LPS; endotoxin) that influence metabolic homeostasis. Rifaximin is a well-tolerated antibiotic that may reduce LPS.

Objective: We sought to develop a method to accurately assess postprandial endotoxemia and to determine whether rifaximin treatment improves metabolic homeostasis in obese humans with metabolic syndrome.

Design and Setting: Plasma LPS, adipose inflammation, glucose and lipid metabolism, and insulin sensitivity were evaluated in a clinical research setting.

Participants: Twelve obese human research participants with prediabetes or three features of metabolic syndrome participated.

Intervention: The research participants were randomized to placebo control or rifaximin soluble solid dispersion (80 mg/d) treatment groups and treated for 12 weeks.

Outcome Measures: We evaluated changes in insulin sensitivity with a euglycemic clamp; changes in lipid and glucose metabolism with oral lipid and glucose tolerance tests; changes in plasma LPS during the lipid tolerance test; and changes in adipose tissue and systemic inflammation by measuring inflammatory cytokines.

Results: Rifaximin treatment slightly worsened insulin sensitivity (P = 0.03), did not improve glucose or lipid homeostasis, and did not significantly improve adipose tissue inflammation. Our efforts to accurately assess plasma LPS using limulus amebocyte lysate assays revealed that the majority of LPS is masked from detection by limulus amebocyte lysate assays, but can be unmasked using a pretreatment step with protease. Unmasked LPS increases during the lipid tolerance test, but rifaximin treatment did not reduce this.

Conclusions: Rifaximin treatment did not lower plasma LPS or improve metabolic homeostasis in obese humans.},
}

@article {pmid31428414,
year = {2019},
author = {Vuik, F and Dicksved, J and Lam, SY and Fuhler, GM and van der Laan, L and van de Winkel, A and Konstantinov, SR and Spaander, M and Peppelenbosch, MP and Engstrand, L and Kuipers, EJ},
title = {Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals.},
journal = {United European gastroenterology journal},
volume = {7},
number = {7},
pages = {897-907},
doi = {10.1177/2050640619852255},
pmid = {31428414},
issn = {2050-6406},
abstract = {Background: Homeostasis of the gastrointestinal tract depends on a healthy bacterial microbiota, with alterations in microbiota composition suggested to contribute to diseases. To unravel bacterial contribution to disease pathology, a thorough understanding of the microbiota of the complete gastrointestinal tract is essential. To date, most microbial analyses have either focused on faecal samples, or on the microbial constitution of one gastrointestinal location instead of different locations within one individual.

Objective: We aimed to analyse the mucosal microbiome along the entire gastrointestinal tract within the same individuals.

Methods: Mucosal biopsies were taken from nine different sites in 14 individuals undergoing antegrade and subsequent retrograde double-balloon enteroscopy. The bacterial composition was characterised using 16 S rRNA sequencing with Illumina Miseq.

Results: At double-balloon enteroscopy, one individual had a caecal adenocarcinoma and one individual had Peutz-Jeghers polyps. The composition of the microbiota distinctively changed along the gastrointestinal tract with larger bacterial load, diversity and abundance of Firmicutes and Bacteroidetes in the lower gastrointestinal tract than the upper gastrointestinal tract, which was predominated by Proteobacteria and Firmicutes.

Conclusions: We show that gastrointestinal location is a larger determinant of mucosal microbial diversity than inter-person differences. These data provide a baseline for further studies investigating gastrointestinal microbiota-related disease.},
}

@article {pmid31428344,
year = {2019},
author = {George, NS and Cheung, L and Luthria, DL and Santin, M and Dawson, HD and Bhagwat, AA and Smith, AD},
title = {Pomegranate peel extract alters the microbiome in mice and dysbiosis caused by Citrobacter rodentium infection.},
journal = {Food science & nutrition},
volume = {7},
number = {8},
pages = {2565-2576},
doi = {10.1002/fsn3.1106},
pmid = {31428344},
issn = {2048-7177},
abstract = {Treatment of mice with a pomegranate peel extract (PPX) decreased the pathogenicity of Citrobacter rodentium (Cr) infections. Here, we investigate the effects of PPX on the microbiome of uninfected or Cr-infected C3H/HeNCr mice by 16S rRNA gene sequencing. Mice were treated with water or PPX for 14 days, feces were collected, and then, the mice were infected with Cr and feces collected again at day 6 postinfection. DNA was isolated from the fecal samples and subjected to 16S rRNA gene sequencing to determine the microbial composition. Differences in the composition of the microbiome were observed for untreated and PPX-treated mice with PPX mice having decreased diversity. PPX treatment decreased the Firmicutes/Bacteroidetes ratio by increasing Bacteroidetes and decreasing Firmicutes levels. The decrease in Firmicutes was driven by a large reduction in Lactobacillus. PPX treatment increased the abundance of Proteobacteria and Verrucomicrobiae and decreased Actinobacteria. The relative abundance of Cr reached 22% in water-treated but only 5% in PPX-treated infected mice. These results suggest that consumption of pomegranate polyphenols altered the microbiome, making it more resistant to displacement by infection with Cr, indicating that pomegranate polyphenols may mitigate the pathogenic effects of food-borne bacterial pathogens.},
}

@article {pmid31428294,
year = {2019},
author = {Vital, M and Rud, T and Rath, S and Pieper, DH and Schlüter, D},
title = {Diversity of Bacteria Exhibiting Bile Acid-inducible 7α-dehydroxylation Genes in the Human Gut.},
journal = {Computational and structural biotechnology journal},
volume = {17},
number = {},
pages = {1016-1019},
doi = {10.1016/j.csbj.2019.07.012},
pmid = {31428294},
issn = {2001-0370},
abstract = {The secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA), formed by gut microbiota from primary bile acids via a multi-step 7α-dehydroxylation reaction, have wide-ranging effects on host metabolism and play an important role in health and disease. A few 7α-dehydroxylating strains have been isolated, where bile acid-inducible (bai) genes were organized in a gene cluster and encoded major enzymes involved. However, only little is known on diversity and abundance of intestinal bacteria catalysing DCA/LCA formation in the human gut in situ. In this study, we took the opportunity to screen metagenome-assembled genomes (MAGs) from sequence data of stool samples provided by two recent studies along with newly available gut-derived isolates for the presence of the bai gene cluster. We revealed in total 765 and 620 MAGs encoding the potential to form DCA/LCA that grouped into 21 and 26 metagenomic species, respectively. The majority of MAGs (92.4 and 90.3%) were associated with a Ruminococcaceae clade that still lacks an isolate, whereas less MAGs belonged to Lachnospiraceae along with eight new isolates (n total = 11) that contained the bai genes. Only a few MAGs were linked to Peptostreptococcaceae. Signatures for horizontal transfer of bai genes were observed. This study gives a comprehensive overview of the diversity of bai-exhibiting bacteria in the human gut highlighting the application of metagenomics to unravel potential functions hidden from current isolates. Eventually, isolates of the identified main MAG clade are required in order to prove their capability of 7α-dehydroxylating primary bile acids.},
}

@article {pmid31428065,
year = {2019},
author = {Sun, L and Jia, H and Li, J and Yu, M and Yang, Y and Tian, D and Zhang, H and Zou, Z},
title = {Cecal Gut Microbiota and Metabolites Might Contribute to the Severity of Acute Myocardial Ischemia by Impacting the Intestinal Permeability, Oxidative Stress, and Energy Metabolism.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1745},
doi = {10.3389/fmicb.2019.01745},
pmid = {31428065},
issn = {1664-302X},
abstract = {Emerging evidence highlights the role of gut microbiota in regulating the pathogenesis of coronary heart disease. Here, we performed 16S rRNA gene sequencing and UPLC-Q-TOF/MS-based metabolomics to investigate the gut microbiome and metabolomes of cecal contents in the isoproterenol (ISO)-induced acute myocardial ischemia (AMI) rats. As expected, considerable gut microbiota alterations were observed in the AMI rats compared with the control rats, paralleling with intestinal inflammation and apoptosis. At phylum level, the abundance of Firmicutes was significantly decreased, whereas the abundance of Bacteroidetes and Spirochaetae was strikingly enriched in the AMI group. At genus level, the significant alteration of genera Treponema 2, Rikenellaceae RC9 gut group, Prevotellaceae UCG-003, and Bacteroides may contribute to the pathogenesis of AMI. These altered microbiota might influence the intestinal permeability and subsequently impair intestinal barrier and stimulate gut inflammation. Consistently, significantly metabolic differences of cecal contents between the AMI and control groups were revealed, and threonic acid, L-urobilin and L-urobilinogen were considered the most associated cecal metabolites with AMI. These strikingly altered metabolites were mainly related to energy metabolism and oxidative stress which could lead to apoptosis and further affect gut barrier. Ultimately, we revealed the potential link of these altered gut microbiota/metabolomes and intestinal inflammatory factors and apoptotic proteins and further confirmed their intimate connections with intestinal inflammation and gut barrier. Our findings depict uncovered potential relationship among the gut microbiome, cecal metabolomes and AMI.},
}

@article {pmid31427744,
year = {2019},
author = {Lee, Y and Sugihara, K and Gillilland, MG and Jon, S and Kamada, N and Moon, JJ},
title = {Hyaluronic acid-bilirubin nanomedicine for targeted modulation of dysregulated intestinal barrier, microbiome and immune responses in colitis.},
journal = {Nature materials},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41563-019-0462-9},
pmid = {31427744},
issn = {1476-1122},
support = {R01EB022563//U.S. Department of Health & Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering (NIBIB)/ ; R01AI127070//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01CA210273//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; R01CA223804//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; U01CA210152//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; R01DK108901//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
abstract = {While conventional approaches for inflammatory bowel diseases mainly focus on suppressing hyperactive immune responses, it remains unclear how to address disrupted intestinal barriers, dysbiosis of the gut commensal microbiota and dysregulated mucosal immune responses in inflammatory bowel diseases. Moreover, immunosuppressive agents can cause off-target systemic side effects and complications. Here, we report the development of hyaluronic acid-bilirubin nanomedicine (HABN) that accumulates in inflamed colonic epithelium and restores the epithelium barriers in a murine model of acute colitis. Surprisingly, HABN also modulates the gut microbiota, increasing the overall richness and diversity and markedly augmenting the abundance of Akkermansia muciniphila and Clostridium XIVα, which are microorganisms with crucial roles in gut homeostasis. Importantly, HABN associated with pro-inflammatory macrophages, regulated innate immune responses and exerted potent therapeutic efficacy against colitis. Our work sheds light on the impact of nanotherapeutics on gut homeostasis, microbiome and innate immune responses for the treatment of inflammatory diseases.},
}

@article {pmid31427714,
year = {2019},
author = {Horvath, A and Rainer, F and Bashir, M and Leber, B and Schmerboeck, B and Klymiuk, I and Groselj-Strele, A and Durdevic, M and Freedberg, DE and Abrams, JA and Fickert, P and Stiegler, P and Stadlbauer, V},
title = {Biomarkers for oralization during long-term proton pump inhibitor therapy predict survival in cirrhosis.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {12000},
doi = {10.1038/s41598-019-48352-5},
pmid = {31427714},
issn = {2045-2322},
support = {P24362//Austrian Science Fund (Fonds zur F&#x00F6;rderung der Wissenschaftlichen Forschung)/ ; },
abstract = {Proton pump inhibitors (PPI) are an invaluable therapy option for acid related diseases; however, PPI therapy is also linked to a series of side effects in cirrhosis, such as microbiome alterations, spontaneous bacterial peritonitis and hepatic encephalopathy. Decision tools to balance benefits and risks of PPI therapy are largely missing. In this study, we tested gut-derived biomarkers to identify PPI-associated dysbiosis, its association with gut barrier function and liver-related mortality. In this observational study, faecal microbiome composition data obtained from 16S rDNA sequencing of 90 cirrhotic patients with and without long-term PPI use and additional potential biomarkers identified from the literature were evaluated for their predictive value regarding PPI-associated dysbiosis and liver-related three-year mortality. In addition, faecal calprotectin, faecal zonulin and serum lipopolysaccharides were assessed as markers for intestinal inflammation, gut permeability and bacterial translocation. Streptococcus salivarius, Veillonella parvula and the genus Streptococcus were significantly increased in patients with long-term PPI therapy and performed well as biomarkers for PPI-associated dysbiosis (accuracy: 74%, 72% and 74%, respectively). The abundance of Streptococcus salivarius was linked to intestinal inflammation and gut barrier dysfunction, whereas the abundance of Veillonella parvula showed associations with liver disease severity; both were independent predictors for liver-related three-year mortality. Gut-derived biomarkers of PPI-associated dysbiosis are linked to worse outcome and a potential option to evaluate the risks of adverse events during long-term PPI therapy.},
}

@article {pmid31427618,
year = {2019},
author = {Yang, Y and Yin, Y and Chen, X and Chen, C and Xia, Y and Qi, H and Baker, PN and Zhang, H and Han, TL},
title = {Evaluating different extraction solvents for GC-MS based metabolomic analysis of the fecal metabolome of adult and baby giant pandas.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {12017},
doi = {10.1038/s41598-019-48453-1},
pmid = {31427618},
issn = {2045-2322},
support = {No. 81370732, 81571453, and 81650110522//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 81370732, 81571453, and 81650110522//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 81370732, 81571453, and 81650110522//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The gut microbiome plays a fundamental role in host health and the fecal metabolome can be analysed to assess microbial activity and can be used as an intermediate phenotype monitoring the host-microbiome relationship. However, there is no established extraction protocol to study the fecal metabolome of giant pandas. The aim of this research is to optimize extraction of the fecal metabolome from adult and baby pandas for high throughput metabolomics analysis using gas chromatography-mass spectrometry (GC-MS). Fecal samples were collected from eight adult pandas and a pair of twin baby pandas. Six different extraction solvents were investigated and evaluated for their reproducibility, metabolite coverage, and extraction efficiency, particularly in relation to the biochemical compound classes such as amino acids, tricarboxylic acid (TCA) cycle intermediates, fatty acids, secondary metabolites, and vitamin and cofactors. Our GC-MS results demonstrated that the extraction solvents with isopropanol: acetonitrile: water (3:2:2 ratio) and 80% methanol were the most appropriate for studying the fecal metabolome of adult and baby giant pandas respectively. These extraction solvents can be used in future study protocols for the analysis of the fecal metabolome in giant pandas.},
}

@article {pmid31427405,
year = {2019},
author = {Zhang, J and Haines, C and Watson, AJM and Hart, AR and Platt, MJ and Pardoll, DM and Cosgrove, SE and Gebo, KA and Sears, CL},
title = {Oral antibiotic use and risk of colorectal cancer in the United Kingdom, 1989-2012: a matched case-control study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2019-318593},
pmid = {31427405},
issn = {1468-3288},
abstract = {BACKGROUND: Microbiome dysbiosis predisposes to colorectal cancer (CRC), but a population-based study of oral antibiotic exposure and risk patterns is lacking.

OBJECTIVE: To assess the association between oral antibiotic use and CRC risk.

DESIGN: A matched case-control study (incident CRC cases and up to five matched controls) was performed using the Clinical Practice Research Datalink from 1989 to 2012.

RESULTS: 28 980 CRC cases and 137 077 controls were identified. Oral antibiotic use was associated with CRC risk, but effects differed by anatomical location. Antibiotic use increased the risk of colon cancer in a dose-dependent fashion (ptrend <0.001). The risk was observed after minimal use, and was greatest in the proximal colon and with antibiotics with anti-anaerobic activity. In contrast, an inverse association was detected between antibiotic use and rectal cancers (ptrend=0.003), particularly with length of antibiotic exposure >60 days (adjusted OR (aOR), 0.85, 95% CI 0.79 to 0.93) as compared with no antibiotic exposure. Penicillins, particularly ampicillin/amoxicillin increased the risk of colon cancer (aOR=1.09 (1.05 to 1.13)), whereas tetracyclines reduced the risk of rectal cancer (aOR=0.90 (0.84 to 0.97)). Significant interactions were detected between antibiotic use and tumour location (colon vs rectum, pinteraction<0.001; proximal colon versus distal colon, pinteraction=0.019). The antibiotic-cancer association was found for antibiotic exposure occurring >10 years before diagnosis (aOR=1.17 (1.06 to 1.31)).

CONCLUSION: Oral antibiotic use is associated with an increased risk of colon cancer but a reduced risk of rectal cancer. This effect heterogeneity may suggest differences in gut microbiota and carcinogenesis mechanisms along the lower intestinal tract.},
}

@article {pmid31427404,
year = {2019},
author = {Misselwitz, B and Butter, M and Verbeke, K and Fox, MR},
title = {Update on lactose malabsorption and intolerance: pathogenesis, diagnosis and clinical management.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2019-318404},
pmid = {31427404},
issn = {1468-3288},
abstract = {Lactose is the main source of calories in milk, an essential nutriedigestion, patients with visceral hypersensitivity nt in infancy and a key part of the diet in populations that maintain the ability to digest this disaccharide in adulthood. Lactase deficiency (LD) is the failure to express the enzyme that hydrolyses lactose into galactose and glucose in the small intestine. The genetic mechanism of lactase persistence in adult Caucasians is mediated by a single C→T nucleotide polymorphism at the LCTbo -13'910 locus on chromosome-2. Lactose malabsorption (LM) refers to any cause of failure to digest and/or absorb lactose in the small intestine. This includes primary genetic and also secondary LD due to infection or other conditions that affect the mucosal integrity of the small bowel. Lactose intolerance (LI) is defined as the onset of abdominal symptoms such as abdominal pain, bloating and diarrhoea after lactose ingestion by an individual with LM. The likelihood of LI depends on the lactose dose, lactase expression and the intestinal microbiome. Independent of lactose digestion, patients with visceral hypersensitivity associated with anxiety or the Irritable Bowel Syndrome (IBS) are at increased risk of the condition. Diagnostic investigations available to diagnose LM and LI include genetic, endoscopic and physiological tests. The association between self-reported LI, objective findings and clinical outcome of dietary intervention is variable. Treatment of LI can include low-lactose diet, lactase supplementation and, potentially, colonic adaptation by prebiotics. The clinical outcome of these treatments is modest, because lactose is just one of a number of poorly absorbed carbohydrates which can cause symptoms by similar mechanisms.},
}

@article {pmid31426820,
year = {2019},
author = {Li, H and Li, H and Wang, J and Guo, L and Fan, H and Zheng, H and Yang, Z and Huang, X and Chu, M and Yang, F and He, Z and Li, N and Yang, J and Wu, Q and Shi, H and Liu, L},
title = {The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites.},
journal = {Virology journal},
volume = {16},
number = {1},
pages = {105},
doi = {10.1186/s12985-019-1211-z},
pmid = {31426820},
issn = {1743-422X},
support = {2016-I2M-1-014//CAMS Innovation Fund for Medical Sciences/ ; 2017-I2M-2-006//CAMS Innovation Fund for Medical Sciences/ ; 2018FB113//Yunnan Applied Basic Research Projects/ ; 2016HC009//Yunnan innovation team in China/ ; },
abstract = {BACKGROUND: The gut microbiome is closely associated with the health of the host; although the interaction between the bacterial microbiome and the whole virome has rarely been studied, it is likely of medical importance. Examination of the interactions between the gut bacterial microbiome and virome of rhesus monkey would significantly contribute to revealing the gut microbiome composition.

METHODS: Here, we conducted a metagenomic analysis of the gut microbiome of rhesus monkeys in a longitudinal cohort treated with an antibiotic cocktail, and we documented the interactions between the bacterial microbiome and virome. The depletion of viral populations was confirmed at the species level by real-time PCR. We also detected changes in the gut metabolome by GC-MS and LC-MS.

RESULTS: A majority of bacteria were depleted after treatment with antibiotics, and the Shannon diversity index decreased from 2.95 to 0.22. Furthermore, the abundance-based coverage estimator (ACE) decreased from 104.47 to 33.84, and the abundance of eukaryotic viruses also changed substantially. In the annotation, 6 families of DNA viruses and 1 bacteriophage family were present in the normal monkeys but absent after gut bacterial microbiome depletion. Intriguingly, we discovered that changes in the gut bacterial microbiome composition may promote changes in the gut virome composition, and tryptophan, arginine, and quinone may play roles in the interaction between the bacterial microbiome and virome.

CONCLUSION: Our results indicated that the clearly altered composition of the virome was correlated with depletion in the bacterial community and that metabolites produced by bacteria possibly play important roles in the interaction.},
}

@article {pmid31426641,
year = {2019},
author = {Zwinsová, B and Brychtová, V and Hrivňáková, M and Zdražilová-Dubská, L and Bencsiková, B and Šefr, R and Nenutil, R and Vídeňská, P and Budinská, E},
title = {Role of the Microbiome in the Formation and Development of Colorectal Cancer.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {32},
number = {4},
pages = {261-269},
doi = {10.14735/amko2019261},
pmid = {31426641},
issn = {1802-5307},
abstract = {BACKGROUND: The clinical, histopathological, and molecular characteristics of colorectal cancer vary considerably. Factors associated with the heterogeneity of this disease and with understanding the effects of heterogeneity on disease progression and response to therapy are critical for the better stratification of patients and the development of new therapeutic methods. Although studies have focused mainly on tumor molecular profiling, current molecular predictive and prognostic factors are relevant to specific groups of colorectal cancer patients and are mostly used to predict the applicability of targeted biological agents rather than to predict their benefits. Molecular profiling fails to capture aspects important for tumor growth and aggressiveness, including the tumor microenvironment. The gut microbiome, consisting of specific communities of all commensal, symbiotic, and pathogenic microorganisms, has been shown to have a significant impact on the development of many diseases, including Crohns disease, type II diabetes, and obesity. Recent studies have indicated that long-term dysbiosis of the intestinal microflora can influence the development and progression of colorectal cancer, as well as tumor aggressiveness and response to treatment.

CONCLUSION: This review article summarizes current knowledge of the gut microbiome in colorectal cancer, including the various mechanisms by which the gut microbiome affects the intestinal wall, thereby contributing to the development and progression of colorectal cancer. This work was supported by Ministry of Health of the Czech Republic (project AZV 16-31966A), project of Ministry of Education, Youth and Sports of the Czech Republic - NPU I - LO1413 a Ministry of Health of the Czech Republic - RVO (MMCI, 00209805). The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers. Submitted: 15. 4. 2019 Accepted: 17. 6. 2019.},
}

@article {pmid31426522,
year = {2019},
author = {Shelake, RM and Pramanik, D and Kim, JY},
title = {Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era.},
journal = {Microorganisms},
volume = {7},
number = {8},
pages = {},
doi = {10.3390/microorganisms7080269},
pmid = {31426522},
issn = {2076-2607},
support = {NRF 2017R1A4A1015515//National Research Foundation of Korea/ ; SSAC, Grant PJ01322601//Rural Development Administration (RDA), Republic of Korea/ ; },
abstract = {Plants and microbes are co-evolved and interact with each other in nature. Plant-associated microbes, often referred to as plant microbiota, are an integral part of plant life. Depending on the health effects on hosts, plant-microbe (PM) interactions are either beneficial or harmful. The role of microbiota in plant growth promotion (PGP) and protection against various stresses is well known. Recently, our knowledge of community composition of plant microbiome and significant driving factors have significantly improved. So, the use of plant microbiome is a reliable approach for a next green revolution and to meet the global food demand in sustainable and eco-friendly agriculture. An application of the multifaceted PM interactions needs the use of novel tools to know critical genetic and molecular aspects. Recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) tools are of great interest to explore PM interactions. A systematic understanding of the PM interactions will enable the application of GE tools to enhance the capacity of microbes or plants for agronomic trait improvement. This review focuses on applying GE techniques in plants or associated microbiota for discovering the fundamentals of the PM interactions, disease resistance, PGP activity, and future implications in agriculture.},
}

@article {pmid31426423,
year = {2019},
author = {Childs, CE and Calder, PC and Miles, EA},
title = {Diet and Immune Function.},
journal = {Nutrients},
volume = {11},
number = {8},
pages = {},
doi = {10.3390/nu11081933},
pmid = {31426423},
issn = {2072-6643},
abstract = {A well-functioning immune system is critical for survival. The immune system must be constantly alert, monitoring for signs of invasion or danger. Cells of the immune system must be able to distinguish self from non-self and furthermore discriminate between non-self molecules which are harmful (e.g., those from pathogens) and innocuous non-self molecules (e.g., from food). This Special Issue of Nutrients explores the relationship between diet and nutrients and immune function. In this preface, we outline the key functions of the immune system, and how it interacts with nutrients across the life course, highlighting the work included within this Special Issue. This includes the role of macronutrients, micronutrients, and the gut microbiome in mediating immunological effects. Nutritional modulation of the immune system has applications within the clinical setting, but can also have a role in healthy populations, acting to reduce or delay the onset of immune-mediated chronic diseases. Ongoing research in this field will ultimately lead to a better understanding of the role of diet and nutrients in immune function and will facilitate the use of bespoke nutrition to improve human health.},
}

@article {pmid31425715,
year = {2019},
author = {Vargas-Pellicer, P and Watrobska, C and Knowles, S and Schroeder, J and Banks-Leite, C},
title = {How should we store avian faecal samples for microbiota analyses? Comparing efficacy and cost-effectiveness.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {105689},
doi = {10.1016/j.mimet.2019.105689},
pmid = {31425715},
issn = {1872-8359},
abstract = {Analyses of bacterial DNA in faecal samples are becoming ever more common, yet we still do not know much about bird microbiomes. These challenges partly lie in the unique chemical nature of their faeces, and in the choice of sample storage method, which affects DNA preservation and the resulting microbiome composition. However, there is little information available on how best to preserve avian faeces for microbial analyses. This study evaluates five widely used methods for preserving nucleic acids and inferring microbiota profiles, for their relative efficacy, cost, and practicality. We tested the five methods (in-situ bead-beating with a TerraLyzer instrument, silica-bead desiccation, ethanol, refrigeration and RNAlater buffer) on 50 fresh faecal samples collected from captive House sparrows (Passer domesticus). In line with other studies, we find that different storage methods lead to distinct bacterial profiles. Storage method had a large effect on community composition and the relative abundance of dominant phyla such as Firmicutes and Proteobacteria, with the most significant changes observed for refrigerated samples. Furthermore, differences in the abundance of aerobic or facultatively aerobic taxa, particularly in refrigerated samples and those stored in ethanol, puts limits on comparisons of bacterial communities across different storage methods. Finally, the methods that did not include in-situ bead-beating did not recover comparable levels of microbiota to the samples that were immediately processed and preserved using a TerraLyzer device. However, this method is also less practical and more expensive under field work circumstances. Our study is the most comprehensive analysis to date on how storage conditions affect subsequent molecular assays applied to avian faeces and provides guidance on cost and practicality of methods under field conditions.},
}

@article {pmid31425594,
year = {2019},
author = {Mougeot, JC and Stevens, CB and Morton, DS and Brennan, MT and Mougeot, FB},
title = {Oral Microbiome and Cancer Therapy-Induced Oral Mucositis.},
journal = {Journal of the National Cancer Institute. Monographs},
volume = {2019},
number = {53},
pages = {},
doi = {10.1093/jncimonographs/lgz002},
pmid = {31425594},
issn = {1745-6614},
abstract = {Characterization of the role of oral microbiome in cancer therapy-induced oral mucositis (CTOM) is critical in preventing the clinically deleterious effects on patients' health that are associated with CTOM. Funding initiatives related to the National Institutes of Health human microbiome project have resulted in groundbreaking advancements in biology and medicine during the last decade. These advancements have shown that a human being is in fact a superorganism made of human cells and associated symbiotic or commensal microbiota. In this review, we describe the state of science as it relates to fundamental knowledge on oral microbiome and its role in CTOM. We also discuss how state-of-the-art technologies and systems biology tools may be used to help tackle the difficult challenges ahead to develop effective treatments or preventive therapies for oral mucositis. We make a clear distinction between disease processes pertaining to the oral microbiome, which includes opportunistic pathogens that may be defined as pathobionts, and those infectious disease processes initiated by exogenous pathogens. We also explored the extent to which knowledge from the gastrointestinal tract in disease and intestinal mucositis could help us better understand CTOM pathobiology. Finally, we propose a model in which the oral microbiome participates in the current five-step CTOM pathobiology model. With the advent of more sophisticated metagenomics technologies and methods of analysis, much hope lies ahead to implement an effective holistic approach to treat cancer patients affected by CTOM.},
}

@article {pmid31425534,
year = {2019},
author = {Lopatto, E and Choi, J and Colina, A and Ma, L and Howe, A and Hinsa-Leasure, S},
title = {Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0220770},
doi = {10.1371/journal.pone.0220770},
pmid = {31425534},
issn = {1932-6203},
abstract = {As agriculture industrializes, concentrated animal feeding operations (CAFOs) are becoming more common. Feces from CAFOs is often used as fertilizer on fields. However, little is known about the effects manure has on the soil microbiome, which is an important aspect of soil health and fertility. In addition, due to the subtherapeutic levels of antibiotics necessary to keep the animals healthy, CAFO manure has elevated levels of antibiotic resistant bacteria. Using 16s rRNA high-throughput sequencing and qPCR, this study sought to determine the impact of swine CAFO manure application on both the soil microbiome and abundance of select antibiotic resistance genes (ARGs) and mobile element genes (erm(B), erm(C), sul1, str(B), intI1, IncW repA) in agricultural soil over the fall and spring seasons. We found the manure community to be distinct from the soil community, with a majority of bacteria belonging to Bacteroidetes and Firmicutes. The soil samples had more diverse communities dominated by Acidobacteria, Actinobacteria, Proteobacteria, Verrucomicrobia, and unclassified bacteria. We observed significant differences in the soil microbiome between all time points, except between the spring samples. However, by tracking manure associated taxa, we found the addition of the manure microbiome to be a minor driver of the shift. Of the measured genes, manure application only significantly increased the abundance of erm(B) and erm(C) which remained elevated in the spring. These results suggest bacteria in the manure do not survive well in soil and that ARG dynamics in soil following manure application vary by resistance gene.},
}

@article {pmid31424606,
year = {2019},
author = {Matsuda, I and Chapman, CA and Clauss, M},
title = {Colobine forestomach anatomy and diet.},
journal = {Journal of morphology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jmor.21052},
pmid = {31424606},
issn = {1097-4687},
support = {//Humboldt Foundation/ ; 17941861 (#JPMJCR17A4)//Japan Science and Technology Agency Core Research for Evolutional Science and Technology/ ; //the Robert Koch Institute and an International Development Research Centre of Canada grant/ ; 19H03308 to IM//JSPS KAKENHI/ ; },
abstract = {Colobine monkeys have complex, multichambered, foregut-fermenting stomachs with either three ("tripartite") or four ("quadripartite," adding the praesaccus) chambers where a commensal microbiome digests plant cell walls and possibly detoxifies defensive plant chemicals. Although different potential functions for the praesaccus have been suggested, little evidence exists to support any of the proposed functions. To address the issue of the function of the praesaccus, we collated literature data on diet and compared tripartite and quadripartite species. Our results suggest that the praesaccus is an adaptation to a dietary niche with a particularly high reliance on leaves as fallback foods in colobine clades with quadripartite stomachs, and a higher reliance on fruits/seeds as foods at times of high fruit availability in clades with tripartite stomachs. This supports the notion that a large gut capacity is an important characteristic by which folivores survive on a high fiber diet, and that this large gut capacity may not be necessary for some species if there are seasonal peaks in fruit availability.},
}

@article {pmid31424444,
year = {2019},
author = {Ahmadi, S and Wang, S and Nagpal, R and Mainali, R and Soleimanian-Zad, S and Kitzman, D and Yadav, H},
title = {An In Vitro Batch-culture Model to Estimate the Effects of Interventional Regimens on Human Fecal Microbiota.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {149},
pages = {},
doi = {10.3791/59524},
pmid = {31424444},
issn = {1940-087X},
abstract = {The emerging role of the gut microbiome in several human diseases demands a breakthrough of new tools, techniques and technologies. Such improvements are needed to decipher the utilization of microbiome modulators for human health benefits. However, the large-scale screening and optimization of modulators to validate microbiome modulation and predict related health benefits may be practically difficult due to the need for large number of animals and/or human subjects. To this end, in vitro or ex vivo models can facilitate preliminary screening of microbiome modulators. Herein, it is optimized and demonstrated an ex vivo fecal microbiota culture system that can be used for examining the effects of various interventions of gut microbiome modulators including probiotics, prebiotics and other food ingredients, aside from nutraceuticals and drugs, on the diversity and composition of the human gut microbiota. Inulin, one of the most widely studied prebiotic compounds and microbiome modulators, is used as an example here to examine its effect on the healthy fecal microbiota composition and its metabolic activities, such as fecal pH and the fecal levels of organic acids including lactate and short-chain fatty acids (SCFAs). The protocol may be useful for studies aimed at estimating the effects of different interventions of modulators on fecal microbiota profiles and at predicting their health impacts.},
}

@article {pmid31423320,
year = {2019},
author = {Malik, F and Wickremesinghe, P and Saverimuttu, J},
title = {Case report and literature review of auto-brewery syndrome: probably an underdiagnosed medical condition.},
journal = {BMJ open gastroenterology},
volume = {6},
number = {1},
pages = {e000325},
doi = {10.1136/bmjgast-2019-000325},
pmid = {31423320},
issn = {2054-4774},
abstract = {Auto-brewery syndrome (ABS), also known as gut fermentation syndrome, is a rarely diagnosed medical condition in which the ingestion of carbohydrates results in endogenous alcohol production. The patient in this case report had fungal yeast forms in the upper small bowel and cecum, which likely fermented carbohydrates to alcohol. Treatment with antifungal agents allowed subsequent ingestion of carbohydrates without symptoms. He had been exposed to a prolonged course of antibiotics before this occurred. We postulate that the antibiotic altered his gut microbiome, allowing fungal growth. This diagnosis should be considered in any patient with positive manifestations of alcohol toxicity who denies alcohol ingestion. The aim of this case report was confirmation and treatment of ABS using a standardised carbohydrate challenge test followed by upper and lower endoscopy to obtain intestinal secretions to detect fungal growth. These fungi were speciated and antifungal sensitivity performed. This allowed the use of appropriate therapy. The patient was kept on a carbohydrate-free diet during the initial 6-week period of therapy. A single-strain probiotic for competitive inhibition of fungal growth was given to the patient. This probiotic was later replaced by a multistrain bacterial probiotic hoping that the multiple bacteria would inhibit fungi better than a single-strain. The beneficial role of probiotics in this condition has not been studied. The patient was rechallenged for endogenous alcohol production prior to reintroducing carbohydrates in his diet.},
}

@article {pmid31423298,
year = {2019},
author = {Casaburi, G and Duar, RM and Vance, DP and Mitchell, R and Contreras, L and Frese, SA and Smilowitz, JT and Underwood, MA},
title = {Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria.},
journal = {Antimicrobial resistance and infection control},
volume = {8},
number = {},
pages = {131},
doi = {10.1186/s13756-019-0583-6},
pmid = {31423298},
issn = {2047-2994},
abstract = {Background: Antibiotic-resistant (AR) bacteria are a global threat. AR bacteria can be acquired in early life and have long-term sequelae. Limiting the spread of antibiotic resistance without triggering the development of additional resistance mechanisms is of immense clinical value. Here, we show how the infant gut microbiome can be modified, resulting in a significant reduction of AR genes (ARGs) and the potentially pathogenic bacteria that harbor them.

Methods: The gut microbiome was characterized using shotgun metagenomics of fecal samples from two groups of healthy, term breastfed infants. One group was fed B. infantis EVC001 in addition to receiving lactation support (n = 29, EVC001-fed), while the other received lactation support alone (n = 31, controls). Coliforms were isolated from fecal samples and genome sequenced, as well as tested for minimal inhibitory concentrations against clinically relevant antibiotics.

Results: Infants fed B. infantis EVC001 exhibited a change to the gut microbiome, resulting in a 90% lower level of ARGs compared to controls. ARGs that differed significantly between groups were predicted to confer resistance to beta lactams, fluoroquinolones, or multiple drug classes, the majority of which belonged to Escherichia, Clostridium, and Staphylococcus. Minimal inhibitory concentration assays confirmed the resistance phenotypes among isolates with these genes. Notably, we found extended-spectrum beta lactamases among healthy, vaginally delivered breastfed infants who had never been exposed to antibiotics.

Conclusions: Colonization of the gut of breastfed infants by a single strain of B. longum subsp. infantis had a profound impact on the fecal metagenome, including a reduction in ARGs. This highlights the importance of developing novel approaches to limit the spread of these genes among clinically relevant bacteria. Future studies are needed to determine whether colonization with B. infantis EVC001 decreases the incidence of AR infections in breastfed infants.

Trial registration: This clinical trial was registered at ClinicalTrials.gov, NCT02457338.},
}

@article {pmid31422890,
year = {2019},
author = {Liu, H and Macdonald, CA and Cook, J and Anderson, IC and Singh, BK},
title = {An Ecological Loop: Host Microbiomes across Multitrophic Interactions.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2019.07.011},
pmid = {31422890},
issn = {1872-8383},
abstract = {Our knowledge of host-associated microorganisms and their role in host functions is rapidly evolving. Stress-affected plants assemble beneficial microbes in their rhizosphere to maximize survival and growth. Similarly, insects have gut microbiomes that extend their functional repertoire in fighting stress. A strong microbial linkage between soil, plants, and pollinators is emerging and this can influence pollination services and overall ecosystem health. Yet, the nature of microbial interactions between different ecosystem components remains poorly understood. Here we highlight the acquisition pathways of beneficial microbes and their functions in protecting hosts against stress. By adopting a new 'eco-holobiont' approach, which explicitly incorporates biotic feedbacks, we can significantly expand our ecological understanding and better develop sustainable environmental management.},
}

@article {pmid31422231,
year = {2019},
author = {Marzall-Pereira, M and Savi, DC and Bruscato, EC and Niebisch, CH and Paba, J and Aluízio, R and Ferreira-Maba, LS and Galli-Terasawa, LV and Glienke, C and Kava, V},
title = {Neopestalotiopsis species presenting wide dye destaining activity: report of a mycelium-associated laccase.},
journal = {Microbiological research},
volume = {228},
number = {},
pages = {126299},
doi = {10.1016/j.micres.2019.126299},
pmid = {31422231},
issn = {1618-0623},
abstract = {Wastewaters from textile dyeing industries represent an ecological concern, notably due to the known toxicity of azo dyes to the local microbiome and human health. Although physicochemical approaches are the rule for the treatment of industrial effluents, biological strategies such as enzyme-mediated dye destaining is a promising alternative. Notwithstanding a broad range of microorganisms, including fungi, algae, yeast, and bacteria, display dye-destaining properties, most of the literature has focused in ligninolytic fungi, leaving other classes of organisms somehow ignored. In this study, six endophytic strains isolated from Maytenus ilicifolia were studied for their destaining activity. The phylogenetic and morphological analysis allowed the identification of strain LGMF1504 as Neopestalotiopsis sp. LGMF1504 that decolorized several commercial dyes as the result of a mycelium-associated laccase. The enzyme expression was modulated by carbon and nitrogen content in the culture medium, it was weakly affected by the presence of aromatic compounds and metal ions while some common laccase mediators improved the destaining activity onto dye substrates. The best culture condition observed for laccase activity was a basic culture medium containing 5 g L-1 starch and 15 g L-1 ammonium tartrate. The laccase activity showed low substrate specificity and almost unaltered performance in a wide range of pH values and NaCl concentrations, suggesting the potential of Neopestalotiopsis sp. LGMF1504 for biodegradation approaches.},
}

@article {pmid31421883,
year = {2019},
author = {Castro, I and Alba, C and Aparicio, M and Arroyo, R and Jiménez, L and Fernández, L and Arias, R and Rodríguez, JM},
title = {Metataxonomic and immunological analysis of milk from ewes with or without a history of mastitis.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2019-16403},
pmid = {31421883},
issn = {1525-3198},
abstract = {Mastitis is a highly prevalent condition that has a great impact on milk production and animal welfare, and often requires substantial management efforts. For this reason, it is generally considered an important threat to the dairy industry. Many microbial, host, and environmental factors can protect against, predispose to, or influence the development of mastitis. The objective of this work was to characterize the milk microbiota of Manchega ewes, and to compare samples from animals with and without a history of mastitis. We analyzed milk samples from 36 ewes belonging to 2 different farms (18 ewes from each farm) using culture-dependent and culture-independent techniques. We also analyzed several immune compounds to investigate associations of mastitis with 3 main variables: farm; history of mastitis or no mastitis; and parity number. Both culture-dependent and culture-independent techniques showed that ewe milk harbored a site-specific complex microbiota and microbiome. Staphylococcus epidermidis was the main species driving the difference between farm A (where it was the dominant species) and B (where it was not). In contrast, samples from farm B were characterized by the presence of a wide spectrum of other coagulase-negative staphylococci. Some of these species have already been associated with subclinical intramammary infections in ruminants. Of the 10 immune compounds assayed in this study, 3 were related to a history of mastitis [IL-8, IFN-γ, and IFN-gamma-induced protein 10 (IP-10)]. Increases in IL-8 concentrations in milk seemed to be a feature of subclinical mastitis in sheep, and in this study, this immune factor was detected only in samples from ewes with some episodes of mastitis and from the group with the highest somatic cell count. We also observed a positive correlation between the samples with the highest somatic cell count and IFN-γ and IP-10 levels. Our results suggest that these 3 compounds could be used as biomarkers for the negative selection of mastitis-prone animals, particularly when somatic cell count is very high.},
}

@article {pmid31421775,
year = {2019},
author = {Keshri, J and Krouptiski, Y and Abu-Fani, L and Achmon, Y and Bauer, TS and Zarka, O and Maler, I and Pinto, R and Sela Saldinger, S},
title = {Dynamics of bacterial communities in alfalfa and mung bean sprouts during refrigerated conditions.},
journal = {Food microbiology},
volume = {84},
number = {},
pages = {103261},
doi = {10.1016/j.fm.2019.103261},
pmid = {31421775},
issn = {1095-9998},
abstract = {Sprouts are considered a healthy ready-to-eat food and has gained popularity in recent years. The objective of the present study was to determine the dynamics of sprouts' microbiome during cold storage to the end of their shelf-life at home. The microbiological quality of fresh alfalfa (Medicago sativa) and mung bean (Vigna radiata) sprouts from two commercial brands was tested and the number of APC ranges from 5.0 to 8.7 log CFU/g in alfalfa and 6.7 to 9.3 log CFU/g in mung bean sprouts. In the case of alfalfa, but not mung beans, there were differences in the mean numbers of APC between the two brands. The number of coliform bacteria ranges from 4.3 to 7.7 log CFU/g in alfalfa and 4.1 to 8.1 log CFU/g in mung bean sprouts. Four independent batches of sprouts were used for DNA preparation and were sampled immediately after purchase and once a week during subsequent storage in refrigerator until the end of their shelf-life. Microbial population of the sprouts was determined using next generation sequencing of 16S rRNA amplicons. Alfalfa sprouts were dominated by Pseudomonas throughout the storage time with relative abundance of >60% at 3 weeks. Fresh mung bean sprouts were dominated by both Pseudomonas and Pantoea, but Pantoea became the dominant taxa after 2 weeks of storage, with >46% of relative abundance. The bacterial communities associated with sprouts were largely dependent on the sprout type, and less dependent on the brand. The species richness and diversity declined during storage and the development of spoilage. Among the 160 genera identified on sprouts, 23 were reported to contain known spoilage-associated species and 30 genera comprise potential human pathogenic species. This study provides new insight into the microbiome dynamics of alfalfa and mung bean sprouts during cold storage.},
}

@article {pmid31421748,
year = {2019},
author = {Vahdatzadeh, M and Deveau, A and Splivallo, R},
title = {Are bacteria responsible for aroma deterioration upon storage of the black truffle Tuber aestivum: A microbiome and volatilome study.},
journal = {Food microbiology},
volume = {84},
number = {},
pages = {103251},
doi = {10.1016/j.fm.2019.103251},
pmid = {31421748},
issn = {1095-9998},
abstract = {Truffle fungi, luxurious food items with captivating aromas, are highly valued in the culinary world. However, truffles are perishable and their aroma undergoes deep changes upon storage. Additionally, truffle aroma might be partially derived from microbes. Hence, we investigated here the influence of storage on two factors, namely the volatile profile and bacterial community composition in the black truffle Tuber aestivum. The possible linkage among those factors was further explored. Our results demonstrate important changes in the volatile profiles of truffles over nine days of storage at room temperature. In the same time frame, dominant bacterial classes characteristic of fresh truffles (α-Proteobacteria, β-Proteobacteria, and Sphingobacteria classes) were gradually replaced by food spoilage bacteria (γ-Proteobacteria and Bacilli classes). Freshness and spoilage volatile markers (i.e. dimethyl sulfide (DMS), butan-2-one, 2- and, 2- and 3-methylbutan-1-ol, and 2-phenylethan-1-ol) were identified. Lastly, network analysis showed correlations between those markers and specific bacterial classes typical of fresh and spoiled truffles. Overall, our results demonstrate the profound effect of storage on the aroma and bacterial community composition of truffles and highlight how the gradual replacement of the commensal microbiome by spoilage microbes mirrors shifts in aroma profile and the possible loss of fresh truffle flavor.},
}

@article {pmid31421123,
year = {2019},
author = {Komesu, YM and Dinwiddie, DL and Richter, HE and Lukacz, ES and Sung, VW and Siddiqui, NY and Zyczynski, HM and Ridgeway, B and Rogers, RG and Arya, LA and Mazloomdoost, D and Levy, J and Carper, B and Gantz, MG and , },
title = {Drelationship Between Vaginal and Urinary Microbiomes.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2019.08.011},
pmid = {31421123},
issn = {1097-6868},
abstract = {BACKGROUND: Although the vaginal and urinary microbiomes have been increasingly well-characterized in health and disease, few have described the relationship between these neighboring environments. Elucidating this relationship has implications for understanding how manipulation of the vaginal microbiome may affect the urinary microbiome and treatment of common urinary conditions.

OBJECTIVE: To describe the relationship between urinary and vaginal microbiomes using 16S rRNA gene sequencing. We hypothesized that the composition of the urinary and vaginal microbiomes would be significantly associated, with similarities in predominant taxa.

STUDY DESIGN: This multicenter study collected vaginal swabs and catheterized urine samples from 186 women with mixed urinary incontinence (MUI) enrolled in a parent study and 84 similarly aged controls. Investigators decided a priori that if vaginal and/or urinary microbiomes differed between continent and incontinent women, the groups would be analyzed separately; if similar, samples from continent and incontinent women would be pooled and analyzed together. A central laboratory sequenced variable regions 1-3 (v1-3) and characterized bacteria to the genus level. Operational taxonomic unit (OTU) abundance was described for paired vaginal and urine samples. Pearson's correlation characterized the relationship between individual OTUs of paired samples. Canonical Correlation Analysis (CCA) evaluated the association between clinical variables (including MUI and control status) and vaginal and urinary OTUs, using the CCA function in the Vegan package (R version 3.5). Linear discriminant analysis effect size (LEfSe) was used to find taxa that discriminated between vaginal and urinary samples.

RESULTS: Urinary and vaginal samples were collected from 212 women [mean age 53 (±11 years)] and results from 197-paired samples were available for analysis. As OTUs in MUI and control samples were related in CCA and since taxa did not discriminate between MUI or controls in either vagina or urine, MUI and control samples were pooled for further analysis. CCA of vaginal and urinary samples indicated that that 60 of the 100 most abundant OTUs in the samples largely overlapped. Lactobacillus was the most abundant genus in both urine and vagina (contributing on average 53% to an individual's urine sample and 64% to an individual's vaginal sample) (Pearson correlation r=0.53). Though less abundant than Lactobacillus, other bacteria with high Pearson correlation coefficients also commonly found in vagina and urine included: Gardnerella (r=0.70), Prevotella (r=0.64), and Ureaplasma (r=0.50). LEfSe analysis identified Tepidomonas and Flavobacterium as bacteria that distinguished the urinary environment for both MUI and controls as these bacteria were absent in the vagina (Tepidimonas effect size 2.38, p<0.001, Flavobacterium effect size 2.15, p<0.001). Though Lactobacillus was the most abundant bacteria in both urine and vagina, it was more abundant in the vagina (LEfSe effect size 2.72, p<0.001).

CONCLUSIONS: Significant associations between vaginal and urinary microbiomes were demonstrated with Lactobacillus being predominant in both urine and vagina. Abundance of other bacteria also correlated highly between the vagina and urine. This inter-relatedness has implications for studying manipulation of the urogenital microbiome in treating conditions such as urgency urinary incontinence and urinary tract infections.},
}

@article {pmid31420885,
year = {2019},
author = {Ma, N and Zhang, J and Reiter, RJ and Ma, X},
title = {Melatonin mediates mucosal immune cells, microbial metabolism, and rhythm crosstalk: A therapeutic target to reduce intestinal inflammation.},
journal = {Medicinal research reviews},
volume = {},
number = {},
pages = {},
doi = {10.1002/med.21628},
pmid = {31420885},
issn = {1098-1128},
support = {B16044//111 Project/ ; 31722054//National Natural Science Foundation of China/ ; 31829004//National Natural Science Foundation of China/ ; xxjc201804//Beijing Nova Programme Interdisciplinary Cooperation Project/ ; 2017DKA001//College of Animal Science and Technology "Young Talents Program" at China Agricultural University/ ; 2017YFD0500501//National Key R&D Program of China/ ; 2018YFD0500601//National Key R&D Program of China/ ; },
abstract = {Nowadays, melatonin, previously considered only as a pharmaceutical product for rhythm regulation and sleep aiding, has shown its potential as a co-adjuvant treatment in intestinal diseases, however, its mechanism is still not very clear. A firm connection between melatonin at a physiologically relevant concentration and the gut microbiota and inflammation has recently established. Herein, we summarize their crosstalk and focus on four novelties. First, how melatonin is synthesized and degraded in the gut and exerts potentially diverse phenotypic effects through its diverse metabolites. Second, how melatonin mediates the activation and proliferation of intestinal mucosal immune cells with paracrine and autocrine properties. By modulating T/B cells, mast cells, macrophages and dendritic cells, melatonin immunomodulatory involved in regulating T-cell differentiation, intervening T/B cell interaction and attenuating the production of pro-inflammatory factors, achieving its antioxidant action via specific receptors. Third, how melatonin exerts antimicrobial action and modulates microbial components, such as lipopolysaccharide, amyloid-β peptides via nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) or signal transducers and activators of transcription (STAT1) pathway to modulate intestinal immune function in immune-pineal axis. The last, how melatonin mediates the effect of intestinal bacterial activity signals on the body rhythm system through the NF-κB pathway and influences the mucosal epithelium oscillation via clock gene expression. These processes are achieved at mitochondrial and nuclear levels to control the host immune cell development. Considering unclear mechanisms and undiscovered actions of melatonin in gut-microbiome-immune axis, it's time to reveal them and provide new insight for the outlook of melatonin as a potential therapeutic target in the treatment and management of intestinal diseases.},
}

@article {pmid31420693,
year = {2019},
author = {Carabeo-Pérez, A and Guerra-Rivera, G and Ramos-Leal, M and Klocke, M and Jiménez-Hernández, J},
title = {Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-019-10052-5},
pmid = {31420693},
issn = {1432-0614},
abstract = {Microbial metagenome analysis has proven its usefulness to investigate the microbiomes present in technical engineered ecosystems such as anaerobic digestion systems. The analysis of the total microbial genomic DNA allows the detailed determination of both the microbial community structure and its functionality. In addition, it enables to study the response of the microbiome to alterations in technical process parameters. Strategies of functional microbial networks to face abiotic stressors, e.g., resistance, resilience, and reorganization, can be evaluated with respect to overall process optimization. The objective of this paper is to review the main metagenomic tools used for effective studies on anaerobic digestion systems in monitoring the dynamic of the microbiomes, as well as the factors that have been identified so far as limiting the metagenomic studies in this ecosystems.},
}

@article {pmid31420578,
year = {2019},
author = {Smith, A and Pierre, JF and Makowski, L and Tolley, E and Lyn-Cook, B and Lu, L and Vidal, G and Starlard-Davenport, A},
title = {Distinct microbial communities that differ by race, stage, or breast-tumor subtype in breast tissues of non-Hispanic Black and non-Hispanic White women.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11940},
doi = {10.1038/s41598-019-48348-1},
pmid = {31420578},
issn = {2045-2322},
abstract = {Growing evidence highlights an association between an imbalance in the composition and abundance of bacteria in the breast tissue (referred as microbial dysbiosis) and breast cancer in women. However, studies on the breast tissue microbiome have not been conducted in non-Hispanic Black (NHB) women. We investigated normal and breast cancer tissue microbiota from NHB and non-Hispanic White (NHW) women to identify distinct microbial signatures by race, stage, or tumor subtype. Using 16S rRNA gene sequencing, we observed that phylum Proteobacteria was most abundant in normal (n = 8), normal adjacent to tumor (normal pairs, n = 11), and breast tumors from NHB and NHW women (n = 64), with fewer Firmicutes, Bacteroidetes, and Actinobacteria. Breast tissues from NHB women had a higher abundance of genus Ralstonia compared to NHW tumors, which could explain a portion of the breast cancer racial disparities. Analysis of tumor subtype revealed enrichment of family Streptococcaceae in TNBC. A higher abundance of genus Bosea (phylum Proteobacteria) increased with stage. This is the first study to identify racial differences in the breast tissue microbiota between NHB and NHW women. Further studies on the breast cancer microbiome are necessary to help us understand risk, underlying mechanisms, and identify potential microbial targets.},
}

@article {pmid31420356,
year = {2019},
author = {},
title = {Tumor Microbiome Composition Influences Pancreatic Cancer Survival.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-RW2019-128},
pmid = {31420356},
issn = {2159-8290},
abstract = {Distinct tumor microbiomes are associated with long- and short-term survival in patients with PDAC.},
}

@article {pmid31420345,
year = {2019},
author = {Lee, K and Walker, AR and Chakraborty, B and Kaspar, JR and Nascimento, MM and Burne, RA},
title = {Exploring novel probiotic mechanisms of Streptococcus A12 with functional genomics.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.01335-19},
pmid = {31420345},
issn = {1098-5336},
abstract = {Health-associated biofilms in the oral cavity are composed of a diverse group of microbial species that can foster an environment that is less favorable for the outgrowth of dental caries pathogens, like Streptococcus mutans. A novel oral bacterium, designated Streptococcus A12, was previously isolated from supragingival dental plaque of a caries-free individual, and was shown to interfere potently with the growth and virulence properties of S. mutans Here, we apply functional genomics to begin to identify molecular mechanisms used by A12 to antagonize, and to resist the antagonistic factors of, S. mutans. Using bioinformatics, genes that could encode factors that enhance the ability of A12 to compete with S. mutans were identified. Selected genes, designated as potential competitive factors (pcf), were deleted. Certain mutant derivatives showed a reduced capacity to compete with S. mutans compared to the parental strain. The A12 pcfO mutant lost the ability to inhibit comX-inducing peptide (XIP) signaling by S. mutans, while mutants in the pcfFEG locus were impaired in sensing of, and were more sensitive to, the lantibiotic nisin. Loss of PcfV, annotated as a colicin V biosynthetic protein, resulted in diminished antagonism of S. mutans. Collectively, the data provide new insights into the complexities and variety of factors that affect biofilm ecology and virulence. Continued exploration of the genomic and physiologic factors that distinguish commensals from truly beneficial members of the oral microbiota will lead to a better understanding of the microbiome and new approaches to promote oral health.Importance Advances in defining the composition of health-associated biofilms have highlighted the important role for beneficial species in maintaining health. Comparatively little, however, has been done to address the genomic and physiological basis underlying the probiotic mechanisms of beneficial commensals. In this study, we explored the ability of a novel oral bacterial isolate, Streptococcus A12, to compete with the dental pathogen Streptococcus mutans using various gene products with diverse functions. A12 displayed enhanced competitiveness by: i) disrupting intercellular communication pathways of S. mutans, ii) sensing and resisting antimicrobial peptides, and iii) producing factors involved in the production of a putative antimicrobial compound. Research on the probiotic mechanisms employed by Streptococcus A12 is providing essential insights into how beneficial bacteria may help maintain oral health, which will aid in the development of biomarkers and therapeutics that can improve the practice of clinical dentistry.},
}

@article {pmid31420081,
year = {2019},
author = {Zhu, T and Liu, X and Kong, FQ and Duan, YY and Yee, AL and Kim, M and Galzote, C and Gilbert, JA and Quan, ZX},
title = {Age and Mothers: Potent Influences of Children's Skin Microbiota.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2019.05.018},
pmid = {31420081},
issn = {1523-1747},
abstract = {The evolution of a child's skin microbiome is associated with the development of the immune system and skin environment. As only few studies have analyzed the microbiota in young children, we investigated changes in the skin microbiota of children (158 subjects; ≤10 years old) and compared the microbiota structures between children and their mothers using 16S rRNA gene amplicon sequencing. Sample location and age were the primary factors determining a child's skin bacterial composition, which differed significantly among the face, ventral forearm, and calf. Relative abundances of Streptococcus and Granulicatella were negatively correlated with age, and the alpha diversity at all body sites examined increased during the first 10 years of life, especially on the face. The facial bacterial composition of 10-year-old children was strongly associated with delivery mode at birth. Among mother-child pairs (50 pairs), the relative abundances of most bacterial genera in children were more similar to those of their own mothers than those of unrelated women. The data indicated that age and site were significantly associated with microbial composition and that maternal factors determine the child's microbiome. Further research is needed to characterize the effects of maturation of the infant microbiome on health in adulthood.},
}

@article {pmid31420049,
year = {2019},
author = {Ryan, FJ},
title = {Application of machine learning techniques for creating urban microbial fingerprints.},
journal = {Biology direct},
volume = {14},
number = {1},
pages = {13},
doi = {10.1186/s13062-019-0245-x},
pmid = {31420049},
issn = {1745-6150},
abstract = {BACKGROUND: Research has found that human associated microbial communities play a role in homeostasis and the disruption of these communities may be important in an array of medical conditions. However outside of the human body many of these communities remain poorly studied. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is characterizing the microbiomes of urban environments with the aim to improve design of mass transit systems. As part of the CAMDA 2018 MetaSUB Forensics Challenge 311 city microbiome samples were provided to create urban microbial fingerprints, as well as a further 3 mystery datasets for validation.

RESULTS: MetaSUB samples were clustered using t-SNE in an unsupervised fashion to almost discrete groups, which upon inspection represented city of origin. Based on this clustering, geographically close metropolitan areas appear to display similar microbial profiles such as those of Auckland and Hamilton. Mystery unlabeled samples were provided part of the challenge. A random forest classifier built on the initial dataset of 311 samples was capable of correctly classifying 83.3% of the mystery samples to their city of origin. Random Forest analyses also identified features with the highest discriminatory power, ranking bacterial species such as Campylobacter jejuni and Staphylococcus argenteus as highly predictive of city of origin. The surface from which the sample was collected displayed little detectable impact on the microbial profiles in the data generated here. The proportion of reads classified per sample varied greatly and so de-novo assembly was applied to recover genomic fragments representing organisms not captured in reference databases.

CONCLUSIONS: Current methods can differentiate urban microbiome profiles from each other with relative ease. De-novo assembly indicated that the MetaSUB metagenomic data contains adequate depth to recover metagenomic assembled genomes and that current databases are not sufficient to fully characterize urban microbiomes. Profiles found here indicate there may be a relationship between geographical distance between areas and the urban microbiome composition although this will need further research. The impact of these different profiles on public health is currently unknown but the MetaSUB consortium is uniquely suited to evaluate these and provide a roadmap for the inclusion of urban microbiome information for city planning and public health policy.

REVIEWERS: This article was reviewed by Dimitar Vassilev, Eran Elhaik and Chengsheng Zhu.},
}

@article {pmid31419763,
year = {2019},
author = {Junkins, EN and Speck, M and Carter, DO},
title = {The microbiology, pH, and oxidation reduction potential of larval masses in decomposing carcasses on Oahu, Hawaii.},
journal = {Journal of forensic and legal medicine},
volume = {67},
number = {},
pages = {37-48},
doi = {10.1016/j.jflm.2019.08.001},
pmid = {31419763},
issn = {1878-7487},
abstract = {Previous studies have begun to characterize the microbial community dynamics of the skin, soil, gut, and oral cavities of decomposing remains. One area that has yet to be explored in great detail is the microbiome of the fly larval mass, the community of immature flies that plays a significant role in decomposition. The current study aimed to characterize the microbiology and chemistry of larval masses established on pig (Sus scrofa domesticus) carcasses and to determine if these characteristics have potential as temporal evidence. Carcasses (n = 3) were decomposed on the soil surface of a tropical habitat on Oahu, Hawaii, USA and sampled over three days at 74 h, 80 h, 98 h, 104 h, 122 h, and 128 h (∼85-142 Accumulated Degree Days) postmortem. Larval masses were analyzed via high-throughput 16S rRNA sequencing and in situ chemical measurements (pH, temperature, oxidation-reduction potential). A trend was observed that resulted in three distinct microbial communities (pre-98 h, 98 h, and post-98 h). The oxidation-reduction potential (Eh) of larval masses apparently regulated microbial community structure with the most negative Eh being associated with the least rich and diverse microbial communities. Overall, a significant interaction between time and taxa was observed, particularly with bacterial phyla Firmicutes and Proteobacteria. The current results provide new insight into the microbial community and chemical parameters of larval masses and indicate a temporal shift that could be further studied as a PMI estimator.},
}

@article {pmid31419428,
year = {2019},
author = {Cox, LM and Abou-El-Hassan, H and Maghzi, AH and Vincentini, J and Weiner, HL},
title = {The sex-specific interaction of the microbiome in neurodegenerative diseases.},
journal = {Brain research},
volume = {},
number = {},
pages = {146385},
doi = {10.1016/j.brainres.2019.146385},
pmid = {31419428},
issn = {1872-6240},
abstract = {Several neurologic diseases exhibit different prevalence and severity in males and females, highlighting the importance of understanding the influence of biologic sex and gender. Beyond host-intrinsic differences in neurologic development and homeostasis, evidence is now emerging that the microbiota is an important environmental factor that may account for differences between men and women in neurologic disease. The gut microbiota is composed of trillions of bacteria, archaea, viruses, and fungi, that can confer benefits to the host or promote disease. There is bidirectional communication between the intestinal microbiota and the brain that is mediated via immunologic, endocrine, and neural signaling pathways. While there is substantial interindividual variation within the microbiota, differences between males and females can be detected. In animal models, sex-specific microbiota differences can affect susceptibility to chronic diseases. In this review, we discuss the ways in which neurologic diseases may be regulated by the microbiota in a sex-specific manner.},
}

@article {pmid31419351,
year = {2019},
author = {Moreno-Arrones, OM and Serrano-Villar, S and Perez-Brocal, V and Saceda-Corralo, D and Morales-Raya, C and Rodrigues-Barata, R and Moya, A and Jaen-Olasolo, P and Vano-Galvan, S},
title = {Analysis of the gut microbiota in alopecia areata: identification of bacterial biomarkers.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.15885},
pmid = {31419351},
issn = {1468-3083},
abstract = {BACKGROUND: Alopecia areata is a T-cell-mediated autoimmune disease with an unknown etiopathogenesis. Gut microbiota has been revealed as a key modulator of systemic immunity.

OBJECTIVE: To determine if patients affected by alopecia universalis present differences in gut bacteria composition compared to healthy controls and investigate possible bacterial biomarkers of the disease.

METHODS: We conducted a cross-sectional study that involved 15 patients affected by alopecia universalis and 15 controls. Gut microbiome of the study subjects was analyzed by sequencing the 16SrRNA of stool samples. We searched for bacterial biomarkers of alopecia universalis using the linear discriminant analysis effect size (LEFse) tool.

RESULTS: In total, 30 study subjects (46.6% female; mean [SD] age, 40.1 [9.8] years) were enrolled. Neither alpha (Shannon diversity index 5.31 ± 0.43 vs. 5.03 ± 0.43, p 0.1) or beta diversity (ADONIS p value: 0.35) of gut microbiota showed statistically significant differences between cases and controls. In patients affected with alopecia, we found an enriched presence (LDA SCORE >2) of Holdemania filiformis, Erysipelotrichacea, Lachnospiraceae, Parabacteroides johnsonii, Clostridiales vadin BB60 group, Bacteroides eggerthii and Parabacteroides distasonis. A predictive model based on the number of bacterial counts of Parabacteroides distasonis and Clostridiales vadin BB60 group correctly predicted disease status in 80% of patients (AUC 0.804 (0.633 - 0.976), p 0.004).

CONCLUSION: Alopecia universalis does not seem to affect broadly gut microbiota structure. Bacterial biomarkers found associated with the disease (Holdemania filiformis, Erysipelotrichacea, Lachnospiraceae, Parabacteroides johnsonii, Eggerthellaceae, Clostridiales vadin BB60 group, Bacteroides eggerthii and Parabacteroides distasonis) should be further studied as they could be involved in its pathophysiology or be used as diagnostic tools. This article is protected by copyright. All rights reserved.},
}

@article {pmid31419350,
year = {2019},
author = {Krieger, Y and Horev, A and Wainstock, T and Sheiner, E and Walfisch, A},
title = {Meconium stained amniotic fluid as a protective factor against childhood dermatitis and skin rash related hospitalization in the offspring - a population based cohort analysis.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.15881},
pmid = {31419350},
issn = {1468-3083},
abstract = {BACKGROUND: Gut microbiome influences cutaneous diseases including atopic dermatitis. Possible impact of intrauterine exposure to meconium on the occurrence of dermatitis and skin rash was proposed.

OBJECTIVE: We investigated the possible influence of intrauterine exposure to meconium stained amniotic fluid (MSAF) on the occurrence of dermatitis and skin rash related hospitalizations throughout childhood.

METHODS: Singleton deliveries occurring between 1991-2014 at a single medical center were divided into two study groups based on presence or lack of MSAF during delivery. Population based cohort analysis, Kaplan-Meier survival analysis, and Cox proportional hazards model were used to study the association between MSAF and cutaneous morbidity related hospitalizations.

RESULTS: A lower rate of the total dermatitis or skin eruption related hospitalization was documented in the MSAF exposed group; 0.78 per 1,000-person years (0.9%, n=312), as compared to 0.98 per 1,000-person years in the unexposed group (1.0%, n=1992) with a hazard ratio of 0.86 (95%CI 0.76-0.96, p=0.011). The survival curve showed lower cumulative hospitalization rate in the MSAF exposed group as compared to the unexposed group (log rank p=0.01). The Cox analysis, controlled for confounders, demonstrated MSAF exposure to be an independent protective factor for dermatitis and skin rash related hospitalizations during childhood (adjusted HR 0.878 (95%CI 0.779-0.990, p=0.034).

CONCLUSION: Fetal exposure to MSAF appears to be an independent protective factor for dermatitis and skin rash related hospitalizations in the offspring throughout childhood and adolescence. This article is protected by copyright. All rights reserved.},
}

@article {pmid31419122,
year = {2019},
author = {Kohne, M and Li, W and Zhu, C and Warncke, K},
title = {Deuterium Kinetic Isotope Effects Resolve Low-Temperature Substrate Radical Reaction Pathways and Steps in B12-Dependent Ethanolamine Ammonia-Lyase.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.9b00588},
pmid = {31419122},
issn = {1520-4995},
abstract = {The first-order reaction kinetics of the cryotrapped 1,1,2,2-2H4-aminoethanol substrate radical intermediate state in the adenosylcobalamin (B12)-dependent ethanolamine ammonia-lyase (EAL) from Salmonella enterica serovar Typhimurium are measured over the range of 203-225 K by using time-resolved, full-spectrum electron paramagnetic resonance spectroscopy. The studies target the fundamental understanding of the mechanism of EAL, the signature enzyme in ethanolamine utilization metabolism associated with microbiome homeostasis and disease conditions in the human gut. Incorporation of 2H into the hydrogen transfer that follows the substrate radical rearrangement step in the substrate radical decay reaction sequence leads to an observed 1H/2H isotope effect of approximately 2 that preserves, with high fidelity, the idiosyncratic piecewise pattern of rate constant versus inverse temperature dependence that was previously reported for the 1H-labeled substrate, including a monoexponential regime (T ≥ 220 K) and two distinct biexponential regimes (T = 203-219 K). In the global kinetic model, reaction at ≥220 K proceeds from the substrate radical macrostate, S• , and at 203-219 K along parallel pathways from the two sequential microstates, S1 • and S2 • , that are distinguished by different protein configurations. Decay from S• , or S1 • and S2 • , is rate-determined by radical rearrangement (1H) or by contributions from both radical rearrangement and hydrogen transfer (2H). Non-native direct decay to products from S1 • is a consequence of the free energy barrier to the native S1 • → S2 • protein configurational transition. At physiological temperatures, this is averted by the fast protein configurational dynamics that guide the S1 • → S2 • transition.},
}

@article {pmid31418980,
year = {2019},
author = {Zhao, R and Huang, R and Long, H and Li, Y and Gao, M and Lai, W},
title = {The dynamics of the oral microbiome and oral health among patients receiving clear aligner orthodontic treatment.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.13175},
pmid = {31418980},
issn = {1601-0825},
abstract = {OBJECTIVES: This 6-month prospective clinical study assessed the impacts of Invisalign appliances on the oral bacterial community and oral health of patients.

METHODS: Salivary samples were obtained from twenty-five adult patients receiving Invisalign aligner treatment before the treatment (Group B) and at a 6-month follow-up (Group P). The bacterial composition of each sample was determined using Illumina MiSeq sequencing of the bacterial 16S rRNA. Intra- and intergroup biodiversity was analyzed. Clinical periodontal parameters and daily oral hygiene habits were recorded.

RESULTS: Reduction of plaque, increased daily brushing frequency and decreased dessert intake were observed in Group P compared to in Group B. 1,853,952 valid reads were obtained from the 50 salivary samples, with 37,904 sequences per sample. No significant differences were detected in the intra- and intergroup biodiversity comparisons between the two groups. By clustering, 8885 OTUs were identified and categorized into six major phyla: Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, Actinobacteria and Candidate_division_TM7_norank. At the genus level, compared with Group B, Group P demonstrated significantly increased Bacillus abundance and decreased Prevotella abundance.

CONCLUSIONS: Our results suggested that the general biodiversity and salivary microbial community structure did not change significantly and that patients had increased beneficial oral hygiene habits and awareness during the first six months of Invisalign treatment. Hence, on the basis of this study, it appears that Invisalign aligner treatment did not induce deterioration of oral health nor significant biodiversity changes in oral bacterial communities, assuming that detailed oral hygiene instructions for both teeth and aligners were provided. This article is protected by copyright. All rights reserved.},
}

@article {pmid31418887,
year = {2019},
author = {Mogilevski, T and Burgell, R and Aziz, Q and Gibson, PR},
title = {Review article: the role of the autonomic nervous system in the pathogenesis and therapy of IBD.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.15433},
pmid = {31418887},
issn = {1365-2036},
abstract = {BACKGROUND: There is a growing body of evidence implicating a role for the brain-gut axis in the pathogenesis of inflammation in patients with IBD.

AIMS: To perform a narrative review of published literature regarding the association of the autonomic nervous system and intestinal inflammation and to describe the rationale for and emerging use of autonomic manipulation as a therapeutic agent METHODS: Current relevant literature was summarised and critically examined.

RESULTS: There is substantial pre-clinical and clinical evidence for a multifaceted anti-inflammatory effect of the vagus at both systemic and local intestinal levels. It acts via acetylcholine-mediated activation of α-7-acetylcholine receptors involving multiple cell types in innate and adaptive immunity and the enteric nervous system with subsequent protective influences on the intestinal barrier, inflammatory mechanisms and the microbiome. In patients with IBD, there is evidence for a sympatho-vagal imbalance, functional enteric neuronal depletion and hyporeactivity of the hypothalamic-pituitary-adrenal axis. Direct or transcutaneous vagal neuromodulation up-regulates the cholinergic anti-inflammatory pathway in pre-clinical and clinical models with down-regulation of systemic and local intestinal inflammation. This is supported by two small studies in Crohn's disease although remains to be investigated in ulcerative colitis.

CONCLUSIONS: Modulating the cholinergic anti-inflammatory pathway influences inflammation both systemically and at a local intestinal level. It represents a potentially underutilised anti-inflammatory therapeutic strategy. Given the likely pathogenic role of the autonomic nervous system in patients with IBD, vagal neuromodulation, an apparently safe and successful means of increasing vagal tone, warrants further clinical exploration.},
}

@article {pmid31418796,
year = {2019},
author = {Eisenhauer, L and Vahjen, W and Dadi, T and Kohn, B and Zentek, J},
title = {Effects of brewer's spent grain and carrot pomace on digestibility, fecal microbiota, and fecal and urinary metabolites in dogs fed low or high protein diets.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skz264},
pmid = {31418796},
issn = {1525-3163},
abstract = {Brewer's spent grain (BSG) and carrot pomace (CAP) were used as fiber sources in low or high protein diets in dogs. Ten adult Beagles were involved in five feeding periods of 19 days in a cross-over design. Experimental diets contained 7.5 % of total dietary fiber from BSG or CAP and 20 % or 40 % of crude protein in dry matter. A diet with 3.5 % total dietary fiber from both fiber sources and 20 % crude protein was used as reference. Fecal dry matter was 27 % higher for diets with BSG compared to CAP (P < 0.001). Apparent fecal digestibility of crude protein was 7-11 % higher in diets with 40 % protein concentration (P < 0.001), while apparent digestibility of crude fat was 2-3 % higher for diets with CAP (P < 0.001). CAP increased the apparent fecal digestibility of total dietary fiber, phosphorus and magnesium (p<0.001), while 40 % protein diets had a positive impact on total dietary fiber and sodium and a negative effect on magnesium apparent fecal digestibility (p<0.001). Inclusion of CAP increased fecal short chain fatty acids (P = 0.010), mainly acetate (P = 0.001). I-butyrate (P = 0.001), i-valerate (P = 0.002), biogenic amines (P < 0.001) and ammonium (P < 0.001) increased with higher dietary protein levels. Diet induced changes in the fecal microbiome were moderate. Relative abundance of Bifidobacteriales was higher for the low protein diets (P = 0.001). To conclude, BSG and CAP can be used as fiber sources in canine diets and are well tolerated even at higher inclusion rates, the effect on microbial protein fermentation seems to be limited compared to the dietary protein level.},
}

@article {pmid31418783,
year = {2019},
author = {Buccheri, MA and Salvo, E and Coci, M and Quero, GM and Zoccarato, L and Privitera, V and Rappazzo, G},
title = {Investigating microbial indicators of anthropogenic marine pollution by 16S and 18S High Throughput Sequencing (HTS) library analysis.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnz179},
pmid = {31418783},
issn = {1574-6968},
abstract = {High Throughput Sequencing technologies are providing unprecedented inventories of microbial communities in aquatic samples, offering an invaluable tool to estimate the impact of anthropogenic pressure on marine communities. In this case study, the Mediterranean touristic site of Aci Castello (Italy) was investigated by High Throughput Sequencing of 16S and 18S rRNA genes. The sampling area falls within a Marine Protected Area and, notwithstanding, features an untreated urban wastewater discharge. Seawater samples were collected close to the wastewater output (COL) and at a second station about 400 m further off (PAN), before and after a summer increase in population. Prokaryotic communities clustered according to stations, rather than to seasons. While PAN showed a typical, not impacted, marine microbial composition, COL was consistently enriched in Epsilonproteobacteria and Firmicutes. Protist communities showed a peculiar clustering, as COL at springtime stood-alone and was dominated by Ciliophora, while the other samples were enriched in Dinophyta. Analysis of alternative, detectable by High Throughput Sequencing, microbial indicators, including both faecal- and sewage associated, allowed uncovering the different sources of pollution in coastal and anthropogenically-impacted marine ecosystems, underpinning the relevance of High Throughput Sequencing -based screening as rapid and precise method for water quality management.},
}

@article {pmid31418624,
year = {2019},
author = {Jones, NP},
title = {Immunosuppression in the Management of Presumed Non-infective Uveitis; Are We Sure What We are Treating? Notes on the Antimicrobial Properties of the Systemic Immunosuppressants.},
journal = {Ocular immunology and inflammation},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/09273948.2019.1643030},
pmid = {31418624},
issn = {1744-5078},
abstract = {Purpose: To describe the antimicrobial effects of immunosuppressants used for presumed autoimmune uveitis, and to discuss the potential importance of these effects in the context of increasing knowledge of the human microbiomes and their influence on inflammation. Methods: Literature review Review of evidence: All immunosuppressants have intrinsic antimicrobial effects; these vary considerably between drugs, and include antibacterial, antiviral and antifungal action. Immunosuppression is known to affect the composition of the gut microbiome, and alterations in microbiome composition are known to affect inflammations including uveitis. Conclusions: Oral immunosuppressants are assumed to act on presumed autoimmune uveitis by downregulation of, or other interference with, an aberrant immune response. However, their antimicrobial properties are usually forgotten, and in the context of increasing knowledge of the involvement of microbes in the initiation of, and also potentially the perpetuation of, tissue inflammation, these effects may prove to be a fundamental part of their action.},
}

@article {pmid31418488,
year = {2019},
author = {Ramayo-Caldas, Y and Zingaretti, L and Popova, M and Estellé, J and Bernard, A and Pons, N and Bellot, P and Mach, N and Rau, A and Roume, H and Perez-Enciso, M and Faverdin, P and Edouard, N and Ehrlich, D and Morgavi, DP and Renand, G},
title = {Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows.},
journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie},
volume = {},
number = {},
pages = {},
doi = {10.1111/jbg.12427},
pmid = {31418488},
issn = {1439-0388},
support = {//APIS-GENE/ ; },
abstract = {Mitigation of greenhouse gas emissions is relevant for reducing the environmental impact of ruminant production. In this study, the rumen microbiome from Holstein cows was characterized through a combination of 16S rRNA gene and shotgun metagenomic sequencing. Methane production (CH4) and dry matter intake (DMI) were individually measured over 4-6 weeks to calculate the CH4 yield (CH4 y = CH4 /DMI) per cow. We implemented a combination of clustering, multivariate and mixed model analyses to identify a set of operational taxonomic unit (OTU) jointly associated with CH4 y and the structure of ruminal microbial communities. Three ruminotype clusters (R1, R2 and R3) were identified, and R2 was associated with higher CH4 y. The taxonomic composition on R2 had lower abundance of Succinivibrionaceae and Methanosphaera, and higher abundance of Ruminococcaceae, Christensenellaceae and Lachnospiraceae. Metagenomic data confirmed the lower abundance of Succinivibrionaceae and Methanosphaera in R2 and identified genera (Fibrobacter and unclassified Bacteroidales) not highlighted by metataxonomic analysis. In addition, the functional metagenomic analysis revealed that samples classified in cluster R2 were overrepresented by genes coding for KEGG modules associated with methanogenesis, including a significant relative abundance of the methyl-coenzyme M reductase enzyme. Based on the cluster assignment, we applied a sparse partial least-squares discriminant analysis at the taxonomic and functional levels. In addition, we implemented a sPLS regression model using the phenotypic variation of CH4 y. By combining these two approaches, we identified 86 discriminant bacterial OTUs, notably including families linked to CH4 emission such as Succinivibrionaceae, Ruminococcaceae, Christensenellaceae, Lachnospiraceae and Rikenellaceae. These selected OTUs explained 24% of the CH4 y phenotypic variance, whereas the host genome contribution was ~14%. In summary, we identified rumen microbial biomarkers associated with the methane production of dairy cows; these biomarkers could be used for targeted methane-reduction selection programmes in the dairy cattle industry provided they are heritable.},
}

@article {pmid31418238,
year = {2019},
author = {Yang, XX and Zhang, L and Huang, XQ and Wu, WX and Zhou, XQ and DU, L and Li, HZ and Liu, Y},
title = {[Difference of the microbial community structure in the rhizosphere of soybean and oilseed rape based on high-throughput pyrosequencing analysis.].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {30},
number = {7},
pages = {2345-2351},
doi = {10.13287/j.1001-9332.201907.028},
pmid = {31418238},
issn = {1001-9332},
abstract = {Clubroot, caused by the soil-borne obligate pathogen Plasmodiophora brassicae, is one of the most severe disease in cruciferous crops. Previous studies showed that when oilseed rape was planted after soybean (namely soybean-oilseed rotation), the incidence and severity of clubroot of oilseed rape could be significantly reduced, compared with that with oilseed rape-oilseed rape conti-nuous cropping. Therefore, the soybean-oilseed rape rotation is a good way to suppress clubroot of oilseed rape. In this study, we compared the rhizosphere microbiome of soybean and oilseed rape rhizosphere soil collected from the field by 16S rRNA (for identification of prokaryotes) and the internal transcribed spacer (ITS) (for identification of fungi) sequencing. The results showed that both soybean and oilseed rape rhizosphere soils had Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Ascomycota, Zygomycota, Basidiomycota and Chytridiomycota. Many microbial genera (e.g., Flavobacterium, Sphingomonas, Bacillus, Streptomyces, Pseudomonas, Trichoderma and Coniothyrium) with activities of biological control and plant growth promotion were more abundant in soybean rhizosphere soil than in the oilseed rape rhizosphere soil. The abundance of plant pathogenic bacteria and fungi was higher in the oilseed rape rhizosphere soil than in the soybean rhizosphere soil. Moreover, the soybean rhizosphere soil was enriched with Rhizobium, Bradyrhizobium (both for nitrogen fixation), and arbuscular mycorrhizal fungus (Glomus). These results indicated that soybean rhizosphere soil could promote the growth and proliferation of beneficial microorga-nisms, but inhibit that of plant pathogens. Our results provide evidence for explanation of the effectiveness of soybean-oilseed rape rotation to control clubroot of oilseed rape and provide potential bio-control resources for clubroot prevention.},
}

@article {pmid31417554,
year = {2019},
author = {Allen, JM and Jaggers, RM and Solden, LM and Loman, BR and Davies, RH and Mackos, AR and Ladaika, CA and Berg, BM and Chichlowski, M and Bailey, MT},
title = {Dietary Oligosaccharides Attenuate Stress-Induced Disruptions in Immune Reactivity and Microbial B-Vitamin Metabolism.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {1774},
doi = {10.3389/fimmu.2019.01774},
pmid = {31417554},
issn = {1664-3224},
abstract = {Background: Exposure to stressful stimuli dysregulates inflammatory processes and alters the gut microbiota. Prebiotics, including long-chain fermentable fibers and milk oligosaccharides, have the potential to limit inflammation through modulation of the gut microbiota. To determine whether prebiotics attenuate stress-induced inflammation and microbiota perturbations, mice were fed either a control diet or a diet supplemented with galactooligosaccharides, polydextrose and sialyllactose (GOS+PDX+SL) or sialyllactose (SL) for 2 weeks prior to and during a 6-day exposure to a social disruption stressor. Spleens were collected for immunoreactivity assays. Colon contents were examined for stressor- and diet- induced changes in the gut microbiome and metabolome through 16S rRNA gene sequencing, shotgun metagenomic sequencing and UPLC-MS/MS. Results: Stress increased circulating IL-6 and enhanced splenocyte immunoreactivity to an ex vivo LPS challenge. Diets containing GOS+PDX+SL or SL alone attenuated these responses. Stress exposure resulted in large changes to the gut metabolome, including robust shifts in amino acids, peptides, nucleotides/nucleosides, tryptophan metabolites, and B vitamins. Multiple B vitamins were inversely associated with IL-6 and were augmented in mice fed either GOS+PDX+SL or SL diets. Stressed mice exhibited distinct microbial communities with lower abundances of Lactobacillus spp. and higher abundances of Bacteroides spp. Diet supplementation with GOS+PDX+SL, but not SL alone, orthogonally altered the microbiome and enhanced the growth of Bifidobacterium spp. Metagenome-assembled genomes (MAGs) from mice fed the GOS+PDX+SL diet unveiled genes in a Bifidobacterium MAG for de novo B vitamin synthesis. B vitamers directly attenuated the stressor-induced exacerbation of cytokine production in LPS-stimulated splenocytes. Conclusions: Overall, these data indicate that colonic metabolites, including B vitamins, are responsive to psychosocial stress. Dietary prebiotics reestablish colonic B vitamins and limit stress-induced inflammation.},
}

@article {pmid31417531,
year = {2019},
author = {Conteville, LC and Oliveira-Ferreira, J and Vicente, ACP},
title = {Gut Microbiome Biomarkers and Functional Diversity Within an Amazonian Semi-Nomadic Hunter-Gatherer Group.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1743},
doi = {10.3389/fmicb.2019.01743},
pmid = {31417531},
issn = {1664-302X},
abstract = {Human groups that still maintain traditional modes of subsistence (hunter-gatherers and rural agriculturalists) represent human groups non-impacted by urban-industrialized lifestyles, and therefore their gut microbiome provides the basis for understanding the human microbiome evolution and its association with human health and disease. The Yanomami is the largest semi-nomadic hunter-gatherer group of the Americas, exploring different niches of the Amazon rainforest in Brazil and Venezuela. Here, based on shotgun metagenomic data, we characterized the gut microbiome of the Yanomami from Brazil and compared taxonomically and functionally with the Yanomami from Venezuela, with other traditional groups from the Amazon and an urban-industrialized group. Taxonomic biomarkers were identified to each South American traditional group studied, including each Yanomami group. Broader levels of functional categories poorly discriminated the traditional and urban-industrialized groups, but the stratification of these categories revealed clear segregation of these groups. The Yanomami/Brazil gut microbiome presented unique functional features, such as a higher abundance of gene families involved in regulation/cell signaling, motility/chemotaxis, and virulence, contrasting with the gut microbiomes from the Yanomami/Venezuela and the other groups. Our study revealed biomarkers, and taxonomic and functional features that distinguished the gut microbiome of Yanomami/Brazil and Yanomami/Venezuela individuals, despite their shared lifestyle, culture, and genetic background. These differences may be a reflection of the environmental and seasonal diversity of the niches they explore. Overall, their microbiome profiles are shared with South American and African traditional groups, probably due to their lifestyle. The unique features identified within the Yanomami highlight the bias imposed by underrepresented sampling, and factors such as variations over space and time (seasonality) that impact, mainly, the hunter-gatherers.},
}

@article {pmid31417524,
year = {2019},
author = {Abbondio, M and Palomba, A and Tanca, A and Fraumene, C and Pagnozzi, D and Serra, M and Marongiu, F and Laconi, E and Uzzau, S},
title = {Fecal Metaproteomic Analysis Reveals Unique Changes of the Gut Microbiome Functions After Consumption of Sourdough Carasau Bread.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1733},
doi = {10.3389/fmicb.2019.01733},
pmid = {31417524},
issn = {1664-302X},
abstract = {Sourdough-leavened bread (SB) is acknowledged for its great variety of valuable effects on consumer's metabolism and health, including a low glycemic index and a reduced content of the possible carcinogen acrylamide. Here, we aimed to investigate how these effects influence the gut microbiota composition and functions. Therefore, we subjected rats to a diet supplemented with SB, baker's yeast leavened bread (BB), or unsupplemented diet (chow), and, after 4 weeks of treatment, their gut microbiota was analyzed using a metaproteogenomic approach. As a result, diet supplementation with SB led to a reduction of specific members of the intestinal microbiota previously associated to low protein diets, namely Alistipes and Mucispirillum, or known as intestinal pathobionts, i.e., Mycoplasma. Concerning functions, asparaginases expressed by Bacteroides were observed as more abundant in SB-fed rats, leading to hypothesize that in their colonic microbiota the enzyme substrate, asparagine, was available in higher amounts than in BB- and chow-fed rats. Another group of protein families, expressed by Clostridium, was detected as more abundant in animal fed SB-supplemented diet. Of these, manganese catalase, small acid-soluble proteins (SASP), Ser/Thr kinase PrkA, and V-ATPase proteolipid subunit have been all reported to take part in Clostridium sporulation, strongly suggesting that the diet supplementation with SB might promote environmental conditions inducing metabolic dormancy of Clostridium spp. within the gut microbiota. In conclusion, our data describe the effects of SB consumption on the intestinal microbiota taxonomy and functions in rats. Moreover, our results suggest that a metaproteogenomic approach can provide evidence of the interplay between metabolites deriving from bread digestion and microbial metabolism.},
}

@article {pmid31417502,
year = {2019},
author = {Bravo, M and Combes, T and Martinez, FO and Cerrato, R and Rey, J and Garcia-Jimenez, W and Fernandez-Llario, P and Risco, D and Gutierrez-Merino, J},
title = {Lactobacilli Isolated From Wild Boar (Sus scrofa) Antagonize Mycobacterium bovis Bacille Calmette-Guerin (BCG) in a Species-Dependent Manner.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1663},
doi = {10.3389/fmicb.2019.01663},
pmid = {31417502},
issn = {1664-302X},
abstract = {Background: Wildlife poses a significant burden for the complete eradication of bovine tuberculosis (bTB). In particular, wild boar (Sus scrofa) is one of the most important reservoirs of Mycobacterium bovis, the causal agent of bTB. Wild boar can display from mild TB lesions, usually found in head lymph nodes, to generalized TB lesions distributed in different anatomical regions; but rarely clinical signs, which complicates the diagnosis of Mycobacterium bovis infection and bTB control. Among the possibilities for this variability in lesion distribution is the influence of the host-beneficial commensal-primed immune barrier. In this respect, beneficial microbes may delay bTB dissemination as a consequence of an antagonistic competition for nutrients and phagocytes. In order to explore this possibility, we have tested whether typical commensals such as lactobacilli have the capacity to reduce the survival rate of the surrogate M. bovis strain Bacillus Calmette-Guerin (BCG); and to modulate its phagocyte intake. Results: Three Lactobacillus species, L. casei, L. plantarum, and L. salivarius, isolated from wild boar feces displayed a pH-dependent inhibitory activity against BCG and influenced its intake by porcine blood phagocytes in a species-dependent manner. All lactobacilli showed a very significant bactericidal effect against BCG at low pH, but only isolates of L. plantarum and L. casei displayed such antimycobacterial activity at neutral pH. The genomes of these isolates revealed the presence of two-peptide bacteriocins whose precursor genes up-regulate in the presence of BCG cells. Furthermore, L. plantarum reduced significantly the BCG phagocytic intake, whereas L. casei had the opposite effect. L. salivarius had no significant influence on the phagocytic response to BCG. Conclusions: Our in vitro results show that lactobacilli isolated from wild boar antagonize BCG as a consequence of their antimycobacterial activity and a competitive phagocytic response. These findings suggest that commensal bacteria could play a beneficial role in influencing the outcome of bTB dissemination. Further work with lactobacilli as a potential competitive pressure to control bTB will need to take into account the complex nature of the commensal microbiome, the specific immunity of the wild boar and the in vivo infection context with pathogenic strains of M. bovis.},
}

@article {pmid31417492,
year = {2019},
author = {Sudo, N},
title = {Biogenic Amines: Signals Between Commensal Microbiota and Gut Physiology.},
journal = {Frontiers in endocrinology},
volume = {10},
number = {},
pages = {504},
doi = {10.3389/fendo.2019.00504},
pmid = {31417492},
issn = {1664-2392},
abstract = {There is increasing interest in the interactions among the gut microbiota, gut, and brain, which is often referred to as the "microbiota-gut-brain" axis. Biogenic amines including dopamine, norepinephrine, serotonin, and histamines are all generated by commensal gut microorganisms and are suggested to play roles as signaling molecules mediating the function of the "microbiota-gut-brain" axis. In addition, such amines generated in the gut have attracted attention in terms of possible clues into the etiologies of depression, anxiety, and even psychosis. This review covers the latest research related to the potential role of microbe-derived amines such as catecholamine, serotonin, histamine, as well as other trace amines, in modulating not only gut physiology but also brain function of the host. Further attention in this field can offer not only insight into expanding the fundamental roles and impacts of the human microbiome, but also further offer new therapeutic strategies for psychological disorders based on regulating the balance of resident bacteria.},
}

@article {pmid31417479,
year = {2019},
author = {Lacorte, E and Gervasi, G and Bacigalupo, I and Vanacore, N and Raucci, U and Parisi, P},
title = {A Systematic Review of the Microbiome in Children With Neurodevelopmental Disorders.},
journal = {Frontiers in neurology},
volume = {10},
number = {},
pages = {727},
doi = {10.3389/fneur.2019.00727},
pmid = {31417479},
issn = {1664-2295},
abstract = {Background and Purpose: A relationship between gut microbiome and central nervous system (CNS), have been suggested. The human microbiome may have an influence on brain's development, thus implying that dysbiosis may contribute in the etiology and progression of some neurological/neuropsychiatric disorders. The objective of this systematic review was to identify evidence on the characterization and potential distinctive traits of the microbiome of children with neurodevelopmental disorders, as compared to healthy children. Methods: The review was performed following the methodology described in the Cochrane handbook for systematic reviews, and was reported based on the PRISMA statement for reporting systematic reviews and meta-analyses. All literature published up to April 2019 was retrieved searching the databases PubMed, ISI Web of Science and the Cochrane Database of Systematic Reviews. Only observational studies, published in English and reporting data on the characterization of the microbiome in humans aged 0-18 years with a neurodevelopmental disorder were included. Neurodevelopmental disorders were categorized according to the definition included in the Diagnostic and Statistical Manual of Mental Disorders, version 5 (DSM-5). Results: Bibliographic searches yielded 9,237 records. One study was identified through other data sources. A total of 16 studies were selected based on their relevance and pertinence to the topic of the review, and were then applied the predefined inclusion and exclusion criteria. A total of 10 case-control studies met the inclusion criteria, and were thus included in the qualitative analysis and applied the NOS score. Two studies reported data on the gut microbiome of children with ADHD, while 8 reported data on either the gut (n = 6) or the oral microbiome (n = 2) of children with ASD. Conclusions: All the 10 studies included in this review showed a high heterogeneity in terms of sample size, gender, clinical issues, and type of controls. This high heterogeneity, along with the small sample size of the included studies, strongly limited the external validity of results. The quality assessment performed using the NOS score showed an overall low to moderate methodological quality of the included studies. To better clarify the potential role of microbiome in patients with neurodevelopmental disorders, further high-quality observational (specifically cohort) studies are needed.},
}

@article {pmid31417197,
year = {2019},
author = {Douglas, AE},
title = {Simple animal models for microbiome research.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41579-019-0242-1},
pmid = {31417197},
issn = {1740-1534},
abstract = {The health and fitness of animals, including humans, are influenced by the presence and composition of resident microbial communities. The development of rational microbial therapies to alleviate chronic immunological, metabolic and neurobiological diseases requires an understanding of the processes underlying microbial community assembly and the mechanisms by which microorganisms influence host traits. For fundamental discovery, simple animal models (that is, lower vertebrate and invertebrate species with low diversity microbiomes) are more cost-effective and time-efficient than mammal models, especially for complex experimental designs and sophisticated genetic screens. Recent research on these simple models demonstrates how microbiome composition is shaped by the interplay between host controls, mediated largely via immune effectors, inter-microorganism competition, and neutral processes of passive dispersal and ecological drift. Parallel research on microbiome-dependent host traits has identified how specific metabolites and proteins released from microorganisms can shape host immune responsiveness, ameliorate metabolic dysfunction and influence behavioural traits. In this Review, the opportunity for microbiome research on the traditional biomedical models zebrafish, Drosophila melanogaster and Caenorhabditis elegans, which command superb research resources and tools, is discussed. Other systems, for example, hydra, squid and the honeybee, are valuable alternative models to address specific questions.},
}

@article {pmid31417100,
year = {2019},
author = {Rosenthal, SB and Bush, KT and Nigam, SK},
title = {A Network of SLC and ABC Transporter and DME Genes Involved in Remote Sensing and Signaling in the Gut-Liver-Kidney Axis.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11879},
doi = {10.1038/s41598-019-47798-x},
pmid = {31417100},
issn = {2045-2322},
support = {U54-HD090259//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; DK109392//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
abstract = {Genes central to drug absorption, distribution, metabolism and elimination (ADME) also regulate numerous endogenous molecules. The Remote Sensing and Signaling Hypothesis argues that an ADME gene-centered network-including SLC and ABC "drug" transporters, "drug" metabolizing enzymes (DMEs), and regulatory genes-is essential for inter-organ communication via metabolites, signaling molecules, antioxidants, gut microbiome products, uremic solutes, and uremic toxins. By cross-tissue co-expression network analysis, the gut, liver, and kidney (GLK) formed highly connected tissue-specific clusters of SLC transporters, ABC transporters, and DMEs. SLC22, SLC25 and SLC35 families were network hubs, having more inter-organ and intra-organ connections than other families. Analysis of the GLK network revealed key physiological pathways (e.g., involving bile acids and uric acid). A search for additional genes interacting with the network identified HNF4α, HNF1α, and PXR. Knockout gene expression data confirmed ~60-70% of predictions of ADME gene regulation by these transcription factors. Using the GLK network and known ADME genes, we built a tentative gut-liver-kidney "remote sensing and signaling network" consisting of SLC and ABC transporters, as well as DMEs and regulatory proteins. Together with protein-protein interactions to prioritize likely functional connections, this network suggests how multi-specificity combines with oligo-specificity and mono-specificity to regulate homeostasis of numerous endogenous small molecules.},
}

@article {pmid31416886,
year = {2019},
author = {Shiels, PG and Buchanan, S and Selman, C and Stenvinkel, P},
title = {Allostatic load and ageing: linking the microbiome and nutrition with age-related health.},
journal = {Biochemical Society transactions},
volume = {},
number = {},
pages = {},
doi = {10.1042/BST20190110},
pmid = {31416886},
issn = {1470-8752},
abstract = {Ageing is a process of decline in physiological function and capability over time. It is an anticipated major burden on societal health-care costs due to an increasingly aged global population. Accelerated biological ageing is a feature of age-related morbidities, which also appear to share common underpinning features, including low-grade persistent inflammation, phosphate toxicity, diminished Nrf2 activity, a depleted metabolic capability, depressed mitochondrial biogenesis and a low diversity gut microbiome.Social, psychological, lifestyle and nutritional risk factors can all influence the trajectory of age-related health, as part of an individual's exposome, which reflects the interplay between the genome and the environment. This is manifest as allostatic (over)load reflecting the burden of lifestyle/disease at both a physiological and molecular level. In particular, age-related genomic methylation levels and inflammatory status reflect exposome differences. These features may be mediated by changes in microbial diversity. This can drive the generation of pro-inflammatory factors, such as TMAO, implicated in the 'diseasome' of ageing. Additionally, it can be influenced by the 'foodome', via nutritional differences affecting the availability of methyl donors required for maintenance of the epigenome and by the provision of nutritionally derived Nrf2 agonists. Both these factors influence age-related physiological resilience and health. This offers novel insights into possible interventions to improve health span, including a rage of emerging senotherapies and simple modifications of the nutritional and environmental exposome. In essence, the emerging strategy is to treat ageing processes common to the diseasome of ageing itself and thus preempt the development or progression of a range of age-related morbidities.},
}

@article {pmid31416862,
year = {2019},
author = {Chen, Y and Brook, TC and Alcon-Giner, C and Clarke, P and Hall, LJ and Hoyles, L},
title = {Draft Genome Sequence of Raoultella ornithinolytica P079F W, Isolated from the Feces of a Preterm Infant.},
journal = {Microbiology resource announcements},
volume = {8},
number = {33},
pages = {},
doi = {10.1128/MRA.00493-19},
pmid = {31416862},
issn = {2576-098X},
abstract = {Here, we describe the draft genome sequence of Raoultella ornithinolytica P079F W, isolated from the feces of an infant residing in a neonatal intensive care unit during an ongoing study to characterize the neonate gut microbiota. P079F W will be used in studies investigating the role of the microbiome in neonatal infections.},
}

@article {pmid31416774,
year = {2019},
author = {Rogers, GB and Taylor, SL and Hoffman, LR and Burr, LD},
title = {The impact of CFTR modulator therapies on CF airway microbiology.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2019.07.008},
pmid = {31416774},
issn = {1873-5010},
abstract = {Major historical advances in cystic fibrosis (CF) respiratory clinical care, including mechanical airway clearance and inhaled medications, have aimed to address the consequences of cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction. In contrast, CFTR modulator therapies instead target the underlying protein defect that leads to CF lung disease. The extent to which these therapies might reduce susceptibility to chronic lung infections remains to be seen. However, by improving airway clearance, reducing the requirement for antibiotics, and in some cases, through direct antimicrobial effects, CFTR modulators are likely to result in substantial changes in CF airway microbiology. These changes could contribute substantially to the clinical benefit associated with modulator therapies, as well as providing an important indicator of treatment efficacy and residual pathophysiology. Indeed, the widespread introduction of modulator therapies might require us to re-consider our models of CF airway microbiology.},
}

@article {pmid31416242,
year = {2019},
author = {Hakimian, JK and Dong, TS and Barahona, JA and Lagishetty, V and Tiwari, S and Azani, D and Barrera, M and Lee, S and Severino, AL and Mittal, N and Cahill, CM and Jacobs, JP and Walwyn, WM},
title = {Dietary Supplementation with Omega-3 Polyunsaturated Fatty Acids Reduces Opioid-Seeking Behaviors and Alters the Gut Microbiome.},
journal = {Nutrients},
volume = {11},
number = {8},
pages = {},
doi = {10.3390/nu11081900},
pmid = {31416242},
issn = {2072-6643},
support = {DA00010/DA/NIDA NIH HHS/United States ; VA CDAII IK2CX001717//Health Services Research and Development/ ; NA//Shirley and Stefan Hatos Foundation/ ; },
abstract = {Opioids are highly addictive substances with a relapse rate of over 90%. While preclinical models of chronic opioid exposure exist for studying opioid dependence, none recapitulate the relapses observed in human opioid addiction. The mechanisms associated with opioid dependence, the accompanying withdrawal symptoms, and the relapses that are often observed months or years after opioid dependence are poorly understood. Therefore, we developed a novel model of chronic opioid exposure whereby the level of administration is self-directed with periods of behavior acquisition, maintenance, and then extinction alternating with reinstatement. This profile arguably mirrors that seen in humans, with initial opioid use followed by alternating periods of abstinence and relapse. Recent evidence suggests that dietary interventions that reduce inflammation, including omega-3 polyunsaturated fatty acids (n-3 PUFAs), may reduce substance misuse liability. Using the self-directed intake model, we characterize the observed profile of opioid use and demonstrate that an n-3-PUFA-enriched diet ameliorates oxycodone-seeking behaviors in the absence of drug availability and reduces anxiety. Guided by the major role gut microbiota have on brain function, neuropathology, and anxiety, we profile the microbiome composition and the effects of chronic opioid exposure and n-3 PUFA supplementation. We demonstrate that the withdrawal of opioids led to a significant depletion in specific microbiota genera, whereas n-3 PUFA supplementation increased microbial richness, phylogenetic diversity, and evenness. Lastly, we examined the activation state of microglia in the striatum and found that n-3 PUFA supplementation reduced the basal activation state of microglia. These preclinical data suggest that a diet enriched in n-3 PUFAs could be used as a treatment to alleviate anxiety induced opioid-seeking behavior and relapse in human opioid addiction.},
}

@article {pmid31416201,
year = {2019},
author = {Cavuoto, KM and Galor, A and Banerjee, S},
title = {Anatomic Characterization of the Ocular Surface Microbiome in Children.},
journal = {Microorganisms},
volume = {7},
number = {8},
pages = {},
doi = {10.3390/microorganisms7080259},
pmid = {31416201},
issn = {2076-2607},
abstract = {The microbiome is important in the evolution of the immune system in children; however, information is lacking regarding the composition of the pediatric ocular microbiome and its surrounding structures. A prospective, cross-sectional study of the ocular microbiome was conducted in children <18 years old. Samples from the inferior conjunctival fornix of both eyes, eyelid margin, and periocular skin underwent DNA amplification and 16S sequencing using Illumina MiSeq 250. The microbiome was analyzed using Qiime. Statistical analysis was performed using a two-sided Student's t-test, diversity indices, and principal coordinate analysis. A total of 15 children were enrolled. The ocular surface microbiome was predominantly composed of Proteobacteria, whereas Bacteroidetes dominated the eyelid margin, and Firmicutes dominated the periocular skin. Despite these variations, no statistically significant compositional differences were found with Bray-Curtis analysis. The conjunctiva had the lowest Shannon diversity index with a value of 2.3, which was significantly lower than those of the eyelid margin (3.4, p = 0.01) and the periocular skin (3.5, p = 0.001). However, the evenness of the species using Faith's phylogenetic diversity index was similar at all sites. Overall, the ocular surface microbiome is dominated by Proteobacteria in children. The niche is similar to the surrounding structures in terms of composition, but has a lower number and relative abundance of species.},
}

@article {pmid31416125,
year = {2019},
author = {Sharma, M and Krammer, F and García-Sastre, A and Tripathi, S},
title = {Moving from Empirical to Rational Vaccine Design in the 'Omics' Era.},
journal = {Vaccines},
volume = {7},
number = {3},
pages = {},
doi = {10.3390/vaccines7030089},
pmid = {31416125},
issn = {2076-393X},
support = {IA/I/18/1/503613//DBT India Alliance/ ; },
abstract = {An ideal vaccine provides long lasting protection against a pathogen by eliciting a well-rounded immune response which engages both innate and adaptive immunity. However, we have a limited understanding of how components of innate immunity, antibody and cell-mediated adaptive immunity interact and function together at a systems level. With advances in high-throughput 'Omics' methodologies it has become possible to capture global changes in the host, at a cellular and molecular level, that are induced by vaccination and infection. Analysis of these datasets has shown the promise of discovering mechanisms behind vaccine mediated protection, immunological memory, adverse effects as well as development of more efficient antigens and adjuvants. In this review, we will discuss how systems vaccinology takes advantage of new technology platforms and big data analysis, to enable the rational development of better vaccines.},
}

@article {pmid31415828,
year = {2019},
author = {Sturød, K and Dhariwal, A and Dahle, UR and Vestrheim, DF and Petersen, FC},
title = {Impact of narrow spectrum Penicillin V on the oral and fecal resistome in a young child treated for otitis media.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2019.08.004},
pmid = {31415828},
issn = {2213-7173},
abstract = {BACKGROUND: Antibiotic overuse has led to a global emergence of resistant bacteria, and children are among the frequent users. Most studies with broad-spectrum antibiotics show severe impact on the resistome development of patients. Although narrow-spectrum antibiotics are believed to have less side-effects, their impact on the microbiome and resistome is mostly unknown. The aim of this study was to investigate the impact of the narrow-spectrum antibiotic phenoxymethylpenicillin (Penicillin V) on the microbiome and resistome of a child treated for acute otitis media (OM).

METHODS: Oral and fecal samples were collected from a one-year child before (day 0) and after (day 5 and 30) receiving Penicillin V against OM. Metagenomic sequencing data was analysed to determine taxonomic profiling, using Kraken and Bracken software, and resistance profiling, using KMA in combination with the ResFinder database.

RESULTS: In the oral samples, antimicrobial resistance genes (ARGs) belonging to four classes were identified at baseline. At day 5, the abundance of some ARGs was increased; some remained unchanged, while others disappeared. At day 30, most ARGs had returned to baseline levels, or lower. In the fecal samples, we observed seven ARGs at baseline and five at day 5. At day 30, the number increased to 21 ARGs from seven different classes.

CONCLUSIONS: Penicillin V had a remarkable impact on the fecal resistome indicating that even narrow-spectrum antibiotics may have important consequences in selecting for a more resistant microbiome.},
}

@article {pmid31415755,
year = {2019},
author = {Tierney, BT and Yang, Z and Luber, JM and Beaudin, M and Wibowo, MC and Baek, C and Mehlenbacher, E and Patel, CJ and Kostic, AD},
title = {The Landscape of Genetic Content in the Gut and Oral Human Microbiome.},
journal = {Cell host & microbe},
volume = {26},
number = {2},
pages = {283-295.e8},
doi = {10.1016/j.chom.2019.07.008},
pmid = {31415755},
issn = {1934-6069},
abstract = {Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.},
}

@article {pmid31415748,
year = {2019},
author = {Pandey, S and Maharana, J and Shukla, AK},
title = {The Gut Feeling: GPCRs Enlighten the Way.},
journal = {Cell host & microbe},
volume = {26},
number = {2},
pages = {160-162},
doi = {10.1016/j.chom.2019.07.018},
pmid = {31415748},
issn = {1934-6069},
abstract = {Host-microbiome interactions affect host physiology, but the underlying mechanisms are not well understood. Recent papers from Chen et al. (2019) and Colosimo et al. (2019) in this issue of Cell Host & Microbe demonstrate that metabolites produced by several members of the gut microbiota can efficiently activate host G protein-coupled receptors and influence host physiology.},
}

@article {pmid31415747,
year = {2019},
author = {Poole, AC},
title = {In the Grand Scheme of Things: Identifying Reproducible Microbial Signatures in Dietary Intervention Studies.},
journal = {Cell host & microbe},
volume = {26},
number = {2},
pages = {158-159},
doi = {10.1016/j.chom.2019.07.012},
pmid = {31415747},
issn = {1934-6069},
abstract = {Nutrition research is plagued by the reproducibility crisis. Reconciling nutrition studies involving microbiome data presents a modern challenge for researchers. In this issue of Cell Host & Microbe, Bisanz et al., 2019 demonstrate a comprehensive methodology for meta-analysis of microbiome sequence data from high-fat-diet intervention studies.},
}

@article {pmid31415231,
year = {2019},
author = {Ross, CM},
title = {Letter by Ross Regarding Article, "The Microbiome, Plasma Metabolites, Dietary Habits, and Cardiovascular Risk Unravelling Their Interplay".},
journal = {Circulation research},
volume = {125},
number = {5},
pages = {e27},
doi = {10.1161/CIRCRESAHA.119.315627},
pmid = {31415231},
issn = {1524-4571},
}

@article {pmid31415219,
year = {2019},
author = {Simon-Soro, A and Sohn, MB and McGinniss, JE and Imai, I and Brown, MC and Knecht, VR and Bailey, A and Clarke, EL and Cantu, E and Li, H and Bittinger, K and Diamond, JM and Christie, JD and Bushman, FD and Collman, RG},
title = {Upper Respiratory Dysbiosis with a Facultative-Dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant.},
journal = {Annals of the American Thoracic Society},
volume = {},
number = {},
pages = {},
doi = {10.1513/AnnalsATS.201904-299OC},
pmid = {31415219},
issn = {2325-6621},
abstract = {RATIONALE: The oropharyngeal microbiome is a primary source of lung microbiota and contributes to lower respiratory infection, and is also a driver of oral health.

OBJECTIVES: We sought to understand oropharyngeal microbial communities in advanced lung disease, community dynamics following lung transplantation, and ecological features of dysbiosis.

METHODS: Oropharyngeal wash (OW) samples were obtained from individuals with end-stage disease awaiting transplantation (n=22), and longitudinally from individuals at 6 weeks, 3 months and 6 months following transplantation (n=33), along with healthy controls (n=14). Bacterial 16S and fungal ITS rRNA regions were deep-sequenced, and bacterial community respiratory patterns were imputed from taxonomic composition.

RESULTS: Healthy subjects' oropharyngeal microbiomes showed a gradient of community types reflecting relative enrichment of strictly anaerobic, aerobic or facultative anaerobic bacteria. End-stage lung disease patients showed severe dysbiosis by both taxonomic composition and respiration phenotypes, with reduced richness and diversity, increased facultative and decreased aerobic bacteria, and absence of communities characterized by obligate aerobes. In patients at 6 weeks and 3 months post-transplant, richness and diversity were intermediate between healthy and pre-transplant subjects, with near-normal distribution of community types. However by six months post-transplant OW resembled the low-diversity facultative-dominated profile of pre-transplant subjects. Community ecotype correlated with Candida abundance.

CONCLUSIONS: End-stage lung disease is associated with marked upper respiratory tract dysbiosis involving both community structure and respiratory metabolism profiles of constituent bacteria. Dynamic changes occur after lung transplantation, with partial normalization early but later appearance of severe dysbiosis similar pre-transplant patients. Aberrant oropharyngeal communities may predispose to abnormal lung microbiota and infection risk both in advanced lung disease and after transplantation.},
}

@article {pmid31415146,
year = {2019},
author = {van de Wouw, M and Stilling, RM and Peterson, VL and Ryan, FJ and Hoban, AE and Shanahan, F and Clarke, G and Claesson, MJ and Dinan, TG and Cryan, JF and Schellekens, H},
title = {Host Microbiota Regulates Central Nervous System Serotonin Receptor 2C Editing in Rodents.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.9b00414},
pmid = {31415146},
issn = {1948-7193},
abstract = {Microbial colonization of the gastrointestinal tract plays a crucial role in the development of enteric and central nervous system functionality. The serotonergic system has been heavily implicated in microbiota-gut-brain axis signaling, particularly in proof-of-principle studies in germ-free (GF) animals. One aspect of the serotonergic system that has been left unexplored in relation to the microbiota is the unique ability of the serotonin receptor 2c (5-HT2C) to undergo post-transcriptional editing, resulting in decreased receptor functionality. We investigated whether GF mice, with absent microbiota from birth, have altered 5-HT2C receptor expression and editing in the brain and if colonization of the microbiota is able to restore editing patterns. Next, we investigated whether microbiota depletion later in life using a chronic antibiotic treatment in rats could affect 5-HT2C receptor editing patterns. We found that GF mice have an increased prevalence of the edited 5-HT2C receptor isoforms in the amygdala, hypothalamus, prefrontal cortex and striatum, which was partially normalized upon colonization post-weaning. However, no alterations were observed in the hypothalamus after microbiota depletion using an antibiotic treatment in adult rats. This suggests that alterations in the microbiome during development, but not later life, could influence 5-HT2C receptor editing patterns. Overall, these results demonstrate that the microbiota affects 5-HT2C receptor editing in the brain and may inform novel therapeutic strategies in conditions in which 5-HT2C receptor editing is altered, such as depression.},
}

@article {pmid31414161,
year = {2019},
author = {Lemoine, L and Verbeke, M and Bernaerts, K and Springael, D},
title = {Impact of the inoculum composition on the structure of the total and active community and its performance in identically operated anaerobic reactors.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-019-10041-8},
pmid = {31414161},
issn = {1432-0614},
support = {13/004 2012//Industrieel Onderzoeksfonds KU Leuven (IOF)/ ; P7/25//Federaal Wetenschapsbeleid/ ; },
abstract = {Anaerobic digestion (AD) is a biological process that is acquiring increasing attention for both solid waste and wastewater treatment, as well as for the production of valuable chemicals. Despite the importance of the inoculum, the relationship between inoculum community composition, reactor performance, and reactor community composition remains vague. To understand the impact of the starting community on the composition and functioning of the AD microbiome, we studied three sets of biologically replicated AD reactors inoculated with different communities, but operated identically, targeting both total and active community compositions. All reactors performed highly similar regarding volatile fatty acid and methane production. The community analyses showed reproducible total and active community compositions in replicate reactors, indicating that particularly deterministic factors shaped the AD community. Moreover, strong variation in community composition between the differently seeded reactors was observed, indicating the role of inoculum composition in community shaping. In all three reactor sets, especially species that were low abundant or even not detected in the inoculum contributed to the reactor communities, supporting the importance of functional redundancy and high diversity in inocula used for AD seeding. The careful start-up of the AD process using initially low organic loading rates likely contributed to the successful assembly of initial low-abundance/rare species into a new cooperative AD community in the reactors.},
}

@article {pmid31413830,
year = {2019},
author = {Hao, H and Zhu, L and Faden, HS},
title = {The milk-based diet of infancy and the gut microbiome.},
journal = {Gastroenterology report},
volume = {7},
number = {4},
pages = {246-249},
doi = {10.1093/gastro/goz031},
pmid = {31413830},
issn = {2052-0034},
abstract = {The composition and the diversity of the gut microbiome play a major role in the health and well-being of humans beginning at birth. The impact of the diet on the structure and the function of the gut microbiome is evident by the changes in the gut microbiome concurrent with the transition from human milk to solid food. Complex oligosaccharides contained in milk are essential nutrients for commensal microbes in the infant gut. The most important commensal bacterium in the infant gut, bifidobacterium, requires α1, 2 fucosylated oligosaccharides for growth. Because not all humans are able to secrete α1, 2 fucosylated oligosaccharides into milk, the gut microbiome of infants and bifidobacteria, in particular, vary considerably between 'secretors' and 'non-secretors'. A paucity of α1, 2 fucosylated oligosaccharides and bifidobacteria in the gut of infants may be associated with poor health.},
}

@article {pmid31413227,
year = {2019},
author = {Hara, S and Matsuda, M and Minamisawa, K},
title = {Growth Stage-dependent Bacterial Communities in Soybean Plant Tissues: Methylorubrum Transiently Dominated in the Flowering Stage of the Soybean Shoot.},
journal = {Microbes and environments},
volume = {},
number = {},
pages = {},
doi = {10.1264/jsme2.ME19067},
pmid = {31413227},
issn = {1347-4405},
abstract = {Plant-associated bacteria are critical for plant growth and health. However, the effects of plant growth stages on the bacterial community remain unclear. Analyses of the microbiome associated with field-grown soybean revealed a marked shift in the bacterial community during the growth stages. The relative abundance of Methylorubrum in the leaf and stem increased from 0.2% to more than 45%, but decreased to approximately 15%, with a peak at the flowering stage at which nitrogen metabolism changed in the soybean plant. These results suggest the significance of a time-series analysis for understanding the relationship between the microbial community and host plant physiology.},
}

@article {pmid31412927,
year = {2019},
author = {Pérez-Jaramillo, JE and de Hollander, M and Ramírez, CA and Mendes, R and Raaijmakers, JM and Carrión, VJ},
title = {Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {114},
doi = {10.1186/s40168-019-0727-1},
pmid = {31412927},
issn = {2049-2618},
support = {568-2012-15517825//Departamento Administrativo de Ciencia, Tecnología e Innovación/ ; Back to the Roots program//Stichting voor de Technische Wetenschappen/ ; Back to the Roots program//Stichting voor de Technische Wetenschappen/ ; 443112/2014-2//CNPq Brazil/ ; },
abstract = {BACKGROUND: Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood.

RESULTS: Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil.

CONCLUSIONS: Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.},
}

@article {pmid31412780,
year = {2019},
author = {Drengenes, C and Wiker, HG and Kalananthan, T and Nordeide, E and Eagan, TML and Nielsen, R},
title = {Laboratory contamination in airway microbiome studies.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {187},
doi = {10.1186/s12866-019-1560-1},
pmid = {31412780},
issn = {1471-2180},
support = {NA//Bergen Medisinske Forskningsstiftelse/ ; NA//GlaxoSmithKline (Norway) through the Norwegian Respiratory Society/ ; NA//the Endowment of timber merchant A. Delphin and wife through the Norwegian Medical Association/ ; NA//Helse Vest/ ; NA//Helse Vest/ ; NA//Helse Vest/ ; },
abstract = {BACKGROUND: The low bacterial load in samples acquired from the lungs, have made studies on the airway microbiome vulnerable to contamination from bacterial DNA introduced during sampling and laboratory processing. We have examined the impact of laboratory contamination on samples collected from the lower airways by protected (through a sterile catheter) bronchoscopy and explored various in silico approaches to dealing with the contamination post-sequencing. Our analyses included quantitative PCR and targeted amplicon sequencing of the bacterial 16S rRNA gene.

RESULTS: The mean bacterial load varied by sample type for the 23 study subjects (oral wash>1st fraction of protected bronchoalveolar lavage>protected specimen brush>2nd fraction of protected bronchoalveolar lavage; p < 0.001). By comparison to a dilution series of know bacterial composition and load, an estimated 10-50% of the bacterial community profiles for lower airway samples could be traced back to contaminating bacterial DNA introduced from the laboratory. We determined the main source of laboratory contaminants to be the DNA extraction kit (FastDNA Spin Kit). The removal of contaminants identified using tools within the Decontam R package appeared to provide a balance between keeping and removing taxa found in both negative controls and study samples.

CONCLUSIONS: The influence of laboratory contamination will vary across airway microbiome studies. By reporting estimates of contaminant levels and taking use of contaminant identification tools (e.g. the Decontam R package) based on statistical models that limit the subjectivity of the researcher, the accuracy of inter-study comparisons can be improved.},
}

@article {pmid31412603,
year = {2019},
author = {Khan, I and Ullah, N and Zha, L and Bai, Y and Khan, A and Zhao, T and Che, T and Zhang, C},
title = {Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome.},
journal = {Pathogens (Basel, Switzerland)},
volume = {8},
number = {3},
pages = {},
doi = {10.3390/pathogens8030126},
pmid = {31412603},
issn = {2076-0817},
support = {(No. BA2016036)//Jiangsu Science and Technology Major Project/ ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic complex inflammatory gut pathological condition, examples of which include Crohn's disease (CD) and ulcerative colitis (UC), which is associated with significant morbidity. Although the etiology of IBD is unknown, gut microbiota alteration (dysbiosis) is considered a novel factor involved in the pathogenesis of IBD. The gut microbiota acts as a metabolic organ and contributes to human health by performing various physiological functions; deviation in the gut flora composition is involved in various disease pathologies, including IBD. This review aims to summarize the current knowledge of gut microbiota alteration in IBD and how this contributes to intestinal inflammation, as well as explore the potential role of gut microbiota-based treatment approaches for the prevention and treatment of IBD. The current literature has clearly demonstrated a perturbation of the gut microbiota in IBD patients and mice colitis models, but a clear causal link of cause and effect has not yet been presented. In addition, gut microbiota-based therapeutic approaches have also shown good evidence of their effects in the amelioration of colitis in animal models (mice) and IBD patients, which indicates that gut flora might be a new promising therapeutic target for the treatment of IBD. However, insufficient data and confusing results from previous studies have led to a failure to define a core microbiome associated with IBD and the hidden mechanism of pathogenesis, which suggests that well-designed randomized control trials and mouse models are required for further research. In addition, a better understanding of this ecosystem will also determine the role of prebiotics and probiotics as therapeutic agents in the management of IBD.},
}

@article {pmid31412298,
year = {2019},
author = {Mahomoodally, MF and Aumeeruddy, MZ and Rengasamy, KRR and Roshan, S and Hammad, S and Pandohee, J and Hu, X and Zengin, G},
title = {Ginger and its Active Compounds in Cancer Therapy: From Folk uses to Nano-therapeutic Applications.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2019.08.009},
pmid = {31412298},
issn = {1096-3650},
abstract = {Ginger is a spice that is renowned for its characteristic aromatic fragrance and pungent taste, with documented healing properties. Field studies conducted in several Asian and African countries revealed that ginger is used traditionally in the management of cancer. The scientific community has probed into the biological validation of its extracts and isolated compounds including the gingerols, shogaols, zingiberene, and zingerone, through in-vitro and in-vivo studies. Nonetheless, an updated compilation of these data together with a deep mechanistic approach is yet to be provided. Accordingly, this review highlights the mechanisms and therapeutics of ginger and its bioactive compounds focused on a cancer context and these evidence are based on the (i) cytotoxic effect against cancer cell lines, (ii) enzyme inhibitory action, (iii) combination therapy with chemotherapeutic and phenolic compounds, (iv) possible links to the microbiome and (v) the use of nano-formulations of ginger bioactive compounds as a more effective drug delivery strategy in cancer therapy.},
}

@article {pmid31412243,
year = {2019},
author = {Huggins, MA and Sjaastad, FV and Pierson, M and Kucaba, TA and Swanson, W and Staley, C and Weingarden, AR and Jensen, IJ and Danahy, DB and Badovinac, VP and Jameson, SC and Vezys, V and Masopust, D and Khoruts, A and Griffith, TS and Hamilton, SE},
title = {Microbial Exposure Enhances Immunity to Pathogens Recognized by TLR2 but Increases Susceptibility to Cytokine Storm through TLR4 Sensitization.},
journal = {Cell reports},
volume = {28},
number = {7},
pages = {1729-1743.e5},
doi = {10.1016/j.celrep.2019.07.028},
pmid = {31412243},
issn = {2211-1247},
abstract = {Microbial exposures can define an individual's basal immune state. Cohousing specific pathogen-free (SPF) mice with pet store mice, which harbor numerous infectious microbes, results in global changes to the immune system, including increased circulating phagocytes and elevated inflammatory cytokines. How these differences in the basal immune state influence the acute response to systemic infection is unclear. Cohoused mice exhibit enhanced protection from virulent Listeria monocytogenes (LM) infection, but increased morbidity and mortality to polymicrobial sepsis. Cohoused mice have more TLR2+ and TLR4+ phagocytes, enhancing recognition of microbes through pattern-recognition receptors. However, the response to a TLR2 ligand is muted in cohoused mice, whereas the response to a TLR4 ligand is greatly amplified, suggesting a basis for the distinct response to Listeria monocytogenes and sepsis. Our data illustrate how microbial exposure can enhance the immune response to unrelated challenges but also increase the risk of immunopathology from a severe cytokine storm.},
}

@article {pmid31412070,
year = {2019},
author = {Arizza, V and Vecchioni, L and Caracappa, S and Sciurba, G and Berlinghieri, F and Gentile, A and Persichetti, MF and Arculeo, M and Alduina, R},
title = {New insights into the gut microbiome in loggerhead sea turtles Caretta caretta stranded on the Mediterranean coast.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0220329},
doi = {10.1371/journal.pone.0220329},
pmid = {31412070},
issn = {1932-6203},
abstract = {Caretta caretta is the most common sea turtle species in the Mediterranean Sea. The species is threatened by anthropomorphic activity that causes thousands of deaths and hundreds of strandings along the Mediterranean coast. Stranded turtles are often cared for in rehabilitation centres until they recover or die. The objective of this study was to characterize the gut microbiome of nine sea turtles stranded along the Sicilian coast of the Mediterranean Sea using high-throughput sequencing analysis targeting V3-V4 regions of the bacterial 16S rRNA gene. Stool samples were collected from eight specimens hosted in the recovery centre after a few days of hospitalization (under 7) and from one hosted for many weeks (78 days). To better explore the role of bacterial communities in loggerhead sea turtles, we compared our data with published fecal microbiomes from specimens stranded along the Tuscan and Ligurian coast. Our results highlight that, despite the different origin, size and health conditions of the animals, Firmicutes, Bacteroidetes and Proteobacteria constitute the main components of the microbiota. This study widens our knowledge on the gut microbiome of sea turtles and could be helpful for the set up of rehabilitation therapies of stranded animals after recovery in specialized centres.},
}

@article {pmid31412044,
year = {2019},
author = {Hyde, J and Gorham, C and Brackney, DE and Steven, B},
title = {Antibiotic resistant bacteria and commensal fungi are common and conserved in the mosquito microbiome.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0218907},
doi = {10.1371/journal.pone.0218907},
pmid = {31412044},
issn = {1932-6203},
abstract = {The emerging and increasing prevalence of bacterial antibiotic resistance is a significant public health challenge. To begin to tackle this problem, it will be critical to not only understand the origins of this resistance but also document environmental reservoirs of antibiotic resistance. In this study we investigated the possibility that both colony and field caught mosquitoes could harbor antibiotic resistant bacteria. Specifically, we characterized the antibiotic resistant bacterial populations from colony-reared Aedes aegypti larvae and adults and two field caught mosquito species Coquillettidia perturbans and Ochlerotatus canadensis. The cultured bacterial populations were dominated by isolates belonging to the class Gammaproteobacteria. Among the antibiotic resistant populations, we found bacteria resistant to carbenicillin, kanamycin, and tetracycline, including bacteria resistant to a cocktail of all three antibiotics in combination. The antibiotic resistant bacteria were numerically rare, at most 5% of total cell counts. Isolates were characterized by 16S rRNA gene sequencing, and clustering into Operational Taxonomic Units (OTUs; 99% sequence identity). 27 antibiotic resistant OTUs were identified, although members of an OTU did not always share the same resistance profile. This suggests the clustering was either not sensitive enough to distinguish different bacteria taxa or different antibiotic resistant sub-populations exist within an OTU. Finally, the antibiotic selection opened up a niche to culture mosquito-associated fungi, and 10 fungal OTUs (28S rRNA gene sequencing) were identified. Two fungal OTUs both classified to the class Microbotryomycetes were commonly identified in the field-caught mosquitoes. Thus, in this study we demonstrate that antibiotic resistant bacteria and certain fungi are common and conserved mosquito microbiome members. These observations highlight the potential of invertebrates to serve as vehicles for the spread of antibiotic resistance throughout the environment.},
}

@article {pmid31411526,
year = {2019},
author = {Peng, M and Tabashsum, Z and Patel, P and Bernhardt, C and Biswas, C and Meng, J and Biswas, D},
title = {Prevention of enteric bacterial infections and modulation of gut microbiota with conjugated linoleic acids producing Lactobacillus in mice.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-20},
doi = {10.1080/19490976.2019.1638724},
pmid = {31411526},
issn = {1949-0984},
abstract = {Probiotics are recognized for outcompeting pathogenic bacteria by competitive receptor-mediated colonization and secretion of functional metabolites which are antimicrobial against certain microbes as well as improving host's gut health and immunity. Recently, we have constructed a bioactive Lactobacillus casei (LC) strain, LC+mcra, by inserting mcra (myosin cross-reactive antigen) gene, which stimulates the conversion of conjugated linoleic acids. In this study, we evaluated the modulation of gut microbiome and protective roles of LC+mcra against pathogenic Salmonella enterica serovar Typhimurium (ST) and enterohemorrhagic E. coli (EHEC) infections in BALB/cJ mice. We observed that LC+mcra colonized efficiently in mice gut intestine and competitively reduced the infection with ST and EHEC in various locations of small and large intestine, specifically cecum, jejunum, and ileum (p < 0.05). Positive modulation of the cecal microbiota, for example, higher relative abundances of Firmicutes, lower relative abundances of Proteobacteria, and increased bacterial species diversity/richness, was detected in ST-challenged mice pretreated with LC+mcra based on 16S metagenomic sequencing. Cytokine gene expression analysis indicated that mice pretreated with LC+mcra associated with attenuated bacterial pathogen-induced gut inflammation. Furthermore, mice fed daily with LC+mcra for one week could protect themselves from the impairments caused by enteric infections with ST or EHEC. These impairments include weight loss, negative hematological changes, intestinal histological alterations, and potential death. This in vivo study suggests that daily consumption of novel conjugated linoleic acids over-producing probiotic effectively improves intestinal microbiota composition and prevents/combats foodborne enteric bacterial infections with pathogenic Salmonella and diarrheagenic E. coli.},
}

@article {pmid31411007,
year = {2019},
author = {Zhu, YX and Song, ZR and Song, YL and Zhao, DS and Hong, XY},
title = {The microbiota in spider mite faeces potentially reflects intestinal bacterial communities in the host.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.12716},
pmid = {31411007},
issn = {1744-7917},
abstract = {Microorganisms provide many physiological functions to herbivorous hosts. Spider mites (genus Tetranychus) are important agricultural pests throughout the world, however, the composition of spider mite microbial community, especially gut microbiome, remains unclear. Here, we investigated the bacterial community in five spider mite species and their associated faeces by deep sequencing of the 16S rRNA gene. The composition of the bacterial community was significantly different among the five prevalent spider mite species, and some bacterial symbionts showed host-species specificity. Moreover, the abundance of the bacterial community in spider mite faeces was significantly higher than that in the corresponding spider mite samples. However, Flavobacterium was detected in all samples, and represent a "core microbiome". Remarkably, the maternally inherited endosymbiont Wolbachia was detected in both spider mite and faeces. Overall, these results offer insight into the complex community of symbionts in spider mites, and give a new direction for future studies. This article is protected by copyright. All rights reserved.},
}

@article {pmid31410991,
year = {2019},
author = {Reza, MM and Finlay, BB and Pettersson, S},
title = {Gut microbes, ageing & organ function: a chameleon in modern biology?.},
journal = {EMBO molecular medicine},
volume = {},
number = {},
pages = {e9872},
doi = {10.15252/emmm.201809872},
pmid = {31410991},
issn = {1757-4684},
support = {//School of Biological Sciences, Nanyang Technological University (NTU), Singapore/ ; //Lee Kong Chian School of Medicine, NTU, Singapore/ ; //Ageing Research Institute for Society and Education (ARISE), NTU, Singapore/ ; //Singapore Centre for Environmental Life Sciences Engineering (SCELSE), NTU, Singapore/ ; //NUHS Centre for Healthy Ageing, Singapore CSIRO, Australia/ ; //Bruker, USA/ ; },
abstract = {All species, including humans, are cohabited by a myriad of microbial species, which massively influences body function in a diet-, exercise- and age-dependent manner. The microbiome composition differs between individuals, partly due to the polymorphic immune system, as well as the environment, making the microbe-host interplay unique in each one of us. Ageing is a gradual loss of function in part due to reduced repair mechanisms and accumulation of tissue damage through mechanisms largely unknown. Accumulating evidence suggests that our indigenous microbes, a known major regulator of human physiology, are also connected to regulate the ageing process through signalling pathways and metabolites though the biological mechanisms are unknown. At an ageing meeting in Singapore in 2018, investigators discussed the current understanding of microbe regulation and its impact on healthy ageing. This review summarizes the highlights from the meeting and conveys some of the new ideas that emerged around gut microbes and the biology of ageing. While highly speculative, an idea emerged in which gut microbes constantly respond and evolve to environmental cues, as part of an ageing process, thus serving as a second messenger to support and attenuate organ decline in a diet-, gender- and age-dependent manner.},
}

@article {pmid31410749,
year = {2019},
author = {Zhang, F and Wang, M and Yang, J and Xu, Q and Liang, C and Chen, B and Zhang, J and Yang, Y and Wang, H and Shang, Y and Wang, Y and Mu, X and Zhu, D and Zhang, C and Yao, M and Zhang, L},
title = {Response of gut microbiota in type 2 diabetes to hypoglycemic agents.},
journal = {Endocrine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12020-019-02041-5},
pmid = {31410749},
issn = {1559-0100},
abstract = {PURPOSE: Accumulated evidence has indicated that the gut microbiome affected the pharmacology of anti-diabetic agents, and their metabolic products induced by the agents transformed the structure of gastrointestinal microbiota in return. However, the studies around heredity, ethnicity, or living condition, referring to human microbiome were mostly represented by an occidental pattern partial and rare studies that focused on the effect of several first-line hypoglycemic agents on the gut flora in a single medical center. Therefore, we aimed to explore the interaction between gut microbiome and type 2 diabetes (T2D) or hypoglycemics in Chinese population.

METHODS: A total of 130 T2D patients with a specific hypoglycemic treatment and 50 healthy volunteers were enrolled in this study. Gut microbiome compositons were analyzed by 16S ribosomal RNA gene-based sequencing protocol.

RESULTS: Hypoglycemic agents contributed to the alteration of specific species in gut bacteria rather than its total diversity. Metformin increased the abundance of Spirochaete, Turicibacter, and Fusobacterium. Insulin also increased Fusobacterium, and α-glucosidase inhibitors (α-GIs) contributed to the plentitude of Bifidobacterium and Lactobacillus. Both metformin and insulin improved taurine and hypotaurine metabolism, and α-GI promoted several amino acid pathways. Although the community of gut microbiota with metformin and insulin showed similarity, significant differences were available in each diabetic group with hypoglycemia.

CONCLUSIONS: Gut microbiota is significantly associated with anti-diabetic agents. The gut microbiome and metabolism have shown respective characteristics in different T2D groups, which were also significantly different from the healthy group. This study provides some new insights for identification and exploration of the pathogenesis of T2D.},
}

@article {pmid31410046,
year = {2019},
author = {Ribaldone, DG and Pellicano, R and Actis, GC},
title = {Inflammation in gastrointestinal disorders: prevalent socioeconomic factors.},
journal = {Clinical and experimental gastroenterology},
volume = {12},
number = {},
pages = {321-329},
doi = {10.2147/CEG.S210844},
pmid = {31410046},
issn = {1178-7023},
abstract = {Western populations harbor a chronic inflammation pattern that lacks organ cardinal signs (edema, increased temperature, pain, and impaired function), releases increased levels of C-reactive protein, and often runs a creeping clinical course with generalized debilitating disease superimposed on system-specific involvement, mostly including nervous tissue (multiple sclerosis, Parkinson's syndromes), joints (arthritis), and skin (psoriasis). A finalistic interpretation may apply to the consideration of the gut as the source of inflammation. In fact, these kind of local events as well as the remote manifestations named above, could be conditioned by the microbiome, the huge cell population indwelling the gut which is under growing scrutiny. The role of the gut as a barrier organ justifies lingering submucosal inflammation as a patrolling activity to maintain bodily integrity; the microbiome, launching inflammogenic signals in response to abrupt diet changes, confers to gut inflammation a socioeconomic vector calling for hitherto unrecognized multi-disciplinary interventions.},
}

@article {pmid31409870,
year = {2019},
author = {Swe, PM and Zakrzewski, M and Waddell, R and Sriprakash, KS and Fischer, K},
title = {High-throughput metagenome analysis of the Sarcoptes scabiei internal microbiota and in-situ identification of intestinal Streptomyces sp.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11744},
doi = {10.1038/s41598-019-47892-0},
pmid = {31409870},
issn = {2045-2322},
support = {1098804//Department of Health | National Health and Medical Research Council (NHMRC)/ ; FT130101875//Centre of Excellence for Electromaterials Science, Australian Research Council (ARC Centre of Excellence for Electromaterials Science)/ ; },
abstract = {Multiple parasitic arthropods of medical importance depend on symbiotic bacteria. While the link between scabies and secondary bacterial infections causing post infective complications of Group A streptococcal and staphylococcal pyoderma is increasingly recognized, very little is known about the microbiota of Sarcoptes scabiei. Here we analyze adult female mite and egg metagenome datasets. The majority of adult mite bacterial reads matched with Enterobacteriaceae (phylum Proteobacteria), followed by Corynebacteriaceae (phylum Actinobacteria). Klebsiella was the most dominant genus (78%) and Corynebacterium constituted 9% of the assigned sequences. Scabies mite eggs had a more diverse microbial composition with sequences from Proteobacteria being the most dominant (75%), while Actinobacteria, Bacteroidetes and Firmicutes accounted for 23% of the egg microbiome sequences. DNA sequences of a potential endosymbiont, namely Streptomyces, were identified in the metagenome sequence data of both life stages. The presence of Streptomyces was confirmed by conventional PCR. Digital droplet PCR indicated higher Streptomyces numbers in adult mites compared to eggs. Streptomyces were localized histologically in the scabies mite gut and faecal pellets by Fluorescent In Situ Hybridization (FISH). Streptomyces may have essential symbiotic roles in the scabies parasite intestinal system requiring further investigation.},
}

@article {pmid31409863,
year = {2019},
author = {Pereira, EM and de Mattos, CS and Dos Santos, OC and Ferreira, DC and de Oliveira, TLR and Laport, MS and de Oliveira Ferreira, E and Dos Santos, KRN},
title = {Staphylococcus hominis subspecies can be identified by SDS-PAGE or MALDI-TOF MS profiles.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11736},
doi = {10.1038/s41598-019-48248-4},
pmid = {31409863},
issn = {2045-2322},
abstract = {Staphylococcus hominis is part of the normal human microbiome. Two subspecies, S. hominis hominis (Shh) and S. hominis novobiosepticus (Shn), have clinical significance. Forty-nine S. hominis isolates were analyzed by the MicroScan automated system, SDS-PAGE and MALDI-TOF methods, followed by partial sequencing of the 16S rDNA gene. The trehalose fermentation test, disk diffusion and broth microdilution tests were used to identify (novobiocin test) and access the susceptibility to oxacillin and vancomycin of isolates. The SCCmec elements and genomic diversity were evaluated by PCR and PFGE methods, respectively. Profiles of 28 (57%; 8 Shh and 20 Shn) isolates corroborated with the results found in all the applied methods of identification. The remaining 21 (43%) isolates were phenotypically identified as Shh by MicroScan; however, they were identified as Shn by SDS-PAGE and mass spectral, and confirmed by 16S rDNA sequencing. Among 41 isolates identified as Shn by the molecular and mass spectrometry methods, 19 (41%) were novobiocin-sensitive, and the trehalose test indicated 11 positive isolates, which are considered atypical phenotypic results for this subspecies. In addition, 92.7% of the isolates identified as Shn by these methods carried mecA gene, while only 12.5% of the Shh isolates were positive. Together, the results highlighted the SDS-PAGE and MALDI-TOF MS methods as promising tools for discriminating S. hominis subspecies.},
}

@article {pmid31409776,
year = {2019},
author = {Luck, H and Khan, S and Kim, JH and Copeland, JK and Revelo, XS and Tsai, S and Chakraborty, M and Cheng, K and Tao Chan, Y and Nøhr, MK and Clemente-Casares, X and Perry, MC and Ghazarian, M and Lei, H and Lin, YH and Coburn, B and Okrainec, A and Jackson, T and Poutanen, S and Gaisano, H and Allard, JP and Guttman, DS and Conner, ME and Winer, S and Winer, DA},
title = {Gut-associated IgA+ immune cells regulate obesity-related insulin resistance.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3650},
doi = {10.1038/s41467-019-11370-y},
pmid = {31409776},
issn = {2041-1723},
support = {119414//Gouvernement du Canada | Instituts de Recherche en Santé du Canada | CIHR Skin Research Training Centre (Skin Research Training Centre)/ ; 142708//Gouvernement du Canada | Instituts de Recherche en Santé du Canada | CIHR Skin Research Training Centre (Skin Research Training Centre)/ ; 148385//Gouvernement du Canada | Instituts de Recherche en Santé du Canada | CIHR Skin Research Training Centre (Skin Research Training Centre)/ ; OG-3-15-5014//Diabetes Canada (DC)/ ; },
abstract = {The intestinal immune system is emerging as an important contributor to obesity-related insulin resistance, but the role of intestinal B cells in this context is unclear. Here, we show that high fat diet (HFD) feeding alters intestinal IgA+ immune cells and that IgA is a critical immune regulator of glucose homeostasis. Obese mice have fewer IgA+ immune cells and less secretory IgA and IgA-promoting immune mediators. HFD-fed IgA-deficient mice have dysfunctional glucose metabolism, a phenotype that can be recapitulated by adoptive transfer of intestinal-associated pan-B cells. Mechanistically, IgA is a crucial link that controls intestinal and adipose tissue inflammation, intestinal permeability, microbial encroachment and the composition of the intestinal microbiome during HFD. Current glucose-lowering therapies, including metformin, affect intestinal-related IgA+ B cell populations in mice, while bariatric surgery regimen alters the level of fecal secretory IgA in humans. These findings identify intestinal IgA+ immune cells as mucosal mediators of whole-body glucose regulation in diet-induced metabolic disease.},
}

@article {pmid31409765,
year = {2019},
author = {Jang, HR and Park, HJ and Kang, D and Chung, H and Nam, MH and Lee, Y and Park, JH and Lee, HY},
title = {A protective mechanism of probiotic Lactobacillus against hepatic steatosis via reducing host intestinal fatty acid absorption.},
journal = {Experimental & molecular medicine},
volume = {51},
number = {8},
pages = {95},
doi = {10.1038/s12276-019-0293-4},
pmid = {31409765},
issn = {2092-6413},
support = {HI14C1135//Korea Health Industry Development Institute (KHIDI)/ ; NRF-2014M3A9D5A01073886//National Research Foundation of Korea (NRF)/ ; NRF-2017R1A2B4009936//National Research Foundation of Korea (NRF)/ ; NRF-2018M3A9F3056405//National Research Foundation of Korea (NRF)/ ; NRF-2018M3A9F3056405//National Research Foundation of Korea (NRF)/ ; },
abstract = {The gut microbiome has been known to contribute up to ~30% of the energy absorption of the host. Although various beneficial mechanisms of probiotics have been suggested for non-alcoholic fatty liver disease (NAFLD), whether and which probiotics impact the host's intestinal energy absorption have not yet been quantitatively studied. Here, we suggest a novel mechanism of probiotics against NAFLD, in which Lactobacillus rhamnosus GG, the most common probiotic, shares intestinal fatty acids and prevents the development of diet-induced hepatic steatosis. By using quantitative methods (radioactive tracers and LC-MS) under both in vitro and in vivo conditions, we found that bacteria and hosts competed for fatty acid absorption in the intestine, resulting in decreased weight gain, body fat mass, and hepatic lipid accumulation without differences in calorie intake and excretion in mice fed the probiotic bacteria.},
}

@article {pmid31409678,
year = {2019},
author = {Edwards, VL and Smith, SB and McComb, EJ and Tamarelle, J and Ma, B and Humphrys, MS and Gajer, P and Gwilliam, K and Schaefer, AM and Lai, SK and Terplan, M and Mark, KS and Brotman, RM and Forney, LJ and Bavoil, PM and Ravel, J},
title = {The Cervicovaginal Microbiota-Host Interaction Modulates Chlamydia trachomatis Infection.},
journal = {mBio},
volume = {10},
number = {4},
pages = {},
doi = {10.1128/mBio.01548-19},
pmid = {31409678},
issn = {2150-7511},
abstract = {The mechanism(s) by which Lactobacillus-dominated cervicovaginal microbiota provide a barrier to Chlamydia trachomatis infection remain(s) unknown. Here we evaluate the impact of different Lactobacillus spp. identified via culture-independent metataxonomic analysis of C. trachomatis-infected women on C. trachomatis infection in a three-dimensional (3D) cervical epithelium model. Lactobacillus spp. that specifically produce d(-) lactic acid were associated with long-term protection against C. trachomatis infection, consistent with reduced protection associated with Lactobacillus iners, which does not produce this isoform, and with decreased epithelial cell proliferation, consistent with the observed prolonged protective effect. Transcriptomic analysis revealed that epigenetic modifications involving histone deacetylase-controlled pathways are integral to the cross talk between host and microbiota. These results highlight a fundamental mechanism whereby the cervicovaginal microbiota modulates host functions to protect against C. trachomatis infection.IMPORTANCE The vaginal microbiota is believed to protect women against Chlamydia trachomatis, the etiologic agent of the most prevalent sexually transmitted infection (STI) in developed countries. The mechanism underlying this protection has remained elusive. Here, we reveal the comprehensive strategy by which the cervicovaginal microbiota modulates host functions to protect against chlamydial infection, thereby providing a novel conceptual mechanistic understanding. Major implications of this work are that (i) the impact of the vaginal microbiota on the epithelium should be considered in future studies of chlamydial infection and other STIs and (ii) a fundamental understanding of the cervicovaginal microbiota's role in protection against STIs may enable the development of novel microbiome-based therapeutic strategies to protect women from infection and improve vaginal and cervical health.},
}

@article {pmid31409661,
year = {2019},
author = {Small, CM and Currey, M and Beck, EA and Bassham, S and Cresko, WA},
title = {Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00331-19},
pmid = {31409661},
issn = {2379-5077},
abstract = {Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach that comprised tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Abundance estimates for rare operational taxonomic units (OTUs), however, showed much lower reproducibility. Gut microbiome composition was highly variable across fish-even among cohoused siblings-relative to technical replicates, but a subtle effect of host genotype (stickleback line) was nevertheless detected for some microbial taxa.IMPORTANCE Our findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major questions in host-microbe ecology and evolution, such as heritability of the microbiome. Our study design and insights should provide a useful example for others desiring to quantify microbiome variation at biological levels in the face of various technical factors in a variety of systems.},
}

@article {pmid31409660,
year = {2019},
author = {Zhang, S and Song, W and Wemheuer, B and Reveillaud, J and Webster, N and Thomas, T},
title = {Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00288-19},
pmid = {31409660},
issn = {2379-5077},
abstract = {Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names "CandidatusUNitrosopumilus hexadellus," "CandidatusUNitrosopumilus detritiferus," and "CandidatusUCenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that "CaUCenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "CaUNitrosopumilus detritiferus" and "CaUNitrosopumilus hexadellus" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.},
}

@article {pmid31409249,
year = {2019},
author = {Becker, CG and Bletz, MC and Greenspan, SE and Rodriguez, D and Lambertini, C and Jenkinson, TS and Guimarães, PR and Assis, APA and Geffers, R and Jarek, M and Toledo, LF and Vences, M and Haddad, CFB},
title = {Low-load pathogen spillover predicts shifts in skin microbiome and survival of a terrestrial-breeding amphibian.},
journal = {Proceedings. Biological sciences},
volume = {286},
number = {1908},
pages = {20191114},
doi = {10.1098/rspb.2019.1114},
pmid = {31409249},
issn = {1471-2954},
abstract = {Wildlife disease dynamics are strongly influenced by the structure of host communities and their symbiotic microbiota. Conspicuous amphibian declines associated with the waterborne fungal pathogen Batrachochytrium dendrobatidis (Bd) have been observed in aquatic-breeding frogs globally. However, less attention has been given to cryptic terrestrial-breeding amphibians that have also been declining in tropical regions. By experimentally manipulating multiple tropical amphibian assemblages harbouring natural microbial communities, we tested whether Bd spillover from naturally infected aquatic-breeding frogs could lead to Bd amplification and mortality in our focal terrestrial-breeding host: the pumpkin toadlet Brachycephalus pitanga. We also tested whether the strength of spillover could vary depending on skin bacterial transmission within host assemblages. Terrestrial-breeding toadlets acquired lethal spillover infections from neighbouring aquatic hosts and experienced dramatic but generally non-protective shifts in skin bacterial composition primarily attributable to their Bd infections. By contrast, aquatic-breeding amphibians maintained mild Bd infections and higher survival, with shifts in bacterial microbiomes that were unrelated to Bd infections. Our results indicate that Bd spillover from even mildly infected aquatic-breeding hosts may lead to dysbiosis and mortality in terrestrial-breeding species, underscoring the need to further investigate recent population declines of terrestrial-breeding amphibians in the tropics.},
}

@article {pmid31409048,
year = {2019},
author = {Drago, L and Panelli, S and Bandi, C and Zuccotti, G and Perini, M and D'Auria, E},
title = {What Pediatricians Should Know Before Studying Gut Microbiota.},
journal = {Journal of clinical medicine},
volume = {8},
number = {8},
pages = {},
doi = {10.3390/jcm8081206},
pmid = {31409048},
issn = {2077-0383},
abstract = {Billions of microorganisms, or "microbiota", inhabit the gut and affect its homeostasis, influencing, and sometimes causing if altered, a multitude of diseases. The genomes of the microbes that form the gut ecosystem should be summed to the human genome to form the hologenome due to their influence on human physiology; hence the term "microbiome" is commonly used to refer to the genetic make-up and gene-gene interactions of microbes. This review attempts to provide insight into this recently discovered vital organ of the human body, which has yet to be fully explored. We herein discuss the rhythm and shaping of the microbiome at birth and during the first years leading up to adolescence. Furthermore, important issues to consider for conducting a reliable microbiome study including study design, inclusion/exclusion criteria, sample collection, storage, and variability of different sampling methods as well as the basic terminology of molecular approaches, data analysis, and clinical interpretation of results are addressed. This basic knowledge aims to provide the pediatricians with a key tool to avoid data dispersion and pitfalls during child microbiota study.},
}

@article {pmid31408948,
year = {2019},
author = {Hayashi, T and Fujita, K and Matsushita, M and Nonomura, N},
title = {Main Inflammatory Cells and Potentials of Anti-Inflammatory Agents in Prostate Cancer.},
journal = {Cancers},
volume = {11},
number = {8},
pages = {},
doi = {10.3390/cancers11081153},
pmid = {31408948},
issn = {2072-6694},
support = {JP18K16693//Japan Society for the Promotion of Science/ ; },
abstract = {Prostate cancer is the most common type of cancer and the leading cause of cancer deaths among men in many countries. Preventing progression is a major concern for prostate cancer patients on active surveillance, patients with recurrence after radical therapies, and patients who acquired resistance to systemic therapies. Inflammation, which is induced by various factors such as infection, microbiome, obesity, and a high-fat diet, is the major etiology in the development of prostate cancer. Inflammatory cells play important roles in tumor progression. Various immune cells including tumor-associated neutrophils, tumor-infiltrating macrophages, myeloid-derived suppressor cells, and mast cells promote prostate cancer via various intercellular signaling. Further basic studies examining the relationship between the inflammatory process and prostate cancer progression are warranted. Interventions by medications and diets to control systemic and/or local inflammation might be effective therapies for prostate cancer progression. Epidemiological investigations and basic research using human immune cells or mouse models have revealed that non-steroidal anti-inflammatory drugs, metformin, statins, soy isoflavones, and other diets are potential interventions for preventing progression of prostate cancer by suppressing inflammation. It is essential to evaluate appropriate indications and doses of each drug and diet.},
}

@article {pmid31408913,
year = {2019},
author = {Sood, A and Singh, A and Mahajan, R and Midha, V and Mehta, V and Gupta, YK and Narang, V and Kaur, K},
title = {Acceptability, Tolerability and Safety of Faecal Microbiota Transplantation in patients with active Ulcerative Colitis (AT&S Study).},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.14829},
pmid = {31408913},
issn = {1440-1746},
abstract = {BACKGROUND: Faecal microbiota transplantation (FMT) targets gut microbiome dysbiosis and is an emerging therapy for ulcerative colitis (UC). Though initial results with FMT in patients with active UC are encouraging, data regarding its acceptability, tolerability and safety are scant.

METHODS: A retrospective analysis of patients with active UC (Mayo clinic score ≥4), who received multisession FMT (at weeks 0, 2, 6, 10, 14, 18 and 22) via colonoscopy between June 2016 and June 2018, was done. Patient acceptability, tolerability and immediate and long term safety of the therapy were assessed.

RESULTS: Of the 129 patients with active UC who were offered FMT, 101 patients consented; giving acceptability of 78.3%. Faecal slurry retention time, improved with each session (3.27 ± 1.06 hours for first session vs 5.12 ± 0.5 hours for seventh session). Abdominal discomfort, flatulence, abdominal distension, borborygmi and low grade fever (30.8%, 15.9%, 9.8%, 7.9% and 7.6% respectively) were the most common post procedural short term adverse events. Long term adverse events included new-onset urticaria (n=2,4.3%), arthritis/arthralgias(n=3, 6.5%), depression (n=1, 2.2%), partial sensorineural hearing loss (n=1, 2.2%), and allergic bronchitis (n=1, 2.2%). Thirteen (12.9%) patients dropped out due to adverse events.

CONCLUSION: FMT appears to be a safe and well tolerated procedure, with good acceptability in patients with active UC.},
}