@article {pmid31121066,
year = {2019},
author = {Hubert, J and Nesvorna, M and Klimov, P and Dowd, SE and Sopko, B and Erban, T},
title = {Differential allergen expression in three Tyrophagus putrescentiae strains inhabited by distinct microbiome.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.13921},
pmid = {31121066},
issn = {1398-9995},
}

@article {pmid31121057,
year = {2019},
author = {Nyangahu, DD and Jaspan, HB},
title = {Influence of maternal microbiota during pregnancy on infant immunity.},
journal = {Clinical and experimental immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/cei.13331},
pmid = {31121057},
issn = {1365-2249},
abstract = {Microbiota from various maternal sites including the gut, vagina and breastmilk, are known to influence colonization in infants. However, emerging evidence suggests that these sites may exert their influence prior to delivery, in turn influencing fetal immune development. The dogma of a sterile womb continues to be challenged. Regardless, there is convincing evidence that the composition of the maternal gut prior to delivery influences neonatal immunity. Therefore, while the presence and function of placental microbiome is not clear, there is consensus that the gut microbiota during pregnancy is a critical determinant of offspring health. Data supporting the notion of bacterial translocation from the maternal gut to extraintestinal sites during pregnancy are emerging, and potentially explain the presence of bacteria in breast milk. Much evidence suggests that the maternal gut microbiota during pregnancy potentially determines the development of atopy and autoimmune phenotypes in offspring. Here, we highlight the role of the maternal microbiota prior to delivery on infant immunity and predisposition to diseases. Moreover, we discuss potential mechanisms that underlie this phenomenon. This article is protected by copyright. All rights reserved.},
}

@article {pmid31120609,
year = {2019},
author = {Sikora, M and Chrabąszcz, M and Waśkiel-Burnat, A and Rakowska, A and Olszewska, M and Rudnicka, L},
title = {Claudin-3 - a new intestinal integrity marker in patients with psoriasis. Association with disease severity.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.15700},
pmid = {31120609},
issn = {1468-3083},
abstract = {BACKGROUND: Gut dysbiosis and increased intestinal permeability play a significant role in the pathogenesis of psoriasis and its comorbidities. Claudin-3 is a key component of tight junctions, which may serve as marker of gut barrier integrity.

OBJECTIVES: The aim of the study was to investigate circulating plasma claudin-3 in patients with psoriasis and to evaluate clinical and metabolic factors, which determine its concentration.

METHODS: This cross-sectional study included 60 patients with psoriasis (39 men and 21 women, mean age: 45.6±12.1 years) and 30 healthy controls (18 men and 12 women, mean age: 46.3±15.5 years) age, sex and body mass index-matched. Plasma claudin-3 concentration was measured using an enzyme-linked immunosorbent assay.

RESULTS: Plasma claudin-3 concentration was significantly higher in patients with psoriasis in comparison to healthy control [median (interquartile range), 50.7 ng/ml (47.3-54.2) vs 43.3 ng/ml (42.3-44.2), p < 0.001]. Patients who achieved ⊗PASI90 response after 16 weeks of treatment showed tendency to decrease in circulating claudin-3 plasma concentration. Positive correlations between claudin-3 concentration and the PASI score (r = 0.828; p < 0.001) as well as claudin-3 and neutrophil-to-lymphocyte ratio (r = 0.847; p < 0.001) were found. A multivariable linear regression analysis confirmed association of claudin-3 with the PASI score (p < 0.001), neutrophil-to-lymphocyte ratio (p < 0.01) and active smoking (p < 0.05).

CONCLUSION: Claudin-3, a biomarker for gut permeability, is increased in psoriasis and correlates with disease severity and smoking. Further investigations are needed to determine whether reinforcing intestinal barrier may be a new therapeutic target in psoriasis. This article is protected by copyright. All rights reserved.},
}

@article {pmid31120342,
year = {2019},
author = {Shurney, D and Pauly, K},
title = {The Gut Microbiome and Food as Medicine: Healthy Microbiomes = Healthy Humans.},
journal = {American journal of health promotion : AJHP},
volume = {33},
number = {5},
pages = {821-824},
doi = {10.1177/0890117119845711b},
pmid = {31120342},
issn = {2168-6602},
}

@article {pmid31120034,
year = {2019},
author = {Armour, CR and Nayfach, S and Pollard, KS and Sharpton, TJ},
title = {A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00332-18},
pmid = {31120034},
issn = {2379-5077},
abstract = {While recent research indicates that human health is affected by the gut microbiome, the functional mechanisms that underlie host-microbiome interactions remain poorly resolved. Metagenomic clinical studies can address this problem by revealing specific microbial functions that stratify healthy and diseased individuals. To improve our understanding of the relationship between the gut microbiome and health, we conducted the first integrative functional analysis of nearly 2,000 publicly available fecal metagenomic samples obtained from eight clinical studies. We identified characteristics of the gut microbiome that associate generally with disease, including functional alpha-diversity, beta-diversity, and beta-dispersion. Using regression modeling, we identified specific microbial functions that robustly stratify diseased individuals from healthy controls. Many of these functions overlapped multiple diseases, suggesting a general role in host health, while others were specific to a single disease and may indicate disease-specific etiologies. Our results clarify potential microbiome-mediated mechanisms of disease and reveal features of the microbiome that may be useful for the development of microbiome-based diagnostics.IMPORTANCE The composition of the gut microbiome associates with a wide range of human diseases, but the mechanisms underpinning these associations are not well understood. To shift toward a mechanistic understanding, we integrated distinct metagenomic data sets to identify functions encoded in the gut microbiome that associate with multiple diseases, which may be important to human health. Additionally, we identified functions that associate with specific diseases, which may elucidate disease-specific etiologies. We demonstrated that the functions encoded in the microbiome can be used to classify disease status, but the inclusion of additional patient covariates may be necessary to obtain sufficient accuracy. Ultimately, this analysis advances our understanding of the gut microbiome functions that constitute a healthy microbiome and identifies potential targets for microbiome-based diagnostics and therapeutics.},
}

@article {pmid31120033,
year = {2019},
author = {Werbner, M and Barsheshet, Y and Werbner, N and Zigdon, M and Averbuch, I and Ziv, O and Brant, B and Elliott, E and Gelberg, S and Titelbaum, M and Koren, O and Avni, O},
title = {Social-Stress-Responsive Microbiota Induces Stimulation of Self-Reactive Effector T Helper Cells.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00292-18},
pmid = {31120033},
issn = {2379-5077},
abstract = {Stressful life events are considered a risk factor for autoimmune disorders, though the mechanisms are unclear. Here we demonstrate that chronic social stress induces virulence-associated transcriptional patterns in the murine gut microbiota. The stress-influenced microbiota increased the presence of effector T helper cells in the mesenteric lymph nodes, including myelin-autoreactive cells. Inhibition of the bacterial quorum sensor QseC, which is also responsive to norepinephrine, diminished the presence of effector T helper cells and bacteria such as Acinetobacter in the mesenteric lymph nodes, without remarkably affecting the gut microbial composition. Together, our results delineate a model in which the immune reaction to stress-responsive microbiota may compromise tolerance to self and therefore may increase the risk for autoimmune diseases in susceptible individuals.IMPORTANCE How do stressful life events increase the risk for autoimmune disorders? Here we show that chronic social stress in mice promotes the expression of virulent genes in the gut microbiota and alters the microbial translocation into the mesenteric lymph nodes. Our results also suggest that the consequent immune response to the stress-affected microbiota may endanger the tolerance for self. The presence of specific translocated bacteria and the immune response in the mesenteric lymph nodes can be diminished using an inhibitor of the bacterial communication system without drastically affecting the gut microbial composition as antibiotics do.},
}

@article {pmid31120032,
year = {2019},
author = {de la Cuesta-Zuluaga, J and Kelley, ST and Chen, Y and Escobar, JS and Mueller, NT and Ley, RE and McDonald, D and Huang, S and Swafford, AD and Knight, R and Thackray, VG},
title = {Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00261-19},
pmid = {31120032},
issn = {2379-5077},
abstract = {Gut microbial diversity changes throughout the human life span and is known to be associated with host sex. We investigated the association of age, sex, and gut bacterial alpha diversity in three large cohorts of adults from four geographical regions: subjects from the United States and United Kingdom in the American Gut Project (AGP) citizen-science initiative and two independent cohorts of Colombians and Chinese. In three of the four cohorts, we observed a strong positive association between age and alpha diversity in young adults that plateaued after age 40 years. We also found sex-dependent differences that were more pronounced in younger adults than in middle-aged adults, with women having higher alpha diversity than men. In contrast to the other three cohorts, no association of alpha diversity with age or sex was observed in the Chinese cohort. The association of alpha diversity with age and sex remained after adjusting for cardiometabolic parameters in the Colombian cohort and antibiotic usage in the AGP cohort. We further attempted to predict the microbiota age in individuals using a machine-learning approach for the men and women in each cohort. Consistent with our alpha-diversity-based findings, U.S. and U.K. women had a significantly higher predicted microbiota age than men, with a reduced difference being seen above age 40 years. This difference was not observed in the Colombian cohort and was observed only in middle-aged Chinese adults. Together, our results provide new insights into the influence of age and sex on the biodiversity of the human gut microbiota during adulthood while highlighting similarities and differences across diverse cohorts.IMPORTANCE Microorganisms in the human gut play a role in health and disease, and in adults higher gut biodiversity has been linked to better health. Since gut microorganisms may be pivotal in the development of microbial therapies, understanding the factors that shape gut biodiversity is of utmost interest. We performed large-scale analyses of the relationship of age and sex to gut bacterial diversity in adult cohorts from four geographic regions: the United States, the United Kingdom, Colombia, and China. In the U.S., U.K., and Colombian cohorts, bacterial biodiversity correlated positively with age in young adults but plateaued at about age 40 years, with no positive association being found in middle-aged adults. Young, but not middle-aged, adult women had higher gut bacterial diversity than men, a pattern confirmed via supervised machine learning. Interestingly, in the Chinese cohort, minimal associations were observed between gut biodiversity and age or sex. Our results highlight the patterns of adult gut biodiversity and provide a framework for future research.},
}

@article {pmid31120031,
year = {2019},
author = {Lutz, HL and Ramírez-Puebla, ST and Abbo, L and Durand, A and Schlundt, C and Gottel, NR and Sjaarda, AK and Hanlon, RT and Gilbert, JA and Mark Welch, JL},
title = {A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00177-19},
pmid = {31120031},
issn = {2379-5077},
abstract = {The European common cuttlefish, Sepia officinalis, is used extensively in biological and biomedical research, yet its microbiome remains poorly characterized. We analyzed the microbiota of the digestive tract, gills, and skin in mariculture-raised S. officinalis using a combination of 16S rRNA amplicon sequencing, quantitative PCR (qPCR), and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) of Vibrionaceae and Piscirickettsiaceae The esophagus was dominated by a single ASV of the genus Vibrio Imaging revealed bacteria in the family Vibrionaceae distributed in a discrete layer that lines the esophagus. This Vibrio was also the primary ASV found in the microbiota of the stomach, cecum, and intestine, but occurred at lower abundance, as determined by qPCR, and was found only scattered in the lumen rather than in a discrete layer via imaging analysis. Treatment of animals with the commonly used antibiotic enrofloxacin led to a nearly 80% reduction of the dominant Vibrio ASV in the esophagus but did not significantly alter the relative abundance of bacteria overall between treated versus control animals. Data from the gills were dominated by a single ASV in the family Piscirickettsiaceae, which imaging visualized as small clusters of cells. We conclude that bacteria belonging to the Gammaproteobacteria are the major symbionts of the cuttlefish Sepia officinalis cultured from eggs in captivity and that the esophagus and gills are major colonization sites.IMPORTANCE Microbes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role of Vibrio (Aliivibrio) fischeri in the light organ of the bobtail squid and the role of Alpha- and Gammaproteobacteria in the reproductive system and egg defense in a variety of cephalopods. We sampled the cuttlefish microbiome throughout the digestive tract, gills, and skin and found dense colonization of an unexpected site, the esophagus, by a microbe of the genus Vibrio, as well as colonization of gills by Piscirickettsiaceae This finding expands the range of organisms and body sites known to be associated with Vibrio and is of potential significance for understanding host-symbiont associations, as well as for understanding and maintaining the health of cephalopods in mariculture.},
}

@article {pmid31120029,
year = {2019},
author = {Zegeye, EK and Brislawn, CJ and Farris, Y and Fansler, SJ and Hofmockel, KS and Jansson, JK and Wright, AT and Graham, EB and Naylor, D and McClure, RS and Bernstein, HC},
title = {Selection, Succession, and Stabilization of Soil Microbial Consortia.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00055-19},
pmid = {31120029},
issn = {2379-5077},
abstract = {Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. In this study, we investigated the successional dynamics of a soil microbiome during 21 weeks of enrichment on chitin and its monomer, N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a homogeneous liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant community structure over time. We also hypothesized that long-term, substrate-driven growth would result in consortia with reduced species richness compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil from that in liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix than in liquid environments.IMPORTANCE The soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. In this study, we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability.},
}

@article {pmid31120028,
year = {2019},
author = {Gibbons, SM},
title = {Defining Microbiome Health through a Host Lens.},
journal = {mSystems},
volume = {4},
number = {3},
pages = {},
doi = {10.1128/mSystems.00155-19},
pmid = {31120028},
issn = {2379-5077},
abstract = {We are walking ecosystems, inoculated at birth with a unique set of microbes that are integral to the functioning of our bodies. The physiology of our commensal microbiota is intertwined with our metabolism, immune function, and mental state. The specifics of this entanglement remain largely unknown and are somewhat unique to individuals, and when any one piece of this complex system breaks, our health can suffer. There appear to be many ways to build a healthy, functional microbiome and several distinct ways in which it can break. Despite the hundreds of associations with human disease, there are only a handful of cases where the exact contribution of the microbiome to the etiology of disease is known. Our laboratory takes a systems approach, integrating dynamic high-throughput host phenotyping with eco-evolutionary dynamics and metabolism of gut microbiota to better define health and disease for each individual at the ecosystem level.},
}

@article {pmid31120027,
year = {2019},
author = {Malmstrom, RR and Eloe-Fadrosh, EA},
title = {Advancing Genome-Resolved Metagenomics beyond the Shotgun.},
journal = {mSystems},
volume = {4},
number = {3},
pages = {},
doi = {10.1128/mSystems.00118-19},
pmid = {31120027},
issn = {2379-5077},
abstract = {Exploration of environmental microbiomes has shed light on the ecological and evolutionary principles at play in natural ecosystems and has been further accelerated through the reconstruction of population genomes to provide genome-centric context. Yet technical challenges with traditional shotgun metagenomics remain for computationally intense short-read assembly, strain heterogeneity within communities, and depth of coverage required for low-abundance microbes. In this Perspective, we highlight three main avenues for promising future developments, including coupling stable isotope probing and genome-resolved metagenomics, applying fluorescence-activated cell sorting approaches to target mini-metagenomes within a larger community, and utilizing single-molecule long-read and synthetic long-read technology to link mobile elements to host microbial cells. These developments on the horizon will undoubtedly advance genome-resolved metagenomic approaches and enable a better understanding of uncultivated microbes in their natural environments.},
}

@article {pmid31120023,
year = {2019},
author = {Dannemiller, KC},
title = {Moving towards a Robust Definition for a "Healthy" Indoor Microbiome.},
journal = {mSystems},
volume = {4},
number = {3},
pages = {},
doi = {10.1128/mSystems.00074-19},
pmid = {31120023},
issn = {2379-5077},
abstract = {Buildings of the future should be designed to support human health, both by promoting the presence of beneficial microbes and by reducing exposure to harmful ones. However, we still do not have a robust definition of what constitutes a "healthy" indoor microbiome. Such a definition would allow us to better understand implications of building design and behavioral decisions of residents, especially for vulnerable populations such as asthmatic children. Relevant assessment methods could then be developed to make microbiome information available to home occupants, environmental health professionals, policy writers, building designers, and building remediation specialists.},
}

@article {pmid31119891,
year = {2019},
author = {Uno, Y},
title = {Prevention of gastric cancer by Helicobacter pylori eradication: A review from Japan.},
journal = {Cancer medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/cam4.2277},
pmid = {31119891},
issn = {2045-7634},
abstract = {Japan introduced a Helicobacter pylori eradication therapy strategy in 2013, with the aim of decreasing the number of gastric cancer-related death, the number of new cases of gastric cancer, and associated medical costs. Five years have passed since then, but no reduction in the annual number of gastric cancer has been observed. In addition, it was suggested that the number of deaths due to gastric cancer could be reduced to 30,000 a year by 2020, but the annual death toll in 2017 remained at more than 45,000. Based on the above evidence, it was examined whether it was possible to reach the target value based on the data from the last 5 years. The number of deaths per year in 2020 is predicted to be more than 40,000, which is clearly different from the target value. Logically, the effect of the strategy might appear by 2023. However, there is a possibility that the risk of gastric cancer may increase in some populations due to the influence of proton pump inhibitors and dysbiosis in the gastric microbiome. To solve these problems, combined therapy with PPIs and aspirin for patients after H pylori eradication should be considered.},
}

@article {pmid31119572,
year = {2019},
author = {Rodgers, K and McLellan, I and Peshkur, T and Williams, R and Tonner, R and Knapp, CW and Henriquez, FL and Hursthouse, AS},
title = {The legacy of industrial pollution in estuarine sediments: spatial and temporal variability implications for ecosystem stress.},
journal = {Environmental geochemistry and health},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10653-019-00316-4},
pmid = {31119572},
issn = {1573-2983},
support = {NE/NO1474/1//Natural Environment Research Council/ ; },
abstract = {The direct impacts of anthropogenic pollution are widely known public and environmental health concerns, and details on the indirect impact of these are starting to emerge, for example affecting the environmental microbiome. Anthropogenic activities throughout history with associated pollution burdens are notable contributors. Focusing on the historically heavily industrialised River Clyde, Scotland, we investigate spatial and temporal contributions to stressful/hostile environments using a geochemical framework, e.g. pH, EC, total organic carbon and potentially toxic elements: As, Co, Cr, Cu, Ni, Pb and Zn and enrichment indicators. With regular breaches of the sediment quality standards in the estuarine system we focused on PTE correlations instead. Multivariate statistical analysis (principle component analysis) identifies two dominant components, PC1: As, Cr, Cu, Pb and Zn, as well as PC2: Ni, Co and total organic carbon. Our assessment confirms hot spots in the Clyde Estuary indicative of localised inputs. In addition, there are sites with high variability indicative of excessive mixing. We demonstrate that industrialised areas are dynamic environmental sites dependant on historical anthropogenic activity with short-scale variation. This work supports the development of 'contamination' mapping to enable an assessment of the impact of historical anthropogenic pollution, identifying specific 'stressors' that can impact the microbiome, neglecting in estuarine recovery dynamics and potentially supporting the emergence of antimicrobial resistance in the environment.},
}

@article {pmid31119399,
year = {2019},
author = {Green, CH and Syn, WK},
title = {Non-nutritive sweeteners and their association with the metabolic syndrome and non-alcoholic fatty liver disease: a review of the literature.},
journal = {European journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00394-019-01996-5},
pmid = {31119399},
issn = {1436-6215},
abstract = {PURPOSE: Non-alcoholic fatty liver disease (NAFLD) is increasing in incidence worldwide, paralleling epidemics in obesity and metabolic syndrome. Widely considered the hepatic manifestation of the metabolic syndrome, NAFLD is associated with significant morbidity, mortality, and increased healthcare costs. There is an abundance of data linking sugar-sweetened beverages, and fructose, in particular, to the metabolic syndrome and NAFLD. As a result, non-nutritive sweeteners (NNSs) are frequently substituted for sugar in drinks and a variety of foods. However, despite the widespread consumption of NNSs, there is growing concern about their impact on metabolic health.

METHODS: This review examines the experimental and clinical evidence on non-nutritive sweetener (NNS) consumption and features of the metabolic syndrome, including NAFLD.

RESULTS: Experimental animal studies show that NNS consumption can induce glucose intolerance, increased food consumption, and weight gain, with proposed mechanisms including altered gut microbiome, inhibition of protective intestinal enzymes, and increased appetite. The evidence from clinical studies is more controversial. Observational studies overwhelmingly show an association between NNS consumption and features of the metabolic syndrome, and this includes NAFLD when analyses are not adjusted for obesity. The evidence from randomized-controlled trials in humans is sparse and conflicting, and primarily evaluates weight-related outcomes.

CONCLUSION: Further research is urgently needed to evaluate NNS consumption and its relationship with NAFLD and the gut microbiome in humans.},
}

@article {pmid31119393,
year = {2019},
author = {Wang, LJ and Yang, CY and Chou, WJ and Lee, MJ and Chou, MC and Kuo, HC and Yeh, YM and Lee, SY and Huang, LH and Li, SC},
title = {Gut microbiota and dietary patterns in children with attention-deficit/hyperactivity disorder.},
journal = {European child & adolescent psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00787-019-01352-2},
pmid = {31119393},
issn = {1435-165X},
support = {CMRPG8E1441//Chang Gung Memorial Hospital Research Grant/ ; MOST 107-2628-B-182-001//Ministry of Science and Technology, Taiwan/ ; },
abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder, but the underlying pathophysiological mechanisms of ADHD remain unclear. Gut microbiota has been recognized to influence brain function and behaviors. Therefore, this study aimed to determine whether imbalanced gut microbiomes identified by a 16S rRNA sequencing approach are involved in the pathophysiology of ADHD. We recruited a total of 30 children with ADHD (mean age: 8.4 years) and a total of 30 healthy controls (mean age: 9.3 years) for this study. The dietary patterns of all participants were assessed with the food frequency questionnaire. The microbiota of fecal samples were investigated using 16S rRNA V3V4 amplicon sequencing, followed by bioinformatics and statistical analyses. We found that the gut microbiota communities in ADHD patients showed a significantly higher Shannon index and Chao index than the control subjects. Furthermore, the linear discriminant analysis effect size (LEfSe) analysis was used to identify differentially enriched bacteria between ADHD patients and healthy controls. The relative abundance of Bacteroides coprocola (B. coprocola) was decreased, while the relative abundance of Bacteroides uniformis (B. uniformis), Bacteroides ovatus (B. ovatus), and Sutterella stercoricanis (S. stercoricanis) were increased in the ADHD group. Of all participants, S. stercoricanis demonstrated a significant association with the intake of dairy, nuts/seeds/legumes, ferritin and magnesium. B. ovatus and S. stercoricanis were positively correlated to ADHD symptoms. In conclusion, we suggest that the gut microbiome community is associated with dietary patterns, and linked to the susceptibility to ADHD.},
}

@article {pmid31119300,
year = {2019},
author = {Kim, H and Worsley, O and Yang, E and Purbojati, RW and Liang, AL and Tan, W and Moses, DID and Hartono, S and Fan, V and Lim, TKH and Schuster, SC and Foo, RS and Chow, PKH and Pettersson, S},
title = {Persistent changes in liver methylation and microbiome composition following reversal of diet-induced non-alcoholic-fatty liver disease.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-019-03114-4},
pmid = {31119300},
issn = {1420-9071},
support = {none//Ministry of Education - Singapore/ ; none//EU grant TORNADO/ ; },
abstract = {Non-alcoholic fatty liver disease (NAFLD) is a metabolic liver disease that is thought to be reversible by changing the diet. To examine the impact of dietary changes on progression and cure of NAFLD, we fed mice a high-fat diet (HFD) or high-fructose diet (HFrD) for 9 weeks, followed by an additional 9 weeks, where mice were given normal chow diet. As predicted, the diet-induced NAFLD elicited changes in glucose tolerance, serum cholesterol, and triglyceride levels in both diet groups. Moreover, the diet-induced NAFLD phenotype was reversed, as measured by the recovery of glucose intolerance and high cholesterol levels when mice were given normal chow diet. However, surprisingly, the elevated serum triglyceride levels persisted. Metagenomic analysis revealed dietary-induced changes of microbiome composition, some of which remained altered even after reversing the diet to normal chow, as illustrated by species of the Odoribacter genus. Genome-wide DNA methylation analysis revealed a "priming effect" through changes in DNA methylation in key liver genes. For example, the lipid-regulating gene Apoa4 remained hypomethylated in both groups even after introduction to normal chow diet. Our results support that dietary change, in part, reverses the NAFLD phenotype. However, some diet-induced effects remain, such as changes in microbiome composition, elevated serum triglyceride levels, and hypomethylation of key liver genes. While the results are correlative in nature, it is tempting to speculate that the dietary-induced changes in microbiome composition may in part contribute to the persistent epigenetic modifications in the liver.},
}

@article {pmid31119299,
year = {2019},
author = {Koedooder, R and Singer, M and Schoenmakers, S and Savelkoul, PHM and Morré, SA and de Jonge, JD and Poort, L and Cuypers, WJSS and Beckers, NGM and Broekmans, FJM and Cohlen, BJ and den Hartog, JE and Fleischer, K and Lambalk, CB and Smeenk, JMJS and Budding, AE and Laven, JSE},
title = {The vaginal microbiome as a predictor for outcome of in vitro fertilization with or without intracytoplasmic sperm injection: a prospective study.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/dez065},
pmid = {31119299},
issn = {1460-2350},
abstract = {STUDY QUESTION: Is the presence or absence of certain vaginal bacteria associated with failure or success to become pregnant after an in vitro fertilization (IVF) or IVF with intracytoplasmic sperm injection (IVF-ICSI) treatment?

SUMMARY ANSWER: Microbiome profiling with the use of interspace profiling (IS-pro) technique enables stratification of the chance of becoming pregnant prior to the start of an IVF or IVF-ICSI treatment.

WHAT IS KNOWN ALREADY: Live-birth rates for an IVF or IVF-ICSI treatment vary between 25 and 35% per cycle and it is difficult to predict who will or will not get pregnant after embryo transfer (ET). Recently, it was suggested that the composition of the vaginal microbiota prior to treatment might predict pregnancy outcome. Analysis of the vaginal microbiome prior to treatment might, therefore, offer an opportunity to improve the success rate of IVF or IVF-ICSI.

STUDY DESIGN, SIZE, DURATION: In a prospective cohort study, 303 women (age, 20-42 years) undergoing IVF or IVF-ICSI treatment in the Netherlands were included between June 2015 and March 2016.

Study subjects provided a vaginal sample before the start of the IVF or IVF-ICSI procedure. The vaginal microbiota composition was determined using the IS-pro technique. IS-pro is a eubacterial technique based on the detection and categorization of the length of the 16S-23S rRNA gene interspace region. Microbiome profiles were assigned to community state types based on the dominant bacterial species. The predictive accuracy of the microbiome profiles for IVF and IVF-ICSI outcome of fresh ET was evaluated by a combined prediction model based on a small number of bacterial species. From this cohort, a model was built to predict outcome of fertility treatment. This model was externally validated in a cohort of 50 women who were undergoing IVF or IVF-ICSI treatment between March 2018 and May 2018 in the Dutch division of the MVZ VivaNeo Kinderwunschzentrum Düsseldorf, Germany.

In total, the vaginal microbiota of 192 women who underwent a fresh ET could be analysed. Women with a low percentage of Lactobacillus in their vaginal sample were less likely to have a successful embryo implantation. The prediction model identified a subgroup of women (17.7%, n = 34) who had a low chance to become pregnant following fresh ET. This failure was correctly predicted in 32 out of 34 women based on the vaginal microbiota composition, resulting in a predictive accuracy of 94% (sensitivity, 26%; specificity, 97%). Additionally, the degree of dominance of Lactobacillus crispatus was an important factor in predicting pregnancy. Women who had a favourable profile as well as <60% L. crispatus had a high chance of pregnancy: more than half of these women (50 out of 95) became pregnant. In the external validation cohort, none of the women who had a negative prediction (low chance of pregnancy) became pregnant.

Because our study uses a well-defined study population, the results will be limited to the IVF or IVF-ICSI population. Whether these results can be extrapolated to the general population trying to achieve pregnancy without ART cannot be determined from these data.

Our results indicate that vaginal microbiome profiling using the IS-pro technique enables stratification of the chance of becoming pregnant prior to the start of an IVF or IVF-ICSI treatment. Knowledge of their vaginal microbiota may enable couples to make a more balanced decision regarding timing and continuation of their IVF or IVF-ICSI treatment cycles.

This study was financed by NGI Pre-Seed 2014-2016, RedMedTech Discovery Fund 2014-2017, STW Valorisation grant 1 2014-2015, STW Take-off early phase trajectory 2015-2016 and Eurostars VALBIOME grant (reference number: 8884). The employer of W.J.S.S.C. has in collaboration with ARTPred acquired a MIND subsidy to cover part of the costs of this collaboration project. The following grants are received but not used to finance this study: grants from Innovatie Prestatie Contract, MIT Haalbaarheid, other from Dutch R&D tax credit WBSO, RedMedTech Discovery Fund, (J.D.d.J.). Grants from Ferring (J.S.E.L., K.F., C.B.L. and J.M.J.S.S.), Merck Serono (K.F. and C.B.L.), Dutch Heart Foundation (J.S.E.L.), Metagenics Inc. (J.S.E.L.), GoodLife (K.F.), Guerbet (C.B.L.). R.K. is employed by ARTPred B.V. during her PhD at Erasmus Medical Centre (MC). S.A.M. has a 100% University appointment. I.S.P.H.M.S., S.A.M. and A.E.B. are co-owners of IS-Diagnostics Ltd. J.D.d.J. is co-owner of ARTPred B.V., from which he reports personal fees. P.H.M.S. reports non-financial support from ARTPred B.V. P.H.M.S., J.D.d.J. and A.E.B. have obtained patents `Microbial population analysis' (9506109) and `Microbial population analysis' (20170159108), both licenced to ARTPred B.V. J.D.d.J. and A.E.B. report patent applications `Method and kit for predicting the outcome of an assisted reproductive technology procedure' (392EPP0) and patent `Method and kit for altering the outcome of an assisted reproductive technology procedure' by ARTPred. W.J.S.S.C. received personal consultancy and educational fees from Goodlife Fertility B.V. J.S.E.L. reports personal consultancy fees from ARTPred B.V., Titus Health B.V., Danone, Euroscreen and Roche during the conduct of the study. J.S.E.L. and N.G.M.B. are co-applicants on an Erasmus MC patent (New method and kit for prediction success of in vitro fertilization) licenced to ARTPred B.V. F.J.M.B. reports personal fees from Advisory Board Ferring, Advisory Board Merck Serono, Advisory Board Gedeon Richter and personal fees from Educational activities for Ferring, outside the submitted work. K.F. reports personal fees from Ferring (commercial sponsor) and personal fees from GoodLife (commercial sponsor). C.B.L. received speakers' fee from Ferring. J.M.J.S.S. reports personal fees and other from Merck Serono and personal fees from Ferring, unrelated to the submitted paper. The other authors declare that they have no competing interests.

TRIAL REGISTRATION NUMBER: ISRCTN83157250. Registered 17 August 2018. Retrospectively registered.},
}

@article {pmid31119104,
year = {2019},
author = {Govender, Y and Gabriel, I and Minassian, V and Fichorova, R},
title = {The Current Evidence on the Association Between the Urinary Microbiome and Urinary Incontinence in Women.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {133},
doi = {10.3389/fcimb.2019.00133},
pmid = {31119104},
issn = {2235-2988},
abstract = {Urinary incontinence (UI) is a burdensome condition with high prevalence in middle-aged to older women and an unclear etiology. Advances in our understanding of host-microbe interactions in the urogenital tract have stimulated interest in the urinary microbiome. DNA sequencing and enhanced urine culture suggest that similarly to other mucosal sites, the urinary bladder of healthy individuals harbors resident microbial communities that may play distinct roles in bladder function. This review focused on the urobiome (expanded quantitative urine culture-based or genomic sequencing-based urinary microbiome) associated with different subtypes of UI, including stress, urgency and mixed urinary incontinence, and related syndromes, such as interstitial cystitis and overactive bladder in women, contrasted to urinary tract infections. Furthermore, we examined clinical evidence for the association of the urinary microbiome with responses to pharmacotherapy for amelioration of UI symptoms. Although published studies are still relatively limited in number, study design and sample size, cumulative evidence suggests that certain Lactobacillus species may play a role in maintaining a healthy bladder milieu. Higher bacterial diversity in the absence of Lactobacillus dominance was associated with urgency UI and resistance to anticholinergic treatment for this condition. UI may also facilitate the persistence of uropathogens following antibiotic treatment, which in turn can alter the commensal/potentially beneficial microbial communities. Risk factors of UI, including age, menopausal status, sex steroid hormones, and body mass index may also impact the urinary microbiome. However, it is yet unclear whether the effects of these risks factors on UI are mediated by urinary host-microbe interactions and a mechanistic link with the female urogenital microbiome is still to be established. Strategies for future research are suggested.},
}

@article {pmid31119076,
year = {2019},
author = {Kaczmarczyk-Ziemba, A and Wagner, GK and Grzywnowicz, K and Kucharczyk, M and Zielińska, S},
title = {The microbiome profiling of fungivorous black tinder fungus beetle Bolitophagus reticulatus reveals the insight into bacterial communities associated with larvae and adults.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6852},
doi = {10.7717/peerj.6852},
pmid = {31119076},
issn = {2167-8359},
abstract = {Saproxylic beetles play a crucial role in key processes occurring in forest ecosystems, and together with fungi contribute to the decomposition and mineralization of wood. Among this group are mycetophilic beetles which associate with wood-decaying fungi and use the fruiting body for nourishment and development. Therefore, their feeding strategy (especially in the case of fungivorous species) requires special digestive capabilities to take advantage of the nutritional value of fungal tissue. Although polypore-beetle associations have been investigated in numerous studies, detailed studies focusing on the microbiome associated with species feeding on fruiting bodies of polypores remain limited. Here we investigated the bacterial communities associated with larvae and adults of Bolitophagus reticulatus collected from Fomes fomentarius growing on two different host tree: beech (Fagus sp.) and birch (Betula sp.), respectively. Among 24 identified bacterial phyla, three were the most relatively abundant (Proteobacteria, Actinobacteria and Bacteroidetes). Moreover, we tried to find unique patterns of bacteria abundances which could be correlated with the long-term field observation showing that the fruiting bodies of F. fomentarius, growing on birch are more inhabited by beetles than fruiting bodies of the same fungus species growing on beech. Biochemical analyses showed that the level of protease inhibitors and secondary metabolites in F. fomentarius is higher in healthy fruiting bodies than in the inhabited ones. However, tested microbiome samples primarily clustered by developmental stage of B. reticulatus and host tree did not appear to impact the taxonomic distribution of the communities. This observation was supported by statistical analyses.},
}

@article {pmid31118956,
year = {2019},
author = {Wang, ZB and Xin, SS and Ding, LN and Ding, WY and Hou, YL and Liu, CQ and Zhang, XD},
title = {The Potential Role of Probiotics in Controlling Overweight/Obesity and Associated Metabolic Parameters in Adults: A Systematic Review and Meta-Analysis.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2019},
number = {},
pages = {3862971},
doi = {10.1155/2019/3862971},
pmid = {31118956},
issn = {1741-427X},
abstract = {Background: The prevalence of overweight/obesity in adults is raised to 39%, which is nearly tripled more than 1975. The alteration of the gut microbiome has been widely accepted as one of the main causal factors. To find an effective strategy for the prevention and treatment of overweight/obesity, a systematic review and meta-analysis were designed.

Methods: In this study, we systematically reviewed the article published from January 2008 to July 2018 and conducted a meta-analysis to examine the effects of probiotics on body weight control, lipid profile, and glycemic control in healthy adults with overweight or obesity. The primary outcomes were body weight, body mass index (BMI), waist circumference, fat mass, fat percentages, plasma lipid profiles, and glucose metabolic parameters.

Results: We systematically searched PubMed, Embase, and the Web of Science and identified 1248 articles, and 7 articles which were manually searched by the references of included studies and previously systematic reviews. Twelve randomized controlled trials (RCTs), including 821 participants, were included in the meta-analysis via full-text screening. Probiotics supplementation resulted in a statistical reduction in body weight (WMD [95% CI]; -0.55 [-0.91, -0.19] kg), BMI (WMD [95% CI]; -0.30 [-0.43, -0.18] kg m-2), waist circumference (WMD [95% CI]; -1.20 [-2.21, -0.19] cm), fat mass (WMD [95% CI]; -0.91 [-1.19, -0.63] kg), and fat percentage (WMD [95% CI]; -0.92 [-1.27, -0.56] %) compared with control groups. As expected, the metabolic parameters were improved significantly, with a pooled standardized mean difference in TC (SMD [95% CI]; -0.43 [-0.80, -0.07]), LDL-C (SMD [95% CI]; -0.41 [-0.77, -0.04]), FPG (SMD [95% CI]; -0.35 [-0.67, -0.02]), insulin (SMD [95% CI]; -0.44 [-0.84, -0.03]), and HOMA-IR (SMD [95% CI]; -0.51 [-0.96, -0.05]), respectively. The changes in TG (SMD [95% CI]; 0.14 [-0.23, 0.50]), HDL-C (SMD [95% CI]; -0.31 [-0.70, 0.07]), and HbA1c (SMD [95% CI]; -0.23 [-0.46, 0.01]) were not significant.

Conclusion: This study suggests that the probiotics supplementation could potentially reduce the weight gain and improve some of the associated metabolic parameters, which may become an effective strategy for the prevention and treatment of obesity in adult individuals.},
}

@article {pmid31118502,
year = {2019},
author = {Durrant, MG and Bhatt, AS},
title = {Microbiome genome structure drives function.},
journal = {Nature microbiology},
volume = {4},
number = {6},
pages = {912-913},
doi = {10.1038/s41564-019-0473-y},
pmid = {31118502},
issn = {2058-5276},
}

@article {pmid31118468,
year = {2019},
author = {Possiel, C and Ortiz-Soto, ME and Ertl, J and Münch, A and Vogel, A and Schmiedel, R and Seibel, J},
title = {Exploring the sequence variability of polymerization-involved residues in the production of levan- and inulin-type fructooligosaccharides with a levansucrase.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {7720},
doi = {10.1038/s41598-019-44211-5},
pmid = {31118468},
issn = {2045-2322},
support = {01DN16034//Bundesministerium f&#x00FC;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 613633//EC | Seventh Framework Programme (EC Seventh Framework Programm)/ ; 613633//EC | Seventh Framework Programme (EC Seventh Framework Programm)/ ; },
abstract = {The connection between the gut microbiome composition and human health has long been recognized, such that the host-microbiome interplay is at present the subject of the so-called "precision medicine". Non-digestible fructooligosaccharides (FOS) can modulate the microbial composition and therefore their consumption occupies a central place in a strategy seeking to reverse microbiome-linked diseases. We created a small library of Bacillus megaterium levansucrase variants with focus on the synthesis of levan- and inulin-type FOS. Modifications were introduced at positions R370, K373 and F419, which are either part of the oligosaccharide elongation pathway or are located in the vicinity of residues that modulate polymerization. These amino acids were exchanged by residues of different characteristics, some of them being extremely low- or non-represented in enzymes of the levansucrase family (Glycoside Hydrolase 68, GH68). F419 seemed to play a minor role in FOS binding. However, changes at R370 abated the levansucrase capacity to synthesize levan-type oligosaccharides, with some mutations turning the product specificity towards neo-FOS and the inulin-like sugar 1-kestose. Although variants retaining the native R370 produced efficiently levan-type tri-, tetra- and pentasaccharides, their capacity to elongate these FOS was hampered by including the mutation K373H or K373L. Mutant K373H, for instance, generated 37- and 5.6-fold higher yields of 6-kestose and 6-nystose, respectively, than the wild-type enzyme, while maintaining a similar catalytic activity. The effect of mutations on the levansucrase product specificity is discussed.},
}

@article {pmid31118434,
year = {2019},
author = {Simintiras, CA and Sánchez, JM and McDonald, M and Lonergan, P},
title = {The influence of progesterone on bovine uterine fluid energy, nucleotide, vitamin, cofactor, peptide, and xenobiotic composition during the conceptus elongation-initiation window.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {7716},
doi = {10.1038/s41598-019-44040-6},
pmid = {31118434},
issn = {2045-2322},
support = {13/IA/1983//Science Foundation Ireland (SFI)/ ; },
abstract = {Conceptus elongation coincides with one of the periods of greatest pregnancy loss in cattle and is characterized by rapid trophectoderm expansion, commencing ~ Day 13 of pregnancy, i.e. before maternal pregnancy recognition. The process has yet to be recapitulated in vitro and does not occur in the absence of uterine gland secretions in vivo. Moreover, conceptus elongation rates are positively correlated to systemic progesterone in maternal circulation. It is, therefore, a maternally-driven and progesterone-correlated developmental phenomenon. This study aimed to comprehensively characterize the biochemical composition of the uterine luminal fluid on Days 12-14 - the elongation-initiation window - in heifers with normal vs. high progesterone, to identify molecules potentially involved in conceptus elongation initiation. Specifically, nucleotide, vitamin, cofactor, xenobiotic, peptide, and energy metabolite profiles of uterine luminal fluid were examined. A total of 59 metabolites were identified, of which 6 and 3 displayed a respective progesterone and day effect, whereas 16 exhibited a day by progesterone interaction, of which 8 were nucleotide metabolites. Corresponding pathway enrichment analysis revealed that pyridoxal, ascorbate, tricarboxylic acid, purine, and pyrimidine metabolism are of likely importance to to conceptus elongation initiation. Moreover, progesterone reduced total metabolite abundance on Day 12 and may alter the uterine microbiome.},
}

@article {pmid31118305,
year = {2019},
author = {Baxter, NT and Lesniak, NA and Sinani, H and Schloss, PD and Koropatkin, NM},
title = {Erratum for Baxter et al., "The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome".},
journal = {mSphere},
volume = {4},
number = {3},
pages = {},
doi = {10.1128/mSphere.00347-19},
pmid = {31118305},
issn = {2379-5042},
}

@article {pmid31118299,
year = {2019},
author = {Sze, MA and Schloss, PD},
title = {The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data.},
journal = {mSphere},
volume = {4},
number = {3},
pages = {},
doi = {10.1128/mSphere.00163-19},
pmid = {31118299},
issn = {2379-5042},
abstract = {PCR amplification of 16S rRNA genes is a critical yet underappreciated step in the generation of sequence data to describe the taxonomic composition of microbial communities. Numerous factors in the design of PCR can impact the sequencing error rate, the abundance of chimeric sequences, and the degree to which the fragments in the product represent their abundance in the original sample (i.e., bias). We compared the performance of high fidelity polymerases and various numbers of rounds of amplification when amplifying a mock community and human stool samples. Although it was impossible to derive specific recommendations, we did observe general trends. Namely, using a polymerase with the highest possible fidelity and minimizing the number of rounds of PCR reduced the sequencing error rate, fraction of chimeric sequences, and bias. Evidence of bias at the sequence level was subtle and could not be ascribed to the fragments' fraction of bases that were guanines or cytosines. When analyzing mock community data, the amount that the community deviated from the expected composition increased with the number of rounds of PCR. This bias was inconsistent for human stool samples. Overall, the results underscore the difficulty of comparing sequence data that are generated by different PCR protocols. However, the results indicate that the variation in human stool samples is generally larger than that introduced by the choice of polymerase or number of rounds of PCR.IMPORTANCE A steep decline in sequencing costs drove an explosion in studies characterizing microbial communities from diverse environments. Although a significant amount of effort has gone into understanding the error profiles of DNA sequencers, little has been done to understand the downstream effects of the PCR amplification protocol. We quantified the effects of the choice of polymerase and number of PCR cycles on the quality of downstream data. We found that these choices can have a profound impact on the way that a microbial community is represented in the sequence data. The effects are relatively small compared to the variation in human stool samples; however, care should be taken to use polymerases with the highest possible fidelity and to minimize the number of rounds of PCR. These results also underscore that it is not possible to directly compare sequence data generated under different PCR conditions.},
}

@article {pmid31118068,
year = {2019},
author = {Angelucci, F and Cechova, K and Amlerova, J and Hort, J},
title = {Antibiotics, gut microbiota, and Alzheimer's disease.},
journal = {Journal of neuroinflammation},
volume = {16},
number = {1},
pages = {108},
doi = {10.1186/s12974-019-1494-4},
pmid = {31118068},
issn = {1742-2094},
support = {LF UK Grant No. 699012//Ipe 2/ ; },
abstract = {Alzheimer's disease (AD) is a neurodegenerative disease whose various pathophysiological aspects are still being investigated. Recently, it has been hypothesized that AD may be associated with a dysbiosis of microbes in the intestine. In fact, the intestinal flora is able to influence the activity of the brain and cause its dysfunctions.Given the growing interest in this topic, the purpose of this review is to analyze the role of antibiotics in relation to the gut microbiota and AD. In the first part of the review, we briefly review the role of gut microbiota in the brain and the various theories supporting the hypothesis that dysbiosis can be associated with AD pathophysiology. In the second part, we analyze the possible role of antibiotics in these events. Antibiotics are normally used to remove or prevent bacterial colonization in the human body, without targeting specific types of bacteria. As a result, broad-spectrum antibiotics can greatly affect the composition of the gut microbiota, reduce its biodiversity, and delay colonization for a long period after administration. Thus, the action of antibiotics in AD could be wide and even opposite, depending on the type of antibiotic and on the specific role of the microbiome in AD pathogenesis.Alteration of the gut microbiota can induce changes in brain activity, which raise the possibility of therapeutic manipulation of the microbiome in AD and other neurological disorders. This field of research is currently undergoing great development, but therapeutic applications are still far away. Whether a therapeutic manipulation of gut microbiota in AD could be achieved using antibiotics is still not known. The future of antibiotics in AD depends on the research progresses in the role of gut bacteria. We must first understand how and when gut bacteria act to promote AD. Once the role of gut microbiota in AD is well established, one can think to induce modifications of the gut microbiota with the use of pre-, pro-, or antibiotics to produce therapeutic effects.},
}

@article {pmid31117952,
year = {2019},
author = {Moore, SG and Ericsson, AC and Behura, SK and Lamberson, WR and Evans, TJ and McCabe, MS and Poock, SE and Lucy, MC},
title = {Concurrent and long-term associations between the endometrial microbiota and endometrial transcriptome in postpartum dairy cows.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {405},
doi = {10.1186/s12864-019-5797-8},
pmid = {31117952},
issn = {1471-2164},
abstract = {BACKGROUND: Fertility in dairy cows depends on ovarian cyclicity and on uterine involution. Ovarian cyclicity and uterine involution are delayed when there is uterine dysbiosis (overgrowth of pathogenic bacteria). Fertility in dairy cows may involve a mechanism through which the uterine microbiota affects ovarian cyclicity as well as the transcriptome of the endometrium within the involuting uterus. The hypothesis was that the transcriptome of the endometrium in postpartum cows would be associated with the cyclicity status of the cow as well as the microbiota during uterine involution. The endometrium of first lactation dairy cows was sampled at 1, 5, and 9 weeks postpartum. All cows were allowed to return to cyclicity without intervention until week 5 and treated with an ovulation synchronization protocol so that sampling at week 9 was on day 13 of the estrous cycle. The endometrial microbiota was measured by 16S rRNA gene sequencing and principal component analysis. The endometrial transcriptome was measured by mRNA sequencing, differential gene expression analysis, and Ingenuity Pathway Analysis.

RESULTS: The endometrial microbiota changed from week 1 to week 5 but the week 5 and week 9 microbiota were similar. The endometrial transcriptome differed for cows that were either cycling or not cycling at week 5 and cyclicity status depended in part on the endometrial microbiota. Compared with cows cycling at week 5, there were large changes in the transcriptome of cows that progressed from non-cycling at week 5 to cycling at week 9. There was evidence for concurrent and longer-term associations between the endometrial microbiota and transcriptome. The week 1 endometrial microbiota had the greatest effect on the subsequent endometrial transcriptome and this effect was greatest at week 5 and diminished by week 9.

CONCLUSIONS: The cumulative response of the endometrial transcriptome to the microbiota represented the combination of past microbial exposure and current microbial exposure. The endometrial transcriptome in postpartum cows, therefore, depended on the immediate and longer-term effects of the uterine microbiota that acted directly on the uterus. There may also be an indirect mechanism through which the microbiome affects the transcriptome through the restoration of ovarian cyclicity postpartum.},
}

@article {pmid31117496,
year = {2019},
author = {Yuan, T and Chu, C and Shi, R and Cui, T and Zhang, X and Zhao, Y and Shi, X and Hui, Y and Pan, J and Qian, R and Dai, X and Liu, Z and Liu, X},
title = {The ApoE-dependent protective effects of sesamol on high-fat diet-induced behavioral disorders: regulation of the microbiome-gut-brain axis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.9b01436},
pmid = {31117496},
issn = {1520-5118},
abstract = {Sesamol, an antioxidant lignan from sesame oil, possesses neuroprotective bioactivities. The present work was aimed to elucidate the systemic protective effects of sesamol on cognitive deficits, and to determine the possible link between gut and brain. Wildtype and ApoE-/- mice were treated with a high-fat diet and sesamol (0.05%, w/w, in drinking water) for 10 weeks. Behavioral tests including Morris-water maze, Y-maze, and elevated plus maze tests indicated that sesamol could only improve cognitive deficits and anxiety behaviors in wildtype. Consistently, sesamol improved synapse ultrastructure and inhibited Aβ accumulation in an ApoE-dependent manner. Moreover, sesamol prevented dietary-induced gut barrier damages and systemic inflammation. Sesamol also re-shaped gut microbiome and improved the generation of microbial metabolites short chain fatty acids. To summarized, this study revealed that the possible mechanism of neuroprotective effects of sesamol might be ApoE-dependent, and its beneficial effects on gut microbiota/metabolites could be translated into neurodegenerative diseases treatment.},
}

@article {pmid31117285,
year = {2019},
author = {Krüger, W and Vielreicher, S and Kapitan, M and Jacobsen, ID and Niemiec, MJ},
title = {Fungal-Bacterial Interactions in Health and Disease.},
journal = {Pathogens (Basel, Switzerland)},
volume = {8},
number = {2},
pages = {},
doi = {10.3390/pathogens8020070},
pmid = {31117285},
issn = {2076-0817},
abstract = {Fungi and bacteria encounter each other in various niches of the human body. There, they interact directly with one another or indirectly via the host response. In both cases, interactions can affect host health and disease. In the present review, we summarized current knowledge on fungal-bacterial interactions during their commensal and pathogenic lifestyle. We focus on distinct mucosal niches: the oral cavity, lung, gut, and vagina. In addition, we describe interactions during bloodstream and wound infections and the possible consequences for the human host.},
}

@article {pmid31117282,
year = {2019},
author = {Gurusinghe, S and Brooks, TL and Barrow, RA and Zhu, X and Thotagamuwa, A and Dennis, PG and Gupta, VVSR and Vanniasinkam, T and Weston, LA},
title = {Technologies for the Selection, Culture and Metabolic Profiling of Unique Rhizosphere Microorganisms for Natural Product Discovery.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {10},
pages = {},
doi = {10.3390/molecules24101955},
pmid = {31117282},
issn = {1420-3049},
support = {UCS 00020//Grains Research and Development Corporation/ ; Honours Support Scheme//Graham Centre for Agricultural Innovation/ ; },
abstract = {Small molecule discovery has benefitted from the development of technologies that have aided in the culture and identification of soil microorganisms and the subsequent analysis of their respective metabolomes. We report herein on the use of both culture dependent and independent approaches for evaluation of soil microbial diversity in the rhizosphere of canola, a crop known to support a diverse microbiome, including plant growth promoting rhizobacteria. Initial screening of rhizosphere soils showed that microbial diversity, particularly bacterial, was greatest at crop maturity; therefore organismal recovery was attempted with soil collected at canola harvest. Two standard media (Mueller Hinton and gellan gum) were evaluated following inoculation with soil aqueous suspensions and compared with a novel "rhizochip" prototype buried in a living canola crop rhizosphere for microbial culture in situ. Following successful recovery and identification of 375 rhizosphere microbiota of interest from all culture methods, isolates were identified by Sanger sequencing and/or characterization using morphological and biochemical traits. Three bacterial isolates of interest were randomly selected as case studies for intensive metabolic profiling. After successful culture in liquid media and solvent extraction, individual extracts were subjected to evaluation by UHPLC-DAD-QToF-MS, resulting in the rapid characterization of metabolites of interest from cultures of two isolates. After evaluation of key molecular features, unique or unusual bacterial metabolites were annotated and are reported herein.},
}

@article {pmid31084747,
year = {2019},
author = {Blikslager, AT},
title = {Colic Prevention to Avoid Colic Surgery: A Surgeon's Perspective.},
journal = {Journal of equine veterinary science},
volume = {76},
number = {},
pages = {1-5},
doi = {10.1016/j.jevs.2019.02.023},
pmid = {31084747},
issn = {0737-0806},
abstract = {Management factors associated with colic, particularly related to stall confinement and nutrition, have been linked to alterations in gastrointestinal mucosal transport, motility, and microbiome, which in turn creates conditions that induce colic. In particular, meal feeding creates large changes in water movement in and out of the colon and alters the microbiome. These conditions may in turn result in colic conditions such as large colon impaction or large colon volvulus. In addition, a range of management and nutritional factors have been found to place horses at risk of select colic conditions such as ileal impaction. Other specific colic conditions, such as strangulating lipomas, may be related to fat metabolism in geldings and ponies, although the association with nutrition and the endocrine system are less well defined. It has long been understood that parasites are associated with colic, and with the advent of highly effective anthelmintics, parasite-induced colic has been markedly reduced. Nonetheless, equine mangers and veterinarians have to be aware of changes in parasite resistance or patterns of activity, such as the resurgence of large strongyles with surveillance-based management of parasites. Overall, understanding management risk factors can lead to recommendations that prevent colic in horses. Additional study of these factors may ultimately lead to reductions in the prevalence of colic by suggesting optimal management practices.},
}

@article {pmid31117025,
year = {2019},
author = {Shi, X and Shao, C and Luo, C and Chu, Y and Wang, J and Meng, Q and Yu, J and Gao, Z and Kang, Y},
title = {Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00198-19},
pmid = {31117025},
issn = {2379-5077},
abstract = {Dysbiosis of airway microbiomes has been found in various respiratory diseases, but its molecular details in terms of taxonomic profile, metabolic characteristics, defensive function, and inhabit adaption are far from clear. Shotgun metagenome sequencing provides detailed information for microbes, whereas its application is rather limited in airways due to host DNA contaminants that overwhelm a minute amount of microbial content. Here, we describe a microfluidics-based enrichment device and an emulsion-based whole-genome amplification procedure (MEEA) for the preparation of DNA from sputa for shotgun sequencing in a metagenomics study. The two protocols coupled in MEEA are first separately assayed with mock samples and are both promising in efficiency and bias. The efficiency and consistency of MEEA are further evaluated in six clinical sputum samples against direct sequencing without enrichment, and MEEA enables 2 to 14 times enrichment for microbial reads, which take 14.68% to 33.52% of total reads. The dominant pathogens detected in MEEA are in excellent agreement with those from clinical etiological tests. Meanwhile, MEEA presents much more microbiome complexity and genome information at a strain level than direct sequencing, exhibiting high sensitivity for identifying prophages and DNA viruses. MEEA provides better microbiome profiling than direct sequencing without a preference for specific microorganisms. The more detailed functional and taxonomic characterization of their species constituents, including both bacterium and virus, facilitates metagenomics studies on the pathogenesis of respiratory microbiomes.IMPORTANCE The airway microbial community, which takes important pathogenic roles for respiratory diseases, is far from clear in terms of taxonomy and gene functions. One of the critical reasons is the heavy contamination of host cell/DNA in airway samples, which hinders the subsequent sequencing of the whole genomic contents of the microbial community-the metagenome. Here, we describe a protocol for airway sample preparation which couples a microbe enrichment microfluidic device and a DNA amplification method performed in numerous droplets. When evaluated with mock and clinical sputum samples, the microfluidics-based enrichment device and emulsion-based whole-genome amplification (MEEA) procedure efficiently removes host cells, amplifies the microbial genome, and shows no obvious bias among microbes. The efficiency of MEEA makes it a promising method in research of respiratory microbial communities and their roles in diseases.},
}

@article {pmid31117024,
year = {2019},
author = {Amato, KR},
title = {Missing Links: the Role of Primates in Understanding the Human Microbiome.},
journal = {mSystems},
volume = {4},
number = {3},
pages = {},
doi = {10.1128/mSystems.00165-19},
pmid = {31117024},
issn = {2379-5077},
abstract = {The gut microbiome can influence host energy balances and metabolic programming. While this information is valuable in a disease context, it also has important implications for understanding host energetics from an ecological and evolutionary perspective. Here I argue that gut microbial influences on host life history-the timing of events that make up an organism's life-are an overlooked but robust area of study given that variation in life history is linked directly to host energetic budgets and allocation patterns. Additionally, while cultural influences on life history complicate the exploration of these links in humans, nonhuman primates represent an alternative system in which more robust associations can be made. By integrating human and nonhuman primate microbiome research within the context of life history theory, we will be able to more effectively pinpoint microbial contributions to host phenotypes. This information will improve our understanding of host-microbe interactions in health and disease and will transform the fields of ecology and evolution more generally.},
}

@article {pmid31117019,
year = {2019},
author = {Kleiner, M},
title = {Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities.},
journal = {mSystems},
volume = {4},
number = {3},
pages = {},
doi = {10.1128/mSystems.00115-19},
pmid = {31117019},
issn = {2379-5077},
abstract = {Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the "expressed" metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.},
}

@article {pmid31116541,
year = {2019},
author = {Nagai, K and Tokita, KI and Ono, H and Uchida, K and Sakamoto, F and Higuchi, H},
title = {Hindgut Bacterial Flora Analysis in Oriental Honey Buzzard (Pernis ptilorhynchus).},
journal = {Zoological science},
volume = {36},
number = {1},
pages = {77-81},
doi = {10.2108/zs180121},
pmid = {31116541},
issn = {0289-0003},
abstract = {The intestinal microbiome is known to affect host health through various effects on nutrition and immunity. The oriental honey buzzard (OHB) is a raptor that feeds on bees and wasps. Due to its restricted diet, we reasoned that the OHB may have a unique microbiome. The aim of this study was to characterize the structure of the intestinal flora of oriental honey buzzards and to investigate the difference of intestinal bacterial flora between individuals in the wild and those reared in captivity. We investigated the intestinal microbiome of seven wild buzzards (Wild), one zoo-reared (Zoo), and one individual reared in captivity for one month (Rearing). Average operational taxonomic units in Wild and Rearing were 69.4 and 113, respectively. Diversity indices such as ACE, Chao 1, Shannon, and Alpha were significantly lower in the Wild than in the Rearing samples. These results suggest that the variety of Wild microbiome is remarkably low. At the phylum level, the composition of the microbiome was similar in all three groups, with firmicutes and bacteroidetes predominating. The third most abundant bacterium in Wild was Proteobacteria, whereas it was Actinobacteria in Rearing and unclassified bacteria in Zoo. Thus, microbiome composition is affected even with just one month of human rearing.},
}

@article {pmid31116403,
year = {2019},
author = {Holman, DB and Gzyl, KE},
title = {A meta-analysis of the bovine gastrointestinal tract microbiota.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz072},
pmid = {31116403},
issn = {1574-6941},
abstract = {The bovine gastrointestinal (GI) tract microbiota has important influences on animal health and production. Presently, a large number of studies have used high-throughput sequencing of the archaeal and bacteria 16S rRNA gene to characterize these microbiota under various experimental parameters. By aggregating publically available archaeal and bacterial 16S rRNA gene datasets from 53 studies we were able to determine taxa that are common to nearly all microbiota samples from the bovine GI tract as well as taxa that are strongly linked to either the rumen or feces. The methanogenic genera Methanobrevibacter and Methanosphaera were identified in nearly all fecal and rumen samples (> 99.1%), as were the bacterial genera Prevotella and Ruminococcus (≥ 92.9%). Bacterial genera such as Alistipes, Bacteroides, Clostridium, Faecalibacterium, and Escherichia/Shigella were associated with feces and Fibrobacter, Prevotella, Ruminococcus, and Succiniclasticum with the rumen. As expected, individual study strongly affected the bacterial community structure, however, fecal and rumen samples did appear separated from each other. This meta-analysis provides the first comparison of high-throughput sequencing 16S rRNA gene datasets generated from the bovine GI tract by multiple studies and may serve as a foundation for improving future microbial community research with cattle.},
}

@article {pmid31116375,
year = {2019},
author = {Ma, A and Sun, M and McDermaid, A and Liu, B and Ma, Q},
title = {MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btz414},
pmid = {31116375},
issn = {1367-4811},
abstract = {MOTIVATION: Metagenomic and metatranscriptomic analyses can provide an abundance of information related to microbial communities. However, straightforward analysis of this data does not provide optimal results, with a required integration of data types being needed to thoroughly investigate these microbiomes and their environmental interactions.

RESULTS: Here, we present MetaQUBIC, an integrated biclustering-based computational pipeline for gene module detection that integrates both metagenomic and metatranscriptomic data. Additionally, we used this pipeline to investigate 735 paired DNA and RNA human gut microbiome samples, resulting in a comprehensive hybrid gene expression matrix of 2.3 million cross-species genes in the 735 human faecal samples and 155 functional enriched gene modules. We believe both the MetaQUBIC pipeline and the generated comprehensive human gut hybrid expression matrix will facilitate further investigations into multiple levels of microbiome studies.

AVAILABILITY: The package is freely available at https://github.com/OSU-BMBL/metaqubic.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid31116134,
year = {2019},
author = {Revolinski, SL and Munoz-Price, LS},
title = {Clostridioides difficile in transplant patients: early diagnosis, treatment, and prevention.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000000560},
pmid = {31116134},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Clostridioides difficile infection is common in solid organ transplant and hematopoietic stem-cell transplant recipients and is associated with significant morbidity and mortality. These populations are also underrepresented in clinical trials, making optimal management difficult. Because of this, management of these populations follows national guideline recommendations. This review aims to summarize the recent relevant literature pertaining to the clinical management of C. difficile infection in transplant patients, with a particular focus on diagnosis, treatment, and prevention.

RECENT FINDINGS: Early diagnosis of C. difficile colonization may mitigate both horizontal and vertical transmission (progression from colonization to colitis) of infection. Once diagnosed, recent literature suggests antibiotic treatment should align with that recommended by national guidelines. Fecal microbiota transplant is an emerging therapy for recurrent C. difficile infection, and recent data have demonstrated safety and efficacy. Prevention strategies including antimicrobial stewardship, probiotic administration, antibiotic administration, and bezlotoxumab may be beneficial in transplant populations, but more data are needed to confirm recent findings.

SUMMARY: Studies evaluating C. difficile infection in transplant patients are only recently starting to emerge. Further research is needed to identify optimal treatment and prevention strategies, and to examine novel strategies such as microbiome manipulation.},
}

@article {pmid31115933,
year = {2019},
author = {Hsu, PI and Pan, CY and Kao, JY and Tsay, FW and Peng, NJ and Kao, SS and Chen, YH and Tsai, TJ and Wu, DC and Tsai, KW},
title = {Short-term and long-term impacts of Helicobacter pylori eradication with reverse hybrid therapy on the gut microbiota.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.14736},
pmid = {31115933},
issn = {1440-1746},
abstract = {BACKGROUND AND AIMS: Anti-H. pylori therapy may lead to the growth of pathogenic or antibiotic-resistant bacteria in the gut. The study aimed to investigate the short-term and long-term impacts of H. pylori eradication with reverse hybrid therapy on the components and macrolide resistance of the gut microbiota.

METHODS: H. pylori-related gastritis patients were administered a 14-day reverse hybrid therapy. Fecal samples were collected before treatment and at the end of week 2, week 8, and week 48. The V3-V4 region of the bacterial 16S rRNA gene in fecal specimens was amplified by polymerase chain reaction and sequenced on Illumina Miseq platform. Additionally, amplification of erm(B) gene (encoding erythromycin resistance methylase) was performed.

RESULTS: Reverse hybrid therapy resulted in decreased relative abundances of Firmicutes (from 62.0% to 30.7%; P < 0.001) and Actinobacteria (from 3.4% to 0.6%; 0.032) at the end of therapy. In contrast, the relative abundance of Proteobacteria increased from 10.2% to 49.1% (0.002). These microbiota alterations did not persist but returned to the initial levels at week 8 and week 48. The amount of erm(B) gene in fecal specimens was comparable to the pretreatment level at week 2 but increased at week 8 (0.025) and then returned to the pretreatment level by week 48.

CONCLUSIONS: H. pylori eradication with reverse hybrid therapy can lead to short-term gut dysbiosis. The amount of erm(B) gene in the stool increased transiently after treatment and returned to the pretreatment level 1-year post-treatment.},
}

@article {pmid31115680,
year = {2019},
author = {Bento-Silva, A and Koistinen, VM and Mena, P and Bronze, MR and Hanhineva, K and Sahlstrøm, S and Kitrytė, V and Moco, S and Aura, AM},
title = {Factors affecting intake, metabolism and health benefits of phenolic acids: do we understand individual variability?.},
journal = {European journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00394-019-01987-6},
pmid = {31115680},
issn = {1436-6215},
support = {FA1403 POSITIVe//European Cooperation in Science and Technology/ ; },
abstract = {INTRODUCTION: Phenolic acids are important phenolic compounds widespread in foods, contributing to nutritional and organoleptic properties.

The bioavailability of these compounds depends on their free or conjugated presence in food matrices, which is also affected by food processing. Phenolic acids undergo metabolism by the host and residing intestinal microbiota, which causes conjugations and structural modifications of the compounds. Human responses, metabolite profiles and health responses of phenolics, show considerable individual variation, which is affected by absorption, metabolism and genetic variations of subjects.

OPINION: A better understanding of the gut-host interplay and microbiome biochemistry is becoming highly relevant in understanding the impact of diet and its constituents. It is common to study metabolism and health benefits separately, with some exceptions; however, it should be preferred that health responders and non-responders are studied in combination with explanatory metabolite profiles and gene variants. This approach could turn interindividual variation from a problem in human research to an asset for research on personalized nutrition.},
}

@article {pmid31114975,
year = {2019},
author = {Sarris, J},
title = {Nutritional Psychiatry: From Concept to the Clinic.},
journal = {Drugs},
volume = {},
number = {},
pages = {},
doi = {10.1007/s40265-019-01134-9},
pmid = {31114975},
issn = {1179-1950},
abstract = {The field of 'nutritional psychiatry' has evolved with rapidity over the past several years, with an increasing amount of dietary or nutrient-based (nutraceutical) intervention studies being initiated, and more preclinical and epidemiological data being available. This emergent paradigm involves the clinical consideration (where appropriate) of prescriptive dietary modification/improvement, and/or the select judicious use of nutrient-based supplementation to prevent or manage psychiatric disorders. In the last several years, significant links have increasingly been established between dietary quality and mental health (although not all data are supportive). Maternal and early-life nutrition may also affect the mental health outcomes in offspring. In respect to nutraceutical research, like with many recent conventional drug studies, results are fairly mixed across the board, and in many cases there is not emphatic evidence to support the use of nutraceuticals in various psychiatric disorders. This may in part be due to a preponderance of recent studies within the field revealing marked placebo effects. Due to current indicators pointing towards mental disorders having an increasing burden of disease, bold and innovative approaches on a societal level are now required. In light of the widespread use of nutrient supplements by those with and without mental disorders, it is also critical that scientifically rigorous methodologies be brought to bear on the assessment of the efficacy of these supplements, and to determine if, or what dose of, a nutrient supplement is required, for whom, and when, and under what circumstances. More simple studies of additional isolated nutrients are not of great benefit to the field (unless studied in supra-dosage in an individualised, biomarker-guided manner), nor, based on recent data, is the research of 'shotgun' formulations of nutraceuticals. The next critical step for the field is to design psychiatric interventional studies for both dietary modification and nutraceuticals, based on more of a personalised medicine approach, using biomarkers (e.g. nutrient deficiencies, inflammatory cytokine levels, genomic assessment, microbiome analysis) and a person's dietary patterns and individual macro/micronutrient requirements.},
}

@article {pmid31114971,
year = {2019},
author = {de Assumpção, PP and Araújo, TMT and de Assumpção, PB and Barra, WF and Khayat, AS and Assumpção, CB and Ishak, G and Nunes, DN and Dias-Neto, E and Coelho, LGV},
title = {Suicide journey of H. pylori through gastric carcinogenesis: the role of non-H. pylori microbiome and potential consequences for clinical practice.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10096-019-03564-5},
pmid = {31114971},
issn = {1435-4373},
abstract = {Despite being one of the most studied cancer-related infections, the relationship between Helicobacter pylori infection and gastric adenocarcinoma (GC) remains, in some points, obscure. Based on a critical analysis of the available literature regarding stomach microbiota, we aimed to shed light to a possible new interpretation of the current understanding about the Helicobacter pylori-related GC carcinogenesis. We analyzed data from the literature on Helicobacter pylori and other potential carcinogenic pathogens, in both benignant conditions and gastric adenocarcinoma. Helicobacter pylori is the dominant microorganism in benignant conditions as non-complicated gastritis. In atrophic gastritis, metaplasia and, mainly, in gastric adenocarcinoma, a strong reduction in Helicobacter pylori abundance, and increased occurrence of other microorganisms is strongly demonstrated by metagenomic experiments. While causing peptic disease and keeping the stomach's high acidity, Helicobacter pylori infection avoids gastric infection by carcinogenic intestinal microbiota. Nevertheless, Helicobacter pylori persistence may also provoke an atrophic gastritis, a condition that causes its own decline, due to a microenvironment modification, including reduced acidity, resulting in Helicobacter pylori substitution by a cancer-prone microbiota. This new interpretation might result in a dramatic modification on clinical management of Helicobacter pylori-related gastric disease.},
}

@article {pmid31114912,
year = {2019},
author = {Avram, O and Rapoport, D and Portugez, S and Pupko, T},
title = {M1CR0B1AL1Z3R-a user-friendly web server for the analysis of large-scale microbial genomics data.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz423},
pmid = {31114912},
issn = {1362-4962},
abstract = {Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a 'one-stop shop' for conducting microbial genomics data analyses via a simple graphical user interface. Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence-absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/.},
}

@article {pmid31114711,
year = {2019},
author = {Day, RL and Harper, AJ and Woods, RM and Davies, OG and Heaney, LM},
title = {Probiotics: current landscape and future horizons.},
journal = {Future science OA},
volume = {5},
number = {4},
pages = {FSO391},
doi = {10.4155/fsoa-2019-0004},
pmid = {31114711},
issn = {2056-5623},
abstract = {In recent years there has been a rapid rise in interest for the application of probiotic supplements to act as mediators in health and disease. This appeal is predominantly due to ever-increasing evidence of the interaction of the microbiota and pathophysiological processes of disease within the human host. This narrative review considers the current landscape of the probiotic industry and its research, and discusses current pitfalls in the lack of translation from laboratory science to clinical application. Future considerations into how industry and academia must adapt probiotic research to maximize success are suggested, including more targeted application of probiotic strains dependent on individual capabilities as well as application of multiple advanced analytical technologies to further understand and accelerate microbiome science.},
}

@article {pmid31114707,
year = {2019},
author = {Heaney, LM and Davies, OG and Selby, NM},
title = {Gut microbial metabolites as mediators of renal disease: do short-chain fatty acids offer some hope?.},
journal = {Future science OA},
volume = {5},
number = {4},
pages = {FSO384},
doi = {10.4155/fsoa-2019-0013},
pmid = {31114707},
issn = {2056-5623},
}

@article {pmid31114705,
year = {2019},
author = {R Wardill, H},
title = {Early career interview: Hannah Wardill.},
journal = {Future science OA},
volume = {5},
number = {4},
pages = {FSO382},
doi = {10.4155/fsoa-2019-0011},
pmid = {31114705},
issn = {2056-5623},
}

@article {pmid31114574,
year = {2019},
author = {Kuhbandner, K and Hammer, A and Haase, S and Terbrack, E and Hoffmann, A and Schippers, A and Wagner, N and Hussain, RZ and Miller-Little, WA and Koh, AY and Stoolman, JS and Segal, BM and Linker, RA and Stüve, O},
title = {MAdCAM-1-Mediated Intestinal Lymphocyte Homing Is Critical for the Development of Active Experimental Autoimmune Encephalomyelitis.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {903},
doi = {10.3389/fimmu.2019.00903},
pmid = {31114574},
issn = {1664-3224},
abstract = {Lymphocyte homing into the intestine is mediated by binding of leukocytes to mucosal addressin cell adhesion molecule 1 (MAdCAM-1), expressed on endothelial cells. Currently, the immune system of the gut is considered a major modulator not only of inflammatory bowel disease, but also of extra-intestinal autoimmune disorders, including multiple sclerosis (MS). Despite intense research in this field, the exact role of the intestine in the pathogenesis of (neuro-)inflammatory disease conditions remains to be clarified. This prompted us to investigate the role of MAdCAM-1 in immunological processes in the intestine during T cell-mediated autoimmunity of the central nervous system (CNS). Using the experimental autoimmune encephalomyelitis model of MS, we show that MAdCAM-1-deficient (MAdCAM-1-KO) mice are less susceptible to actively MOG35-55-induced disease. Protection from disease was accompanied by decreased numbers of immune cells in the lamina propria and Peyer's patches as well as reduced immune cell infiltration into the spinal cord. MOG35-55-recall responses were intact in other secondary lymphoid organs of MAdCAM-1-KO mice. The composition of specific bacterial groups within the microbiome did not differ between MAdCAM-1-KO mice and controls, while MAdCAM-1-deficiency severely impaired migration of MOG35-55-activated lymphocytes to the gut. Our data indicate a critical role of MAdCAM-1 in the development of CNS inflammation by regulating lymphocyte homing to the intestine, and may suggest a role for the intestinal tract in educating lymphocytes to become encephalitogenic.},
}

@article {pmid31114571,
year = {2019},
author = {Haussner, F and Chakraborty, S and Halbgebauer, R and Huber-Lang, M},
title = {Challenge to the Intestinal Mucosa During Sepsis.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {891},
doi = {10.3389/fimmu.2019.00891},
pmid = {31114571},
issn = {1664-3224},
abstract = {Sepsis is a complex of life-threating organ dysfunction in critically ill patients, with a primary infectious cause or through secondary infection of damaged tissues. The systemic consequences of sepsis have been intensively examined and evidences of local alterations and repercussions in the intestinal mucosal compartment is gradually defining gut-associated changes during sepsis. In the present review, we focus on sepsis-induced dysfunction of the intestinal barrier, consisting of an increased permeability of the epithelial lining, which may facilitate bacterial translocation. We discuss disturbances in intestinal vascular tonus and perfusion and coagulopathies with respect to their proposed underlying molecular mechanisms. The consequences of enzymatic responses by pancreatic proteases, intestinal alkaline phosphatases, and several matrix metalloproteases are also described. We conclude our insight with a discussion on novel therapeutic interventions derived from crucial aspects of the gut mucosal dynamics during sepsis.},
}

@article {pmid31114550,
year = {2019},
author = {Martinez-Fernandez, G and Denman, SE and McSweeney, CS},
title = {Sample Processing Methods Impacts on Rumen Microbiome.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {861},
doi = {10.3389/fmicb.2019.00861},
pmid = {31114550},
issn = {1664-302X},
abstract = {The standardization of collection and processing methods for rumen samples is crucial to reduce the level of errors that may affect the analysis and interpretation of the data. The aim of this study was to compare two processing methods and their impacts on the microbial community composition analysis, from material that was either immediately frozen or samples that were stored as cell pellets after removing the supernatant prior to freezing. Eight rumen-fistulated Brahman steers received chloroform as an antimethanogenic compound for 21 days. Rumen fluid samples (60 mL per animal) were collected using a probe covered with two layers of cheesecloth at 3 h post feeding at day 0 prior-treatment (control period) and day 21 of treatment. One sub-set of samples were placed in dry ice and stored at -80°C (Method 1) for subsequent DNA extraction, while a second subset of samples was centrifuged, the supernatant removed and the microbial pellet and rumen contents placed in dry ice and stored at -80°C (Method 2) prior to DNA extractions. Phylogenetic based methods (Illumina Miseq) targeting the 16S rRNA gene were used to characterize the bacterial and archaeal communities from both collection methods for the control and treatment periods. The results from this study showed that the chloroform treatment was significantly different for all beta diversity measures regardless of the processing method used. Significant differences in the relative abundances of some bacteria and archaea, such as Elusimicrobia, Fibrobacteres, Lentisphaerae, Spirochaetes, and Verrucomicrobia and Methanomassiliicoccaceae, were observed at higher levels in the Method 2. These microbial populations are known to have fragile cell wall structures and are susceptible to cell lysis. Regardless of the processing method used, both identified the key microbial groups and can be used to compare the relative shifts in the rumen microbiome between treatments. However, immediately freezing samples might alter the abundance of material from species that are more readily lysed and will not be suitable for studies that aim to assign absolute abundance values to these species within the rumen.},
}

@article {pmid31113768,
year = {2019},
author = {Ryan, PM and Stanton, C and Ross, RP and Kelly, AL and Dempsey, E and Ryan, CA},
title = {Paediatrician's perspective of infant gut microbiome research: current status and challenges.},
journal = {Archives of disease in childhood},
volume = {},
number = {},
pages = {},
doi = {10.1136/archdischild-2019-316891},
pmid = {31113768},
issn = {1468-2044},
abstract = {Due to its innately intriguing nature and recent genomic technological advances, gut microbiome research has been at the epicentre of medical research for over a decade now. Despite the degree of publicisation, a comprehensive understanding and, therefore, acceptance of the area as a whole may be somewhat lacking within the broader medical community. This paper summarises the main analytical techniques and tools currently applied to compositional microbiome research. In addition, we outline five major lessons learnt from a decade of infant microbiome research, along with the current research gaps. Finally, we aim to provide an introduction and general guidelines relating to infant gut microbiome research for the practising paediatrician.},
}

@article {pmid31113486,
year = {2019},
author = {Bedognetti, D and Ceccarelli, M and Galluzzi, L and Lu, R and Palucka, K and Samayoa, J and Spranger, S and Warren, S and Wong, KK and Ziv, E and Chowell, D and Coussens, LM and De Carvalho, DD and DeNardo, DG and Galon, J and Kaufman, HL and Kirchhoff, T and Lotze, MT and Luke, JJ and Minn, AJ and Politi, K and Shultz, LD and Simon, R and Thórsson, V and Weidhaas, JB and Ascierto, ML and Ascierto, PA and Barnes, JM and Barsan, V and Bommareddy, PK and Bot, A and Church, SE and Ciliberto, G and De Maria, A and Draganov, D and Ho, WS and McGee, HM and Monette, A and Murphy, JF and Nisticò, P and Park, W and Patel, M and Quigley, M and Radvanyi, L and Raftopoulos, H and Rudqvist, NP and Snyder, A and Sweis, RF and Valpione, S and Butterfield, LH and Disis, ML and Fox, BA and Cesano, A and Marincola, FM and , },
title = {Toward a comprehensive view of cancer immune responsiveness: a synopsis from the SITC workshop.},
journal = {Journal for immunotherapy of cancer},
volume = {7},
number = {1},
pages = {131},
doi = {10.1186/s40425-019-0602-4},
pmid = {31113486},
issn = {2051-1426},
abstract = {Tumor immunology has changed the landscape of cancer treatment. Yet, not all patients benefit as cancer immune responsiveness (CIR) remains a limitation in a considerable proportion of cases. The multifactorial determinants of CIR include the genetic makeup of the patient, the genomic instability central to cancer development, the evolutionary emergence of cancer phenotypes under the influence of immune editing, and external modifiers such as demographics, environment, treatment potency, co-morbidities and cancer-independent alterations including immune homeostasis and polymorphisms in the major and minor histocompatibility molecules, cytokines, and chemokines. Based on the premise that cancer is fundamentally a disorder of the genes arising within a cell biologic process, whose deviations from normality determine the rules of engagement with the host's response, the Society for Immunotherapy of Cancer (SITC) convened a task force of experts from various disciplines including, immunology, oncology, biophysics, structural biology, molecular and cellular biology, genetics, and bioinformatics to address the complexity of CIR from a holistic view. The task force was launched by a workshop held in San Francisco on May 14-15, 2018 aimed at two preeminent goals: 1) to identify the fundamental questions related to CIR and 2) to create an interactive community of experts that could guide scientific and research priorities by forming a logical progression supported by multiple perspectives to uncover mechanisms of CIR. This workshop was a first step toward a second meeting where the focus would be to address the actionability of some of the questions identified by working groups. In this event, five working groups aimed at defining a path to test hypotheses according to their relevance to human cancer and identifying experimental models closest to human biology, which include: 1) Germline-Genetic, 2) Somatic-Genetic and 3) Genomic-Transcriptional contributions to CIR, 4) Determinant(s) of Immunogenic Cell Death that modulate CIR, and 5) Experimental Models that best represent CIR and its conversion to an immune responsive state. This manuscript summarizes the contributions from each group and should be considered as a first milestone in the path toward a more contemporary understanding of CIR. We appreciate that this effort is far from comprehensive and that other relevant aspects related to CIR such as the microbiome, the individual's recombined T cell and B cell receptors, and the metabolic status of cancer and immune cells were not fully included. These and other important factors will be included in future activities of the taskforce. The taskforce will focus on prioritization and specific actionable approach to answer the identified questions and implementing the collaborations in the follow-up workshop, which will be held in Houston on September 4-5, 2019.},
}

@article {pmid31113268,
year = {2019},
author = {Keskin, M and Goksan Pabuccu, E and Sahin, O and Cakmak, D and Oral, S and Kiseli, M and Yarcı Gursoy, A},
title = {Oral antibiotic prophylaxis in elective cesarean deliveries: pilot analysis in tertiary Care Hospital.},
journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians},
volume = {},
number = {},
pages = {1-151},
doi = {10.1080/14767058.2019.1622670},
pmid = {31113268},
issn = {1476-4954},
abstract = {INTRODUCTION: Puerperal infection remains a significant cause of maternal morbidity and mortality. Those infections occur more likely after cesarean delivery (CD). Prophylactic antibiotics are administered at the time of CD to prevent complications. In addition to intraoperative prophylaxis; prescription of antibiotics during hospital discharge to prevent surgical site infections (SSI) is quite common. Purpose of this study is to determine the utility of prophylactic oral antibiotic prescription in a cohort of low-risk women undergoing CD.

MATERIALS AND METHODS: A prospective observational study was conducted between 2014 and 2018 at Ufuk University School of Medicine, Department of Obstetrics and Gynaecology. Total of 389 low risk elective cesarean deliveries were selected. All cases received intraoperative prophylaxis. In group I (157 subjects), no further antibiotics were given and in group II (232 cases), oral cephuroxime 500 mg was given during hospital discharge. Primary outcome was SSI. Secondary outcomes were endometritis and other infectious conditions.

RESULTS: Overall SSI rate was 2.5%. Only 2 SSIs were noted in group 1 (1.2%) compared to eight in group II (3.4%). There was no statistical difference in SSI rate between two groups. Secondary outcomes were also comparable.

CONCLUSION: In this study we failed to reveal any beneficial effect of oral antibiotic prescription during hospital discharge in low risk elective CDs. Therefore, use of oral antibiotics in addition to intraoperative prophylaxis should be questioned in terms of increased costs, emergence of bacterial resistance and long term effects on new born as a consequence of changes in gut microbiome.},
}

@article {pmid31113222,
year = {2019},
author = {Lew, KN and Starkweather, A and Cong, X and Judge, M},
title = {A Mechanistic Model of Gut-Brain Axis Perturbation and High-Fat Diet Pathways to Gut Microbiome Homeostatic Disruption, Systemic Inflammation, and Type 2 Diabetes.},
journal = {Biological research for nursing},
volume = {},
number = {},
pages = {1099800419849109},
doi = {10.1177/1099800419849109},
pmid = {31113222},
issn = {1552-4175},
abstract = {Type 2 diabetes (T2D) is a highly prevalent metabolic disease, affecting nearly 10% of the American population. Although the etiopathogenesis of T2D remains poorly understood, advances in DNA sequencing technologies have allowed for sophisticated interrogation of the human microbiome, providing insight into the role of the gut microbiome in the development and progression of T2D. An emerging body of research reveals that gut-brain axis (GBA) perturbations and a high-fat diet (HFD), along with other modifiable and nonmodifiable risk factors, contribute to gut microbiome homeostatic imbalance. Homeostatic imbalance or disruption increases gut wall permeability and facilitates translocation of endotoxins (lipopolysaccharides) into the circulation with resultant systemic inflammation. Chronic, low-grade systemic inflammation ensues with pro-inflammatory pathways activated, contributing to obesity, insulin resistance (IR), pancreatic β-cell decline, and, thereby, T2D. While GBA perturbations and HFD are implicated in provoking these conditions, prior mechanistic models have tended to examine HFD and GBA pathways exclusively without considering their shared pathways to T2D. Addressing this gap, this article proposes a mechanistic model informed by animal and human studies to advance scientific understanding of (1) modifiable and nonmodifiable risk factors for gut microbiome homeostatic disruption, (2) HFD and GBA pathways contributing to homeostatic disruption, and (3) shared GBA and HFD pro-inflammatory pathways to obesity, IR, β-cell decline, and T2D. The proposed mechanistic model, based on the extant literature, proposes a framework for studying the complex relationships of the gut microbiome to T2D to advance study in this promising area of research.},
}

@article {pmid31112983,
year = {2019},
author = {Claudel, JP and Auffret, N and Leccia, MT and Poli, F and Corvec, S and Dréno, B},
title = {Staphylococcus epidermidis: A Potential New Player in the Physiopathology of Acne?.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-8},
doi = {10.1159/000499858},
pmid = {31112983},
issn = {1421-9832},
abstract = {BACKGROUND: Cutibacterium acnes has been identified as one of the main triggers of acne. However, increasing knowledge of the human skin microbiome raises questions about the role of other skin commensals, such as Staphylococcus epidermidis, in the physiopathology of this skin disease.

SUMMARY: This review provides an overview of current knowledge of the potential role of S. epidermidis in the physiopathology of acne. Recent research indicates that acne might be the result of an unbalanced equilibrium between C. acnes and S. epidermidis,according to dedicated interactions. Current treatments act on C. acnesonly. Other treatment options may be considered, such as probiotics derived from S. epidermidis to restore the naturally balanced microbiota or through targeting the regulation of the host's AMP mediators. Key Messages: Research seems to confirm the beneficial role of S. epidermidis in acne by limiting C. acnes over-colonisation and inflammation.},
}

@article {pmid31112880,
year = {2019},
author = {Gopinath, D and Menon, RK and Banerjee, M and Su Yuxiong, R and Botelho, MG and Johnson, NW},
title = {Culture-independent studies on bacterial dysbiosis in oral and oropharyngeal squamous cell carcinoma: A systematic review.},
journal = {Critical reviews in oncology/hematology},
volume = {139},
number = {},
pages = {31-40},
doi = {10.1016/j.critrevonc.2019.04.018},
pmid = {31112880},
issn = {1879-0461},
abstract = {Imbalance within the resident bacterial community (dysbiosis), rather than the presence and activity of a single organism, has been proposed to be associated with, and to influence, the development and progression of various diseases; however, the existence and significance of dysbiosis in oral/oropharyngeal cancer is yet to be clearly established. A systematic search (conducted on 25/01/2018 and updated on 25/05/2018) was performed on three databases (Pubmed, Web of Science & Scopus) to identify studies employing culture-independent methods which investigated the bacterial community in oral/oropharyngeal cancer patients compared to control subjects. Of the 1546 texts screened, only fifteen publications met the pre-determined selection criteria. Data extracted from 731 cases and 809 controls overall, could not identify consistent enrichment of any particular taxon in oral/oropharyngeal cancers, although common taxa could be identified between studies. Six studies reported the enrichment of Fusobacteria in cancer at different taxonomic levels whereas four studies reported an increase in Parvimonas. Changes in microbial diversity remained inconclusive, with four studies showing a higher diversity in controls, three studies showing a higher diversity in tumors and three additional studies showing no difference between tumors and controls. Even though most studies identified a component of dysbiosis in oral/oropharyngeal cancer, methodological and analytical variations prevented a standardized summary, which highlights the necessity for studies of superior quality and magnitude employing standardized methodology and reporting. Indeed an holistic metagenomic approach is likely to be more meaningful, as is understanding of the overall metabolome, rather than a mere enumeration of the organisms present.},
}

@article {pmid31112792,
year = {2019},
author = {Nathalie, M and de Wiele Tom, V and Fiona, F and Siobhain, O and Gerard, C and James, K},
title = {Gut microbiome patterns depending on children's psychosocial stress: reports versus biomarkers.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2019.05.024},
pmid = {31112792},
issn = {1090-2139},
abstract = {AIM: Chronic stress increases disease vulnerability factors including inflammation, a pathological characteristic potentially regulated by the gut microbiota. We checked the association between the gut microbiome and psychosocial stress in children/adolescents and investigated which stress parameter (negative versus positive emotion, self-report versus parental report, events versus emotions, biomarker cortisol versus parasympathetic activity) is the most relevant indicator herein.

METHODS: Gut microbiome sequencing was completed in fecal samples from 93 Belgian 8-16y olds. Stress measures included negative events, negative emotions, emotional problems reported by parents, happiness, hair cortisol and heart rate variability (pnn50 parameter reflecting parasympathetic activity). Alpha diversity, beta diversity and linear discriminant analysis were the unadjusted analyses. Age, sex, socio-economic status, diet, physical activity, sleep and weight status were adjusted for via a redundancy analysis and differential abundance via zero-inflated negative binomial regression.

RESULTS: High stress as reflected by low pnn50 and more negative events were associated with a lower alpha diversity as indicated by the Simpson index. Happiness and pnn50 showed significant differences between high and low stress groups based on weighted UniFrac distance, and this remained significant after confounder adjustment. Adjusted and unadjusted taxonomic differences were also most pronounced for happiness and pnn50 being associated respectively with 24 OTU (=11.8% of bacterial counts) and 31 OTU (=13.0%). As a general pattern, high stress was associated with lower Firmicutes at the phylum level and higher Bacteroides, Parabacteroides, Rhodococcus, Methanobrevibacter and Roseburia but lower Phascolarctobacterium at genus level. Several genera gave conflicting results between different stress measures e.g. Ruminococcaceae UCG014, Tenericutes, Eubacterium coprostanoligenes, Prevotella 9 and Christensenellaceae R7. Differential results in preadolescents versus adolescents were also evident.

CONCLUSION: Even in this young healthy population, stress parameters were cross-sectionally associated with gut microbial composition but this relationship was instrument specific. Positive emotions and parasympathetic activity appeared the strongest parameters and should be integrated in future microbiota projects amongst other stress measures.},
}

@article {pmid31111967,
year = {2019},
author = {Chang, AM and Liu, Q and Hajjar, AM and Greer, A and McLean, JS and Darveau, RP},
title = {Toll-like receptor 2 and toll-like receptor 4 responses regulate neutrophil infiltration into the junctional epithelium and significantly contribute to the composition of the oral microbiota.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/JPER.18-0719},
pmid = {31111967},
issn = {1943-3670},
abstract = {BACKGROUND: Oral gingival tissue, especially the junctional epithelium (JE), is constantly exposed to sub-gingival plaque. A key component of gingival health is the regulation of the number of neutrophils that migrate into the gingival crevice to counteract its harmful effects. This report investigates the contribution of innate defense receptors, Toll-like receptor 2 (TLR), TLR4 and both (TLR2/4) to the maintenance of neutrophil homeostasis in the JE.

METHODS: Bacterial composition was analyzed from whole oral swabs collected from 12-14-week-old TLR2, TLR4, TLR2/4 double knock-out (KO) mice using a MiSeq platform targeting the V3-V4 region of the 16S ribosomal RNA gene. Mandibles were histologically examined for quantification of neutrophils in the JE and bone loss. Lastly, total bacterial load was quantitated using quantitative real-time PCR.

RESULTS: Compared to wild-type (WT), all TLR KO mice displayed significantly increased recruitment of neutrophils (p = 0.0079) into the JE. In addition, TLR4 and TLR2/4 KO mice demonstrated a significant increase in the number of bacteria (p = 0.022 and p = 0.0152, respectively). Lastly, comparative compositional analyses of the oral microbiome revealed that each KO strain harbored unique microbial communities that are distinct from each other but maintained similar levels of alveolar bone.

CONCLUSIONS: Neutrophil migration into healthy mouse JE does not require TLR2 or TLR4. However, a significant increase in the number of neutrophils as well as a significant change in the oral microbial composition in both TLR2 and TLR4 KO mice demonstrate that these TLRs contribute to the homeostatic relationship between bacteria and the host in healthy mice periodontal tissue. This article is protected by copyright. All rights reserved.},
}

@article {pmid31111902,
year = {2019},
author = {Keller, MJ and Huber, A and Espinoza, L and Serrano, MG and Parikh, HI and Buck, GA and Gold, JA and Wu, Y and Wang, T and Herold, BC},
title = {Impact of Herpes Simplex Virus Type 2 and Human Immunodeficiency Virus Dual Infection on Female Genital Tract Mucosal Immunity and the Vaginal Microbiome.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiz203},
pmid = {31111902},
issn = {1537-6613},
abstract = {BACKGROUND: Mechanisms linking herpes simplex virus type 2 (HSV-2) with human immunodeficiency virus (HIV) are not fully defined. We tested the hypothesis that HSV-2 and HIV dual infection is associated with cervicovaginal inflammation and/or vaginal dysbiosis.

METHODS: Genital tract samples were obtained weekly over a 12-week period from 30 women seropositive (+) for HIV and HSV-2 and 15 women each who were seropositive for one or seronegative (-) for both viruses. Immune mediators, antimicrobial activity, and microbial composition and diversity were compared.

RESULTS: Significant differences in the concentrations of interferon-γ (P = .002), tumor necrosis factor-α (P = .03), human beta defensin 1 (P = .001), secretory leukocyte protease inhibitor (P = .01), and lysozyme (P = .03) were observed across the 4 groups (Kruskal-Wallis). There were also significant differences in vaginal microbial alpha diversity (Simpson index) (P = .0046). Specifically, when comparing HIV-1+/HSV-2+ to HIV-1-/HSV-2- women, a decrease in Lactobacillus crispatus and increase in diverse anaerobes was observed. The number of genital HSV outbreaks was greater in HIV+ versus HIV- women (39 versus 12) (P = .04), but there were no significant differences when comparing outbreak to non-outbreak visits.

CONCLUSIONS: Increased microbial diversity and cervicovaginal inflammation in HIV and HSV-2 dually infected women may adversely impact genital health and, in the absence of antiretroviral therapy, facilitate HIV shedding.},
}

@article {pmid31111901,
year = {2019},
author = {Little, RF and Uldrick, TS},
title = {Are There Clues to Oral KSHV Shedding and Kaposi Sarcoma Oncogenesis in the Oral Microbiome?.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiz250},
pmid = {31111901},
issn = {1537-6613},
}

@article {pmid31111169,
year = {2019},
author = {Reiger, M and Schwierzeck, V and Traidl-Hoffmann, C},
title = {[Atopic eczema and microbiome].},
journal = {Der Hautarzt; Zeitschrift fur Dermatologie, Venerologie, und verwandte Gebiete},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00105-019-4424-6},
pmid = {31111169},
issn = {1432-1173},
abstract = {BACKGROUND: Atopic eczema is a chronic inflammatory skin disease characterized by skin barrier disruption, inflammation and dysbiosis. Furthermore, atopic eczema is associated with other diseases of the atopic group, such as allergies, rhinoconjunctivitis and asthma. The skin microbiome consists of bacteria, viruses and fungi. Patients suffering from atopic eczema often show an imbalance (dysbiosis) of the microbiome.

OBJECTIVE: It is not yet completely clarified what influence dysbiosis and the cutaneous microbiome have on the development and severity of atopic eczema. Modern sequencing methods will be used to investigate the role of the skin microbiome in the pathogenesis of atopic eczema in the future.

MATERIAL AND METHODS: This article presents and discusses the results of current basic research.

RESULTS: The human skin microbiome differs according to body region, age and gender. It interacts with the skin barrier and the cutaneous immune system. Patients suffering from atopic eczema develop dysbiosis consisting of an increased load of Staphylococcus aureus and a reduction of commensal skin bacteria. The altered skin microbiome in patients suffering from atopic eczema may also affect skin barrier function and inflammatory reactions.

CONCLUSION: Knowledge of the skin microbiome has improved in recent years. This will certainly improve the understanding of the pathogenesis causing atopic eczema. These findings may also form the foundation of new treatment and prevention strategies for atopic eczema in the future.},
}

@article {pmid31111150,
year = {2019},
author = {Boix-Amorós, A and Collado, MC and Van't Land, B and Calvert, A and Le Doare, K and Garssen, J and Hanna, H and Khaleva, E and Peroni, DG and Geddes, DT and Kozyrskyj, AL and Warner, JO and Munblit, D},
title = {Reviewing the evidence on breast milk composition and immunological outcomes.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuz019},
pmid = {31111150},
issn = {1753-4887},
abstract = {A large number of biologically active components have been found in human milk (HM), and in both human and animal models, studies have provided some evidence suggesting that HM composition can be altered by maternal exposures, subsequently influencing health outcomes for the breastfed child. Evidence varies from the research studies on whether breastfeeding protects the offspring from noncommunicable diseases, including those associated with immunological dysfunction. It has been hypothesized that the conflicting evidence results from HM composition variations, which contain many immune active molecules, oligosaccharides, lactoferrin, and lysozyme in differing concentrations, along with a diverse microbiome. Determining the components that influence infant health outcomes in terms of both short- and long-term sequelae is complicated by a lack of understanding of the environmental factors that modify HM constituents and thereby offspring outcomes. Variations in HM immune and microbial composition (and the differing infantile responses) may in part explain the controversies that are evidenced in studies that aim to evaluate the prevalence of allergy by prolonged and exclusive breastfeeding. HM is a "mixture" of immune active factors, oligosaccharides, and microbes, which all may influence early immunological outcomes. This comprehensive review provides an in-depth overview of existing evidence on the studied relationships between maternal exposures, HM composition, vaccine responses, and immunological outcomes.},
}

@article {pmid31111067,
year = {2019},
author = {Chowdhry, R and Singh, N and Sahu, DK and Tripathi, RK and Mishra, A and Singh, A and Mukerjee, I and Lal, N and Bhatt, MLB and Kant, R},
title = {Dysbiosis and Variation in Predicted Functions of the Granulation Tissue Microbiome in HPV Positive and Negative Severe Chronic Periodontitis.},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {8163591},
doi = {10.1155/2019/8163591},
pmid = {31111067},
issn = {2314-6141},
abstract = {Retrospective analysis has already shown correlation between severe Chronic Periodontitis (CP) cases with human papiloma virus (HPV). Hence, we aimed to explore deep-seated infected granulation tissue removed during periodontal flap surgery procedures for residential bacterial species between HPV+ and HVP- CP cases, which may serve as good predisposition marker for oral cancer. All CP-granulation samples showed the prominence of Firmicutes, Proteobacteria, and Bacteroidetes phyla with an abundance of gram negative anaerobes, except Streptococcus. In Beta diversity nonmetric multidimensional scaling plot, the random distribution of species was observed between HPV+ and HPV- CP granulation-samples. However, an abundance of Capnocytophaga ochracea was observed in HPV+ CP samples (p<0.05), while Porphyromonas endodontalis, Macellibacteroides fermentas, Treponema phagedenis, and Campylobacter rectus species were highly abundant in HPV- CP samples (p<0.05). The differential species richness leads altered functions related to mismatch-repair and nucleotide excision-repair and cytoskeleton-proteins. Hence, differential abundance of gram negative bacterial species between HPV+ and HPV- granulation-samples under anaerobic conditions may release virulence factors which may alter pathways favouring carcinogenesis. Hence, these species may serve as good predisposition marker for oral-cancer.},
}

@article {pmid31110496,
year = {2019},
author = {Rizzato, C and Torres, J and Kasamatsu, E and Camorlinga-Ponce, M and Bravo, MM and Canzian, F and Kato, I},
title = {Potential Role of Biofilm Formation in the Development of Digestive Tract Cancer With Special Reference to Helicobacter pylori Infection.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {846},
doi = {10.3389/fmicb.2019.00846},
pmid = {31110496},
issn = {1664-302X},
abstract = {Bacteria are highly social organisms that communicate via signaling molecules and can assume a multicellular lifestyle to build biofilm communities. Until recently, complications from biofilm-associated infection have been primarily ascribed to increased bacterial resistance to antibiotics and host immune evasion, leading to persistent infection. In this theory and hypothesis article we present a relatively new argument that biofilm formation has potential etiological role in the development of digestive tract cancer. First, we summarize recent new findings suggesting the potential link between bacterial biofilm and various types of cancer to build the foundation of our hypothesis. To date, evidence has been particularly convincing for colorectal cancer and its precursor, i.e., polyps, pointing to several key individual bacterial species, such as Bacteroides fragilis, Fusobacterium nucleatum, and Streptococcus gallolyticus subsp. Gallolyticus. Then, we further extend this hypothesis to one of the most common bacterial infection in humans, Helicobacter pylori (Hp), which is considered a major cause of gastric cancer. Thus far, there has been no direct evidence linking in vivo Hp gastric biofilm formation to gastric carcinogenesis. Yet, we synthesize the information to support an argument that biofilm associated-Hp is potentially more carcinogenic, summarizing biological characteristics of biofilm-associated bacteria. We also discuss mechanistic pathways as to how Hp or other biofilm-associated bacteria control biofilm formation and highlight recent findings on Hp genes that influence biofilm formation, which may lead to strain variability in biofilm formation. This knowledge may open a possibility of developing targeted intervention. We conclude, however, that this field is still in its infancy. To test the hypothesis rigorously and to link it ultimately to gastric pathologies (e.g., premalignant lesions and cancer), studies are needed to learn more about Hp biofilms, such as compositions and biological properties of extracellular polymeric substance (EPS), presence of non-Hp microbiome and geographical distribution of biofilms in relation to gastric gland types and structures. Identification of specific Hp strains with enhanced biofilm formation would be helpful not only for screening patients at high risk for sequelae from Hp infection, but also for development of new antibiotics to avoid resistance, regardless of its association with gastric cancer.},
}

@article {pmid31110428,
year = {2019},
author = {Deo, PN and Deshmukh, R},
title = {Oral microbiome: Unveiling the fundamentals.},
journal = {Journal of oral and maxillofacial pathology : JOMFP},
volume = {23},
number = {1},
pages = {122-128},
doi = {10.4103/jomfp.JOMFP_304_18},
pmid = {31110428},
issn = {0973-029X},
abstract = {The oral cavity has the second largest and diverse microbiota after the gut harboring over 700 species of bacteria. It nurtures numerous microorganisms which include bacteria, fungi, viruses and protozoa. The mouth with its various niches is an exceptionally complex habitat where microbes colonize the hard surfaces of the teeth and the soft tissues of the oral mucosa. In addition to being the initiation point of digestion, the oral microbiome is crucial in maintaining oral as well as systemic health. Because of the ease of sample collection, it has become the most well-studied microbiome till date. Previously, studying the microbiome was limited to the conventional culture-dependent techniques, but the abundant microflora present in the oral cavity could not be cultured. Hence, studying the microbiome was difficult. The emergence of new genomic technologies including next-generation sequencing and bioinformatics has revealed the complexities of the oral microbiome. It has provided a powerful means of studying the microbiome. Understanding the oral microbiome in health and disease will give further directions to explore the functional and metabolic alterations associated with the diseased states and to identify molecular signatures for drug development and targeted therapies which will ultimately help in rendering personalized and precision medicine. This review article is an attempt to explain the different aspects of the oral microbiome in health.},
}

@article {pmid31109338,
year = {2019},
author = {Wei, MY and Shi, S and Liang, C and Meng, QC and Hua, J and Zhang, YY and Liu, J and Zhang, B and Xu, J and Yu, XJ},
title = {The microbiota and microbiome in pancreatic cancer: more influential than expected.},
journal = {Molecular cancer},
volume = {18},
number = {1},
pages = {97},
doi = {10.1186/s12943-019-1008-0},
pmid = {31109338},
issn = {1476-4598},
support = {81625016//National Science Foundation for Distinguished Young Scholars of China/ ; 17YF1402500//Shanghai Sailing Program/ ; },
abstract = {Microbiota is just beginning to be recognized as an important player in carcinogenesis and the interplay among microbes is greater than expected. Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease for which mortality closely parallels incidence. Early detection would provide the best opportunity to increase survival rates. Specific well-studied oral, gastrointestinal, and intrapancreatic microbes and some kinds of hepatotropic viruses and bactibilia may have potential etiological roles in pancreatic carcinogenesis, or modulating individual responses to oncotherapy. Concrete mechanisms mainly involve perpetuating inflammation, regulating the immune system-microbe-tumor axis, affecting metabolism, and altering the tumor microenvironment. The revolutionary technology of omics has generated insight into cancer microbiomes. A better understanding of the microbiota in PDAC might lead to the establishment of screening or early-stage diagnosis methods, implementation of cancer bacteriotherapy, adjustment of therapeutic efficacy even alleviating the adverse effects, creating new opportunities and fostering hope for desperate PDAC patients.},
}

@article {pmid31109269,
year = {2019},
author = {Olmedo-Martín, RV and González-Molero, I and Olveira, G and Amo-Trillo, V and Jiménez-Pérez, M},
title = {Vitamin D in inflammatory bowel disease: Biological, clinical and therapeutic aspects.},
journal = {Current drug metabolism},
volume = {},
number = {},
pages = {},
doi = {10.2174/1389200220666190520112003},
pmid = {31109269},
issn = {1875-5453},
abstract = {BACKGROUND: Vitamin D has an immunoregulatory action in inflammatory bowel disease (IBD) as well as other immune-mediated disorders. Its influence on intestinal permeability, innate and adaptive immunity, and the composition and diversity of the microbiota contribute to the maintenance of intestinal homeostasis. Patients with IBD have a greater prevalence of vitamin D deficiency than the general population and a possible association between this deficit and a worse course of the disease. However, intervention studies in patients with IBD have proved inconclusive.

OBJECTIVE: To review all the evidence concerning the role of vitamin D as an important factor in the pathophysiology of IBD, review the associations found between its deficiency and the prognosis of the disease, and draw conclusions for the practical application from the main intervention studies undertaken.

METHOD: Structured search and review of basic, epidemiological, clinical and intervention studies evaluating the influence of vitamin D in IBD, following the basic principles of scientific data.

RESULTS: Vitamin D deficiency is associated with disease activity, quality of life, the consumption of social and healthcare resources, and the durability of anti-TNFα biological treatment. The determination of new metabolites of vitamin D, the measurement of its absorption capacity and questionnaires about sun exposure could help identify groups of IBD patients with a special risk of vitamin D deficiency.

CONCLUSION: Well-designed intervention studies are needed in IBD, with probably higher objective plasma doses of vitamin D to establish its efficacy as a therapeutic agent with immunomodulatory properties. Meanwhile, vitamin D deficiency should be screened for and corrected in affected patients in order to achieve adequate bone and phosphocalcic metabolism.},
}

@article {pmid31108813,
year = {2019},
author = {Shikano, A and Kuda, T and Shibayama, J and Toyama, A and Ishida, Y and Takahashi, H and Kimura, B},
title = {Effects of Lactobacillus plantarum Uruma-SU4 fermented green loofah on plasma lipid levels and gut microbiome of high-fat diet fed mice.},
journal = {Food research international (Ottawa, Ont.)},
volume = {121},
number = {},
pages = {817-824},
doi = {10.1016/j.foodres.2018.12.065},
pmid = {31108813},
issn = {1873-7145},
abstract = {To clarify the effect of loofah Luffa cylindrica and fermented loofah on hyperlipidemia, the in vitro bile acid lowering capacity and blood lipid levels of ddY mice fed high-fat diet supplemented with loofah were determined. Furthermore, the caecal microbiomes patterns were analysed using 16S rDNA amplicon sequencing with a next generation sequencer (MiSeq) system. Green loofah was homogenized and autoclaved (LH), and subsequently fermented with Lactobacillus plantarum Uruma-SU4 (FL). In vitro bile acid (taurocholic, glycocholic and deoxycholic acids (DCA)) lowering capacity was significantly high in FL. The levels of plasma triacylglyceride in mice which were fed a high-fat diet containing 17% beef tallow was lowered by 5% dried FL (FLD) and was unaffected by dried LH (LHD). Caecal Lactobacillus johnsonii and Clostridium disporicum known as predominant lactic acid bacteria in mice gut and urso-DCA producer, respectively, were increased by FLD. On the other hand, Flintibacter butyricus was lowered by both LHD and FLD. These results suggest that if green loofah cannot be consumed as a fresh vegetable, lactic acid fermentation may be useful in generating effective nutritional supplements and functional foods.},
}

@article {pmid31108361,
year = {2019},
author = {Regar, RK and Gaur, VK and Bajaj, A and Tambat, S and Manickam, N},
title = {Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities.},
journal = {The Science of the total environment},
volume = {681},
number = {},
pages = {413-423},
doi = {10.1016/j.scitotenv.2019.05.090},
pmid = {31108361},
issn = {1879-1026},
abstract = {Microbial communities play a crucial role in bioremediation of pollutants in contaminated ecosystem. In addition to pure culture isolation and bacterial 16S rRNA based community studies, the focus has now shifted employing the omics technologies enormously for understanding the microbial diversity and functional potential of soil samples. Our previous report on two pesticide-contaminated sites revealed the diversity of both culturable and unculturable bacteria. In the present study, we have observed distinct taxonomic and functional communities in contaminated soil with respect to an uncontaminated soil as control by using shotgun metagenomic sequencing method. Our data demonstrated that Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Acidobacteria significantly dominated the microbial diversity with their cumulative abundance percentage in the range of 98.61, 87.38, and 80.52 for Hindustan Insecticides Limited (HIL), India Pesticides Limited (IPL), and control respectively. Functional gene analysis demonstrated the presence of large number of both substrate specific upper pathway and common lower pathway degradative genes. Relatively lower number of genes was found encoding the degradation of styrene, atrazine, bisphenol, dioxin, and naphthalene. When three bacteria were augumentated with rhamnolipid (20-100 μM) and Triton X-100 (84-417 μM) surfactants in HIL soil, an enhanced degradation to 76%, 70%, and 58% of HCH, Endosulfan, and DDT respectively was achieved. The overall data obtained from two heavily contaminated soil suggest the versatility of the microbial communities for the xenobiotic pollutant degradation which may help in exploiting their potential applications in bioremediation.},
}

@article {pmid31108132,
year = {2019},
author = {Zeng, Q and Junli Gong, and Liu, X and Chen, C and Sun, X and Li, H and Zhou, Y and Cui, C and Wang, Y and Yang, Y and Wu, A and Shu, Y and Hu, X and Lu, Z and Zheng, SG and Qiu, W and Lu, Y},
title = {Gut dysbiosis and lack of short chain fatty acids in a Chinese cohort of patients with multiple sclerosis.},
journal = {Neurochemistry international},
volume = {},
number = {},
pages = {104468},
doi = {10.1016/j.neuint.2019.104468},
pmid = {31108132},
issn = {1872-9754},
abstract = {BACKGROUND: Recent studies, mostly conducted in Western countries, showed that gut microbes are involved in the pathogenesis of multiple sclerosis (MS).

OBJECTIVE: The aim of this study was to investigate whether gut dysbiosis is relevant to the initiation and progression of MS in a Chinese population.

METHODS: Next-generation sequencing (NGS) and gas chromatography (GC) were integrated and used to compare the fecal bacterial communities and the short-chain fatty acid (SCFA) levels among relapsing-remitting MS (RRMS) patients (n = 34), neuromyelitis optica spectrum disorder (NMOSD) patients (n = 34), and healthy controls (HCs) (n = 34). T-cell profile analyses were performed by flow cytometry for MS patients and matched controls (n = 12).

RESULTS: (1) The gut microbiome of MS patients was characterized by an increase of Streptococcus and a decrease of Prevotella_9; additionally, compared to NMOSD patients, Prevotella_9 was found to be much more abundant in MS patients. (2) A striking depletion of fecal acetate, propionate, and butyrate was observed in MS patients compared to HCs. (3) The abundance of Streptococcus was negatively correlated with the proportion of pTregs (P < 0.05) and positively correlated with Th17 cells (P < 0.05) in the peripheral blood, while the abundance of Prevotella_9 was negatively correlated with the Th17 cell frequency (P < 0.01), and the fecal SCFA level was positively correlated with pTreg frequency (P < 0.05).

CONCLUSIONS: Gut dysbiosis and a lack of SCFAs exist in Chinese MS patients, which might be related to an aberrant immune response of MS; this relationship may have a diagnostic and therapeutic value for patients with MS.},
}

@article {pmid31107972,
year = {2019},
author = {Herbert, RA and Eng, T and Martinez, U and Wang, B and Langley, S and Wan, K and Pidatala, V and Hoffman, E and Chen, JC and Bissell, MJ and Brown, JB and Mukhopadhyay, A and Mortimer, JC},
title = {Rhizobacteria mediate the phytotoxicity of a range of biorefinery-relevant compounds.},
journal = {Environmental toxicology and chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/etc.4501},
pmid = {31107972},
issn = {1552-8618},
abstract = {Advances in engineering biology have expanded the list of renewable compounds that can be produced at scale via biological routes from plant biomass. In most cases, these chemical products have not been evaluated for effects on biological systems, defined here as bioactivity, that may be relevant to their manufacture. For sustainable chemical and fuel production, the industry needs to transition from fossil to renewable carbon sources, resulting in unprecedented expansion in the production and environmental distribution of chemicals used in biomanufacturing. Further, while some chemicals have been assessed for mammalian toxicity, environmental and agricultural hazards are largely unknown. We assessed six compounds that are representative of the emerging biofuel and bioproduct manufacturing process for their effect on model plants (Arabidopsis thaliana, Sorghum bicolor) and show that several alter plant seedling physiology at sub-millimolar concentrations. However, these responses change in the presence of individual bacterial species from the A. thaliana root microbiome. We identified two individual microbes that change the effect of chemical treatment on root architecture, and a pooled microbial community with different effects relative to its constituents individually. Our findings indicate that screening industrial chemicals for bioactivity on model organisms in the presence of their microbiomes is important for biologically and ecologically relevant risk analyses. This article is protected by copyright. All rights reserved.},
}

@article {pmid31107879,
year = {2019},
author = {Duvallet, C and Larson, K and Snapper, S and Iosim, S and Lee, A and Freer, K and May, K and Alm, E and Rosen, R},
title = {Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0216453},
doi = {10.1371/journal.pone.0216453},
pmid = {31107879},
issn = {1932-6203},
abstract = {BACKGROUND: Children with oropharyngeal dysphagia have impaired airway protection mechanisms and are at higher risk for pneumonia and other pulmonary complications. Aspiration of gastric contents is often implicated as a cause for these pulmonary complications, despite being supported by little evidence. The goal of this study is to determine the relative contribution of oropharyngeal and gastric microbial communities to perturbations in the lung microbiome of children with and without oropharyngeal dysphagia and aspiration.

METHODS: We conducted a prospective cohort study of 220 patients consecutively recruited from a tertiary aerodigestive center undergoing simultaneous esophagogastroduodenoscopy and flexible bronchoscopy. Bronchoalveolar lavage, gastric and oropharyngeal samples were collected from all recruited patients and 16S sequencing was performed. A subset of 104 patients also underwent video fluoroscopic swallow studies to assess swallow function and were categorized as aspiration/no aspiration. To ensure the validity of the results, we compared the microbiome of these aerodigestive patients to the microbiome of pediatric patients recruited to a longitudinal cohort study of children with suspected GERD; patients recruited to this study had oropharyngeal, gastric and/or stool samples available. The relationships between microbial communities across the aerodigestive tract were described by analyzing within- and between-patient beta diversities and identifying taxa which are exchanged between aerodigestive sites within patients. These relationships were then compared in patients with and without aspiration to evaluate the effect of aspiration on the aerodigestive microbiome.

RESULTS: Within all patients, lung, oropharyngeal and gastric microbiomes overlap. The degree of similarity is the lowest between the oropharynx and lungs (median Jensen-Shannon distance (JSD) = 0.90), and as high between the stomach and lungs as between the oropharynx and stomach (median JSD = 0.56 for both; p = 0.6). Unlike the oropharyngeal microbiome, lung and gastric communities are highly variable across people and driven primarily by person rather than body site. In patients with aspiration, the lung microbiome more closely resembles oropharyngeal rather than gastric communities and there is greater prevalence of microbial exchange between the lung and oropharynx than between gastric and lung sites (p = 0.04 and 4x10-5, respectively).

CONCLUSIONS: The gastric and lung microbiomes display significant overlap in patients with intact airway protective mechanisms while the lung and oropharynx remain distinct. In patients with impaired swallow function and aspiration, the lung microbiome shifts towards oropharyngeal rather than gastric communities. This finding may explain why antireflux surgeries fail to show benefit in pediatric pulmonary outcomes.},
}

@article {pmid31107866,
year = {2019},
author = {Mainali, K and Bewick, S and Vecchio-Pagan, B and Karig, D and Fagan, WF},
title = {Detecting interaction networks in the human microbiome with conditional Granger causality.},
journal = {PLoS computational biology},
volume = {15},
number = {5},
pages = {e1007037},
doi = {10.1371/journal.pcbi.1007037},
pmid = {31107866},
issn = {1553-7358},
abstract = {Human microbiome research is rife with studies attempting to deduce microbial correlation networks from sequencing data. Standard correlation and/or network analyses may be misleading when taken as an indication of taxon interactions because "correlation is neither necessary nor sufficient to establish causation"; environmental filtering can lead to correlation between non-interacting taxa. Unfortunately, microbial ecologists have generally used correlation as a proxy for causality although there is a general consensus about what constitutes a causal relationship: causes both precede and predict effects. We apply one of the first causal models for detecting interactions in human microbiome samples. Specifically, we analyze a long duration, high resolution time series of the human microbiome to decipher the networks of correlation and causation of human-associated microbial genera. We show that correlation is not a good proxy for biological interaction; we observed a weak negative relationship between correlation and causality. Strong interspecific interactions are disproportionately positive, whereas almost all strong intraspecific interactions are negative. Interestingly, intraspecific interactions also appear to act at a short time-scale causing vast majority of the effects within 1-3 days. We report how different taxa are involved in causal relationships with others, and show that strong interspecific interactions are rarely conserved across two body sites whereas strong intraspecific interactions are much more conserved, ranging from 33% between the gut and right-hand to 70% between the two hands. Therefore, in the absence of guiding assumptions about ecological interactions, Granger causality and related techniques may be particularly helpful for understanding the driving factors governing microbiome composition and structure.},
}

@article {pmid31107796,
year = {2019},
author = {Rendina, DN and Lubach, GR and Phillips, GJ and Lyte, M and Coe, CL},
title = {Maternal and Breast Milk Influences on the Infant Gut Microbiome, Enteric Health and Growth Outcomes of Rhesus Monkeys.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPG.0000000000002394},
pmid = {31107796},
issn = {1536-4801},
abstract = {OBJECTIVES: Gut bacteria play an essential role during infancy and are strongly influenced by the mode of birth and feeding. A primate model was used to investigate the benefits of exposure to the mother or conversely the negative impact of early nursery rearing on microbial colonization.

METHOD: Rectal swabs were obtained from rhesus macaques born vaginally and mother-reared (MR, N = 35) or delivered primarily via cesarean-section and human-reared (HR, N = 19). Microbiome composition was determined by rRNA gene amplicon sequencing at 2, 4 and 8 weeks of age and KEGG orthologs used to assess influences on functional metabolic pathways in the gut. Growth trajectories and incidence of diarrheic symptoms were evaluated.

RESULTS: The microbial community structure was different between MR and HR infants with respect to phylogeny and abundance at all 3 ages. When examining dominant phyla, HR infants had a higher Firmicutes-to-Bacteroidetes ratio. At the genus level, breast milk-dependent commensal taxa and adult-typical genera were more abundant in MR infants. This difference resulted in a corresponding shift in the predicted metabolic effects, specifically for microbial genes associated with metabolism and immune function. HR infants had faster growth trajectories (p < 0.001), but more diarrheic symptoms by 6 months postnatal (p = 0.008).

CONCLUSIONS: MR infants acquired adult-typical microbiota more quickly, and had higher levels of several beneficial commensal taxa. Cesarean-delivered and formula-fed infants had different developmental trajectories of bacterial colonization. Establishment of the gut microbiome was associated with an infant's growth trajectory, and implicated in the subsequent vulnerability to Campylobacter infections associated with diarrhea in infant monkeys.},
}

@article {pmid31107724,
year = {2019},
author = {Hiremath, G and Shilts, MH and Boone, HH and Correa, H and Acra, S and Tovchigrechko, A and Rajagopala, SV and Das, SR},
title = {The Salivary Microbiome Is Altered in Children With Eosinophilic Esophagitis and Correlates With Disease Activity.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000000039},
pmid = {31107724},
issn = {2155-384X},
abstract = {OBJECTIVES: Eosinophilic esophagitis (EoE) is an allergen-mediated inflammatory disease affecting the esophagus. Although microbial communities may affect the host immune responses, little is known about the role of the microbiome in EoE. We compared the composition of the salivary microbiome in children with EoE with that of non-EoE controls to test the hypotheses that the salivary microbiome is altered in children with EoE and is associated with disease activity.

METHODS: Saliva samples were collected from 26 children with EoE and 19 non-EoE controls comparable for age and ethnicity. The salivary microbiome was profiled using 16S rRNA gene sequencing. Disease activity was assessed using the Eosinophilic Esophagitis Endoscopic Reference Score and the Eosinophilic Esophagitis Histologic Scoring System (EoEHSS).

RESULTS: A trend toward lower microbial richness and alpha diversity was noted in children with EoE. Although the overall salivary microbiome composition was similar between children with and without EoE, specific taxa such as Streptococcus (q value = 0.06) tended to be abundant in children with active EoE compared with non-EoE controls. Haemophilus was significantly abundant in children with active EoE compared with inactive EoE (q value = 0.0008) and increased with the increasing EoEHSS and Eosinophilic Esophagitis Histology Scoring System (q value = 5e-10). In addition, 4 broad salivary microbial communities correlated with the EoEHSS.

DISCUSSION: The composition of the salivary microbiome community structure can be altered in children with EoE. A relative abundance of Haemophilus positively correlates with the disease activity. These findings indicate that perturbations in the salivary microbiome may have a role in EoE pathobiology and could serve as a noninvasive marker of disease activity.This is an open access article distributed under the Creative Commons Attribution License 4.0 (CCBY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.},
}

@article {pmid31107258,
year = {2019},
author = {Lunjani, N and Hlela, C and O'Mahony, L},
title = {Microbiome and skin biology.},
journal = {Current opinion in allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ACI.0000000000000542},
pmid = {31107258},
issn = {1473-6322},
abstract = {PURPOSE OF REVIEW: The skin is home to a diverse milieu of bacteria, fungi, viruses, bacteriophages, and archaeal communities. The application of culture-independent approaches has revolutionized the characterization of the skin microbiome and have revealed a previously underappreciated phylogenetic and functional granularity of skin-associated microbes in both health and disease states.

RECENT FINDINGS: The physiology of a given skin-niche drives the site-specific differences in bacterial phyla composition of healthy skin. Changes in the skin microbiome have consistently been associated with atopic dermatitis. In particular, Staphylococcus aureus overgrowth with concomitant decline in Staphylococcus epidermidis is a general feature associated with atopic dermatitis and is not restricted to eczematous lesions. Changes in fungal species are now also being described. Changes in the composition and metabolic activity of the gut microbiota are associated with skin health.

SUMMARY: We are now beginning to appreciate the intimate and intricate interactions between microbes and skin health. Multiple studies are currently focused on the manipulation of the skin or gut microbiome to explore their therapeutic potential in the prevention and treatment of skin inflammation.},
}

@article {pmid31106972,
year = {2019},
author = {Ogunrinde, E and Zhou, Z and Luo, Z and Alekseyenko, A and Li, QZ and Macedo, D and Kamen, DL and Oates, JC and Gilkeson, GS and Jiang, W},
title = {A link between plasma microbial translocation, microbiome, and autoantibody development in first-degree relatives of systemic lupus erythematosus patients.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.40935},
pmid = {31106972},
issn = {2326-5205},
abstract = {OBJECTIVE: Systemic lupus erythematosus (SLE) is characterized by antibody production against self-antigens. However, the events underlying autoantibody formation in SLE remains unclear. This study investigated the role of plasma autoantibody levels, microbial translocation, and the microbiome in SLE.

METHODS: Plasma samples from two cohorts, one with 18 unrelated healthy controls (UHCs) and 18 first-degree relatives (FDRs) and the other with 19 healthy controls and 21 SLE patients were assessed for autoantibody levels by autoantigen microarrays, lipopolysaccharide (LPS) levels by limulus amebocyte assay and microbiome composition by microbial 16S rDNA sequencing.

RESULTS: FDRs and SLE patients exhibited increased plasma autoantibodies compared to their control groups. Parents and children of lupus patients exhibited elevated plasma LPS levels in comparison to controls (p = 0.02). Plasma LPS levels positively correlated with plasma anti-dsDNA IgG levels in FDRs (r=0.51, p=0.03) but not in SLE patients. Circulating microbiome analysis revealed that FDRs (Observed species, p=0.004; Chao1 index, p=0.005) but not patients had significantly reduced microbiome diversity compared to their controls. The majority of differentially abundant bacteria identified between UHCs and FDRs were in the Firmicutes phylum, while bacteria from several different phyla were identified between HCs and SLE patients. Bacteria in the Paenibacillus genus was the only overlapping differentially abundant bacteria in both cohorts, and it was reduced in FDRs (p.adj = 2.13 x 10-12) and SLE patients (p.adj = 0.008) but elevated in controls.

CONCLUSIONS: These results indicate a possible role for plasma microbial translocation and microbiome composition in influencing autoantibody development in SLE. This article is protected by copyright. All rights reserved.},
}

@article {pmid31106877,
year = {2019},
author = {Petrullo, L and Jorgensen, MJ and Snyder-Mackler, N and Lu, A},
title = {Composition and stability of the vervet monkey milk microbiome.},
journal = {American journal of primatology},
volume = {},
number = {},
pages = {e22982},
doi = {10.1002/ajp.22982},
pmid = {31106877},
issn = {1098-2345},
support = {Turner Fellowship program//Stony Brook University/ ; //University of Washington/ ; UL1-TR001420//National Institutes of Health CTSA pilot/ ; OD010965//a P40/ ; },
abstract = {The human milk microbiome is vertically transmitted to offspring during the postnatal period and has emerged as a critical driver of infant immune and metabolic development. Despite this importance in humans, the milk microbiome of nonhuman primates remains largely unexplored. This dearth of comparative work precludes our ability to understand how species-specific differences in the milk microbiome may differentially drive maternal effects and limits how translational models can be used to understand the role of vertically transmitted milk microbes in human development. Here, we present the first culture-independent data on the milk microbiome of a nonhuman primate. We collected milk and matched fecal microbiome samples at early and late lactation from a cohort of captive lactating vervet monkeys (N = 15). We found that, similar to humans, the vervet monkey milk microbiome comprises a shared community of taxa that are universally present across individuals. However, unlike in humans, this shared community is dominated by the genera Lactobacillus, Bacteroides, and Prevotella. We also found that, in contrast to previous culture-dependent studies in humans, the vervet milk microbiome exhibits greater alpha-diversity than the gut microbiome across lactation. Finally, we did not find support for the translocation of microbes from the gut to the mammary gland within females (i.e., "entero-mammary pathway"). Taken together, our results show that the vervet monkey milk microbiome is taxonomically diverse, distinct from the gut microbiome, and largely stable. These findings demonstrate that the milk microbiome is a unique substrate that may selectively favor the establishment and persistence of particular microbes across lactation and highlights the need for future experimental studies on the origin of microbes in milk.},
}

@article {pmid31106639,
year = {2019},
author = {Zhong, S and Zhou, Z and Liang, Y and Cheng, X and Li, Y and Teng, W and Zhao, M and Liu, C and Guan, M and Zhao, C},
title = {Targeting strategies for chemotherapy-induced peripheral neuropathy: does gut microbiota play a role?.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/1040841X.2019.1608905},
pmid = {31106639},
issn = {1549-7828},
abstract = {Chemotherapy-induced peripheral neuropathy (CIPN) is a progressive, often irreversible condition that produces severe neurological deficits. Emerging data suggest that chemotherapy also exerts detrimental effects on gut microbiota composition and intestinal permeability, contributing to dysbiosis and inflammation. Compared with other complications associated with chemotherapy, such as diarrhoea and mucositis, CIPN is of particular concern because it is the most common reason for terminating or suspending treatment. However, specific and effective curative treatment strategies are lacking. In this review, we provide an update on current preclinical and clinical understandings about the role of gut microbiota in CIPN. The gut microbiota serves as an intersection between the microbiome-gut-brain and the neuroimmune-endocrine axis, forming a complex network that can directly or indirectly affect key components involved in the manifestations of CIPN. Herein, we discuss several potential mechanisms within the context of the networks and summarize alterations in gut microbiome induced by chemotherapeutic drugs, providing great potential for researchers to target pathways associated with the gut microbiome and overcome CIPN.},
}

@article {pmid31106155,
year = {2019},
author = {Montironi, R and Santoni, M and Cimadamore, A and Lopez-Beltran, A and Cheng, L},
title = {Editorial: Emerging Biomarkers in Genitourinary Tumors.},
journal = {Frontiers in oncology},
volume = {9},
number = {},
pages = {326},
doi = {10.3389/fonc.2019.00326},
pmid = {31106155},
issn = {2234-943X},
}

@article {pmid31106110,
year = {2019},
author = {Sakai, Y and Seki, N and Hamano, H and Ochi, H and Abe, F and Shimizu, F and Masuda, K and Iino, H},
title = {A study of the prebiotic effect of lactulose at low dosages in healthy Japanese women.},
journal = {Bioscience of microbiota, food and health},
volume = {38},
number = {2},
pages = {69-72},
doi = {10.12938/bmfh.18-013},
pmid = {31106110},
issn = {2186-6953},
abstract = {To investigate the prebiotic effect of lactulose at low dosages, we assessed changes in defaecation frequency following ingestion of 1, 2, or 3 g/day of lactulose for 2 weeks. Each test was carried out after a 2-week washout period. This was an open-label, before-after trial that enrolled 26 healthy Japanese women. The defaecation frequency, number of defaecation days, and number of faecal bifidobacteria increased significantly compared with before ingestion of 1, 2, and 3 g/day of lactulose. These results suggest that even 1 g/day of lactulose could have a prebiotic effect.},
}

@article {pmid31106061,
year = {2019},
author = {Xiao, Y and Xiao, G and Liu, H and Zhao, X and Sun, C and Tan, X and Sun, K and Liu, S and Feng, J},
title = {Captivity causes taxonomic and functional convergence of gut microbial communities in bats.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6844},
doi = {10.7717/peerj.6844},
pmid = {31106061},
issn = {2167-8359},
abstract = {Background: Diet plays a crucial role in sculpting microbial communities. Similar diets appear to drive convergence of gut microbial communities between host species. Captivity usually provides an identical diet and environment to different animal species that normally have similar diets. Whether different species' microbial gut communities can be homogenized by a uniform diet in captivity remains unclear.

Methods: In this study, we compared gut microbial communities of three insectivorous bat species (Rhinolophus ferrumequinum, Vespertilio sinensis, and Hipposideros armiger) in captivity and in the wild using 16S rDNA sequencing. In captivity, R. ferrumequinum and V. sinensis were fed yellow mealworms, while H. armiger was fed giant mealworms to rule out the impact of an identical environment on the species' gut microbial communities.

Results: We found that the microbial communities of the bat species we studied clustered by species in the wild, while the microbial communities of R. ferrumequinum and V. sinensis in captivity clustered together. All microbial functions found in captive V. sinensis were shared by R. ferrumequinum. Moreover, the relative abundances of all metabolism related KEGG pathways did not significantly differ between captive R. ferrumequinum and V. sinensis; however, the relative abundance of "Glycan Biosynthesis and Metabolism" differed significantly between wild R. ferrumequinum and V. sinensis.

Conclusion: Our results suggest that consuming identical diets while in captivity tends to homogenize the gut microbial communities among bat species. This study further highlights the importance of diet in shaping animal gut microbiotas.},
}

@article {pmid31105729,
year = {2019},
author = {Cicatelli, A and Ferrol, N and Rozpadek, P and Castiglione, S},
title = {Editorial: Effects of Plant-Microbiome Interactions on Phyto- and Bio-Remediation Capacity.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {533},
doi = {10.3389/fpls.2019.00533},
pmid = {31105729},
issn = {1664-462X},
}

@article {pmid31105675,
year = {2019},
author = {Wang, J and Lang, T and Shen, J and Dai, J and Tian, L and Wang, X},
title = {Core Gut Bacteria Analysis of Healthy Mice.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {887},
doi = {10.3389/fmicb.2019.00887},
pmid = {31105675},
issn = {1664-302X},
abstract = {Previous studies revealed that there existed great individual variations of gut microbiota in mice, and the gut bacteria of mice were changed with the occurrence and development of diseases. To identify the core gut bacteria in healthy mice and explore their relationships with the host phenotypes would help to understand the underlying mechanisms. In this study, we identified 37 genus-level core bacteria from feces of 101 healthy mice with different ages, sexes, and mouse strains in three previous studies. They collectively represented nearly half of the total sequences, and predominantly included carbohydrate- and amino acids-metabolizing bacteria and immunomodulatory bacteria. Among them, Anaerostipes indwelt the gut of all healthy mice. Co-abundance analysis showed that these core genera were clustered into five groups (Group C1-C5), which were ecologically related. For example, the abundances of Group C2 including probiotics Bifidobacterium and Lactobacillus slightly positively correlated with those of Group C1. Principal component analysis (PCA) and multivariate analysis of variance test revealed that these core gut genera were distinguished with age and sex, and also associated with their health/disease state. Linear discriminant analysis effect size (LEfSe) method showed that bacteria in Group C1 and C2/C3 increased with the age in infancy and early adulthood, and were more abundant in female mice than in male ones. The metabolic syndrome (MS) induced by high fat diet (HFD) and accelerated postnatal growth would decrease Group C2 genera, whereas probiotics intervention would reverse HFD-induced reduction of Group C2. Spearman correlation analysis indicated that the principal components based on the abundance of the 37 core genera were significantly correlated with host characteristic parameters of MS. These results demonstrated that the 37 core genera in five co-abundance groups from healthy mice were related to host phenotypes. It was indicated that these prevalent gut bacterial genera could be representative of the healthy gut microbiome in gnotobiotic animal models, and might also be candidates of probiotics and fecal microbiota transplantation.},
}

@article {pmid31105659,
year = {2019},
author = {Fuertes, A and Pérez-Burillo, S and Apaolaza, I and Vallès, Y and Francino, MP and Rufián-Henares, JÁ and Planes, FJ},
title = {Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {848},
doi = {10.3389/fmicb.2019.00848},
pmid = {31105659},
issn = {1664-302X},
abstract = {Predicting the metabolic behavior of the human gut microbiota in different contexts is one of the most promising areas of constraint-based modeling. Recently, we presented a supra-organismal approach to build context-specific metabolic networks of bacterial communities using functional and taxonomic assignments of meta-omics data. In this work, this algorithm is applied to elucidate the metabolic changes induced over the first year after birth in the gut microbiota of a cohort of Spanish infants. We used metagenomics data of fecal samples and nutritional data of 13 infants at five time points. The resulting networks for each time point were analyzed, finding significant alterations once solid food is introduced in the diet. Our work shows that solid food leads to a different pattern of output metabolites that can be potentially released from the gut microbiota to the host. Experimental validation is presented for ferulate, a neuroprotective metabolite involved in the gut-brain axis.},
}

@article {pmid31105654,
year = {2019},
author = {Calon, TGA and Trobos, M and Johansson, ML and van Tongeren, J and van der Lugt-Degen, M and Janssen, AML and Savelkoul, PHM and Stokroos, RJ and Budding, AE},
title = {Microbiome on the Bone-Anchored Hearing System: A Prospective Study.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {799},
doi = {10.3389/fmicb.2019.00799},
pmid = {31105654},
issn = {1664-302X},
abstract = {The bone-anchored hearing system (BAHS) has evolved to a common treatment option for various types of hearing revalidation. The BAHS consists of an implant in the skull that breeches the skin. Soft tissue reactions are a common complication associated with BAHS and are generally poorly understood. This study aims to investigate the influence of BAHS and associated skin reactions around the implant. A total of 45 patients were prospectively followed from implantation up to at least 1 year. Swabs were obtained at baseline, 12 weeks follow-up and during cases of inflammation (Holgers score ≥2). The microbiota was assessed using IS-proTM, a bacterial profiling method based on the interspace region between the 16S-23S rRNA genes. Detection of operational taxonomic units, the Shannon Diversity Index, sample similarity analyses and Partial Least Squares Discriminant Analysis (PLS-DA) were employed. Staphylococcus epidermidis, Streptococcus pneumoniae/mitis, Propionibacterium acnes, Staphylococcus capitis, Staphylococcus hominis, Bifidobacterium longum, Haemophilus parainfluenzae, Lactobacillus rhamnosus, Bordetella spp., Streptococcus sanguinis, Peptostreptococcus anaerobius, Staphylococcus aureus, Lactococcus lactis, Enterobacter cloacae, and Citrobacter koseri were the most commonly found bacterial species. S. pneumoniae/mitis was significantly more often observed after implantation, whereas P. acnes was significantly less observed after implantation compared with baseline. The relative abundance of S. epidermidis (17%) and S. aureus (19.4%) was the highest for the group of patients with inflammation. The Shannon Diversity Index was significantly increased after implantation compared with pre-surgical swabs for Firmicutes, Actinobacteria, Fusobacteria, Verrucomicrobia (FAFV), but not for other phyla. When combining all phyla, there was no significant increase in the Shannon Diversity Index. The diversity index was similar post-surgically for patients experiencing inflammation and for patients without inflammation. With a supervised classifier (PLS-DA), patients prone to inflammation could be identified at baseline with an accuracy of 91.7%. In addition, PLS-DA could classify post-surgical abutments as non-inflamed or inflamed with an accuracy of 97.7%. This study shows the potential of using IS-proTM to describe and quantify the microbiota associated with the percutaneous BAHS. Furthermore, the results indicate the possibility of an early identification of patients susceptible to adverse skin reaction following implantation. Both S. aureus and S. epidermidis should be considered as relevant bacteria for BAHS-associated inflammation.},
}

@article {pmid31105489,
year = {2019},
author = {Shurney, D},
title = {The Gut Microbiome: Unleashing the Doctor Within.},
journal = {American journal of lifestyle medicine},
volume = {13},
number = {3},
pages = {265-268},
doi = {10.1177/1559827619826551},
pmid = {31105489},
issn = {1559-8284},
}

@article {pmid31105269,
year = {2019},
author = {Gyongyosi, B and Cho, Y and Lowe, P and Calenda, CD and Iracheta-Vellve, A and Satishchandran, A and Ambade, A and Szabo, G},
title = {Alcohol-induced IL-17A production in Paneth cells amplifies endoplasmic reticulum stress, apoptosis, and inflammasome-IL-18 activation in the proximal small intestine in mice.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41385-019-0170-4},
pmid = {31105269},
issn = {1935-3456},
abstract = {Gut microbial translocation contributes to alcoholic hepatitis. Using a mouse model of alcoholic hepatitis, we investigated the effects of chronic alcohol plus binge and found increased abundance of Paneth cells and IL-17A in the proximal small intestine (PSI). Alcohol increased IL-17A production and pro-apoptotic signaling evidenced by Bax, Bim, caspase-3, and caspase-8 increases via endoplasmic reticulum (ER) stress indicated by C/EBP homologous protein (CHOP) upregulation; this was prevented by the ER stress inhibitor, 4-PBA, in isolated crypts in vitro and in vivo. Mechanistically, IL-17 augmented alcohol-induced ER stress in isolated crypts. In vivo IL-17A blocking antibody administration in alcohol-treated mice attenuated ER stress-mediated apoptosis and IL-18 induction and prevented alcohol-induced impairment of tight junctions in the PSI and LPS translocation to the liver. Acute-on-chronic alcohol resulted in inflammasome activation, caspase-1 cleavage, and IL-18 production in the PSI. In vivo treatment with antibiotics or 4-PBA prevented CHOP upregulation and inflammasome activation. Our data suggest that alcohol upregulates innate immune mechanisms by increasing Paneth cell numbers and IL-17A release contributing to apoptosis amplification, inflammasome activation, and gut leakiness in the PSI. Binge alcohol-induced Paneth cell expansion, ER stress, and inflammasome activation in the PSI are modulated by the gut microbiome.},
}

@article {pmid31104970,
year = {2019},
author = {Zeineldin, M and Lowe, J and Aldridge, B},
title = {Contribution of the Mucosal Microbiota to Bovine Respiratory Health.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2019.04.005},
pmid = {31104970},
issn = {1878-4380},
abstract = {Recognizing the respiratory tract as a dynamic and complex ecosystem has enhanced our understanding of the pathophysiology of bovine respiratory disease (BRD). There is widespread evidence showing that disease-predisposing factors often disrupt the respiratory microbial ecosystem, provoking atypical colonization patterns and a progressive dysbiosis. The ecological factors that shape the respiratory microbiota, and the influence of these complex communities on bovine respiratory health, are a rich area for research exploration. Here, we review the current status of understanding of the bovine respiratory microbiota, the factors that influence its development and stability, its role in maintaining mucosal homeostasis, and ultimately its contribution to bovine health and disease. Finally, we explore the limitations of current research approaches to the microbiome and discuss potential directions for future research that can help us better understand the role of the respiratory microbiota in the health, welfare, and productivity of livestock.},
}

@article {pmid31103138,
year = {2018},
author = {Gottlieb, A and Bechmann, L and Canbay, A},
title = {The Presence and Severity of Nonalcoholic Steatohepatitis Is Associated with Specific Changes in Circulating Bile Acids.},
journal = {Annals of hepatology},
volume = {17},
number = {3},
pages = {341-342},
doi = {10.5604/01.3001.0011.7378},
pmid = {31103138},
issn = {1665-2681},
abstract = {Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease nowadays with currently no approved therapies for the disease. The liver plays a pivotal role in lipid and glucose metabolism. The interactions of molecular mechanisms on the gut for example influences the development still needs to be understood. Bile acids (BA) have been shown to impact metabolic homeostasis and insulin sensitivity. Here, we comment on a study analyzing BA profiles in NAFLD patients addressing novel pathways involved in NAFLD progression.},
}

@article {pmid31104215,
year = {2019},
author = {Li, P and Wu, H and Jin, Y and Huang, X and Chen, Y and Yang, X and Wang, R and Zhang, W},
title = {Exploring the diversity and dynamic of bacterial community vertically distributed in Tongguling National Nature Reserve in Hainan Island, China.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
doi = {10.1007/s42770-019-00078-2},
pmid = {31104215},
issn = {1678-4405},
abstract = {National nature reserves are important for preserving ecological resources and constructing national ecological security barriers. Tongguling National Nature Reserve (TNNR) is known for its unique tropical island ecosystem and abundant biological resources. This study was conducted to characterize and compare its bacterial community diversity and composition in soils from 10, 20, and 30 cm in depth using high-throughput sequencing of 16S rDNA genes. We found that soils from 20 cm had the highest diversity and might serve as a "middle bridge" to the dynamic distribution between the 10- and 30-cm soil samples. The diversity pattern indicated that the main abundant groups varied distinctly and significantly among soils of different depths. Moreover, Chloroflexi was the most dynamic group in TNNR soils, together with another abundant but rarely reported group, Verrucomicrobia, which greatly enhanced the microbial diversity of TNNR soils. Overall, the results of this study emphasize the urgent need for greater understanding of bacterial community variations in response to human activities and climate change.},
}

@article {pmid31104156,
year = {2019},
author = {Bajic, P and Dornbier, RA and Doshi, CP and Wolfe, AJ and Farooq, AV and Bresler, L},
title = {Implications of the Genitourinary Microbiota in Prostatic Disease.},
journal = {Current urology reports},
volume = {20},
number = {7},
pages = {34},
doi = {10.1007/s11934-019-0904-6},
pmid = {31104156},
issn = {1534-6285},
abstract = {PURPOSE OF REVIEW: To summarize recent investigation into associations between the genitourinary microbiota and prostatic disease.

RECENT FINDINGS: The genitourinary tract is not sterile. There are microbial communities (microbiota) in each niche of the genitourinary tract including the bladder, prostate, and urethra, which have been the subject of increasing scientific interest. Investigators have utilized several unique methods to study them, resulting in a highly heterogeneous body of literature. To characterize these genitourinary microbiota, diverse clinical specimens have been analyzed, including urine obtained by various techniques, seminal fluid, expressed prostatic secretions, and prostatic tissue. Recent studies have attempted to associate the microbiota detected from these samples with urologic disease and have implicated the genitourinary microbiota in many common conditions, including benign prostatic hyperplasia (BPH), prostate cancer, and chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). In this review, we summarize the recent literature pertaining to the genitourinary microbiota and its relationship to the pathophysiology and management of three common prostatic conditions: BPH, prostate cancer, and CP/CPPS.},
}

@article {pmid31103967,
year = {2019},
author = {Mukhtar, I and Anwar, H and Hussain, G and Rasul, A and Naqvi, SAR and Faisal, MN and Mustafa, I and Malik, S and Shaukat, A and Mirza, OA and Sohail, MU},
title = {Detection of Paracetamol as substrate of the gut microbiome.},
journal = {Pakistan journal of pharmaceutical sciences},
volume = {32},
number = {2 (Supplementary)},
pages = {751-757},
pmid = {31103967},
issn = {1011-601X},
abstract = {Gut microbiome, a new organ; represent targets to alter pharmacokinetics of orally administered drugs. Recently, in vitro trials endorsed the idea that orally administered drugs interact and some of their quantity may be taken up by normal microbiome during transit through gut. Such transport mechanisms in microbiome may compete for drug with the host itself. Currently, no data confirms specific transport system for paracetamol uptake by gut microbiome. In vivo trial was conducted in normal healthy male rats (n=36). Paracetamol was administered orally in a single dose of 75mg/kg to isolate microbial mass after transit of 2, 3, 4, 5 and 6 hours post drug administration. Paracetamol absorbance by microbiome was pursued by injecting extracted microbial lysate in RP-HPLC-UV with C18 column under isocratic conditions at 207nm using acetonitrile and water (25:75 v/v) pH 2.50 as mobile phase. Paracetamol absorbance (14.10±0.75μg/mg of microbial mass) and percent dose recovery (13.16±0.55%) seen at transit of 4 hours was significantly higher (P<0.05) compared to other groups. Study confirms the hypothesis of homology between membrane transporters of the gut microbiome and intestinal epithelium. Orally administered drugs can be absorbed by gut microbes competitively during transit in small intestine and it varies at various transit times.},
}

@article {pmid31103040,
year = {2019},
author = {Veach, AM and Morris, R and Yip, DZ and Yang, ZK and Engle, NL and Cregger, MA and Tschaplinski, TJ and Schadt, CW},
title = {Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {76},
doi = {10.1186/s40168-019-0668-8},
pmid = {31103040},
issn = {2049-2618},
support = {DE-AC05-00OR22725//Biological and Environmental Research/ ; },
abstract = {BACKGROUND: Plants have developed defense strategies for phytopathogen and herbivore protection via coordinated metabolic mechanisms. Low-molecular weight metabolites produced within plant tissues, such as salicylic acid, represent one such mechanism which likely mediates plant - microbe interactions above and below ground. Salicylic acid is a ubiquitous phytohormone at low levels in most plants, yet are concentrated defense compounds in Populus, likely acting as a selective filter for rhizosphere microbiomes. We propagated twelve Populus trichocarpa genotypes which varied an order of magnitude in salicylic acid (SA)-related secondary metabolites, in contrasting soils from two different origins. After four months of growth, plant properties (leaf growth, chlorophyll content, and net photosynthetic rate) and plant root metabolomics specifically targeting SA metabolites were measured via GC-MS. In addition, rhizosphere microbiome composition was measured via Illumina MiSeq sequencing of 16S and ITS2 rRNA-genes.

RESULTS: Soil origin was the primary filter causing divergence in bacterial/archaeal and fungal communities with plant genotype secondarily influential. Both bacterial/archaeal and fungal evenness varied between soil origins and bacterial/archaeal diversity and evenness correlated with at least one SA metabolite (diversity: populin; evenness: total phenolics). The production of individual salicylic acid derivatives that varied by host genotype resulted in compositional differences for bacteria /archaea (tremuloidin) and fungi (salicylic acid) within one soil origin (Clatskanie) whereas soils from Corvallis did not illicit microbial compositional changes due to salicylic acid derivatives. Several dominant bacterial (e.g., Betaproteobacteria, Acidobacteria, Verrucomicrobia, Chloroflexi, Gemmatimonadete, Firmicutes) and one fungal phyla (Mortierellomycota) also correlated with specific SA secondary metabolites; bacterial phyla exhibited more negative interactions (declining abundance with increasing metabolite concentration) than positive interactions.

CONCLUSIONS: These results indicate microbial communities diverge most among soil origin. However, within a soil origin, bacterial/archaeal communities are responsive to plant SA production within greenhouse-based rhizosphere microbiomes. Fungal microbiomes are impacted by root SA-metabolites, but overall to a lesser degree within this experimental context. These results suggest plant defense strategies, such as SA and its secondary metabolites, may partially drive patterns of both bacterial/archaeal and fungal taxa-specific colonization and assembly.},
}

@article {pmid31102465,
year = {2019},
author = {Birer, C and Wright, ES},
title = {Capturing the complex interplay between drugs and the intestinal microbiome.},
journal = {Clinical pharmacology and therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1002/cpt.1505},
pmid = {31102465},
issn = {1532-6535},
abstract = {Predicting drug interactions, disposition, and side effects is central to the practice of clinical pharmacology. Until recently, the human microbiome has been an underappreciated player in the dynamics of drug metabolism. It is now clear that humans are 'superorganisms' with about tenfold more microbial cells than human cells and harboring an immense diversity of microbial enzymes. Owing to the advent of new technologies, we are beginning to understand the human microbiome's impact on clinical pharmacology. This article is protected by copyright. All rights reserved.},
}

@article {pmid31102430,
year = {2019},
author = {Pathirana, E and McPherson, A and Whittington, R and Hick, P},
title = {The Role of Tissue Type, Sampling and Nucleic Acid Purification Methodology on the Inferred Composition of Pacific Oyster (Crassostrea gigas) Microbiome.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jam.14326},
pmid = {31102430},
issn = {1365-2672},
abstract = {AIMS: This study evaluated methods to sample and extract nucleic acids from Pacific oysters to accurately determine the microbiome associated with different tissues.

METHODS AND RESULTS: Samples were collected from haemolymph, gill, gut and adductor-muscle, using swabs and homogenates of solid tissues. Nucleic acids were extracted from fresh and frozen samples using three different commercial kits. The bacterial DNA yield varied between methods (P < 0.05) and each tissue harboured a unique microbiota, except for gill and muscle. Higher bacterial DNA yields were obtained by swabbing compared to tissue homogenates and from fresh tissues compared to frozen tissues, without impacting the bacterial community composition estimated by 16S rRNA gene (V1-V3 region) sequencing. Despite the higher bacterial DNA yields with QIAamp® DNA microbiome kit, the E.Z.N.A.® Mollusc DNA kit identified twice as many operational taxonomic units (OTUs) and eliminated PCR inhibition from gut tissues.

CONCLUSIONS: Sampling and nucleic acid purification substantially affected the quantity and diversity of bacteria identified in Pacific oyster microbiome studies and a fit-for-purpose strategy is recommended.

Accurate identification of Pacific oyster microbial diversity is instrumental for understanding the polymicrobial aetiology of Pacific oyster mortality diseases which greatly impact oyster production. This article is protected by copyright. All rights reserved.},
}

@article {pmid31102416,
year = {2019},
author = {Yu, XL and Chan, Y and Zhuang, L and Lai, HC and Lang, NP and Leung, WK and Watt, RM},
title = {Intra-oral single site comparisons of periodontal and peri-implant microbiota in health and disease.},
journal = {Clinical oral implants research},
volume = {},
number = {},
pages = {},
doi = {10.1111/clr.13459},
pmid = {31102416},
issn = {1600-0501},
abstract = {OBJECTIVE: Periodontitis and peri-implantitis are oral infectious-inflammatory diseases that share similarities in their pathology and etiology. Our objective was to characterize the single-site subgingival and submucosal microbiomes of implant-rehabilitated, partially dentate Chinese subjects (n=18) presenting with both periodontitis and peri-implantitis.

MATERIALS AND METHODS: Subgingival/submucosal plaque samples were collected from four clinically-distinct sites in each subject: peri-implantitis submucosa (DI), periodontal pocket (DT), clinically-healthy (unaffected) peri-implant submucosa (HI), and clinically-healthy (unaffected) subgingival sulcus (HT). The bacterial microbiota present was analysed using Illumina MiSeq sequencing.

RESULTS: 26 phyla and 5,726 Operational Taxonomic Units (OTUs, 97% sequence similarity cut-off) were identified. Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, Actinobacteria, Synergistetes, TM7 and Spirochaetes comprised 99.6% of the total reads detected. Bacterial communities within the DI, DT, HI and HT sites shared high levels of taxonomic similarity. 31 'core species' were present in >90% sites; with Streptococcus infantis/mitis/oralis (HMT-070/HMT-071/HMT-638/HMT-677) and Fusobacterium sp. HMT-203/HMT-698 being particularly prevalent and abundant. Beta-diversity analyses (Permanova-test, weighted-UniFrac) revealed the largest variance in the microbiota was at the subject level (46%), followed by periodontal health status (4%). Differing sets of OTUs were associated with periodontitis and peri-implantitis sites, respectively. This included putative 'periodontopathogens, such as Prevotella, Porphyromonas, Tannerella, Bacteroidetes [G-5] and Treponema spp. Interaction network analysis identified several putative patterns underlying dysbiosis in periodontitis/peri-implantitis sites.

CONCLUSIONS: Species (OTU) composition of the periodontal and peri-implant microbiota varied widely between subjects. The inter-subject variations in subgingival/submucosal microbiome composition outweighed differences observed between implant versus tooth sites, or between diseased versus healthy (unaffected) peri-implant/periodontal sites. This article is protected by copyright. All rights reserved.},
}

@article {pmid31101975,
year = {2019},
author = {Eble, H and Joswig, M and Lamberti, L and Ludington, WB},
title = {Cluster partitions and fitness landscapes of the Drosophila fly microbiome.},
journal = {Journal of mathematical biology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00285-019-01381-0},
pmid = {31101975},
issn = {1432-1416},
abstract = {The concept of genetic epistasis defines an interaction between two genetic loci as the degree of non-additivity in their phenotypes. A fitness landscape describes the phenotypes over many genetic loci, and the shape of this landscape can be used to predict evolutionary trajectories. Epistasis in a fitness landscape makes prediction of evolutionary trajectories more complex because the interactions between loci can produce local fitness peaks or troughs, which changes the likelihood of different paths. While various mathematical frameworks have been proposed to investigate properties of fitness landscapes, Beerenwinkel et al. (Stat Sin 17(4):1317-1342, 2007a) suggested studying regular subdivisions of convex polytopes. In this sense, each locus provides one dimension, so that the genotypes form a cube with the number of dimensions equal to the number of genetic loci considered. The fitness landscape is a height function on the coordinates of the cube. Here, we propose cluster partitions and cluster filtrations of fitness landscapes as a new mathematical tool, which provides a concise combinatorial way of processing metric information from epistatic interactions. Furthermore, we extend the calculation of genetic interactions to consider interactions between microbial taxa in the gut microbiome of Drosophila fruit flies. We demonstrate similarities with and differences to the previous approach. As one outcome we locate interesting epistatic information on the fitness landscape where the previous approach is less conclusive.},
}

@article {pmid31101887,
year = {2019},
author = {DiLegge, MJ and Manter, DK and Vivanco, JM},
title = {A novel approach to determine generalist nematophagous microbes reveals Mortierella globalpina as a new biocontrol agent against Meloidogyne spp. nematodes.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {7521},
doi = {10.1038/s41598-019-44010-y},
pmid = {31101887},
issn = {2045-2322},
abstract = {Root-knot nematodes (RKN) such as Meloidogyne spp. are among the most detrimental pests in agriculture affecting several crops. New methodologies to manage RKN are needed such as efficient discovery of nematophagous microbes. In this study, we developed an in vitro high-throughput method relying on the free-living nematode Caenorhabditis elegans and the infection of those nematodes with a soil slurry containing a microbiome likely to house nematophagous microbes. Nematodes were monitored for presence of infection and sub-cultured repeatedly for the purpose of isolating pure cultures of the microbe responsible for conferring the nematicidal activity. Once soil microbes were confirmed to be antagonistic to C. elegans, they were tested for pathogenicity against Meloidogyne chitwoodi. Using this methodology, the fungal isolate Mortierella globalpina was confirmed to be pathogenic in vitro against M. chitwoodi by nematode trapping via hyphal adhesion to the cuticle layer, penetration of the cuticle layer, and subsequently digestion of its cellular contents. M. globalpina was also observed to reduce disease symptomology of RKNs in vivo via significant reduction of root-galls on tomato (Solanum lycopersicum var. Rutgers).},
}

@article {pmid31101866,
year = {2019},
author = {Cho, EJ and Leem, S and Kim, SA and Yang, J and Lee, YB and Kim, SS and Cheong, JY and Cho, SW and Kim, JW and Kim, SM and Yoon, JH and Park, T},
title = {Circulating Microbiota-Based Metagenomic Signature for Detection of Hepatocellular Carcinoma.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {7536},
doi = {10.1038/s41598-019-44012-w},
pmid = {31101866},
issn = {2045-2322},
support = {HI16C2037//Korea Health Industry Development Institute (KHIDI)/ ; NRF-2017R1D1A1B03034639//National Research Foundation of Korea (NRF)/ ; 04-2017-0640//Seoul National University Hospital (SNUH)/ ; },
abstract = {Circulating microbial dysbiosis is associated with chronic liver disease including nonalcoholic steatohepatitis and alcoholic liver disease. In this study, we evaluated whether disease-specific alterations of circulating microbiome are present in patients with cirrhosis and hepatocellular carcinoma (HCC), and their potential as diagnostic biomarkers for HCC. We performed cross-sectional metagenomic analyses of serum samples from 79 patients with HCC, 83 with cirrhosis, and 201 matching healthy controls, and validated the results in the same number of subjects. Serum bacterial DNA was analyzed using high-throughput pyrosequencing after amplification of the V3-V4 hypervariable regions of 16S rDNA. Blood microbial diversity was significantly reduced in HCC, compared with cirrhosis and control. There were significant differences in the relative abundances of several bacterial taxa that correlate with the presence of HCC, thus defining a specific blood microbiome-derived metagenomic signature of HCC. We identified 5 microbial gene markers-based model which distinguished HCC from controls with an area under the receiver-operating curve (AUC) of 0.879 and a balanced accuracy of 81.6%. In the validation, this model accurately distinguished HCC with an AUC of 0.875 and an accuracy of 79.8%. In conclusion, circulating microbiome-based signatures may be potential biomarkers for the detection HCC.},
}