@article {pmid30901692,
year = {2019},
author = {Zhang, Y and Li, X},
title = {Salicylic acid: biosynthesis, perception, and contributions to plant immunity.},
journal = {Current opinion in plant biology},
volume = {50},
number = {},
pages = {29-36},
doi = {10.1016/j.pbi.2019.02.004},
pmid = {30901692},
issn = {1879-0356},
abstract = {Salicylic acid (SA) has emerged as a key plant defense hormone with critical roles in different aspects of plant immunity. Analysis of Arabidopsis mutants revealed complex regulation of pathogen-induced SA biosynthesis. Studies on SA-insensitive mutants led to the identification of the SA receptors and how SA regulates defense gene expression. Consistent with its critical roles in plant immunity, SA is required for the assembly of a normal root microbiome and various pathogen effectors have evolved to target components of SA biosynthesis or signaling. This review discusses recent advances in SA biology, focusing in particular on the regulation of SA biosynthesis and SA perception.},
}

@article {pmid30901468,
year = {2019},
author = {Balakrishnan, B and Luckey, D and Taneja, V},
title = {Autoimmunity-Associated Gut Commensals Modulate Gut Permeability and Immunity in Humanized Mice.},
journal = {Military medicine},
volume = {184},
number = {Supplement_1},
pages = {529-536},
doi = {10.1093/milmed/usy309},
pmid = {30901468},
issn = {1930-613X},
abstract = {OBJECTIVE: Although the etiology of rheumatoid arthritis (RA) is unknown, recent studies have led to the concept that gut dysbiosis may be involved in onset. In this study, we aimed to determine if human gut commensals modulate the immune response and gut epithelial integrity in DQ8 mice.

METHODS: DQ8 mice were orally gavaged with RA-associated (Eggerthella lenta or Collinsella aerofaciens) and non-associated (Prevotella histicola or Bifidobacterium sp.) on alternate days for 1 week in naïve mice. Some mice were immunized with type II collagen and oral gavage continued for 6 weeks and followed for arthritis. Epithelial integrity was done by FITC-Dextran assay. In addition, cytokines were measured in sera by ELISA and various immune cells were quantified using flow cytometry.

RESULTS: Gut permeability was increased by the RA-associated bacteria and was sex and age-dependent. In vivo and in vitro observations showed that the RA-non-associated bacteria outgrow the RA-associated bacteria when gavaged or cultured together. Mice gavaged with the RA-non-associated bacteria produced lower levels of pro-inflammatory MCP-1 and MCP-3 and had lower numbers of Inflammatory monocytes CD11c+Ly6c+, when compared to controls. E. lenta treated naïve mice produce Th17 cytokines.

CONCLUSIONS: Our studies suggest that gut commensals influence immune response in and away from the gut by changing the gut permeability and immunity. Dysbiosis helps the growth of RA-associated bacteria and reduces the beneficial bacteria.},
}

@article {pmid30901358,
year = {2019},
author = {Jeanne, T and Parent, SÉ and Hogue, R},
title = {Using a soil bacterial species balance index to estimate potato crop productivity.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0214089},
doi = {10.1371/journal.pone.0214089},
pmid = {30901358},
issn = {1932-6203},
abstract = {The development of 'molecular-omic' tools and computing analysis platforms have greatly enhanced our ability to assess the impacts of agricultural practices and crop management protocols on soil microbial diversity. However, biotic factors are rarely factored into agricultural management models. Today it is possible to identify specific microbiomes and define biotic components that contribute to soil quality. We assessed the bacterial diversity of soils in 51 potato production plots. We describe a strategy for identifying a potato-crop-productivity bacterial species balance index based on amplicon sequence variants. We observed a significant impact of soil texture balances on potato yields; however, the Shannon and Chao1 richness indices and Pielou's evenness index poorly correlated with these yields. Nonetheless, we were able to estimate the portion of the total bacterial microbiome related to potato yield using an integrated species balances index derived from the elements of the bacterial microbiome that positively or negatively correlate with residual potato yields. This innovative strategy based on a microbiome selection procedure greatly enhances our ability to interpret the impact of agricultural practices and cropping system management choices on microbial diversity and potato yield. This strategy provides an additional tool that will aid growers and the broader agricultural sector in their decision-making processes concerning the soil quality and crop productivity.},
}

@article {pmid30901046,
year = {2019},
author = {Sordillo, JE and Korrick, S and Laranjo, N and Carey, V and Weinstock, GM and Gold, DR and O'Connor, G and Sandel, M and Bacharier, LB and Beigelman, A and Zeiger, R and Litonjua, AA and Weiss, ST},
title = {Association of the Infant Gut Microbiome With Early Childhood Neurodevelopmental Outcomes: An Ancillary Study to the VDAART Randomized Clinical Trial.},
journal = {JAMA network open},
volume = {2},
number = {3},
pages = {e190905},
doi = {10.1001/jamanetworkopen.2019.0905},
pmid = {30901046},
issn = {2574-3805},
abstract = {Importance: In animal models, the early life gut microbiome influences later neurodevelopment. Corresponding data in human populations are lacking.

Objective: To study associations between the gut microbiome in infants and development at preschool age measured by the Ages and Stages Questionnaire, third edition (ASQ-3).

This ancillary cohort study of the Vitamin D Antenatal Asthma Reduction Trial (VDAART) used data from 715 participants who had development assessed at 3 years of age by the ASQ-3, which included scores in 5 domains (gross motor skills, fine motor skills, problem solving, communication, and personal and social skills). A total of 309 stool samples were collected from infants aged 3 to 6 months for microbiome analysis using 16S rRNA gene sequencing.

Exposures: Infant gut microbiome.

Main Outcomes and Measures: Continuous ASQ-3 scores and typical vs potential delay in the 5 developmental domains. Factor scores for bacterial coabundance groups were used as predictors in regression models of continuous ASQ-3 scores. Logistic regression was used to examine bacterial coabundance scores and odds of scoring below the threshold for typical development. Multivariate analysis examined the abundance of individual taxa and ASQ-3 scores.

Results: The 309 participants (170 [55.0%] male) with ASQ-3 scores and stool samples were ethnically diverse (136 [44.0%] black, 41 [13.3%] Hispanic, 86 [27.8%] white, and 46 [14.9%] other race/ethnicity); the mean (SD) age at ASQ-3 assessment was 3.0 (0.07) years. Coabundance scores dominated by Clostridiales (Lachnospiraceae genera and other, unclassified Clostridiales taxa) were associated with poorer ASQ-3 communication (β, -1.12; 95% CI, -2.23 to -0.01; P = .05) and personal and social (β, -1.44; 95% CI, -2.47 to -0.40; P = .01) scores and with increased odds of potential delay for communication (odds ratio [OR], 1.69; 95% CI, 1.06 to 2.68) and personal and social skills (OR, 1.96; 95% CI, 1.22 to 3.15) per unit increase in coabundance score. The Bacteroides-dominated coabundance grouping was associated with poorer fine motor scores (β, -2.42; 95% CI, -4.29 to -0.55; P = .01) and with increased odds of potential delay for fine motor skills (OR, 1.52; 95% CI, 1.07 to 2.16) per unit increase in coabundance score. Multivariate analysis detected similar family-level and order-level associations.

Conclusions and Relevance: These findings suggest an association between infant gut microbiome composition and communication, personal and social, and fine motor skills at age 3 years. The majority of associations were driven by taxa within the order Clostridiales.},
}

@article {pmid30900475,
year = {2019},
author = {Walker, MM and Talley, NJ and Keely, S},
title = {Follow up on atopy and the gastrointestinal tract - a review of a common association 2018.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2019.1596025},
pmid = {30900475},
issn = {1747-4132},
abstract = {INTRODUCTION: Primary atopic disorders can be classified as heritable genetic disorders presenting with deregulated pathogenic allergic effector responses irrespective of sensitization. In the last decade, there are parallel rises in the burden of atopic and gastrointestinal (GI) diseases. Areas covered: There is increasing recognition of an association between atopy and GI disease through immune dysregulation, the microbiome and shared genetic pathways. Since the first article on atopy and the GI tract in 2014 in this journal, many more studies have shed light on the shared pathways in these diseases, particularly in the field of eosinophilic GI disease, functional GI disorders and inflammatory bowel disease. Expert opinion: Understanding the links with common mechanisms in atopy and GI diseases that may lead to better targeting of treatment through manipulation of immune mechanisms, the microbiome, genetics, food allergens and specific GI diseases such as inflammatory bowel disease, functional GI disorders.},
}

@article {pmid30900360,
year = {2019},
author = {Robinson, DA and Hopmans, JW and Filipovic, V and van der Ploeg, M and Lebron, I and Jones, SB and Reinsch, S and Jarvis, N and Tuller, M},
title = {Global Environmental Changes Impact Soil Hydraulic Functions through Biophysical Feedbacks.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.14626},
pmid = {30900360},
issn = {1365-2486},
abstract = {Although only representing 0.05% of global freshwater, or 0.001% of all global water, soil water supports all terrestrial biological life. Soil moisture behaviour in most models is constrained by hydraulic parameters that do not change. Here we argue that biological feedbacks from plants, macro-fauna and the microbiome influence soil structure, and thus the soil hydraulic parameters and the soil water content signals we observe. Incorporating biological feedbacks into soil hydrological models is therefore important for understanding environmental change and its impacts on ecosystems. We anticipate that environmental change will accelerate and modify soil hydraulic function. Increasingly we understand the vital role that soil moisture exerts on the carbon cycle and other environmental threats such as heatwaves, droughts and floods, wildfires, regional precipitation patterns, disease regulation and infrastructure stability, in addition to agricultural production. Biological feedbacks may result in changes to soil hydraulic function that could be irreversible, resulting in alternative stable states (ASS) of soil moisture. To explore this, we need models that consider all the major feedbacks between soil properties and soil-plant-faunal-microbial-atmospheric processes, which is something we currently do not have. Therefore, a new direction is required to incorporate a dynamic description of soil structure and hydraulic property evolution into soil-plant-atmosphere, or land surface, models that consider feedbacks from land use and climate drivers of change, so as to better model ecosystem dynamics. This article is protected by copyright. All rights reserved.},
}

@article {pmid30899699,
year = {2019},
author = {Myles, IA},
title = {Allergy as a Disease of Dysbiosis: Is It Time to Shift the Treatment Paradigm?.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {50},
doi = {10.3389/fcimb.2019.00050},
pmid = {30899699},
issn = {2235-2988},
}

@article {pmid30899534,
year = {2019},
author = {Greathouse, KL and White, JR and Padgett, RN and Perrotta, BG and Jenkins, GD and Chia, N and Chen, J},
title = {Gut microbiome meta-analysis reveals dysbiosis is independent of body mass index in predicting risk of obesity-associated CRC.},
journal = {BMJ open gastroenterology},
volume = {6},
number = {1},
pages = {e000247},
doi = {10.1136/bmjgast-2018-000247},
pmid = {30899534},
issn = {2054-4774},
abstract = {Objective: Obesity is a risk factor for colorectal cancer (CRC), accounting for more than 14% of CRC incidence. Microbial dysbiosis and chronic inflammation are common characteristics in both obesity and CRC. Human and murine studies, together, demonstrate the significant impact of the microbiome in governing energy metabolism and CRC development; yet, little is understood about the contribution of the microbiome to development of obesity-associated CRC as compared to individuals who are not obese.

Design: In this study, we conducted a meta-analysis using five publicly available stool and tissue-based 16S rRNA and whole genome sequencing (WGS) data sets of CRC microbiome studies. High-resolution analysis was employed for 16S rRNA data, which allowed us to achieve species-level information to compare with WGS.

Results: Characterisation of the confounders between studies, 16S rRNA variable region and sequencing method did not reveal any significant effect on alpha diversity in CRC prediction. Both 16S rRNA and WGS were equally variable in their ability to predict CRC. Results from diversity analysis confirmed lower diversity in obese individuals without CRC; however, no universal differences were found in diversity between obese and non-obese individuals with CRC. When examining taxonomic differences, the probability of being classified as CRC did not change significantly in obese individuals for all taxa tested. However, random forest classification was able to distinguish CRC and non-CRC stool when body mass index was added to the model.

Conclusion: Overall, microbial dysbiosis was not a significant factor in explaining the higher risk of colon cancer among individuals with obesity.},
}

@article {pmid30899393,
year = {2019},
author = {Gutiérrez-Repiso, C and Moreno-Indias, I and de Hollanda, A and Martín-Núñez, GM and Vidal, J and Tinahones, FJ},
title = {Gut microbiota specific signatures are related to the successful rate of bariatric surgery.},
journal = {American journal of translational research},
volume = {11},
number = {2},
pages = {942-952},
pmid = {30899393},
issn = {1943-8141},
abstract = {Bariatric surgery (BS) success rates vary in the long-time. A better understanding of weight-loss response may help improve the outcomes of BS. Gut microbiome could be implicated in the successful rate of BS. The aim of the study is to analyze the role of gut microbiome in the successful rate of BS. This is a cross-sectional study of a prospective cohort of 24 patients who underwent gastric bypass. Patients were classified based on excess weight loss (EWL) as: Success (EWL50% at nadir weight and throughout follow-up), Primary Failure (EWL<50% at nadir weight and thereafter), and Weight Regain (EWL>50% at nadir weight, but <50% at last follow-up visit). Gut microbiome analysis was assessed by High Throughput Sequencing. Cholesterol metabolism was shown as the most affected parameter among groups. Studied groups registered minor changes between their gut microbiome abundances, with Butyrivibrio, Lachnospira and Sarcina among them. However, Success group shared a more diverse core microbiome than the other groups. We showed evidence of a possible role of gut microbiome in the cholesterol metabolism, possibly through bile acids, relative to the success or failure of BS outcomes. Acinetobacter and Serratia, from Primary Failure core microbiome, could have implications in its successful rate. Sarcina abundance was presented as the best genera related to the body mass index (BMI) post-surgery. Gut microbiota could mediate, at least partially, the success rate of BS through their interaction with the bile acids milieu. Further studies are necessary to validate this probe of concept.},
}

@article {pmid30899262,
year = {2019},
author = {He, B and Hoang, TK and Tian, X and Taylor, CM and Blanchard, E and Luo, M and Bhattacharjee, MB and Freeborn, J and Park, S and Couturier, J and Lindsey, JW and Tran, DQ and Rhoads, JM and Liu, Y},
title = {Lactobacillus reuteri Reduces the Severity of Experimental Autoimmune Encephalomyelitis in Mice by Modulating Gut Microbiota.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {385},
doi = {10.3389/fimmu.2019.00385},
pmid = {30899262},
issn = {1664-3224},
abstract = {The gut microbiome plays an important role in immune function and has been implicated in multiple sclerosis (MS). However, how and if the modulation of microbiota can prevent or treat MS remain largely unknown. In this study, we showed that probiotic Lactobacillus reuteri DSM 17938 (L. reuteri) ameliorated the development of murine experimental autoimmune encephalomyelitis (EAE), a widely used animal model of MS, a model which is primarily mediated by TH17 and TH1 cells. We discovered that L. reuteri treatment reduced TH1/TH17 cells and their associated cytokines IFN-γ/IL-17 in EAE mice. We also showed that the loss of diversity of gut microbiota induced by EAE was largely restored by L. reuteri treatment. Taxonomy-based analysis of gut microbiota showed that three "beneficial" genera Bifidobacterium, Prevotella, and Lactobacillus were negatively correlated with EAE clinical severity, whereas the genera Anaeroplasma, Rikenellaceae, and Clostridium were positively correlated with disease severity. Notably, L. reuteri treatment coordinately altered the relative abundance of these EAE-associated taxa. In conclusion, probiotic L. reuteri changed gut microbiota to modulate immune responses in EAE, making it a novel candidate in future studies to modify the severity of MS.},
}

@article {pmid30899109,
year = {2019},
author = {Cryan, JF and Dinan, TG},
title = {Talking about a microbiome revolution.},
journal = {Nature microbiology},
volume = {4},
number = {4},
pages = {552-553},
doi = {10.1038/s41564-019-0422-9},
pmid = {30899109},
issn = {2058-5276},
}

@article {pmid30899005,
year = {2019},
author = {Elovitz, MA and Gajer, P and Riis, V and Brown, AG and Humphrys, MS and Holm, JB and Ravel, J},
title = {Cervicovaginal microbiota and local immune response modulate the risk of spontaneous preterm delivery.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1305},
doi = {10.1038/s41467-019-09285-9},
pmid = {30899005},
issn = {2041-1723},
abstract = {Failure to predict and understand the causes of preterm birth, the leading cause of neonatal morbidity and mortality, have limited effective interventions and therapeutics. From a cohort of 2000 pregnant women, we performed a nested case control study on 107 well-phenotyped cases of spontaneous preterm birth (sPTB) and 432 women delivering at term. Using innovative Bayesian modeling of cervicovaginal microbiota, seven bacterial taxa were significantly associated with increased risk of sPTB, with a stronger effect in African American women. However, higher vaginal levels of β-defensin-2 lowered the risk of sPTB associated with cervicovaginal microbiota in an ethnicity-dependent manner. Surprisingly, even in Lactobacillus spp. dominated cervicovaginal microbiota, low β-defensin-2 was associated with increased risk of sPTB. These findings hold promise for diagnostics to accurately identify women at risk for sPTB early in pregnancy. Therapeutic strategies could include immune modulators and microbiome-based therapeutics to reduce this significant health burden.},
}

@article {pmid30898652,
year = {2019},
author = {O'Connor, KM and Lucking, EF and Golubeva, AV and Strain, CR and Fouhy, F and Cenit, MC and Dhaliwal, P and Bastiaanssen, TFS and Burns, DP and Stanton, C and Clarke, G and Cryan, JF and O'Halloran, KD},
title = {Manipulation of gut microbiota blunts the ventilatory response to hypercapnia in adult rats.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ebiom.2019.03.029},
pmid = {30898652},
issn = {2352-3964},
abstract = {BACKGROUND: It is increasingly evident that perturbations to the diversity and composition of the gut microbiota have significant consequences for the regulation of integrative physiological systems. There is growing interest in the potential contribution of microbiota-gut-brain signalling to cardiorespiratory control in health and disease.

METHODS: In adult male rats, we sought to determine the cardiorespiratory effects of manipulation of the gut microbiota following a 4-week administration of a cocktail of antibiotics. We subsequently explored the effects of administration of faecal microbiota from pooled control (vehicle) rat faeces, given by gavage to vehicle- and antibiotic-treated rats.

FINDINGS: Antibiotic intervention depressed the ventilatory response to hypercapnic stress in conscious animals, owing to a reduction in the respiratory frequency response to carbon dioxide. Baseline frequency, respiratory timing variability, and the expression of apnoeas and sighs were normal. Microbiota-depleted rats had decreased systolic blood pressure. Faecal microbial transfer to vehicle- and antibiotic-treated animals also disrupted the gut microbiota composition, associated with depressed ventilatory responsiveness to hypercapnia. Chronic antibiotic intervention or faecal microbial transfer both caused significant disruptions to brainstem monoamine neurochemistry, with increased homovanillic acid:dopamine ratio indicative of increased dopamine turnover, which correlated with the abundance of several bacteria of six different phyla.

INTERPRETATION: Chronic antibiotic administration and faecal microbial transfer disrupt gut microbiota, brainstem monoamine concentrations and the ventilatory response to hypercapnia. We suggest that aberrant microbiota-gut-brain axis signalling has a modulatory influence on respiratory behaviour during hypercapnic stress. FUND: Department of Physiology and APC Microbiome Ireland, University College Cork, Ireland.},
}

@article {pmid30898603,
year = {2019},
author = {Ogawa, M and Hoshina, T and Haro, K and Kumadaki, T and Ishii, M and Fujino, Y and Fukuda, K and Kusuhara, K},
title = {The microbiological characteristics of lower respiratory tract infection in patients with neuromuscular disorders: An investigation based on a multiplex polymerase chain reaction to detect viruses and a clone library analysis of the bacterial 16S rRNA gene sequence in sputum samples.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmii.2019.01.002},
pmid = {30898603},
issn = {1995-9133},
abstract = {We performed gene amplification methods for the detections of bacteria and viruses using sputum samples to clarify the microbiological characteristics of lower respiratory tract infection in patients with neuromuscular disorders. The tendencies of higher proportion of respiratory virus detection and lower diversity of bacteria in sputum were observed.},
}

@article {pmid30898151,
year = {2019},
author = {Labus, JS and Osadchiy, V and Hsiao, EY and Tap, J and Derrien, M and Gupta, A and Tillisch, K and Le Nevé, B and Grinsvall, C and Ljungberg, M and Öhman, L and Törnblom, H and Simren, M and Mayer, EA},
title = {Evidence for an association of gut microbial Clostridia with brain functional connectivity and gastrointestinal sensorimotor function in patients with irritable bowel syndrome, based on tripartite network analysis.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {45},
doi = {10.1186/s40168-019-0656-z},
pmid = {30898151},
issn = {2049-2618},
support = {DK048351//National Institutes of Health/ ; DK064539//National Institutes of Health/ ; DK096606//National Institutes of Health/ ; 13409//Vetenskapsrådet/ ; 21691//Vetenskapsrådet/ ; 21692//Vetenskapsrådet/ ; },
abstract = {BACKGROUND AND AIMS: Evidence from preclinical and clinical studies suggests that interactions among the brain, gut, and microbiota may affect the pathophysiology of irritable bowel syndrome (IBS). As disruptions in central and peripheral serotonergic signaling pathways have been found in patients with IBS, we explored the hypothesis that the abundance of serotonin-modulating microbes of the order Clostridiales is associated with functional connectivity of somatosensory brain regions and gastrointestinal (GI) sensorimotor function.

METHODS: We performed a prospective study of 65 patients with IBS and 21 healthy individuals (controls) recruited from 2011 through 2013 at a secondary/tertiary care outpatient clinic in Sweden. Study participants underwent functional brain imaging, rectal balloon distension, a nutrient and lactulose challenge test, and assessment of oroanal transit time within a month. They also submitted stool samples, which were analyzed by 16S ribosomal RNA gene sequencing. A tripartite network analysis based on graph theory was used to investigate the interactions among bacteria in the order Clostridiales, connectivity of brain regions in the somatosensory network, and GI sensorimotor function.

RESULTS: We found associations between GI sensorimotor function and gut microbes in stool samples from controls, but not in samples from IBS patients. The largest differences between controls and patients with IBS were observed in the Lachnospiraceae incertae sedis, Clostridium XIVa, and Coprococcus subnetworks. We found connectivity of subcortical (thalamus, caudate, and putamen) and cortical (primary and secondary somatosensory cortices) regions to be involved in mediating interactions among these networks.

CONCLUSIONS: In a comparison of patients with IBS and controls, we observed disruptions in the interactions between the brain, gut, and gut microbial metabolites in patients with IBS-these involve mainly subcortical but also cortical regions of brain. These disruptions may contribute to altered perception of pain in patients with IBS and may be mediated by microbial modulation of the gut serotonergic system.},
}

@article {pmid30897381,
year = {2018},
author = {Liu, Z and Li, J and Liu, H and Tang, Y and Zhan, Q and Lai, W and Ao, L and Meng, X and Ren, H and Xu, D and Zeng, Q},
title = {The intestinal microbiota associated with cardiac valve calcification differs from that of coronary artery disease.},
journal = {Atherosclerosis},
volume = {284},
number = {},
pages = {121-128},
doi = {10.1016/j.atherosclerosis.2018.11.038},
pmid = {30897381},
issn = {1879-1484},
abstract = {BACKGROUND AND AIMS: Although most risk factors for cardiac valve calcification (VC) are similar to those for coronary artery disease (CAD), they differ regarding lesions and clinical symptoms. Recently, increasing evidence suggests that intestinal bacteria play essential roles in cardiovascular disease (CVD). It is plausible that the gut microbiota is linked to the occurrence of different CVDs under similar risk factors. Thus, we aimed to explore the gut microbiomes in patients with VC or CAD and determine their underlying connections.

METHODS: We collected samples from 119 subjects and performed 16S rRNA gene sequencing to analyze the gut microbiomes in VC and CAD patients and in control volunteers.

RESULTS: The gut microbiomes of VC and CAD patients were significantly different in terms of beta-diversity. Bacteria from Veillonella dispar, Bacteroides plebeius and Fusobacterium were enriched in the VC group, while members of Collinsella aerofaciens, Megamonas, Enterococcus, Megasphaera, Dorea and Blautia were decreased. According to the association with dyslipidemia, seven operational taxonomic units (OTUs), including Parabacteroides distasonis, Megamonas, Fusobacterium, Bacteroides sp., Bacteroides plebeius, Lactobacillus and Prevotella copri, were regarded as potential pathogens for CVDs. Additionally, Prevotella copri might be a keystone of CVDs, especially in VC patients, while Collinsella aerofaciens is a possible keystone of CAD, based on the multi-correlations of these bacteria with other OTUs in microbial communities.

CONCLUSIONS: Patients with VC and CAD suffer from different gut microbial dysbiosis. The gut microbiomes are associated with the clinical characteristics in these diseases and might be potential therapeutic targets.},
}

@article {pmid30896565,
year = {2019},
author = {Li, T and Liu, ZH and Li, K and Bai, HH},
title = {Evaluation of the vaginal microbiome in clinical diagnosis and management of vaginal infectious diseases.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/CM9.0000000000000211},
pmid = {30896565},
issn = {2542-5641},
abstract = {OBJECTIVE: The Vaginal Microecology Evaluation System (VMES) is a technical and economically feasible tool to assess the vaginal microbiomes of gynecological outpatients. The aim of this review was to introduce knowledge on the potential changes that can occur in the vaginal microbiome and how to use the Evaluation System to diagnose and manage a broad range of vaginal infections.

DATA SOURCES: This review was based on data in articles published in PubMed up to December 10, 2018, with the following keywords: "Vaginal microecosystem", "vaginal microbiome", "vaginal microbiota", and "vaginal flora".

STUDY SELECTION: Original articles and critical reviews on VMES and vaginal microbiota selected for this review. References of the retrieved articles were also screened to search for potentially relevant papers.

RESULTS: Any imbalance in the naturally occurring vaginal bacterial flora may result in infections such as bacterial vaginitis, aerobic vaginitis, vulvovaginal candidiasis, or Trichomonas vaginalis. VMES is mainly composed of morphological and functional microecological indicators. The former diagnostic modality includes bacterial density, flora diversity, dominant bacterial flora, indicators of inflammation, pathogenic microorganisms, Nugent score, and AV score. Functional indicators consist of two main components: metabolites and microbial enzymes.

CONCLUSIONS: The establishment of VMES has a high clinical value in the treatment of vaginal infections. It opens up new opportunities for the comprehensive management of dysbacteriosis when such infections occur.This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0.},
}

@article {pmid30895930,
year = {2019},
author = {Leavis, HL},
title = {Friend or foe: how intestinal microbiome contribute to health and disease states.},
journal = {The Netherlands journal of medicine},
volume = {77},
number = {2},
pages = {40-41},
pmid = {30895930},
issn = {1872-9061},
}

@article {pmid30895716,
year = {2019},
author = {Denis, S and Aurélie, D and Jun, N and Pierre, M and Amarante, V and Marco, M and Alexandre, B and Richard, S},
title = {Linking soil's volatilome to microbes and plant roots highlights the importance of microbes as emitters of belowground volatile signals.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14599},
pmid = {30895716},
issn = {1462-2920},
abstract = {Plants and microbes release a plethora of volatiles that act as signals in plant-microbe interactions. Characterizing soil's volatilome and microbiome might shed light on the nature of relevant volatile signals and on their emitters. This hypothesis was tested by characterizing plant cover, soil's volatilome, nutrient content and microbiomes in three grasslands of the Swiss Jura Mountains. The fingerprints of soil's volatiles were generated by solid-phase micro-extraction gas chromatography/mass spectrometry, whereas high-throughput sequencing was used to create a snapshot of soil's microbial communities. A high similarity was observed in plant communities of two out of three sites, which was mirrored by the soil's volatilome. Multiple factor analysis evidenced a strong association among soil's volatilome, plant and microbial communities. The proportion of volatiles correlated to single bacterial and fungal taxon was higher than for plants. This suggests that those organisms might be major contributors to the volatilome of grassland soils. These findings illustrate that key volatiles in grassland soils might be emitted by a handful of organisms that include specific plants and microbes. Further work will be needed to unravel the structure of belowground volatiles and understand their implications for plant health and development. This article is protected by copyright. All rights reserved.},
}

@article {pmid30895681,
year = {2019},
author = {Fernández-Bayo, JD and Hestmark, KV and Claypool, JT and Harrold, DR and Randall, TE and Achmon, Y and Stapleton, JJ and Simmons, CW and VanderGheynst, JS},
title = {The initial soil microbiota impacts the potential for lignocellulose degradation during soil solarization.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jam.14258},
pmid = {30895681},
issn = {1365-2672},
abstract = {AIMS: Soil biosolarization (SBS) is a pest control technology that includes the incorporation of organic matter into soil prior to solarization. The objective of this study was to measure the impact of the initial soil microbiome on the temporal evolution of genes encoding lignocellulose-degrading enzymes during SBS.

METHODS AND RESULTS: SBS field experiments were completed using green waste as a soil amendment and in the presence and absence of compost activating inoculum. Samples were collected over time and at two different soil depths for measurement of the microbial community and the predicted lignocellulosic-degrading microbiome. Compost inoculum had a significant positive effect on several predicted genes encoding enzymes involved in cellulose, hemicellulose and lignin degradation. These included beta-glucosidase, endo-1,3(4)-beta-glucanase, alpha-galactosidase and laccase.

CONCLUSION: Amendment of microorganisms found in compost to soil prior to soil biosolarization enhanced the degradation potential of cellulose, hemicellulose and lignin found in green waste.

The type of organic matter amended and its biotransformation by soil microorganisms impact the efficacy of SBS. The results suggest that co-amending highly recalcitrant biomass with microorganisms found in compost improves biomass conversion during soil biosolarization. This article is protected by copyright. All rights reserved.},
}

@article {pmid30895635,
year = {2019},
author = {Olaisen, M and Spigset, O and Flatberg, A and Granlund, AVB and Brede, WR and Albrektsen, G and Røyset, ES and Gilde, B and Sandvik, AK and Martinsen, TC and Fossmark, R},
title = {Mucosal 5-aminosalicylic acid concentration, drug formulation and mucosal microbiome in patients with quiescent ulcerative colitis.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.15227},
pmid = {30895635},
issn = {1365-2036},
support = {//Liaison Committee between Central Norway Regional Health Authority (RHA) and Norwegian University of Science and Technology (NTNU)/ ; //St.Olav´s Hospital, Trondheim University Hospital/ ; //Faculty of Medicine and Health Sciences at NTNU and RHA/ ; },
abstract = {BACKGROUND: 5-aminosalicylic acid (5-ASA) is the first-line therapy for ulcerative colitis (UC). 5-ASA acts locally in the colonic mucosa by numerous proposed mechanisms, and is metabolised by N-acetyltransferase (NAT). Large variations in mucosal 5-ASA concentrations have been reported, but the underlying mechanisms are not understood.

AIMS: To study the relationship between 5-ASA concentration, 5-ASA formulation, NAT genotype and bacterial microbiome in patients with UC.

METHODS: Patients with quiescent UC, using monotherapy of Mezavant (n = 18), Asacol (n = 14) or Pentasa (n = 10), 4.0-4.8 g/day were included. 5-ASA was measured in colonic mucosal biopsies and serum by ultra-high performance liquid chromatography. NAT genotypes were determined by Sanger sequencing. Bacterial microbiome was sequenced from faeces and mucosa by 16S rRNA sequencing using Illumina Miseq.

RESULTS: Mezavant provided the highest mucosal 5-ASA levels (geometric mean 2.39 ng/mg), followed by Asacol (1.60 ng/mg, 33% lower, P = 0.50) and Pentasa (0.57 ng/mg, 76% lower, P = 0.033). Mucosal 5-ASA concentration was not associated with NAT genotype, but serum 5-ASA concentration and NAT1 genotype was associated (P = 0.044). Mucosal 5-ASA concentration was positively associated with mucosal bacterial diversity (P = 0.0005) and bacterial composition. High mucosal 5-ASA concentration was related to reduced abundance of pathogenic bacteria such as Proteobacteria, and increased abundance of several favourable bacteria such as Faecalibacterium.

CONCLUSIONS: Mucosal 5-ASA concentration is positively associated with bacterial diversity and a mucosal bacterial composition that are perceived favourable in UC. Mezavant yielded higher mucosal 5-ASA concentrations than Pentasa. 5-ASA may have beneficial effects on the mucosal microbiome, and high concentrations possibly amend dysbiosis in UC.},
}

@article {pmid30895406,
year = {2019},
author = {Nguyen, VD and Nguyen, TT and Pham, TT and Packianather, M and Le, CH},
title = {Molecular screening and genetic diversity analysis of anticancer Azurin-encoding and Azurin-like genes in human gut microbiome deduced through cultivation-dependent and cultivation-independent studies.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10123-019-00070-8},
pmid = {30895406},
issn = {1618-1905},
support = {106-YS.04-2014.40//National Foundation for Science and Technology Development/ ; },
abstract = {Azurin, a bacteriocin produced by a human gut bacterium Pseudomonas aeruginosa, can reveal selectively cytotoxic and induce apoptosis in cancer cells. After overcoming two phase I trials, a functional region of Azurin called p28 has been approved as a drug for the treatment of brain tumor glioma by FDA. The present study aims to improve a screening procedure and assess genetic diversity of Azurin genes in P. aeruginosa and Azurin-like genes in the gut microbiome of a specific population in Vietnam and global populations. Firstly, both cultivation-dependent and cultivation-independent techniques based on genomic and metagenomic DNAs extracted from fecal samples of the healthy specific population were performed and optimized to detect Azurin genes. Secondly, the Azurin gene sequences were analyzed and compared with global populations by using bioinformatics tools. Finally, the screening procedure improved from the first step was applied for screening Azurin-like genes, followed by the protein synthesis and NCI in vitro screening for anticancer activity. As a result, this study has successfully optimized the annealing temperatures to amplify DNAs for screening Azurin genes and applying to Azurin-like genes from human gut microbiota. The novelty of this study is the first of its kind to classify Azurin genes into five different genotypes at a global scale and confirm the potential anticancer activity of three Azurin-like synthetic proteins (Cnazu1, Dlazu11, and Ruazu12). The results contribute to the procedure development applied for screening anticancer proteins from human microbiome and a comprehensive understanding of their therapeutic response at a genetic level.},
}

@article {pmid30895203,
year = {2019},
author = {Oldenburg, CE and Sié, A and Coulibaly, B and Ouermi, L and Dah, C and Tapsoba, C and Bärnighausen, T and Lebas, E and Arzika, AM and Cummings, S and Zhong, L and Lietman, TM and Keenan, JD and Doan, T},
title = {Indirect Effect of Azithromycin Use on the Intestinal Microbiome Diversity of Untreated Children: A Randomized Trial.},
journal = {Open forum infectious diseases},
volume = {6},
number = {3},
pages = {ofz061},
doi = {10.1093/ofid/ofz061},
pmid = {30895203},
issn = {2328-8957},
abstract = {Cohabiting children may share components of their intestinal microbiome. We evaluated whether receipt of azithromycin in one sibling confers changes to the intestinal microbiome in an untreated sibling compared with placebo in a randomized controlled trial. We found no evidence of an indirect effect of antibiotic use in cohabiting children. Clinical Trials Registrations: NCT03187834.},
}

@article {pmid30895172,
year = {2019},
author = {Ma, B and Liang, J and Dai, M and Wang, J and Luo, J and Zhang, Z and Jing, J},
title = {Altered Gut Microbiota in Chinese Children With Autism Spectrum Disorders.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {40},
doi = {10.3389/fcimb.2019.00040},
pmid = {30895172},
issn = {2235-2988},
abstract = {The link between gut microbes and autism spectrum disorders (ASD) has been already observed in some studies, but some bacterial families/species were found to be inconsistently up or down regulated. This issue has been rarely explored in the Chinese population. In this study, we assessed whether or not gut microbiota dysbiosis was associated with children with ASD in China. We enrolled 45 children with ASD (6-9 years of age; 39 boys and 6 girls) and 45 sex- and age-matched neurotypical children. Dietary and other socio-demographic information was obtained via questionnaires. We characterized the composition of the fecal microbiota using bacterial 16S ribosomal RNA (16S rRNA) gene sequencing. The ASD group showed less diversity and richness of gut microbiota than the neurotypical group, as estimated by the abundance-based coverage estimator index and the phylogenetic diversity index. The analysis of beta diversity showed an altered microbial community structure in the ASD group. After adjustment for confounders and multiple testing corrections, no significant group difference was found in the relative abundance of microbiota on the level of the phylum. At the family level, children with ASD had a lower relative abundance of Acidaminococcaceae than the healthy controls. Moreover, a decrease in the relative abundance of genera Lachnoclostridium, Tyzzerella subgroup 4, Flavonifractor, and unidentified Lachnospiraceae was observed in ASD group. This study provides further evidence of intestinal microbial dysbiosis in ASD and sheds light on the characteristics of the gut microbiome of autistic children in China.},
}

@article {pmid30894858,
year = {2019},
author = {Liberti, A and Cannon, JP and Litman, GW and Dishaw, LJ},
title = {A Soluble Immune Effector Binds Both Fungi and Bacteria via Separate Functional Domains.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {369},
doi = {10.3389/fimmu.2019.00369},
pmid = {30894858},
issn = {1664-3224},
abstract = {The gut microbiome of animals consists of diverse microorganisms that include both prokaryotes and eukaryotes. Complex interactions occur among these inhabitants, as well as with the immune system of the host, and profoundly influence the overall health of both the host and its microbial symbionts. Despite the enormous importance for the host to regulate its gut microbiome, the extent to which animals generate immune-related molecules with the capacity to directly influence polymicrobial interactions remains unclear. The urochordate, Ciona robusta, is a model organism that has been adapted to experimental studies of host/microbiome interactions. Ciona variable-region containing chitin-binding proteins (VCBPs) are innate immune effectors, composed of immunoglobulin (Ig) variable regions and a chitin-binding domain (CBD) and are expressed in high abundance in the gut. It was previously shown that VCBP-C binds bacteria and influences both phagocytosis by granular amoebocytes and biofilm formation via its Ig domains. We show here that the CBD of VCBP-C independently recognizes chitin molecules present in the cell walls, sporangia (spore-forming bodies), and spores of a diverse set of filamentous fungi isolated from the gut of Ciona. To our knowledge, this is the first description of a secreted Ig-containing immune molecule with the capacity to directly promote transkingdom interactions through simultaneous binding by independent structural domains and could have broad implications in modulating the establishment, succession, and homeostasis of gut microbiomes.},
}

@article {pmid30894847,
year = {2019},
author = {Brown, EEF and Cooper, A and Carrillo, C and Blais, B},
title = {Selection of Multidrug-Resistant Bacteria in Medicated Animal Feeds.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {456},
doi = {10.3389/fmicb.2019.00456},
pmid = {30894847},
issn = {1664-302X},
abstract = {Exposure to antimicrobial resistant (AMR) bacteria is a major public health issue which may, in part, have roots in food production practices that are conducive to the selection of AMR bacteria ultimately impacting the human microbiome through food consumption. Of particular concern is the prophylactic use of antibiotics in animal husbandry, such as the medication of feeds with sulfonamides and other antibiotics not considered clinically relevant, but which may nonetheless co-select for multi-drug resistant (MDR) bacteria harboring resistance to medically important antibiotics. Using a MDR Klebsiella pneumoniae strain exhibiting resistance to sulfonamides and beta-lactams (including carbapenem) as a model, we examined the ability of non-medicated and commercially medicated (sulfonamide) animal feeds to select for the model strain when inoculated at low levels by measuring its recovery along with key AMR markers, sul1(sulfonamide) and blaKPC-3 (meropenem), under different incubation conditions. When non-medicated feeds were supplemented with defined amounts of sulfadiazine the model strain was significantly enriched after incubation in Mueller Hinton Broth at 37°C overnight, or in same at room temperature for a week, with consistent detection of both the sul1 and blaKPC-3 markers as determined by polymerase chain reaction (PCR) techniques to screen colony isolates recovered on plating media. Significant recoveries of the inoculated strain and the sul1 and blaKPC-3 markers were observed with one of three commercially medicated (sulfamethazine) feeds tested under various incubation conditions. These results demonstrate that under certain conditions the prophylactic use of so-called non-priority antibiotics in feeds can potentially lead to co-selection of environmental AMR bacteria with resistance to medically important antibiotics, which may have far-reaching implications for human health.},
}

@article {pmid30894688,
year = {2019},
author = {Ma, ZS and Li, L and Gotelli, NJ},
title = {Diversity-disease relationships and shared species analyses for human microbiome-associated diseases.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-019-0395-y},
pmid = {30894688},
issn = {1751-7370},
abstract = {Diversity indices have been routinely computed in the study of human microbiome-associated diseases (MADs). However, it is still unclear whether there is a consistent diversity-disease relationship (DDR) for the human MADs, and whether there are consistent differences in the taxonomic composition of microbiomes sampled from healthy versus diseased individuals. Here we reanalyzed raw data and used a meta-analysis to compare the microbiome diversity and composition of healthy versus diseased individuals in 41 comparisons extracted from 27 previously published studies of human MADs. In the DDR analysis, the average effect size across studies did not differ from zero for a comparison of healthy versus diseased individuals. In 30 of 41 comparisons (73%) there was no significant difference in microbiome diversity of healthy versus diseased individuals, or of different disease classes. For the species composition analysis (shared species analysis), the effect sizes were significantly different from zero. In 33 of 41 comparisons (80%), there were fewer OTUs (operational taxonomic units) shared between healthy and diseased individuals than expected by chance, but with 49% (20 of 41 comparisons) statistically significant. These results imply that the taxonomic composition of disease-associated microbiomes is often distinct from that of healthy individuals. Because species composition changes with disease state, some microbiome OTUs may serve as potential diagnostic indicators of disease. However, the overall species diversity of human microbiomes is not a reliable indicator of disease.},
}

@article {pmid30894650,
year = {2019},
author = {Zhu, B and Macleod, LC and Newsome, E and Liu, J and Xu, P},
title = {Aggregatibacter actinomycetemcomitans mediates protection of Porphyromonas gingivalis from Streptococcus sanguinis hydrogen peroxide production in multi-species biofilms.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {4944},
doi = {10.1038/s41598-019-41467-9},
pmid = {30894650},
issn = {2045-2322},
support = {R01DE023078//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
abstract = {Mixed species biofilms are shaped and influenced by interactions between species. In the oral cavity, dysbiosis of the microbiome leads to diseases such as periodontitis. Porphyromonas gingivalis is a keystone pathogen of periodontitis. In this study, we showed that polymicrobial biofilm formation promoted the tolerance of Porphyromonas gingivalis to oxidative stress under micro-aerobic conditions. The presence of Streptococcus sanguinis, an oral commensal bacterium, inhibited the survival of P. gingivalis in dual-species biofilms via the secretion of hydrogen peroxide (H2O2). Interestingly, this repression could be attenuated by the presence of Aggregatibacter actinomycetemcomitans in tri-species biofilms. It was also shown that the katA gene, encoding a cytoplasmic catalase in A. actinomycetemcomitans, was responsible for the reduction of H2O2 produced by S. sanguinis, which consequently increased the biomass of P. gingivalis in tri-species biofilms. Collectively, these findings reveal that polymicrobial interactions play important roles in shaping bacterial community in biofilm. The existence of catalase producers may support the colonization of pathogens vulnerable to H2O2, in the oral cavity. The catalase may be a potential drug target to aid in the prevention of periodontitis.},
}

@article {pmid30894633,
year = {2019},
author = {Guevara, T and Rodríguez-Banqueri, A and Lasica, AM and Ksiazek, M and Potempa, BA and Potempa, J and Gomis-Rüth, FX},
title = {Structural determinants of inhibition of Porphyromonas gingivalis gingipain K by KYT-36, a potent, selective, and bioavailable peptidase inhibitor.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {4935},
doi = {10.1038/s41598-019-41354-3},
pmid = {30894633},
issn = {2045-2322},
abstract = {Porphyromonas gingivalis is a member of the dysbiotic oral microbiome and a "keystone pathogen" that causes severe periodontal disease, which is among the most prevalent infectious diseases. Part of the virulence factors secreted by P. gingivalis are the essential cysteine peptidases gingipain K (Kgp) and R (RgpA and RgpB), which account for 85% of the extracellular proteolytic activity of the pathogen and are thus prime targets for inhibition. We report the high-resolution (1.20 Å) complex structure of Kgp with KYT-36, a peptide-derived, potent, bioavailable and highly selective inhibitor, which is widely used for studies in vitro, in cells and in vivo. Sub-nanomolar inhibition of Kgp is achieved by tight binding to the active-site cleft, which is covered for its sub-sites S3 through S1' under establishment of nine hydrophobic interactions, 14 hydrogen bonds and one salt bridge. In addition, an inhibitor carbonyl carbon that mimics the scissile carbonyl of substrates is pyramidalized and just 2.02 Å away from the catalytic nucleophile of Kgp, C477Sγ. Thus, the crystal structure emulates a reaction intermediate of the first nucleophilic attack during catalysis of cysteine peptidases. The present study sets the pace for the development of tailored next-generation drugs to tackle P. gingivalis.},
}

@article {pmid30894435,
year = {2019},
author = {Majta, J and Odrzywolek, K and Milanovic, B and Hubar, V and Wrobel, S and Strycharz-Angrecka, E and Wojciechowski, S and Milanowska, K},
title = {Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population.},
journal = {mSphere},
volume = {4},
number = {2},
pages = {},
doi = {10.1128/mSphereDirect.00152-19},
pmid = {30894435},
issn = {2379-5042},
abstract = {A variety of autoimmune and allergy events are becoming increasingly common, especially in Western countries. Some pieces of research link such conditions with the composition of microbiota during infancy. In this period, the predominant form of nutrition for gut microbiota is oligosaccharides from human milk (HMO). A number of gut-colonizing strains, such as Bifidobacterium and Bacteroides, are able to utilize HMO, but only some Bifidobacterium strains have evolved to digest the specific composition of human oligosaccharides. Differences in the proportions of the two genera that are able to utilize HMO have already been associated with the frequency of allergies and autoimmune diseases in the Finnish and the Russian populations. Our results show that differences in terms of the taxonomic annotation do not explain the reason for the differences in the Bifidobacterium/Bacteroides ratio between the Finnish and the Russian populations. In this paper, we present the results of function-level analysis. Unlike the typical workflow for gene abundance analysis, BiomeScout technology explains the differences in the Bifidobacterium/Bacteroides ratio. Our research shows the differences in the abundances of the two enzymes that are crucial for the utilization of short type 1 oligosaccharides.IMPORTANCE Knowing the limitations of taxonomy-based research, there is an emerging need for the development of higher-resolution techniques. The significance of this research is demonstrated by the novel method used for the analysis of function-level metagenomes. BiomeScout-the presented technology-utilizes proprietary algorithms for the detection of differences between functionalities present in metagenomic samples.},
}

@article {pmid30894139,
year = {2019},
author = {Szafrańska, AK and Junker, V and Steglich, M and Nübel, U},
title = {Rapid cell division of Staphylococcus aureus during colonization of the human nose.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {229},
doi = {10.1186/s12864-019-5604-6},
pmid = {30894139},
issn = {1471-2164},
support = {643476//Horizon 2020 Framework Programme/ ; },
abstract = {BACKGROUND: Staphylococcus aureus is an important opportunistic pathogen and a commensal bacterium, thriving in the nasal cavities of 20% of the human population. Little is known about the dynamics of asymptomatic colonization and the occasional transition to infectious disease.

RESULTS: In this study, we inferred that S. aureus cells replicate every one to three hours on average while colonizing the human nose, based on two independent lines of genomic evidence. First, we collected nasal swab samples from human subjects, extracted and sequenced metagenomic DNA, and analyzed the distribution of sequencing coverage along the staphylococcal chromosome. Calibration of this data by comparison to a laboratory culture enabled measuring S. aureus cell division rates in nasal samples. Second, we applied mutation accumulation experiments paired with genome sequencing to measure spontaneous mutation rates at a genome scale. Relating these mutation rates to annual evolutionary rates confirmed that nasal S. aureus continuously pass several thousand cell divisions per year when averaged over large, globally distributed populations and over many years, corresponding to generation times of less than two hours.

CONCLUSIONS: The cell division rates we determined were higher than the fastest documented rates during fulminant disease progression (in a mouse model of systemic infection) and much higher than those previously measured in expectorated sputum from cystic fibrosis patients. This paper supplies absolute in-vivo generation times for an important bacterial commensal, indicating that colonization of the human upper respiratory tract is characterized by a highly dynamic equilibrium between bacterial growth and removal.},
}

@article {pmid30894042,
year = {2019},
author = {Bor, B and Bedree, JK and Shi, W and McLean, JS and He, X},
title = {Saccharibacteria (TM7) in the Human Oral Microbiome.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {22034519831671},
doi = {10.1177/0022034519831671},
pmid = {30894042},
issn = {1544-0591},
abstract = {Bacteria from the Saccharibacteria phylum (formerly known as TM7) are ubiquitous members of the human oral microbiome and are part of the Candidate Phyla Radiation. Recent studies have revealed remarkable 16S rRNA diversity in environmental and mammalian host-associated members across this phylum, and their association with oral mucosal infectious diseases has been reported. However, due to their recalcitrance to conventional cultivation, TM7's physiology, lifestyle, and role in health and diseases remain elusive. The recent cultivation and characterization of Nanosynbacter lyticus type strain TM7x (HMT_952)-the first Saccharibacteria strain coisolated as an ultrasmall obligate parasite with its bacterial host from the human oral cavity-provide a rare glimpse into the novel symbiotic lifestyle of these enigmatic human-associated bacteria. TM7x is unique among all bacteria: it has an ultrasmall size and lives on the surface of its host bacterium. With a highly reduced genome, it lacks the ability to synthesize any of its own amino acids, vitamins, or cell wall precursors and must parasitize other oral bacteria. TM7x displays a highly dynamic interaction with its bacterial hosts, as reflected by the reciprocal morphologic and physiologic changes in both partners. Furthermore, depending on environmental conditions, TM7x can exhibit virulent killing of its host bacterium. Thus, Saccharibacteria potentially affect oral microbial ecology by modulating the oral microbiome structure hierarchy and functionality through affecting the bacterial host's physiology, inhibiting the host's growth dynamics, or affecting the relative abundance of the host via direct killing. At this time, several other uncharacterized members of this phylum have been detected in various human body sites at high prevalence. In the oral cavity alone, at least 6 distinct groups vary widely in relative abundance across anatomic sites. Here, we review the current knowledge on the diversity and unique biology of this recently uncovered group of ultrasmall bacteria.},
}

@article {pmid30893890,
year = {2019},
author = {Tatsika, S and Karamanoli, K and Karayanni, H and Genitsaris, S},
title = {Metagenomic Characterization of Bacterial Communities on Ready-to-Eat Vegetables and Effects of Household Washing on their Diversity and Composition.},
journal = {Pathogens (Basel, Switzerland)},
volume = {8},
number = {1},
pages = {},
doi = {10.3390/pathogens8010037},
pmid = {30893890},
issn = {2076-0817},
abstract = {Ready-to-eat (RTE) leafy salad vegetables are considered foods that can be consumed immediately at the point of sale without further treatment. The aim of the study was to investigate the bacterial community composition of RTE salads at the point of consumption and the changes in bacterial diversity and composition associated with different household washing treatments. The bacterial microbiomes of rocket and spinach leaves were examined by means of 16S rRNA gene high-throughput sequencing. Overall, 886 Operational Taxonomic Units (OTUs) were detected in the salads' leaves. Proteobacteria was the most diverse high-level taxonomic group followed by Bacteroidetes and Firmicutes. Although they were processed at the same production facilities, rocket showed different bacterial community composition than spinach salads, mainly attributed to the different contributions of Proteobacteria and Bacteroidetes to the total OTU number. The tested household decontamination treatments proved inefficient in changing the bacterial community composition in both RTE salads. Furthermore, storage duration of the salads at refrigeration temperatures affected the microbiome, by decreasing the bacterial richness and promoting the dominance of psychrotropic bacteria. Finally, both salads were found to be a reservoir of opportunistic human pathogens, while washing methods usually applied at home proved to be inefficient in their removal.},
}

@article {pmid30893436,
year = {2019},
author = {Cattoir, V and Felden, B},
title = {Future antibacterial strategies: from basic concepts to clinical challenges.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiz134},
pmid = {30893436},
issn = {1537-6613},
abstract = {Conventional antibiotics have cured more diseases than all other drug classes combined. However, the pipeline of novel antibiotics is running dry while multi-drug resistance (MDR) is increasing at an alarming rate. Even though vaccines and antibodies are part of the toolkit against antimicrobial resistance, broadening the concept of 'antibiotic' is essential for innovation. Original roadmaps are needed to tackle the overwhelming MDR bacterial infections. The majority of 'in-use' antibacterial drugs derived from secondary metabolites that are produced by cultured soil microorganisms. Ongoing investigations extend large scale microbiome analyses to new natural sources, target the host-pathogen interface, include nanotechnologies and rejuvenate old paths, such as phages and bacteriocins. Host immune modulators and virulence-resistance suppressors are also being developed, with RNA therapeutics. These strategies should help to improve future prevention and treatment of MDR bacterial infections, but numerous challenges limit their introduction into clinical practice.},
}

@article {pmid30893143,
year = {2019},
author = {Kumar, PS},
title = {Systemic Risk Factors for the Development of Periimplant Diseases.},
journal = {Implant dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1097/ID.0000000000000873},
pmid = {30893143},
issn = {1538-2982},
abstract = {PURPOSE: Although periimplantitis results from the tissue destructive effects of a dysbiotic periimplant microbiome, several factors may either contribute to the dysbiosis or influence the host response to this bacterial challenge and thereby increase the risk of disease. The goal of this narrative review is examine extrinsic factors that might increase the risk at both subject and site levels.

MATERIALS AND METHODS: The PubMed (MEDLINE) database was searched for articles examining the influence of systemic conditions on periimplantitis or implant failure. Key search terms included "systemic," "medications," "periodontitis," "dental implant," "periimplantitis," "implant failure" and related terms. Manual searches were also performed for the following journals: Clinical Oral Implants Research, International Journal of Periodontics and Restorative Dentistry, Journal of Clinical Periodontology, International Journal of Oral and Maxillofacial Implants, Implant Dentistry, and Journal of Periodontology. The inclusion criteria were cohort studies and case-control studies with at least 10 participants per group and with at least 6 months of follow-up.

RESULTS: Certain systemic diseases, medications, radiotherapy, and behavioral factors, such as oral hygiene and compliance with periodontal maintenance therapy, appear to significantly increase the risk of disease.},
}

@article {pmid30893089,
year = {2019},
author = {Lewies, A and Zandberg, L and Baumgartner, J},
title = {Interventions to prevent iron deficiency during the first 1000 days in low-income and middle-income countries: recent advances and challenges.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCO.0000000000000557},
pmid = {30893089},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: Iron deficiency remains highly prevalent in women and young children in low-income and middle-income countries. To prevent the potentially life-long consequences of iron deficiency when occurring during early life, the WHO recommends iron supplementation of pregnant women and young children. However, increasing evidence of limited efficacy and risk of current iron intervention strategies are cause of concern. This review aims to highlight recent advances and challenges of established and novel intervention strategies for the prevention of iron deficiency during the first 1000 days in low-income and middle-income countries.

RECENT FINDINGS: Recent meta-analyses and trials challenged the WHO's current recommendation to provide iron-folic acid rather than multiple micronutrient supplements during routine antenatal care. Furthermore, several studies explored optimal windows for iron supplementation, such as prior to conception. Studies are demonstrating that infectious and noninfectious inflammation is compromising the efficacy of iron interventions in vulnerable groups. Therefore, strategies addressing iron deficiency should focus on targeting infection and inflammation while simultaneously providing additional iron. Furthermore, both iron deficiency and iron supplementation may promote an unfavourable gut microbiota. Recent trials in infants indicate that the provision of a prebiotic together with iron may alleviate the adverse effects of iron on the gut microbiome and gut inflammation, and may even enhance iron absorption.

SUMMARY: Recent studies highlight the need for and potential of novel intervention strategies that increase the efficacy and limit the potential harm of universal iron supplementation.},
}

@article {pmid30893085,
year = {2019},
author = {Pali-Schöll, I and Jensen-Jarolim, E},
title = {Gender aspects in food allergy.},
journal = {Current opinion in allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ACI.0000000000000529},
pmid = {30893085},
issn = {1473-6322},
abstract = {PURPOSE OF REVIEW: The difference of food allergy prevalence between male and female individuals is well documented and should have more impact for personalized diagnosis and management. Although in younger age male sex dominates, in adults more women are affected by food allergies. This sex disparity diminishes again around menopause, underlining the influence of sex hormones, but in addition, also metabolic gender-specific factors and differences in microbiome composition might contribute to the different expression of food allergy in the two genders. The sex-dependent and gender-dependent influence on development of food allergy, disease severity, as well as on social, dietary and neuropsychological factors in studies mainly published within past 18 months are discussed in this review.

RECENT FINDINGS: Sex and gender differences likely play a role in food allergy development, for instance via influence on immune cells and mediators, or on the composition of the microbiome, but only few controlled studies on this specific topic are available.

SUMMARY: Future prospective studies need to clearly take into account the sex and gender difference in order to provide personalized diagnosis, management and treatment of food allergy.},
}

@article {pmid30892954,
year = {2019},
author = {Tarantino, P and Curigliano, G},
title = {Defining the immunogram of breast cancer: a focus on clinical trials.},
journal = {Expert opinion on biological therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14712598.2019.1598372},
pmid = {30892954},
issn = {1744-7682},
abstract = {In the phase III ImPassion130 trial the addition of immunotherapy to chemotherapy improved overall survival in mTNBC patients. This benefit was significant only in patients harboring PD-L1-positive tumors, suggesting that stratification according to response biomarkers is needed to achieve consistent responses. Besides PD-L1 expression, a variety of potential biomarkers are under investigation for predicting immunotherapy efficacy in breast cancer, such as tumor-infiltrating lymphocytes, gene signatures, tumor mutational burden, microsatellite instability and gut microbiome. Enriching future trials through these biomarkers could help identifying the population of responders, realizing what has been called precision immunotherapy.},
}

@article {pmid30892771,
year = {2019},
author = {Slots, J},
title = {Focal infection of periodontal origin.},
journal = {Periodontology 2000},
volume = {79},
number = {1},
pages = {233-235},
doi = {10.1111/prd.12258},
pmid = {30892771},
issn = {1600-0757},
abstract = {Periodontology has evolved from a predominantly mechanical to a sophisticated infectious disease-based discipline. Research has paved the way for a greater understanding of the periodontal microbiome, improvement in periodontal diagnostics and therapies, and the recognition of periodontitis being associated with more than 50 systemic diseases. The etiopathology of progressive periodontitis includes active herpesviruses, specific bacterial pathogens, and proinflammatory immune responses. This article points to a role of periodontal herpesviruses in the development of systemic diseases and proposes treatment of severe periodontitis not only to avoid tooth loss, but also to reduce the risk for systemic diseases. An efficient, safe, and reliable anti-infective treatment of severe periodontitis is presented, which targets both herpesviruses and bacterial pathogens and which can be carried out in minimal time with minimal cost.},
}

@article {pmid30891612,
year = {2019},
author = {Cockerham, S and Lee, B and Orben, RA and Suryan, RM and Torres, LG and Warzybok, P and Bradley, R and Jahncke, J and Young, HS and Ouverney, C and Shaffer, SA},
title = {Microbial Ecology of the Western Gull (Larus occidentalis).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-019-01352-4},
pmid = {30891612},
issn = {1432-184X},
abstract = {Avian species host diverse communities of microorganisms which have important roles in the life of birds, including increased metabolism, protection from disease, and immune system development. Along with high human populations and a diversity of human uses of coastal zones, anthropogenic food sources are becoming increasingly available to some species, including gulls. Anthropogenic associations increase the likelihood of encountering foreign or pathogenic bacteria. Diseases in birds caused by bacteria are a substantial source of avian mortality; therefore, it is essential to characterize the microbiome of seabirds. Here, we determined both core and environmentally derived microbial communities of breeding western gulls (Larus occidentalis) from six colonies in California and Oregon. Using DNA extracted from bacterial swabs of the bill, cloaca, and feet of gulls, 16S rRNA gene sequencing was performed targeting the V4 region. We identified a total of 8542 operational taxonomic units (OTUs) from 75 gulls. Sixty-eight OTUs were identified in gulls from all six colonies with the greatest representation from phyla's of Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Overall, microbial richness based on Chao's Abundance-based Coverage Estimator (ACE) index was similar for all colonies (mean = 2347 OTUs) with the smallest coastal colonies having the highest richness (mean = 2626 OTUs) and the largest colonies, located farther off-shore, having the lowest (mean = 2068 OTUs). This survey represents the most in-depth assessment to date of microbes associated with western gulls, and the first study to identify both species-specific and environmentally derived bacteria across multiple populations.},
}

@article {pmid30891563,
year = {2018},
author = {Li, Z and Zhu, H and Zhang, L and Qin, C},
title = {The intestinal microbiome and Alzheimer's disease: A review.},
journal = {Animal models and experimental medicine},
volume = {1},
number = {3},
pages = {180-188},
doi = {10.1002/ame2.12033},
pmid = {30891563},
issn = {2576-2095},
abstract = {Alzheimer's disease (AD) is an increasingly common neurodegenerative disease. Since the intestinal microbiome is closely related to nervous system diseases, alterations in the composition of intestinal microbiota could potentially contribute to the pathophysiology of AD. However, how the initial interactions with intestinal microbes alter events later in life, such as during neurodegenerative diseases, is still unclear. This review summarizes what is known about the relationship between the intestinal microbiome and AD.},
}

@article {pmid30891538,
year = {2019},
author = {Ghanchi, A and James, PT and Cerami, C},
title = {Guts, Germs, and Iron: A Systematic Review on Iron Supplementation, Iron Fortification, and Diarrhea in Children Aged 4-59 Months.},
journal = {Current developments in nutrition},
volume = {3},
number = {3},
pages = {nzz005},
doi = {10.1093/cdn/nzz005},
pmid = {30891538},
issn = {2475-2991},
abstract = {Background: The impact of iron supplements and iron fortification on diarrhea in children is controversial, with some studies reporting an increase and others reporting no effect.

Objective: The aim of the study was systematically assess the published literature on oral iron supplementation and fortification to evaluate its impact on diarrhea incidence among children aged 4-59 mo.

Methods: Randomized controlled trials of oral iron supplementation or iron fortification that reported diarrheal outcomes in children aged 4-59 mo were identified from a systematic search of 5 databases.

Results: Of the 906 records identified, 19 studies were found to fit the inclusion criteria for this systematic review. However, variable case definitions for diarrhea made meta-analysis impossible. Of the 19 studies, 7 (37%) studies showed a significant increase, either in overall diarrhea incidence or within a specific subgroup of the population, between iron-supplemented and control groups. Subgroups included children who were iron-replete and children undergoing their first month of iron intervention. Two studies reported an increase in bloody diarrhea. The remaining 12 (63%) studies showed no difference between iron-supplemented and control groups.

Conclusions: Studies on iron supplementation and fortification use divergent case definitions for diarrhea. A number of studies (37%) showed an increase in overall diarrhea incidence or within a specific subgroup of the population, between iron-supplemented and control groups, but the majority (63%) did not. In addition, there was no clear relation between diarrhea and type of intervention or amount of iron administered observed. In future studies, we recommend that diarrhea be clearly defined and consistently recorded as a secondary outcome. Antibiotic status of participants receiving iron should also be collected to help assess possible drug interactions resulting in a "red stool effect." Finally, further microbiome research is required to better understand the effects of oral iron on specific bacterial species in the colon.},
}

@article {pmid30891246,
year = {2019},
author = {Togo, AH and Diop, A and Dubourg, G and Khelaifia, S and Richez, M and Armstrong, N and Maraninchi, M and Fournier, PE and Raoult, D and Million, M},
title = {Anaerotruncusmassiliensis sp. nov., a succinate-producing bacterium isolated from human stool from an obese patient after bariatric surgery.},
journal = {New microbes and new infections},
volume = {29},
number = {},
pages = {100508},
doi = {10.1016/j.nmni.2019.01.004},
pmid = {30891246},
issn = {2052-2975},
abstract = {A new bacterium, strain AT3T, was isolated by microbial culturomics from a faecal sample from a Frenchman after bariatric surgery. The isolate exhibited 96.6% 16S ribosomal RNA gene nucleotide sequence similarity with Anaerotruncus colihominis strain WAL 14565T = CCUG 45055T = CIP 107754T. Phenotypic and genomic characteristics showed that the new strain represents a novel species, for which the name Anaerotruncus massiliensis sp. nov. is proposed. The type strain is strain AT3T = CSUR P2007T = DSM 100567T.},
}

@article {pmid30891159,
year = {2019},
author = {Mougeot, JC and Stevens, CB and Almon, KG and Paster, BJ and Lalla, RV and Brennan, MT and Mougeot, FB},
title = {Caries-associated oral microbiome in head and neck cancer radiation patients: a longitudinal study.},
journal = {Journal of oral microbiology},
volume = {11},
number = {1},
pages = {1586421},
doi = {10.1080/20002297.2019.1586421},
pmid = {30891159},
issn = {2000-2297},
abstract = {Head and neck cancer (HNC) therapy often leads to caries development. Our goal was to characterize the oral microbiome of HNC patients who underwent radiation therapy (RT) at baseline (T0), and 6 (T6) and 18 (T18) months post-RT, and to determine if there was a relationship with increased caries. HOMINGS was used to determine the relative abundance (RA) of >600 bacterial species in oral samples of 31 HNC patients. The DMFS score was used to define patient groups with tooth decay increase (DMFS[+]) or no increase (DMFS[-]).A change in microbiome beta-diversity was observed at T6 and T18. The Streptococcus mutans RA increased at T6 in both DMFS[+] and DMFS[-] groups. The RA of Prevotella melaninogenica, the species often associated with caries in young children, decreased at T6 in the DMFS[-] group. The RA of the health-associated species, Abiotrophia defective, decreased in the DMFS[+] group. The oral microbiome underwent significant changes in radiation-treated HNC patients, whether they developed caries or not. Caries rates were not associated with a difference in salivary flow reduction between DMFS[+] andDMFS[-] groups. Patients who develop caries might be more susceptible to certain species associated with oral disease or have fewer potentially protective oral species.},
}

@article {pmid30891151,
year = {2019},
author = {Kyriachenko, Y and Falalyeyeva, T and Korotkyi, O and Molochek, N and Kobyliak, N},
title = {Crosstalk between gut microbiota and antidiabetic drug action.},
journal = {World journal of diabetes},
volume = {10},
number = {3},
pages = {154-168},
doi = {10.4239/wjd.v10.i3.154},
pmid = {30891151},
issn = {1948-9358},
abstract = {Type 2 diabetes (T2D) is a disorder characterized by chronic inflated blood glucose levels (hyperglycemia), at first due to insulin resistance and unregulated insulin secretion but with tendency towards global spreading. The gut microbiota is recognized to have an influence on T2D, although surveys have not formed a clear overview to date. Because of the interactions between gut microbiota and host homeostasis, intestinal bacteria are believed to play a large role in various diseases, including metabolic syndrome, obesity and associated disease. In this review, we highlight the animal and human studies which have elucidated the roles of metformin, α-glucosidase inhibitors, glucagon-like peptide-1 agonists, peroxisome proliferator-activated receptors γ agonists, inhibitors of dipeptidyl peptidase-4, sodium/glucose cotransporter inhibitors, and other less studied medications on gut microbiota. This review is dedicated to one of the most widespread diseases, T2D, and the currently used antidiabetic drugs and most promising new findings. In general, the gut microbiota has been shown to have an influence on host metabolism, food consumption, satiety, glucose homoeostasis, and weight gain. Altered intestinal microbiota composition has been noticed in cardiovascular diseases, colon cancer, rheumatoid arthritis, T2D, and obesity. Therefore, the main effect of antidiabetic drugs is on the microbiome composition, basically increasing the short-chain fatty acids-producing bacteria, responsible for losing weight and suppressing inflammation.},
}

@article {pmid30891034,
year = {2019},
author = {Bello-Gil, D and Audebert, C and Olivera-Ardid, S and Pérez-Cruz, M and Even, G and Khasbiullina, N and Gantois, N and Shilova, N and Merlin, S and Costa, C and Bovin, N and Mañez, R},
title = {The Formation of Glycan-Specific Natural Antibodies Repertoire in GalT-KO Mice Is Determined by Gut Microbiota.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {342},
doi = {10.3389/fimmu.2019.00342},
pmid = {30891034},
issn = {1664-3224},
abstract = {Gut commensal bacteria are known to have a significant role in regulating the innate and adaptive immune homeostasis. Alterations in the intestinal microbial composition have been associated with several disease states, including autoimmune and inflammatory conditions. However, it is not entirely clear how commensal gut microbiota modulate and contribute to the systemic immunity, and whether circulating elements of the host immune system could regulate the microbiome. Thus, we have studied the diversity and abundance of specific taxons in the gut microbiota of inbred GalT-KO mice during 7 months of animal life by metagenetic high-throughput sequencing (16S rRNA gene, variable regions V3-V5). The repertoire of glycan-specific natural antibodies, obtained by printed glycan array technology, was then associated with the microbial diversity for each animal by metagenome-wide association studies (MWAS). Our data show that the orders clostridiales (most abundant), bacteriodales, lactobacillales, and deferribacterales may be associated with the development of the final repertoire of natural anti-glycan antibodies in GalT-KO mice. The main changes in microbiota diversity (month-2 and month-3) were related to important changes in levels and repertoire of natural anti-glycan antibodies in these mice. Additionally, significant positive and negative associations were found between the gut microbiota and the pattern of specific anti-glycan antibodies. Regarding individual features, the gut microbiota and the corresponding repertoire of natural anti-glycan antibodies showed differences among the examined animals. We also found redundancy in different taxa associated with the development of specific anti-glycan antibodies. Differences in microbial diversity did not, therefore, necessarily influence the overall functional output of the gut microbiome of GalT-KO mice. In summary, the repertoire of natural anti-carbohydrate antibodies may be partially determined by the continuous antigenic stimulation produced by the gut bacterial population of each GalT-KO mouse. Small differences in gut microbiota diversity could determine different repertoire and levels of natural anti-glycan antibodies and consequently might induce different immune responses to pathogens or other potential threats.},
}

@article {pmid30891012,
year = {2019},
author = {Zhao, Y and Yang, S and Li, B and Li, W and Wang, J and Chen, Z and Yang, J and Tan, H and Li, J},
title = {Alterations of the Mice Gut Microbiome via Schistosoma japonicum Ova-Induced Granuloma.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {352},
doi = {10.3389/fmicb.2019.00352},
pmid = {30891012},
issn = {1664-302X},
abstract = {Schistosomiasis, also called bilharziasis, is a neglected tropical disease induced by Schistosoma spp. that causes hundreds of millions of infections. Although Schistosoma ova-induced granulomas commonly cause inflammation, hyperplasia, ulceration, micro abscess formation, and polyposis, the role of the egg granuloma on the gut microbiome remains unclear. To explore the role, gut microbial communities in mice infected with Schistosoma japonicum were surveyed. Female C57BL/6 and BALB/c mice were exposed to cercariae of S. japonicum for 45 and 65 days and then sacrificed. Intestinal contents and feces were collected, DNA was extracted, and high-throughput 16S rRNA gene-based pyrosequencing was used to provide a comparative analysis of gut microbial diversity. The intestinal mucosal tissues were also examined. Histopathologic analysis demonstrated that the basic structure of the colonic mucosa was damaged by ova-induced granuloma. Regarding the gut microbiome, 2,578,303 good-quality sequences were studied and assigned to 25,278 Operational Taxonomic Units (OTUs) at a threshold of 97% similarity. The average number of OTUs for C57BL/6 and BALB/c were 545 and 530, respectively. At the phylum level, intestinal microbial communities were dominated by Firmicutes, Bacteroidetes, Proteobacteria, and Verrucomicrobia. Infection with S. japonicum modified bacterial richness in the fecal associated microbiota. Exposure significantly modified bacterial community composition among different groups. At the phylogenetic levels, LEfSe analysis revealed that several bacterial taxa were significantly associated with the S. japonicum-infected mice. The present results suggest that egg granulomas in the intestine influence differentiation of the gut microbial community under pathophysiological conditions. This result suggests that intestinal microbiome-based strategies should be considered for early diagnosis, clinical treatment, and prognosis evaluation of schistosomiasis.},
}

@article {pmid30891007,
year = {2019},
author = {Tian, X and Hellman, J and Prakash, A},
title = {Elevated Gut Microbiome-Derived Propionate Levels Are Associated With Reduced Sterile Lung Inflammation and Bacterial Immunity in Mice.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {159},
doi = {10.3389/fmicb.2019.00159},
pmid = {30891007},
issn = {1664-302X},
abstract = {Short-chain fatty acids (SCFA) are important dietary and microbiome metabolites that can have roles in gut immunity as well as further afield. We previously observed that gut microbiome alteration via antibiotics led to attenuated lung inflammatory responses. The rationale for this study was to identify gut microbiome factors that regulate lung immune homeostasis. We first investigated key factors within mouse colonic lumen filtrates (CLF) which could elicit direct inflammatory effects in vitro. We identified lipopolysaccharide (LPS) and SCFAs as key CLF ingredients whose levels and inflammatory capacity changed after antibiotic exposure in mice. Specifically, the SCFA propionate appeared to be a key regulator of LPS responses in vitro. Elevated propionate: acetate ratios, as seen in CLF after antibiotic exposure, strongly blunted inflammatory responses in vitro. In vivo, exposure of lungs to high dose propionate, to mimic how prior antibiotic exposure changed SCFA levels, resulted in diminished immune containment of Staphylococcus aureus pneumonia. Finally, we discovered an enrichment of propionate-producing gut bacteria in mice with reduced lung inflammation following lung ischemia reperfusion injury in vivo. Overall, our data show that propionate levels can distinctly modulate lung immune responses in vitro and in vivo and that gut microbiome increased production of propionate is associated with reduced lung inflammation.},
}

@article {pmid30890906,
year = {2019},
author = {Hewel, C and Kaiser, J and Wierczeiko, A and Linke, J and Reinhardt, C and Endres, K and Gerber, S},
title = {Common miRNA Patterns of Alzheimer's Disease and Parkinson's Disease and Their Putative Impact on Commensal Gut Microbiota.},
journal = {Frontiers in neuroscience},
volume = {13},
number = {},
pages = {113},
doi = {10.3389/fnins.2019.00113},
pmid = {30890906},
issn = {1662-4548},
abstract = {With the rise of Next-Generation-Sequencing (NGS) methods, Micro-RNAs (miRNAs) have achieved an important position in the research landscape and have been found to present valuable diagnostic tools in various diseases such as multiple sclerosis or lung cancer. There is also emerging evidence that miRNAs play an important role in the pathogenesis of neurodegenerative diseases such as Alzheimer's disease (AD) or Parkinson's disease (PD). Apparently, these diseases come along with changes in miRNA expression patterns which led to attempts from researchers to use these small RNA species from several body fluids for a better diagnosis and in order to observe disease progression. Additionally, it became evident that microbial commensals might play an important role for pathology development and were shown to have a significantly different composition in patients suffering from neurodegeneration compared with healthy controls. As it could recently be shown that secreted miRNAs are able to enter microbial organisms, it is conceivable that the host's miRNA might affect the gut microbial ecosystem. As such, miRNAs may inherit a central role in shaping the "diseased microbiome" and thereby mutually act on the characteristics of these neurodegenerative diseases. We have therefore (1) compiled a list of miRNAs known to be associated with AD and/or PD, (2) performed an in silico target screen for binding sites of these miRNA on human gut metagenome sequences and (3) evaluated the hit list for interesting matches potentially relevant to the etiology of AD and or PD. The examination of protein identifiers connected to bacterial secretion system, lipopolysaccharide biosynthesis and biofilm formation revealed an overlap of 37 bacterial proteins that were targeted by human miRNAs. The identified links of miRNAs to the biological processes of bacteria connected to AD and PD have yet to be validated via in vivo experiments. However, our results show a promising new approach for understanding aspects of these neurodegenerative diseases in light of the regulation of the microbiome.},
}

@article {pmid30890706,
year = {2019},
author = {Hannula, SE and Zhu, F and Heinen, R and Bezemer, TM},
title = {Foliar-feeding insects acquire microbiomes from the soil rather than the host plant.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1254},
doi = {10.1038/s41467-019-09284-w},
pmid = {30890706},
issn = {2041-1723},
abstract = {Microbiomes of soils and plants are linked, but how this affects microbiomes of aboveground herbivorous insects is unknown. We first generated plant-conditioned soils in field plots, then reared leaf-feeding caterpillars on dandelion grown in these soils, and then assessed whether the microbiomes of the caterpillars were attributed to the conditioned soil microbiomes or the dandelion microbiome. Microbiomes of caterpillars kept on intact plants differed from those of caterpillars fed detached leaves collected from plants growing in the same soil. Microbiomes of caterpillars reared on detached leaves were relatively simple and resembled leaf microbiomes, while those of caterpillars from intact plants were more diverse and resembled soil microbiomes. Plant-mediated changes in soil microbiomes were not reflected in the phytobiome but were detected in caterpillar microbiomes, however, only when kept on intact plants. Our results imply that insect microbiomes depend on soil microbiomes, and that effects of plants on soil microbiomes can be transmitted to aboveground insects feeding later on other plants.},
}

@article {pmid30890566,
year = {2019},
author = {Clarke, G and Sandhu, KV and Griffin, BT and Dinan, TG and Cryan, JF and Hyland, NP},
title = {Gut Reactions: Breaking Down Xenobiotic-Microbiome Interactions.},
journal = {Pharmacological reviews},
volume = {71},
number = {2},
pages = {198-224},
doi = {10.1124/pr.118.015768},
pmid = {30890566},
issn = {1521-0081},
abstract = {The microbiome plays a key role in health and disease, and there has been considerable interest in therapeutic targeting of the microbiome as well as mining this rich resource in drug discovery efforts. However, a growing body of evidence suggests that the gut microbiota can itself influence the actions of a range of xenobiotics, in both beneficial and potentially harmful ways. Traditionally, clinical studies evaluating the pharmacokinetics of new drugs have mostly ignored the important direct and indirect effects of the gut microbiome on drug metabolism and efficacy. Despite some important observations from xenobiotic metabolism in general, there is only an incomplete understanding of the scope of influence of the microbiome specifically on drug metabolism and absorption, and how this might influence systemic concentrations of parent compounds and toxic metabolites. The significance of both microbial metabolism of xenobiotics and the impact of the gut microbiome on host hepatic enzyme systems is nonetheless gaining traction and presents a further challenge in drug discovery efforts, with implications for improving treatment outcomes or counteracting adverse drug reactions. Microbial factors must now be considered when determining drug pharmacokinetics and the impact that an evolving and dynamic microbiome could have in this regard. In this review, we aim to integrate the contribution of the gut microbiome in health and disease to xenobiotic metabolism focusing on therapeutic interventions, pharmacological drug action, and chemical biotransformations that collectively will have implications for the future practice of precision medicine.},
}

@article {pmid30890551,
year = {2019},
author = {Özdemir, BC and Dotto, GP},
title = {Sex hormones and anticancer immunity.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-19-0137},
pmid = {30890551},
issn = {1078-0432},
abstract = {The impact of sex hormones on anticancer immunity deserves attention due to the importance of the immune system in cancer therapy and the recognition of sex differences in immunity. Cancer is ultimately the result of failed immune surveillance and diverging effects of male and female sex hormones on anticancer immunity could contribute to the higher cancer incidence and poorer outcome in men. Estrogens and androgens affect the number and function of immune cells, an effect that depends on cell type, tumor microenvironment, and the age and reproductive status of the individual. Despite the recent progress in immunooncology our current understanding of the interplay between sex hormones and anticancer immune responses is in its infancy. In this review we will focus on the impact of sex hormones on anticancer immunity and immunotherapy. We will discuss the potential role of the changing hormone levels in anticancer immunity during aging and in the context of menopausal hormone therapies and oral contraception. We will review emerging data on sex differences in PD-L1 expression and potential biomarkers predictive for the efficacy of immune checkpoint inhibitors such as the microbiome and consider ongoing clinical trials evaluating the potential impact of hormone deprivation therapies to increase response to immune checkpoint inhibitors in breast and prostate cancer. Lastly, we will point to areas of future research.},
}

@article {pmid30890361,
year = {2019},
author = {Qiu, Z and Egidi, E and Liu, H and Kaur, S and Singh, BK},
title = {New frontiers in agriculture productivity: Optimised microbial inoculants and in situ microbiome engineering.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biotechadv.2019.03.010},
pmid = {30890361},
issn = {1873-1899},
abstract = {Increasing agricultural productivity is critical to feed the ever-growing human population. Being linked intimately to plant health, growth and productivity, harnessing the plant microbiome is considered a potentially viable approach for the next green revolution, in an environmentally sustainable way. In recent years, our understanding of drivers, roles, mechanisms, along with knowledge to manipulate the plant microbiome, have significantly advanced. Yet, translating this knowledge to expand farm productivity and sustainability requires the development of solutions for a number of technological and logistic challenges. In this article, we propose new and emerging strategies to improve the survival and activity of microbial inoculants, including using selected indigenous microbes and optimising microbial delivery methods, as well as modern gene editing tools to engineer microbial inoculants. In addition, we identify multiple biochemical and molecular mechanisms and/approaches which can be exploited for microbiome engineering in situ to optimise plant-microbiome interactions for improved farm yields. These novel biotechnological approaches can provide effective tools to attract and maintain activities of crop beneficial microbiota that increase crop performance in terms of nutrient acquisition, and resistance to biotic and abiotic stresses, resulting in an increased agricultural productivity and sustainability.},
}

@article {pmid30890301,
year = {2019},
author = {Chen, QL and Cui, HL and Su, JQ and Penuelas, J and Zhu, YG},
title = {Antibiotic Resistomes in Plant Microbiomes.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2019.02.010},
pmid = {30890301},
issn = {1878-4372},
abstract = {Microorganisms associated with plants may alter the traits of the human microbiome important for human health, but this alteration has largely been overlooked. The plant microbiome is an interface between plants and the environment, and provides many ecosystem functions such as improving nutrient uptake and protecting against biotic and abiotic stress. The plant microbiome also represents a major pathway by which humans are exposed to microbes and genes consumed with food, such as pathogenic bacteria, antibiotic-resistant bacteria, and antibiotic-resistance genes. In this review we highlight the main findings on the composition and function of the plant microbiome, and underline the potential of plant microbiomes in the dissemination of antibiotic resistance via food consumption or direct contact.},
}

@article {pmid30890187,
year = {2019},
author = {Tovaglieri, A and Sontheimer-Phelps, A and Geirnaert, A and Prantil-Baun, R and Camacho, DM and Chou, DB and Jalili-Firoozinezhad, S and de Wouters, T and Kasendra, M and Super, M and Cartwright, MJ and Richmond, CA and Breault, DT and Lacroix, C and Ingber, DE},
title = {Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {43},
doi = {10.1186/s40168-019-0650-5},
pmid = {30890187},
issn = {2049-2618},
abstract = {BACKGROUND: Species-specific differences in tolerance to infection are exemplified by the high susceptibility of humans to enterohemorrhagic Escherichia coli (EHEC) infection, whereas mice are relatively resistant to this pathogen. This intrinsic species-specific difference in EHEC infection limits the translation of murine research to human. Furthermore, studying the mechanisms underlying this differential susceptibility is a difficult problem due to complex in vivo interactions between the host, pathogen, and disparate commensal microbial communities.

RESULTS: We utilize organ-on-a-chip (Organ Chip) microfluidic culture technology to model damage of the human colonic epithelium induced by EHEC infection, and show that epithelial injury is greater when exposed to metabolites derived from the human gut microbiome compared to mouse. Using a multi-omics approach, we discovered four human microbiome metabolites-4-methyl benzoic acid, 3,4-dimethylbenzoic acid, hexanoic acid, and heptanoic acid-that are sufficient to mediate this effect. The active human microbiome metabolites preferentially induce expression of flagellin, a bacterial protein associated with motility of EHEC and increased epithelial injury. Thus, the decreased tolerance to infection observed in humans versus other species may be due in part to the presence of compounds produced by the human intestinal microbiome that actively promote bacterial pathogenicity.

CONCLUSION: Organ-on-chip technology allowed the identification of specific human microbiome metabolites modulating EHEC pathogenesis. These identified metabolites are sufficient to increase susceptibility to EHEC in our human Colon Chip model and they contribute to species-specific tolerance. This work suggests that higher concentrations of these metabolites could be the reason for higher susceptibility to EHEC infection in certain human populations, such as children. Furthermore, this research lays the foundation for therapeutic-modulation of microbe products in order to prevent and treat human bacterial infection.},
}

@article {pmid30890060,
year = {2019},
author = {Colombo, APV and Tanner, ACR},
title = {The Role of Bacterial Biofilms in Dental Caries and Periodontal and Peri-implant Diseases: A Historical Perspective.},
journal = {Journal of dental research},
volume = {98},
number = {4},
pages = {373-385},
doi = {10.1177/0022034519830686},
pmid = {30890060},
issn = {1544-0591},
abstract = {Over the last hundred years, groundbreaking research in oral microbiology has provided a broad and deep understanding about the oral microbiome, its interactions with our body, and how the community can affect our health, be protective, or lead to the development of dental diseases. During this exciting journey, hypotheses were proposed, and concepts were established, discarded, and later revisited from updated perspectives. Dental plaque, previously considered a polymicrobial community of unspecific pathogenicity, is recognized as microbial biofilms with healthy, cariogenic, or periodontopathogenic profiles, resulting from specific ecologic determinants and host factors. The "one pathogen, one disease" paradigm of oral infections has been replaced by a holistic concept of a microbial community as the entity of pathogenicity. Cutting-edge technology can now explore large microbial communities related to different clinical conditions, which has led to finding several novel disease-associated species and potential pathobionts and pathobiomes. This vast amount of data generated over time has widened our view of the etiology of caries and periodontal and peri-implant diseases and has promoted updated strategies to treat and prevent the oral diseases.},
}

@article {pmid30881245,
year = {2017},
author = {Gasta, MG and Gossard, CM and Williamson, CB and Dolan, KE and Finley, HJ and Burns, CM and Parker, EC and Pizano, JM and Lipski, EA},
title = {Probiotics and Disease: A Comprehensive Summary-Part 5, Respiratory Conditions of the Ears, Nose, and Throat.},
journal = {Integrative medicine (Encinitas, Calif.)},
volume = {16},
number = {3},
pages = {28-40},
pmid = {30881245},
issn = {1546-993X},
abstract = {This article series provides a literature review of the disease-specific probiotic strains studied in published clinical trials in humans and animals. The goal of the series is to provide clinically useful tools. The table design allows for quick access to supportive data and will be helpful as a guide for both researchers and clinicians. The first article (part 1) focused on mental health and neurological conditions and the second article (part 2) explored cultured and fermented foods that are commonly available in the United States. The third article (part 3) explored the relationship between bacterial strains and 2 of the most prevalent diseases we have in modern society, cardiometabolic disease and fatigue syndromes. The fourth article (part 4) elucidated the role of the microbiome in infectious diseases, and this fifth article (part 5) investigates probiotic strains on respiratory conditions that affect the ears, nose, and throat. Future articles will review conditions related to autoimmunity and dermatological conditions; the influence of the microbiome on cancer development and prognosis; gastrointestinal and genitourinary diseases associated with dysbiosis conditions; followed by an article focused on probiotic supplements. This literature review is specific to disease condition, probiotic classification, and individual strain.},
}

@article {pmid30889240,
year = {2019},
author = {Cui, HL and Duan, GL and Zhang, H and Cheng, W and Zhu, YG},
title = {Microbiota in Non-flooded and Flooded Rice Culms.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz036},
pmid = {30889240},
issn = {1574-6941},
abstract = {Rice plants are the habitat for large and diverse populations of microbes, which play important roles on rice health and productivity. However, the response of microbiome on rice culm to water flooding is poorly understood. In this study, the bacterial community on non-flooded (RSA) and flooded (RSB) rice culms was investigated through 16S rRNA gene sequencing. The results showed that RSA and RSB had significantly distinct bacterial communities. In RSA, Gammaproteobacteria and Pantoea were the most abundant class (57%), genus (37.06%), respectively, while in RSB, the most abundant phylum and genus was Firmicutes (54%) and Bacillus (52.63%), respectively. Compared with RSA, the abundance of 27 genera significantly increased and 21 genera significantly decreased in RSB, and some remarkably changed species, such as Aeromonas, Bacillus were identified, which are sensitive to non-flooded or flooded conditions. In addition, rare operational taxonomic units (OTUs) was much more than abundant OTUs in all samples, and RSB had significantly higher bacterial richness than RSA due to having more rare taxa. Our study would advance the insights into the microbiome of rice culms and its response to flooding, which would help to identify potential beneficial bacteria for improving crop health and sustainable productivity in agroecosystems.},
}

@article {pmid30889229,
year = {2019},
author = {Portillo, A and Palomar, AM and de Toro, M and Santibáñez, S and Santibáñez, P and Oteo, JA},
title = {Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213384},
doi = {10.1371/journal.pone.0213384},
pmid = {30889229},
issn = {1932-6203},
abstract = {OBJECTIVE: The aim of this study was to characterize the bacterial microbiome of hard ticks with affinity to bite humans in La Rioja (North of Spain).

METHODS: A total of 88 adult ticks (22 Rhipicephalus sanguineus sensu lato, 27 Haemaphysalis punctata, 30 Dermacentor marginatus and 9 Ixodes ricinus) and 120 I. ricinus nymphs (CRETAV collection, La Rioja, Spain), representing the main anthropophilic species in our environment, were subjected to a metagenomic analysis of the V3-V4 region of the 16S rRNA gene using an Illumina MiSeq platform. Data obtained with Greengenes database were refined with BLAST. Four groups of samples were defined, according to the four tick species.

RESULTS: Proteobacteria was the predominant phylum observed in all groups. Gammaproteobacteria was the most abundant class, followed by Alphaproteobacteria for R. sanguineus, H. punctata and D. marginatus but the relative abundance of reads for these classes was reversed for I. ricinus. This tick species showed more than 46% reads corresponding to 'not assigned' OTUs (Greengenes), and >97% of them corresponded to 'Candidatus Midichloriaceae' using BLAST. Within Rickettsiales, 'Candidatus Midichloria', Rickettsia, Ehrlichia, 'Candidatus Neoehrlichia' and Wolbachia were detected. I. ricinus was the most alpha-diverse species. Regarding beta-diversity, I. ricinus and H. punctata samples grouped according to their tick species but microbial communities of some R. sanguineus and D. marginatus specimens clustered together.

CONCLUSIONS: The metagenomics approach seems useful to discover the spectrum of tick-related bacteria. More studies are needed to identify and differentiate bacterial species, and to improve the knowledge of tick-borne diseases in Spain.},
}

@article {pmid30888695,
year = {2019},
author = {Foysal, MJ and Momtaz, F and Kawser, AQMR and Chaklader, MR and Siddik, MAB and Lamichhane, B and Tay, ACY and Rahman, MM and Fotedar, R},
title = {Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish (Tenualosa ilisha) marketed for human consumption in Bangladesh.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jam.14257},
pmid = {30888695},
issn = {1365-2672},
abstract = {AIMS: This study conducted bacterial community, virulence and antibiogram profiling inside the hindgut and skin of freshly caught hilsa fish and those sold at markets.

METHODS AND RESULTS: The results of 16S rRNA-based high-throughput sequencing showed a higher number of bacterial genera in marketed fish samples than in fresh fish samples. The total operational taxonomic units (OTU), genus counts and diversity index were significantly higher (p > 0.05) in marketed fish, which also had abundant pathogenic bacterial groups. Skin samples had a lower profusion of pathogenic bacteria than gut samples. A total of 52 bacterial isolates from nine species were identified in this study, of which 25 were from a Chittagong market and 22 were from a Dhaka market, while only five were from fresh hilsa. The PCR amplification of 12 species-specific virulence genes in the 52 isolates, namely, aer, hly, chxA, toxB, rtxC, sfa, uge, norB, trx, toxA, ipaH, sigA and coa, indicated a high number of positive samples containing Vibrio cholerae, Aeromonas spp., Klebsiella pneumoniae, Escherichia coli and Staphylococcus aureus. Antibiogram profiling of these bacteria against ten commercial antibiotics showed high resistance patterns of the isolates against sulfamethoxazole, kanamycin, neomycin, ampicillin and tetracycline.

CONCLUSION: The results reveal the spread of multidrug-resistant bacteria in hilsa fish marketed for human consumption in Bangladesh.

The present study highlights the risk of spreading environmentally- and clinically-pathogenic bacteria in fish sold for human consumption in Bangladesh. Such bacteria come from aquatic pollution and poor handling, storage and transportation practices that may predispose fish to major outbreaks of infectious and waterborne diseases. This article is protected by copyright. All rights reserved.},
}

@article {pmid30888065,
year = {2019},
author = {Wang, G and Yu, Y and Wang, YZ and Wang, JJ and Guan, R and Sun, Y and Shi, F and Gao, J and Fu, XL},
title = {Role of SCFAs in gut microbiome and glycolysis for colorectal cancer therapy.},
journal = {Journal of cellular physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jcp.28436},
pmid = {30888065},
issn = {1097-4652},
support = {No. 81673827//National Natural Science Foundation of China/ ; No. 2016JP008//Shanghai health development planning commission research project of traditional Chinese medicine/ ; SHXH201640//Shanghai Xuhui science and technology commission research project/ ; },
abstract = {Increased risk of colorectal cancer (CRC) is associated with altered intestinal microbiota as well as short-chain fatty acids (SCFAs) reduction of output The energy source of colon cells relies mainly on three SCFAs, namely butyrate (BT), propionate, and acetate, while CRC transformed cells rely mainly on aerobic glycolysis to provide energy. This review summarizes recent research results for dysregulated glucose metabolism of SCFAs, which could be initiated by gut microbiome of CRC. Moreover, the relationship between SCFA transporters and glycolysis, which may correlate with the initiation and progression of CRC, are also discussed. Additionally, this review explores the linkage of BT to transport of SCFAs expressions between normal and cancerous colonocyte cell growth for tumorigenesis inhibition in CRC. Furthermore, the link between gut microbiota and SCFAs in the metabolism of CRC, in addition, the proteins and genes related to SCFAs-mediated signaling pathways, coupled with their correlation with the initiation and progression of CRC are also discussed. Therefore, targeting the SCFA transporters to regulate lactate generation and export of BT, as well as applying SCFAs or gut microbiota and natural compounds for chemoprevention may be clinically useful for CRCs treatment. Future research should focus on the combination these therapeutic agents with metabolic inhibitors to effectively target the tumor SCFAs and regulate the bacterial ecology for activation of potent anticancer effect, which may provide more effective application prospect for CRC therapy.},
}

@article {pmid30887889,
year = {2019},
author = {Wang, L and Mazzola, M},
title = {Field evaluation of reduced rate Brassicaceae seed meal amendment and rootstock genotype on the microbiome and control of apple replant disease.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-02-19-0045-R},
pmid = {30887889},
issn = {0031-949X},
abstract = {An orchard field trial was conducted to assess the utility of reduced rate Brassicaceae seed meal (SM) amendment in concert with specific rootstock genotypes for effective control of apple replant disease. Three amendment rates of a 1:1 formulation of Brassica juncea/Sinapis alba SM were compared to pre-plant 1,3-dichloropropene/chloropicrin soil fumigation for disease control efficacy. When applied at the highest rate (6.6 t ha-1) in the spring of planting, SM caused significant phytotoxicity and tree mortality, which was higher for Gala.M26 than Gala.G41 but was not observed at SM application rates of 2.2 or 4.4 t ha-1. SM treatment resulted in growth and yield increases of Gala.M.26 and Gala.G.41 trees in a manner similar to the fumigation treatment and significantly greater than the no treatment control. Tree growth in soils treated with SM at 4.4 t ha-1 was similar or superior to that obtained with SM at 6.6 t ha-1 and superior to that attained at a SM application rate of 2.2 t ha-1. Soil fumigation and all SM treatments reduced Pratylenchus penetrans root infestation relative to the control treatment at the end of the initial growing season. Lesion nematode root densities in the fumigation treatment, but not SM treatments, rapidly recovered and were indistinguishable from the control at the end of the second growing season. Soil fumigation and all SM treatments significantly suppressed Pythium spp. root infection relative to the control. Trees grafted to rootstock G.41 possessed lower P. penetrans root densities relative to trees grafted to rootstock M.26. One year after planting, composition of microbial communities from SM-amended soils was distinct from those detected in control and fumigated soils, and the differences were amplified with increasing SM application rate. Specific fungal and bacterial phyla associated with suppression of plant pathogens were more abundant in SM-treated soil relative to the control and were similar in abundance in 4.4 and 6.6 t ha-1 SM treatments. Findings from this study demonstrated that use of the appropriate apple rootstock genotype will allow for effective replant disease control at SM application rates significantly less than that utilized previously (6.6 t ha-1).},
}

@article {pmid30887551,
year = {2019},
author = {Dąbrowska, K},
title = {Phage therapy: What factors shape phage pharmacokinetics and bioavailability? Systematic and critical review.},
journal = {Medicinal research reviews},
volume = {},
number = {},
pages = {},
doi = {10.1002/med.21572},
pmid = {30887551},
issn = {1098-1128},
support = {UMO-2012/05/E/NZ6/03314//National Science Centre/ ; UMO-2015/18/M/NZ6/00412//National Science Centre/ ; UMO-2018/29/B/NZ6/01659//National Science Centre/ ; },
abstract = {Bacteriophages are not forgotten viruses anymore: scientists and practitioners seek to understand phage pharmacokinetics in animals and humans, investigating bacteriophages as therapeutics, nanocarriers or microbiome components. This review provides a comprehensive overview of factors that determine phage circulation, penetration, and clearance, and that in consequence determine phage applicability for medicine. It makes use of experimental data collected by the phage community so far (PubMed 1924-2016, including non-English reports), combining elements of critical and systematic review. This study covers phage ability to enter a system by various routes of administration, how (and if) the phage may access various tissues and organs, and finally what mechanisms determine the courses of phage clearance. The systematic review method was applied to analyze (i) phage survival in the gut (gut transit) and (ii) phage ability to enter the mammalian system by many administration routes. Aspects that have not yet been covered by a sufficient number of reports for mathematical analysis, as well as mechanisms underlying trends, are discussed in the form of a critical review. In spite of the extraordinary diversity of bacteriophages and possible phage applications, the analysis revealed that phage morphology, phage specificity, phage dose, presence of sensitive bacteria or the characteristics of treated individuals (age, taxonomy) may affect phage bioavailability in animals and humans. However, once phages successfully enter the body, they reach most organs, including the central nervous system. Bacteriophages are cleared mainly by the immune system: innate immunity removes phages even when no specific response to bacteriophages has yet developed.},
}

@article {pmid30887257,
year = {2019},
author = {Fayfman, M and Flint, K and Srinivasan, S},
title = {Obesity, Motility, Diet, and Intestinal Microbiota-Connecting the Dots.},
journal = {Current gastroenterology reports},
volume = {21},
number = {4},
pages = {15},
doi = {10.1007/s11894-019-0680-y},
pmid = {30887257},
issn = {1534-312X},
abstract = {PURPOSE OF REVIEW: The goal of the present review is to explore the relationship between dietary changes and alterations in gut microbiota that contribute to disorders of gut motility and obesity.

RECENT FINDINGS: We review the microbiota changes that are seen in obesity, diarrhea, and constipation and look at potential mechanisms of how dysbiosis can predispose to these. We find that microbial metabolites, particularly short chain fatty acids, can lead to signaling changes in the host enterocytes. Microbial alteration leading to both motility disorders and obesity may be mediated by the release of hormones including glucagon-like peptides 1 and 2 (GLP-1, GLP-2) and polypeptide YY (PYY). These pathways provide avenues for microbiota-targeted interventions that can treat both disorders of motility and obesity. In summary, multiple mechanisms contribute to the interplay between the microbial dysbiosis, obesity, and dysmotility.},
}

@article {pmid30887254,
year = {2019},
author = {Gu, L and Xu, Y and Xu, W and Li, M and Su, H and Li, C and Liu, Z},
title = {The exosome secretion inhibitor neticonazole suppresses intestinal dysbacteriosis-induced tumorigenesis of colorectal cancer.},
journal = {Investigational new drugs},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10637-019-00759-7},
pmid = {30887254},
issn = {1573-0646},
support = {81272720//the National Natural Science Foundation of China/ ; },
abstract = {Colorectal cancer (CRC) is the most frequently encountered malignancy associated with the rectum or colon, and accumulating evidences have implicated intestinal dysbacteriosis (IDB, disruption of gut microbiome) and exosomes in the pathology of CRC. We aimed to investigate the effect of IDB on exosome secretion in a CRC xenograft mouse model. An IDB mouse model was established and was inoculated with the CRC cell line SW480 as a xenograft tumor. Tumor growth was monitored for 15 days in sham and IDB mice, after which blood was collected to assess serum exosome secretion. A novel exosome secretion inhibitor, neticonazole, was administered to IDB mice bearing CRC xenograft tumors, followed by monitoring of tumor growth and mouse survival. Western blot analysis was performed in xenograft tumors to investigate the underlying molecular mechanism. IDB promoted CRC xenograft tumor growth and exosome secretion, which could be inhibited by the exosome secretion inhibitor neticonazole. Moreover, neticonazole treatment significantly improved the survival of IDB mice with CRC xenograft tumors, likely through increasing apoptosis of CRC xenograft tumor cells. The exosome secretion inhibitor neticonazole may serve as a promising therapeutic candidate against CRC by suppressing IDB-induced CRC tumorigenesis.},
}

@article {pmid30887236,
year = {2019},
author = {Gong, J and Chehrazi-Raffle, A and Placencio-Hickok, V and Guan, M and Hendifar, A and Salgia, R},
title = {The gut microbiome and response to immune checkpoint inhibitors: preclinical and clinical strategies.},
journal = {Clinical and translational medicine},
volume = {8},
number = {1},
pages = {9},
doi = {10.1186/s40169-019-0225-x},
pmid = {30887236},
issn = {2001-1326},
support = {P30CA033572//National Cancer Institute/ ; 1U54CA209978-01A1//National Cancer Institute/ ; },
abstract = {There is growing interest in identifying predictive biomarkers for inhibitors of programmed cell death protein 1 receptor (PD-1), programmed death ligand 1 (PD-L1), and cytotoxic T-lymphocyte associated protein 4 (CTLA-4). Given the links between the stool microbiota, anticancer immunosurveillance, and general health, the composition of the gut microbiome has recently undergone investigation as a biomarker for immunotherapy. In this review, we highlight published results from preclinical and clinical studies to date supporting a relationship between the gut microbiome and antitumor efficacy of immune checkpoint inhibitors. Despite the promising and hypothesis-generating findings that have been produced in this arena to date, there remain some inconsistencies amongst present data that may need to be resolved to contribute to further development. Among these, a better understanding of the immunomodulatory function of the microbiome, standardization in sampling, sequencing techniques, and data analysis, and ensuring uniformity across various aspects of study design are warranted in conducting future prospective studies seeking to validate the gut microbiome as a potential biomarker of response to checkpoint blockade.},
}

@article {pmid30886779,
year = {2019},
author = {Eisenhofer, R and Weyrich, LS},
title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6594},
doi = {10.7717/peerj.6594},
pmid = {30886779},
issn = {2167-8359},
abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.},
}

@article {pmid30885933,
year = {2019},
author = {Scott, JE and O'Toole, GA},
title = {The Yin and Yang of Streptococcus Lung Infections in Cystic Fibrosis: A Model for Studying Polymicrobial Interactions.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JB.00115-19},
pmid = {30885933},
issn = {1098-5530},
abstract = {The streptococci are increasingly recognized as a core component of the cystic fibrosis (CF) lung microbiome, yet the role that they play in CF lung disease is unclear. The presence of Streptococcus milleri group (SMG, also known as the anginosus group streptococci, AGS) correlates with exacerbation when these microbes are the predominant species in the lung. In contrast, microbiome studies have indicated that increased relative abundance of streptococci in the lung, including members of the oral microflora, correlates with less severe impacts on lung disease compared to other CF-associated microflora, indicating a complex role for this genus in the context of CF. Recent findings suggest that streptococci in the CF lung microenvironment may influence the growth and/or virulence of other CF pathogens as evidenced by increased virulence factor production by Pseudomonas aeruginosa when grown in coculture with oral streptococci. Conversely, the presence of P. aeruginosa can enhance the growth of streptococci, including members of the SMG, a phenomenon that could be exacerbated by the fact that streptococci are not susceptible to some of the front-line antibiotics used to treat P. aeruginosa Collectively, these studies indicate the necessity for further investigation into the role of streptococci in the CF airway to determine how these microbes, alone or via interactions with other CF-associated pathogens, might influence CF lung disease, for better or for worse. We also propose that studying the interactions of streptococci with other CF pathogens is an ideal model to study clinically relevant microbial interactions.},
}

@article {pmid30885927,
year = {2019},
author = {Kirakodu, S and Chen, J and Gonzalez Martinez, J and Gonzalez, OA and Ebersole, J},
title = {Microbiome Profiles of Ligature-Induced Periodontitis in Nonhuman Primates Across the Lifespan.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1128/IAI.00067-19},
pmid = {30885927},
issn = {1098-5522},
abstract = {This investigation compared the microbiome colonizing teeth during the initiation, progression and resolution of periodontitis in nonhuman primates (Macaca mulatta) at different ages. Subgingival plaque samples were collected at baseline, and at 0.5, 1 and 3 months following ligature-induced periodontitis and following naturally-occurring disease resolution at 5 months. Samples were analyzed using 16S amplicon sequencing to identify bacterial profiles across age groups: young (<3 yrs), adolescent (3-7 yrs.), adult (12-15 yrs.) aged (17-23 yrs.). α-diversity of the microbiomes was greater in the adult/aged samples compared to the young/adolescent samples. β-diversity of the samples demonstrated clear age group differences, albeit, individual variation in microbiomes between animals within the age categories was noted. Phyla distribution differed between the young/adolescent group animals and the adult/aged animals at each of the time points showing an enrichment of Spirochetes, Fusobacteria, and Bacteroidetes phyla associated with periodontitis. Major differences in the top 50 OTUs were noted in the young and adolescent microbiomes during the initiation and progression post-ligation compared to the adult and aged animals. A large number of species in the top 50 OTUs were lower at baseline and in resolved disease microbiomes in the young samples, while profiles in adolescent animals were more consistent with the disease microbiomes. Microbiome profiles for resolution for adults and aged animals appeared more resilient and generally maintained a pattern similar to disease. Use of the model can expand our understanding of the crucial interactions of the oral microbiome and host responses in periodontitis.},
}

@article {pmid30885813,
year = {2019},
author = {Christian, LM},
title = {At the Forefront of Psychoneuroimmunology in Pregnancy: Implications for Racial Disparities in Birth Outcomes: PART 2: Biological Mechanisms.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neubiorev.2019.03.010},
pmid = {30885813},
issn = {1873-7528},
abstract = {As reviewed in Part I of this two part review, birth prior to full term is a substantial public health issue. In the US, ˜400,000 babies per year are born preterm (< 37 weeks), while >1 million are early term (37-386/7 weeks) and remarkable racial disparities in shortened gestation are observed among African Americans as compared to Whites. Biomechanisms linking stressor exposures with birth outcomes are increasingly being explicated. The current paper reviews the mechanistic role of maternal biological functioning in the link between behavioral exposures and birth outcomes. These include the inter-related roles of neuroendocrine function, inflammatory regulation, biological aging, and the microbiome. An integrative approach which addresses both behavioral and biological factors within the same study, carefully considers the role of race/ethnicity, and rigorously defines birth outcomes (e.g., spontaneous versus medically-indicated and inclusive of early term birth) is needed to move research in this field toward better mechanistic understanding and clinical application.},
}

@article {pmid30885792,
year = {2019},
author = {Sampson, T},
title = {The impact of indigenous microbes on Parkinson's disease.},
journal = {Neurobiology of disease},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbd.2019.03.014},
pmid = {30885792},
issn = {1095-953X},
abstract = {The gastrointestinal tract is inhabited by trillions of individual microbes, representing hundreds to thousands of distinct species. These indigenous organisms are not simply spectators to host activity, but instead actively modulate critical aspects of host physiology. From digestion and the production of small molecules, to the maturation and tuning of immune responses, the gastrointestinal microbiome influences every organ system in the body. Growing experimental evidence demonstrates microbial influence on neurological function in both health and disease. Furthermore, sequencing of the intestinal microbe population reveals altered community structures in various neurological conditions. Here, we provide a perspective on the potential roles for the intestinal microbiome in modulating Parkinson's disease. While Parkinson's disease has been historically studied as a disease of the central nervous system, there is growing appreciation for the roles of both gastrointestinal function and its resident microbes within this disease state. Recent studies focused on the microbiome during Parkinson's disease may advance our understanding of disease etiology and provide perspective for previously unrecognized therapeutic avenues through modulation of intestinal microbes.},
}

@article {pmid30885720,
year = {2019},
author = {LaPierre, N and Ju, CJ and Zhou, G and Wang, W},
title = {MetaPheno: A Critical Evaluation of Deep Learning and Machine Learning in Metagenome-Based Disease Prediction.},
journal = {Methods (San Diego, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymeth.2019.03.003},
pmid = {30885720},
issn = {1095-9130},
abstract = {The human microbiome plays a number of critical roles, impacting almost every aspect of human health and well-being. Conditions in the microbiome have been linked to a num-ber of significant diseases. Additionally, revolutions in sequencing technology have led to a rapid increase in publicly-available sequencing data. Consequently, there have been grow-ing efforts to predict disease status from metagenomic sequencing data, with a proliferation of new approaches in the last few years. Some of these efforts have explored utilizing a powerful form of machine learning called deep learning, which has been applied successfully in several biological domains. Here, we review some of these methods and the algorithms that they are based on, with a particular focus on deep learning methods. We also per-form a deeper analysis of Type 2 Diabetes and obesity datasets that have eluded improved results, using a variety of machine learning and feature extraction methods. We conclude by offering perspectives on study design considerations that may impact results and future directions the field can take to improve results and offer more valuable conclusions. The scripts and extracted features for the analyses conducted in this paper are available via GitHub: https://github.com/nlapier2/metapheno.},
}

@article {pmid30885689,
year = {2019},
author = {Hildonen, M and Kodama, M and Puetz, L and Gilbert, MTP and Limborg, MT},
title = {A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss).},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mimet.2019.03.010},
pmid = {30885689},
issn = {1872-8359},
abstract = {Immediate freezing is perhaps the most preferred method used for preserving gut microbial samples, but research on sample preservation has been principally based around samples from mammalian species, and little is known about the advantages or disadvantages relating to different storage methods for fish guts. Fish gut samples may pose additional challenges due to the different chemical and enzymatic profile, as well as the higher water content, which might affect the yield and purity of DNA recovered. To explore this, we took gut content and mucosal scrape samples from 10 rainbow trout (Oncorhynchus mykiss), and tested whether different preservation methods have any effect on the ability to construct high quality genomic libraries for shotgun and 16S rRNA gene sequencing. Four different storage methods were compared for the gut content samples (immediate freezing on dry ice, 96% ethanol, RNAlater and DNA/RNA shield), while two different methods were compared for mucosal scrape samples (96% ethanol and RNAlater). The samples were thereafter stored at -80 °C. Our findings concluded that 96% ethanol outperforms the other storage methods when considering DNA quantity, quality, cost and labor. Ethanol works consistently well for both gut content and mucosal scrape samples, and enables construction of DNA sequencing libraries of sufficient quantity and with a fragment length distribution suitable for shotgun sequencing. Two main conclusions from our study are i) sample storage optimisation is an important part of establishing a microbiome research program in a new species or sample type system, and ii) 96% ethanol is the preferred method for storing rainbow trout gut content and mucosal scrape samples.},
}

@article {pmid30885621,
year = {2019},
author = {Rogers, GB},
title = {The nasopharyngeal microbiome and LRTIs in infants.},
journal = {The Lancet. Respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2213-2600(18)30495-8},
pmid = {30885621},
issn = {2213-2619},
}

@article {pmid30885591,
year = {2019},
author = {Kokai-Kun, JF and Roberts, T and Coughlin, O and Le, C and Whalen, H and Stevenson, R and Wacher, VJ and Sliman, J},
title = {Use of ribaxamase (SYN-004), a β-lactamase, to prevent Clostridium difficile infection in β-lactam-treated patients: a double-blind, phase 2b, randomised placebo-controlled trial.},
journal = {The Lancet. Infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1473-3099(18)30731-X},
pmid = {30885591},
issn = {1474-4457},
abstract = {BACKGROUND: Infections with Clostridium difficile are a health threat, yet no products are currently licensed for prevention of primary C difficile infections. Intravenous β-lactam antibiotics are considered to confer a high risk of C difficile infection because of their biliary excretion into the gastrointestinal tract and disruption of the gut microbiome. ribaxamase (SYN-004) is an orally administered β-lactamase that was designed to be given with intravenous β-lactam antibiotics to degrade excess antibiotics in the upper gastrointestinal tract before they disrupt the gut microbiome and lead to C difficile infection. We therefore aimed to determine whether administration of ribaxamase could prevent C difficile infection in patients being treated with intravenous ceftriaxone for a lower respiratory tract infection, thereby supporting continued clinical development.

METHODS: In this parallel-group, double-blind, multicentre, phase 2b, randomised placebo-controlled trial, we recruited patients who had been admitted to a hospital with a lower respiratory tract infection with a pneumonia index score of 90-130 and who were expected to be treated with ceftriaxone for at least 5 days. Patients were recruited from 54 clinical sites in the USA, Canada, Bulgaria, Hungary, Poland, Romania, and Serbia. We randomly assigned patients older than 50 years to groups (1:1) in blocks of four by use of an interactive web portal; these groups were assigned to receive either 150 mg ribaxamase or placebo four times per day during, and for 72 h after, treatment with ceftriaxone. All patients, clinical investigators, study staff, and sponsor personnel were masked to the study drug assignments. The primary endpoint was the incidence of C difficile infection, as diagnosed by the local laboratory, in patients who received at least one treatment dose, and this outcome was assessed during treatment and for 4 weeks after treatment. This study is registered with ClinicalTrials.gov, number NCT02563106.

FINDINGS: Between Nov 16, 2015, and Nov 10, 2016, we screened 433 patients for inclusion in the study. Of these patients, 20 (5%) patients were excluded from the study (16 [4%] patients did not meet inclusion criteria; four [1%] patients because of dosing restrictions). We enrolled and randomly assigned 413 patients to groups, of whom 207 patients were assigned to receive ceftriaxone plus ribaxamase and 206 patients were assigned to receive ceftriaxone plus placebo. However, one (<1%) patient in the ribaxamase group withdrew consent and was not treated with ribaxamase. During the study and within the 4 weeks after antibiotic treatment, two (1·0%) patients in the ribaxamase group and seven (3·4%) patients in the placebo group were diagnosed with an infection with C difficile (risk reduction 2·4%, 95% CI -0·6 to 5·9; one-sided p=0·045). Adverse events were similar between groups but more deaths were reported in the ribaxamase group (11 deaths vs five deaths in the placebo group). This disparity was due to the higher incidence of deaths attributed to cardiac-associated causes in the ribaxamase group (six deaths vs one death in the placebo group).

INTERPRETATION: In patients treated with intravenous ceftriaxone for lower respiratory tract infections, oral ribaxamase reduced the incidence of C difficile infections compared with placebo. The imbalance in deaths between the groups appeared to be related to the underlying health of the patients. Ribaxamase has the potential to prevent C difficile infection in patients treated with intravenous β-lactam antibiotics, and our findings support continued clinical development of ribaxamase to prevent C difficile infection.

FUNDING: Synthetic Biologics.},
}

@article {pmid30885590,
year = {2019},
author = {Goldenberg, SD},
title = {A solution to the problem of antibiotic induced collateral damage to the gut microbiome.},
journal = {The Lancet. Infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1473-3099(18)30784-9},
pmid = {30885590},
issn = {1474-4457},
}

@article {pmid30885328,
year = {2019},
author = {Zhao, S and Gao, G and Li, W and Li, X and Zhao, C and Jiang, T and Jia, Y and He, Y and Li, A and Su, C and Ren, S and Chen, X and Zhou, C},
title = {Antibiotics are associated with attenuated efficacy of anti-PD-1/PD-L1 therapies in Chinese patients with advanced non-small cell lung cancer.},
journal = {Lung cancer (Amsterdam, Netherlands)},
volume = {130},
number = {},
pages = {10-17},
doi = {10.1016/j.lungcan.2019.01.017},
pmid = {30885328},
issn = {1872-8332},
abstract = {OBJECTIVES: Gut microbiome plays a dominant role in modulating therapeutic efficacy of immune checkpoint inhibitors (ICIs) targeting the programmed cell death receptor/ligand-1 (PD-1/PD-L1) pathway, suggesting that co-administration of antibiotics (Abx), which might result in dysbacteriosis, can attenuate the clinical outcomes of ICIs. The current study aimed to investigate the predictive role of Abx on ICIs treatment in patients with advanced non-small cell lung cancer (NSCLC). The impact of proton pump inhibitors (PPIs), another medication that can induce dysbacteriosis, was also investigated.

MATERIALS AND METHODS: We retrospectively reviewed the medical records of eligible patients who received anti-PD-1-based therapies in our hospital. Tumor responses, patients' survival, the incidence of immune-related adverse events (irAEs) and other baseline variables were examined. The application of Abx or PPIs treatment were also collected. Clinical outcomes and clinicopathologic features were compared according to the status of Abx or PPIs co-administration.

RESULTS: A total of 109 patients were included. Of them, 20 (18.3%) patients were categorized in Abx-treated group. No major difference in baseline characteristics was observed between Abx-treated and -untreated groups. Concomitant Abx treatment was significantly associated with shorter progression-free survival (PFS) (p < 0.0001) and overall survival (OS) (p = 0.0021). And primary disease progression tended to increase in Abx-treated group (p = 0.092). Yet, the occurrence and grades of irAEs were comparable between two groups. In multivariable analysis, Abx treatment was markedly associated with worse PFS (HR=0.32, 95%CI 0.18-0.59, p < 0.0001) and OS (HR=0.35, 95%CI 0.16-0.77, p = 0.009). Regarding the use of PPIs, no significant difference was observed in clinical outcomes between the patients with or without concomitant PPIs treatment.

CONCLUSIONS: Abx treatment was significantly associated with attenuated clinical outcomes derived from anti-PD-1-based ICIs in a Chinese cohort of patients with advanced NSCLC.},
}

@article {pmid30885294,
year = {2019},
author = {Prodan, A and Levin, E and Nieuwdorp, M},
title = {Does disease start in the mouth, the gut or both?.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
doi = {10.7554/eLife.45931},
pmid = {30885294},
issn = {2050-084X},
abstract = {Oral bacteria colonize the gut more frequently than previously thought.},
}

@article {pmid30885266,
year = {2019},
author = {Westreich, ST and Ardeshir, A and Alkan, Z and Kable, ME and Korf, I and Lemay, DG},
title = {Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {41},
doi = {10.1186/s40168-019-0664-z},
pmid = {30885266},
issn = {2049-2618},
support = {UC Davis Signature Research in Genomics Award//University of California, Davis/ ; UC Davis Signature Research in Genomics Award//University of California, Davis/ ; P51OD011107-56//National Institutes of Health (US)/ ; 2032-53000-001-00-D//U.S. Department of Agriculture/ ; 2032-53000-001-00-D//U.S. Department of Agriculture/ ; UC Davis Signature Research in Genomics Award//University of California Davis/ ; },
abstract = {BACKGROUND: Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease.

RESULTS: Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes.

CONCLUSIONS: The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites.},
}

@article {pmid30884883,
year = {2019},
author = {Spence, JD},
title = {Nutrition and Risk of Stroke.},
journal = {Nutrients},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/nu11030647},
pmid = {30884883},
issn = {2072-6643},
abstract = {Nutrition is far more important in stroke risk than most physcians suppose. Healthy lifestyle choices reduce the risk of stroke by ~80%, and of the factors that increase the risk of stroke, the worst is diet: only ~0.1% of Americans consume a healthy diet, and only 8.3% consume a somewhat healthy diet. The situation is probably not much better in most other countries. A Cretan Mediterranean diet, high in olive oil, whole grains, fruits, vegetables and legumes, and low in cholesterol and saturated fat, can reduce stroke by 40% or more in high-risk patients. The role of the intestinal microbiome in cardiovascular risk is emerging; high levels of toxic metabolites produced by intestinal bacteria from meat (particularly red meat) and egg yolk are renally excreted. Patients with renal impairment, including the elderly, should limit red meat and avoid egg yolk, as should other patients at high risk of stroke. Salt intake should be limited to 2⁻3 grams per day. Metabolic B12 deficiency is common and usually missed. It has serious neurological consequences, including an increase in the risk of stroke. It now clear that B vitamins to lower homocysteine reduce the risk of stroke, but we should probably be using methylcobalamin instead of cyanocobalamin.},
}

@article {pmid30884651,
year = {2019},
author = {Blanco-Míguez, A and Fdez-Riverola, F and Lourenço, A and Sánchez, B},
title = {In silico prediction reveals the existence of potential bioactive neuropeptides produced by the human gut microbiota.},
journal = {Food research international (Ottawa, Ont.)},
volume = {119},
number = {},
pages = {221-226},
doi = {10.1016/j.foodres.2019.01.069},
pmid = {30884651},
issn = {1873-7145},
abstract = {This work reports on a large-scale potential neuropeptide activity screening in human gut microbiomes deposited in public databases. In our experimental approach, the sequences of the bioactive peptides collected in the MAHMI database, mainly predicted as immunomodulatory or antitumoral, were crossed with those of the neuroactive/digestive peptides. From 91,325,790 potential bioactive peptides, only 581 returned a match when crossed against the 5949 neuroactive peptides from the NeuroPep database and the 15 digestive hormones. Relevant bacterial taxa, such as Ruminococcus sp., Clostridium sp. were found among the main producers of the matching sequences, and many of the matches corresponded to adiponectin and the hormone produced by adipocites, which is involved in glucose homeostasis. These results show, for the first time, the presence of potentially bioactive peptides produced by gut microbiota members over the nervous cells, most notably, peptides with already predicted immunomodulatory or anti-inflammatory activity. Classical (Lactobacillus sp.) and next-generation (Faecalibacterium sp.) probiotics are shown to produce these peptides, which are proposed as a potential mechanism of action of psychobiotics. Our previous experimental results showed that many of these peptides were active when incubated with immune cells, such as dendritic cells, so their effect over the nervous system innervating the gut mucosa holds significant potential and should be explored.},
}

@article {pmid30882042,
year = {2018},
author = {Siemer, S and Hahlbrock, A and Vallet, C and McClements, DJ and Balszuweit, J and Voskuhl, J and Docter, D and Wessler, S and Knauer, SK and Westmeier, D and Stauber, RH},
title = {Nanosized food additives impact beneficial and pathogenic bacteria in the human gut: a simulated gastrointestinal study.},
journal = {NPJ science of food},
volume = {2},
number = {1},
pages = {22},
doi = {10.1038/s41538-018-0030-8},
pmid = {30882042},
issn = {2396-8370},
abstract = {Nanotechnology provides the food industry with new ways to modulate various aspects of food. Hence, engineered nanoparticles (NPs) are increasingly added to food and beverage products as functional ingredients. However, the impact of engineered as well as naturally occurring NPs on both commensal and pathogenic microorganisms within the gastrointestinal tract (GI) is not fully understood. Here, well-defined synthetic NPs and bacterial models were used to probe nanoparticle-bacteria interactions, from analytical to in situ to in vitro. NP-bacteria complexation occurred most efficiently for small NPs, independent of their core material or surface charge, but could be reduced by NPs' steric surface modifications. Adsorption to bacteria could also be demonstrated for naturally occurring carbon NPs isolated from beer. Complex formation affected the (patho)biological behavior of both the NPs and bacteria, including their cellular uptake into epithelial cells and phagocytes, pathogenic signaling pathways, and NP-induced cell toxicity. NP-bacteria complex formation was concentration-dependently reduced when the NPs became coated with biomolecule coronas with sequential simulation of first oral uptake and then the GI. However, efficient NP adsorption was restored when the pH was sufficiently low, such as in simulating the conditions of the stomach. Collectively, NP binding to enteric bacteria may impact their (patho)biology, particularly in the stomach. Nanosized-food additives as well as naturally occurring NPs may be exploited to (rationally) shape the microbiome. The information contained in this article should facilitate a "safe by design" strategy for the development and application of engineered NPs as functional foods ingredients.},
}

@article {pmid30881255,
year = {2017},
author = {Dolan, KE and Pizano, JM and Gossard, CM and Williamson, CB and Burns, CM and Gasta, MG and Finley, HJ and Parker, EC and Lipski, EA},
title = {Probiotics and Disease: A Comprehensive Summary-Part 6, Skin Health.},
journal = {Integrative medicine (Encinitas, Calif.)},
volume = {16},
number = {4},
pages = {32-41},
pmid = {30881255},
issn = {1546-993X},
abstract = {This article series provides a literature review of the disease-specific probiotic strains associated with dermatological disorders and conditions that have been studied in published clinical trials in humans and animals. This is not an exhaustive review. The table design allows for quick access to supportive data and will be helpful as a guide for both researchers and clinicians. The goal of the probiotics and disease series is to provide clinically useful tools. The first article (part 1) focused on mental health and neurological conditions, and the second article (part 2) explored cultured and fermented foods that are commonly available in the United States. The third article (part 3) explored the relationship between bacterial strains and 2 of the most prevalent diseases we have in modern society: cardiometabolic disease and fatigue syndromes. The fourth article (part 4) elucidated the role of the microbiome in infectious diseases, and the fifth article (part 5) examined respiratory conditions and conditions of the ears, nose, and throat. This sixth article (part 6) article explores the relationship between the microbiome and skin disorders. Future articles will review conditions related to autoimmunity and dermatological conditions; the influence of the microbiome on cancer development and prognosis, gastrointestinal and genitourinary diseases associated with dysbiosis conditions; followed by an article focused on probiotic supplements. This literature review is specific to disease condition, probiotic classification, and individual strain.},
}

@article {pmid30884189,
year = {2019},
author = {Jiang, CL and Jin, WZ and Tao, XH and Zhang, Q and Zhu, J and Feng, SY and Xu, XH and Li, HY and Wang, ZH and Zhang, ZJ},
title = {Black soldier fly larvae (Hermetia illucens) strengthen the metabolic function of food waste biodegradation by gut microbiome.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.13393},
pmid = {30884189},
issn = {1751-7915},
support = {2018-0AG-045//YuHang Initiative for Eco-Agriculture Development/ ; 41673081//the National Natural Science Foundation of China/ ; 2015C03009//ZheJiang Science and Technology Innovation Program of China/ ; },
abstract = {Vermicomposting using black soldier fly (BSF) larvae (Hermetia illucens) has gradually become a promising biotechnology for waste management, but knowledge about the larvae gut microbiome is sparse. In this study, 16S rRNA sequencing, SourceTracker, and network analysis were leveraged to decipher the influence of larvae gut microbiome on food waste (FW) biodegradation. The microbial community structure of BSF vermicompost (BC) changed greatly after larvae inoculation, with a peak colonization traceable to gut bacteria of 66.0%. The relative abundance of 11 out of 21 metabolic function groups in BC were significantly higher than that in natural composting (NC), such as carbohydrate-active enzymes. In addition, 36.5% of the functional genes in BC were significantly higher than those in NC. The changes of metabolic functions and functional genes were significantly correlated with the microbial succession. Moreover, the bacteria that proliferated in vermicompost, including Corynebacterium, Vagococcus, and Providencia, had strong metabolic abilities. Systematic and complex interactions between the BSF gut and BC bacteria occurred over time through invasion, altered the microbial community structure, and thus evolved into a new intermediate niche favourable for FW biodegradation. The study highlights BSF gut microbiome as an engine for FW bioconversion, which is conducive to bioproducts regeneration from wastes.},
}

@article {pmid30883790,
year = {2019},
author = {Fernández, I and Cosme, M and Stringlis, IA and Yu, K and de Jonge, R and Van Wees, SCM and Pozo, MJ and Pieterse, CMJ and Van der Heijden, MGA},
title = {Molecular dialogue between arbuscular mycorrhizal fungi and the non-host plant Arabidopsis thaliana switches from initial detection to antagonism.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.15798},
pmid = {30883790},
issn = {1469-8137},
abstract = {Approximately 29% of all vascular plant species are unable to establish an arbuscular mycorrhizal (AM) symbiosis. Despite this, AM fungi (Rhizophagus spp.) are enriched in the root microbiome of the non-host Arabidopsis thaliana and Arabidopsis roots become colonized when AM networks nurtured by host plants are available. Here, we investigated the non-host-AM fungus interaction by analyzing transcriptional changes in Rhizophagus, Arabidopsis, and the host plant Medicago truncatula while growing in the same mycorrhizal network. In early interaction stages, Rhizophagus activated the Arabidopsis strigolactone biosynthesis genes CCD7 and CCD8, suggesting that detection of AM fungi is not completely impaired. However, in colonized Arabidopsis roots, fungal nutrient transporter genes GintPT, GintAMT2, GintMST2 and GintMST4, essential for AM symbiosis, were not activated. RNA-seq transcriptome analysis pointed to activation of costly defenses in colonized Arabidopsis roots. Moreover, Rhizophagus colonization caused a 50% reduction in shoot biomass, but also led to enhanced systemic immunity against Botrytis cinerea. This suggests that early signaling between AM fungi and Arabidopsis is not completely impaired and that incompatibility appears at later interaction stages. Moreover, Rhizophagus-mediated defenses coincide with reduced Arabidopsis growth, but also with systemic disease resistance, highlighting the multifunctional role of AM fungi in host and non-host interactions. This article is protected by copyright. All rights reserved.},
}

@article {pmid30883572,
year = {2019},
author = {Sugino, KY and Paneth, N and Comstock, SS},
title = {Michigan cohorts to determine associations of maternal pre-pregnancy body mass index with pregnancy and infant gastrointestinal microbial communities: Late pregnancy and early infancy.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213733},
doi = {10.1371/journal.pone.0213733},
pmid = {30883572},
issn = {1932-6203},
abstract = {BACKGROUND: About 25% of women in the United States are obese prior to becoming pregnant. Although there is some knowledge about the relationship between the gastrointestinal microbiota and obesity, little is known about the relationship between pre-pregnancy obesity and the gastrointestinal microbiota in pregnancy or its impact on infant gut microbiota. However, the composition of the gut microbiota early in life may influence childhood health. Thus, the objective of this research was to identify associations between maternal pre-pregnancy obesity and the pregnancy (n = 39) or early infancy (n = 39) microbiotas.

RESULTS: Fecal bacterial communities from overweight women had lower microbiota diversity (Chao1: p = 0.02; inverse Simpson: p = 0.05; Shannon: p = 0.02) than communities from normal weight or obese women. The within-group microbiota composition of overweight women differed from those of normal and obese women at the genus and phylum levels (p = 0.003 and p = 0.02, respectively). Pre-pregnancy overweight women had higher abundances of Bacteroides and lower Phascolarctobacterium than women who were normal weight or obese prior to becoming pregnant. Normal weight women had lower abundances of Acidaminococcus and Dialister than overweight and obese women. Infant community composition tended to differ in membership (Sorensen index) by maternal pre-pregnancy BMI category, and significantly differed by delivery mode and breastfeeding exclusivity (p = 0.06, p = 0.001, p = 0.008, respectively). Infants from normal weight women had lower abundances of Megasphaera than infants from overweight or obese women. Streptococcus was lowest in infants from overweight women, and Staphylococcus was lowest in infants from obese women.

CONCLUSION: Maternal and infant microbiotas are associated with and might be affected by maternal pre-pregnancy BMI. Future work should determine if there are also functional differences in the infant microbiome, if those functional differences are related to maternal pre-pregnancy BMI, and whether differences in composition or traits persist over time.},
}

@article {pmid30883471,
year = {2019},
author = {Mailing, LJ and Allen, JM and Buford, TW and Fields, CJ and Woods, JA},
title = {Exercise and the Gut Microbiome: A Review of the Evidence, Potential Mechanisms, and Implications for Human Health.},
journal = {Exercise and sport sciences reviews},
volume = {47},
number = {2},
pages = {75-85},
doi = {10.1249/JES.0000000000000183},
pmid = {30883471},
issn = {1538-3008},
abstract = {The gastrointestinal tract contains trillions of microbes (collectively known as the gut microbiota) that play essential roles in host physiology and health. Studies from our group and others have demonstrated that exercise independently alters the composition and functional capacity of the gut microbiota. Here, we review what is known about the gut microbiota, how it is studied, and how it is influenced by exercise training and discuss the potential mechanisms and implications for human health and disease.},
}

@article {pmid30883466,
year = {2019},
author = {Neu, J},
title = {Multiomics-based strategies for taming intestinal inflammation in the neonate.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCO.0000000000000559},
pmid = {30883466},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: The purpose of this review is to discuss evolving research into intestinal inflammatory responses as they relate to the developing microbiome and to provide insights into developing multiomic tools that are being used to describe these relationships. Intestinal inflammatory conditions are common, and in the neonate present special challenges, especially in the form of necrotizing enterocolitis (NEC) and other conditions that involve damage or breakdown of the mucosal barrier, leading to systemic inflammation and damage to distal sites, such as the liver and brain.

RECENT STUDIES: Recent studies show that when a dysbiosis (microbial imbalance or impaired microbiota) occurs, an inflammatory response that can affect the entire body is frequently the result. We are recognizing that not only the microbial diversity and relative abundance of certain taxa play a role in dysbiosis and inflammation, but their functional capabilities in terms of metabolite production and interaction with the immune system of the host afre critical in future health and disease.

SUMMARY: A multiomic approach to evaluate these microorgansims as well as their interaction with the host by using systems-based concepts is becoming possible and is likely to shed new light on various disease entities and how we can best prevent and treat them.},
}

@article {pmid30883192,
year = {2019},
author = {Man, WH and Clerc, M and de Steenhuijsen Piters, WAA and van Houten, MA and Chu, MLJN and Kool, J and Keijser, BJF and Sanders, EAM and Bogaert, D},
title = {Loss of Microbial Topography between Oral and Nasopharyngeal Microbiota and Development of Respiratory Infections Early in Life.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.201810-1993OC},
pmid = {30883192},
issn = {1535-4970},
abstract = {RATIONALE: The respiratory microbiota is increasingly being appreciated as an important mediator in the susceptibility to childhood respiratory tract infections (RTIs). Pathogens are presumed to originate from the nasopharyngeal ecosystem.

OBJECTIVES: To investigate the association between early-life respiratory microbiota and development of childhood RTIs.

METHODS: In a prospective birth cohort (Microbiome Utrecht Infant Study: MUIS), we characterized the oral microbiota longitudinally from birth until six months of age of 112 infants (9 regular samples/subject) and compared them with nasopharyngeal microbiota using 16S-rRNA-based sequencing. We also characterized oral and nasopharynx samples during RTI episodes in the first half year of life.

MEASUREMENTS AND MAIN RESULTS: Oral microbiota were driven mostly by feeding type, followed by age, mode of delivery and season of sampling. In contrast to our previously published associations between nasopharyngeal microbiota development and susceptibility to RTIs, oral microbiota development was not directly associated with susceptibility to RTI development. However, we did observe an influx of oral taxa, such as Neisseria lactamica, Streptococcus, Prevotella nanceiensis, Fusobacterium and Janthinobacterium lividum, in the nasopharyngeal microbiota prior to and during RTIs, which was accompanied by reduced presence and abundance of Corynebacterium, Dolosigranulum and Moraxella spp. Moreover, this phenomenon was accompanied by reduced niche differentiation indicating loss of ecological topography preceding confirmed RTIs. This loss of ecological topography was further augmented by start of daycare, and linked to consecutive development of symptomatic infections.

CONCLUSIONS: Together, our results link the loss of topography to subsequent development of RTI episodes. This may lead to new insights for prevention of RTIs and antibiotic utilization in childhood.},
}

@article {pmid30882766,
year = {2019},
author = {Ferrarello, D and Froh, EB and Hinson, TD and Spatz, DL},
title = {Nurses' Views on Using Pasteurized Donor Human Milk for Hypoglycemic Term Infants.},
journal = {MCN. The American journal of maternal child nursing},
volume = {},
number = {},
pages = {},
doi = {10.1097/NMC.0000000000000525},
pmid = {30882766},
issn = {1539-0683},
abstract = {PURPOSE: The purpose of this study was to explore maternal child nurses' knowledge and beliefs about using pasteurized donor human milk (PDHM) to treat newborns with hypoglycemia. Pasteurized donor human milk has been used for decades in neonatal intensive care units, but its use is relatively new in the well-baby population.

STUDY DESIGN AND METHODS: Focus groups of maternal child nurses were conducted to explore this topic.

RESULTS: Six focus groups that included a total 20 nurses were held. Four themes were identified: 1) nurses presumed safety of PDHM but lacked knowledge, 2) nurses' role as patient-family advocate, 3) nurses' logistical concerns about implementation of PDHM, and 4) nurses lacked clarity on formal milk sharing versus PDHM.

CLINICAL IMPLICATIONS: As the use of PDHM increases for well babies, nurses will need more education about PDHM, its safety profile, its use in breastfeeding support and protection of the infant microbiome, and how PDHM differs from informal milk sharing. Nurses play an important role in helping parents weigh risks and benefits of using PDHM or formula when supplementation is needed during the hospital stay. It is important that nurses feel confident in their own knowledge and ability to address parental concerns so they can advocate for their patients and support parental decisionmaking.},
}

@article {pmid30882743,
year = {2019},
author = {Shaw, L and Klein, N},
title = {The Microbiome-The Explanation for (Almost) Everything?.},
journal = {The Pediatric infectious disease journal},
volume = {38},
number = {4},
pages = {e69-e71},
doi = {10.1097/INF.0000000000002261},
pmid = {30882743},
issn = {1532-0987},
}

@article {pmid30882489,
year = {2019},
author = {Maurice, JB and Garvey, L and Tsochatzis, EA and Wiltshire, M and Cooke, G and Guppy, N and McDonald, J and Marchesi, J and Nelson, M and Kelleher, P and Goldin, R and Thursz, M and Lemoine, M},
title = {Monocyte-macrophage activation is associated with nonalcoholic fatty liver disease and liver fibrosis in HIV monoinfection independently of the gut microbiome and bacterial translocation.},
journal = {AIDS (London, England)},
volume = {33},
number = {5},
pages = {805-814},
doi = {10.1097/QAD.0000000000002133},
pmid = {30882489},
issn = {1473-5571},
abstract = {BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is common among people living with HIV. There are limited data available on the pathophysiology of NAFLD and the development of fibrosis in this population.

OBJECTIVES: The aim of this study was to investigate the association of bacterial translocation, adipose tissue dysfunction, monocyte activation and gut dysbiosis in patients with HIV monoinfection and NAFLD.

METHODS: Cases with biopsy-proven NAFLD and HIV monoinfection were age and sex-matched to HIV-positive and HIV-negative controls. Markers of bacterial translocation [lipopolysaccharide-binding protein (LBP), bacterial DNA and lipopolysaccharide (LPS)], adipose tissue dysfunction (leptin, adiponectin) and monocyte activation (sCD14 and sCD163) were measured by ELISA. Hepatic patterns of macrophage activation were explored with immunohistochemistry. 16 s rRNA sequencing was performed with stool.

RESULTS: Thirty-three cases were included (≥F2 fibrosis n = 16), matched to HIV-positive (n = 29) and HIV-negative (n = 17) controls. Cases with NAFLD were more obese (BMI 31.0 ± 4.4 vs. 24.1 ± 2.8 kg/m, P < 0.001) and had significantly increased levels of sCD14, sCD163 and higher leptin to adiponectin ratio vs. HIV-positive controls. Cases with ≥F2 verses < F2 fibrosis had increased sCD14 (1.4 ± 0.4 vs. 1.1 ± 0.3 μg/ml, P = 0.023) and sCD163 (1.0 ± 0.3 vs. 0.8 ± 0.3 μg/ml, P = 0.060), which correlated with waist circumference (sCD14 P = 0.022, sCD163 P = 0.011). Immunohistochemistry showed increased hepatic portal macrophage clusters in patients with fibrosis. No markers of bacterial translocation or changes to the microbiome were associated with NAFLD or fibrosis.

CONCLUSION: NAFLD fibrosis stage in HIV monoinfected patients is associated with monocyte activation in the context of obesity, which may be independent of bacterial translocation and gut microbiome.},
}

@article {pmid30882461,
year = {2019},
author = {Wang, Z and Xu, CM and Liu, YX and Wang, XQ and Zhang, L and Li, M and Zhu, SW and Xie, ZJ and Wang, PH and Duan, LP and Zhu, HQ},
title = {Characteristic dysbiosis of gut microbiota of chinese patients with diarrhea-predominant irritable bowel syndrome by an insight into the pan-microbiome.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/CM9.0000000000000192},
pmid = {30882461},
issn = {2542-5641},
abstract = {BACKGROUND: Irritable bowel syndrome (IBS) is reported associated with the alteration of gut microbial composition termed as dysbiosis. However, the pathogenic mechanism of IBS remains unclear, while the studies of Chinese individuals are scarce. This study aimed to understand the concept of dysbiosis among Chinese diarrhea-predominant IBS (IBS-D) patients, as a degree of variance between the gut microbiomes of IBS-D population and that of healthy population.

METHODS: The IBS-D patients were recruited (assessed according to the Rome III criteria, by IBS symptom severity score) from the Outpatient Department of Gastroenterology of Peking University Third Hospital, and volunteers as healthy controls (HC) were enrolled, during 2013. The 16S rRNA sequences were extracted from fecal samples. RDP resources, BLAST and SparCC software were used to obtain the phylotype composition of samples and the internal interactions of the microbial community. Herein, the nonparametric test, Wilcoxon rank-sum test was carried out to find the statistical significance between HC and IBS-D groups. All the P values were adjusted to q values to decrease the error rate.

RESULTS: The study characterized the gut microbiomes of Chinese IBS-D patients, and demonstrated that the dysbiosis could be characterized as directed alteration of the microbiome composition leading to greater disparity between relative abundance of two phyla, Bacteroidetes (Z = 4.77, q = 1.59 × 10) and Firmicutes (Z = -3.87, q = 5.83 × 10). Moreover it indicated that the IBS symptom features were associated with the dysbiosis of whole gut microbiome, instead of one or several certain genera even they were dominating. Two genera, Bacteroides and Lachnospiracea incertae sedis, were identified as the core genera, meanwhile the non-core genera contribute to a larger pan-microbiome of the gut microbiome. Furthermore the dysbiosis in IBS-D patients was associated with a reduction of network complexity of the interacted microbial community (HC vs. IBS-D: 639 vs. 154). The disordered metabolic functions of IBS-D patients were identified as the potential influence of gut microbiome on the host (significant difference with q < 0.01 between HC and IBS-D).

CONCLUSIONS: This study supported the view of the potential influence of gut microbiome on the symptom of Chinese IBS-D patients, and further characterized dysbiosis in Chinese IBS-D patients, thus provided more pathological evidences for IBS-D with the further understanding of dysbiosis.This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0.},
}

@article {pmid30881970,
year = {2019},
author = {Mima, K and Baba, H},
title = {The gut microbiome, antitumor immunity, and liver cancer.},
journal = {Hepatobiliary surgery and nutrition},
volume = {8},
number = {1},
pages = {67-68},
doi = {10.21037/hbsn.2018.11.09},
pmid = {30881970},
issn = {2304-3881},
}

@article {pmid30881924,
year = {2019},
author = {Tribble, GD and Angelov, N and Weltman, R and Wang, BY and Eswaran, SV and Gay, IC and Parthasarathy, K and Dao, DV and Richardson, KN and Ismail, NM and Sharina, IG and Hyde, ER and Ajami, NJ and Petrosino, JF and Bryan, NS},
title = {Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {39},
doi = {10.3389/fcimb.2019.00039},
pmid = {30881924},
issn = {2235-2988},
abstract = {The oral microbiome has the potential to provide an important symbiotic function in human blood pressure physiology by contributing to the generation of nitric oxide (NO), an essential cardiovascular signaling molecule. NO is produced by the human body via conversion of arginine to NO by endogenous nitric oxide synthase (eNOS) but eNOS activity varies by subject. Oral microbial communities are proposed to supplement host NO production by reducing dietary nitrate to nitrite via bacterial nitrate reductases. Unreduced dietary nitrate is delivered to the oral cavity in saliva, a physiological process termed the enterosalivary circulation of nitrate. Previous studies demonstrated that disruption of enterosalivary circulation via use of oral antiseptics resulted in increases in systolic blood pressure. These previous studies did not include detailed information on the oral health of enrolled subjects. Using 16S rRNA gene sequencing and analysis, we determined whether introduction of chlorhexidine antiseptic mouthwash for 1 week was associated with changes in tongue bacterial communities and resting systolic blood pressure in healthy normotensive individuals with documented oral hygiene behaviors and free of oral disease. Tongue cleaning frequency was a predictor of chlorhexidine-induced changes in systolic blood pressure and tongue microbiome composition. Twice-daily chlorhexidine usage was associated with a significant increase in systolic blood pressure after 1 week of use and recovery from use resulted in an enrichment in nitrate-reducing bacteria on the tongue. Individuals with relatively high levels of bacterial nitrite reductases had lower resting systolic blood pressure. These results further support the concept of a symbiotic oral microbiome contributing to human health via the enterosalivary nitrate-nitrite-NO pathway. These data suggest that management of the tongue microbiome by regular cleaning together with adequate dietary intake of nitrate provide an opportunity for the improvement of resting systolic blood pressure.},
}

@article {pmid30881899,
year = {2019},
author = {Ashton, JJ and Mossotto, E and Ennis, S and Beattie, RM},
title = {Personalising medicine in inflammatory bowel disease-current and future perspectives.},
journal = {Translational pediatrics},
volume = {8},
number = {1},
pages = {56-69},
doi = {10.21037/tp.2018.12.03},
pmid = {30881899},
issn = {2224-4344},
abstract = {Up to 25% of inflammatory bowel disease (IBD) presents during childhood, often with severe and extensive disease, leading to significant morbidity including delayed growth and nutritional impairment. The classical approach to management has centred on differentiation into Crohn's disease (CD) or ulcerative colitis (UC), with subsequent treatment based on symptoms, results and complications. However, IBD is a heterogeneous condition with substantial variation in phenotype, disease course and outcome, so whilst effective treatment exists one size does not fit all. The ability to predict disease course at diagnosis, alongside tailoring medications based on response gives the potential for a more 'personalised approach'. The move to a pre-emptive strategy to prevent IBD-related complications, whilst simultaneously minimising side effects and long-term toxicity from therapy, particularly in those with relatively indolent disease, has the potential to revolutionise care. In very early-onset IBD, personalised approaches to diagnosis and management have become the standard of treatment enabling clinicians to significantly alter the outcomes of the few children with monogenic disease. However, the promise of discoveries in genomics, microbiome and transcriptomics in paediatric IBD has not yet translated to clinical application for the vast majority of patients. Despite this, the opportunity presents itself to apply data gathered at diagnosis and follow-up to predict which patients are likely to progress to complicated disease, which will respond well and which will require additional therapy. Using complex mathematics and innovative, cutting-edge machine learning (ML) techniques gives the potential to use this data to develop personalised clinical care algorithms to treat patients more effectively, reduce toxicity and improve outcome. In this review, we will consider current management of paediatric IBD, discuss how precision medicine is making inroads into clinical practice already, examine the contemporary studies applying data to stratify patients and explore how future management may be revolutionised by personalisation with clinical, genomic and other multi-omic data.},
}

@article {pmid30881898,
year = {2019},
author = {Ledder, O},
title = {Antibiotics in inflammatory bowel diseases: do we know what we're doing?.},
journal = {Translational pediatrics},
volume = {8},
number = {1},
pages = {42-55},
doi = {10.21037/tp.2018.11.02},
pmid = {30881898},
issn = {2224-4344},
abstract = {Despite the revolution in inflammatory bowel disease (IBD) treatment over the past two decades with the advent of biological therapies, there remains a substantial proportion of patients with inadequate or unsustained response to existent therapies. The overwhelming focus of IBD therapeutics has been targeting mucosal immunity, however with the developing evidence base pointing to the role of gut microbes in the inflammatory process, renewed focus should be placed on the impact of manipulating the microbiome in IBD management. This review provides an overview of the evidence implicating bacteria in the pathogenesis of gut inflammation in IBD and provides an overview of the evidence of antibiotics in IBD treatment. We also suggest a potential role of antibiotics in clinical practice based on available evidence and clinical experience.},
}

@article {pmid30880449,
year = {2019},
author = {Dohlman, AB and Shen, X},
title = {Mapping the microbial interactome: Statistical and experimental approaches for microbiome network inference.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {},
number = {},
pages = {1535370219836771},
doi = {10.1177/1535370219836771},
pmid = {30880449},
issn = {1535-3699},
abstract = {IMPACT STATEMENT: This review provides a comprehensive description of experimental and statistical tools used for network analyses of the human gut microbiome. Understanding the system dynamics of microbial interactions may lead to the improvement of therapeutic approaches for managing microbiome-associated diseases. Microbiome network inference tools have been developed and applied to both cross-sectional and longitudinal experimental designs, as well as to multi-omic datasets, with the goal of untangling the complex web of microbe-host, microbe-environmental, and metabolism-mediated microbial interactions. The characterization of these interaction networks may lead to a better understanding of the systems dynamics of the human gut microbiome, augmenting our knowledge of the microbiome's role in human health, and guiding the optimization of effective, precise, and rational therapeutic strategies for managing microbiome-associated disease.},
}

@article {pmid30880022,
year = {2019},
author = {Cohen, LJ and Cho, JH and Gevers, D and Chu, H},
title = {Genetic Factors and the Intestinal Microbiome Guide Development of Microbe-based Therapies for Inflammatory Bowel Diseases.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2019.03.017},
pmid = {30880022},
issn = {1528-0012},
abstract = {The intestinal microbiota is a dynamic community of bacteria, fungi, and viruses that mediates mucosal homeostasis and physiology. Imbalances in the microbiome and aberrant immune responses to gut bacteria can disrupt homeostasis and are associated with inflammatory bowel diseases (IBD) in humans and colitis in mice. We review genetic variants associated with IBD and their effects on the intestinal microbiome, the immune response, and disease pathogenesis. The intestinal microbiome, which includes microbial antigens, adjuvants, and metabolic products, affects the development and function of the intestinal mucosa and inflammatory responses in the gut. Strategies to manipulate the microbiome might therefore be used in treatment of IBD. We review microbe-based therapies for IBD and the potential to engineer patients' intestinal microbiota. We discuss how studies of patients with IBD and mouse models have advanced our understanding of the interactions between genetic factors and the gut microbiome, and challenges to development of microbe-based therapies for IBD.},
}

@article {pmid30879880,
year = {2019},
author = {Nunn, KL and Ridenhour, BJ and Chester, EM and Vitzthum, VJ and Fortenberry, JD and Forney, LJ},
title = {Vaginal Glycogen, Not Estradiol, Is Associated With Vaginal Bacterial Community Composition in Black Adolescent Women.},
journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jadohealth.2019.01.010},
pmid = {30879880},
issn = {1879-1972},
abstract = {PURPOSE: The purpose of this study was to characterize the composition of vaginal bacterial communities in a cohort of black adolescent women and to determine how the species composition of these communities correlates with levels of estradiol, glycogen, and stress.

METHODS: Twenty-one black adolescent women were sampled longitudinally. The composition of their vaginal communities was determined by analyzing the sequences of the V1-V3 regions of 16S rRNA genes, and they were grouped based on patterns in species abundances. The relationships between estradiol, glycogen, psychosocial stress, and the composition of these communities were assessed.

RESULTS: Vaginal communities could be distinguished and classified into three groups that differed in the abundances of Lactobacillus. Eighty-one percent of study participants had communities dominated by species of Lactobacillus. Glycogen levels were higher in communities dominated by one or multiple species of Lactobacillus compared with those having low proportions of Lactobacillus. Estradiol and psychosocial stress measurements did not differ among the three groups, whereas estradiol and glycogen exhibited a weak positive relationship that was not statistically significant.

CONCLUSIONS: The findings of this pilot study suggest that glycogen levels are associated with vaginal community composition in young black women; however, estradiol and psychosocial stress are not. In addition, the results suggest there is no simple relationship between levels of estradiol and the production of vaginal glycogen.},
}