@article {pmid31711172,
year = {2019},
author = {Becraft, AR and Sturm, ML and Mendez, RL and Park, SH and Lee, SI and Shay, NF},
title = {Intake of Watermelon or Its Byproducts Alters Glucose Metabolism, the Microbiome, and Hepatic Proinflammatory Metabolites in High-Fat-Fed Male C57BL/6 J Mice.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1093/jn/nxz267},
pmid = {31711172},
issn = {1541-6100},
abstract = {BACKGROUND: Watermelon intake has demonstrated effects on blood pressure regulation along with other health benefits.

OBJECTIVE: We hypothesized that intake of whole watermelon and products made from watermelon rind (WR) and watermelon skin (WS) would remediate metabolic complications in C57BL/6 J male mice fed a diet modeling a Western-style diet.

METHODS: Ten-week-old male C57BL/6 J mice were provided either a low-fat (LF) diet [10% fat (by energy), 8% sucrose (by energy) and no added cholesterol], a high-fat (HF) diet [45% fat (by energy), 20% kcal sucrose (by energy), and 1% (w/w) cholesterol], or an HF diet plus WS, WR, or watermelon flesh (WF) for 10 wk. Dried WF was provided at 8% of total energy (equivalent to 2 servings/d) and watermelon skin and rind were added at 2.25% (w/w, dry weight of additives) of diet. Animals were provided experimental diets ad libitum. Body weights, food intake, and glucose tolerance were determined. Serum insulin, inflammatory markers, microbiome, and the relative hepatic concentrations of 709 biochemicals were measured postmortem.

RESULTS: The final body weight of the LF control group was significantly lower than that of the HF-fed control group (32.8 ± 0.9 g compared with 43.0 ± 1.7 g, P ≤ 0.05). Mice in treatment groups fed HF supplemented with watermelon products had final body weights similar to those of the HF-fed control mice. Serum insulin concentrations were reduced by ∼40% in mice fed an HF diet with WR supplementation compared with mice fed an HF diet alone (P ≤ 0.05). Depending on the individual species or group, microbiome populations changed significantly. Supplementation with WF resulted in a return to the basal hepatic concentrations of monohydroxy fatty acids and eicosanoids observed in LF-fed mice (P ≤ 0.05).

CONCLUSIONS: In obese male mice, supplementation with each of the watermelon products to an HF diet improved fasting blood glucose, circulating serum insulin concentrations, and changes in hepatic metabolite accumulation. At a modest level of supplementation to an HF diet, fiber-rich additives made from WR and WS further improved glucose metabolism and energy efficiency and shifted the microbiome composition.},
}

@article {pmid31710600,
year = {2019},
author = {Wilkins, LGE and Leray, M and O'Dea, A and Yuen, B and Peixoto, R and Pereira, TJ and Bik, HM and Coil, DA and Duffy, JE and Herre, EA and Lessios, H and Lucey, NM and Mejia, LC and Rasher, DB and Sharp, K and Sogin, EM and Thacker, RW and Vega Thurber, R and Wcislo, WT and Wilbanks, EG and Eisen, JA},
title = {Host-associated microbiomes drive structure and function of marine ecosystems.},
journal = {PLoS biology},
volume = {17},
number = {11},
pages = {e3000533},
doi = {10.1371/journal.pbio.3000533},
pmid = {31710600},
issn = {1545-7885},
abstract = {The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth's most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host-microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies.},
}

@article {pmid31710301,
year = {2019},
author = {Bai, J and Jhaney, I and Wells, J},
title = {Developing a Reproducible Microbiome Data Analysis Pipeline Using the Amazon Web Services Cloud for a Cancer Research Group: Proof-of-Concept Study.},
journal = {JMIR medical informatics},
volume = {7},
number = {4},
pages = {e14667},
doi = {10.2196/14667},
pmid = {31710301},
issn = {2291-9694},
abstract = {BACKGROUND: Cloud computing for microbiome data sets can significantly increase working efficiencies and expedite the translation of research findings into clinical practice. The Amazon Web Services (AWS) cloud provides an invaluable option for microbiome data storage, computation, and analysis.

OBJECTIVE: The goals of this study were to develop a microbiome data analysis pipeline by using AWS cloud and to conduct a proof-of-concept test for microbiome data storage, processing, and analysis.

METHODS: A multidisciplinary team was formed to develop and test a reproducible microbiome data analysis pipeline with multiple AWS cloud services that could be used for storage, computation, and data analysis. The microbiome data analysis pipeline developed in AWS was tested by using two data sets: 19 vaginal microbiome samples and 50 gut microbiome samples.

RESULTS: Using AWS features, we developed a microbiome data analysis pipeline that included Amazon Simple Storage Service for microbiome sequence storage, Linux Elastic Compute Cloud (EC2) instances (ie, servers) for data computation and analysis, and security keys to create and manage the use of encryption for the pipeline. Bioinformatics and statistical tools (ie, Quantitative Insights Into Microbial Ecology 2 and RStudio) were installed within the Linux EC2 instances to run microbiome statistical analysis. The microbiome data analysis pipeline was performed through command-line interfaces within the Linux operating system or in the Mac operating system. Using this new pipeline, we were able to successfully process and analyze 50 gut microbiome samples within 4 hours at a very low cost (a c4.4xlarge EC2 instance costs $0.80 per hour). Gut microbiome findings regarding diversity, taxonomy, and abundance analyses were easily shared within our research team.

CONCLUSIONS: Building a microbiome data analysis pipeline with AWS cloud is feasible. This pipeline is highly reliable, computationally powerful, and cost effective. Our AWS-based microbiome analysis pipeline provides an efficient tool to conduct microbiome data analysis.},
}

@article {pmid31710124,
year = {2019},
author = {Furuya, S and Argemi, J and Uehara, T and Katou, Y and Fouts, DE and Schnabl, B and Dubuquoy, L and Belorkar, A and Vadigepalli, R and Kono, H and Bataller, R and Rusyn, I},
title = {A novel mouse model of acute-on-chronic cholestatic alcoholic liver disease: A systems biology comparison with human alcoholic hepatitis.},
journal = {Alcoholism, clinical and experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.14234},
pmid = {31710124},
issn = {1530-0277},
abstract = {BACKGROUND: Alcohol-related liver disease is the main cause of liver-related mortality worldwide. The development of novel targeted therapies for patients with advanced forms (i.e., alcoholic hepatitis, AH) is hampered by the lack of suitable animal models. Here, we developed a novel mouse model of acute-on-chronic alcohol liver injury with cholestasis and fibrosis and performed an extensive molecular comparative analysis with human AH.

METHODS: For the mouse model of acute-on-chronic liver injury, we used 3, 5-diethoxycarbonyl-1,4-dihydrocollidine (DDC, 0.05% w/w) diet for 8 weeks to establish cholestatic liver fibrosis. After one-week washout period, male mice were fed intragastrically for 4 weeks with up to 24 g/kg of ethyl alcohol in a high-fat diet. This animal model was phenotyped using histopathology, clinical chemistry, microbiome and gene expression approaches. Data were compared to the phenotypes of human alcohol-related liver disease, including AH.

RESULTS: Mice with cholestatic liver fibrosis and subsequent alcohol exposure (DDC + EtOH) exhibited exacerbated liver fibrosis with a pericellular pattern, increased neutrophil infiltration and ductular proliferation, all characteristics of human AH. DDC administration had no effect on urine alcohol concentration or liver steatosis. Importantly, DDC and alcohol treated mice showed a transcriptomic signature that resembled that of patients with AH. Finally, we show that mice in the DDC + EtOH group had an increased gut barrier dysfunction, mimicking an important pathophysiological mechanism of human AH.

CONCLUSIONS: We developed a novel mouse model of acute-on chronic cholestatic alcoholic liver injury that has considerable translational potential and can be used to test novel therapeutic modalities for AH.},
}

@article {pmid31709760,
year = {2019},
author = {Collens, A and Kelley, E and Katz, LA},
title = {The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.b.22915},
pmid = {31709760},
issn = {1552-5015},
support = {1541511//Division of Environmental Biology/ ; 1651908//Division of Environmental Biology/ ; R15HG010409/GM/NIGMS NIH HHS/United States ; R15HG010409/GF/NIH HHS/United States ; },
abstract = {John Tyler Bonner's call to re-evaluate evolutionary theory in light of major transitions in life on Earth (e.g., from the first origins of microbial life to the evolution of sex, and the origins of multicellularity) resonate with recent discoveries on epigenetics and the concept of the hologenome. Current studies of genome evolution often mistakenly focus only on the inheritance of DNA between parent and offspring. These are in line with the widely accepted Neo-Darwinian framework that pairs Mendelian genetics with an emphasis on natural selection as explanations for the evolution of biodiversity on Earth. Increasing evidence for widespread symbioses complicates this narrative, as is seen in Scott Gilbert's discussion of the concept of the holobiont in this series: Organisms across the tree of life coexist with substantial influence on one another through endosymbiosis, symbioses, and host-associated microbiomes. The holobiont theory, coupled with observations from molecular studies, also requires us to understand genomes in a new way-by considering the interactions underlain by the genome of a host plus its associated microbes, a conglomerate entity referred to as the hologenome. We argue that the complex patterns of inheritance of these genomes coupled with the influence of symbionts on host gene expression make the concept of the hologenome an epigenetic phenomenon. We further argue that the aspects of the hologenome challenge of the modern evolutionary synthesis, which requires updating to remain consistent with Darwin's intent of providing natural laws that underlie the evolution of life on Earth.},
}

@article {pmid31709683,
year = {2019},
author = {Mayneris-Perxachs, J and Fernández-Real, JM},
title = {How the joint study of the microbiota and metabolites in different body fluids may aid in the identification of novel disease mechanisms.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.15130},
pmid = {31709683},
issn = {1742-4658},
abstract = {Thanks to the emergence and recent advances in high-throughput sequencing technologies, it is becoming more evident every day that changes in the microbiome composition are linked to a myriad of health conditions. Despite this, the mechanisms of host-microbiota signalling remain largely unknown. The microbiome has an extensive metabolic activity that leads to the generation of a large number of compounds that are likely to influence host health. Therefore, the microbiome-host cross-talk is in part mediated by microbial-derived metabolites. Unlike metagenomics, which only provides information about microbial genes and thus the microbiome functional potential, metabolic phenotyping is well suited to capture their actual metabolic activity. Here we provide an overview of these approaches and propose an integration of metagenomics, as a microbiome compositional readout, with faecal and plasma/urine metabolomics, as a functional readout, to unravel novel mechanisms linking the microbiome to host health and disease.},
}

@article {pmid31709681,
year = {2019},
author = {Damjanovic, K and Menéndez, P and Blackall, LL and van Oppen, MJH},
title = {Mixed mode bacterial transmission in the common brooding coral Pocillopora acuta.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14856},
pmid = {31709681},
issn = {1462-2920},
abstract = {Reef-building corals form associations with a huge diversity of microorganisms, which are essential for the survival and well-being of their host. While the acquisition patterns of Symbiodiniaceae microalgal endosymbionts are strongly linked to the coral's reproductive strategy, few studies have investigated the transmission mode of bacteria, especially in brooding species. Here, we relied on 16S rRNA gene and ITS2 marker metabarcoding in conjunction with fluorescence in situ hybridisation microscopy to describe the onset of microbial associations in the common brooding coral Pocillopora acuta. We analysed the bacterial and Symbiodiniaceae community composition in five adult colonies, their larvae, and 4-day old recruits. Larvae and recruits inherited Symbiodiniaceae, as well as a small number of bacterial strains, from their parents. Rhodobacteraceae and Endozoicomonas were among the most abundant taxa that were likely maternally transmitted to the offspring. The presence of bacterial aggregates in newly released larvae was observed with confocal microscopy, confirming the occurrence of vertical transmission of bacteria in P. acuta. We concluded that host factors as well as the environmental bacterial pool influenced the microbiome of P. acuta. This article is protected by copyright. All rights reserved.},
}

@article {pmid31709649,
year = {2019},
author = {Lee, SH and Lee, SB and Heo, JH and Yoon, HS and Byun, JW and Choi, GS and Shin, J},
title = {Sebaceous Glands participate in the inflammation of Rosacea.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.16055},
pmid = {31709649},
issn = {1468-3083},
abstract = {Rosacea is a chronic inflammatory dermatosis that can present with a variety of cutaneous manifestations.1 Recently, mast cells are known to be importantly related to the pathogenesis of rosacea.2 The disease characteristically presents a centrofacial distribution1,3 , an area rich in sebaceous glands.},
}

@article {pmid31709269,
year = {2019},
author = {Badman, J and Daly, K and Kelly, J and Moran, AW and Cameron, J and Watson, I and Newbold, J and Shirazi-Beechey, SP},
title = {The Effect of Milk Replacer Composition on the Intestinal Microbiota of Pre-ruminant Dairy Calves.},
journal = {Frontiers in veterinary science},
volume = {6},
number = {},
pages = {371},
doi = {10.3389/fvets.2019.00371},
pmid = {31709269},
issn = {2297-1769},
abstract = {The impact of dietary composition and prebiotics, in promoting the growth of beneficial groups of gut bacteria, is increasingly apparent. Using Illumina MiSeq sequencing of bacterial 16S rRNA genes, this study has aimed to characterize and compare the establishment of the gastrointestinal microbiota in dairy calves given two different commercial milk replacer (MR) diets. MR1 and MR2 contain different levels of macronutrients such as protein and fat. Moreover, differences in manufacturing methods infer that MR2 may contain a greater proportion of conjugated milk oligosaccharides (OS), while MR1 contains more free milk OS. A total of 10 dairy calves, five in each group, were assigned to one of the two MR diets. Freshly voided fecal samples were taken at 0, 7, 14, 28, and 49 days after first consumption of milk replacer. The relative abundance of two individual Bifidobacterium species, which are known to utilize milk OS, and Faecalibacterium prausnitzii were significantly higher at day 7 in the fecal microbiome of calves fed MR2 compared with MR1. These commensal bacteria are widely regarded as probiotic organisms that confer a health benefit on the host. Our findings suggest that the composition of bovine milk replacers can have significant effects on the establishment of the gut microbiota in pre-weaned (neonatal) dairy calves. Better understanding of milk composition-microbiota-host interactions in early life will inform targeted interventions to increase growth and reduce mortality in young animals.},
}

@article {pmid31709198,
year = {2019},
author = {Sun, Y and Chen, Q and Lin, P and Xu, R and He, D and Ji, W and Bian, Y and Shen, Y and Li, Q and Liu, C and Dong, K and Tang, YW and Pei, Z and Yang, L and Lu, H and Guo, X and Xiao, L},
title = {Characteristics of Gut Microbiota in Patients With Rheumatoid Arthritis in Shanghai, China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {369},
doi = {10.3389/fcimb.2019.00369},
pmid = {31709198},
issn = {2235-2988},
abstract = {Little is known regarding differences in the gut microbiomes of rheumatoid arthritis (RA) patients and healthy cohorts in China. This study aimed to identify differences in the fecal microbiomes of 66 Chinese patients with RA and 60 healthy Chinese controls. The V3-V4 variable regions of bacterial 16S rRNA genes were sequenced with the Illumina system to define the bacterial composition. The alpha-diversity index of the microbiome of the RA patients was significantly lower than that of the control group. The bacterial genera Bacteroides (p = 0.02202) and Escherichia-Shigella (p = 0.03137) were more abundant in RA patients. In contrast, Lactobacillus (p = 0.000014), Alloprevotella (p = 0.0000008615), Enterobacter (p = 0.000005759), and Odoribacter (p = 0.0000166) were less abundant in the RA group than in the control group. Spearman correlation analysis of blood physiological measures of RA showed that bacterial genera such as Dorea and Ruminococcus were positively correlated with RF-IgA and anti-CCP antibodies. Furthermore, Alloprevotella and Parabacteroides were positively correlated with the erythrocyte sedimentation rate, and Prevotella-2 and Alloprevotella were positively correlated with C-reactive protein, both biomarkers of inflammation. These findings suggest that the gut microbiota may contribute to RA development via interactions with the host immune system.},
}

@article {pmid31709196,
year = {2019},
author = {Metz, P and Tjan, MJH and Wu, S and Pervaiz, M and Hermans, S and Shettigar, A and Sears, CL and Ritschel, T and Dutilh, BE and Boleij, A},
title = {Drug Discovery and Repurposing Inhibits a Major Gut Pathogen-Derived Oncogenic Toxin.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {364},
doi = {10.3389/fcimb.2019.00364},
pmid = {31709196},
issn = {2235-2988},
abstract = {Objective: The human intestinal microbiome plays an important role in inflammatory bowel disease (IBD) and colorectal cancer (CRC) development. One of the first discovered bacterial mediators involves Bacteroides fragilis toxin (BFT, also named as fragilysin), a metalloprotease encoded by enterotoxigenic Bacteroides fragilis (ETBF) that causes barrier disruption and inflammation of the colon, leads to tumorigenesis in susceptible mice, and is enriched in the mucosa of IBD and CRC patients. Thus, targeted inhibition of BFT may benefit ETBF carrying patients. Design: By applying two complementary in silico drug design techniques, drug repositioning and molecular docking, we predicted potential BFT inhibitory compounds. Top candidates were tested in vitro on the CRC epithelial cell line HT29/c1 for their potential to inhibit key aspects of BFT activity, being epithelial morphology changes, E-cadherin cleavage (a marker for barrier function) and increased IL-8 secretion. Results: The primary bile acid and existing drug chenodeoxycholic acid (CDCA), currently used for treating gallstones, cerebrotendinous xanthomatosis, and constipation, was found to significantly inhibit all evaluated cell responses to BFT exposure. The inhibition of BFT resulted from a direct interaction between CDCA and BFT, as confirmed by an increase in the melting temperature of the BFT protein in the presence of CDCA. Conclusion: Together, our results show the potential of in silico drug discovery to combat harmful human and microbiome-derived proteins and more specifically suggests a potential for retargeting CDCA to inhibit the pro-oncogenic toxin BFT.},
}

@article {pmid31709051,
year = {2019},
author = {Nakagawa, S and Inoue, S and Kryukov, K and Yamagishi, J and Ohno, A and Hayashida, K and Nakazwe, R and Kalumbi, M and Mwenya, D and Asami, N and Sugimoto, C and Mutengo, MM and Imanishi, T},
title = {Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia.},
journal = {Clinical & translational immunology},
volume = {8},
number = {11},
pages = {e01087},
doi = {10.1002/cti2.1087},
pmid = {31709051},
issn = {2050-0068},
abstract = {Objectives: We have developed a portable system for the rapid determination of bacterial composition for the diagnosis of infectious diseases. Our system comprises of a nanopore technology-based sequencer, MinION, and two laptop computers. To examine the accuracy and time efficiency of our system, we provided a proof-of-concept for the detection of the causative bacteria of 11 meningitis patients in Zambia.

Methods: We extracted DNA from cerebrospinal fluid samples of each patient and amplified the 16S rRNA gene regions. The sequencing library was prepared, and the sequenced reads were simultaneously processed for bacterial composition determination using the minimap2 software and the representative prokaryote genomes.

Results: The sequencing results of four of the six culture-positive samples were consistent with those of conventional culture-based methods. The dominant bacterial species in each of these samples were identified from the sequencing data within only 3 min. Although the major bacterial species were also detected from the other two culture-positive samples and five culture-negative samples, their presence could not be confirmed. Moreover, as a whole, although the number of sequencing reads obtained within a short sequencing run was small, there was no change in the major bacterial species over time with prolonged sequencing. In addition, the processing time strongly correlated with the number of sequencing reads used for the analysis.

Conclusion: Our results suggest that time-effective analysis could be achieved by determining the number of sequencing reads required for the rapid diagnosis of infectious bacterial species depending on the complexity of bacterial species in a sample.},
}

@article {pmid31709044,
year = {2019},
author = {Quigley, EMM},
title = {Microbiome Modulation in Liver Disease.},
journal = {Clinical liver disease},
volume = {14},
number = {4},
pages = {149-151},
doi = {10.1002/cld.862},
pmid = {31709044},
issn = {2046-2484},
}

@article {pmid31708944,
year = {2019},
author = {Lucaciu, R and Pelikan, C and Gerner, SM and Zioutis, C and Köstlbacher, S and Marx, H and Herbold, CW and Schmidt, H and Rattei, T},
title = {A Bioinformatics Guide to Plant Microbiome Analysis.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {1313},
doi = {10.3389/fpls.2019.01313},
pmid = {31708944},
issn = {1664-462X},
abstract = {Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.},
}

@article {pmid31708891,
year = {2019},
author = {Zhao, F and Song, S and Ma, Y and Xu, X and Zhou, G and Li, C},
title = {A Short-Term Feeding of Dietary Casein Increases Abundance of Lactococcus lactis and Upregulates Gene Expression Involving Obesity Prevention in Cecum of Young Rats Compared With Dietary Chicken Protein.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2411},
doi = {10.3389/fmicb.2019.02411},
pmid = {31708891},
issn = {1664-302X},
abstract = {Casein and chicken are assessed to contain high quality proteins, which are essential for human health. Studies have shown that ingestion of the two dietary proteins resulted in distinct effects on physiology, liver transcriptome and gut microbiota. However, its underlying mechanism is not fully understood, in particular for a crosstalk between gut microbiota and host under a specific diet intervention. We fed young rats with a casein or a chicken protein-based diet (CHPD) for 7 days, and characterized cecal microbiota composition and cecal gene expression. We found that a short-term intervention with a casein-based diet (CAD) induced a higher relative abundance of beneficial bacterium Lactococcus lactis as well as Bifidobacterium pseudolongum, which upregulated galactose metabolism of the microbiome compared with a CHPD. The CAD also upregulated gene expression involved in obesity associated pathways (e.g., Adipoq and Irs1) in cecal tissue of rats. These genes and the bacterial taxon were reported to play an important role in protecting development of obesity. Furthermore, the differentially represented bacterial taxon L. lactis was positively associated with these differentially expressed genes in the gut tissue. Our results provide a new insight into the crosstalk between gut microbiota and host in response to dietary proteins, indicating a potential mechanism of obesity prevention function by casein.},
}

@article {pmid31708890,
year = {2019},
author = {Bosman, ES and Albert, AY and Lui, H and Dutz, JP and Vallance, BA},
title = {Skin Exposure to Narrow Band Ultraviolet (UVB) Light Modulates the Human Intestinal Microbiome.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2410},
doi = {10.3389/fmicb.2019.02410},
pmid = {31708890},
issn = {1664-302X},
abstract = {The recent worldwide rise in idiopathic immune and inflammatory diseases such as multiple sclerosis (MS) and inflammatory bowel diseases (IBD) has been linked to Western society-based changes in lifestyle and environment. These include decreased exposure to sunlight/UVB light and subsequent impairment in the production of vitamin D, as well as dysbiotic changes in the makeup of the gut microbiome. Despite their association, it is unclear if there are any direct links between UVB light and the gut microbiome. In this study we investigated whether exposing the skin to Narrow Band Ultraviolet B (NB-UVB) light to increase serum vitamin D levels would also modulate the makeup of the human intestinal microbiota. The effects of NB-UVB light were studied in a clinical pilot study using a healthy human female cohort (n = 21). Participants were divided into those that took vitamin D supplements throughout the winter prior to the start of the study (VDS+) and those who did not (VDS-). After three NB-UVB light exposures within the same week, the serum 25(OH)D levels of participants increased on average 7.3 nmol/L. The serum response was negatively correlated to the starting 25-hydroxy vitamin D [25(OH)D] serum concentration. Fecal microbiota composition analysis using 16S rRNA sequencing showed that exposure to NB-UVB significantly increased alpha and beta diversity in the VDS- group whereas there were no changes in the VDS+ group. Bacteria from several families were enriched in the VDS- group after the UVB exposures according to a Linear Discriminant Analysis (LDA) prediction, including Lachnospiracheae, Rikenellaceae, Desulfobacteraceae, Clostridiales vadinBB60 group, Clostridia Family XIII, Coriobacteriaceae, Marinifilaceae, and Ruminococcus. The serum 25(OH)D concentrations showed a correlation with the relative abundance of the Lachnospiraceae, specifically members of the Lachnopsira and Fusicatenibacter genera. This is the first study to show that humans with low 25(OH)D serum levels display overt changes in their intestinal microbiome in response to NB-UVB skin exposure and increases in 25(OH)D levels, suggesting the existence of a novel skin-gut axis that could be used to promote intestinal homeostasis and health. Clinical Trial Registration: clinicaltrials.gov, NCT03962673. Registered 23 May 2019 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT03962673?term=NCT03962673&rank=1.},
}

@article {pmid31708889,
year = {2019},
author = {Tang, KY and Wang, ZW and Wan, QH and Fang, SG},
title = {Metagenomics Reveals Seasonal Functional Adaptation of the Gut Microbiome to Host Feeding and Fasting in the Chinese Alligator.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2409},
doi = {10.3389/fmicb.2019.02409},
pmid = {31708889},
issn = {1664-302X},
abstract = {As a natural hibernator, the Chinese alligator (Alligator sinensis) is an ideal and intriguing model to investigate changes in microbial community structure and function caused by hibernation. In this study, we used 16S rRNA profiling and metagenomic analysis to compare the composition, diversity, and functional capacity in the gut microbiome of hibernating vs. active Chinese alligators. Our results show that gut microbial communities undergo seasonal restructuring in response to seasonal cycles of feeding and fasting in the Chinese alligator, but this animal harbors a core gut microbial community primarily dominated by Proteobacteria, Fusobacteria, Bacteroidetes, and Firmicutes across the gut regions. During hibernation, there is an increase in the abundance of bacterial taxa (e.g., the genus Bacteroides) that can degrade host mucin glycans, which allows adaptation to winter fasting. This is accompanied by the enrichment of mucin oligosaccharide-degrading enzyme and carbohydrate-active enzyme families. In contrast, during the active phase (feeding), active Chinese alligators exhibit a carnivore gut microbiome dominated by Fusobacteria, and there is an increase in the relative abundance of bacteria (e.g., Cetobacterium somerae) with known proteolytic and amino acids-fermentating functions that improve host protein-rich food digestion efficiency. In addition, seasonal variations in the expression of β-defensins play a protective role in intestinal immunity. These findings provide insights into the functional adaptations of host-gut microbe symbioses to seasonal dietary shifts to maintain gut homeostasis and health, especially in extreme physiological states.},
}

@article {pmid31708879,
year = {2019},
author = {Schürmann, M and Oppel, F and Gottschalk, M and Büker, B and Jantos, CA and Knabbe, C and Hütten, A and Kaltschmidt, B and Kaltschmidt, C and Sudhoff, H},
title = {The Therapeutic Effect of 1,8-Cineol on Pathogenic Bacteria Species Present in Chronic Rhinosinusitis.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2325},
doi = {10.3389/fmicb.2019.02325},
pmid = {31708879},
issn = {1664-302X},
abstract = {Chronic rhinosinusitis (CRS) is marked by an inflamed mucosa of sinuses and is accompanied by a significantly reduced quality of live. Since no guidelines for the treatment of CRS are available, long lasting clinical histories with health care costs adding up to dozens of billion $ annually are caused by CRS. The progression of CRS is often induced by bacterial infections and/or a shift in microbiome as well as biofilm formation. The exact microbiome alterations are still unclear and the impenetrable biofilm renders the treatment with common antibiotics ineffective. This study focuses on characterizing the microbiome changes in CRS and investigating the inhibition of biofilm growth by 1,8-Cineol, a small, non-polar and hence biofilm penetrating molecule with known antimicrobial potential. We performed MALDI-TOF MS based characterization of the microbiomes of healthy individuals and CRS patients (n = 50). The microbiome in our test group was shifted to pathogens (Staphylococcus aureus, Escherichia coli, and Moraxella catarrhalis). In contrast to published studies, solely based on cell culture techniques, we could not verify the abundance of Pseudomonas aeruginosa in CRS. The inhibition of bacterial proliferation and biofilm growth by 1,8-Cineol was measured for these three pathogens. Interestingly, S. aureus, the most prominent germ in CRS, showed a biofilm inhibition not simply correlated to its inhibition of proliferation. RT-qPCR confirmed that this was due to the downregulations of major key players in biofilm generation (agrA, SarA and σB) by 1,8-Cineol. Furthermore we verified this high biofilm inhibition potential in a model host system consisting out of S. aureus biofilm grown on mature respiratory epithelium. A second host model, comprising organotypic slices, was utilized to investigate the reaction of the innate immune system present in the nasal mucosa upon biofilm formation and treatment with 1,8-Cineol. Interestingly Staphylococcus epidermidis, the cause of very common catheter infections, possesses a biofilm generation pathway very similar to S. aureus and might be treatable in a similar fashion. The two presented in vitro model systems might be transferred to combinations of every biofilm forming bacterial with most kind of epithelium and mucosa.},
}

@article {pmid31708226,
year = {2019},
author = {Wang, L and Wang, LA and Zhan, X and Huang, Y and Wang, J and Wang, X},
title = {Response mechanism of microbial community to the environmental stress caused by the different mercury concentration in soils.},
journal = {Ecotoxicology and environmental safety},
volume = {},
number = {},
pages = {109906},
doi = {10.1016/j.ecoenv.2019.109906},
pmid = {31708226},
issn = {1090-2414},
abstract = {Despite the toxicity of mercury for mammal has been widely studied in recent years, little is known on its impact on the soil microbiome. In this paper, the effects of mercury in soils microbial communities along a gradient of contamination from no to high concentration was assessed by the richness and diversity of microbial community using high throughput sequencing method. The richness of microbial community decreased gradually with the increase of culture time, while the low and medium concentration of mercury had little effect on the evenness of soil microbial community. Proteobacteria tolerated the mercury contamination, while Acidobacteria, Planctomycetes and Chloroflexi were sensitive to mercury pollution in phylum level. Omnitrophica and Ignavibacteriae microorganisms were very sensitive to mercury contamination and dead quickly when contaminated with mercury. Mercury contamination selected two mercury tolerance genuses which were Massilia and Burkholderia in genus level and at least 22 microorganisms such as Alkanindiges, Geothrix, Polycyclovorans and Sporichthya in genus which mainly from the Acidobacteria, Proteobacteria, Bacteroides, Chloroflexi and Omnitrophica phylum were sensitive to mercury. The bacteria tolerant to mercury in soil were Massilia and Burkholderia from Betaproteobacteria and Lysobacter, Luteimonas from Gammaproteobacteria, separately, they were Gram-negative bacteria with thin cell walls and complex ingredients that responded quickly to pollution stress.},
}

@article {pmid31708009,
year = {2019},
author = {Huang, T and Gao, W and Lv, J and Yu, C and Wu, T and Wang, S and Liao, C and Meng, L and Wang, D and Wang, Z and Pang, Z and Yu, M and Wang, H and Wu, X and Dong, Z and Wu, F and Jiang, G and Wang, X and Liu, Y and Deng, J and Lu, L and Cao, W and Li, L},
title = {The Chinese National Twin Registry: A Unique Data Source for Systems Epidemiology of Complex Disease.},
journal = {Twin research and human genetics : the official journal of the International Society for Twin Studies},
volume = {},
number = {},
pages = {1-4},
doi = {10.1017/thg.2019.85},
pmid = {31708009},
issn = {1832-4274},
abstract = {The Chinese National Twin Registry (CNTR), initiated in 2001, has now become the largest twin registry in Asia. From 2015 to 2018, the CNTR continued to receive Chinese government funding and had recruited 61,566 twin-pairs by 2019 to study twins discordant for specific exposures such as environmental factors, and twins discordant for disease outcomes or measures of morbidity. Omic data, including genetics, genomics, metabolomics, and proteomics, and gut microbiome will be tested. The integration of omics and digital technologies in public health will advance our understanding of precision public health. This review introduces the updates of the CNTR, including study design, sample size, biobank, zygosity assessment, advances in research and future systems epidemiologic research.},
}

@article {pmid31707624,
year = {2019},
author = {Schoeler, M and Caesar, R},
title = {Dietary lipids, gut microbiota and lipid metabolism.},
journal = {Reviews in endocrine & metabolic disorders},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11154-019-09512-0},
pmid = {31707624},
issn = {1573-2606},
support = {(2017-02001//Svenska Forskningsrådet Formas/ ; },
abstract = {The gut microbiota is a central regulator of host metabolism. The composition and function of the gut microbiota is dynamic and affected by diet properties such as the amount and composition of lipids. Hence, dietary lipids may influence host physiology through interaction with the gut microbiota. Lipids affect the gut microbiota both as substrates for bacterial metabolic processes, and by inhibiting bacterial growth by toxic influence. The gut microbiota has been shown to affect lipid metabolism and lipid levels in blood and tissues, both in mice and humans. Furthermore, diseases linked to dyslipidemia, such as non-alcoholic liver disease and atherosclerosis, are associated with changes in gut microbiota profile. The influence of the gut microbiota on host lipid metabolism may be mediated through metabolites produced by the gut microbiota such as short-chain fatty acids, secondary bile acids and trimethylamine and by pro-inflammatory bacterially derived factors such as lipopolysaccharide. Here we will review the association between gut microbiota, dietary lipids and lipid metabolism.},
}

@article {pmid31707507,
year = {2019},
author = {Le Bastard, Q and Chapelet, G and Javaudin, F and Lepelletier, D and Batard, E and Montassier, E},
title = {The effects of inulin on gut microbial composition: a systematic review of evidence from human studies.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10096-019-03721-w},
pmid = {31707507},
issn = {1435-4373},
abstract = {BACKGROUND: Inulin, consisting of repetitive fructosyl units linked by β(2,1) bonds, is a readily fermentable fiber by intestinal bacteria that generates large quantities of short-chain fatty acids (SCFA). In individuals with constipation, it was reported that inulin ingestion was associated with a significant increase in stool frequency, suggesting a potential impact of inulin on human gut microbiota composition. Progress in high-throughput technologies allow assessment of human-associated microbiomes in terms of diversity and taxonomic or functional composition, and can identify changes in response to a specific supplementation. Hence, to understand the effects of inulin on the human gut microbiome is pivotal to gain insight into their mechanisms of action.

METHODS: Here, we conducted a systematic review of human studies in adult individuals showing the effects of inulin on the gut microbiome. We searched in MEDLINE, EMBASE, Web of Science, and Scopus databases for articles in English published in peer-reviewed journals and indexed up until March 2019. We used multiple search terms capturing gut microbiome, gut microflora, intestinal microbiota, intestinal flora, gut microbiota, gut flora, microbial gut community, gut microbial composition, and inulin.

RESULTS: Overall, nine original articles reported the effects of inulin on microbiome composition in adult humans, most of them being randomized, double-blind, placebo-controlled trials (n = 7). Studies varied significantly in design (3 studies associated inulin and oligofructose), supplementation protocols (from 5 to 20 gr per day of inulin consumed) and in microbiome assessment methods (16S sequencing, n = 7). The most consistent change was an increase in Bifidobacterium. Other concordant results included an increase in relative abundance of Anaerostipes, Faecalibacterium, and Lactobacillus, and a decrease in relative abundance of Bacteroides after inulin supplementation.

CONCLUSIONS: Our systematic review assessed the evidence for the effects of inulin supplementation on the human gut microbiome. However, these in vivo studies did not confirm in vitro experiments as the taxonomic alterations were not associated with increase in short-chain fatty acids levels.},
}

@article {pmid31707496,
year = {2019},
author = {Shukla, A and Sobel, JD},
title = {Vulvovaginitis Caused by Candida Species Following Antibiotic Exposure.},
journal = {Current infectious disease reports},
volume = {21},
number = {11},
pages = {44},
doi = {10.1007/s11908-019-0700-y},
pmid = {31707496},
issn = {1523-3847},
abstract = {PURPOSE OF REVIEW: Goal was to review epidemiology, pathophysiology, and prevention of post-antibiotic Candida vulvovaginitis (VVC).

RECENT FINDINGS: Antibacterial therapy, whether systemic or locally applied to the vagina, represents the single most frequent and predictable cause or triggering mechanism of symptomatic vulvovaginal candidiasis (VVC). Such initiating mechanisms may precipitate sporadic or recurrent episodes of VVC. In spite of this widely recognized association, the exact mechanism whereby antibiotics of all classes cause acute exacerbation of symptomatic vaginal disease remains largely unstudied and therefore largely unknown. Pathophysiology is hypothesized to be reduction or alteration of vaginal microbiome restraints of yeast colonization, proliferation, and expression of virulence characteristics. The predictable link between antibiotic use and post-antibiotic VVC affords practitioners an opportunity for timely intervention using selective, convenient antimycotics usually drugs but possibly probiotic measures. Indications and limitation of these steps are discussed.},
}

@article {pmid31707334,
year = {2019},
author = {Alexandrov, PN and Hill, JM and Zhao, Y and Bond, T and Taylor, CM and Percy, ME and Li, W and Lukiw, WJ},
title = {Aluminum-induced generation of lipopolysaccharide (LPS) from the human gastrointestinal (GI)-tract microbiome-resident Bacteroides fragilis.},
journal = {Journal of inorganic biochemistry},
volume = {203},
number = {},
pages = {110886},
doi = {10.1016/j.jinorgbio.2019.110886},
pmid = {31707334},
issn = {1873-3344},
abstract = {Gram-negative bacteria of the human gastrointestinal (GI) tract microbiome: (i) are capable of generating a broad-spectrum of highly neurotoxic, pro-inflammatory and potentially pathogenic molecules; and (ii) these include a highly immunogenic class of amphipathic surface glycolipids known as lipopolysaccharide (LPS). Bacteroides fragilis (B. fragilis), a commensal, Gram negative, non-motile, non-spore forming obligatory anaerobic bacillus, and one of the most abundant bacteria found in the human GI tract, produces a particularly pro-inflammatory and neurotoxic LPS (BF-LPS). BF-LPS: (i) is known to be secreted from the B. fragilis outer membrane into the external-medium; (ii) can damage biophysiological barriers via cleavage of zonula adherens cell-cell adhesion proteins, thereby disrupting both the GI-tract barrier and the blood-brain barrier (BBB); (iii) is able to transit GI-tract barriers into the systemic circulation and cross the BBB into the human CNS; and (iv) accumulates within CNS neurons in neurodegenerative disorders such as Alzheimer's disease (AD). This short communication provides evidence that the incubation of B. fragilis with aluminum sulfate [Al2(SO4)3] is a potent inducer of BF-LPS. The results suggest for the first time that the pro-inflammatory properties of aluminum may not only be propagated by aluminum itself, but by a stimulation in the production of microbiome-derived BF-LPS and other pro-inflammatory pathogenic microbial products normally secreted from human GI-tract-resident microorganisms.},
}

@article {pmid31707234,
year = {2019},
author = {Marx, W and Hockey, M and McGuinness, AJ and Lane, M and Christodoulou, J and van der Mei, I and Berk, M and Dean, OM and Taylor, B and Broadley, S and Lechner-Scott, J and Jacka, FN and Lucas, RM and Ponsonby, AL and , },
title = {The effect of emerging nutraceutical interventions for clinical and biological outcomes in multiple sclerosis: A systematic review.},
journal = {Multiple sclerosis and related disorders},
volume = {37},
number = {},
pages = {101486},
doi = {10.1016/j.msard.2019.101486},
pmid = {31707234},
issn = {2211-0356},
abstract = {BACKGROUND: Due to the considerable burden of multiple sclerosis (MS)-related symptoms and the need to identify effective interventions to prevent disease progression, various nutraceutical interventions have been trialed as adjunctive treatments. The aim of this review was to investigate the efficacy and safety of nutraceutical interventions for clinical and biological outcomes in people with MS.

METHODS: In accordance with PRISMA reporting guidelines, a systematic literature search was conducted using three electronic literature databases. Risk of bias was assessed using the Jadad scale.

RESULTS: Thirty-seven randomized controlled trials, investigating fourteen nutraceuticals, were included in the review. Trials that investigated alpha lipoic acid (n = 4/6), ginkgo biloba (n = 3/5), vitamin A (n = 2/2), biotin (n = 1/2), carnitine (n = 1/2), green tea (n = 1/2), coenzyme Q10 (n = 1/1), probiotics (n = 1/1), curcumin (n = 1/1), Andrographis paniculata (n = 1/1), ginseng (n = 1/1), and lemon verbena (n = 1/1) were reported to improve biological (e.g. MRI brain volume change, antioxidant capacity) and/or clinical (e.g. fatigue, depression, Expanded Disability Status Scale) outcomes in multiple sclerosis compared to control. However, most trials were relatively small (average study sample size across included studies, n = 55) and there were few replicate studies per nutraceutical to validate the reported results. Furthermore, some nutraceuticals (e.g. green tea and inosine) should be used with caution due to reported adverse events. Risk of bias across most studies was low, with 31 studies receiving a score between 4 and 5 (out of 5) on the Jadad Scale.

CONCLUSION: The existing literature provides preliminary support for the use of a number of nutraceutical interventions in MS. However, sufficiently powered long-term trials are required to expand the currently limited literature and to investigate unexplored nutraceuticals that may target relevant pathways involved in MS such as the gut microbiome and mitochondrial dysfunction. Prospero ID: CRD42018111736.},
}

@article {pmid31707219,
year = {2019},
author = {Stubbendieck, RM and Li, H and Currie, CR},
title = {Convergent evolution of signal-structure interfaces for maintaining symbioses.},
journal = {Current opinion in microbiology},
volume = {50},
number = {},
pages = {71-78},
doi = {10.1016/j.mib.2019.10.001},
pmid = {31707219},
issn = {1879-0364},
abstract = {Symbiotic microbes are essential to the ecological success and evolutionary diversification of multicellular organisms. The establishment and stability of bipartite symbioses are shaped by mechanisms ensuring partner fidelity between host and symbiont. In this minireview, we demonstrate how the interface of chemical signals and host structures influences fidelity between legume root nodules and rhizobia, Hawaiian bobtail squid light organs and Allivibrio fischeri, and fungus-growing ant crypts and Pseudonocardia. Subsequently, we illustrate the morphological diversity and widespread phylogenetic distribution of specialized structures used by hosts to house microbial symbionts, indicating the importance of signal-structure interfaces across the history of multicellular life. These observations, and the insights garnered from well-studied bipartite associations, demonstrate the need to concentrate on the signal-structure interface in complex and multipartite systems, including the human microbiome.},
}

@article {pmid31707206,
year = {2019},
author = {Leveau, JH},
title = {A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome.},
journal = {Current opinion in microbiology},
volume = {49},
number = {},
pages = {41-49},
doi = {10.1016/j.mib.2019.10.002},
pmid = {31707206},
issn = {1879-0364},
abstract = {The plant leaf surface, or phyllosphere, represents a unique and challenging microbial biome with a diverse and dynamic community of commensal, parasitic, and mutualistic agents of microscopic proportions. This mini-review offers a digest of recently published research dedicated to the study of phyllosphere microbiota, framed in the context of processes and outcomes of microbial community assembly, structure, and (inter)activity in the phyllosphere, with particular focus on the contributions of environment, plant, and microbe, and on the potential benefits of interrogating those contributions at finer resolutions.},
}

@article {pmid31706747,
year = {2019},
author = {Fan, Y and Qin, Y and Chen, M and Li, X and Wang, R and Huang, Z and Xu, Q and Yu, M and Zhang, Y and Han, X and Du, G and Xia, Y and Wang, X and Lu, C},
title = {Prenatal low-dose DEHP exposure induces metabolic adaptation and obesity: Role of hepatic thiamine metabolism.},
journal = {Journal of hazardous materials},
volume = {},
number = {},
pages = {121534},
doi = {10.1016/j.jhazmat.2019.121534},
pmid = {31706747},
issn = {1873-3336},
abstract = {Di-(2-ethylhexyl)-phthalate (DEHP) is a ubiquitous environmental pollutant and is widely used in industrial plastics. However, the long-term health implications of prenatal exposure to DEHP remains unclear. We set out to determine whether prenatal DEHP exposure can induce metabolic syndrome in offspring and investigate the underlying mechanisms. A mouse model of prenatal DEHP exposure (0.2, 2, and 20 mg/kg/day) was established to evaluate the long-term metabolic disturbance in offspring. The mice were profiled for the hepatic metabolome, transcriptome and gut microbiota to determine the underlying mechanisms. Thiamine supplementation (50 mg/kg/day) was administered to offspring to investigate the role of thiamine in ameliorating metabolic syndrome. Prenatal exposure to low-dose DEHP (0.2 mg/kg/day) resulted in metabolic syndrome, including abnormal adipogenesis, energy expenditure and glucose metabolism, along with dysbiosis of the gut microbiome, in male offspring. Notably, hepatic thiamine metabolism was disrupted in these offspring due to the dysregulation of thiamine transport enzymes, which caused abnormal glucose metabolism. Prenatal low-dose DEHP exposure caused life-long metabolic consequences in a sex-dependent manner, and these consequences were be attenuated by thiamine supplementation in offspring. Our findings suggest low-dose DEHP exposure during early life stages is a potential risk factor for later obesity and metabolic syndrome.},
}

@article {pmid31706024,
year = {2019},
author = {Gui, Q and Hoffman, PS and Lewis, JP},
title = {Amixicile targets anaerobic bacteria within the oral microbiome.},
journal = {Journal of oral biosciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.job.2019.10.004},
pmid = {31706024},
issn = {1880-3865},
abstract = {OBJECTIVES: Anaerobic bacteria are the major causative agents of periodontal disease. However, so far, targeted therapy aimed at reducing those pathogens has not been widely implemented. We have previously reported on a novel antimicrobial, amixicile, that targets anaerobic bacteria through inhibition of the function of the major anaerobic metabolic enzyme pyruvate ferredoxin oxidoreductase (PFOR), while not affecting aerotolerant organisms. It effectively inhibited the growth of oral anaerobes both in monocultures as well as in mixed in vitro mixed cultured however, amixicile's activity in in vivo-like conditions remained to be established.

METHODS: Here, we expand our study using an ex vivo oral microbiome combined with metagenomic sequencing to determine the effect of amixicile treatment on the composition of the microbiome and compare it to that of metronidazole.

RESULTS: Our results show that in the complex microbiomes, anaerobic bacteria are selectively inhibited, while the growth of aerotolerant ones, such as Streptococcus, Klebsiella, Neisseria, and Rothia is unaffected. Veillonella was the most abundant anaerobic genus in our ex vivo microbiome, and we observed complete inhibition of its growth. In addition, growth of other anaerobes, Fusobacterium and Prevotella, was significantly inhibited. Lactobacillus was inhibited only at high concentrations of amixicile. It is noteworthy that a change in abundance of bacteriophages, such as Siphoviridae and Myoviridae, associated with the oral microbiome was observed.

CONCLUSIONS: Collectively, our data expand on the so far reported inhibitory spectrum of amixicile and demonstrates that it inhibits anaerobic bacteria, including both clinical isolates and laboratory strains.},
}

@article {pmid31705881,
year = {2019},
author = {Scaglione, GL and Fania, L and De Paolis, E and De Bonis, M and Mazzanti, C and Di Zenzo, G and Lechiancole, S and Messinese, S and Capoluongo, E},
title = {Evaluation of cutaneous, oral and intestinal microbiota in patients affected by pemphigus and bullous pemphigoid: A pilot study.},
journal = {Experimental and molecular pathology},
volume = {},
number = {},
pages = {104331},
doi = {10.1016/j.yexmp.2019.104331},
pmid = {31705881},
issn = {1096-0945},
abstract = {BACKGROUND: Significant alterations of the cutaneous microbiota (CM) have been recently demonstrated in bullous pemphigoid (BP). Microbiome data of both oral cavity (OM) and gut (GM) from patients affected by bullous disease are not available yet and, further consistent studies focused on the role of such microbial populations are still missing.

OBJECTIVE: Objective: In this pilot study we characterized and compared GM, OM and CM of patients affected by pemphigus vulgaris (PV) and BP to investigate a distinctive microbiome composition in this two rare dermatological disorders.

METHODS: High-throughput sequencing of the V3-V4 hyper-variable regions of 16S rRNA was used to compare the bacterial community composition of stool, skin and oral mucosae swabs in a cohort of PV and BP patients. A dedicated bioinformatics software coupled with in-house pipeline was implemented to analyse and compare diseases dataset.

RESULTS: GM samples of both PV and BP patients were principally characterized by Firmicutes and Bacteroidetes phyla. Interestingly, the Firmicutes phylum and Staphylococcus genus were mainly represented in cutaneous samples. The diversity of phyla in oral mucosae was higher than those of gut and skin samples and, Bacteroidetes phylum was significantly underrepresented in all PV samples.

CONCLUSION: Firmicutes phylum and Staphilococcus genus were the most represented in OM and CM swabs of PV and BP microbial populations. Moreover, we argue the quantitative imbalance linked to the decrease of Bacteriodetes in the oral cavity of PV patients might be associated to disease typical fetor. To shed light on this peculiar feature further studies are still required.},
}

@article {pmid31705536,
year = {2019},
author = {Tobin, AM},
title = {Unravelling the microbiome in psoriasis.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bjd.18547},
pmid = {31705536},
issn = {1365-2133},
}

@article {pmid31705258,
year = {2019},
author = {Branchereau, M and Burcelin, R and Heymes, C},
title = {The gut microbiome and heart failure: A better gut for a better heart.},
journal = {Reviews in endocrine & metabolic disorders},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11154-019-09519-7},
pmid = {31705258},
issn = {1573-2606},
abstract = {Despite the development of new drugs and therapeutic strategies, mortality and morbidity related to heart failure (HF) remains high. It is also the leading cause of global mortality. Several concepts have been proposed to explore the underlying pathogenesis of HF, but there is still a strong need for more specific and complementary therapeutic options. In recent years, accumulating evidence has demonstrated that changes in the composition of gut microbiota, referred to as dysbiosis, might play a pivotal role in the development of several diseases, including HF. HF-associated decreased cardiac output, resulting in bowell wall oedema and intestine ischaemia, can alter gut structure, peamibility and function. These changes would favour bacterial translocation, exacerbating HF pathogenesis at least partly through activation of systemic inflammation. Although our knowledge of the precise molecular mechanisms by which gut dysbiosis influance HF is still limited, a growing body of evidence has recently demonstrated the impact of a series of gut microbiome-derived metabolites, such as trimetylamine N-oxide, short-chain fatty acids or secondary bile acids, which have been shown to play critical roles in cardiac health and disease. This review will summarize the role of gut microbiota and its metabolites in the pathogenesis of HF. Current and future preventive and therapeutic strategies to prevent HF by an adequate modulation of the microbiome and its derived metabolites are also discussed.},
}

@article {pmid31705042,
year = {2019},
author = {Kundu, P and Manna, B and Majumder, S and Ghosh, A},
title = {Species-wide Metabolic Interaction Network for Understanding Natural Lignocellulose Digestion in Termite Gut Microbiota.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16329},
doi = {10.1038/s41598-019-52843-w},
pmid = {31705042},
issn = {2045-2322},
abstract = {The structural complexity of lignocellulosic biomass hinders the extraction of cellulose, and it has remained a challenge for decades in the biofuel production process. However, wood-feeding organisms like termite have developed an efficient natural lignocellulolytic system with the help of specialized gut microbial symbionts. Despite having an enormous amount of high-throughput metagenomic data, specific contributions of each individual microbe to achieve this lignocellulolytic functionality remains unclear. The metabolic cross-communication and interdependence that drives the community structure inside the gut microbiota are yet to be explored. We have contrived a species-wide metabolic interaction network of the termite gut-microbiome to have a system-level understanding of metabolic communication. Metagenomic data of Nasutitermes corniger have been analyzed to identify microbial communities in different gut segments. A comprehensive metabolic cross-feeding network of 205 microbes and 265 metabolites was developed using published experimental data. Reconstruction of inter-species influence network elucidated the role of 37 influential microbes to maintain a stable and functional microbiota. Furthermore, in order to understand the natural lignocellulose digestion inside N. corniger gut, the metabolic functionality of each influencer was assessed, which further elucidated 15 crucial hemicellulolytic microbes and their corresponding enzyme machinery.},
}

@article {pmid31705027,
year = {2019},
author = {Ventura, RE and Iizumi, T and Battaglia, T and Liu, M and Perez-Perez, GI and Herbert, J and Blaser, MJ},
title = {Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16396},
doi = {10.1038/s41598-019-52894-z},
pmid = {31705027},
issn = {2045-2322},
abstract = {Although the intestinal microbiome has been increasingly implicated in autoimmune diseases, much is unknown about its roles in Multiple Sclerosis (MS). Our aim was to compare the microbiome between treatment-naïve MS subjects early in their disease course and controls, and between Caucasian (CA), Hispanic (HA), and African American (AA) MS subjects. From fecal samples, we performed 16S rRNA V4 sequencing and analysis from 45 MS subjects (15 CA, 16 HA, 14 AA) and 44 matched healthy controls, and whole metagenomic shotgun sequencing from 24 MS subjects (all newly diagnosed, treatment-naïve, and steroid-free) and 24 controls. In all three ethnic groups, there was an increased relative abundance of the same single genus, Clostridium, compared to ethnicity-matched controls. Analysis of microbiota networks showed significant changes in the network characteristics between combined MS cohorts and controls, suggesting global differences not restricted to individual taxa. Metagenomic analysis revealed significant enrichment of individual species within Clostridia as well as particular functional pathways in the MS subjects. The increased relative abundance of Clostridia in all three early MS cohorts compared to controls provides candidate taxa for further study as biomarkers or as etiologic agents in MS.},
}

@article {pmid31704981,
year = {2019},
author = {Li, YF and Chen, YW and Xu, JK and Ding, WY and Shao, AQ and Zhu, YT and Wang, C and Liang, X and Yang, JL},
title = {Temperature elevation and Vibrio cyclitrophicus infection reduce the diversity of haemolymph microbiome of the mussel Mytilus coruscus.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16391},
doi = {10.1038/s41598-019-52752-y},
pmid = {31704981},
issn = {2045-2322},
abstract = {Haemolymph microbiome was considered to be unique to healthy invertebrates and beneficial to the host against external pathogens, including disease resistance and maintenance of homeostasis. Here, we investigated the effects of elevated water temperature on infection of haemolymph microbiome of the hard-shelled mussel (Mytilus coruscus). Exposure to Vibrio. cyclitrophicus resulted in high mortality of mussels on day nine at 27 °C. The haemolymph was collected to determine the microbiota by 16 S rRNA gene sequencing. Exposure to waterborne V. cyclitrophicus increased the mortality of mussels that was associated with a reduction in the diversity of their microbial community. Principal coordinate analysis (PCoA) revealed that temperature was an essential factor in shaping microbial communities in mussel haemolymph. Vibrio exposure promoted the proliferation of opportunistic pathogens (e.g., Arcobacter and Francisella) at a lower temperature. A high abundance of Vibrio present in live and dead mussels, at 27 °C might contribute greatly to mortality, as indicated by linear discriminant analysis effect size (LEfSe). These data suggested that the dynamics of microbial community have unique biomarker species in mussel haemolymph that could be used as health indicators. An elevated temperature may reduce the ability of bacterial elimination function against infection in mussel haemolymph.},
}

@article {pmid31704882,
year = {2019},
author = {Banskar, S and Detzner, AA and Juarez-Rodriguez, MD and Hozo, I and Gupta, D and Dziarski, R},
title = {The Pglyrp1-Regulated Microbiome Enhances Experimental Allergic Asthma.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {},
number = {},
pages = {},
doi = {10.4049/jimmunol.1900711},
pmid = {31704882},
issn = {1550-6606},
abstract = {Changes in intestinal or respiratory microbiomes in infants correlate with increased incidence of asthma, but the causative role of microbiome in the susceptibility to asthma and the host genes that regulate these changes in microbiome are mostly unknown. In this study, we show that decreased responsiveness to allergic asthma in Pglyrp1-/- mice (lacking bactericidal peptidoglycan recognition protein 1) could be transferred to germ-free wild-type mice by colonization of mothers and newborns with microbiota from Pglyrp1-/- mice. These colonized mice had decreased airway resistance and fewer inflammatory cells, less severe histopathology, and lower levels of IgE and proallergic cytokines and chemokines in the lungs. This microbiome-dependent decreased responsiveness to asthma was most pronounced in colonized germ-free BALB/c mice (genetically predisposed to asthma), only partially evident in outbred germ-free Swiss Webster mice, and marginal in conventional BALB/c mice following depletion of microbiome with antibiotics. Mice with a low asthmatic response colonized with microbiota from Pglyrp1-/- mice had increased abundance of Bacteroidetes and decreased abundance of Firmicutes, Tenericutes, Deferribacteres, and Spirochaetes in the feces and increased abundance of Pasteurella in the oropharynx. These changes in bacterial abundance in the feces and oropharynx correlated with lower asthmatic responses in the lungs. Thus, our results show that Pglyrp1 enhances allergic asthmatic responses primarily through its effect on the host intestinal microbiome and identify several bacteria that may increase or decrease sensitivity to asthma. This effect of microbiome is strong in asthma-prone BALB/c mice and weak in asthma-resistant outbred mice and requires germ-free conditions before colonization with microbiota from Pglyrp1-/- mice.},
}

@article {pmid31704684,
year = {2019},
author = {Scarborough, MJ and Myers, KS and Donohue, TJ and Noguera, DR},
title = {Medium-chain fatty acid synthesis by Candidatus Weimeria bifida, gen. nov., sp. nov., and Candidatus Pseudoramibacter fermentans, sp. nov.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02242-19},
pmid = {31704684},
issn = {1098-5336},
abstract = {Chain elongation is emerging as a bioprocess to produce valuable medium-chain fatty acids (MCFA; 6 to 8 carbons in length) from organic waste streams by harnessing the metabolism of anaerobic microbiomes. Although our understanding of chain elongation physiology is still evolving, the reverse β-oxidation pathway has been identified as a key metabolic function to elongate the intermediate products of fermentation to MCFA. Here, we describe two uncultured chain-elongating microorganisms that were enriched in an anaerobic microbiome transforming the residues from a lignocellulosic biorefining process. Based on a multi-omic analysis, we describe Candidatus Weimeria bifida, gen. nov., sp. nov. and Candidatus Pseudoramibacter fermentans, sp. nov., both predicted to produce MCFA but using different substrates. The analysis of a time-series meta-transcriptomic dataset suggests that Ca. W. bifida is an effective xylose utilizer since both the pentose phosphate pathway and the Bifid shunt are active. Furthermore, the metatranscriptomic data suggests that energy conservation during MCFA production in this organism is essential and occurs via the creation of an ion motive force using both the RNF complex and an energy-conserving hydrogenase. For Ca. P. fermentans, predicted to produce MCFA from lactate, the meta-transcriptomic analysis reveals the activity of an electron-confurcating lactate dehydrogenase, energy conservation via the RNF complex, H2 production for redox balance, and glycerol utilization. A thermodynamic analysis also suggests the possibility of glycerol being a substrate for MCFA production by Ca. P. fermentans. In total, this work reveals unknown characteristics of MCFA production in two novel organisms.IMPORTANCE Chain elongation by medium chain fatty acid (MCFA)-producing microbiomes offer an opportunity to produce valuable chemicals from organic streams that would otherwise be considered waste. However, the physiology and energetics of chain elongation is only beginning to be studied, and many of these organisms remain uncultured. We analyzed MCFA production by two uncultured organisms that were identified as the main MCFA producers in a microbial community enriched from an anaerobic digester; this characterization, which is based on meta-multi-omic analysis, complements the knowledge that has been acquired from pure culture studies. The analysis revealed previously unreported features of the metabolism of MCFA-producing organisms.},
}

@article {pmid31704676,
year = {2019},
author = {Allwood, JS and Fierer, N and Dunn, RR},
title = {The Future of Environmental DNA in Forensic Science.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.01504-19},
pmid = {31704676},
issn = {1098-5336},
abstract = {DNA sequencing technologies continue to improve and there has been a corresponding expansion of DNA-based applications in the forensic sciences. DNA recovered from dust and environmental debris can be used to identify the organisms associated with these sample types, including bacteria, plant, fungi and insects. Such results can then be leveraged to discern sample origin or geolocation and investigate individual identification. Here we will take a critical look at the current DNA-based technologies using microbiome and environmental sample sources that are focused on the generation of some investigative tools for use in forensic science. We discuss the pitfalls and contentions associated with the use of these techniques and highlight some of the future research required to expand the utility of these methods in the forensic sciences.},
}

@article {pmid31704674,
year = {2019},
author = {Zhang, YJ and Hu, HW and Chen, QL and Yan, H and Wang, JT and Chen, D and He, JZ},
title = {Manure application did not enrich antibiotic resistance genes in root endophytic bacterial microbiota of cherry radish.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02106-19},
pmid = {31704674},
issn = {1098-5336},
abstract = {Growing evidence suggests that livestock manure used as organic fertilizer in agriculture may lead to potential propagation of antibiotic resistance genes (ARGs) from "farm to fork". However, little is known about the impacts of manure fertilization on the incidence of ARGs in the plant-associated microbiomes (including rhizosphere, endosphere and phyllosphere), which hampers our ability to assess the dissemination of antibiotic resistance in the soil-plant system. Here, we constructed a pot experiment to explore the effects of poultry and cattle manure applications on the shifts of resistome in the plant microbiome of harvested cherry radish. A total of 144 ARGs conferring resistance to eight major classes of antibiotics were detected among all the samples. Rhizosphere and phyllosphere microbiomes harbored significantly higher diversity and abundance of ARGs than root endophytic microbiomes of cherry radish. Manure application significantly increased the abundance of ARGs in the rhizosphere and phyllosphere, but not in the endophytes of root, which is the edible part of cherry radish. Soil and plant microbiomes changed dramatically after manure applications and clustered separately according to different sample types and treatments. Structural equation modelling revealed that bacterial abundance was the most important factor modulating the distribution patterns of soil and plant resistomes after accounting for multiple drivers. Taken together, we provide evidence that the enrichment of resistome in the rhizosphere and phyllosphere of cherry radish is more obvious compared with the endosphere after manure application, suggesting that manure amendment might not enhance the ARGs dissemination into the root of vegetables in the pot experiment.Importance Our study provides important evidence that manure application increased the occurrence of ARGs in the rhizosphere and phyllosphere of cherry radish, compared with the endophytic bacterial microbiota of root, which is the edible part of cherry radish. Our findings suggest that although manure amendment is a significant route of ARGs entering agricultural soils, these manure-derived ARGs may be at low risk of migrating into the endophytes of root vegetables.},
}

@article {pmid31704528,
year = {2019},
author = {Chen, X and Wang, Y and Li, W and Zhang, J and Qi, W and Lu, Y and Ding, Z},
title = {Coupling changes of disinfectant and bacteria induced by the water stagnation and disinfection strategy.},
journal = {Chemosphere},
volume = {242},
number = {},
pages = {125190},
doi = {10.1016/j.chemosphere.2019.125190},
pmid = {31704528},
issn = {1879-1298},
abstract = {This paper studied stagnation-induced changes of disinfectant and bacteria using an orthogonal test and kinetic analysis, and then proposed a disinfection strategy. Tap water from a drinking water distribution system and ultrafiltrated water were collected and disinfected with four disinfectants (concentrations were set 0.2-1 mg/L as Cl2. The study had several findings. First, disinfectants expanded lag phases and shortened generation times of the microbiome. Reduction in culturability, substrate responsiveness, respiratory activity, membrane potential and integrity subsequently occurred with increasing disinfection concentration. Second, the disinfectant decay rate decreased with initial disinfection concentration, and the effective disinfection phase (heterotrophic plate count (HPC) was less than 100 cfu/mL) was longer in water samples with lower organic matter. Moreover, the disinfection process was divided into an effective phase and an invalid phase (HPC>100 cfu/mL). Then a disinfection efficiency model was built and the regulation of disinfection by-products (DBPs) production was studied in chlorinated water samples, which provides a general method for other disinfectant studies. The average trihalomethanes (THMs) production during the effective phase (marked as THM/th) and THMs production during the invalid phase (marked as ΔTHM) were proposed to evaluate the DBPs production. The level of THM/th and ΔTHM were lower in ultrafiltrated water than those in tap water. THM/th were negatively correlated with initial chlorine concentration while ΔTHM were positively correlated with initial chlorine concentration. Finally, for the purpose of raising disinfection efficiency and decreasing DBPs, we propose periodic pulse disinfection.},
}

@article {pmid31704465,
year = {2019},
author = {Shi, S and Qi, Z and Jiang, W and Quan, S and Sheng, T and Tu, J and Shao, Y and Qi, K},
title = {Effects of probiotics on cecal microbiome profile altered by duck Escherichia coli 17 infection in Cherry Valley ducks.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {103849},
doi = {10.1016/j.micpath.2019.103849},
pmid = {31704465},
issn = {1096-1208},
abstract = {Avian colibacillosis is one of the most serious infectious bacterial diseases that endanger the modern poultry industry. Lactobacillus is believed to inhibit intestinal pathogens and maintain a healthy gut microbiota. This study aimed to investigate Lactobacillus supplementation in Cherry Valley ducks to prevent the intestinal flora dysbiosis caused by Duck Escherichia coli 17. One hundred and twenty healthy one day old Cherry Valley ducks were randomized to three study groups (Group I = the control group; Group II = duck Escherichia coli 17 challenge group and Group III = DE17 challenge group supplemented with lactic acid bacteria composite preparation). Cherry Valley ducks in Group II and Group III were gavage challenged with DE17 (1 × 105 CFU/mL) on day 14. Pyrosequencing of the V3/V4 variable regions of the genes encoding for 16S rRNA was used for sequence analysis. The results showed that the normal intestinal microecology was affected by DE17, including a relative increase in proteobacteria. At the same time, the Lactobacillales were increased and harmful bacteria were decreased in different intestinal segments of ducks in Group III, compared to those in Group II. Network analysis showed that dietary lactic acid bacteria addition improved the interaction pattern within the cecal microbiota of ducks and the result showed that in Ruminococcus_2 was independently present in the group III and Lachnospiraceae_NK4A136_group species correlation existed between group I and group III. This study proved that oral supplementation with Lactobacillus casei 1.2435, Lactobacillus rhamnosus 621 and Lactobacillus rhamnosus A4 can mitigate DE17 induced intestinal flora dysbiosis.},
}

@article {pmid31704402,
year = {2019},
author = {Liddicoat, C and Sydnor, H and Cando-Dumancela, C and Dresken, R and Liu, J and Gellie, NJC and Mills, JG and Young, JM and Weyrich, LS and Hutchinson, MR and Weinstein, P and Breed, MF},
title = {Naturally-diverse airborne environmental microbial exposures modulate the gut microbiome and may provide anxiolytic benefits in mice.},
journal = {The Science of the total environment},
volume = {701},
number = {},
pages = {134684},
doi = {10.1016/j.scitotenv.2019.134684},
pmid = {31704402},
issn = {1879-1026},
abstract = {Growing epidemiological evidence links natural green space exposure with a range of health benefits, including for mental health. Conversely, greater urbanisation associates with increased risk of mental health disorders. Microbiomes are proposed as an important but understudied link that may help explain many green space-human health associations. However, there remains a lack of controlled experimental evidence testing possible beneficial effects from passive exposure to natural biodiversity via airborne microbiota. Previous mouse model studies have used unrealistic environmental microbial exposures-including excessive soil and organic matter contact, feed supplements and injections-to demonstrate host microbiota, immune biomarker, and behavioural changes. Here, in a randomised controlled experiment, we demonstrate that realistic exposures to trace-level dust from a high biodiversity soil can change mouse gut microbiota, in comparison to dust from low biodiversity soil or no soil (control) (n = 54 total mice, comprising 3 treatments × 18 mice, with 9 females + 9 males per group). Furthermore, we found a nominal soil-derived anaerobic spore-forming butyrate-producer, Kineothrix alysoides, was supplemented to a greater extent in the gut microbiomes of high biodiversity treatment mice. Also, increasing relative abundance of this rare organism correlated with reduced anxiety-like behaviour in the most anxious mice. Our results point to an intriguing new hypothesis: that biodiverse soils may represent an important supplementary source of butyrate-producing bacteria capable of resupplying the mammalian gut microbiome, with potential for gut health and mental health benefits. Our findings have potential to inform cost-effective population health interventions through microbiome-conscious green space design and, ultimately, the mainstreaming of biodiversity into health care.},
}

@article {pmid31704194,
year = {2019},
author = {Kuźniar, A and Włodarczyk, K and Grządziel, J and Goraj, W and Gałązka, A and Wolińska, A},
title = {Culture-independent analysis of an endophytic core microbiome in two species of wheat: Triticum aestivum L. (cv. 'Hondia') and the first report of microbiota in Triticum spelta L. (cv. 'Rokosz').},
journal = {Systematic and applied microbiology},
volume = {},
number = {},
pages = {126025},
doi = {10.1016/j.syapm.2019.126025},
pmid = {31704194},
issn = {1618-0984},
abstract = {The main goal of the study was to determine the structure of endophytic bacteria inhabiting different parts (endosperm, germ, roots, coleoptiles, and leaves) of two wheat species, Triticum aestivum L. (cv. 'Hondia') and Triticum spelta L. (cv. 'Rokosz'), in order to provide new knowledge about the stability and/or changeability of the core microbiome in different plant organs. The endophytic core microbiome is associated with plants throughout their whole life cycle; however, plant organs can determine the actual endophytic community. Therefore, next generation sequencing with MiSeq Illumina technology was applied to identify the endophytic microbiome of T. aestivum and T. spelta. Bioinformatic analyses were performed with the use of the DADA2(1.8) package and R software (3.5.1). It was demonstrated that wheat, which is an important crop plant, was associated with beneficial endophytic bacteria inside the endosperms, germs, roots, leaves, and coleoptiles. Importantly, for the first time, biodiversity was recognized in the coleoptiles of the investigated wheat species. Flavobacterium, Pseudomonas and Janthinobacterium were shown to be common genera for both tested wheat cultivars. Among them, Pseudomonas was found to be the only endophytic genus accompanying both wheat species from the endosperm stage to the development of the leaf. Paenibacillus was recognized as a core genus for the 'Hondia' cv., whereas Pedobacter and Duganella constituted the core microbiome in the 'Rokosz' cv. In addition, the first insight into the unique and yet unrecognized endophytic microbiome of T. spelta is presented.},
}

@article {pmid31703107,
year = {2019},
author = {Kozik, AJ and Nakatsu, CH and Chun, H and Jones-Hall, YL},
title = {Comparison of the fecal, cecal, and mucus microbiome in male and female mice after TNBS-induced colitis.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0225079},
doi = {10.1371/journal.pone.0225079},
pmid = {31703107},
issn = {1932-6203},
abstract = {Crohn's Disease and Ulcerative Colitis are chronic, inflammatory conditions of the digestive tract, collectively known as Inflammatory Bowel Disease (IBD). The combined influence of lifestyle factors, genetics, and the gut microbiome contribute to IBD pathogenesis. Studies of the gut microbiome have shown significant differences in its composition between healthy individuals and those with IBD. Due to the high inter-individual microbiome variation seen in humans, mouse models of IBD are often used to investigate potential IBD mechanisms and their interplay between host, microbial, and environmental factors. While fecal samples are the predominant material used for microbial community analysis, they may not be the ideal sample to use for analysis of the microbiome of mice with experimental colitis, such as that induced by 2, 4, 6 trinitrobenzesulfonic acid (TNBS). As TNBS is administered intrarectally to induce colitis and inflammation is confined to the colon in this model, we hypothesized that the microbiome of the colonic mucus would most closely correlate with TNBS colitis severity. Based on our previous research, we also hypothesized that sex would be associated with both disease severity and microbial differences in mice with chronic TNBS colitis. We examined and compared the fecal, cecal content, and colonic mucus microbiota of 8-week old male and female C57BL/6J wild-type mice prior to and after the induction of TNBS colitis via 16S rRNA gene sequencing. We found that the colonic mucus microbiome was more closely correlated with disease severity than were alterations in the fecal and cecal microbiomes. We also found that the microbiomes of the feces, cecum, and mucus were distinct, but found no significant differences that were associated with sex in either compartment. Our findings highlight the importance of sampling colonic mucus in TNBS-induced colitis. Moreover, consideration of the differential impact of sex on the microbiome across mouse strains may be critical for the appropriate application of TNBS colitis models and robust comparisons across studies in the future.},
}

@article {pmid31703071,
year = {2019},
author = {Subotic, S and Boddicker, AM and Nguyen, VM and Rivers, J and Briles, CE and Mosier, AC},
title = {Honey bee microbiome associated with different hive and sample types over a honey production season.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0223834},
doi = {10.1371/journal.pone.0223834},
pmid = {31703071},
issn = {1932-6203},
abstract = {Western honey bees (Apis mellifera) are important pollinators in natural and agricultural ecosystems, and yet are in significant decline due to several factors including parasites, pathogens, pesticides, and habitat loss. A new beehive construction called the FlowTM hive was developed in 2015 to allow honey to be harvested directly from the hive without opening it, resulting in an apparent decrease in stress to the bees. Here, we compared the Flow and traditional Langstroth hive constructions to determine if there were any significant differences in the bee microbiome. The bee-associated bacterial communities did not differ between hive constructions and varied only slightly over the course of a honey production season. Samples were dominated by taxa belonging to the Lactobacillus, Bifidobacterium, Bartonella, Snodgrassella, Gilliamella, and Frischella genera, as observed in previous studies. The top ten most abundant taxa made up the majority of the sequence data; however, many low abundance organisms were persistent across the majority of samples regardless of sampling time or hive type. We additionally compared different preparations of whole bee and dissected bee samples to elaborate on previous bee microbiome research. We found that bacterial sequences were overwhelming derived from the bee guts, and microbes on the bee surfaces (including pollen) contributed little to the overall microbiome of whole bees. Overall, the results indicate that different hive constructions and associated disturbance levels do not influence the bee gut microbiome, which has broader implications for supporting hive health.},
}

@article {pmid31702998,
year = {2019},
author = {Meier, R and Thompson, JA and Chung, M and Zhao, N and Kelsey, KT and Michaud, DS and Koestler, DC},
title = {A Bayesian framework for identifying consistent patterns of microbial abundance between body sites.},
journal = {Statistical applications in genetics and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1515/sagmb-2019-0027},
pmid = {31702998},
issn = {1544-6115},
abstract = {Recent studies have found that the microbiome in both gut and mouth are associated with diseases of the gut, including cancer. If resident microbes could be found to exhibit consistent patterns between the mouth and gut, disease status could potentially be assessed non-invasively through profiling of oral samples. Currently, there exists no generally applicable method to test for such associations. Here we present a Bayesian framework to identify microbes that exhibit consistent patterns between body sites, with respect to a phenotypic variable. For a given operational taxonomic unit (OTU), a Bayesian regression model is used to obtain Markov-Chain Monte Carlo estimates of abundance among strata, calculate a correlation statistic, and conduct a formal test based on its posterior distribution. Extensive simulation studies demonstrate overall viability of the approach, and provide information on what factors affect its performance. Applying our method to a dataset containing oral and gut microbiome samples from 77 pancreatic cancer patients revealed several OTUs exhibiting consistent patterns between gut and mouth with respect to disease subtype. Our method is well powered for modest sample sizes and moderate strength of association and can be flexibly extended to other research settings using any currently established Bayesian analysis programs.},
}

@article {pmid31702462,
year = {2019},
author = {Garnaas, KR and Kittelsrud, J and Behnke, M},
title = {Theme 6 Tissue biomarkers.},
journal = {Amyotrophic lateral sclerosis & frontotemporal degeneration},
volume = {20},
number = {sup1},
pages = {206-216},
doi = {10.1080/21678421.2019.1646994},
pmid = {31702462},
issn = {2167-9223},
abstract = {Background: Glutamate excitotoxicity is a longstanding hypothesis in the pathophysiology of ALS. Prior studies have demonstrated increased plasma glutamate levels in ALS patients, which suggest a systemic defect in glutamate metabolism (1). The most abundant amino acid consumed in our diet is glutamate. Studies in healthy human subjects have demonstrated efficient metabolism of dietary glutamate via metabolism by enzymes present in the liver, gut lumen and residential gut bacteria. There is increasing evidence that the gut microbiota has significant CNS effects and intestinal dysbiosis has been found in the ALS transgenic SOD1G93A mouse model (2). If intestinal dysbiosis altered the prevalence of glutamine synthetase (GS) producing bacteria, dietary glutamate homeostasis could be impaired, leading to elevated plasma glutamate levels.Objectives: This study examined the degree of fluctuation in plasma glutamate levels seen with consumption of a protein shake in a cohort of ALS patients and family members from a single ALS center.Methods: Twenty six patients (87% of total cohort followed in the ALS center) underwent measurement of plasma amino acid analysis prior to and 1 hour following consumption of a 75 gm protein shake. A subset of 16 patients went on to receive a probiotic with high GS activity and completed serial protein challenges and amino acid analysis during the study. Ten unaffected family members of ALS patients underwent a similar protein challenge. Glutamate Metabolism Dysfunction (GMD) was defined as >30 umol difference post-prandially compared to fasting, and graded as mild (>30-60), moderate (>60-90) or severe (>90).Results: At baseline, 65.4% (17/26) ALS patients screened were GMD positive, compared to 30% (3/10) of tested family members. The severity of GMD in ALS patients was 41% mild, 29% moderate, 29% severe with only mild severity identified in family members. In the six month treatment phase, 75% (6/8) of patients with stable or improving GMD status saw significant improvements in their ALSFRS-R rate of decline, while 71.4% (5/7) with worsening or remaining severe GMD status experienced worsening of their rate of progression.Discussion and conclusions: Although limited by small sample size, this study does represent an excellent sampling within a single ALS center and is the first of its kind to investigate whether impairment in dietary glutamate metabolism exists in ALS patients. If validated in a larger ALS population, detection of glutamate metabolism dysfunction (GMD) could represent a novel biomarker linked to a potential therapeutic target in ALS patients. Planned microbiome analysis will also help in validating this hypothesis.},
}

@article {pmid31701990,
year = {2019},
author = {Zhang, J and Tyler, HL and Haron, MH and Jackson, CR and Pasco, DS and Pugh, ND},
title = {Macrophage activation by edible mushrooms is due to the collaborative interaction of toll-like receptor agonists and dectin-1b activating beta glucans derived from colonizing microorganisms.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/c9fo01707k},
pmid = {31701990},
issn = {2042-650X},
abstract = {Research supports the theory that the microbiome of plants and mushrooms produce potent activators of pathogen recognition receptors which are principal contributors to the stimulation of macrophages. We have previously reported that the in vitro macrophage stimulatory activity of water-soluble extracts from 13 different types of edible mushrooms is predominantly due to bacterial components originating from the naturally occurring bacterial communities within these materials. The purpose of the current study was to further investigate the bacterial-dependent activity of the water-soluble extracts and assess whether these 13 types of mushrooms contain water-insoluble beta glucans that activate the dectin-1b signaling pathway. Activity of the water-soluble extracts was predominantly due to Toll-like receptor 2 (TLR2) and TLR4 agonists. For dectin-1b-dependent activity (indicative of water-insoluble beta glucans), culinary mushrooms (Agaricus bisporus varieties) were essentially inactive, whereas most of the medicinal mushrooms (Lentinula edodes, Grifola frondosa, Hypsizygus marmoreus varieties, Flammulina velutipes) exhibited potent activation. A. bisporus samples with no detectable dectin-1b-dependent activity had yeast colony forming units that were 687 times lower than L. edodes exhibiting high activity, indicating that the active insoluble beta glucans are derived from colonizing yeast. In addition, co-stimulation of macrophages with the TLR agonists and insoluble beta glucan was found to result in a synergistic enhancement of in vitro cytokine production. Taken together, these findings indicate that the in vitro macrophage activating potential of edible mushrooms is due to the collaborative interaction of water-soluble TLR agonists (derived from colonizing bacteria) and water-insoluble beta glucans (derived from colonizing yeast).},
}

@article {pmid31701433,
year = {2019},
author = {Venegas-Borsellino, C and Kwon, M},
title = {Impact of Soluble Fiber in the Microbiome and Outcomes in Critically Ill Patients.},
journal = {Current nutrition reports},
volume = {},
number = {},
pages = {},
doi = {10.1007/s13668-019-00299-9},
pmid = {31701433},
issn = {2161-3311},
abstract = {PURPOSE OF REVIEW: To discuss the controversy over the effect of dietary fiber (DF) on (1) outcomes in critical illness, (2) microbiome and metabolic homeostasis, and (3) current evidence and guidelines regarding supplementation in critically ill patients.

RECENT FINDINGS: In healthy individuals, consumption of DF is widely known as a long-term protecting factor against colon cancer, cardiovascular disease, and other metabolic disorders like obesity, type 2 diabetes, and fatty liver disease; in hospitalized patients, DF may have a beneficial effect in the incidence of diarrhea, infections, and length of stay. But, what does that mean for critically ill patients? What is the recommended DF intake and what are current guidelines? There are many confounding factors that limit the evidence of beneficial effects from fiber supplementation in critically ill patients, including the side effects critical care therapies can have on gut microbiota, but after extrapolating data from healthy and hospitalized non-critical patients and considering that its administration appears to be safe, it may be wise to administer fiber-containing enteral feedings in ICU patients. Analysis of those confounders requires future research.},
}

@article {pmid31701171,
year = {2019},
author = {Ni, J and Hatori, S and Wang, Y and Li, YY and Kubota, K},
title = {Uncovering Viable Microbiome in Anaerobic Sludge Digesters by Propidium Monoazide (PMA)-PCR.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-019-01449-w},
pmid = {31701171},
issn = {1432-184X},
support = {NA//Strategic International Collaborative Research Program/ ; NA//Ministry of Land, Infrastructure, Transport and Tourism/ ; KAKENHI Grant Number JP18H01564//Japan Society for the Promotion of Science/ ; },
abstract = {Use of anaerobic sludge digester is a common practice around the world for solids digestion and methane generation from municipal sewage sludge. Understanding microbial community structure is vital to get better insight into the anaerobic digestion process and to gain better process control. However, selective analysis of viable microorganisms is limited by DNA-based assays. In this study, propidium monoazide (PMA)-PCR with 16S rRNA gene sequencing analysis was used to distinguish live and dead microorganisms based on cell membrane integrity. Microbial community structures of PMA-treated and PMA-untreated anaerobic digester sludge samples were compared. Quantitative PCR revealed that 5-30% of the rRNA genes were derived from inactive or dead cells in anaerobic sludge digesters. This caused a significant decrease in the numbers of operational taxonomic units and Chao1 and Shannon indices compared with that of the PMA-untreated sludge. Microbial community analysis showed that majority of the viable microbiome consisted of Euryarchaeota, Bacteroidetes, Deltaproteobacteria, Chloroflexi, Firmicutes, WWE1, Spirochaetes, Synergistetes, and Caldiserica. On the other hand, after the PMA treatment, numbers of Alphaproteobacteria and Betaproteobacteria declined. These were considered residual microbial members. The network analysis also revealed a relationship among the OTUs belonging to WWE1 and Bacteroidales. PMA-PCR-based 16S rRNA gene sequencing analysis is an effective tool for uncovering viable microbiome in complex environmental samples.},
}

@article {pmid31701169,
year = {2019},
author = {Tribius, S and Würdemann, N and Laban, S and Hoffmann, TK and Sharma, SJ and Klussmann, JP},
title = {[Update on HPV-associated head and neck cancer-highlights from the 2019 ASCO Annual Meeting].},
journal = {HNO},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00106-019-00766-3},
pmid = {31701169},
issn = {1433-0458},
abstract = {At this year's Annual Meeting of the American Society for Clinical Oncology (ASCO), the keyword search "HPV-associated head and neck cancer" resulted in 920 hits-74% of the hits on human papillomavirus (HPV). This underlines the relevance of the topic. The spectrum ranged from validation and separation of the prognostic groups of patients with HPV-associated oropharyngeal carcinoma (OPSCC) according to TNM 8, to the characterization of new tumor markers and tumor mutational burden for possible de-escalation strategies to avoid toxicity of standard multimodal treatments. It has been shown that the separation of p16-positive OPSCC into Union for International Cancer Control (UICC) stages I and II with the current TNM 8 classification without further markers is not sufficiently successful to justify de-escalation strategies. Following publication of the results of the De-ESCALaTE- and RTOG-1016 trials in 2018, which confirm the current standard of care for p16-positive OPSCC, no further phase III studies on de-escalation were presented. In a presented prospective phase II study (NCT02281955), the radiotherapy dose was reduced to cumulative 60 Gy, whereby the simultaneous chemotherapy regimen with cisplatin 30 mg/m2 weekly is not standard of care and could be administered as an alternative to cisplatin cetuximab. Some work dealt with the oral and intestinal microbiota as prognostic markers or their treatment-related changes, particularly under immunotherapy. Modification seems to have a positive impact on the success of therapy. However, robust data are still lacking for the various modified treatments for HPV-associated OPSCC, which are needed before their implementation in daily practice.},
}

@article {pmid31700900,
year = {2019},
author = {Han, MM and Zhu, XY and Peng, YF and Lin, H and Liu, DC and Li, L},
title = {The alterations of gut microbiota in mice with chronic pancreatitis.},
journal = {Annals of translational medicine},
volume = {7},
number = {18},
pages = {464},
doi = {10.21037/atm.2019.08.18},
pmid = {31700900},
issn = {2305-5839},
abstract = {Background: The changes of intestinal microbiome are associated with inflammatory, metabolic, and malignant disorders, and there are no studies assessing the intestinal microbiota of mice with chronic pancreatitis (CP). Thus, we aim to investigate the variations in diversity, composition and function of intestinal microbiota in CP mice.

Methods: Sixteen male C57BL/6 mice were randomly selected, and divided into two groups, treated intraperitoneally with saline (normal control group, CT group) or ethanol + cerulein (experimental group, CP group) for 6 weeks. Body weight as measured in entire processes. Histopathological examination of CP index was conducted to verify the CP induction. Extracted DNA from colon samples was used for Illumina HiSeq sequencing of the bacterial V4 region of 16S rRNA gene and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Functional profiling of microbial communities was predicted with BugBase.

Results: Significant alterations of the gut microbiota were found in the CP mice compared to CT groups, as revealed by significant decrease in bacterial richness and diversity, declined the relative abundance of Lachnospiraceae_NK4A136, Ruminiclostridium and Roseburia, and increased the relative abundances of Bacteroides and Alloprevotella genera. Analysis of microbial community-level phenotypes revealed significant differences in nine phenotypes (aerobic, anaerobic, containing mobile elements, facultatively anaerobic, biofilm forming, gram-negative, gram-positive, potentially pathogenic, and stress tolerant) between CP group and CT group.

Conclusions: This study indicated that mice with CP had a distinct microbiota profile.},
}

@article {pmid31700190,
year = {2019},
author = {Singer, JR and Blosser, EG and Zindl, CL and Silberger, DJ and Conlan, S and Laufer, VA and DiToro, D and Deming, C and Kumar, R and Morrow, CD and Segre, JA and Gray, MJ and Randolph, DA and Weaver, CT},
title = {Preventing dysbiosis of the neonatal mouse intestinal microbiome protects against late-onset sepsis.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-019-0640-y},
pmid = {31700190},
issn = {1546-170X},
support = {P30AR050948//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P30AR050948//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; T32GM008361//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32GM008361//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32GM008361//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Late-onset sepsis (LOS) is thought to result from systemic spread of commensal microbes from the intestines of premature infants. Clinical use of probiotics for LOS prophylaxis has varied owing to limited efficacy, reflecting an incomplete understanding of relationships between development of the intestinal microbiome, neonatal dysbiosis and LOS. Using a model of LOS, we found that components of the developing microbiome were both necessary and sufficient to prevent LOS. Maternal antibiotic exposure that eradicated or enriched transmission of Lactobacillus murinus exacerbated and prevented disease, respectively. Prophylactic administration of some, but not all Lactobacillus spp. was protective, as was administration of Escherichia coli. Intestinal oxygen level was a major driver of colonization dynamics, albeit via mechanisms distinct from those in adults. These results establish a link between neonatal dysbiosis and LOS, and provide a basis for rational selection of probiotics that modulate primary succession of the microbiome to prevent disease.},
}

@article {pmid31699813,
year = {2019},
author = {Kishikawa, T and Maeda, Y and Nii, T and Motooka, D and Matsumoto, Y and Matsushita, M and Matsuoka, H and Yoshimura, M and Kawada, S and Teshigawara, S and Oguro, E and Okita, Y and Kawamoto, K and Higa, S and Hirano, T and Narazaki, M and Ogata, A and Saeki, Y and Nakamura, S and Inohara, H and Kumanogoh, A and Takeda, K and Okada, Y},
title = {Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1136/annrheumdis-2019-215743},
pmid = {31699813},
issn = {1468-2060},
abstract = {OBJECTIVE: The causality and pathogenic mechanism of microbiome composition remain elusive in many diseases, including autoimmune diseases such as rheumatoid arthritis (RA). This study aimed to elucidate gut microbiome's role in RA pathology by a comprehensive metagenome-wide association study (MWAS).

METHODS: We conducted MWAS of the RA gut microbiome in the Japanese population (ncase=82, ncontrol=42) by using whole-genome shotgun sequencing of high depth (average 13 Gb per sample). Our MWAS consisted of three major bioinformatic analytic pipelines (phylogenetic analysis, functional gene analysis and pathway analysis).

RESULTS: Phylogenetic case-control association tests showed high abundance of multiple species belonging to the genus Prevotella (e.g., Prevotella denticola) in the RA case metagenome. The non-linear machine learning method efficiently deconvoluted the case-control phylogenetic discrepancy. Gene functional assessments showed that the abundance of one redox reaction-related gene (R6FCZ7) was significantly decreased in the RA metagenome compared with controls. A variety of biological pathways including those related to metabolism (e.g., fatty acid biosynthesis and glycosaminoglycan degradation) were enriched in the case-control comparison. A population-specific link between the metagenome and host genome was identified by comparing biological pathway enrichment between the RA metagenome and the RA genome-wide association study results. No apparent discrepancy in alpha or beta diversities of metagenome was found between RA cases and controls.

CONCLUSION: Our shotgun sequencing-based MWAS highlights a novel link among the gut microbiome, host genome and pathology of RA, which contributes to our understanding of the microbiome's role in RA aetiology.},
}

@article {pmid31699806,
year = {2019},
author = {Ramsheh, MY and Haldar, K and Bafadhel, M and George, L and Free, RC and John, C and Reeve, NF and Ziegler-Heitbrock, L and Gut, I and Singh, D and Mistry, V and Tobin, MD and Oggioni, MR and Brightling, C and Barer, MR},
title = {Resistome analyses of sputum from COPD and healthy subjects reveals bacterial load-related prevalence of target genes.},
journal = {Thorax},
volume = {},
number = {},
pages = {},
doi = {10.1136/thoraxjnl-2019-213485},
pmid = {31699806},
issn = {1468-3296},
abstract = {BACKGROUND: Antibiotic resistance is a major global threat. We hypothesised that the chronic obstructive pulmonary disease (COPD) airway is a reservoir of antimicrobial resistance genes (ARGs) that associate with microbiome-specific COPD subgroups.

OBJECTIVE: To determine the resistance gene profiles in respiratory samples from COPD patients and healthy volunteers.

METHODS: Quantitative PCR targeting 279 specific ARGs was used to profile the resistomes in sputum from subjects with COPD at stable, exacerbation and recovery visits (n=55; COPD-BEAT study), healthy controls with (n=7) or without (n=22) exposure to antibiotics in the preceding 12 months (EXCEED study) and in bronchial brush samples from COPD (n=8) and healthy controls (n=7) (EvA study).

RESULTS: ARG mean (SEM) prevalence was greater in stable COPD samples (35.2 (1.6)) than in healthy controls (27.6 (1.7); p=0.004) and correlated with total bacterial abundance (r2=0.23; p<0.001). Prevalence of ARG positive signals in individuals was not related to COPD symptoms, lung function or their changes at exacerbation. In the COPD subgroups designated High γProteobacteria and High Firmicutes, ARG prevalence was not different at stable state but significantly declined from stable through exacerbation to recovery in the former (p=0.011) without changes in total bacterial abundance. The ARG patterns were similar in COPD versus health, COPD microbiome-subgroups and between sputum and bronchoscopic samples independent of antibiotic exposure in the last 12 months.

CONCLUSIONS: ARGs are highly prevalent in sputum, broadly in proportion to bacterial abundance in both healthy and COPD subjects. Thus, COPD appears to be an ARG reservoir due to high levels of bacterial colonisation.},
}

@article {pmid31699194,
year = {2019},
author = {Li, NN and Bai, CM and Zhao, L and Ge, YP},
title = {[Gut Microbiome Differences between Gastrointestinal Cancer Patients and Healthy People].},
journal = {Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae},
volume = {41},
number = {5},
pages = {636-645},
doi = {10.3881/j.issn.1000-503X.11372},
pmid = {31699194},
issn = {1000-503X},
abstract = {Objective To compare the differences in fecal flora among patients with esophageal cancer,gastric cancer,or colorectal cancer and between patients with gastrointestinal tumors and healthy people.Methods The 16S rRNA method was used to analyze the differences in fecal flora among 13 patients with esophageal squamous cell carcinoma,23 patients with gastric cancer,6 patients with colorectal cancer,and 49 healthy persons.Results Bifidobacterium,Faecalibacterium prausnitzii,and Ruminococcus callidus were less abundant in the fecal flora of cancer patients than in those of healthy controls(all P<0.05).Some species of Firmicutes and Actinobacteria were significantly reduced in the feces of patients with esophageal cancer or gastric cancer than in healthy people(P<0.05),whereas others showed consistency with the intestinal cancer group.Anti-tumor treatment,antibiotics,and lactic acid could affect the fecal flora of cancer patients.Conclusion The gut microbiota compositions(mainly Firmicutes and Actinobacteria)and some specific bacteria species in the feces of patients with esophageal cancer and gastric cancer are similar to those in the feces of patients with intestinal cancer,suggesting these bacteria may be involved in the development of upper gastrointestinal tumors.},
}

@article {pmid31699155,
year = {2019},
author = {Coller, E and Cestaro, A and Zanzotti, R and Bertoldi, D and Pindo, M and Larger, S and Albanese, D and Mescalchin, E and Donati, C},
title = {Microbiome of vineyard soils is shaped by geography and management.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {140},
doi = {10.1186/s40168-019-0758-7},
pmid = {31699155},
issn = {2049-2618},
support = {ADP P1611051I//Provincia Autonoma di Trento (IT)/ ; },
abstract = {BACKGROUND: Despite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities and the extent by which these are impacted by cultivation are still poorly understood. Using 16S rRNA gene and ITS sequencing, we characterized the soil microbiota of vineyards and of neighboring permanent grassland soils in the Italian province of Trentino, and correlated their structure and composition to location, chemical properties of the soil, and land management.

RESULTS: Bacterial communities had a core of conserved taxa accounting for more than 60% of the reads of each sample, that was influenced both by geography and cultivation. The core fungal microbiota was much smaller and dominated by geography alone. Cultivation altered the structure and composition of the soil microbiota both for bacteria and fungi, with site-specific effects on their diversity. The diversity of bacterial and fungal communities was generally inversely correlated across locations. We identified several taxa that were impacted by the chemical properties and texture of the soil.

CONCLUSIONS: Our results highlight the different responses of bacterial and fungal communities to environmental factors and highlight the need to characterize both components of the soil microbiota to fully understand the factors that drive their variability.},
}

@article {pmid31699146,
year = {2019},
author = {He, B and Liu, Y and Hoang, TK and Tian, X and Taylor, CM and Luo, M and Tran, DQ and Tatevian, N and Rhoads, JM},
title = {Antibiotic-modulated microbiome suppresses lethal inflammation and prolongs lifespan in Treg-deficient mice.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {145},
doi = {10.1186/s40168-019-0751-1},
pmid = {31699146},
issn = {2049-2618},
support = {R01AT007083/GF/NIH HHS/United States ; 0601N18072//Shanghai General Hospital/ ; DK56338//Texas Medical Center Digestive Diseases Center/ ; 81974256//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Regulatory T cell (Treg) deficiency leads to IPEX syndrome, a lethal autoimmune disease, in Human and mice. Dysbiosis of the gut microbiota in Treg-deficient scurfy (SF) mice has been described, but to date, the role of the gut microbiota remains to be determined.

RESULTS: To examine how antibiotic-modified microbiota can inhibit Treg deficiency-induced lethal inflammation in SF mice, Treg-deficient SF mice were treated with three different antibiotics. Different antibiotics resulted in distinct microbiota and metabolome changes and led to varied efficacy in prolonging lifespan and reducing inflammation in the liver and lung. Moreover, antibiotics altered plasma levels of several cytokines, especially IL-6. By analyzing gut microbiota and metabolome, we determined the microbial and metabolomic signatures which were associated with the antibiotics. Remarkably, antibiotic treatments restored the levels of several primary and secondary bile acids, which significantly reduced IL-6 expression in RAW macrophages in vitro. IL-6 blockade prolonged lifespan and inhibited inflammation in the liver and lung. By using IL-6 knockout mice, we further identified that IL-6 deletion provided a significant portion of the protection against inflammation induced by Treg dysfunction.

CONCLUSION: Our results show that three antibiotics differentially prolong survival and inhibit lethal inflammation in association with a microbiota-IL-6 axis. This pathway presents a potential avenue for treating Treg deficiency-mediated autoimmune disorders.},
}

@article {pmid31699144,
year = {2019},
author = {Park, R and Dzialo, MC and Spaepen, S and Nsabimana, D and Gielens, K and Devriese, H and Crauwels, S and Tito, RY and Raes, J and Lievens, B and Verstrepen, KJ},
title = {Microbial communities of the house fly Musca domestica vary with geographical location and habitat.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {147},
doi = {10.1186/s40168-019-0748-9},
pmid = {31699144},
issn = {2049-2618},
abstract = {House flies (Musca domestica) are widespread, synanthropic filth flies commonly found on decaying matter, garbage, and feces as well as human food. They have been shown to vector microbes, including clinically relevant pathogens. Previous studies have demonstrated that house flies carry a complex and variable prokaryotic microbiota, but the main drivers underlying this variability and the influence of habitat on the microbiota remain understudied. Moreover, the differences between the external and internal microbiota and the eukaryotic components have not been examined. To obtain a comprehensive view of the fly microbiota and its environmental drivers, we sampled over 400 flies from two geographically distinct countries (Belgium and Rwanda) and three different environments-farms, homes, and hospitals. Both the internal as well as external microbiota of the house flies were studied, using amplicon sequencing targeting both bacteria and fungi. Results show that the house fly's internal bacterial community is very diverse yet relatively consistent across geographic location and habitat, dominated by genera Staphylococcus and Weissella. The external bacterial community, however, varies with geographic location and habitat. The fly fungal microbiota carries a distinct signature correlating with the country of sampling, with order Capnodiales and genus Wallemia dominating Belgian flies and genus Cladosporium dominating Rwandan fly samples. Together, our results reveal an intricate country-specific pattern for fungal communities, a relatively stable internal bacterial microbiota and a variable external bacterial microbiota that depends on geographical location and habitat. These findings suggest that vectoring of a wide spectrum of environmental microbes occurs principally through the external fly body surface, while the internal microbiome is likely more limited by fly physiology.},
}

@article {pmid31699101,
year = {2019},
author = {Kumpitsch, C and Koskinen, K and Schöpf, V and Moissl-Eichinger, C},
title = {The microbiome of the upper respiratory tract in health and disease.},
journal = {BMC biology},
volume = {17},
number = {1},
pages = {87},
doi = {10.1186/s12915-019-0703-z},
pmid = {31699101},
issn = {1741-7007},
abstract = {The human upper respiratory tract (URT) offers a variety of niches for microbial colonization. Local microbial communities are shaped by the different characteristics of the specific location within the URT, but also by the interaction with both external and intrinsic factors, such as ageing, diseases, immune responses, olfactory function, and lifestyle habits such as smoking. We summarize here the current knowledge about the URT microbiome in health and disease, discuss methodological issues, and consider the potential of the nasal microbiome to be used for medical diagnostics and as a target for therapy.},
}

@article {pmid31698863,
year = {2019},
author = {Lugli, GA and Duranti, S and Milani, C and Mancabelli, L and Turroni, F and Sinderen, DV and Ventura, M},
title = {Uncovering Bifidobacteria via Targeted Sequencing of the Mammalian Gut Microbiota.},
journal = {Microorganisms},
volume = {7},
number = {11},
pages = {},
doi = {10.3390/microorganisms7110535},
pmid = {31698863},
issn = {2076-2607},
support = {15/JP-HDHL/3280//Joint Programming Initiative A healthy diet for a healthy life/ ; SFI/12/RC/2273a and SFI/12/RC/2273b//Science Fondation Ireland/ ; },
abstract = {Bifidobacteria are among the most prevalent gut commensals in mammals, playing crucial functional roles that start from their early colonization of the infant gastrointestinal tract and last throughout the life span of their host. Metagenomic approaches have been employed to unveil the genetic features of bifidobacteria in order to understand how they participate in the correct development of a healthy microbiome. Nevertheless, their low relative abundance in many environmental samples may represent a major limitation for metagenomics approaches. To overcome this restriction, we applied an enrichment method that allows amplification of bifidobacterial DNA obtained from human or animal fecal samples for up to 26,500-fold, resulting in the metagenomic reconstruction of genomes belonging to bifidobacterial strains, present at very low abundance in collected samples. Functional predictions of the genes from these reconstructed genomes allows us to identify unique signatures among members of the same bifidobacterial species, highlighting genes correlated with the uptake of nutrients and adhesion to the intestinal mucosa.},
}

@article {pmid31683617,
year = {2019},
author = {Kim, SW and Holanda, DM and Gao, X and Park, I and Yiannikouris, A},
title = {Efficacy of a Yeast Cell Wall Extract to Mitigate the Effect of Naturally Co-Occurring Mycotoxins Contaminating Feed Ingredients Fed to Young Pigs: Impact on Gut Health, Microbiome, and Growth.},
journal = {Toxins},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/toxins11110633},
pmid = {31683617},
issn = {2072-6651},
support = {2019//Alltech/ ; },
abstract = {Mycotoxins are produced by fungi and are potentially toxic to pigs. Yeast cell wall extract (YCWE) is known to adsorb mycotoxins and improve gut health in pigs. One hundred and twenty growing (56 kg; experiment 1) and 48 nursery piglets (6 kg; experiment 2) were assigned to four dietary treatments in a 2 × 2 factorial design for 35 and 48 days, respectively. Factors were mycotoxins (no addition versus experiment 1: 180 μg/kg aflatoxins and 14 mg/kg fumonisins; or experiment 2: 180 μg/kg aflatoxins and 9 mg/kg fumonisins, and 1 mg/kg deoxynivalenol) and YCWE (0% versus 0.2%). Growth performance, blood, gut health and microbiome, and apparent ileal digestibility (AID) data were evaluated. In experiment 1, mycotoxins reduced ADG and G:F, and duodenal IgG, whereas in jejunum, YCWE increased IgG and reduced villus width. In experiment 2, mycotoxins reduced BW, ADG, and ADFI. Mycotoxins reduced ADG, which was recovered by YCWE. Mycotoxins reduced the AID of nutrients evaluated and increased protein carbonyl, whereas mycotoxins and YCWE increased the AID of the nutrients and reduced protein carbonyl. Mycotoxins reduced villus height, proportion of Ki-67-positive cells, and increased IgA and the proportion of bacteria with mycotoxin-degrading ability, whereas YCWE tended to increase villus height and reduced IgA and the proportion of pathogenic bacteria in jejunum. The YCWE effects were more evident in promoting gut health and growth in nursery pigs, which showed higher susceptibility to mycotoxin effects.},
}

@article {pmid31698527,
year = {2019},
author = {Roesch, LFW and Dobbler, PT and Pylro, VS and Kolaczkowski, B and Drew, JC and Triplett, EW},
title = {PIME: A package for discovery of novel differences among microbial communities.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13116},
pmid = {31698527},
issn = {1755-0998},
abstract = {The data used for profiling microbial communities is usually sparse with some microbes having high abundance in a few samples and being nearly absent in others. However, current bioinformatics tools able to deal with this sparsity are missing. PIME (Prevalence Interval for Microbiome Evaluation) was designed for remove those taxa that may be high in relative abundance in just a few samples but have a low prevalence overall. The reliability and robustness of PIME were compared against existing methods and tested using 16S rRNA independent datasets. PIME filters microbial taxa not shared in a per treatment prevalence interval starting at 5% prevalence with increasing increments of 5% at each filtering step. For each prevalence interval, hundreds of decision trees are calculated to predict the likelihood of detecting differences in treatments. The best prevalence-filtered dataset is user-selected by choosing the prevalence interval that keeps a large portion of the 16S rRNA sequences in the dataset while also showing the lowest error rate. To obtain the likelihood of introducing type I error while building prevalence-filtered datasets, an error detection step based is also included. A PIME reanalysis of published datasets uncovered other expected microbial associations then previously reported, which may be masked when only relative abundance was considered.},
}

@article {pmid31698213,
year = {2019},
author = {Carvalho, JRS and Amaral, FM and Florencio, L and Kato, MT and Delforno, TP and Gavazza, S},
title = {Microaerated UASB reactor treating textile wastewater: The core microbiome and removal of azo dye Direct Black 22.},
journal = {Chemosphere},
volume = {242},
number = {},
pages = {125157},
doi = {10.1016/j.chemosphere.2019.125157},
pmid = {31698213},
issn = {1879-1298},
abstract = {Sequential anaerobic and aerobic processes have been recommended to treat textile wastewater reliably. In this work, the focus was on finding an energetically more competitive system to remove tetra-azo dye Direct Black 22 (DB22). We operated two upflow anaerobic sludge blanket (UASB) reactors (R1 and R2) in three phases (PI, PII, and PIII). R1 was operated as a conventional UASB, while R2 was microaerated in the upper part (0.18 ± 0.05 mg O2. L-1), aiming to remove DB22 simultaneously with the aromatic amine byproducts. PI consisted of feeding reactors with synthetic textile wastewater (STW), PII had higher salinity in the STW, and PIII was the same as PII, plus sulfate. The results showed that color and COD removal efficiencies were similar for both reactors (67-72% for R1 and 59-78% for R2) without a substantial influence of oxygen in R2. However, microaeration played a crucial role in R2 by removing the anaerobically formed aromatic amines; during PIII, the effluent was 16 times less toxic than that of R1. The microbial community that developed in the sludge bed of both reactors was quite similar, with the core microbiome represented by Trichococcus, Syntrophus and Methanosaeta genera. The increase in salinity in PII and PIII promoted a shift in the microbial community, excluding salty-sensitive genera from the core microbiome. The putative genera Brevundimonas and Ornatilinea were associated to aromatic amine microaerobic removal. Therefore, there is a potential application of a compact microaerated anaerobic system for textile wastewater treatment.},
}

@article {pmid31698175,
year = {2019},
author = {Horton, AA and Newbold, LK and Palacio-Cortés, AM and Spurgeon, DJ and Pereira, MG and Carter, H and Gweon, HS and Vijver, MG and van Bodegom, PM and Navarro da Silva, MA and Lahive, E},
title = {Accumulation of polybrominated diphenyl ethers and microbiome response in the great pond snail Lymnaea stagnalis with exposure to nylon (polyamide) microplastics.},
journal = {Ecotoxicology and environmental safety},
volume = {188},
number = {},
pages = {109882},
doi = {10.1016/j.ecoenv.2019.109882},
pmid = {31698175},
issn = {1090-2414},
abstract = {Microplastics attract widespread attention, including for their potential to transport toxic chemicals in the form of plasticisers and associated hydrophobic organic chemicals, such as polybrominated diphenyl ethers (PBDEs). The aims of this study were to investigate how nylon (polyamide) microplastics may affect PBDE accumulation in snails, and the acute effects of nylon particles and PBDEs on survival, weight change and inherent microbiome diversity and community composition of the pond snail Lymnaea stagnalis. Snails were exposed for 96 h to BDEs-47, 99, 100 and 153 in the presence and absence of 1% w/w nylon microplastics in quartz sand sediment. No mortality was observed over the exposure period. Snails not exposed to microplastics lost significantly more weight compared to those exposed to microplastics. Increasing PBDE concentration in the sediment resulted in an increased PBDE body burden in the snails, however microplastics did not significantly influence total PBDE uptake. Based on individual congeners, uptake of BDE 47 by snails was significantly reduced in the presence of microplastics. The diversity and composition of the snail microbiome was not significantly altered by the presence of PBDEs nor by the microplastics, singly or combined. Significant effects on a few individual operational taxonomic units (OTUs) occurred when comparing the highest PBDE concentration with the control treatment, but in the absence of microplastics only. Overall within these acute experiments, only subtle effects on weight loss and slight microbiome alterations occurred. These results therefore highlight that L. stagnalis are resilient to acute exposures to microplastics and PBDEs, and that microplastics are unlikely to influence HOC accumulation or the microbiome of this species over short timescales.},
}

@article {pmid31697779,
year = {2019},
author = {Artim, SC and Sheh, A and Burns, MA and Fox, JG},
title = {Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus).},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224950},
doi = {10.1371/journal.pone.0224950},
pmid = {31697779},
issn = {1932-6203},
abstract = {The common marmoset (Callithrix jacchus) is increasingly used as an animal model for biomedical research; however, gastrointestinal diseases causing significant morbidity are endemic in many captive marmoset colonies. Establishing gut microbiome patterns in a marmoset colony may aid in clinical decision-making and model reproducibility. A standardized method of sample collection and storage is essential for proper interpretation of microbiome data. While microbiome studies commonly utilize fecal samples, the goal of this study was to determine whether the microbiome profile from a rectal swab performed on a sedated animal was comparable to the microbiome profile from a fecal sample. During routine physical exams, paired fecal and rectal swab samples were collected from each of 23 marmosets. DNA was extracted from all fecal and rectal swab samples and 16S ribosomal RNA gene sequences were amplified and analyzed. Initial comparison of the relative abundance of bacterial phyla between paired samples had a r2 value of 0.70 with S of 0.08 with no significant differences in α and β diversity metrics between fecal and rectal samples. Initial analysis however, revealed 5 discordant fecal-rectal pairs which corresponded only with the 5 rectal swabs that were classified as free of visible fecal matter during collection. Exclusion of these 5 pairs resulted in an optimized fit of the data as evidenced by a r2 value of 0.91 with S of 0.05. These results demonstrate that rectal swabs are a reliable method for profiling the fecal microbiome in the marmoset since the bacterial composition from a rectal swab with visible fecal contents correlated well with the bacterial composition from a fecal sample from the same marmoset. This study highlights the importance of standardized sample collection methods and exclusion of inappropriate samples.},
}

@article {pmid31697694,
year = {2019},
author = {Hattenrath-Lehmann, TK and Jankowiak, J and Koch, F and Gobler, CJ},
title = {Prokaryotic and eukaryotic microbiomes associated with blooms of the ichthyotoxic dinoflagellate Cochlodinium (Margalefidinium) polykrikoides in New York, USA, estuaries.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0223067},
doi = {10.1371/journal.pone.0223067},
pmid = {31697694},
issn = {1932-6203},
abstract = {While harmful algal blooms caused by the ichthyotoxic dinoflagellate, Cochlodinium (Margalefidinium) polykrikoides, are allelopathic and may have unique associations with bacteria, a comprehensive assessment of the planktonic communities associated with these blooms has been lacking. Here, we used high-throughput amplicon sequencing to assess size fractionated (0.2 and 5 μm) bacterial (16S) and phytoplankton assemblages (18S) associated with blooms of C. polykrikoides during recurrent blooms in NY, USA. Over a three-year period, samples were collected inside ('patch') and outside ('non-patch') dense accumulations of C. polykrikoides to assess the microbiome associated with these blooms. Eukaryotic plankton communities of blooms had significantly lower diversity than non-bloom samples, and non-bloom samples hosted 30 eukaryotic operational taxonomic units (OTUs) not found within blooms, suggesting they may have been allelopathically excluded from blooms. Differential abundance analyses revealed that C. polykrikoides blooms were significantly enriched in dinoflagellates (p<0.001) and the experimental enrichment of C. polykrikoides led to a significant increase in the relative abundance of eight genera of dinoflagellates but a significant decline in other eukaryotic plankton. Amoebophrya co-dominated both within- and near- C. polykrikoides blooms and was more abundant in bloom patches. The core bacterial microbiome of the >0.2μm fraction of blooms was dominated by an uncultured bacterium from the SAR11 clade, while the >5μm size fraction was co-dominated by an uncultured bacterium from Rhodobacteraceae and Coraliomargarita. Two bacterial lineages within the >0.2μm fraction, as well as the Gammaproteobacterium, Halioglobus, from the >5μm fraction were unique to the microbiome of blooms, while there were 154 bacterial OTUs only found in non-bloom waters. Collectively, these findings reveal the unique composition and potential function of eukaryotic and prokaryotic communities associated with C. polykrikoides blooms.},
}

@article {pmid31697678,
year = {2019},
author = {Srivathsan, A and Nagarajan, N and Meier, R},
title = {Boosting natural history research via metagenomic clean-up of crowdsourced feces.},
journal = {PLoS biology},
volume = {17},
number = {11},
pages = {e3000517},
doi = {10.1371/journal.pbio.3000517},
pmid = {31697678},
issn = {1545-7885},
abstract = {Biodiversity is in crisis due to habitat destruction and climate change. The conservation of many noncharismatic species is hampered by the lack of data. Yet, natural history research-a major source of information on noncharismatic species-is in decline. We here suggest a remedy for many mammal species, i.e., metagenomic clean-up of fecal samples that are "crowdsourced" during routine field surveys. Based on literature data, we estimate that this approach could yield natural history information for circa 1,000 species within a decade. Metagenomic analysis would simultaneously yield natural history data on diet and gut parasites while enhancing our understanding of host genetics, gut microbiome, and the functional interactions between traditional and new natural history data. We document the power of this approach by carrying out a "metagenomic clean-up" on fecal samples collected during a single night of small mammal trapping in one of Alfred Wallace's favorite collecting sites.},
}

@article {pmid31697315,
year = {2019},
author = {McGregor, K and Labbe, A and Greenwood, CMT},
title = {MDiNE: A model to estimate differential co-occurrence networks in microbiome studies.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btz824},
pmid = {31697315},
issn = {1367-4811},
abstract = {MOTIVATION: The human microbiota is the collection of microorganisms colonizing the human body, and plays an integral part in human health. A growing trend in microbiome analysis is to construct a network to estimate the co-occurrence patterns among taxa through precision matrices. Existing methods do not facilitate investigation into how these networks change with respect to covariates.

RESULTS: We propose a new model called Microbiome Differential Network Estimation (MDiNE) to estimate network changes with respect to a binary covariate. The counts of individual taxa in the samples are modelled through a multinomial distribution whose probabilities depend on a latent Gaussian random variable. A sparse precision matrix over all the latent terms determines the co-occurrence network among taxa. The model fit is obtained and evaluated using Hamiltonian Monte Carlo methods. The performance of our model is evaluated through an extensive simulation study, and is shown to outperform existing methods in terms of estimation of network parameters. We also demonstrate an application of the model to estimate changes in the intestinal microbial network topology with respect to Crohn's disease.

AVAILABILITY: MDiNE is implemented in a freely available R package: https://github.com/kevinmcgregor/mdine.

SUPPLEMENTARY INFORMATION: A file containing supplemental material has been submitted with this manuscript.},
}

@article {pmid31697231,
year = {2019},
author = {Sydenham, TV and Overballe-Petersen, S and Hasman, H and Wexler, H and Kemp, M and Justesen, US},
title = {Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids.},
journal = {Microbial genomics},
volume = {},
number = {},
pages = {},
doi = {10.1099/mgen.0.000312},
pmid = {31697231},
issn = {2057-5858},
abstract = {Bacteroides fragilis constitutes a significant part of the normal human gut microbiota and can also act as an opportunistic pathogen. Antimicrobial resistance (AMR) and the prevalence of AMR genes are increasing, and prediction of antimicrobial susceptibility based on sequence information could support targeted antimicrobial therapy in a clinical setting. Complete identification of insertion sequence (IS) elements carrying promoter sequences upstream of resistance genes is necessary for prediction of AMR. However, de novo assemblies from short reads alone are often fractured due to repeat regions and the presence of multiple copies of identical IS elements. Identification of plasmids in clinical isolates can aid in the surveillance of the dissemination of AMR, and comprehensive sequence databases support microbiome and metagenomic studies. We tested several short-read, hybrid and long-lead assembly pipelines by assembling the type strain B. fragilis CCUG4856T (=ATCC25285=NCTC9343) with Illumina short reads and long reads generated by Oxford Nanopore Technologies (ONT) MinION sequencing. Hybrid assembly with Unicycler, using quality filtered Illumina reads and Filtlong filtered and Canu-corrected ONT reads, produced the assembly of highest quality. This approach was then applied to six clinical multidrug-resistant B. fragilis isolates and, with minimal manual finishing of chromosomal assemblies of three isolates, complete, circular assemblies of all isolates were produced. Eleven circular, putative plasmids were identified in the six assemblies, of which only three corresponded to a known cultured Bacteroides plasmid. Complete IS elements could be identified upstream of AMR genes; however, there was not complete correlation between the absence of IS elements and antimicrobial susceptibility. As our knowledge on factors that increase expression of resistance genes in the absence of IS elements is limited, further research is needed prior to implementing AMR prediction for B. fragilis from whole-genome sequencing.},
}

@article {pmid31696774,
year = {2019},
author = {Astbury, S and Atallah, E and Vijay, A and Aithal, GP and Grove, JI and Valdes, AM},
title = {Lower gut microbiome diversity and higher abundance of proinflammatory genus Collinsella are associated with biopsy-proven nonalcoholic steatohepatitis.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/19490976.2019.1681861},
pmid = {31696774},
issn = {1949-0984},
abstract = {There is increasing evidence for the role of gut microbial composition in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Nonalcoholic steatohepatitis (NASH) is the most serious form of NAFLD where inflammation causes liver damage that can progress to cirrhosis. We have characterized the gut microbiome composition in UK patients with biopsy-proven NASH (n = 65) and compared it to that in healthy controls (n = 76). We report a 7% lower Shannon alpha diversity in NASH patients without cirrhosis (n = 40) compared to controls (p = 2.7x 10-4) and a 14% drop in NASH patients with cirrhosis (n = 25, p = 5.0x 10-4). Beta diversity (Unweighted UniFrac distance) was also significantly reduced in both NASH (p = 5.6x 10-25) and NASH-cirrhosis (p = 8.1x 10-7) groups. The genus most strongly associated with NASH in this study was Collinsella (0.29% abundance in controls, 3.45% in NASH without cirrhosis (False Discovery Rate (FDR) p = .008), and 4.38% in NASH with cirrhosis (FDR p = .02)). This genus, which has been linked previously to obesity and atherosclerosis, was also positively correlated with fasting levels of triglycerides (p = .01) and total cholesterol (p = 1.2x 10-4) and negatively correlated with high-density lipoprotein cholesterol (p = 2.8x 10-6) suggesting that some of the pathways present in this microbial genus may influence lipid metabolism in the host. In patients, we also found decreased abundance of some of the Ruminococcaceae which are known to produce high levels of short-chain fatty acids which can lower inflammation. This may thus contribute to pathology associated with NASH.},
}

@article {pmid31696646,
year = {2019},
author = {Galand, PE and Remize, M and Meistertzheim, AL and Pruski, AM and Peru, E and Suhrhoff, TJ and Le Bris, N and Vétion, G and Lartaud, F},
title = {Diet shapes cold-water corals bacterial communities.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14852},
pmid = {31696646},
issn = {1462-2920},
abstract = {Different cold-water coral (CWC) species harbor distinct microbial communities and the community composition is thought to be linked to the ecological strategies of the host. Here we test whether diet shapes the composition of bacterial communities associated with CWC. We compared the microbiomes of two common CWC species in aquaria, Lophelia pertusa and Madrepora oculata, when they were either starved, or fed respectively with a carnivorous diet, two different herbivorous diets, or a mix of the 3. We targeted both the standing stock (16SrDNA) and the active fraction (16SrRNA) of the bacterial communities and showed that in both species, the corals' microbiome was specific to the given diet. A part of the microbiome remained, however, species-specific, which indicates that the microbiome's plasticity is framed by the identity of the host. In addition, the storage lipid content of the coral tissue showed that different diets had different effects on the corals' metabolisms. The combined results suggest that L. pertusa may be preying preferentially on zooplankton while M. oculata may in addition use phytoplankton and detritus. The results cast a new light on coral microbiomes as they indicate that a portion of the CWC's bacterial community could represent a food influenced microbiome. This article is protected by copyright. All rights reserved.},
}

@article {pmid31696621,
year = {2019},
author = {Mueller, NT and Dominguez-Bello, MG and Appel, LJ and Hourigan, SK},
title = {'Vaginal seeding' after a caesarean section provides benefits to newborn children: FOR: Does exposing caesarean-delivered newborns to the vaginal microbiome affect their chronic disease risk? The critical need for trials of 'vaginal seeding' during caesarean section.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1471-0528.15979},
pmid = {31696621},
issn = {1471-0528},
}

@article {pmid31696602,
year = {2019},
author = {Aronoff, DM and Blaser, MJ},
title = {Disturbing the neonatal microbiome is a small price to pay for preventing early onset neonatal GBS disease: AGAINST: Against relying on antibiotics to prevent GBS EOD.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1471-0528.15988},
pmid = {31696602},
issn = {1471-0528},
}

@article {pmid31696235,
year = {2019},
author = {Mitchell, AL and Almeida, A and Beracochea, M and Boland, M and Burgin, J and Cochrane, G and Crusoe, MR and Kale, V and Potter, SC and Richardson, LJ and Sakharova, E and Scheremetjew, M and Korobeynikov, A and Shlemov, A and Kunyavskaya, O and Lapidus, A and Finn, RD},
title = {MGnify: the microbiome analysis resource in 2020.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz1035},
pmid = {31696235},
issn = {1362-4962},
abstract = {MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.},
}

@article {pmid31696209,
year = {2019},
author = {Di Rienzi, SC and Britton, RA},
title = {Adaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/advances/nmz118},
pmid = {31696209},
issn = {2156-5376},
abstract = {The consumption of sugar has become central to the Western diet. Cost and health concerns associated with sucrose spurred the development and consumption of other sugars and sweeteners, with the average American consuming 10 times more sugar than 100 y ago. In this review, we discuss how gut microbes are affected by changes in the consumption of sugars and other sweeteners through transcriptional, abundance, and genetic adaptations. We propose that these adaptations result in microbes taking on different metabolic, ecological, and genetic profiles along the intestinal tract. We suggest novel approaches to assess the consequences of these changes on host-microbe interactions to determine the safety of novel sugars and sweeteners.},
}

@article {pmid31696186,
year = {2019},
author = {Che, L and Zhou, Q and Liu, Y and Hu, L and Peng, X and Wu, C and Zhang, R and Tang, J and Wu, F and Fang, Z and Lin, Y and Xu, S and Feng, B and Li, J and Jiang, P and Wu, and Chen, D},
title = {Flaxseed oil supplementation improves intestinal function and immunity, associated with altered intestinal microbiome and fatty acid profile in pigs with intrauterine growth retardation.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/c9fo01877h},
pmid = {31696186},
issn = {2042-650X},
abstract = {Flaxseed oil (FO), enriched in n-3 polyunsaturated fatty acids (PUFAs), is an important oil source for intestinal development and health. We aimed to study the different effects of FO versus soybean oil (SO) on growth, intestinal health and immune function of neonates with intrauterine growth retardation (IUGR) using a weaned piglet model. Forty pairs of male IUGR and normal birth weight piglets, weaned at 21 ± 1 d, were fed diets containing either 4% FO or SO for 3 weeks consecutively. Growth performance, nutrient digestibility and intestinal function parameters, immunology and microbiota composition were determined. IUGR led to a poor growth rate, nutrient digestibility and abnormal immunology variables, whereas feeding FO diet improved systemic and gut immunity, as indicated by increased plasma concentration of immunoglobulin G and decreased CD3+CD8+ T lymphocytes, and down-regulated intestinal expression of genes (MyD88, NF-κB, TNF-α, IL-10). Although IUGR tended to decrease villous height, feeding FO diet tended to increase the villi-crypt ratio and up-regulated expressions of tight junction genes (Claudin-1 and ZO-1), together with increased mucosa contents of n-3 PUFAs and a lower Σn-6/Σn-3 ratio. Besides, FO diet decreased the abundance of pathogenic bacteria Spirochaetes, and increased phylum Actinobacteria, and genera Blautia and Bifidobacterium in colonic digesta. Our findings indicate that IUGR impairs growth rate, nutrient digestibility, and partly immunology variables, whereas feeding FO-supplemented diet could improve intestinal function and immunity of both IUGR and NBW pigs, associated with the altered gut microbiome and mucosal fatty acid profile.},
}

@article {pmid31696151,
year = {2019},
author = {Lee, P and Oleszak, F and Nihalani, A and Velayudhan, V and McFarlane, IM},
title = {Acute Psychosis Precipitated by Urinary Tract Infection in a Patient with Gliosis of the Basal Ganglia.},
journal = {American journal of medical case reports},
volume = {7},
number = {12},
pages = {329-333},
doi = {10.12691/ajmcr-7-12-7},
pmid = {31696151},
issn = {2374-216X},
abstract = {Background: Urinary tract infections (UTI) have been found to be associated with a variety of neuropsychiatric disorders, and could play a role in the pathophysiology of relapse of affective and nonaffective psychosis. In addition, prior history of infarction in areas of the brain such as the cerebellum, basal ganglia, and mid-brain have been reported in patients with new onset psychotic symptoms.

Case presentation: A 29-year-old woman was brought to the hospital with acute mental status changes and signs of sepsis. Infectious work-up was initiated including blood cultures, brain imaging, lumbar tap and urinalysis. Brain MRI revealed abnormalities in the basal ganglia and the urinalysis revealed signs of a urinary tract infection (UTI). Further history revealed episodes of mania and depression compatible with bipolar disorder with psychotic features that had acutely worsened. The patient's condition improved with intravenous antibiotics and the introduction of anti-psychotics. She was discharged in stable condition with outpatient psychiatric follow-up.

Conclusion: Infectious diseases (UTIs in particular) are not only more prevalent among patients with acute relapse of psychiatric disorders, but have also been found to have triggered acute psychosis among stable psychiatric patients. Organic brain lesions must be thoroughly investigated among patients presenting with new psychiatric disorders in order to initiate appropriate therapy to control the symptoms.},
}

@article {pmid31695961,
year = {2019},
author = {Buwembo, W and Munabi, IG and Kaddumukasa, M and Kiryowa, H and Nankya, E and Johnson, WE and Okello, E and Sewankambo, N},
title = {Periodontitis and Rheumatoid Arthritis in sub-Saharan Africa, gaps and way forward: a systematic review and meta-analysis.},
journal = {Open journal of stomatology},
volume = {9},
number = {10},
pages = {215-226},
doi = {10.4236/ojst.2019.910023},
pmid = {31695961},
issn = {2160-8709},
abstract = {Background: This review identified papers that described periodontitis and rheumatoid arthritis in sub-Saharan Africa. Only English language publications from January 2010 to December 2017 describing original research in sub-Saharan Africa on the association between periodontitis and rheumatoid arthritis were considered for this study.

Methods: Published databases: PubMed, Science direct and Google scholar, were searched using terms "periodontitis", "rheumatoid arthritis" and "Sub-Saharan Africa" to generate a set of putative studies. Articles with data on both rheumatoid arthritis and periodontitis compared to controls were selected. Studies on the association of periodontitis with cardiovascular disease, arthritis or rheumatoid arthritis alone were excluded. Data were extracted, critically appraised, and analyzed using a random-effect Mantel-Haenszel meta-analysis on plaque index, gingival index, pocket depth and clinical attachment loss.

Results: Three publications were selected for the systematic review and 2 for the meta-analysis. Two studies were from Sudan, and one was from Burina Faso. There was a significant increase in pocket depth (mean difference: 0.31; 95% CI: 0.21, 0.41; N= 274; (p ≤ 0.001) and clinical attachment loss (mean difference: 0.47; 95% CI: 0.22, 0.75; N= 274; (p ≤ 0.001) in participants with rheumatoid arthritis compared to normal controls.

Conclusion: Findings from these combined studies show a significant relationship between periodontal disease and rheumatoid arthritis with increased periodontal pocket depth and clinical attachment loss. They also highlight the need for additional work especially in the area of associating rheumatoid arthritis with P. gingivalis, the oral microbiome and treating periodontal diseases to help in the management of rheumatoid arthritis.},
}

@article {pmid31695928,
year = {2019},
author = {Lee, NK and Kim, WS and Paik, HD},
title = {Bacillus strains as human probiotics: characterization, safety, microbiome, and probiotic carrier.},
journal = {Food science and biotechnology},
volume = {28},
number = {5},
pages = {1297-1305},
doi = {10.1007/s10068-019-00691-9},
pmid = {31695928},
issn = {2092-6456},
abstract = {Both spore and vegetative forms of Bacillus species have been used as probiotics, and they have high stability to the surrounding atmospheric conditions such as heat, gastric conditions, and moisture. The commercial Bacillus probiotic strains in use are B. cereus, B. clausii, B. coagulans, B. licheniformis, B. polyfermenticus, B. pumilus, and B. subtilis. These strains have antimicrobial, anticancer, antioxidant, and vitamin production properties. However, Bacillus probiotics can also produce toxins and biogenic amines and transfer antibiotic resistance genes; therefore, their safety is a concern. Studies on the microbiome using probiotic Bacillus strains are limited in humans. Most microbiome research has been conducted in chicken, mouse, and pig. Some Bacillus probiotics are used as fermentation starters in plant and soybean and dietary supplement of baking foods as a probiotic carrier. This review summarizes the characterization of Bacillus species as probiotics for human use and their safety, microbiome, and probiotic carrier.},
}

@article {pmid31695897,
year = {2019},
author = {Horgan, FG and Srinivasan, TS and Crisol-Martínez, E and Almazan, MLP and Ramal, AF and Oliva, R and Quibod, IL and Bernal, CC},
title = {Microbiome responses during virulence adaptation by a phloem-feeding insect to resistant near-isogenic rice lines.},
journal = {Ecology and evolution},
volume = {9},
number = {20},
pages = {11911-11929},
doi = {10.1002/ece3.5699},
pmid = {31695897},
issn = {2045-7758},
abstract = {The microbiomes of phloem-feeding insects include functional bacteria and yeasts essential for herbivore survival and development. Changes in microbiome composition are implicated in virulence adaptation by herbivores to host plant species or host populations (including crop varieties). We examined patterns in adaptation by the green leafhopper, Nephotettix virescens, to near-isogenic rice lines (NILs) with one or two resistance genes and the recurrent parent T65, without resistance genes. Only the line with two resistance genes was effective in reducing leafhopper fitness. After 20 generations on the resistant line, selected leafhoppers attained similar survival, weight gain, and egg laying to leafhoppers that were continually reared on the susceptible recurrent parent, indicating that they had adapted to the resistant host. By sequencing the 16s rRNA gene, we described the microbiome of leafhoppers from colonies associated with five collection sites, and continually reared or switched between NILs. The microbiomes included 69-119 OTUs of which 44 occurred in ≥90% of samples. Of these, 14 OTUs were assigned to the obligate symbiont Candidatus sulcia clade. After 20 generations of selection, collection site had a greater effect than host plant on microbiome composition. Six bacteria genera, including C. sulcia, were associated with leafhopper virulence. However, there was significant within-treatment, site-related variability in the prevalence of these taxa such that the mechanisms underlying their association with virulence remain to be determined. Our results imply that these taxa are associated with leafhopper nutrition. Ours is the first study to describe microbiome diversity and composition in rice leafhoppers. We discuss our results in light of the multiple functions of herbivore microbiomes during virulence adaptation in insect herbivores.},
}

@article {pmid31695782,
year = {2019},
author = {Cao, Q and Gao, X and Lin, Y and Yue, C and Wang, Y and Quan, F and Zhang, Z and Liu, X and Lu, Y and Zhan, Y and Yang, H and Li, X and Qin, D and Birnbaumer, L and Hao, K and Yang, Y},
title = {Thymopentin ameliorates dextran sulfate sodium-induced colitis by triggering the production of IL-22 in both innate and adaptive lymphocytes.},
journal = {Theranostics},
volume = {9},
number = {25},
pages = {7490-7505},
doi = {10.7150/thno.35015},
pmid = {31695782},
issn = {1838-7640},
abstract = {Background: Ulcerative colitis (UC) is a chronic inflammatory gastrointestinal disease, notoriously challenging to treat. Previous studies have found a positive correlation between thymic atrophy and colitis severity. It was, therefore, worthwhile to investigate the effect of thymopentin (TP5), a synthetic pentapeptide corresponding to the active domain of the thymopoietin, on colitis. Methods: Dextran sulfate sodium (DSS)-induced colitis mice were treated with TP5 by subcutaneous injection. Body weight, colon length, colon weight, immune organ index, disease activity index (DAI) score, and the peripheral blood profile were examined. The immune cells of the spleen and colon were analyzed by flow cytometry. Histology was performed on isolated colon tissues for cytokine analysis. Bacterial DNA was extracted from mouse colonic feces to assess the intestinal microbiota. Intestinal lamina propria mononuclear cells (LPMCs), HCT116, CT26, and splenocytes were cultured and treated with TP5. Results: TP5 treatment increased the body weight and colon length, decreased the DAI score, and restored colon architecture of colitic mice. TP5 also decreased the infiltration of immune cells and expression levels of pro-inflammatory cytokines such as IL-6. Importantly, the damaged thymus and compromised lymphocytes in peripheral blood were significantly restored by TP5. Also, the production of IL-22, both in innate and adaptive lymphoid cells, was triggered by TP5. Given the critical role of IL-22 in mucosal host defense, we tested the effect of TP5 on mucus barrier and gut microbiota and found that the number of goblet cells and the level of Mucin-2 expression were restored, and the composition of the gut microbiome was normalized after TP5 treatment. The critical role of IL-22 in the protective effect of TP5 on colitis was further confirmed by administering the anti-IL-22 antibody (αIL-22), which completely abolished the effect of TP5. Furthermore, TP5 significantly increased the expression level of retinoic acid receptor-related orphan receptor γ (RORγt), a transcription factor for IL-22. Consistent with this, RORγt inhibitor abrogated the upregulation of IL-22 induced by TP5. Conclusion: TP5 exerts a protective effect on DSS-induced colitis by triggering the production of IL-22 in both innate and adaptive lymphocytes. This study delineates TP5 as an immunomodulator that may be a potential drug for the treatment of UC.},
}

@article {pmid31695687,
year = {2019},
author = {Browne, PD and Aparicio, M and Alba, C and Hechler, C and Beijers, R and Rodríguez, JM and Fernández, L and de Weerth, C},
title = {Human Milk Microbiome and Maternal Postnatal Psychosocial Distress.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2333},
doi = {10.3389/fmicb.2019.02333},
pmid = {31695687},
issn = {1664-302X},
abstract = {Human milk contains many bioactive components, including bacteria, which are transferred to the developing infant through breastfeeding. Milk bacteria appear to, amongst others, originate from the maternal gut. A mother's postnatal psychosocial distress may alter maternal gut microbiota, which in turn may affect the bacteria present in milk. The aim of this study was to explore whether maternal postnatal psychosocial distress was related to alterations in the relative abundances of specific bacteria and to milk microbial diversity. Healthy mothers (N = 77; N = 51 with complete data) collected breast milk samples at 2, 6, and 12 weeks postpartum and filled in mood questionnaires on experienced stress, anxiety, and depressive symptoms at 6 weeks postpartum. A metataxonomic approach (16S rRNA gene sequencing (region V3 and V4) using Illumina MiSeq technology) was used to assess bacterial abundances and diversity. For the group as a whole, an increase in diversity of the milk bacterial community was observed during the first 3 months of breastfeeding (Shannon index). This general increase in diversity appears to be explained by an increase of Lactobacillus and other minor genera, together with a decrease in Staphylococcus. With respect to psychological distress and milk microbial composition, no significant differences in the relative abundance of major bacterial genera were detected between women with high (N = 13) and low (N = 13) psychosocial distress. However, progressive and distinct changes in the content of Firmicutes, Proteobacteria, and Bacteroidetes at the phylum level and Acinetobacter, Flavobacterium, and Lactobacillus at the genera level were observed in milk samples of women with low psychosocial distress. With respect to milk microbial diversity, high maternal psychosocial distress, compared to low maternal psychosocial distress, was related to significantly lower bacterial diversity in milk at 3 months post-delivery. Anxiety, stress, and depressive symptoms separately were unrelated to specific bacterial profiles. The current study suggests a potential relation between maternal psychosocial distress and milk microbiota, providing first evidence of a possible mechanism through which post-partum psychological symptoms may affect infant development and health.},
}

@article {pmid31695359,
year = {2019},
author = {Clancy, RL and Cripps, AW},
title = {An Oral Whole-Cell Killed Nontypeable Haemophilus influenzae Immunotherapeutic For The Prevention Of Acute Exacerbations Of Chronic Airway Disease.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {14},
number = {},
pages = {2423-2431},
doi = {10.2147/COPD.S217317},
pmid = {31695359},
issn = {1178-2005},
abstract = {In subjects with chronic bronchitis, protection against acute bronchitis following oral administration of a whole-cell killed nontypeable Haemophilus influenzae (NTHi) preparation was demonstrated in the mid-1980s. Subsequently, studies aiming to validate clinical efficacy of this oral treatment were complicated by a number of factors, including the modification of clinical definitions, the implications of which were not recognized at that time. The objective of this review is to integrate our pre-clinical and clinical research in this field conducted over the past 30 years to demonstrate the evolution of the idea of communication between mucosal surfaces through the common mucosal immune system and the development of an effective oral NTHi immunotherapy. Our earliest studies recruited subjects with chronic sputum production and high levels of culture-positive sputum for Gram-negative bacteria but by 2000, the clinical diagnostic focus had switched from "chronic bronchitis" to "chronic obstructive pulmonary disease" (COPD), which was functionally defined using spirometry. This change led to variable clinical trial results, confirming the importance of chronic sputum production and culture-positive sputum. Additional conditioning factors such as patient age and gender were influential in study populations with low culture-positive sputum production. Through this period, studies in human and in rodent models provided new insights into airway protection mechanisms and the pathogenesis of airway inflammation. Key findings were the importance of a dysbiosis within the airway microbiome, and the critical role of an interdependence between the bronchus and the gut, with a Peyer's patch-dependent extra-bronchus "loop" controlling the composition of the bronchus microbiome. Within this context, intercurrent virus infections initiate a microbiome-dependant hypersensitivity reaction involving Peyer's patch-derived Th17 cells. We conclude that whole-cell killed NTHi immunotherapy has consistent and significant benefits when examined in the context of changing clinical disease definitions, age and gender, and has the potential to change the natural history of chronic airway disease.},
}

@article {pmid31695050,
year = {2019},
author = {Jo, R and Nishimoto, Y and Umezawa, K and Yama, K and Aita, Y and Ichiba, Y and Murakami, S and Kakizawa, Y and Kumagai, T and Yamada, T and Fukuda, S},
title = {Comparison of oral microbiome profiles in stimulated and unstimulated saliva, tongue, and mouth-rinsed water.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16124},
doi = {10.1038/s41598-019-52445-6},
pmid = {31695050},
issn = {2045-2322},
abstract = {Epidemiological studies using saliva have revealed relationships between the oral microbiome and many oral and systemic diseases. However, when collecting from a large number of participants such as a large-scale cohort study, the time it takes to collect saliva can be a problem. Mouth-rinsed water, which is water that has been used to rinse the oral cavity, can be used as an alternative method for collecting saliva for oral microbiome analysis because it can be collected in a shorter time than saliva. The purpose of this study was to verify whether mouth-rinsed water is a suitable saliva substitute for analyzing the oral microbiome. We collected samples of mouth-rinsed water, stimulated saliva, unstimulated saliva, and tongue coating from 10 systemic healthy participants, and compared the microbial diversity and composition of the samples using next-generation sequencing of 16S rRNA-encoding genes. The results showed that the microbial diversity of mouth-rinsed water was similar to that of unstimulated and stimulated saliva, and significantly higher than that of tongue-coating samples. The microbial composition at the species level of mouth-rinsed water also showed a very high correlation with the composition of unstimulated and stimulated saliva. These results suggest that the mouth-rinsed water is a suitable collection method instead of saliva for oral microbiome analysis.},
}

@article {pmid31695033,
year = {2019},
author = {Johnson, JS and Spakowicz, DJ and Hong, BY and Petersen, LM and Demkowicz, P and Chen, L and Leopold, SR and Hanson, BM and Agresta, HO and Gerstein, M and Sodergren, E and Weinstock, GM},
title = {Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5029},
doi = {10.1038/s41467-019-13036-1},
pmid = {31695033},
issn = {2041-1723},
abstract = {The 16S rRNA gene has been a mainstay of sequence-based bacterial analysis for decades. However, high-throughput sequencing of the full gene has only recently become a realistic prospect. Here, we use in silico and sequence-based experiments to critically re-evaluate the potential of the 16S gene to provide taxonomic resolution at species and strain level. We demonstrate that targeting of 16S variable regions with short-read sequencing platforms cannot achieve the taxonomic resolution afforded by sequencing the entire (~1500 bp) gene. We further demonstrate that full-length sequencing platforms are sufficiently accurate to resolve subtle nucleotide substitutions (but not insertions/deletions) that exist between intragenomic copies of the 16S gene. In consequence, we argue that modern analysis approaches must necessarily account for intragenomic variation between 16S gene copies. In particular, we demonstrate that appropriate treatment of full-length 16S intragenomic copy variants has the potential to provide taxonomic resolution of bacterial communities at species and strain level.},
}

@article {pmid31694700,
year = {2019},
author = {Mei, R and Liu, WT},
title = {Quantifying the contribution of microbial immigration in engineered water systems.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {144},
doi = {10.1186/s40168-019-0760-0},
pmid = {31694700},
issn = {2049-2618},
abstract = {Immigration is a process that can influence the assembly of microbial communities in natural and engineered environments. However, it remains challenging to quantitatively evaluate the contribution of this process to the microbial diversity and function in the receiving ecosystems. Currently used methods, i.e., counting shared microbial species, microbial source tracking, and neutral community model, rely on abundance profile to reveal the extent of overlapping between the upstream and downstream communities. Thus, they cannot suggest the quantitative contribution of immigrants to the downstream community function because activities of individual immigrants are not considered after entering the receiving environment. This limitation can be overcome by using an approach that couples a mass balance model with high-throughput DNA sequencing, i.e., ecogenomics-based mass balance. It calculates the net growth rate of individual microbial immigrants and partitions the entire community into active populations that contribute to the community function and inactive ones that carry minimal function. Linking activities of immigrants to their abundance further provides quantification of the contribution from an upstream environment to the downstream community. Considering only active populations can improve the accuracy of identifying key environmental parameters dictating process performance using methods such as machine learning.},
}

@article {pmid31694652,
year = {2019},
author = {Kyo, M and Nishioka, K and Nakaya, T and Kida, Y and Tanabe, Y and Ohshimo, S and Shime, N},
title = {Unique patterns of lower respiratory tract microbiota are associated with inflammation and hospital mortality in acute respiratory distress syndrome.},
journal = {Respiratory research},
volume = {20},
number = {1},
pages = {246},
doi = {10.1186/s12931-019-1203-y},
pmid = {31694652},
issn = {1465-993X},
support = {18K16518//Japan Society for the Promotion of Science/ ; 18K16184//Japan Society for the Promotion of Science/ ; 18H03040//Japan Society for the Promotion of Science/ ; 17K17053//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: The lung microbiome maintains the homeostasis of the immune system within the lungs. In acute respiratory distress syndrome (ARDS), the lung microbiome is enriched with gut-derived bacteria; however, the specific microbiome associated with morbidity and mortality in patients with ARDS remains unclear. This study investigated the specific patterns of the lung microbiome that are correlated with mortality in ARDS patients.

METHODS: We analyzed the lung microbiome from the bronchoalveolar lavage fluid (BALF) of patients with ARDS and control subjects. We measured the copy numbers of 16S rRNA and the serum and BALF cytokines (interleukin [IL]-6, IL-8, receptor for advanced glycation end products, and angiopoietin-2).

RESULTS: We analyzed 47 mechanically ventilated patients diagnosed with (n = 40) or without (n = 7; control) ARDS. The alpha diversity was significantly decreased in ARDS patients compared with that of the controls (6.24 vs. 8.07, P = 0.03). The 16S rRNA gene copy numbers tended to be increased in the ARDS group compared with the controls (3.83 × 106 vs. 1.01 × 105 copies/mL, P = 0.06). ARDS patients were subdivided into the hospital survivor (n = 24) and non-survivor groups (n = 16). Serum IL-6 levels were significantly higher in the non-survivors than in the survivors (567 vs. 214 pg/mL, P = 0.027). The 16S rRNA copy number was significantly correlated with serum IL-6 levels in non-survivors (r = 0.615, P < 0.05). The copy numbers and relative abundance of betaproteobacteria were significantly lower in the non-survivors than in the survivors (713 vs. 7812, P = 0.012; 1.22% vs. 0.08%, P = 0.02, respectively). Conversely, the copy numbers of Staphylococcus, Streptococcus and Enterobacteriaceae were significantly correlated with serum IL-6 levels in the non-survivors (r = 0.579, P < 0.05; r = 0.604, P < 0.05; r = 0.588, P < 0.05, respectively).

CONCLUSIONS: The lung bacterial burden tended to be increased, and the alpha diversity was significantly decreased in ARDS patients. The decreased Betaproteobacteria and increased Staphylococcus, Streptococcus and Enterobacteriaceae might represent a unique microbial community structure correlated with increased serum IL-6 and hospital mortality.

TRIAL REGISTRATION: The institutional review boards of Hiroshima University (Trial registration: E-447-4, registered 16 October 2019) and Kyoto Prefectural University of Medicine (Trial registration: ERB-C-973, registered 19 October 2017) approved an opt-out method of informed consent.},
}

@article {pmid31694321,
year = {2019},
author = {Zhao, S and Min, L and Zheng, N and Wang, J},
title = {Effect of Heat Stress on Bacterial Composition and Metabolism in the Rumen of Lactating Dairy Cows.},
journal = {Animals : an open access journal from MDPI},
volume = {9},
number = {11},
pages = {},
doi = {10.3390/ani9110925},
pmid = {31694321},
issn = {2076-2615},
support = {2017YFD0500502//National Key Research and Development Program :/ ; ASTIP-IAS12//Agricultural Science and Technology Innovation Program :/ ; CARS-36//Modern Agro-Industry Technology Research System of PR China :/ ; CAAS-ZDXT2019004//Scientific Research Project for Major Achievements of The Agricultural Science and Technology Innovation Program :/ ; },
abstract = {Heat stress negatively impacts the health and milk production of dairy cows, and ruminal microbial populations play an important role in dairy cattle's milk production. Currently there are no available studies that investigate heat stress-associated changes in the rumen microbiome of lactating dairy cattle. Improved understanding of the link between heat stress and the ruminal microbiome may be beneficial in developing strategies for relieving the influence of heat stress on ruminants by manipulating ruminal microbial composition. In this study, we investigated the ruminal bacterial composition and metabolites in heat stressed and non-heat stressed dairy cows. Eighteen lactating dairy cows were divided into two treatment groups, one with heat stress and one without heat stress. Dry matter intake was measured and rumen fluid from all cows in both groups was collected. The bacterial 16S rRNA genes in the ruminal fluid were sequenced, and the rumen pH and the lactate and acetate of the bacterial metabolites were quantified. Heat stress was associated with significantly decreased dry matter intake and milk production. Rumen pH and rumen acetate concentrations were significantly decreased in the heat stressed group, while ruminal lactate concentration increased. The influence of heat stress on the microbial bacterial community structure was minor. However, heat stress was associated with an increase in lactate producing bacteria (e.g., Streptococcus and unclassified Enterobacteriaceae), and with an increase in Ruminobacter, Treponema, and unclassified Bacteroidaceae, all of which utilize soluble carbohydrates as an energy source. The relative abundance of acetate-producing bacterium Acetobacter decreased during heat stress. We concluded that heat stress is associated with changes in ruminal bacterial composition and metabolites, with more lactate and less acetate-producing species in the population, which potentially negatively affects milk production.},
}

@article {pmid31694316,
year = {2019},
author = {Prescott, SL and Hancock, T and Bland, J and van den Bosch, M and Jansson, JK and Johnson, CC and Kondo, M and Katz, D and Kort, R and Kozyrskyj, A and Logan, AC and Lowry, CA and Nanan, R and Poland, B and Robinson, J and Schroeck, N and Sinkkonen, A and Springmann, M and Wright, RO and Wegienka, G},
title = {Eighth Annual Conference of inVIVO Planetary Health: From Challenges to Opportunities.},
journal = {International journal of environmental research and public health},
volume = {16},
number = {21},
pages = {},
doi = {10.3390/ijerph16214302},
pmid = {31694316},
issn = {1660-4601},
abstract = {inVIVO Planetary Health (inVIVO) is a progressive scientific movement providing evidence, advocacy, and inspiration to align the interests and vitality of people, place, and planet. Our goal is to transform personal and planetary health through awareness, attitudes, and actions, and a deeper understanding of how all systems are interconnected and interdependent. Here, we present the abstracts and proceedings of our 8th annual conference, held in Detroit, Michigan in May 2019, themed "From Challenges, to Opportunities". Our far-ranging discussions addressed the complex interdependent ecological challenges of advancing global urbanization, including the biopsychosocial interactions in our living environment on physical, mental, and spiritual wellbeing, together with the wider community and societal factors that govern these. We had a strong solutions focus, with diverse strategies spanning from urban-greening and renewal, nature-relatedness, nutritional ecology, planetary diets, and microbiome rewilding, through to initiatives for promoting resilience, positive emotional assets, traditional cultural narratives, creativity, art projects for personal and community health, and exploring ways of positively shifting mindsets and value systems. Our cross-sectoral agenda underscored the importance and global impact of local initiatives everywhere by contributing to new normative values as part of a global interconnected grass-roots movement for planetary health.},
}

@article {pmid31694288,
year = {2019},
author = {Castelán-Sánchez, HG and Elorrieta, P and Romoacca, P and Liñan-Torres, A and Sierra, JL and Vera, I and Batista-García, RA and Tenorio-Salgado, S and Lizama-Uc, G and Pérez-Rueda, E and Quispe-Ricalde, MA and Dávila-Ramos, S},
title = {Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses.},
journal = {Genes},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/genes10110891},
pmid = {31694288},
issn = {2073-4425},
support = {227-2015-FONDECYT//Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica/ ; 227229//Consejo Nacional de Ciencia y Tecnología/ ; NI-201117//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; UAEMOR-PTC-344//Secretaría de Educación Pública/ ; },
abstract = {Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent opportunity to increase our understanding of these ecosystems. The main goal of this study was to assess the structure and functional diversity of the communities of microorganisms in an intermediate-salinity environment, and we used a metagenomic shotgun approach for this analysis. These Andean hypersaline systems exhibited high bacterial diversity and abundance of the phyla Proteobacteria, Bacteroidetes, Balneolaeota, and Actinobacteria; in contrast, Archaea from the phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota were identified in low abundance. Acos harbored a more diverse prokaryotic community and a higher number of unique species compared with Maras. In addition, we obtained the draft genomes of two bacteria, Halomonas elongata and Idiomarina loihiensis, as well as the viral genomes of Enterobacteria lambda-like phage and Halomonas elongata-like phage and 27 partial novel viral halophilic genomes. The functional metagenome annotation showed a high abundance of sequences associated with detoxification, DNA repair, cell wall and capsule formation, and nucleotide metabolism; sequences for these functions were overexpressed mainly in bacteria and also in some archaea and viruses. Thus, their metabolic profiles afford a decrease in oxidative stress as well as the assimilation of nitrogen, a critical energy source for survival. Our work represents the first microbial characterization of a community structure in samples collected from Peruvian hypersaline systems.},
}

@article {pmid31694154,
year = {2019},
author = {Anderson, G and Rodriguez, M and Reiter, RJ},
title = {Multiple Sclerosis: Melatonin, Orexin, and Ceramide Interact with Platelet Activation Coagulation Factors and Gut-Microbiome-Derived Butyrate in the Circadian Dysregulation of Mitochondria in Glia and Immune Cells.},
journal = {International journal of molecular sciences},
volume = {20},
number = {21},
pages = {},
doi = {10.3390/ijms20215500},
pmid = {31694154},
issn = {1422-0067},
abstract = {Recent data highlight the important roles of the gut microbiome, gut permeability, and alterations in mitochondria functioning in the pathophysiology of multiple sclerosis (MS). This article reviews such data, indicating two important aspects of alterations in the gut in the modulation of mitochondria: (1) Gut permeability increases toll-like receptor (TLR) activators, viz circulating lipopolysaccharide (LPS), and exosomal high-mobility group box (HMGB)1. LPS and HMGB1 increase inducible nitric oxide synthase and superoxide, leading to peroxynitrite-driven acidic sphingomyelinase and ceramide. Ceramide is a major driver of MS pathophysiology via its impacts on glia mitochondria functioning; (2) Gut dysbiosis lowers production of the short-chain fatty acid, butyrate. Butyrate is a significant positive regulator of mitochondrial function, as well as suppressing the levels and effects of ceramide. Ceramide acts to suppress the circadian optimizers of mitochondria functioning, viz daytime orexin and night-time melatonin. Orexin, melatonin, and butyrate increase mitochondria oxidative phosphorylation partly via the disinhibition of the pyruvate dehydrogenase complex, leading to an increase in acetyl-coenzyme A (CoA). Acetyl-CoA is a necessary co-substrate for activation of the mitochondria melatonergic pathway, allowing melatonin to optimize mitochondrial function. Data would indicate that gut-driven alterations in ceramide and mitochondrial function, particularly in glia and immune cells, underpin MS pathophysiology. Aryl hydrocarbon receptor (AhR) activators, such as stress-induced kynurenine and air pollutants, may interact with the mitochondrial melatonergic pathway via AhR-induced cytochrome P450 (CYP)1b1, which backward converts melatonin to N-acetylserotonin (NAS). The loss of mitochnodria melatonin coupled with increased NAS has implications for altered mitochondrial function in many cell types that are relevant to MS pathophysiology. NAS is increased in secondary progressive MS, indicating a role for changes in the mitochondria melatonergic pathway in the progression of MS symptomatology. This provides a framework for the integration of diverse bodies of data on MS pathophysiology, with a number of readily applicable treatment interventions, including the utilization of sodium butyrate.},
}

@article {pmid31693963,
year = {2019},
author = {Kasahara, K and Rey, FE},
title = {The emerging role of gut microbial metabolism on cardiovascular disease.},
journal = {Current opinion in microbiology},
volume = {50},
number = {},
pages = {64-70},
doi = {10.1016/j.mib.2019.09.007},
pmid = {31693963},
issn = {1879-0364},
abstract = {The gut microbiome has been implicated in the progression of cardiovascular diseases (CVD) including hypertension, dyslipidemia, atherosclerosis, thrombosis, heart failure, and ischemic stroke. Metabolomics studies in humans and diverse mouse populations have revealed associations between diet-derived gut bacterial metabolites, including trimethylamine-N-oxide, short-chain fatty acids, and intermediates of aromatic amino acid breakdown, with progression of CVD. Functional studies in animals fed diets of defined composition have been instrumental for establishing causal links between these metabolites, the microbes that produce them, dietary substrates and disease. The purpose of this review is to discuss recent progress in our understanding of how gut microbial metabolism of food influences the development of CVD and to outline experimental approaches that can be useful for addressing crucial knowledge gaps in the field. Together, this body of work supports the notion that the gut microbiomes mediate many of the effects of diet.},
}

@article {pmid31693918,
year = {2019},
author = {Fernando, JR and Butler, CA and Adams, GG and Mitchell, HL and Dashper, SG and Escobar, K and Hoffmann, B and Shen, P and Walker, GD and Yuan, Y and Reynolds, C and Reynolds, EC},
title = {The Prebiotic Effect of CPP-ACP Sugar-Free Chewing Gum.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {103225},
doi = {10.1016/j.jdent.2019.103225},
pmid = {31693918},
issn = {1879-176X},
abstract = {OBJECTIVES: To determine if chewing gum containing casein phosphopeptide stabilised amorphous calcium phosphate (CPP-ACP) promoted an increase in the abundance ofStreptococcus sanguinis and other species associated with dental health in supragingival plaque in a clinical study.

MATERIALS AND METHODS: Nineteen participants were recruited for a three-leg cross-over, randomised, controlled clinical trial. Participants chewed a sugar-free gum with or without CPP-ACP six times daily for 20 min over two weeks. The study also involved no gum chewing (no gum) for the same two week period. Participants were randomly assigned to one of the test gums or no gum for each intervention period. Participants abstained from oral hygiene and had washout periods of two weeks between intervention periods. After each intervention period, supragingival plaque was collected and analysed for bacterial composition by sequencing the V4 variable region of the 16S rRNA gene. Data were analysed using a linear mixed model.

RESULTS: The CPP-ACP gum intervention produced a significant (p < 0.01) increase in the proportions of S. sanguinis (112%), as well as the commensal species Rothia dentocariosa (127%), Corynebacterium durum (80%) and Streptococcus mitis (55%) when compared with the no gum intervention. All the species that were promoted by the CPP-ACP gum are known to possess one or both of the alkali-producing enzymes arginine deiminase and nitrate reductase.

CONCLUSION: This clinical study demonstrated that chewing a sugar-free gum containing CPP-ACP promoted prebiosis by significantly increasing the proportion of S. sanguinis and other health-associated bacterial species in supragingival plaque.

CLINICAL SIGNIFICANCE: Regular chewing of CPP-ACP sugar-free gum increases the proportions of health-associated commensal species in supragingival plaque to promote prebiosis and oral homeostasis.},
}

@article {pmid31693706,
year = {2019},
author = {Dmitrieva, AS and Ivnitsky, SB and Maksimova, IA and Panchenko, PL and Kachalkin, AV and Markov, AV},
title = {Yeasts affect tolerance of Drosophila melanogaster to food substrate with high NaCl concentration.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224811},
doi = {10.1371/journal.pone.0224811},
pmid = {31693706},
issn = {1932-6203},
abstract = {The ability of model animal species, such as Drosophila melanogaster, to adapt quickly to various adverse conditions has been shown in many experimental evolution studies. It is usually assumed by default that such adaptation is due to changes in the gene pool of the studied population of macroorganisms. At the same time, it is known that microbiome can influence biological processes in macroorganisms. In order to assess the possible impact of microbiome on adaptation, we performed an evolutionary experiment in which some D. melanogaster lines were reared on a food substrate with high NaCl concentration while the others were reared on the standard (favourable) substrate. We evaluated the reproductive efficiency of experimental lines on the high salt substrate three years after the experiment started. Our tests confirmed that the lines reared on the salty substrate became more tolerant to high NaCl concentration. Moreover, we found that pre-inoculation of the high salt medium with homogenized salt-tolerant flies tended to improve reproductive efficiency of naïve flies on this medium (compared to pre-inoculation with homogenized control flies). The analysis of yeast microbiome in fly homogenates revealed significant differences in number and species richness of yeasts between salt-tolerant and control lines. We also found that some individual yeast lines extracted from the salt-tolerant flies improved reproductive efficiency of naïve flies on salty substrate (compared to baker's yeast and no yeast controls), whereas the effect of the yeast lines extracted from the control flies tended to be smaller. The yeast Starmerella bacillaris extracted from the salt-tolerant flies showed the strongest positive effect. This yeast is abundant in all salt-tolerant lines, and very rare or absent in all control lines. The results are consistent with the hypothesis that some components of the yeast microbiome of D. melanogaster contribute to to flies' tolerance to food substrate with high NaCl concentration.},
}

@article {pmid31693591,
year = {2019},
author = {Schmiechen, ZC and Weissler, KA and Frischmeyer-Guerrerio, PA},
title = {Recent developments in understanding the mechanisms of food allergy.},
journal = {Current opinion in pediatrics},
volume = {31},
number = {6},
pages = {807-814},
doi = {10.1097/MOP.0000000000000806},
pmid = {31693591},
issn = {1531-698X},
abstract = {PURPOSE OF REVIEW: The prevalence of food allergy is rising globally. This review will discuss recent discoveries regarding the immunologic mechanisms that drive the initial sensitization and allergic response to food antigens, which may inform prevention and treatment strategies.

RECENT FINDINGS: Tolerance to food antigens is antigen-specific and promoted by oral exposure early in life and maternal transfer of immune complexes via breast milk. IgG can inhibit both the initiation and effector phases of allergic responses to food antigens in mice, and high levels of food-specific IgG4 are associated with acquisition of tolerance in humans. Disruption of the skin barrier provides a route for food sensitization through the actions of mast cells, type 2 innate lymphoid cells, and IL-33 signaling. Regulatory T cells (Tregs) promote acquisition of oral tolerance, although defects in circulating allergen-specific Tregs are not evident in children with established food allergy. Certain microbes can offer protection against the development of IgE and food allergic responses, while dysbiosis increases susceptibility to food allergy.

SUMMARY: Tolerance to food antigens is antigen-specific and is promoted by oral exposure early in life, maternal transfer of immune complexes, food-specific IgG, Tregs, an intact skin barrier, and a healthy microbiome.},
}

@article {pmid31693497,
year = {2019},
author = {Romero, R and Gomez-Lopez, N and Winters, AD and Jung, E and Shaman, M and Bieda, J and Panaitescu, B and Pacora, P and Erez, O and Greenberg, JM and Ahmad, MM and Hsu, CD and Theis, KR},
title = {Evidence that intra-amniotic infections are often the result of an ascending invasion - a molecular microbiological study.},
journal = {Journal of perinatal medicine},
volume = {47},
number = {9},
pages = {915-931},
doi = {10.1515/jpm-2019-0297},
pmid = {31693497},
issn = {1619-3997},
abstract = {Background Microbial invasion of the amniotic cavity resulting in intra-amniotic infection is associated with obstetrical complications such as preterm labor with intact or ruptured membranes, cervical insufficiency, as well as clinical and histological chorioamnionitis. The most widely accepted pathway for intra-amniotic infection is the ascension of microorganisms from the lower genital tract. However, hematogenous dissemination of microorganisms from the oral cavity or intestine, retrograde seeding from the peritoneal cavity through the fallopian tubes, and introduction through invasive medical procedures have also been suggested as potential pathways for intra-amniotic infection. The primary reason that an ascending pathway is viewed as most common is that the microorganisms most often detected in the amniotic fluid are those that are typical inhabitants of the vagina. However, thus far, no studies have shown that microorganisms in the amniotic cavity are simultaneously present in the vagina of the woman from which they were isolated. The objective of the study was to determine the frequency with which microorganisms isolated from women with intra-amniotic infection are also present in the lower genital tract. Methods This was a cross-sectional study of women with intra-amniotic infection with intact membranes. Intra-amniotic infection was defined as a positive culture and elevated concentrations of interleukin-6 (IL-6) (>2.6 ng/mL) in amniotic fluid and/or acute histologic chorioamnionitis and funisitis. Microorganisms isolated from bacterial cultures of amniotic fluid were taxonomically identified through matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) and 16S ribosomal RNA (rRNA) gene sequencing. Vaginal swabs were obtained at the time of amniocentesis for the identification of microorganisms in the lower genital tract. The overall bacterial profiles of amniotic fluids and vaginal swabs were characterized through 16S rRNA gene sequencing. The bacterial profiles of vaginal swabs were interrogated for the presence of bacteria cultured from amniotic fluid and for the presence of prominent (>1% average relative abundance) operational taxonomic units (OTUs) within the overall 16S rRNA gene bacterial profiles of amniotic fluid. Results (1) A total of 75% (6/8) of women had bacteria cultured from their amniotic fluid that are typical residents of the vaginal ecosystem. (2) A total of 62.5% (5/8) of women with bacteria cultured from their amniotic fluid also had these bacteria present in their vagina. (3) The microorganisms cultured from amniotic fluid and also detected in the vagina were Ureaplasma urealyticum, Escherichia coli, and Streptococcus agalactiae. (4) 16S rRNA gene sequencing revealed that the amniotic fluid of women with intra-amniotic infection had bacterial profiles dominated by Sneathia, Ureaplasma, Prevotella, Lactobacillus, Escherichia, Gardnerella, Peptostreptococcus, Peptoniphilus, and Streptococcus, many of which had not been cultured from the amniotic fluid samples. (5) Seventy percent (7/10) of the prominent (>1% average relative abundance) OTUs found in amniotic fluid were also prominent in the vagina. Conclusion The majority of women with intra-amniotic infection had bacteria cultured from their amniotic fluid that were typical vaginal commensals, and these bacteria were detected within the vagina at the time of amniocentesis. Molecular microbiological interrogation of amniotic fluid from women with intra-amniotic infection revealed that the bacterial profiles of amniotic fluid were largely consistent with those of the vagina. These findings indicate that ascension from the lower genital tract is the primary pathway for intra-amniotic infection.},
}

@article {pmid31693153,
year = {2019},
author = {Yubuki, N and Galindo, LJ and Reboul, G and López-García, P and Brown, MW and Pollet, N and Moreira, D},
title = {Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina - Blastocystis Stramenopile Lineage.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz250},
pmid = {31693153},
issn = {1537-1719},
abstract = {Lateral gene transfer (LGT) is a very common process in bacterial and archaeal evolution, playing an important role in the adaptation to new environments. In eukaryotes, its role and frequency remain highly debated, although recent research supports that gene transfer from bacteria to diverse eukaryotes may be much more common than previously appreciated. However, most of this research focused on animals and the true phylogenetic and functional impact of bacterial genes in less-studied microbial eukaryotic groups remains largely unknown. Here, we have analyzed transcriptome data from the deep-branching stramenopile Opalinidae, common members of frog gut microbiomes and distantly related to the well-known genus Blastocystis. Phylogenetic analyses suggest the early acquisition of several bacterial genes in a common ancestor of both lineages. Those LGTs most likely facilitated the adaptation of the free-living ancestor of the Opalinidae-Blastocystis symbiotic group to new niches in the oxygen-depleted animal gut environment.},
}

@article {pmid31692741,
year = {2019},
author = {Renu, and Gupta, SK and Rai, AK and Sarim, KM and Sharma, A and Budhlakoti, N and Arora, D and Verma, DK and Singh, DP},
title = {Metaproteomic data of maize rhizosphere for deciphering functional diversity.},
journal = {Data in brief},
volume = {27},
number = {},
pages = {104574},
doi = {10.1016/j.dib.2019.104574},
pmid = {31692741},
issn = {2352-3409},
abstract = {Metaproteomics is a powerful tool for obtaining data on all proteins recovered directly from environmental samples at a given time. It provides a direct evidence of functional diversity and structure among microbiota present in niches and significant insights into microbial activity together with metabolomics, which is the study of the intermediate and end-products of cellular processes. Metaproteomics is a comparatively new approach which is facing a number of empirical, technical, computational and experimental design challenges that needs to be addressed. Presently only little efforts have been made to have information on microbial proteins in rhizospheric soil of maize through metagemonics approach but there is no direct evidence on functions of microbial community in this very important niche. Since rhizosphere microbiome plays important role in plant growth and development the present study is conducted to optimize the metaproteomic extraction protocol from maize rhizosphere and analyse functionality of microbial communities. We present metaproteome data from maize rhizospheric soil. Isolation of metaproteome from maize rhizosphere collected from ICAR-IISS, Mau experimental Farm was done with the standardized protocol at our laboratory and metaproteome analysis was done with the standardized pipeline. In total 696 proteins with different functions representing 244 genus and 393 species were identified. The proteome data provides direct evidence on the biological processes in soil ecosystem and is the first reported reference data from maize rhizosphere. The LC MS/MS proteomic data are available via ProteomeXchange with identifier PXD014519.},
}

@article {pmid31692435,
year = {2019},
author = {Seo, M and Anderson, G},
title = {Gut-Amygdala Interactions in Autism Spectrum Disorders: Developmental Roles via regulating Mitochondria, Exosomes, Immunity and microRNAs.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/1381612825666191105102545},
pmid = {31692435},
issn = {1873-4286},
abstract = {BACKGROUND: Autism Spectrum Disorder (ASD) have long been conceived as a developmental disorder. A growing body of data highlights a role for alterations in the gut in the pathoetiology and/or pathophysiology of ASD. Recent work shows alterations in the gut microbiome to have a significant impact on amygdala development in infancy, suggesting that the alterations in the gut microbiome may act to modulate not only amygdala development but how the amygdala modulates the development of the frontal cortex and other brain regions.

METHODS: This article reviews wide bodies of data pertaining to the developmental roles of the maternal and foetal gut and immune systems in the regulation of offspring brain development.

RESULTS: A number of processes seem to be important in mediating how genetic, epigenetic and environmental factors interact in early development to regulate such gut-mediated changes in the amygdala, wider brain functioning and inter-area connectivity, including via regulation of microRNA (miR)-451, 14-3-3 proteins, cytochrome P450 (CYP)1B1 and the melatonergic pathways. As well as a decrease in the activity of monoamine oxidase, heightened levels of in miR-451 and CYP1B1, coupled to decreased 14-3-3 act to inhibit the synthesis of N-acetylserotonin and melatonin, contributing to the hyperserotonemia that is often evident in ASD, with consequences for mitochondria functioning and the content of released exosomes. These same factors are likely to play a role in regulating placental changes that underpin the association of ASD with preeclampsia and other perinatal risk factors, including exposure to heavy metals and air pollutants. Such alterations in placental and gut processes act to change the amygdala-driven biological underpinnings of affect-cognitive and affect-sensory interactions in the brain.

CONCLUSION: Such a perspective readily incorporates previously disparate bodies of data in ASD, including the role of the mu-opioid receptor, dopamine signalling and dopamine receptors, as well as the changes occurring to oxytocin and taurine levels. This has a number of treatment implications, the most readily applicable being the utilization of sodium butyrate and melatonin.},
}