@article {pmid30231244,
year = {2018},
author = {Liu, J and Cui, L and Yan, X and Zhao, X and Cheng, J and Zhou, L and Gao, J and Cao, Z and Ye, X and Hu, S},
title = {Analysis of Oral Microbiota Revealed High Abundance of Prevotella Intermedia in Gout Patients.},
journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology},
volume = {49},
number = {5},
pages = {1804-1812},
doi = {10.1159/000493626},
pmid = {30231244},
issn = {1421-9778},
abstract = {BACKGROUND/AIMS: Microbes reside in a number of body sites, including the oral cavity, and are associated with the progression of many systemic diseases. In this study, we aimed to investigate the effects of gout and hyperuricemia (HUA) on the composition of oral microbiomes.

METHODS: Analysis of the oral microbiota from 12 gout patients, 11 HUA patients, and 19 healthy control subjects was performed using a deep sequencing approach, and validation of significant changes in Prevotella intermedia and Serratia marcescens in new patient cohorts was performed using quantitative PCR (qPCR).

RESULTS: Our analysis indicated that both gout and HUA significantly altered the composition of the oral microbiome in patients. Patients with gout or HUA had significantly greater levels of salivary Prevotella intermedia but significantly lower levels of Serratia marcescens than healthy control subjects.

CONCLUSION: We demonstrated the association between the oral microbiome and gout and HUA for the first time. In particular, 16S sequencing and qPCR analysis revealed significantly higher levels of oral Prevotella intermedia in gout/HUA patients, which suggests that these patients might be at risk for the development of periodontitis.},
}

@article {pmid30231060,
year = {2018},
author = {Beyer, K and Zaura, E and Brandt, BW and Buijs, MJ and Brun, JG and Crielaard, W and Bolstad, AI},
title = {Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0202278},
doi = {10.1371/journal.pone.0202278},
pmid = {30231060},
issn = {1932-6203},
abstract = {OBJECTIVE: Rheumatoid arthritis (RA) and periodontitis are chronic inflammatory diseases that share common risk factors. However, the bidirectional relationship between RA and periodontal disease is not fully understood. This study was undertaken to describe the bacterial component of the subgingival microbiome in RA patients and to relate this to RA disease activity and periodontal status.

METHODS: Patients with chronic established RA (N = 78) were periodontally examined and their subgingival plaque samples were collected; their clinical and laboratory data on RA status and medication were obtained from medical records. Bacterial DNA was quantified by universal 16S rDNA qPCR, and Porphyromonas gingivalis by species-specific qPCR. For microbiome assessment, 16S rDNA amplicon sequencing was performed.

RESULTS: Active RA was diagnosed in 58% of the patients and periodontitis in 82% (mild: 9%, moderate: 55%, severe: 18%). P. gingivalis was present in 14% of the samples. Different levels of gingival bleeding, periodontal probing depth, RA disease status, prednisolone use and smoking were associated with significantly different microbiome compositions. Two subgingival microbial community types were discerned.

CONCLUSION: In RA patients with active disease, anti-inflammatory medication as part of RA therapy was associated with better oral health status and a healthier subgingival microbiome compared to that of RA patients in remission, especially those in remission who were current smokers. RA patients in remission with current smoking status may particularly benefit from a systematic periodontal treatment program. The potential role of microbial community types in patient stratification and personalized therapy should be assessed in longitudinal studies.},
}

@article {pmid30230652,
year = {2018},
author = {Little, MS and Ervin, SM and Walton, WG and Tripathy, A and Xu, Y and Liu, J and Redinbo, MR},
title = {Active Site Flexibility Revealed in Crystal Structures of Parabacteroides merdae β-Glucuronidase from the Human Gut Microbiome.},
journal = {Protein science : a publication of the Protein Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/pro.3507},
pmid = {30230652},
issn = {1469-896X},
abstract = {β-Glucuronidase (GUS) enzymes in the gastrointestinal tract are involved in maintaining mammalian-microbial symbiosis and can play key roles in drug efficacy and toxicity. Parabacteroides merdae GUS was identified as an abundant mini-Loop 2 (mL2) type GUS enzyme in the Human Microbiome Project gut metagenomic database. Here, we report the crystal structure of P. merdae GUS and highlight the differences between this enzyme and extant structures of gut microbial GUS proteins. We find that P. merdae GUS exhibits a distinct tetrameric quaternary structure and that the mL2 motif traces a unique path within the active site, which also includes two arginines distinctive to this GUS. We observe two states of the P. merdae GUS active site; a loop repositions itself by more than 50 Å to place a functionally-relevant residue into the enzyme's catalytic site. Finally, we find that P. merdae GUS is able to bind to homo- and heteropolymers of the polysaccharide alginic acid. Together, these data broaden our understanding of the structural and functional diversity in the GUS family of enzymes present in the human gut microbiome and point to specialization as an important feature of microbial GUS orthologs. This article is protected by copyright. All rights reserved.},
}

@article {pmid30230220,
year = {2018},
author = {Nichols, RG and Cai, J and Murray, IA and Koo, I and Smith, PB and Perdew, GH and Patterson, AD},
title = {Structural and Functional Analysis of the Gut Microbiome for Toxicologists.},
journal = {Current protocols in toxicology},
volume = {},
number = {},
pages = {e54},
doi = {10.1002/cptx.54},
pmid = {30230220},
issn = {1934-9262},
support = {ES028244//National Institutes of Health/ ; ES028288//National Institutes of Health/ ; ES026684//National Institutes of Health/ ; //National Institute of Food and Agriculture/ ; 2914-38420-21822//U.S. Department of Agriculture/ ; },
abstract = {Characterizing the reciprocal interactions between toxicants, the gut microbiota, and the host, holds great promise for improving our mechanistic understanding of toxic endpoints. Advances in culture-independent sequencing analysis (e.g., 16S rRNA gene amplicon sequencing) combined with quantitative metabolite profiling (i.e., metabolomics) have provided new ways of studying the gut microbiome and have begun to illuminate how toxicants influence the structure and function of the gut microbiome. Developing a standardized protocol is important for establishing robust, reproducible, and importantly, comparative data. This protocol can be used as a foundation for examining the gut microbiome via sequencing-based analysis and metabolomics. Two main units follow: (1) analysis of the gut microbiome via sequencing-based approaches; and (2) functional analysis of the gut microbiome via metabolomics. © 2018 by John Wiley & Sons, Inc.},
}

@article {pmid30228778,
year = {2018},
author = {Van der Jeught, K and Xu, HC and Li, YJ and Lu, XB and Ji, G},
title = {Drug resistance and new therapies in colorectal cancer.},
journal = {World journal of gastroenterology},
volume = {24},
number = {34},
pages = {3834-3848},
doi = {10.3748/wjg.v24.i34.3834},
pmid = {30228778},
issn = {2219-2840},
abstract = {Colorectal cancer (CRC) is often diagnosed at an advanced stage when tumor cell dissemination has taken place. Chemo- and targeted therapies provide only a limited increase of overall survival for these patients. The major reason for clinical outcome finds its origin in therapy resistance. Escape mechanisms to both chemo- and targeted therapy remain the main culprits. Here, we evaluate major resistant mechanisms and elaborate on potential new therapies. Amongst promising therapies is α-amanitin antibody-drug conjugate targeting hemizygous p53 loss. It becomes clear that a dynamic interaction with the tumor microenvironment exists and that this dictates therapeutic outcome. In addition, CRC displays a limited response to checkpoint inhibitors, as only a minority of patients with microsatellite instable high tumors is susceptible. In this review, we highlight new developments with clinical potentials to augment responses to checkpoint inhibitors.},
}

@article {pmid30228776,
year = {2018},
author = {Oikonomou, T and Papatheodoridis, GV and Samarkos, M and Goulis, I and Cholongitas, E},
title = {Clinical impact of microbiome in patients with decompensated cirrhosis.},
journal = {World journal of gastroenterology},
volume = {24},
number = {34},
pages = {3813-3820},
doi = {10.3748/wjg.v24.i34.3813},
pmid = {30228776},
issn = {2219-2840},
abstract = {Cirrhosis is an increasing cause of morbidity and mortality. Recent studies are trying to clarify the role of microbiome in clinical exacerbation of patients with decompensated cirrhosis. Nowadays, it is accepted that patients with cirrhosis have altered salivary and enteric microbiome, characterized by the presence of dysbiosis. This altered microbiome along with small bowel bacterial overgrowth, through translocation across the gut, is associated with the development of decompensating complications. Studies have analyzed the correlation of certain bacterial families with the development of hepatic encephalopathy in cirrhotics. In general, stool and saliva dysbiosis with reduction of autochthonous bacteria in patients with cirrhosis incites changes in bacterial defenses and higher risk for bacterial infections, such as spontaneous bacterial peritonitis, and sepsis. Gut microbiome has even been associated with oncogenic pathways and under circumstances might promote the development of hepatocarcinogenesis. Lately, the existence of the oral-gut-liver axis has been related with the development of decompensating events. This link between the liver and the oral cavity could be via the gut through impaired intestinal permeability that allows direct translocation of bacteria from the oral cavity to the systemic circulation. Overall, the contribution of the microbiome to pathogenesis becomes more pronounced with progressive disease and therefore may represent an important therapeutic target in the management of cirrhosis.},
}

@article {pmid30228377,
year = {2018},
author = {Rupf, S and Laczny, CC and Galata, V and Backes, C and Keller, A and Umanskaya, N and Erol, A and Tierling, S and Lo Porto, C and Walter, J and Kirsch, J and Hannig, M and Hannig, C},
title = {Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situ biofilm model.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14010},
doi = {10.1038/s41598-018-32361-x},
pmid = {30228377},
issn = {2045-2322},
support = {RU 866/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; HA 2718/11-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; HA 5192/7-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Dental caries is caused by acids released from bacterial biofilms. However, the in vivo formation of initial biofilms in relation to caries remains largely unexplored. The aim of this study was to compare the oral microbiome during the initial phase of bacterial colonization for individuals with (CC) and without (NC) cavitated dentin caries lesions. Bovine enamel slabs on acrylic splints were worn by the volunteers (CC: 14, NC: 13) for in situ biofilm formation (2 h, 4 h, 8 h, 1 ml saliva as reference). Sequencing of the V1/V2 regions of the 16S rRNA gene was performed (MiSeq). The relative abundances of individual operational taxonomic units (OTUs) were compared between samples from the CC group and the NC group. Random forests models were furthermore trained to separate the groups. While the overall heterogeneity did not differ substantially between CC and NC individuals, several individual OTUs were found to have significantly different relative abundances. For the 8 h samples, most of the significant OTUs showed higher relative abundances in the CC group, while the majority of significant OTUs in the saliva samples were more abundant in the NC group. Furthermore, using OTU signatures enabled a separation between both groups, with area-under-the-curve (AUC) values of ~0.8. In summary, the results suggest that initial oral biofilms provide the potential to differentiate between CC and NC individuals.},
}

@article {pmid30228282,
year = {2018},
author = {Zhang, M and Ma, W and Zhang, J and He, Y and Wang, J},
title = {Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13981},
doi = {10.1038/s41598-018-32219-2},
pmid = {30228282},
issn = {2045-2322},
support = {81473236//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Autism spectrum disorder (ASD) is a set of complex neurodevelopmental disorders. Recent studies reported that children with ASD have altered gut microbiota profiles compared with typical development (TD) children. However, few studies on gut bacteria of children with ASD have been conducted in China. Here, in order to elucidate changes of fecal microbiota in children with ASD, 16S rRNA sequencing was conducted and the 16S rRNA (V3-V4) gene tags were amplified. We investigated differences in fecal microbiota between 35 children with ASD and 6 TD children. At the phylum level, the fecal microbiota of ASD group indicated a significant increase of the Bacteroidetes/Firmicutes ratio. At the genus level, we found that the relative abundance of Sutterella, Odoribacter and Butyricimonas was much more abundant in the ASD group whereas the abundance of Veillonella and Streptococcus was decreased significantly compared to the control group. Functional analysis demonstrated that butyrate and lactate producers were less abundant in the ASD group. In addition, we downloaded the association data set of microbe-disease from human microbe-disease association database and constructed a human disease network including ASD using our gut microbiome results. In this microbe-disease network based on microbe similarity of diseases, we found that ASD is positively correlated with periodontal, negatively related to type 1 diabetes. Therefore, these results suggest that microbe-based disease analysis is able to predict novel connection between ASD and other diseases and may play a role in revealing the pathogenesis of ASD.},
}

@article {pmid30228238,
year = {2018},
author = {Namasivayam, S and Sher, A and Glickman, MS and Wipperman, MF},
title = {The Microbiome and Tuberculosis: Early Evidence for Cross Talk.},
journal = {mBio},
volume = {9},
number = {5},
pages = {},
doi = {10.1128/mBio.01420-18},
pmid = {30228238},
issn = {2150-7511},
abstract = {Tuberculosis (TB) is an ancient infectious disease of humans that has been extensively studied both clinically and experimentally. Although susceptibility to Mycobacterium tuberculosis infection is clearly influenced by factors such as nutrition, immune status, and both mycobacterial and host genetics, the variable pathogenesis of TB in infected individuals remains poorly understood. During the past two decades, it has become clear that the microbiota-the trillion organisms that reside at mucosal surfaces within and on the body-can exert a major influence on disease outcome through its effects on host innate and adaptive immune function and metabolism. This new recognition of the potentially pleiotropic participation of the microbiome in immune responses has raised the possibility that the microbiota may influence M. tuberculosis infection and/or disease. Similarly, treatment of TB may alter the healthy steady-state composition and function of the microbiome, possibly affecting treatment outcome in addition to other host physiological parameters. Herein, we review emerging evidence for how the microbiota may influence the transition points in the life cycle of TB infection, including (i) resistance to initial infection, (ii) initial infection to latent tuberculosis (LTBI), (iii) LTBI to reactivated disease, and (iv) treatment to cure. A major goal of this review is to frame questions to guide future scientific and clinical studies in this largely unexplored but increasingly important area of TB research.},
}

@article {pmid30227799,
year = {2018},
author = {Rifaat, M and Depmeier, C and Jeger, V and Schneemann, M and Anagnostopoulos, A},
title = {[CME: Fusobacterium nucleatum/naviforme - a Rare but Serious Cause for Pyogenic Liver Abscesses].},
journal = {Praxis},
volume = {107},
number = {19},
pages = {1007-1012},
doi = {10.1024/1661-8157/a002995},
pmid = {30227799},
issn = {1661-8157},
abstract = {CME: Fusobacterium nucleatum/naviforme - a Rare but Serious Cause for Pyogenic Liver Abscesses Abstract. Pyogenic liver abscesses belong to the most common abdominal infections. Beside the most common pathogens, also rare forms like Fusobacteria, which can also be part of the natural oropharyngeal and enteral microbiome, may be considered to cause severe forms of abscesses of the liver. Since they may be more difficult to detect, they could become a challenge during diagnosis and therapy.},
}

@article {pmid30122997,
year = {2018},
author = {Zhu, Y and Zhao, F and Li, Z and Yu, J},
title = {Current landscape and future directions of biomarkers for predicting responses to immune checkpoint inhibitors.},
journal = {Cancer management and research},
volume = {10},
number = {},
pages = {2475-2488},
doi = {10.2147/CMAR.S167400},
pmid = {30122997},
issn = {1179-1322},
abstract = {Immune checkpoint inhibitors (ICIs), represented by anti-CTLA-4 or anti-PD-1/anti-PD-L1 pathway antibodies, have led to a revolution in cancer treatment modalities. ICIs have unique clinical benefits, such as effectiveness against a broad range of tumor types, strong overall impact on survival, and persistent responses after the cessation of therapy. However, only a subset of patients responds to these therapies, and a small proportion of patients even experience rapid progression or an increased risk of death. Therefore, it is imperative to optimize patient selection for treatment. This review focuses on the mechanisms of tumor escape from immune surveillance, the composition and activity of a preexisting immune infiltrate, the degree of tumor foreignness (as reflected by the mutational burden, expression of viral genes, and driver gene mutations), and host factors (including peripheral blood biomarkers, genetic polymorphisms, and gut microbiome) to summarize current evidence on the biomarkers of responses to ICIs and explore the future prospects in this field.},
}

@article {pmid30227431,
year = {2018},
author = {Johnson, MM and Fernandez-Bussy, S},
title = {Deciphering the Lung Microbiome: Implications for Lung Health and Disease.},
journal = {Respiration; international review of thoracic diseases},
volume = {},
number = {},
pages = {1-3},
doi = {10.1159/000492753},
pmid = {30227431},
issn = {1423-0356},
}

@article {pmid30227422,
year = {2018},
author = {Reininghaus, EZ and Wetzlmair, LC and Fellendorf, FT and Platzer, M and Queissner, R and Birner, A and Pilz, R and Hamm, C and Maget, A and Koidl, C and Riedrich, K and Klampfer, K and Ferk, K and Dalkner, N},
title = {The Impact of Probiotic Supplements on Cognitive Parameters in Euthymic Individuals with Bipolar Disorder: A Pilot Study.},
journal = {Neuropsychobiology},
volume = {},
number = {},
pages = {1-8},
doi = {10.1159/000492537},
pmid = {30227422},
issn = {1423-0224},
abstract = {INTRODUCTION: Cognitive dysfunction is prevalent in depressive as well as manic episodes in individuals with Bipolar Disorder (BD). Even more, after symptom remission, many individuals with BD experience persisting cognitive impairment also in euthymic periods, leading to high illness burden and low quality of life. According to a recent research in animals and healthy humans, microbiota may influence cognitive processes via the brain-gut axis. A strategy to examine the role of the microbiota in different diseases is the intake of supplements that modulate the gut microbiome. The aim of this pilot study was to analyze the impact of probiotic supplements on cognitive parameters in a cohort of euthymic individuals with BD, receiving daily probiotic treatment over a time period of 3 months.

METHODS: A total of 20 euthymic individuals with BD received probiotic supplement over a time period of 3 months and completed a cognitive test battery at 3 time points (t1 at time of inclusion, t2 after one month and t3 after 3 months of probiotic intake).

RESULTS: We found a significant improvement of performance concerning attention and psychomotor processing speed measured with the Digit Symbol Test after one (t2) as well as after 3 months (t3) of treatment (F = 8.60; η2 = 0.49, p < 0.01). Furthermore, executive function measured with the TMT-B, increased significantly over 3 months (F = 3.68; η2 = 0.29, p < 0.05).

CONCLUSION: The results confirm the hypotheses that probiotic supplement might help stable individuals with BD to improve the cognitive function, which in turn might lead to better psychosocial, occupational, work and financial functioning. Nevertheless, the idea of this potential new treatment is challenging because of the variety of the human's gut microbiota.},
}

@article {pmid30227294,
year = {2018},
author = {Crognale, S and Casentini, B and Amalfitano, S and Fazi, S and Petruccioli, M and Rossetti, S},
title = {Biological As(III) oxidation in biofilters by using native groundwater microorganisms.},
journal = {The Science of the total environment},
volume = {651},
number = {Pt 1},
pages = {93-102},
doi = {10.1016/j.scitotenv.2018.09.176},
pmid = {30227294},
issn = {1879-1026},
abstract = {Arsenic (As) contamination in drinking water represents a worldwide threat to human health. During last decades, the exploitation of microbial As-transformations has been proposed for bioremediation applications. Among biological methods for As-contaminated water treatment, microbial As(III)-oxidation is one of the most promising approaches since it can be coupled to commonly used adsorption removal technologies, without requiring the addition of chemicals and producing toxic by-products. Despite the As(III) oxidation capability has been described in several bacterial pure or enrichment cultures, very little is known about the real potentialities of this process when mixed microbial communities, naturally occurring in As contaminated waters, are used. This study highlighted the contribution of native groundwater bacteria to As(III)-oxidation in biofilters, under conditions suitable for a household-scale treatment system. This work elucidated the influence of a variety of experimental conditions (i.e., various filling materials, flow rates, As(III) inflow concentration, As(III):As(V) ratio, filter volumes) on the microbially-mediated As(III)-oxidation process in terms of oxidation efficiency and rate. The highest oxidation efficiencies (up to 90% in 3 h) were found on coarse sand biofilters treating total initial As concentration of 100 μg L-1. The detailed microbial characterization of the As(III) oxidizing biofilms revealed the occurrence of several OTUs affiliated with families known to oxidize As(III) (e.g., Burkholderiaceae, Comamonadaceae, Rhodobacteraceae, Xanthomonadaceae). Furthermore, As-related functional genes increased in biofilter systems in line with the observed oxidative performances.},
}

@article {pmid30227174,
year = {2018},
author = {Ahn, Y and Jung, JY and Veach, BT and Khare, S and Gokulan, K and Piñeiro, SA and Cerniglia, CE},
title = {In vitro test systems to determine tetracycline residue binding to human feces.},
journal = {Regulatory toxicology and pharmacology : RTP},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.yrtph.2018.09.013},
pmid = {30227174},
issn = {1096-0295},
abstract = {The use of antimicrobials, such as tetracycline, in food-producing animals may result in antimicrobial drug residues (ADR) in edible tissues from treated animals and contribute to the emergence of antibiotic resistant bacteria. The Veterinary International Conference on Harmonization (VICH) document (VICH GL36(R)/FDA-CVM Guidance for Industry#159) provides guidance on evaluating the safety of veterinary ADR in the human foods as related to effects on the human intestinal microbiome. One recognized research gap is a need for additional data and testing requirements to determine the fraction of an oral dose of ADR available to intestinal microorganisms. In the present study, we address this need by examining the binding of tetracycline to human feces using chemical and microbiological assays. High-performance liquid chromatography and liquid chromatography mass spectrometry assays showed that 25% (w/v) diluted steam sterilized feces dosed with 0.15 and 1.5 μg/ml tetracycline had binding of 58.2 ± 10.8% and 56.9 ± 9.1%, respectively. Tetracycline binding to fecal slurries gave similar results. Microbiological assays with two reference bacterial strains validated the results of the chemical assays. Based on data from chemical and microbiological assays methods, the fraction of dose available to microorganisms was 0.418 and 0.431 of the 0.15 and 1.5 μg/ml tetracycline treatments, respectively. This study also proposes factors to be considered when designing and conducting experiments to determine the percent of an antimicrobial agents that is available to microorganisms in the gastrointestinal tract.},
}

@article {pmid30226423,
year = {2018},
author = {Wulff, NAA and Fassini, CG and Marques, VV and Martins, EC and Coletti, DAB and Teixeira, DDC and Sanches, MM and Bové, JM},
title = {Molecular characterization and detection of 16SrIII group phytoplasma associated with Huanglongbing symptoms.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-03-18-0081-R},
pmid = {30226423},
issn = {0031-949X},
abstract = {When Huanglongbing (HLB) was found in Brazil in 2004, 'Candidatus Liberibacter americanus' (Lam) was infecting most of the trees while 'Ca. L. asiaticus' (Las) was present in minor proportion. Currently, 'Ca. L. asiaticus' is the predominant bacterium associated with HLB in citrus trees in São Paulo (SP) and Minas Gerais (MG) States, the major citrus growing regions in Brazil. A phytoplasma from 16Sr group IX was associated with HLB symptoms in Brazil in 2007, in plants free of Liberibacter. In this report, HLB-samples testing negative for Las, Lam and 16SrIX phytoplasma, were infected with 16SrIII phytoplasmas. Co-infection with Las and 16SrIII was also found. The 16S rRNA gene sequences from 22 samples were obtained and sequenced, confirming that 16Sr group III phytoplasma is associated with HLB symptoms in SP and MG States. Ten single nucleotide polymorphisms (SNPs) were found in the 1,427 bp 16SrDNA sequences from 16SrIII phytoplasmas from citrus, while none was detected in 16SrDNA sequences among 16SrIX phytoplasma from citrus. Ribosomal protein (rp) rpsSrplVrpsC gene sequences were amplified with 16SrIII group specific primers and sequenced from a subset of nine samples and assembled into three groups based on eight SNPs. SNPs in 16S rRNA and rp gene sequences are common in 16SrIII phytoplasmas from other hosts and this phytoplasma group is widespread in South America. 16SrIII phytoplasmas highly related are commonly found in Melia azedarach, a widespread tree in Brazil and Argentina. The finding of a new phytoplasma associated with HLB symptoms, belonging to the 16SrIII group reinforces the need to develop diagnostic tools to assess HLB associated microbiome.},
}

@article {pmid30226189,
year = {2018},
author = {Wexler, AG and Schofield, WB and Degnan, PH and Folta-Stogniew, E and Barry, NA and Goodman, AL},
title = {Human gut Bacteroides capture vitamin B12 via cell surface-exposed lipoproteins.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
doi = {10.7554/eLife.37138},
pmid = {30226189},
issn = {2050-084X},
support = {GM118159//National Institutes of Health/ ; 1014860//Burroughs Wellcome Fund/ ; 55108526//Howard Hughes Medical Institute/United States ; Graduate Student Fellowship//Gruber Foundation/ ; GM103574//National Institutes of Health/ ; },
abstract = {Human gut Bacteroides use surface-exposed lipoproteins to bind and metabolize complex polysaccharides. Although vitamins and other nutrients are also essential for commensal fitness, much less is known about how commensal bacteria compete with each other or the host for these critical resources. Unlike in Escherichia coli, transport loci for vitamin B12 (cobalamin) and other corrinoids in human gut Bacteroides are replete with conserved genes encoding proteins whose functions are unknown. Here we report that one of these proteins, BtuG, is a surface-exposed lipoprotein that is essential for efficient B12 transport in B. thetaiotaomicron. BtuG binds B12 with femtomolar affinity and can remove B12 from intrinsic factor, a critical B12 transport protein in humans. Our studies suggest that Bacteroides use surface-exposed lipoproteins not only for capturing polysaccharides, but also to acquire key vitamins in the gut.},
}

@article {pmid30225164,
year = {2018},
author = {Dranse, HJ and Zheng, A and Comeau, AM and Langille, MGI and Zabel, BA and Sinal, CJ},
title = {The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5494},
doi = {10.7717/peerj.5494},
pmid = {30225164},
issn = {2167-8359},
abstract = {Chemerin is an adipocyte derived signalling molecule (adipokine) that serves as a ligand activator of Chemokine-like receptor 1(CMKLR1). Chemerin/CMKLR1 signalling is well established to regulate fundamental processes in metabolism and inflammation. The composition and function of gut microbiota has also been shown to impact the development of metabolic and inflammatory diseases such as obesity, diabetes and inflammatory bowel disease. In this study, we assessed the microbiome composition of fecal samples isolated from wildtype, chemerin, or CMKLR1 knockout mice using Illumina-based sequencing. Moreover, the knockout mice and respective wildtype mice used in this study were housed at different universities allowing us to compare facility-dependent effects on microbiome composition. While there was no difference in alpha diversity within samples when compared by either facility or genotype, we observed a dramatic difference in the presence and abundance of numerous taxa between facilities. There were minor differences in bacterial abundance between wildtype and chemerin knockout mice, but significantly more differences in taxa abundance between wildtype and CMKLR1 knockout mice. Specifically, CMKLR1 knockout mice exhibited decreased abundance of Akkermansia and Prevotella, which correlated with body weight in CMKLR1 knockout, but not wildtype mice. This is the first study to investigate a linkage between chemerin/CMKLR1 signaling and microbiome composition. The results of our study suggest that chemerin/CMKLR1 signaling influences metabolic processes through effects on the gut microbiome. Furthermore, the dramatic difference in microbiome composition between facilities might contribute to discrepancies in the metabolic phenotype of CMKLR1 knockout mice reported by independent groups. Considered altogether, these findings establish a foundation for future studies to investigate the relationship between chemerin signaling and the gut microbiome on the development and progression of metabolic and inflammatory disease.},
}

@article {pmid30224943,
year = {2018},
author = {Randolph, TW and Zhao, S and Copeland, W and Hullar, M and Shojaie, A},
title = {KERNEL-PENALIZED REGRESSION FOR ANALYSIS OF MICROBIOME DATA.},
journal = {The annals of applied statistics},
volume = {12},
number = {1},
pages = {540-566},
doi = {10.1214/17-AOAS1102},
pmid = {30224943},
issn = {1932-6157},
abstract = {The analysis of human microbiome data is often based on dimension-reduced graphical displays and clusterings derived from vectors of microbial abundances in each sample. Common to these ordination methods is the use of biologically motivated definitions of similarity. Principal coordinate analysis, in particular, is often performed using ecologically defined distances, allowing analyses to incorporate context-dependent, non-Euclidean structure. In this paper, we go beyond dimension-reduced ordination methods and describe a framework of high-dimensional regression models that extends these distance-based methods. In particular, we use kernel-based methods to show how to incorporate a variety of extrinsic information, such as phylogeny, into penalized regression models that estimate taxonspecific associations with a phenotype or clinical outcome. Further, we show how this regression framework can be used to address the compositional nature of multivariate predictors comprised of relative abundances; that is, vectors whose entries sum to a constant. We illustrate this approach with several simulations using data from two recent studies on gut and vaginal microbiomes. We conclude with an application to our own data, where we also incorporate a significance test for the estimated coefficients that represent associations between microbial abundance and a percent fat.},
}

@article {pmid30224442,
year = {2018},
author = {Tun, MH and Tun, HM and Mahoney, JJ and Konya, TB and Guttman, DS and Becker, AB and Mandhane, PJ and Turvey, SE and Subbarao, P and Sears, MR and Brook, JR and Lou, W and Takarao, TK and Scott, JA and Kozyrskyj, AL and , },
title = {Postnatal exposure to household disinfectants, infant gut microbiota and subsequent risk of overweight in children.},
journal = {CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne},
volume = {190},
number = {37},
pages = {E1097-E1107},
doi = {10.1503/cmaj.170809},
pmid = {30224442},
issn = {1488-2329},
abstract = {BACKGROUND: Emerging links between household cleaning products and childhood overweight may involve the gut microbiome. We determined mediating effects of infant gut microbiota on associations between home use of cleaning products and future overweight.

METHODS: From the Canadian Healthy Infant Longitudinal Development (CHILD) birth cohort, we tested associations between maternal report of cleaning product use and overweight at age 3, and whether associations were mediated by microbial profiles of fecal samples in 3- to 4-month-old infants.

RESULTS: Among 757 infants, the abundance of specific gut microbiota was associated with household cleaning with disinfectants and eco-friendly products in a dose-dependent manner. With more frequent use of disinfectants, Lachnospiraceae increasingly became more abundant (highest v. lowest quintile of use: adjusted odds ratio [AOR] 1.93, 95% confidence interval [CI] 1.08 to 3.45) while genus Haemophilus declined in abundance (highest v. lowest quintile of use: AOR 0.36, 95% CI 0.20 to 0.65). Enterobacteriaceae were successively depleted with greater use of eco-friendly products (AOR 0.45, 95% CI 0.27 to 0.74). Lachnospiraceae abundance significantly mediated associations of the top 30th centile of household disinfectant use with higher body mass index (BMI) z score (p = 0.02) and with increased odds of overweight or obesity (p = 0.04) at age 3. Use of eco-friendly products was associated with decreased odds of overweight or obesity independently of Enterobacteriaceae abundance (AOR 0.44, 95% CI 0.22 to 0.86), with no significant mediation (p = 0.2).

INTERPRETATION: Exposure to household disinfectants was associated with higher BMI at age 3, mediated by gut microbial composition at age 3-4 months. Although child overweight was less common in households that cleaned with eco-friendly products, the lack of mediation by infant gut microbiota suggests another pathway for this association.},
}

@article {pmid30224347,
year = {2018},
author = {Leiva-Gea, I and Sánchez-Alcoholado, L and Martín-Tejedor, B and Castellano-Castillo, D and Moreno-Indias, I and Cardona, AU and Tinahones, FJ and Fernández-García, JC and Queipo-Ortuño, MI},
title = {Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes, MODY2, and Healthy Control Subjects: A Case-Control Study.},
journal = {Diabetes care},
volume = {},
number = {},
pages = {},
doi = {10.2337/dc18-0253},
pmid = {30224347},
issn = {1935-5548},
abstract = {OBJECTIVE: Type 1 diabetes is associated with compositional differences in gut microbiota. To date, no microbiome studies have been performed in maturity-onset diabetes of the young 2 (MODY2), a monogenic cause of diabetes. Gut microbiota of type 1 diabetes, MODY2, and healthy control subjects was compared.

RESEARCH DESIGN AND METHODS: This was a case-control study in 15 children with type 1 diabetes, 15 children with MODY2, and 13 healthy children. Metabolic control and potential factors modifying gut microbiota were controlled. Microbiome composition was determined by 16S rRNA pyrosequencing.

RESULTS: Compared with healthy control subjects, type 1 diabetes was associated with a significantly lower microbiota diversity, a significantly higher relative abundance of Bacteroides, Ruminococcus, Veillonella, Blautia, and Streptococcus genera, and a lower relative abundance of Bifidobacterium, Roseburia, Faecalibacterium, and Lachnospira. MODY2 showed a significantly higher Prevotella abundance and a lower Ruminococcus and Bacteroides abundance. Proinflammatory cytokines and lipopolisaccharides were increased in type 1 diabetes, and gut permeability (determined by zonulin levels) was significantly increased in type 1 diabetes and MODY2. The PICRUSt analysis found an increment of genes related to lipid and amino acid metabolism, ABC transport, lipopolysaccharide biosynthesis, arachidonic acid metabolism, antigen processing and presentation, and chemokine signaling pathways in type 1 diabetes.

CONCLUSIONS: Gut microbiota in type 1 diabetes differs at taxonomic and functional levels not only in comparison with healthy subjects but fundamentally with regard to a model of nonautoimmune diabetes. Future longitudinal studies should be aimed at evaluating if the modulation of gut microbiota in patients with a high risk of type 1 diabetes could modify the natural history of this autoimmune disease.},
}

@article {pmid30224089,
year = {2018},
author = {Carthey, AJR and Gillings, MR and Blumstein, DT},
title = {The Extended Genotype: Microbially Mediated Olfactory Communication.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2018.08.010},
pmid = {30224089},
issn = {1872-8383},
abstract = {Microbes are now known to influence inter- and intraspecific olfactory signaling systems. They do so by producing metabolites that function as odorants. A unique attribute of such odorants is that they arise as a product of microbial-host interactions. These interactions need not be mutualistic, and indeed can be antagonistic. We develop an integrated ecoevolutionary model to explore microbially mediated olfactory communication and a process model that illustrates the various ways that microbial products might contribute to odorants. This novel approach generates testable predictions, including that selection to incorporate microbial products should be a common feature of infochemicals that communicate identity but not those that communicate fitness or quality. Microbes extend an individual's genotype, but also enhance vulnerability to environmental change.},
}

@article {pmid30223906,
year = {2018},
author = {Bredon, M and Dittmer, J and Noël, C and Moumen, B and Bouchon, D},
title = {Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {162},
doi = {10.1186/s40168-018-0536-y},
pmid = {30223906},
issn = {2049-2618},
abstract = {BACKGROUND: Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the environment together with other macroarthropods. Lignocellulose is the main component of plants and is composed of cellulose, lignin and hemicellulose. Its digestion requires the action of multiple Carbohydrate-Active enZymes (called CAZymes), typically acting together as a cocktail with complementary, synergistic activities and modes of action. Some invertebrates express a few endogenous lignocellulose-degrading enzymes but in most species, an efficient degradation and digestion of lignocellulose can only be achieved through mutualistic associations with endosymbionts. Similar to termites, it has been suspected that several bacterial symbionts may be involved in lignocellulose degradation in terrestrial isopods, by completing the CAZyme repertoire of their hosts.

RESULTS: To test this hypothesis, host transcriptomic and microbiome shotgun metagenomic datasets were obtained and investigated from the pill bug Armadillidium vulgare. Many genes of bacterial and archaeal origin coding for CAZymes were identified in the metagenomes of several host tissues and the gut content of specimens from both laboratory lineages and a natural population of A. vulgare. Some of them may be involved in the degradation of cellulose, hemicellulose, and lignin. Reconstructing a lignocellulose-degrading microbial community based on the prokaryotic taxa contributing relevant CAZymes revealed two taxonomically distinct but functionally redundant microbial communities depending on host origin. In parallel, endogenous CAZymes were identified from the transcriptome of the host and their expression in digestive tissues was demonstrated by RT-qPCR, demonstrating a complementary enzyme repertoire for lignocellulose degradation from both the host and the microbiome in A. vulgare.

CONCLUSIONS: Our results provide new insights into the role of the microbiome in the evolution of terrestrial isopods and their adaptive radiation in terrestrial habitats.},
}

@article {pmid30223892,
year = {2018},
author = {Sitaraman, R},
title = {Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {163},
doi = {10.1186/s40168-018-0551-z},
pmid = {30223892},
issn = {2049-2618},
abstract = {The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.},
}

@article {pmid30223687,
year = {2018},
author = {Lin, H and He, QY and Shi, L and Sleeman, M and Baker, MS and Nice, EC},
title = {Proteomics and the microbiome: pitfalls and potential.},
journal = {Expert review of proteomics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14789450.2018.1523724},
pmid = {30223687},
issn = {1744-8387},
abstract = {INTRODUCTION: Human symbiotic microbiota are now known to play important roles in human health and disease. Significant progress in our understanding of the human microbiome has been driven by recent technological advances in the fields of genomics, transcriptomics and proteomics. As a complementary method to metagenomics, proteomics is enabling detailed protein profiling of the microbiome to decipher its structure and function and to analyse its relationship with the human body. Faecal proteomics is being increasingly applied to discover and validate potential health and disease biomarkers, and TGA approved instrumentation and a range of clinical assays are being developed that will collectively play key roles in advancing personalized medicine. Areas covered: This review will introduce the complexity of the microbiome and its role in health and disease (in particular the gastrointestinal tract or gut microbiome), discuss current genomic and proteomic methods for studying this system, including the discovery of potential biomarkers, and outline the development of clinically accepted protocols leading to personalized medicine. Expert commentary: Recognition of the important role the microbiome plays in both health and disease is driving current research in this key area. A proteogenomics approach will be essential to unravel the biologies underlying this complex network.},
}

@article {pmid30223529,
year = {2018},
author = {Lee, SH and Yun, Y and Kim, SJ and Lee, EJ and Chang, Y and Ryu, S and Shin, H and Kim, HL and Kim, HN and Lee, JH},
title = {Association between Cigarette Smoking Status and Composition of Gut Microbiota: Population-Based Cross-Sectional Study.},
journal = {Journal of clinical medicine},
volume = {7},
number = {9},
pages = {},
doi = {10.3390/jcm7090282},
pmid = {30223529},
issn = {2077-0383},
support = {NRF-2017R1D1A1B03035501//National Research Foundation of Korea/ ; NRF-2016R1A6A3A11932719//National Research Foundation of Korea/ ; HI14C0072//Ministry of Health and Welfare/ ; 2010-0027945//National Research Foundation of Korea/ ; },
abstract = {There have been few large-scale studies on the relationship between smoking and gut microbiota. We investigated the relationship between smoking status and the composition of gut microbiota. This was a population-based cross-sectional study using Healthcare Screening Center cohort data. A total of 758 men were selected and divided into three groups: never (n = 288), former (n = 267), and current smokers (n = 203). Among the three groups, there was no difference in alpha diversity, however, Jaccard-based beta diversity showed significant difference (p = 0.015). Pairwise permutational multivariate analysis of variance (PERMANOVA) tests between never and former smokers did not show a difference; however, there was significant difference between never and current smokers (p = 0.017) and between former and current smokers (p = 0.011). Weighted UniFrac-based beta diversity also showed significant difference among the three groups (p = 0.038), and pairwise PERMANOVA analysis of never and current smokers showed significant difference (p = 0.01). In the analysis of bacterial composition, current smokers had an increased proportion of the phylum Bacteroidetes with decreased Firmicutes and Proteobacteria compared with never smokers, whereas there were no differences between former and never smokers. In conclusion, gut microbiota composition of current smokers was significantly different from that of never smokers. Additionally, there was no difference in gut microbiota composition between never and former smokers.},
}

@article {pmid30223263,
year = {2018},
author = {Mörkl, S and Wagner-Skacel, J and Lahousen, T and Lackner, S and Holasek, SJ and Bengesser, SA and Painold, A and Holl, AK and Reininghaus, E},
title = {The Role of Nutrition and the Gut-Brain Axis in Psychiatry: A Review of the Literature.},
journal = {Neuropsychobiology},
volume = {},
number = {},
pages = {1-9},
doi = {10.1159/000492834},
pmid = {30223263},
issn = {1423-0224},
abstract = {INTRODUCTION: Individuals suffering from psychiatric disorders experience high levels of illness burden and a significantly reduced quality of life. Despite targeted psychopharmacological strategies and complementary psychotherapeutic procedures only moderate effects are obtained, and the risk of relapse is high in many patients. Worldwide, psychiatric diseases such as depression are continuously increasing, challenging the personal life of the affected as well as their families, but also whole societies by increasing disability, early retirement and hospitalization. According to current scientific knowledge psychiatric disorders are caused by a multifactorial pathogenesis, including genetics, inflammation and neurotransmitter imbalance; furthermore, also lifestyle-associated factors gain rising importance. In line with this, there is growing evidence that the gut microbiota and nutrition have an impact on the onset and course of psychiatric disorders.

AIM: This narrative review highlights the important role of nutrition in psychiatric care and underlines the significance of nutritional advice in the multifactorial, biopsychosocial treatment of patients. It focuses on current dietary interventions such as the Mediterranean diet, dietary supplements and modifications of the gut microbiota with pre-, pro- and postbiotics.

RESULTS: Recent studies support the connection between the quality of diet, gut microbiota and mental health through regulation of metabolic functions, anti-inflammatory and antiapoptotic properties and the support of neurogenesis. Dietary coaching to improve mental health seems to be an additional, cost-effective, practical, nonpharmacological intervention for individuals with psychiatric disorders.

CONCLUSION: The use of nutritional interventions in psychiatry equips therapists with a promising tool for both the prevention and treatment of psychiatric disorders. Besides pharmacological therapy, psychotherapy and physical activity, nutritional interventions are an important pillar in the multifactorial, biopsychosocial treatment of psychiatric disease and could be used as a potential therapeutic target.},
}

@article {pmid30222209,
year = {2018},
author = {Heilmann, RM and Steiner, JM},
title = {Clinical utility of currently available biomarkers in inflammatory enteropathies of dogs.},
journal = {Journal of veterinary internal medicine},
volume = {},
number = {},
pages = {},
doi = {10.1111/jvim.15247},
pmid = {30222209},
issn = {1939-1676},
support = {//Leipzig University/ ; //German Research Foundation/ ; },
abstract = {Chronic inflammatory enteropathies (CIE) in dogs are a group of disorders that are characterized by chronic persistent or recurrent signs of gastrointestinal disease and histologic evidence of mucosal inflammation. These CIEs are classified as either food-responsive, antibiotic-responsive, or immunosuppressant-responsive enteropathy. Patients not clinically responding to immunomodulatory treatment are grouped as nonresponsive enteropathy and dogs with intestinal protein loss as protein-losing enteropathy. Disease-independent clinical scoring systems were established in dogs for assessment of clinical disease severity and patient monitoring during treatment. Histopathologic and routine clinicopathologic findings are usually not able to distinguish the subgroups of CIE. Treatment trials are often lengthy and further diagnostic tests are usually at least minimally invasive. Biomarkers that can aid in defining the presence of disease, site of origin, severity of the disease process, response to treatment, or a combination of these would be clinically useful in dogs with CIE. This article summarizes the following biomarkers that have been evaluated in dogs with CIE during the last decade, and critically evaluates their potential clinical utility in dogs with CIE: functional biomarkers (cobalamin, methylmalonic acid, folate, α1 -proteinase inhibitor, immunoglobulin A), biochemical biomarkers (C-reactive protein, perinuclear anti-neutrophilic cytoplasmic antibodies, 3-bromotyrosine, N-methylhistamine, calprotectin, S100A12, soluble receptor of advanced glycation end products, cytokines and chemokines, alkaline phosphatase), microbiomic biomarkers (microbiome changes, dysbiosis index), metabolomic biomarkers (serum metabolome), genetic biomarkers (genomic markers, gene expression changes), and cellular biomarkers (regulatory T cells). In addition, important performance criteria of diagnostic tests are briefly reviewed.},
}

@article {pmid30222202,
year = {2018},
author = {Sikora, M and Chrabąszcz, M and Maciejewski, C and Zaremba, M and Waśkiel, A and Olszewska, M and Rudnicka, L},
title = {Intestinal barrier integrity in patients with plaque psoriasis.},
journal = {The Journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1346-8138.14647},
pmid = {30222202},
issn = {1346-8138},
support = {//Ministry of Science and Higher Education/ ; 1M4/NM3/17/17//Medical University of Warsaw/ ; },
abstract = {Psoriasis is a chronic inflammatory systemic disease. Growing evidence suggests that human homeostasis depends on a mutualistic relationship with gut bacteria that produce a number of biologically active compounds. Therefore, enteric microbiota dysbiosis with gut barrier disruption may be an important factor in the development of chronic inflammatory diseases. The aim of our study was to assess non-invasive markers of intestinal barrier integrity in patients with moderate to severe psoriasis. Concentrations of claudin-3 (intestinal epithelial tight junction structure) and intestinal fatty acid binding protein (I-FABP; marker of enterocyte damage) were determined in the blood of patients with chronic plaque psoriasis (n = 20) and healthy individuals (n = 20) using commercially available enzyme-linked immunoassay test kits. Claudin-3 concentration was higher in patients with psoriasis compared with healthy control (median, 54.07 vs 42.36 ng/mL; P < 0.001). Patients with psoriasis also had elevated concentration of plasma I-FABP (median, 708.8 vs 147.1 pg/mL; P < 0.05). Our results support the hypothesis that dysfunction of the intestinal barrier in psoriasis disturbs the homeostatic equilibrium between the microbiota and immune system. Further studies are needed in order to develop new therapeutic interventions based on modulation of intestinal permeability.},
}

@article {pmid30221733,
year = {2018},
author = {Vida, A and Kardos, G and Kovács, T and Bodrogi, BL and Bai, P},
title = {Deletion of poly(ADP‑ribose) polymerase-1 changes the composition of the microbiome in the gut.},
journal = {Molecular medicine reports},
volume = {},
number = {},
pages = {},
doi = {10.3892/mmr.2018.9474},
pmid = {30221733},
issn = {1791-3004},
abstract = {Poly(adenosine diphosphate‑ribose) polymerase (PARP)‑1 is the prototypical PARP enzyme well known for its role in DNA repair and as a pro‑inflammatory protein. Since PARP1 is an important co‑factor of several other pro‑inflammatory proteins, in the present study the possible changes in microbial flora of PARP1 knockout mice were investigated. Samples from the duodenum, cecum and feces from wild type and PARP1 knockout C57BL/6J male mice were collected and 16S ribosomal RNA genes were sequenced. Based on the sequencing results, the microbiome and compared samples throughout the lower part of the gastrointestinal system were reconstructed. The present results demonstrated that the lack of PARP1 enzyme only disturbed the microbial flora of the duodenum, where the biodiversity increased in the knockout animals on the species level but decreased on the order level. The most prominent change was the overwhelming abundance of the family Porphyromonadaceae in the duodenum of PARP1‑/‑ animals, which disappeared in the cecum and feces where families were spread out more evenly than in the wild type animals. The findings of the present study may improve current understanding of the role of PARP1 in chronic inflammatory diseases.},
}

@article {pmid30221593,
year = {2018},
author = {Vargas-Albores, F and Martínez-Córdova, LR and Martínez-Porchas, M and Calderón, K and Lago-Lestón, A},
title = {Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences.},
journal = {Biotechnology & genetic engineering reviews},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/02648725.2018.1513230},
pmid = {30221593},
issn = {2046-5556},
abstract = {The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.},
}

@article {pmid30221488,
year = {2018},
author = {Zhou, D and Huang, XF and Guo, J and Dos-Santos, ML and Vivanco, JM},
title = {Trichoderma gamsii affected herbivore feeding behaviour on Arabidopsis thaliana by modifying the leaf metabolome and phytohormones.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.13310},
pmid = {30221488},
issn = {1751-7915},
support = {201206850028//China Scholarship Council/ ; //Colorado State University Agricultural Experiment Station/ ; },
abstract = {Plants can re-programme their transcriptome, proteome and metabolome to deal with environmental and biotic stress. It has been shown that the rhizosphere microbiome has influence on the plant metabolome and on herbivore behaviour. In the present study, Trichoderma gamsii was isolated from Arabidopsis thaliana rhizosphere soil. The inoculation of roots of Arabidopsis thaliana with T. gamsii significantly inhibited the feeding behaviour of Trichoplusia ni and affected the metabolome as well as the content of phytohormones in Arabidopsis leaves. T. gamsii-treated plant leaves had higher levels of amino acids and lower concentrations of sugars. In addition, T. gamsii-treated plant leaves had more abscisic acid (ABA) and lower levels of salicylic acid (SA) and indole-3-acetic acid (IAA) in comparison with the untreated plants. Furthermore, the inoculation with T. gamsii on different signalling mutants showed that the induction of defences were SA-dependent. These findings indicate that T. gamsii has potential as a new type of biocontrol agent to promote plant repellence to insect attacks.},
}

@article {pmid30221070,
year = {2018},
author = {Holtorf, A and Conrad, A and Holzmann, B and Janssen, KP},
title = {Cell-type specific MyD88 signaling is required for intestinal tumor initiation and progression to malignancy.},
journal = {Oncoimmunology},
volume = {7},
number = {8},
pages = {e1466770},
doi = {10.1080/2162402X.2018.1466770},
pmid = {30221070},
issn = {2162-4011},
abstract = {The signal adapter MyD88, an essential component of Toll-like receptor (TLR) signaling, is important for gut-microbiome interactions. However, its contribution to cancer and its cell-type specific functions are controversially discussed. Therefore, we generated new tissue-specific mouse models and analyzed the clinical importance in human colorectal cancer. A gene-trap was inserted into the murine Myd88 gene (Myd88LSL), yielding MyD88-deficient background with Cre-mediated re-expression in myeloid (MYEL) or intestinal epithelial cells (IECs). These lines were bred with the Apc1638N model that develops invasive adenocarcinoma and analyzed at 12 months. Further, two patient collectives of colorectal cancer (n = 61, and n = 633) were analyzed for expression of Myd88 and TLRs. MyD88 expression was significantly increased in carcinomas, and increased intratumoral levels of MyD88 and TLR pathway components were associated with significantly shorter disease-free (P = .011), and overall survival (P < .0001). In accordance, fully MyD88-deficient mice showed highly significantly decreased tumor incidence, tumor numbers, increased survival, and, importantly, fully lacked malignant lesions. Thus, MyD88 is essential for tumorigenesis and especially progression to malignancy. Tissue-specific re-expression of MyD88 highly significantly increased tumor initiation by differing mechanisms. In intestinal epithelia, MyD88 enhanced epithelial turnover, whereas in myeloid cells, it led to increased production of tumor- and stemness-enhancing cytokines, significantly associated with altered expression of adaptive immune genes. However, neither re-expression of MyD88 in IECs or myeloid cells was sufficient for malignant progression to carcinoma. Thus, MyD88 crucially contributes to colorectal cancer initiation and progression with non-redundant and cell-type specific functions, constituting an attractive therapeutic target.},
}

@article {pmid30220912,
year = {2018},
author = {Dhoble, AS and Lahiri, P and Bhalerao, KD},
title = {Machine learning analysis of microbial flow cytometry data from nanoparticles, antibiotics and carbon sources perturbed anaerobic microbiomes.},
journal = {Journal of biological engineering},
volume = {12},
number = {},
pages = {19},
doi = {10.1186/s13036-018-0112-9},
pmid = {30220912},
issn = {1754-1611},
abstract = {Background: Flow cytometry, with its high throughput nature, combined with the ability to measure an increasing number of cell parameters at once can surpass the throughput of prevalent genomic and metagenomic approaches in the study of microbiomes. Novel computational approaches to analyze flow cytometry data will result in greater insights and actionability as compared to traditional tools used in the analysis of microbiomes. This paper is a demonstration of the fruitfulness of machine learning in analyzing microbial flow cytometry data generated in anaerobic microbiome perturbation experiments.

Results: Autoencoders were found to be powerful in detecting anomalies in flow cytometry data from nanoparticles and carbon sources perturbed anaerobic microbiomes but was marginal in predicting perturbations due to antibiotics. A comparison between different algorithms based on predictive capabilities suggested that gradient boosting (GB) and deep learning, i.e. feed forward artificial neural network with three hidden layers (DL) were marginally better under tested conditions at predicting overall community structure while distributed random forests (DRF) worked better for predicting the most important putative microbial group(s) in the anaerobic digesters viz. methanogens, and it can be optimized with better parameter tuning. Predictive classification patterns with DL (feed forward artificial neural network with three hidden layers) were found to be comparable to previously demonstrated multivariate analysis. The potential applications of this approach have been demonstrated for monitoring the syntrophic resilience of the anaerobic microbiomes perturbed by synthetic nanoparticles as well as antibiotics.

Conclusion: Machine learning can benefit the microbial flow cytometry research community by providing rapid screening and characterization tools to discover patterns in the dynamic response of microbiomes to several stimuli.},
}

@article {pmid30220344,
year = {2018},
author = {Dickson, K and Liu, S and Zhou, J and Langille, M and Holbein, BE and Lehmann, C},
title = {Selective sensitivity of the gut microbiome to iron chelators in polybacterial abdominal sepsis.},
journal = {Medical hypotheses},
volume = {120},
number = {},
pages = {68-71},
doi = {10.1016/j.mehy.2018.08.018},
pmid = {30220344},
issn = {1532-2777},
abstract = {Iron chelation has been proposed as a potential therapy for polybacterial abdominal sepsis. Treatment with iron chelation is known to be able to attenuate bacterial growth. It is hypothesized that the different types of bacteria will exhibit variations in their sensitivity to iron chelation based on differences in their iron metabolism. Bacteria with weaker iron access systems might have their growth reduced initially, but stronger species may also be suppressed. Gram-positive and Gram-negative bacteria are known to possess different iron acquisition systems, which may affect their response to iron chelation. Bacteria which can produce siderophores are at a particular advantage for iron acquisition. Novel iron chelators, which do not act as xenosiderophores, may be effective in depriving these bacteria of iron. This has implications for the treatment of polybacterial sepsis, which might be enhanced if the sensitivity to iron chelation of the primary causative agents is known.},
}

@article {pmid30220333,
year = {2018},
author = {Sandgren, AM and Brummer, RJM},
title = {ADHD-originating in the gut? The emergence of a new explanatory model.},
journal = {Medical hypotheses},
volume = {120},
number = {},
pages = {135-145},
doi = {10.1016/j.mehy.2018.08.022},
pmid = {30220333},
issn = {1532-2777},
abstract = {The microbiome-gut-brain axis paradigm explains that alterations in the central nervous system and behavior may be secondary to functional changes in the gut in general and more specifically the enteric nervous system. An unfavorable development of the intestinal microbial ecosystem, leading to e.g. a diminished microbial diversity, may play a central role. This paper outlines, and describes the theoretical basis of, a novel integrative model explaining the etiology and pathogenesis of ADHD in a microbiota-gut-brain context, taking into account the complexity of the bi-directional signaling between the gut and the brain.},
}

@article {pmid30217275,
year = {2018},
author = {Fenner, J and Silverberg, NB},
title = {Skin diseases associated with atopic dermatitis.},
journal = {Clinics in dermatology},
volume = {36},
number = {5},
pages = {631-640},
doi = {10.1016/j.clindermatol.2018.05.004},
pmid = {30217275},
issn = {1879-1131},
abstract = {Atopic dermatitis is a common chronic pruritic inflammatory skin disorder, characterized by an abnormal skin barrier, immune dysfunction, and an altered skin microbiome. Atopic dermatitis may be seen in conjunction with a variety of other skin disorders due to the complex pathogenesis of atopic dermatitis, involving genetic and environmental factors that are associated with immune dysfunction, barrier defects, and altered skin microbiomes. Skin disorders associated with atopic dermatitis include diseases sharing similar genetic origins like ichthyosis vulgaris, infectious diseases such as impetigo, and eczema herpeticum, in addition to the cutaneous autoimmune diseases, alopecia areata, and vitiligo. Atopic dermatitis is also often linked to such benign conditions as pityriasis alba and keratosis pilaris. This review discusses the cutaneous comorbidities of atopic dermatitis and their relationship via their occurrence in conjunction with atopic dermatitis.},
}

@article {pmid30219863,
year = {2018},
author = {Espina, MDT and Gabarrini, G and Harmsen, HJM and Westra, J and van Winkelhoff, AJ and van Dijl, JM},
title = {Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuy035},
pmid = {30219863},
issn = {1574-6976},
abstract = {Microbial communities inhabiting the human body, collectively called the microbiome, are critical modulators of immunity. This notion is underpinned by associations between changes in the microbiome and particular autoimmune disorders. Specifically, in rheumatoid arthritis, one of the most frequently occurring autoimmune disorders worldwide, changes in the oral and gut microbiomes have been implicated in the loss of tolerance against self-antigens and in increased inflammatory events promoting the damage of joints. In the present review, we highlight recently gained insights in the roles of microbes in the etiology of rheumatoid arthritis. In addition, we address important immunomodulatory processes, including biofilm formation and neutrophil function, which have been implicated in host-microbe interactions relevant for rheumatoid arthritis. Lastly, we present recent advances in the development and evaluation of emerging microbiome-based therapeutic approaches. Altogether, we conclude that the key to uncovering the etiopathogenesis of rheumatoid arthritis will lie in the immunomodulatory functions of the oral and gut microbiomes.},
}

@article {pmid30219275,
year = {2018},
author = {Riquelme, JA and Ferreccio, C and Lavandero, S},
title = {Editorial commentary: Cardiometabolic diseases and gut microbiota-removing the veil.},
journal = {Trends in cardiovascular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tcm.2018.08.009},
pmid = {30219275},
issn = {1873-2615},
}

@article {pmid30219104,
year = {2018},
author = {Nygaard, AB and Charnock, C},
title = {Longitudinal development of the dust microbiome in a newly opened Norwegian kindergarten.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {159},
doi = {10.1186/s40168-018-0553-x},
pmid = {30219104},
issn = {2049-2618},
abstract = {BACKGROUND: In Norway, 91% of children aged 1-5 attend kindergarten where they are exposed to indoor microbiomes which can have relevance for development and health. In order to gain a better understanding of the composition of the indoor microbiome and how it is affected by occupancy over time, floor dust samples from a newly opened kindergarten were investigated. Samples were collected during an 11-month period. Samples were analyzed for bacterial composition using 16S rRNA gene sequencing. Samples were also screened for four clinically relevant antibiotic resistance genes. In addition, Petrifilm analyses were used to evaluate surface hygiene.

RESULTS: Significant changes in the microbial community composition were observed over time (PERMANOVA, P < 0.05). Particularly, changes in the abundance and the proportions of human associated bacteria were found. A decrease in the prevalence of Propionibacterium from over 16% abundance to less than 1% and an increase in Streptococcus from 10 to 16% were the most significant findings. Four classes of clinically relevant antibiotic resistance genes were tested for; three were detected in the dust, indicating the presence of resistant bacteria and a potential for resistance spread. Petrifilm analysis showed that some surfaces in the kindergarten were of consistent poor hygienic quality, and new hygienic routines are required.

CONCLUSIONS: This study, which is the first of its kind performed at a newly opened kindergarten, reveals changes in the microbiome over time as well as the presence of antibiotic resistance genes and hygiene issues which are of relevance for occupant health.},
}

@article {pmid30219094,
year = {2018},
author = {Bope, A and Weir, MH and Pruden, A and Morowitz, M and Mitchell, J and Dannemiller, KC},
title = {Translating research to policy at the NCSE 2017 symposium "Microbiology of the Built Environment: Implications for Health and Design".},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {160},
doi = {10.1186/s40168-018-0552-y},
pmid = {30219094},
issn = {2049-2618},
support = {G-2016-7221//Alfred P. Sloan Foundation/ ; },
abstract = {Here, we summarize a symposium entitled "Microbiology of the Built Environment: Implications for Health and Design" that was presented at the National Council for Science and the Environment (NCSE) 17th National Conference and Global Forum in January 2017. We covered topics including indoor microbial exposures and childhood asthma, the influence of hospital design on neonatal development, the role of the microbiome in our premise (i.e., building) plumbing systems, antibiotic resistance, and quantitative microbial risk assessment. This symposium engaged the broader scientific and policy communities in a discussion to increase awareness of this critical research area and translate findings to practice.},
}

@article {pmid30218543,
year = {2018},
author = {Zhan, X and Xue, L and Zheng, H and Plantinga, A and Wu, MC and Schaid, DJ and Zhao, N and Chen, J},
title = {A small-sample kernel association test for correlated data with application to microbiome association studies.},
journal = {Genetic epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/gepi.22160},
pmid = {30218543},
issn = {1098-2272},
support = {//US Public Health Service/ ; GM065450//National Institutes of Health/ ; //Mayo Clinic Center for Individualized Medicine/ ; },
abstract = {Recent research has highlighted the importance of the human microbiome in many human disease and health conditions. Most current microbiome association analyses focus on unrelated samples; such methods are not appropriate for analysis of data collected from more advanced study designs such as longitudinal and pedigree studies, where outcomes can be correlated. Ignoring such correlations can sometimes lead to suboptimal results or even possibly biased conclusions. Thus, new methods to handle correlated outcome data in microbiome association studies are needed. In this paper, we propose the correlated sequence kernel association test (CSKAT) to address such correlations using the linear mixed model. Specifically, random effects are used to account for the outcome correlations and a variance component test is used to examine the microbiome effect. Compared to existing genetic association tests for longitudinal and family samples, we implement a correction procedure to better calibrate the null distribution of the score test statistic to accommodate the small sample size nature of data collected from a typical microbiome study. Comprehensive simulation studies are conducted to demonstrate the validity and efficiency of our method, and we show that CSKAT achieves a higher power than existing methods while correctly controlling the Type I error rate. We also apply our method to a microbiome data set collected from a UK twin study to illustrate its potential usefulness. A free implementation of our method in R software is available at https://github.com/jchen1981/SSKAT.},
}

@article {pmid30218470,
year = {2018},
author = {Hurgobin, B and de Jong, E and Bosco, A},
title = {Insights into respiratory disease through bioinformatics.},
journal = {Respirology (Carlton, Vic.)},
volume = {},
number = {},
pages = {},
doi = {10.1111/resp.13401},
pmid = {30218470},
issn = {1440-1843},
support = {//National Health and Medical Research Council/ ; //Simon Lee Foundation/ ; },
abstract = {Respiratory diseases such as asthma, chronic obstructive pulmonary disease and lung cancer represent a critical area for medical research as millions of people are affected globally. The development of new strategies for treatment and/or prevention, and the identification of biomarkers for patient stratification and early detection of disease inception are essential to reducing the impact of lung diseases. The successful translation of research into clinical practice requires a detailed understanding of the underlying biology. In this regard, the advent of next-generation sequencing and mass spectrometry has led to the generation of an unprecedented amount of data spanning multiple layers of biological regulation (genome, epigenome, transcriptome, proteome, metabolome and microbiome). Dealing with this wealth of data requires sophisticated bioinformatics and statistical tools. Here, we review the basic concepts in bioinformatics and genomic data analysis and illustrate the application of these tools to further our understanding of lung diseases. We also highlight the potential for data integration of multi-omic profiles and computational drug repurposing to define disease subphenotypes and match them to targeted therapies, paving the way for personalized medicine.},
}

@article {pmid30218426,
year = {2018},
author = {Dong, T and Pisegna, J},
title = {Passing the "Acid Test": Do Proton Pump Inhibitors Affect the Composition of the Microbiome?.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-018-5273-3},
pmid = {30218426},
issn = {1573-2568},
}

@article {pmid30217998,
year = {2018},
author = {Ren, R and Wang, Z and Sun, H and Gao, X and Sun, G and Peng, L and Yan, B and Yang, Y},
title = {The gastric mucosal-associated microbiome in patients with gastric polyposis.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13817},
doi = {10.1038/s41598-018-31738-2},
pmid = {30217998},
issn = {2045-2322},
abstract = {The characteristics of the gastric microbiota in patients with gastric polyposis (GP) remain unclear. Given this we collected gastric antrum and gastric body biopsies from healthy controls (HC.A and HC.B group) and gastric antrum, gastric body and polyp biopsies from patients with multiple gastric polyps (GP.A, GP.B and GP.P group) for 16S rDNA sequencing. The results showed that the diversity of the gastric flora in the GP group was significantly lower than that of the HC group. The gastric flora composition of the GP group was significantly different from the HC group. However, flora diversity and compositions in different parts of the stomach (gastric antrum, gastric body or polyp tissue) were not significantly different. H. pylori abundance could influence the composition of gastric microbiota. Meanwhile, patients with fundic gland polyps (FGPs) and those with hyperplastic polyps (HPs) had considerably similar gastric bacterial compositions. We constructed a microbial dysbiosis index (MDI) based on the gastric microbiota at the genus level as a predictive model, and it was able to distinguish between individuals in the GP and HC groups. These findings showed that intragastric flora dysbiosis may be closely related to the occurrence and development of gastric polyps.},
}

@article {pmid30217851,
year = {2018},
author = {Stough, JMA and Kolton, M and Kostka, JE and Weston, DJ and Pelletier, DA and Wilhelm, SW},
title = {Diversity of active viral infections within the Sphagnum microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.01124-18},
pmid = {30217851},
issn = {1098-5336},
abstract = {Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of 6 Sphagnum plants were obtained from a peatland in northern Minnesota and total RNA extracted and sequenced. Metatranscriptomes were assembled and contigs screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein, gp23, as a marker for phage diversity, we identified 33 contigs representing undocumented phage s that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) major capsid protein were used as markers for ssRNA viruses and NCLDV, respectively. In total 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent near-complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinto-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades, and suggest viruses may play a considerable role in the ecology of the Sphagnum microbiome.SignificanceSphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor its own growth over other plant species. This slows rates of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome, and identifying new potential model systems to study virus-host interactions in the peatland ecosystem.},
}

@article {pmid30217839,
year = {2018},
author = {Han, W and He, P and Shao, L and Lü, F},
title = {Metabolic Interactions of a Chain Elongation Microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.01614-18},
pmid = {30217839},
issn = {1098-5336},
abstract = {Carbon chain elongation (CCE), a reaction within the carboxylate platform that elongates short-chain to medium-chain carboxylates by mixed culture, has attracted worldwide interest. The present study provides insights into the microbial diversity and predictive microbial metabolic pathways of a mixed-culture CCE microbiome based on comparative analysis of the metagenome and metatranscriptome. We found that the acclimated chain elongation microbiome shared a highly similar microbial structure with the original inoculating biogas reactor culture; however, the metabolic activities were completely different, demonstrating the high stability of the microbial structure and flexibility of its functions. Additionally, the fatty acid biosynthesis pathway (FAB pathway), rather than the well-known reverse β-oxidation pathway (RBO pathway) for CCE, was more active and pivotal, though the FAB pathway had more steps and was more ATP consuming, which is a phenomenon that has rarely been observed in previous CCE studies. Total 91 draft genomes were reconstructed from the metagenomic reads, of which three were near-completed (completeness > 97 %) and were assigned to unknown strains of Methanolinea tarda, Bordetella avium and Planctomycetaceae. The last two strains are probably the new-found active participators of CCE in the mixed culture. Finally, a conceptual framework of CCE, including both two pathways and potential participators, was proposed.Importance Carbon chain elongation means the conversion of short-chain volatile fatty acids to medium-chain carboxylates, such as n-caproate and n-caprylate with electron donors under anaerobic condition. This bio-reaction can both expand the resource of valuable biochemicals and broaden the utilization of low-grade organic residues in a sustainable biorefinery context. Clostridium kluyveri is conventionally considered as model microbe for carbon chain elongation which uses the reverse β-oxidation pathway. However, little is known about the detailed microbial structure and function of other abundant microorganism in a mixed culture (or open culture) of chain elongation. We conducted the comparative metagenomic and metatranscriptomic analysis of a chain elongation microbiome to throw light on the underlying functional microbes and alternative pathways.},
}

@article {pmid30216146,
year = {2018},
author = {Rodríguez Hernáez, J and Cerón Cucchi, ME and Cravero, S and Martinez, MC and Gonzalez, S and Puebla, A and Dopazo, J and Farber, M and Paniego, N and Rivarola, M},
title = {The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid.},
journal = {Microbial genomics},
volume = {},
number = {},
pages = {},
doi = {10.1099/mgen.0.000216},
pmid = {30216146},
issn = {2057-5858},
abstract = {Butyrivibrio fibrisolvens forms part of the gastrointestinal microbiome of ruminants and other mammals, including humans. Indeed, it is one of the most common bacteria found in the rumen and plays an important role in ruminal fermentation of polysaccharides, yet, to date, there is no closed reference genome published for this species in any ruminant animal. We successfully assembled the nearly complete genome sequence of B. fibrisolvens strain INBov1 isolated from cow rumen using Illumina paired-end reads, 454 Roche single-end and mate pair sequencing technology. Additionally, we constructed an optical restriction map of this strain to aid in scaffold ordering and positioning, and completed the first genomic structure of this species. Moreover, we identified and assembled the first chromid of this species (pINBov266). The INBov1 genome encodes a large set of genes involved in the cellulolytic process but lacks key genes. This seems to indicate that B. fibrisolvens plays an important role in ruminal cellulolytic processes, but does not have autonomous cellulolytic capacity. When searching for genes involved in the biohydrogenation of unsaturated fatty acids, no linoleate isomerase gene was found in this strain. INBov1 does encode oleate hydratase genes known to participate in the hydrogenation of oleic acids. Furthermore, INBov1 contains an enolase gene, which has been recently determined to participate in the synthesis of conjugated linoleic acids. This work confirms the presence of a novel chromid in B. fibrisolvens and provides a new potential reference genome sequence for this species, providing new insight into its role in biohydrogenation and carbohydrate degradation.},
}

@article {pmid30215734,
year = {2018},
author = {Jun, S},
title = {Ethnicity May Be Important for Studying the Role of the Microbiome and Vitamin D Receptor in IBD.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izy285},
pmid = {30215734},
issn = {1536-4844},
}

@article {pmid30215698,
year = {2018},
author = {Kang, C and LeRoith, D and Gallagher, EJ},
title = {Diabetes, obesity and breast cancer.},
journal = {Endocrinology},
volume = {},
number = {},
pages = {},
doi = {10.1210/en.2018-00574},
pmid = {30215698},
issn = {1945-7170},
abstract = {The rates of obesity and diabetes are increasing worldwide while the age of onset for both obesity and diabetes are decreasing steadily. Obesity and diabetes are associated with multiple factors that contribute to the increased risk of a number of different cancers, including breast cancer. These factors are hyperinsulinemia, elevated insulin-like growth factors, hyperglycemia, dyslipidemia, adipokines, inflammatory cytokines and the gut microbiome. In this review we discuss the current understanding of the complex signaling pathways underlying these multiple factors involved in the obesity/diabetes-breast cancer link, with a focus particularly on the roles of insulin / IGF system and dyslipidemia in pre-clinical breast cancer models. We review some of the therapeutic strategies to target these metabolic derangements in cancer. Future research directions and potential therapeutic strategies are also discussed.},
}

@article {pmid30215540,
year = {2018},
author = {Mainz, JG and Jaudszus, A and Pletz, MW},
title = {Development of a clinical decision rule for diagnosing sinus infections - to reduce unnecessary antibiotic prescribing.},
journal = {Expert review of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17512433.2018.1524753},
pmid = {30215540},
issn = {1751-2441},
}

@article {pmid30215383,
year = {2018},
author = {Flume, PA and Chalmers, JD and Olivier, KN},
title = {Advances in bronchiectasis: endotyping, genetics, microbiome, and disease heterogeneity.},
journal = {Lancet (London, England)},
volume = {392},
number = {10150},
pages = {880-890},
doi = {10.1016/S0140-6736(18)31767-7},
pmid = {30215383},
issn = {1474-547X},
abstract = {Bronchiectasis is characterised by pathological dilation of the airways. More specifically, the radiographic demonstration of airway enlargement is the common feature of a heterogeneous set of conditions and clinical presentations. No approved therapies exist for the condition other than for bronchiectasis caused by cystic fibrosis. The heterogeneity of bronchiectasis is a major challenge in clinical practice and the main reason for difficulty in achieving endpoints in clinical trials. Recent observations of the past 2 years have improved the understanding of physicians regarding bronchiectasis, and have indicated that it might be more effective to classify patients in a different way. Patients could be categorised according to a heterogeneous group of endotypes (defined by a distinct functional or pathobiological mechanism) or by clinical phenotypes (defined by relevant and common features of the disease). In doing so, more specific therapies needed to effectively treat patients might finally be developed. Here, we describe some of the recent advances in endotyping, genetics, and disease heterogeneity of bronchiectasis including observations related to the microbiome.},
}

@article {pmid30215118,
year = {2018},
author = {Weichert, W},
title = {[Molecular predictors in immune oncology].},
journal = {Der Pathologe},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00292-018-0508-9},
pmid = {30215118},
issn = {1432-1963},
abstract = {The current rapid development of novel therapeutic approaches in immune oncology (IO) and specifically in the field of immune checkpoint inhibition is accompanied by an equally dynamic development of novel biomarker approaches for the identification of responding/non-responding patients under IO treatment. In addition to the measurement of the expression of checkpoint ligands/receptors, complex molecular predictors are gaining increasing attention in certain IO treatment constellations. This includes the entity informed identification of molecularly defined biological tumor subtypes (e.g., microsatellite instable neoplasms), the measurement of tumor mutational load and immune cell effector signatures as relatively routine diagnostic compatible novel biomarker strategies. In addition, a multitude of even more complex molecular IO biomarker approaches is emerging. This development is accompanied by new patient selection strategies which are based on the simultaneous combinatorial evaluation of more than one parameter. This article provides a comprehensive overview on currently relevant aspects in the field of IO biomarkers.},
}

@article {pmid30214898,
year = {2018},
author = {Trinh, P and Zaneveld, JR and Safranek, S and Rabinowitz, PM},
title = {One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review.},
journal = {Frontiers in public health},
volume = {6},
number = {},
pages = {235},
doi = {10.3389/fpubh.2018.00235},
pmid = {30214898},
issn = {2296-2565},
abstract = {The One Health concept stresses the ecological relationships between human, animal, and environmental health. Much of the One Health literature to date has examined the transfer of pathogens from animals (e.g., emerging zoonoses) and the environment to humans. The recent rapid development of technology to perform high throughput DNA sequencing has expanded this view to include the study of entire microbial communities. Applying the One Health approach to the microbiome allows for consideration of both pathogenic and non-pathogenic microbial transfer between humans, animals, and the environment. We review recent research studies of such transmission, the molecular and statistical methods being used, and the implications of such microbiome relationships for human health. Our review identified evidence that the environmental microbiome as well as the microbiome of animals in close contact can affect both the human microbiome and human health outcomes. Such microbiome transfer can take place in the household as well as the workplace setting. Urbanization of built environments leads to changes in the environmental microbiome which could be a factor in human health. While affected by environmental exposures, the human microbiome also can modulate the response to environmental factors through effects on metabolic and immune function. Better understanding of these microbiome interactions between humans, animals, and the shared environment will require continued development of improved statistical and ecological modeling approaches. Such enhanced understanding could lead to innovative interventions to prevent and manage a variety of human health and disease states.},
}

@article {pmid30214266,
year = {2018},
author = {Sunkara, T and Rawla, P and Ofosu, A and Gaduputi, V},
title = {Fecal microbiota transplant - a new frontier in inflammatory bowel disease.},
journal = {Journal of inflammation research},
volume = {11},
number = {},
pages = {321-328},
doi = {10.2147/JIR.S176190},
pmid = {30214266},
issn = {1178-7031},
abstract = {Inflammatory bowel disease (IBD) is a chronic multifactorial disease that affects the gastrointestinal tract and results from an aberrant immune response toward luminal antigens in genetically susceptible people. Most of the current therapies for IBD focus on the management of the inflammation by using corticosteroids, immune modulators, and more recently, monoclonal antibodies (biological therapy). Although these therapies provide benefit in most cases, there are still a significant number of patients who do not respond or become refractory over time, suggesting the need for alternative therapeutic options. In the last decade, it has been recognized that "dysbiosis," an imbalanced gut microbiota, is a key element in IBD suggesting microbiome-based therapies as an attractive approach. Recently, fecal microbiota transplant (FMT) has been successfully used for the treatment of Clostridium difficile infection, and it is now under investigation for the treatment of IBD. Clinical trials data are still poor but strongly support a future introduction of FMT in therapy to manage IBD microbiome. More studies are needed to assess the optimal route of administration and the frequency of FMT, the best matched donor for each patient as well as the risks associated with FMT in IBD.},
}

@article {pmid30214170,
year = {2018},
author = {Ticinesi, A and Tana, C and Nouvenne, A and Prati, B and Lauretani, F and Meschi, T},
title = {Gut microbiota, cognitive frailty and dementia in older individuals: a systematic review.},
journal = {Clinical interventions in aging},
volume = {13},
number = {},
pages = {1497-1511},
doi = {10.2147/CIA.S139163},
pmid = {30214170},
issn = {1178-1998},
abstract = {Cognitive frailty, defined as the coexistence of mild cognitive impairment symptoms and physical frailty phenotype in older persons, is increasingly considered the main geriatric condition predisposing to dementia. Recent studies have demonstrated that gut microbiota may be involved in frailty physiopathology by promoting chronic inflammation and anabolic resistance. The contribution of gut microbiota to the development of cognitive impairment and dementia is less defined, even though the concept of "gut-brain axis" has been well demonstrated for other neuropsychiatric disorders. The aim of this systematic review was to summarize the current state-of-the-art literature on the gut microbiota alterations associated with cognitive frailty, mild cognitive impairment and dementia and elucidate the effects of pre- or probiotic administration on cognitive symptom modulation in animal models of aging and human beings. We identified 47 papers with original data (31 from animal studies and 16 from human studies) suitable for inclusion according to our aims. We concluded that several observational and intervention studies performed in animal models of dementia (mainly Alzheimer's disease) support the concept of a gut-brain regulation of cognitive symptoms. Modulation of vagal activity and bacterial synthesis of substances active on host neural metabolism, inflammation and amyloid deposition are the main mechanisms involved in this physiopathologic link. Conversely, there is a substantial lack of human data, both from observational and intervention studies, preventing to formulate any clinical recommendation on this topic. Gut microbiota modulation of cognitive function represents, however, a promising area of research for identifying novel preventive and treatment strategies against dementia.},
}

@article {pmid30214028,
year = {2018},
author = {Meredith, LK and Ogée, J and Boye, K and Singer, E and Wingate, L and von Sperber, C and Sengupta, A and Whelan, M and Pang, E and Keiluweit, M and Brüggemann, N and Berry, JA and Welander, PV},
title = {Soil exchange rates of COS and CO18O differ with the diversity of microbial communities and their carbonic anhydrase enzymes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0270-2},
pmid = {30214028},
issn = {1751-7370},
support = {1331214//NSF | Directorate for Geosciences (GEO)/ ; CSP 2033//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-76SF00515//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; 338264//EC | European Research Council (ERC)/ ; Early Postdoc Mobility Fellowship//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {Differentiating the contributions of photosynthesis and respiration to the global carbon cycle is critical for improving predictive climate models. Carbonic anhydrase (CA) activity in leaves is responsible for the largest biosphere-atmosphere trace gas fluxes of carbonyl sulfide (COS) and the oxygen-18 isotopologue of carbon dioxide (CO18O) that both reflect gross photosynthetic rates. However, CA activity also occurs in soils and will be a source of uncertainty in the use of COS and CO18O as carbon cycle tracers until process-based constraints are improved. In this study, we measured COS and CO18O exchange rates and estimated the corresponding CA activity in soils from a range of biomes and land use types. Soil CA activity was not uniform for COS and CO2, and patterns of divergence were related to microbial community composition and CA gene expression patterns. In some cases, the same microbial taxa and CA classes catalyzed both COS and CO2 reactions in soil, but in other cases the specificity towards the two substrates differed markedly. CA activity for COS was related to fungal taxa and β-D-CA expression, whereas CA activity for CO2 was related to algal and bacterial taxa and α-CA expression. This study integrates gas exchange measurements, enzyme activity models, and characterization of soil taxonomic and genetic diversity to build connections between CA activity and the soil microbiome. Importantly, our results identify kinetic parameters to represent soil CA activity during application of COS and CO18O as carbon cycle tracers.},
}

@article {pmid30213625,
year = {2018},
author = {Grayson, MH and Feldman, S and Prince, BT and Patel, PJ and Matsui, EC and Apter, AJ},
title = {Advances in asthma in 2017: Mechanism, biologics, and genetics.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2018.08.033},
pmid = {30213625},
issn = {1097-6825},
abstract = {This review summarizes some of the most significant advances in asthma research over the past year. We first focus on novel discoveries in the mechanism of asthma development and exacerbation. This is followed by a discussion of potential new biomarkers, including the use of radiographic markers of disease. Several new biologics have become available to the clinician in the past year, and we summarize these advances and how they may influence the clinical delivery of asthma care. Following this, important findings in the genetics of asthma and heterogeneity in phenotypes of the disease are explored, as is the role the environment plays in shaping the development and exacerbation of asthma. Finally, we conclude with a discussion of advances in health literacy and how they will impact asthma care.},
}

@article {pmid30213352,
year = {2018},
author = {Pahel, BT and Rowan-Legg, A and Quinonez, RB},
title = {A Developmental Approach to Pediatric Oral Health.},
journal = {Pediatric clinics of North America},
volume = {65},
number = {5},
pages = {885-907},
doi = {10.1016/j.pcl.2018.05.003},
pmid = {30213352},
issn = {1557-8240},
abstract = {Orofacial growth and development is a complex process spanning the life course. This article provides an oral health overview in the context of overall growth, physical and social development from infancy through adolescence. It reviews oral health-specific developmental milestones during childhood (0-12 years) and adolescence (≥13 years). It examines issues particular to each age category or spanning multiple ages (eg, pediatric overweight and obesity, tobacco use, and dental trauma) in relation to oral health and development. In addition, the oral microbiome and its potential role in informing personalized oral health care across the life course is discussed.},
}

@article {pmid30212959,
year = {2018},
author = {Huang, Q and Wang, Y and Xia, Y and Li, L and Luo, J and Xia, S and Sun, Y and Miao, Y and Wang, K and Chen, Y},
title = {Testing the neutral theory of biodiversity with the microbiome dataset from cystic fibrosis patients.},
journal = {Medicine},
volume = {97},
number = {37},
pages = {e12248},
doi = {10.1097/MD.0000000000012248},
pmid = {30212959},
issn = {1536-5964},
abstract = {Cystic fibrosis (CF) is a hereditary disease that is characterized by defective mucociliary clearance, airway obstruction, chronic infection, and persistent inflammation. Cystic fibrosis pulmonary exacerbation (CFPE) majorly causes the morbidity of CF patients. Although CF has been demonstrated to change the composition of lung microbial community, previous studies have not made efforts to study the differences in the mechanism of assembly and diversity maintenance of lung microbial community in CF patients. In this study, we applied the neutral theory of biodiversity to comparatively investigate the assembly and diversity maintenance of the lung microbial community before and after the antibiotic treatment by reanalyzing the dataset from Fodor et al's study. We found that no one sample in the lung microbial communities of the sputum samples of Exacerbation group, nor those of End-of-treatment group satisfied the predictions of neutral model, suggesting that the neutral-process does not dominate in CF patients before and after antibiotic treatments. By comparing the biodiversity parameter between Exacerbation and End-of-treatment group, we found that the former had the significantly higher biodiversity, but the change in diversity parameter is slight and the P value is close to.05 (P value = .41). Therefore, our second finding is that although CFPE may increase the biodiversity of lung microbial community, the change is not essential.},
}

@article {pmid30180541,
year = {2018},
author = {Hill, AB and Beitelshees, M and Nayerhoda, R and Pfeifer, BA and Jones, CH},
title = {Engineering a Next-Generation Glycoconjugate-Like Streptococcus pneumoniae Vaccine.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.8b00100},
pmid = {30180541},
issn = {2373-8227},
abstract = {We detail the development of a next-generation Streptococcus pneumoniae liposomal encapsulation of polysaccharides (LEPS) vaccine, with design characteristics geared toward best-in-class efficacy. The first generation LEPS vaccine, which contained 20 encapsulated pneumococcal capsular polysaccharides (CPSs) and two surface-displayed virulence-associated proteins (GlpO and PncO), enabling prophylactic potency against 70+ serotypes of Streptococcus pneumoniae (the causative agent of pneumococcal disease), was rationally redesigned for advanced clinical readiness and best-in-class coverage. In doing so, the virulent-specific GlpO protein antigen was removed from the final formulation due to off-target immunogenicity toward bacterial species within the human microbiome, while directed protection was maintained by increasing the dose of PncO from 17 to 68 μg. LEPS formulation parameters also readily facilitated an increase in CPS valency (to a total of 24) and systematic variation in protein-liposome attachment mechanisms in anticipation of clinical translation. An additional safety assessment study demonstrated that LEPS does not exhibit appreciable toxicological effects even when administered at ten times the effective dose. In summary, this new design offers the broadest, safest, and most-complete protection while maintaining desirable glycoconjugate-like features, positioning the LEPS vaccine platform for clinical success and a global health impact.},
}

@article {pmid30212750,
year = {2018},
author = {Wang, CZ and Yao, H and Zhang, CF and Chen, L and Wan, JY and Huang, WH and Zeng, J and Zhang, QH and Liu, Z and Yuan, J and Bi, Y and Sava-Segal, C and Du, W and Xu, M and Yuan, CS},
title = {American ginseng microbial metabolites attenuate DSS-induced colitis and abdominal pain.},
journal = {International immunopharmacology},
volume = {64},
number = {},
pages = {246-251},
doi = {10.1016/j.intimp.2018.09.005},
pmid = {30212750},
issn = {1878-1705},
abstract = {Inflammatory bowel disease (IBD) is a significant public health problem in the United States. Abdominal pain is a major complaint among individuals with IBD. Successful IBD management not only controls enteric inflammation, but also reduces abdominal discomfort. Recently, increased attention has been focused on alternative strategies for IBD management. HPLC/Q-TOF-MS analysis was employed to evaluate the intestinal microbiome's biotransformation of parent American ginseng compounds into their metabolites. Using a DSS mouse model, the effects of American ginseng microbial metabolites on chemically induced colitis was investigated with disease activity index and histological assessment. Expressions of inflammatory cytokines were determined using real-time PCR and ELISA. Abdominal pain was evaluated using the von Frey filament test. After the gut microbiome's biotransformation, the major metabolites were found to be the compound K and ginsenoside Rg3. Compared with the DSS animal group, American ginseng treatment significantly attenuated experimental colitis, as supported by the histological assessment. The enteric microbiome-derived metabolites of ginseng significantly attenuated the abdominal pain. American ginseng treatment significantly reduced gut inflammation, consistent with pro-inflammatory cytokine level changes. The gut microbial metabolite compound K showed significant anti-inflammatory effects even at low concentrations, compared to its parent ginsenoside Rb1. American ginseng intestinal microbial metabolites significantly reduced chemically-induced colitis and abdominal pain, as mediated by the inhibition of pro-inflammatory cytokine expression. Intestinal microbial metabolism plays a critical role in American ginseng mediated colitis management.},
}

@article {pmid30212730,
year = {2018},
author = {Roodt, AP and Naudé, Y and Stoltz, A and Rohwer, E},
title = {Human skin volatiles: Passive sampling and GC × GC-ToFMS analysis as a tool to investigate the skin microbiome and interactions with anthropophilic mosquito disease vectors.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1097-1098},
number = {},
pages = {83-93},
doi = {10.1016/j.jchromb.2018.09.002},
pmid = {30212730},
issn = {1873-376X},
abstract = {Volatile organic compounds (VOCs) emanating from the surfaces of human skin are of great interest to researchers in medical and forensic fields, as well as to biologists studying the ecology of blood-feeding insect vectors of human disease. Research involving the comparison of relative abundances of VOCs emanating from human skin is currently limited by the methodology used for sample collection and pre-concentration. The use of in-house developed silicone rubber (polydimethylsiloxane (PDMS)) passive sampling devices constructed in the form of bracelets and anklets was explored to address this need. The easy-to-use samplers were employed as non-invasive passive sampling devices for the non-targeted collection and concentration of volatile human skin emissions prior to thermal desorption thereof coupled with comprehensive gas chromatographic time-of-flight mass spectrometric (GC × GC-TOFMS) analysis. Compounds collected were from a wide range of compound classes. Several compounds, notably cyclic ketones, identified have not been previously reported in skin volatile literature. Comparison of normalized unique mass peak area signals has revealed relative quantitative differences and similarities between the samples collected from two individuals' wrists and as well as between an individual's wrist and ankle. The sampling method was evaluated based on its ability to provide many candidate compounds for potential biomarker discovery. The results show the ability of the new sampling method for augmenting the current knowledge on human skin volatile emissions. The samplers are both easy to use and economical. Applications explored include the study of the complex relationships between the human skin microbiome and the attractiveness of individuals to anthropophilic blood host seeking mosquitoes.},
}

@article {pmid30212648,
year = {2018},
author = {Teo, SM and Tang, HHF and Mok, D and Judd, LM and Watts, SC and Pham, K and Holt, BJ and Kusel, M and Serralha, M and Troy, N and Bochkov, YA and Grindle, K and Lemanske, RF and Johnston, SL and Gern, JE and Sly, PD and Holt, PG and Holt, KE and Inouye, M},
title = {Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease.},
journal = {Cell host & microbe},
volume = {24},
number = {3},
pages = {341-352.e5},
doi = {10.1016/j.chom.2018.08.005},
pmid = {30212648},
issn = {1934-6069},
abstract = {Repeated cycles of infection-associated lower airway inflammation drive the pathogenesis of persistent wheezing disease in children. In this study, the occurrence of acute respiratory tract illnesses (ARIs) and the nasopharyngeal microbiome (NPM) were characterized in 244 infants through their first five years of life. Through this analysis, we demonstrate that >80% of infectious events involve viral pathogens, but are accompanied by a shift in the NPM toward dominance by a small range of pathogenic bacterial genera. Unexpectedly, this change frequently precedes the detection of viral pathogens and acute symptoms. Colonization of illness-associated bacteria coupled with early allergic sensitization is associated with persistent wheeze in school-aged children, which is the hallmark of the asthma phenotype. In contrast, these bacterial genera are associated with "transient wheeze" that resolves after age 3 years in non-sensitized children. Thus, to complement early allergic sensitization, monitoring NPM composition may enable early detection and intervention in high-risk children.},
}

@article {pmid30212521,
year = {2018},
author = {Pauer, H and Hardoim, CCP and Teixeira, FL and Miranda, KR and Barbirato, DDS and Carvalho, DP and Antunes, LCM and Leitão, ÁADC and Lobo, LA and Domingues, RMCP},
title = {Impact of violacein from Chromobacterium violaceum on the mammalian gut microbiome.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0203748},
doi = {10.1371/journal.pone.0203748},
pmid = {30212521},
issn = {1932-6203},
abstract = {Violacein is a violet pigment produced by Chromobacterium violaceum that possesses several functions such as antibacterial, antiviral, antifungal, and antioxidant activities. The search for potential compounds and therapies that may interfere with and modulate the gut microbial consortia without causing severe damage and increased resistance is important for the treatment of inflammatory, allergic, and metabolic diseases. The aim of the present work was to evaluate the ability of violacein to change microbial patterns in the mammalian gut by favoring certain groups over the others in order to be used as a therapy for diseases associated with changes in the intestinal microflora. To do this, we used male Wistar rats, and administered violacein orally, in low (50 μg/ml) and high (500 μg/ml) doses for a month. Initially, the changes in the microbial diversity were observed by DGGE analyses that showed that the violacein significantly affects the gut microbiota of the rats. Pyrosequencing of 16S rDNA was then employed using a 454 GS Titanium platform, and the results demonstrated that higher taxonomic richness was observed with the low violacein treatment group, followed by the control group and high violacein treatment group. Modulation of the microbiota at the class level was observed in the low violacein dose, where Bacilli and Clostridia (Firmicutes) were found as dominant. For the high violacein dose, Bacilli followed by Clostridia and Actinobacteria were present as the major components. Further analyses are crucial for a better understanding of how violacein affects the gut microbiome and whether this change would be beneficial to the host, providing a framework for the development of alternative treatment strategies for intestinal diseases using this compound.},
}

@article {pmid30212271,
year = {2018},
author = {Ossorio, PN and Zhou, Y},
title = {Regulating stool for microbiota transplantation.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-4},
doi = {10.1080/19490976.2018.1502537},
pmid = {30212271},
issn = {1949-0984},
abstract = {In 2017 Gut Microbes published "A proposed definition of microbiota transplantation for regulatory purposes," in which the authors suggest that regulators should draw a line between microbiota transplants and biologic drugs composed of microbial communities (or other products derived from the human microbiome). They develop a definition of microbiota transplantation (MT) to help regulators draw such a line, and suggest that MT need not be, and cannot be, regulated as a biologic drug (a live biotherapeutic product). However, an agency's regulatory scrutiny of a medical product should be commensurate with that product's degree of risk to patients. Products for MT, such as stool, are likely to be as or more dangerous than more highly manipulated microbial products that scientists and regulators agree should be regulated as biologic drugs. Therefore, we argue that MT, as defined by the authors, should receive the same regulatory oversight as any other biologic product intended to cure, mitigate, treat, or prevent disease. We also suggest that regulators might not be able to operationalize the proposed definition of MT.},
}

@article {pmid30212253,
year = {2018},
author = {Karl, JP and Berryman, CE and Young, AJ and Radcliffe, PN and Branck, TA and Pantoja-Feliciano, IG and Rood, JC and Pasiakos, SM},
title = {Associations between the gut microbiota and host responses to high altitude.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00253.2018},
pmid = {30212253},
issn = {1522-1547},
abstract = {Hypobaric hypoxia, and dietary protein and fat intakes have been independently associated with an altered gastrointestinal (GI) environment and gut microbiota, but little is known regarding host-gut microbiota interactions at high altitude (HA) and the impact of diet macronutrient composition. This study aimed to determine the effect dietary protein:fat ratio manipulation on the gut microbiota and GI barrier function during weight loss at high altitude (HA), and to identify associations between the gut microbiota and host responses to HA. Following sea level (SL) testing, 17 healthy males were transported to HA (4300m) and randomly assigned to consume provided standard-protein (SP; 1.1g/kg/d, 39% fat) or higher-protein (HP; 2.1g/kg/d, 23% fat) carbohydrate-matched hypocaloric diets for 22d. Fecal microbiota composition and metabolites, GI barrier function, GI symptoms, and acute mountain sickness (AMS) severity were measured. Macronutrient intake did not impact fecal microbiota composition, had only transient effects on microbiota metabolites, and had no effect on increases in small intestinal permeability, GI symptoms, and inflammation observed at HA. AMS severity was also unaffected by diet, but in exploratory analyses was associated with higher SL relative abundance of Prevotella, a known driver of inter-individual variability in human gut microbiota composition, and greater microbiota diversity after AMS onset. Findings suggest that the gut microbiota may contribute to variability in host responses to HA independent of the dietary protein:fat ratio, but should be considered preliminary and hypothesis-generating due to the small sample size and exploratory nature of analyses associating the fecal microbiota and host responses to HA.},
}

@article {pmid30212017,
year = {2018},
author = {Deurvorst, SE and Alberga, JJ and van Tellingen, A and Flens, MJ},
title = {[Oxalate nephropathy due to malabsorption syndrome].},
journal = {Nederlands tijdschrift voor geneeskunde},
volume = {162},
number = {},
pages = {},
pmid = {30212017},
issn = {1876-8784},
abstract = {Enteric oxalate nephropathy is caused by hyperoxaluria. Factors which contribute to excessive oxalate absorption are an abundance of free fatty acids in the intestine due to malabsorption, changes in the microbiome, and bowel inflammation. We present two cases that illustrate different pathophysiological aspects of this disease. The first patient was a 70-year-old male who developed oxalate nephropathy through malabsorption caused by chronic pancreatitis. It is plausible that the oxalate nephropathy was set off by antibiotic treatment which influenced the microbiome. The second patient was a 63-year-old male who underwent a Roux-en-Y gastric bypass. The associated malabsorption resulted in oxalate nephropathy. Kidney biopsies from both patients showed typical oxalate crystals. Therapeutic regimens using calcium supplementation, steroids, and a low oxalate diet are rational treatments, which have proven to prevent deterioration of renal function in some patients.},
}

@article {pmid30211673,
year = {2018},
author = {Morin, M and Pierce, EC and Dutton, RJ},
title = {Changes in the genetic requirements for microbial interactions with increasing community complexity.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
doi = {10.7554/eLife.37072},
pmid = {30211673},
issn = {2050-084X},
support = {#2016-65131//David and Lucile Packard Foundation/ ; Pew Scholar in Biomedical Sciences//Pew Charitable Trusts/ ; P50 GM068763//National Institutes of Health/ ; 5 T32 GM 7240-40//National Institutes of Health/ ; },
abstract = {Microbial community structure and function rely on complex interactions whose underlying molecular mechanisms are poorly understood. To investigate these interactions in a simple microbiome, we introduced E. coli into an experimental community based on a cheese rind and identified the differences in E. coli's genetic requirements for growth in interactive and non-interactive contexts using Random Barcode Transposon Sequencing (RB-TnSeq) and RNASeq. E. coli's genetic requirements varied among pairwise growth conditions and between pairwise and community conditions. Our analysis points to mechanisms by which growth conditions change as a result of increasing community complexity and suggests that growth within a community relies on a combination of pairwise and higher order interactions. Our work provides a framework for using the model organism E. coli as a readout to investigate microbial interactions regardless of the genetic tractability of members of the studied ecosystem.},
}

@article {pmid30211604,
year = {2018},
author = {Hoisington, AJ and Billera, DM and Bates, KL and Stamper, CE and Stearns-Yoder, KA and Lowry, CA and Brenner, LA},
title = {Exploring service dogs for rehabilitation of veterans with PTSD: A microbiome perspective.},
journal = {Rehabilitation psychology},
volume = {},
number = {},
pages = {},
doi = {10.1037/rep0000237},
pmid = {30211604},
issn = {1939-1544},
abstract = {PURPOSE/OBJECTIVE: Recently, there has been an increase in the use of therapy animals, often dogs, to assist individuals with challenges associated with managing stressful social situations (i.e., psychological rehabilitation). Potential applications are wide-ranging from elementary schools to airports to hospitals. Here we present an overview of the present knowledge and provide recommendations for future research aimed at exploring the impact of therapy dogs on the rehabilitation of Veterans with posttraumatic stress disorder (PTSD) with a focus on the microbiome. Research Method/Design: In this review we searched the literature for studies that were conducted involving Veterans and service dogs. Because of the limited number of studies, we conducted a nonsystematic review to include the topics of the microbiome and psychological mechanisms that may play a role in rehabilitation of Veterans with dogs.

RESULTS: Whether dogs can be used as an intervention to increase function among those with PTSD remains a question. Nonetheless, it has been suggested that dog ownership may improve mental health outcomes via multiple mechanisms, such as decreasing social isolation and increasing physical activity and exposure to green spaces. The presence of a dog in the home may alter the human inhabitants' microbiomes, thereby, potentially providing an additional mechanism through which service dogs may influence human health and well-being.

CONCLUSIONS/IMPLICATIONS: Theoretically, the use of service dogs for rehabilitation of Veterans with PTSD could improve mental health outcomes. To the best of our knowledge the impact that therapy dogs have on the microbiome of the owners, as well as their built environments, has yet to be explored. (PsycINFO Database Record},
}

@article {pmid30211234,
year = {2018},
author = {Glueck, B and Han, Y and Cresci, GAM},
title = {Tributyrin Supplementation Protects Immune Responses and Vasculature and Reduces Oxidative Stress in the Proximal Colon of Mice Exposed to Chronic-Binge Ethanol Feeding.},
journal = {Journal of immunology research},
volume = {2018},
number = {},
pages = {9671919},
doi = {10.1155/2018/9671919},
pmid = {30211234},
issn = {2314-7156},
abstract = {Excessive ethanol consumption causes adverse effects and contributes to organ dysfunction. Ethanol metabolism triggers oxidative stress, altered immune function, and gut dysbiosis. The gut microbiome is known to contribute to the maintenance of intestinal homeostasis, and disturbances are associated with pathology. A consequence of gut dysbiosis is also alterations in its metabolic and fermentation byproducts. The gut microbiota ferments undigested dietary polysaccharides to yield short-chain fatty acids, predominantly acetate, propionate, and butyrate. Butyrate has many biological mechanisms of action including anti-inflammatory and immunoprotective effects, and its depletion is associated with intestinal injury. We previously showed that butyrate protects gut-liver injury during ethanol exposure. While the intestine is the largest immune organ in the body, little is known regarding the effects of ethanol on intestinal immune function. This work is aimed at investigating the effects of butyrate supplementation, in the form of the structured triglyceride tributyrin, on intestinal innate immune responses and oxidative stress following chronic-binge ethanol exposure in mice. Our work suggests that tributyrin supplementation preserved immune responses and reduced oxidative stress in the proximal colon during chronic-binge ethanol exposure. Our results also indicate a possible involvement of tributyrin in maintaining the integrity of intestinal villi vasculature disrupted by chronic-binge ethanol exposure.},
}

@article {pmid30211213,
year = {2018},
author = {Alves, LF and Westmann, CA and Lovate, GL and de Siqueira, GMV and Borelli, TC and Guazzaroni, ME},
title = {Metagenomic Approaches for Understanding New Concepts in Microbial Science.},
journal = {International journal of genomics},
volume = {2018},
number = {},
pages = {2312987},
doi = {10.1155/2018/2312987},
pmid = {30211213},
issn = {2314-436X},
abstract = {Over the past thirty years, since the dawn of metagenomic studies, a completely new (micro) universe was revealed, with the potential to have profound impacts on many aspects of the society. Remarkably, the study of human microbiome provided a new perspective on a myriad of human traits previously regarded as solely (epi-) genetically encoded, such as disease susceptibility, immunological response, and social and nutritional behaviors. In this context, metagenomics has established a powerful framework for understanding the intricate connections between human societies and microbial communities, ultimately allowing for the optimization of both human health and productivity. Thus, we have shifted from the old concept of microbes as harmful organisms to a broader panorama, in which the signal of the relationship between humans and microbes is flexible and directly dependent on our own decisions and practices. In parallel, metagenomics has also been playing a major role in the prospection of "hidden" genetic features and the development of biotechnological applications, through the discovery of novel genes, enzymes, pathways, and bioactive molecules with completely new or improved biochemical functions. Therefore, this review highlights the major milestones over the last three decades of metagenomics, providing insights into both its potentialities and current challenges.},
}

@article {pmid30211174,
year = {2018},
author = {Trudeau, MP and Zhou, Y and Leite, FL and Gomez, A and Urriola, PE and Shurson, GC and Chen, C and Isaacson, RE},
title = {Fecal Hyodeoxycholic Acid Is Correlated With Tylosin-Induced Microbiome Changes in Growing Pigs.},
journal = {Frontiers in veterinary science},
volume = {5},
number = {},
pages = {196},
doi = {10.3389/fvets.2018.00196},
pmid = {30211174},
issn = {2297-1769},
abstract = {The changes in the gut microbiome play an important role in the promoting effects of antibiotics, such as tylosin, to the health, and productivity of farm animals. Microbial metabolites are expected to be key mediators between antibiotics-induced microbiome changes and growth-promoting effects. The objective of this study was to extend the identification of tylosin-responsive microbes to the identification of tylosin-responsive metabolites in growing pigs. The feeding trial was conducted on a commercial farm using two pens of pigs fed diets with and without tylosin (40 mg/kg of diet). Fecal samples were collected from 10 pigs per pen at weeks 10, 13, 16, 19, and 22 of age, and subsequently analyzed using liquid chromatography-mass spectrometry (LC-MS) analysis. The multivariate model of LC-MS data showed that time-dependent changes occurred in the fecal metabolome of both control and tylosin-treated pigs. More importantly, the metabolomic profiles were similar between the tylosin treatment and control groups in weeks 10 and 22, but diverged during weeks 13-19. Subsequent analyses of the fecal metabolites contributing to the separation of two groups of pigs showed that hyodeoxycholic acid (HDCA), together with tylosin and its metabolites in feces, was greatly increased during weeks 13-19 (P < 0.05) in the group of pigs fed tylosin. The integration of current metabolomics data and the microbiome data from a previous study revealed the consistency between HDCA and a specific genus of microbes in the Clostridia family. Further studies are required to determine the causative relations between tylosin-elicited changes in HDCA and the microbiome as well as the role of HDCA in the growth promoting effects of tylosin.},
}

@article {pmid30210803,
year = {2018},
author = {Wang, Z and Lou, H and Wang, Y and Shamir, R and Jiang, R and Chen, T},
title = {GePMI: A statistical model for personal intestinal microbiome identification.},
journal = {NPJ biofilms and microbiomes},
volume = {4},
number = {},
pages = {20},
doi = {10.1038/s41522-018-0065-2},
pmid = {30210803},
issn = {2055-5008},
abstract = {Human gut microbiomes consist of a large number of microbial genomes, which vary by diet and health conditions and from individual to individual. In the present work, we asked whether such variation or similarity could be measured and, if so, whether the results could be used for personal microbiome identification (PMI). To address this question, we herein propose a method to estimate the significance of similarity among human gut metagenomic samples based on reference-free, long k-mer features. Using these features, we find that pairwise similarities between the metagenomes of any two individuals obey a beta distribution and that a p value derived accordingly well characterizes whether two samples are from the same individual or not. We develop a computational framework called GePMI (Generating inter-individual similarity distribution for Personal Microbiome Identification) and apply it to several human gut metagenomic datasets (>300 individuals and >600 samples in total). From the results of GePMI, most of the human gut microbiomes can be identified (auROC = 0.9470, auPRC = 0.8702). Even after antibiotic treatment or fecal microbiota transplantation, the individual k-mer signature still maintains a certain specificity.},
}

@article {pmid30210540,
year = {2018},
author = {Alwardat, N and Di Renzo, L and De Lorenzo, A},
title = {Comment on "The Gut Microbiome Profile in Obesity: A Systematic Review".},
journal = {International journal of endocrinology},
volume = {2018},
number = {},
pages = {6015278},
doi = {10.1155/2018/6015278},
pmid = {30210540},
issn = {1687-8337},
}

@article {pmid30210530,
year = {2018},
author = {Li, Y},
title = {Epigenetic Mechanisms Link Maternal Diets and Gut Microbiome to Obesity in the Offspring.},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {342},
doi = {10.3389/fgene.2018.00342},
pmid = {30210530},
issn = {1664-8021},
abstract = {Nutrition is the most important environmental factor that can influence early developmental processes through regulation of epigenetic mechanisms during pregnancy and neonatal periods. Maternal diets or nutritional compositions contribute to the establishment of the epigenetic profiles in the fetus that have a profound impact on individual susceptibility to certain diseases or disorders in the offspring later in life. Obesity is considered a global epidemic that impairs human life quality and also increases risk of development of many human diseases such as diabetes and cardiovascular diseases. Studies have shown that maternal nutrition status is closely associated with obesity in progenies indicating obesity has a developmental origin. Maternal diets may also impact the early establishment of the fetal and neonatal microbiome leading to specific epigenetic signatures that may potentially predispose to the development of late-life obesity. This article will review the association of different maternal dietary statuses including essential nutritional quantity and specific dietary components with gut microbiome in determining epigenetic impacts on offspring susceptibility to obesity.},
}

@article {pmid30210480,
year = {2018},
author = {Xu, J and Li, Y and Yang, Z and Li, C and Liang, H and Wu, Z and Pu, W},
title = {Yeast Probiotics Shape the Gut Microbiome and Improve the Health of Early-Weaned Piglets.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2011},
doi = {10.3389/fmicb.2018.02011},
pmid = {30210480},
issn = {1664-302X},
abstract = {Weaning is one of the most stressful challenges in the pig's life, which contributes to dysfunctions of intestinal and immune system, disrupts the gut microbial ecosystem, and therefore compromises the growth performance and health of piglets. To mitigate the negative impact of the stress on early-weaned piglets, effective measures are needed to promote gut health. Toward this end, we tamed a Saccharomyces cerevisiae strain and developed a probiotic Duan-Nai-An, which is a yeast culture of the tamed S. cerevisiae on egg white. In this study, we tested the performance of Duan-Nai-An on growth and health of early-weaned piglets and analyzed its impact on fecal microbiota. The results showed that Duan-Nai-An significantly improved weight gain and feed intake, and reduced diarrhea and death of early-weaned piglets. Analysis of the gut microbiota showed that the bacterial community was shaped by Duan-Nai-An and maintained as a relatively stable structure, represented by a higher core OTU number and lower unweighted UniFrac distances across the early weaned period. However, fungal community was not significantly shaped by the yeast probiotics. Notably, 13 bacterial genera were found to be associated with Duan-Nai-An feeding, including Enterococcus, Succinivibrio, Ruminococcus, Sharpea, Desulfovibrio, RFN20, Sphaerochaeta, Peptococcus, Anaeroplasma, and four other undefined genera. These findings suggest that Duan-Nai-An has the potential to be used as a feed supplement in swine production.},
}

@article {pmid30210479,
year = {2018},
author = {Xu, H and Tian, J and Hao, W and Zhang, Q and Zhou, Q and Shi, W and Qin, M and He, X and Chen, F},
title = {Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2009},
doi = {10.3389/fmicb.2018.02009},
pmid = {30210479},
issn = {1664-302X},
abstract = {As one of the most prevalent human infectious diseases, dental caries results from dysbiosis of the oral microbiota driven by multiple factors. However, most of caries studies were cross-sectional and mainly focused on the differences in the oral microbiota between caries-free (CF) and caries-affected (CA) populations, while little is known about the dynamic shift in microbial composition, and particularly the change in species association pattern during disease transition. Here, we reported a longitudinal study of a 12-month follow-up of a cohort of 3-year-old children. Oral examinations and supragingival plaque collections were carried out at the beginning and every subsequent 6 months, for a total of three time points. All the children were CF at enrollment. Children who developed caries at 6-month follow-up but had not received any dental treatment until the end of the study were incorporated into the CA group. Children who remained CF at the end of the study were incorporated into the CF group. Using Illumina Miseq Sequencing of the 16S rRNA gene, we monitored the shift of supragingival microbiome during caries initiation and progression in children who developed caries over the 12-month study period. Intriguingly, principle coordinates analyses revealed two major shifting patterns in microbial structures during caries initiation and progression in CA group, but not in CF group. Dynamic co-occurring OTU network study showed that compared to CF group, there was significant increase in both number and intensity of correlations between microbial taxa, as well as the formation of tight clusters of specific bacteria in CA group. Furthermore, there were enhanced correlations, positive ones between CA-enriched taxa, and negative ones between CF-enriched and CA-enriched species within CA group. Our data suggested coordinated microbial interactions could be essential to caries pathogenesis. Most importantly, our study indicated that significant microbial shifts occur not only during caries development, but even in the sub-clinical state. Using supragingival microbiome profiles, we were able to construct a caries-onset prediction model with a prediction accuracy of 93.1%. Our study indicated that the microbial shifts prior to the onset of caries might potentially be used for the early diagnosis and prediction of caries.},
}

@article {pmid30210475,
year = {2018},
author = {Jones, J and DiBattista, JD and Stat, M and Bunce, M and Boyce, MC and Fairclough, DV and Travers, MJ and Huggett, MJ},
title = {The Microbiome of the Gastrointestinal Tract of a Range-Shifting Marine Herbivorous Fish.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2000},
doi = {10.3389/fmicb.2018.02000},
pmid = {30210475},
issn = {1664-302X},
abstract = {Globally, marine species' distributions are being modified due to rising ocean temperatures. Increasing evidence suggests a circum-global pattern of poleward extensions in the distributions of many tropical herbivorous species, including the ecologically important rabbitfish Siganus fuscescens. Adaptability of a species to such new environments may be heavily influenced by the composition of their gastrointestinal microbe fauna, which is fundamentally important to animal health. Siganus fuscescens thus provides an opportunity to assess the stability of gastrointestinal microbes under varying environmental conditions. The gastrointestinal microbial communities of S. fuscescens were characterized over 2,000 km of Australia's western coast, from tropical to temperate waters, including near its current southern distributional limit. Sequencing of the 16S rRNA gene demonstrated that each population had a distinct hindgut microbial community, and yet, 20 OTUs occurred consistently in all samples. These OTUs were considered the 'core microbiome' and were highly abundant, composing between 31 and 54% of each population. Furthermore, levels of short chain fatty acids, an indicator of microbial fermentation activity, were similar among tropical and temperate locations. These data suggest that flexibility in the hindgut microbiome may play a role in enabling such herbivores to colonize new environments beyond their existing range.},
}

@article {pmid30210474,
year = {2018},
author = {Zehavi, T and Probst, M and Mizrahi, I},
title = {Insights Into Culturomics of the Rumen Microbiome.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1999},
doi = {10.3389/fmicb.2018.01999},
pmid = {30210474},
issn = {1664-302X},
abstract = {Cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. In this study, we aimed to discover the potential of culturomics for characterizing the rumen microbiome and for identifying factors, specifically sample dilution and media type, which affect microbial richness on agar plates. Our cultivation experiment captured 23% of all operational taxonomic units (OTUs) found in the rumen microbiome in this study. The use of different media increased the number of cultured OTUs by up to 40%. Sample dilution had the strongest effect on increasing richness on the plates, while abundance and phylogeny were the main factors determining cultivability of rumen microbes. Our findings from phylogenetic analysis of cultured OTUs on the lower branches of the phylogenetic tree suggest that multifactorial traits govern cultivability. Interestingly, most of our cultured OTUs belonged to the rare rumen biosphere. These cultured OTUs could not be detected in the rumen microbiome, even when we surveyed it across a 38 rumen microbiome samples. These findings add another unique dimension to the complexity of the rumen microbiome and suggest that a large number of different organisms can be cultured in a single cultivation effort.},
}

@article {pmid30210470,
year = {2018},
author = {Li, Y and Fu, X and Ma, X and Geng, S and Jiang, X and Huang, Q and Hu, C and Han, X},
title = {Intestinal Microbiome-Metabolome Responses to Essential Oils in Piglets.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1988},
doi = {10.3389/fmicb.2018.01988},
pmid = {30210470},
issn = {1664-302X},
abstract = {This study investigated the effects of dietary essential oils (EOs) on intestinal microbial composition and metabolic profiles in weaned piglets. The piglets were fed the same basal diet supplemented with EOs (EO) or without EOs (Con) in the current study. The results showed that the body weight gain was significantly increased, while the diarrhea incidence was significantly reduced in the EO group. In addition, EOs could modify the intestinal microbial composition of weaned piglets. The relative abundances of some beneficial bacterial species such as Bacilli, Lactobacillales, Streptococcaceae, and Veillonellaceae were significantly increased in the EO group. Metabolomics analysis indicated that protein biosynthesis, amino acid metabolism, and lipid metabolism were enriched in the EO group. And correlation analysis demonstrated that some gut bacterial genera were highly correlated with altered gut microbiota-related metabolites. Taken together, this study indicated that dietary EOs not only altered microbial composition and function but modulated the microbial metabolic profiles in the colon, which might help us understand EOs' beneficial effects on intestinal health of weaned piglets.},
}

@article {pmid30210099,
year = {2018},
author = {Sarhan, MS and Patz, S and Hamza, MA and Youssef, HH and Mourad, EF and Fayez, M and Murphy, B and Ruppel, S and Hegazi, NA},
title = {G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla.},
journal = {Microbes and environments},
volume = {},
number = {},
pages = {},
doi = {10.1264/jsme2.ME18023},
pmid = {30210099},
issn = {1347-4405},
abstract = {The rapid development of high-throughput techniques and expansion of bacterial databases have accelerated efforts to bring plant microbiomes into cultivation. We introduced plant-only-based culture media as a successful candidate to mimic the nutritional matrices of plant roots. We herein employed a G3 PhyloChip microarray to meticulously characterize the culture-dependent and -independent bacterial communities of the maize root compartments, the endo- and ecto-rhizospheres. An emphasis was placed on the preference of the growth of unculturable candidate divisions/phyla on plant-only-based culture media over standard culture media (nutrient agar). A total of 1,818 different operational taxonomic units (OTUs) were resolved representing 67 bacterial phyla. Plant-only-based culture media displayed particular affinity towards recovering endophytic over ectophytic rhizobacteria. This was shown by the slightly higher recovery of CFUs for endophytes on plant-only-based culture media (26%) than on standard culture media (10%) as well as the higher taxa richness and numbers of exclusive families of unculturable divisions/phyla. Out of 30 bacterial phyla (comprising >95% of the whole population), 13 were of a significantly higher incidence on plant-only-based culture media, 6 phyla of which were not-yet-cultured (Atribacteria, OP9; Dependentiae, TM6; Latescibacteria, WS3; Marinimicrobia, SAR406; Omnitrophica, OP3; BRC1). Furthermore, plant-only-based culture media significantly enriched less abundant and/or hard-to-culture bacterial phyla (Acidobacteria, Gemmatimonadetes, and Tenericutes). These results present conclusive evidence of the ability of plant-only-based culture media to bring the plant-fed in situ microbiome into the status of plant-fed in vitro cultures, and to widen the scope of cultivation of heretofore-unculturable bacterial divisions/phyla.},
}

@article {pmid30209587,
year = {2018},
author = {Hernández-Gómez, O and Briggler, JT and Williams, RN},
title = {Captivity-Induced Changes in the Skin Microbial Communities of Hellbenders (Cryptobranchus alleganiensis).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1258-1},
pmid = {30209587},
issn = {1432-184X},
abstract = {Variation in environmental conditions can result in disparate associations between hosts and microbial symbionts. As such, it is imperative to evaluate how environmental variables (e.g., habitat quality) can influence host-associated microbiome composition. Within wildlife conservation programs, captive conditions can negatively influence the establishment and maintenance of "wild-type" microbiotas within a host. Alternative microbial communities can result in the proliferation of disease among captive stock or upon reintroduction. Hellbenders (Cryptobranchus alleganiensis) are a threatened salamander for which extensive captive management is currently employed. Using metabarcoding, we characterized the skin microbiota of wild and captive hellbenders from two subspecies in the state of Missouri, the eastern (C. a. alleganiensis) and the Ozark hellbender (C. a. bishopi). Both subspecies in our study included wild adults and captive juveniles that were collected from the wild as eggs. Our objectives were to investigate differences in the skin microbial communities' richness/diversity, composition, and functional profiles of microbes between wild and captive individuals. Captive eastern hellbenders possessed richer communities than wild cohorts, whereas the opposite pattern was observed within the Ozark subspecies. We found significant microbial community structure between wild and captive populations of both subspecies. Microbiota structure translated into differences in the predicted metagenome of wild and captive individuals as well. As such, we can expect captive hellbenders to experience alternative microbial structure and function upon reintroduction into the wild. Our study provides a baseline for the effect of captivity on the skin microbial communities of hellbenders, and highlights the need to incorporate microbiota management in current captive-rearing programs.},
}

@article {pmid30209176,
year = {2018},
author = {MacDuff, DA and Baldridge, MT and Qaqish, AM and Nice, TJ and Darbandi, AD and Hartley, VL and Peterson, ST and Miner, JJ and Iwai, K and Virgin, HW},
title = {HOIL1 is essential for the induction of type I and III interferons by MDA5 and regulates persistent murine norovirus infection.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JVI.01368-18},
pmid = {30209176},
issn = {1098-5514},
abstract = {The Linear Ubiquitin Chain Assembly Complex (LUBAC), composed of heme-oxidized IRP2 ubiquitin ligase-1 (HOIL1), HOIL-1-interacting protein (HOIP) and SHANK-associated RH-domain-interacting protein (SHARPIN), is a crucial regulator of multiple immune signaling pathways. In humans, HOIL1- or HOIP-deficiency is associated with an immune disorder involving auto-inflammation, immunodeficiency and inflammatory bowel disease (IBD)-like symptoms. During viral infection, LUBAC is reported to inhibit the induction of interferon (IFN) by the cytosolic RNA sensor, RIG-I. Surprisingly, we found that HOIL1 is essential for the induction of both type I and type III IFNs, as well as the phosphorylation of IFN regulatory factor (IRF3), during murine norovirus (MNoV) infection in cultured dendritic cells. The RIG-I-like receptor, MDA5, is also required for IFN induction and IRF3 phosphorylation during MNoV infection. Furthermore, HOIL1 and MDA5 were required for IFN induction after Theiler's murine encephalomyelitis virus infection and poly(I:C) transfection, but not Sendai virus or vesicular stomatitis virus infection, indicating that HOIL1 and LUBAC are required specifically for MDA5 signaling. Moreover, Hoil1-/- mice exhibited defective control of acute and persistent murine norovirus (MNoV) infection, and defective regulation of MNoV persistence by the microbiome as also observed previously for IFN-λ receptor-, STAT1- and IRF3-deficient mice. These data indicate that LUBAC plays a critical role in IFN induction to control RNA viruses sensed by MDA5.IMPORTANCE Human noroviruses are a leading cause of gastroenteritis throughout the world, but are challenging to study in vivo and in vitro Murine norovirus (MNoV) provides a tractable genetic and small animal model to study norovirus biology and immune responses. Interferons are critical mediators of anti-viral immunity, but excessive expression can dysregulate the immune system. IFN-λ plays an important role at mucosal surfaces including the gastrointestinal tract, and both IFN-λ and commensal enteric bacteria are important modulators of persistent MNoV infection. The LUBAC complex, of which HOIL1 is a component, is reported to inhibit type I IFN induction after RIG-I stimulation. We show, in contrast, that HOIL1 is critical for type I and III IFN induction during infection with MNoV, a virus that preferentially activates MDA5. Moreover, HOIL1 regulates MNoV infection in vivo These data reveal distinct functions for LUBAC in these closely related signaling pathways and in modulation of IFN expression.},
}

@article {pmid30209011,
year = {2018},
author = {Shade, A and Dunn, RR and Blowes, SA and Keil, P and Bohannan, BJM and Herrmann, M and Küsel, K and Lennon, JT and Sanders, NJ and Storch, D and Chase, J},
title = {Macroecology to Unite All Life, Large and Small.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2018.08.005},
pmid = {30209011},
issn = {1872-8383},
abstract = {Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. Research in microbial ecology and macroecology have long been detached. Here, we argue that it is time to bridge the gap, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity. Microbial ecology and macroecology will mutually benefit from a unified research agenda and shared datasets that span the entirety of the biodiversity of life and the geographic expanse of the Earth.},
}

@article {pmid30208962,
year = {2018},
author = {Yuan, J and Zhao, J and Wen, T and Zhao, M and Li, R and Goossens, P and Huang, Q and Bai, Y and Vivanco, JM and Kowalchuk, GA and Berendsen, RL and Shen, Q},
title = {Root exudates drive the soil-borne legacy of aboveground pathogen infection.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {156},
doi = {10.1186/s40168-018-0537-x},
pmid = {30208962},
issn = {2049-2618},
support = {2015CB150500//Ministry of Science and Technology of the People's Republic of China/ ; 31330069//National Nature Science Foundation of China/ ; BX201600075//National Postdoctoral Program for Innovative Talents/ ; BK20170724//Nature Science Foundation of Jiangsu Province/ ; },
abstract = {BACKGROUND: Plants are capable of building up beneficial rhizosphere communities as is evidenced by disease-suppressive soils. However, it is not known how and why soil bacterial communities are impacted by plant exposure to foliar pathogens and if such responses might improve plant performance in the presence of the pathogen. Here, we conditioned soil by growing multiple generations (five) of Arabidopsis thaliana inoculated aboveground with Pseudomonas syringae pv tomato (Pst) in the same soil. We then examined rhizosphere communities and plant performance in a subsequent generation (sixth) grown in pathogen-conditioned versus control-conditioned soil. Moreover, we assessed the role of altered root exudation profiles in shaping the root microbiome of infected plants.

RESULTS: Plants grown in conditioned soil showed increased levels of jasmonic acid and improved disease resistance. Illumina Miseq 16S rRNA gene tag sequencing revealed that both rhizosphere and bulk soil bacterial communities were altered by Pst infection. Infected plants exhibited significantly higher exudation of amino acids, nucleotides, and long-chain organic acids (LCOAs) (C > 6) and lower exudation levels for sugars, alcohols, and short-chain organic acids (SCOAs) (C ≤ 6). Interestingly, addition of exogenous amino acids and LCOA also elicited a disease-suppressive response.

CONCLUSION: Collectively, our data suggest that plants can recruit beneficial rhizosphere communities via modification of plant exudation patterns in response to exposure to aboveground pathogens to the benefit of subsequent plant generations.},
}

@article {pmid30208950,
year = {2018},
author = {Ho, TTB and Groer, MW and Kane, B and Yee, AL and Torres, BA and Gilbert, JA and Maheshwari, A},
title = {Dichotomous development of the gut microbiome in preterm infants.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {157},
doi = {10.1186/s40168-018-0547-8},
pmid = {30208950},
issn = {2049-2618},
support = {NR015446//National Institutes of Health/ ; HL124078//National Institutes of Health/ ; HL133022//National Institutes of Health/ ; T32GM007281//National Institutes of Health/ ; },
abstract = {BACKGROUND: Preterm infants are at risk of developing intestinal dysbiosis with an increased proportion of Gammaproteobacteria. In this study, we sought the clinical determinants of the relative abundance of feces-associated Gammaproteobacteria in very low birth weight (VLBW) infants. Fecal microbiome was characterized at ≤ 2 weeks and during the 3rd and 4th weeks after birth, by 16S rRNA amplicon sequencing. Maternal and infant clinical characteristics were extracted from electronic medical records. Data were analyzed by linear mixed modeling and linear regression.

RESULTS: Clinical data and fecal microbiome profiles of 45 VLBW infants (gestational age 27.9 ± 2.2 weeks; birth weight 1126 ± 208 g) were studied. Three stool samples were analyzed for each infant at mean postnatal ages of 9.9 ± 3, 20.7 ± 4.1, and 29.4 ± 4.9 days. The average relative abundance of Gammaproteobacteria was 42.5% (0-90%) at ≤ 2 weeks, 69.7% (29.9-86.9%) in the 3rd, and 75.5% (54.5-86%) in the 4th week (p < 0.001). Hierarchical and K-means clustering identified two distinct subgroups: cluster 1 started with comparatively low abundance that increased with time, whereas cluster 2 began with a greater abundance at ≤ 2 weeks (p < 0.001) that decreased over time. Both groups resembled each other by the 3rd week. Single variants of Klebsiella and Staphylococcus described variance in community structure between clusters and were shared between all infants, suggesting a common, hospital-derived source. Fecal Gammaproteobacteria was positively associated with vaginal delivery and antenatal steroids.

CONCLUSIONS: We detected a dichotomy in gut microbiome assembly in preterm infants: some preterm infants started with low relative gammaproteobacterial abundance in stool that increased as a function of postnatal age, whereas others began with and maintained high abundance. Vaginal birth and antenatal steroids were identified as predictors of Gammaproteobacteria abundance in the early (≤ 2 weeks) and later (3rd and 4th weeks) stool samples, respectively. These findings are important in understanding the development of the gut microbiome in premature infants.},
}

@article {pmid30208917,
year = {2018},
author = {Zumwalde, NA and Haag, JD and Gould, MN and Gumperz, JE},
title = {Mucosal associated invariant T cells from human breast ducts mediate a Th17-skewed response to bacterially exposed breast carcinoma cells.},
journal = {Breast cancer research : BCR},
volume = {20},
number = {1},
pages = {111},
doi = {10.1186/s13058-018-1036-5},
pmid = {30208917},
issn = {1465-542X},
support = {PF-17-002-01-CCE//American Cancer Society/ ; },
abstract = {BACKGROUND: Antimicrobial T cells play key roles in the disease progression of cancers arising in mucosal epithelial tissues, such as the colon. However, little is known about microbe-reactive T cells within human breast ducts and whether these impact breast carcinogenesis.

METHODS: Epithelial ducts were isolated from primary human breast tissue samples, and the associated T lymphocytes were characterized using flow cytometric analysis. Functional assays were performed to determine T-cell cytokine secretion in response to bacterially treated human breast carcinoma cells.

RESULTS: We show that human breast epithelial ducts contain mucosal associated invariant T (MAIT) cells, an innate T-cell population that recognizes specific bacterial metabolites presented by nonclassical MR1 antigen-presenting molecules. The MAIT cell population from breast ducts resembled that of peripheral blood in its innate lymphocyte phenotype (i.e., CD161, PLZF, and interleukin [IL]-18 receptor coexpression), but the breast duct MAIT cell population had a distinct T-cell receptor Vβ use profile and was markedly enriched for IL-17-producing cells compared with blood MAIT cells. Breast carcinoma cells that had been exposed to Escherichia coli activated MAIT cells in an MR1-dependent manner. However, whereas phorbol 12-myristate 13-acetate/ionomycin stimulation induced the production of both interferon-γ and IL-17 by breast duct MAIT cells, bacterially exposed breast carcinoma cells elicited a strongly IL-17-biased response. Breast carcinoma cells also showed upregulated expression of natural killer group 2 member D (NKG2D) ligands compared with primary breast epithelial cells, and the NKG2D receptor contributed to MAIT cell activation by the carcinoma cells.

CONCLUSIONS: These results demonstrate that MAIT cells from human breast ducts mediate a selective T-helper 17 cell response to human breast carcinoma cells that were exposed to E. coli. Thus, cues from the breast microbiome and the expression of stress-associated ligands by neoplastic breast duct epithelial cells may shape MAIT cell responses during breast carcinogenesis.},
}

@article {pmid30208886,
year = {2018},
author = {Gregory, AC and Sullivan, MB and Segal, LN and Keller, BC},
title = {Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome.},
journal = {Respiratory research},
volume = {19},
number = {1},
pages = {174},
doi = {10.1186/s12931-018-0878-9},
pmid = {30208886},
issn = {1465-993X},
support = {T32 AI112542//National Institutes of Health/ ; K23 AI102970//National Institutes of Health/ ; 2T-32HL007317-36//National Institutes of Health/ ; T32 HL07317//National Institutes of Health/ ; GBMF#3790//Gordon and Betty Moore Foundation/ ; },
abstract = {BACKGROUND: The role of commensal viruses in humans is poorly understood, and the impact of the virome on lung health and smoking-related disease is particularly understudied.

METHODS: Genetic material from acellular bronchoalveolar lavage fluid was sequenced to identify and quantify viral members of the lower respiratory tract which were compared against concurrent bronchoalveolar lavage bacterial, metabolite, cytokine and cellular profiles, and clinical data. Twenty smoker and 10 nonsmoker participants with no significant comorbidities were studied.

RESULTS: Viruses that infect bacteria (phages) represented the vast majority of viruses in the lung. Though bacterial communities were statistically indistinguishable across smokers and nonsmokers as observed in previous studies, lung viromes and metabolic profiles were significantly different between groups. Statistical analyses revealed that changes in viral communities correlate most with changes in levels of arachidonic acid and IL-8, both potentially relevant for chronic obstructive pulmonary disease (COPD) pathogenesis based on prior studies.

CONCLUSIONS: Our assessment of human lung DNA viral communities reveals that commensal viruses are present in the lower respiratory tract and differ between smokers and nonsmokers. The associations between viral populations and local immune and metabolic tone suggest a significant role for virome-host interaction in smoking related lung disease.},
}

@article {pmid30208875,
year = {2018},
author = {Wang, Q and Li, F and Liang, B and Liang, Y and Chen, S and Mo, X and Ju, Y and Zhao, H and Jia, H and Spector, TD and Xie, H and Guo, R},
title = {A metagenome-wide association study of gut microbiota in asthma in UK adults.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {114},
doi = {10.1186/s12866-018-1257-x},
pmid = {30208875},
issn = {1471-2180},
support = {105022/Z/14/Z//Wellcome Trust/United Kingdom ; JSGG20140702161403250, DRC-SZ [2015]162, CXB201108250098A, JSGG20160229172752028, and JCYJ20160229172757249//Shenzhen Municipal Government of China/ ; 077/ 2014/A2//Science and Technology Development/ ; },
abstract = {BACKGROUND: Asthma, one of the most common chronic respiratory disorders, is associated with the hyper-activation of the T-cell subset of adaptive immunity. The gut microbiota may be involved in the development of asthma through the production of short-chain fatty acids (SCFAs), exhibiting modulatory effects on Th. So, we performed a metagenome-wide association study (MWAS) of the fecal microbiota from individuals with asthma and healthy controls. And that was the first case to resolve the relationship between asthma and microbiome among UK adults.

RESULTS: The microbiota of the individuals with asthma consisted of fewer microbial entities than the microbiota of healthy individuals. Faecalibacterium prausnitzii, Sutterella wadsworthensis and Bacteroides stercoris were depleted in cases, whereas Clostridiums with Eggerthella lenta were over-represented in individuals with asthma. Functional analysis shows that the SCFAs might be altered in the microbiota of asthma patients.

CONCLUSION: In all, the adult human gut microbiome of asthma patients is clearly different from healthy controls. The functional and taxa results showed that the change of asthma patients might related to SCFAs.},
}

@article {pmid30208844,
year = {2018},
author = {Kosina, SM and Greiner, AM and Lau, RK and Jenkins, S and Baran, R and Bowen, BP and Northen, TR},
title = {Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {115},
doi = {10.1186/s12866-018-1256-y},
pmid = {30208844},
issn = {1471-2180},
support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; },
abstract = {BACKGROUND: As microbiome research becomes increasingly prevalent in the fields of human health, agriculture and biotechnology, there exists a need for a resource to better link organisms and environmental chemistries. Exometabolomics experiments now provide assertions of the metabolites present within specific environments and how the production and depletion of metabolites is linked to specific microbes. This information could be broadly useful, from comparing metabolites across environments, to predicting competition and exchange of metabolites between microbes, and to designing stable microbial consortia. Here, we introduce Web of Microbes (WoM; freely available at: http://webofmicrobes.org), the first exometabolomics data repository and visualization tool.

DESCRIPTION: WoM provides manually curated, direct biochemical observations on the changes to metabolites in an environment after exposure to microorganisms. The web interface displays a number of key features: (1) the metabolites present in a control environment prior to inoculation or microbial activation, (2) heatmap-like displays showing metabolite increases or decreases resulting from microbial activities, (3) a metabolic web displaying the actions of multiple organisms on a specified metabolite pool, (4) metabolite interaction scores indicating an organism's interaction level with its environment, potential for metabolite exchange with other organisms and potential for competition with other organisms, and (5) downloadable datasets for integration with other types of -omics datasets.

CONCLUSION: We anticipate that Web of Microbes will be a useful tool for the greater research community by making available manually curated exometabolomics results that can be used to improve genome annotations and aid in the interpretation and construction of microbial communities.},
}

@article {pmid30208569,
year = {2018},
author = {Johnson, TR and Gómez, BI and McIntyre, MK and Dubick, MA and Christy, RJ and Nicholson, SE and Burmeister, DM},
title = {The Cutaneous Microbiome and Wounds: New Molecular Targets to Promote Wound Healing.},
journal = {International journal of molecular sciences},
volume = {19},
number = {9},
pages = {},
doi = {10.3390/ijms19092699},
pmid = {30208569},
issn = {1422-0067},
abstract = {The ecological community of microorganisms in/on humans, termed the microbiome, is vital for sustaining homeostasis. While culture-independent techniques have revealed the role of the gut microbiome in human health and disease, the role of the cutaneous microbiome in wound healing is less defined. Skin commensals are essential in the maintenance of the epithelial barrier function, regulation of the host immune system, and protection from invading pathogenic microorganisms. In this review, we summarize the literature derived from pre-clinical and clinical studies on how changes in the microbiome of various acute and chronic skin wounds impact wound healing tissue regeneration. Furthermore, we review the mechanistic insights garnered from model wound healing systems. Finally, in the face of growing concern about antibiotic-resistance, we will discuss alternative strategies for the treatment of infected wounds to improve wound healing and outcomes. Taken together, it has become apparent that commensals, symbionts, and pathogens on human skin have an intimate role in the inflammatory response that highlights several potential strategies to treat infected, non-healing wounds. Despite these promising results, there are some contradictory and controversial findings from existing studies and more research is needed to define the role of the human skin microbiome in acute and chronic wound healing.},
}

@article {pmid30208103,
year = {2018},
author = {Passmore, IJ and Letertre, MPM and Preston, MD and Bianconi, I and Harrison, MA and Nasher, F and Kaur, H and Hong, HA and Baines, SD and Cutting, SM and Swann, JR and Wren, BW and Dawson, LF},
title = {Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria.},
journal = {PLoS pathogens},
volume = {14},
number = {9},
pages = {e1007191},
doi = {10.1371/journal.ppat.1007191},
pmid = {30208103},
issn = {1553-7374},
abstract = {Clostridium difficile is a Gram-positive spore-forming anaerobe and a major cause of antibiotic-associated diarrhoea. Disruption of the commensal microbiota, such as through treatment with broad-spectrum antibiotics, is a critical precursor for colonisation by C. difficile and subsequent disease. Furthermore, failure of the gut microbiota to recover colonisation resistance can result in recurrence of infection. An unusual characteristic of C. difficile among gut bacteria is its ability to produce the bacteriostatic compound para-cresol (p-cresol) through fermentation of tyrosine. Here, we demonstrate that the ability of C. difficile to produce p-cresol in vitro provides a competitive advantage over gut bacteria including Escherichia coli, Klebsiella oxytoca and Bacteroides thetaiotaomicron. Metabolic profiling of competitive co-cultures revealed that acetate, alanine, butyrate, isobutyrate, p-cresol and p-hydroxyphenylacetate were the main metabolites responsible for differentiating the parent strain C. difficile (630Δerm) from a defined mutant deficient in p-cresol production. Moreover, we show that the p-cresol mutant displays a fitness defect in a mouse relapse model of C. difficile infection (CDI). Analysis of the microbiome from this mouse model of CDI demonstrates that colonisation by the p-cresol mutant results in a distinctly altered intestinal microbiota, and metabolic profile, with a greater representation of Gammaproteobacteria, including the Pseudomonales and Enterobacteriales. We demonstrate that Gammaproteobacteria are susceptible to exogenous p-cresol in vitro and that there is a clear divide between bacterial Phyla and their susceptibility to p-cresol. In general, Gram-negative species were relatively sensitive to p-cresol, whereas Gram-positive species were more tolerant. This study demonstrates that production of p-cresol by C. difficile has an effect on the viability of intestinal bacteria as well as the major metabolites produced in vitro. These observations are upheld in a mouse model of CDI, in which p-cresol production affects the biodiversity of gut microbiota and faecal metabolite profiles, suggesting that p-cresol production contributes to C. difficile survival and pathogenesis.},
}

@article {pmid30208025,
year = {2018},
author = {Rees, T and Bosch, T and Douglas, AE},
title = {The microbiome and the human: A reply to Parke and colleagues.},
journal = {PLoS biology},
volume = {16},
number = {9},
pages = {e2006974},
doi = {10.1371/journal.pbio.2006974},
pmid = {30208025},
issn = {1545-7885},
}

@article {pmid30207838,
year = {2018},
author = {Matthews, C and Crispie, F and Lewis, E and Reid, M and O'Toole, PW and Cotter, PD},
title = {The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/19490976.2018.1505176},
pmid = {30207838},
issn = {1949-0984},
abstract = {Methane is generated in the foregut of all ruminant animals by the microorganisms present. Dietary manipulation is regarded as the most effective and most convenient way to reduce methane emissions (and in turn energy loss in the animal) and increase nitrogen utilization efficiency. This review examines the impact of diet on bovine rumen function and outlines what is known about the rumen microbiome. Our understanding of this area has increased significantly in recent years due to the application of omics technologies to determine microbial composition and functionality patterns in the rumen. This information can be combined with data on nutrition, rumen physiology, nitrogen excretion and/or methane emission to provide comprehensive insights into the relationship between rumen microbial activity, nitrogen utilisation efficiency and methane emission, with an ultimate view to the development of new and improved intervention strategies.},
}

@article {pmid30207437,
year = {2018},
author = {Guerra, F and Mazur, M and Ndokaj, A and Corridore, D and La Torre, G and Polimeni, A and Ottolenghi, L},
title = {Periodontitis and the microbiome: a systematic review and meta-analysis.},
journal = {Minerva stomatologica},
volume = {},
number = {},
pages = {},
doi = {10.23736/S0026-4970.18.04198-5},
pmid = {30207437},
issn = {1827-174X},
abstract = {INTRODUCTION: The association between the oral microbiome and periodontal diseases is still unclear. We performed a systematic review and meta-analysis to quantify the association between the specific pathogens and periodontitis.

EVIDENCE ACQUISITION: A computerized medical search was performed using MEDLINE and SCOPUS database between 1950 and May 2017 to identify all case-control studies that evaluated the association between specific pathogens and periodontitis. The pooled Odds Ratio with relative 95% confidence interval (95% CI) was calculated and plotted in the forest plot.

EVIDENCE SYNTHESIS: 11 RCTs involving 2111 patients were included. The retrieved case-control studies evaluated the presence or absence of different targeted pathogens. Among the microrganisms evaluated Porphyromonas gengivalis [OR (95% CI) 2.93(0.98,8.87); P< 0.0001] and Streptococcus mutans [OR (95% CI) 1.77 (0.89-3.54); P=0.03] were found to be risk factors for the development of periodontitis, while Aggregatibacter actinomycetemcomitans [OR (95% CI) 0.52 (0.33-0.83)] played a protective role for periodontitis.

CONCLUSIONS: It seems that changes in the taxonomic composition of the microbiome rather than single targeted pathogens is the key determinant of periodontitis.},
}

@article {pmid30207256,
year = {2018},
author = {Hooks, KB and Konsman, JP and O'Malley, MA},
title = {Microbiota-gut-brain research: a critical analysis.},
journal = {The Behavioral and brain sciences},
volume = {},
number = {},
pages = {1-40},
doi = {10.1017/S0140525X18002133},
pmid = {30207256},
issn = {1469-1825},
abstract = {Microbiota-gut-brain (MGB) research is a fast-growing field of inquiry with important implications for how human brain function and behaviour are understood. Researchers manipulate gut microbes ('microbiota') to reveal connections between intestinal microbiota and normal brain functions (e.g., cognition, emotion, memory) or pathological states (e.g., anxiety and mood disorders, neural developmental disorders such as autism). Many claims are made about causal relationships between gut microbiota and human behaviour. By uncovering these relationships, MGB research aims to offer new explanations of mental health and potential avenues of treatment.So far, limited evaluation has been made of MGB's methods and its core experimental findings, many of which are extensively reiterated in copious reviews of the field. These factors, plus the self-help potential of MGB, have combined to encourage uncritical public uptake of MGB discoveries. Both social and professional media focus on the potential for dietary intervention in mental health, and causal relationships are assumed to be established.Our target article has two main aims. One is to examine critically the core practices and findings of experimental MGB research, and to raise questions about them for brain and behavioural scientists who may not be familiar with the field. The other is to challenge the way in which MGB findings are presented. Our positive goal is to suggest how current problems and weaknesses may be addressed, in order for both scientific and public audiences to gain a clearer picture of MGB research and its strengths and limitations.},
}

@article {pmid30206827,
year = {2018},
author = {Cai, J and Bai, C and Tang, X and Dai, J and Gong, Y and Hu, Y and Shao, K and Zhou, L and Gao, G},
title = {Characterization of bacterial and microbial eukaryotic communities associated with an ephemeral hypoxia event in Taihu Lake, a shallow eutrophic Chinese lake.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-018-2987-x},
pmid = {30206827},
issn = {1614-7499},
support = {2017ZX07203-004//National Water Pollution Control and Management of Science and Technology Major Projects/ ; 41471040//National Natural Science Foundation of China/ ; 41501101//National Natural Science Foundation of China/ ; 41571462//National Natural Science Foundation of China/ ; 41621002//National Natural Science Foundation of China/ ; 41661134036//National Natural Science Foundation of China/ ; BK20151059//Natural Science Foundation of Jiangsu Province/ ; QYZDJ-SSW-DQC008//Key Research Program of Frontier Sciences, CAS/ ; },
abstract = {While the important roles of microbial communities in oceanic hypoxic zones were beginning to be understood, little is known about microbial community associated with this phenomenon in shallow lakes. To address this deficit, both the bacterial and microbial eukaryotic communities of an ephemeral hypoxic area of Taihu Lake were characterized. The hypoxia provided nutritional niches for various bacteria, which results in high abundance and diversity. Specific bacterial groups, such as vadinBC27 subgroup of Bacteroidetes, Burkholderiales, Rhodocyclales, Pseudomonas, and Parcubacteria, were dominated in hypoxic sites and relevant to the fermentation, denitrification, nitrification, and sulfur metabolism. Conversely, most of microbial eukaryotes disappeared along with the decline of DO. An unexpected dominance of fungi was observed during hypoxia, which partly explained by the accumulation of toxic algae. Mucor was the single dominant genus in the hypoxic zone. We proposed that this group might cooperate with bacterial communities in the anaerobic degradation of algal biomass and woody materials. Generally, the hypoxic microbiome in shallow lakes is mainly involved in fermentative metabolism depending on phytodetritus and is potentially influenced by terrestrial sources. This study provided new insights into the unique microbiome in short-term hypoxia in shallow lakes and lays the foundation for studies that will enhance our understanding of the microbial players associated with hypoxia and their adaption strategy on the global scale.},
}

@article {pmid30206704,
year = {2018},
author = {Tarkka, MT and Drigo, B and Deveau, A},
title = {Mycorrhizal microbiomes.},
journal = {Mycorrhiza},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00572-018-0865-5},
pmid = {30206704},
issn = {1432-1890},
abstract = {This Mycorrhiza issue groups topical papers based on presentations and discussions at the Mycorrhizal Microbiomes session at 9th International Conference on Mycorrhiza, Prague, Czech Republic, August 2017. The five articles that appear in this special issue advance the field of mycorrhizal microbiomes, not simply by importing ideas from an emerging area, but by using them to inform rich and methodologically grounded research. The aim of this special issue is to explore the interactions between mycorrhizal fungi and surrounding complex environments from a distinct but complementary point of view, highlighting the large spectrum of unknowns that still need to be explored. In this editorial, we first introduce the level of knowledge in this thematic area, then describe major results from the five manuscripts and characterise their importance to mycorrhizal research, and finally discuss the developing topics in this rapidly emerging thematic area.},
}

@article {pmid30206171,
year = {2018},
author = {Gaulke, CA and Arnold, HK and Humphreys, IR and Kembel, SW and O'Dwyer, JP and Sharpton, TJ},
title = {Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota.},
journal = {mBio},
volume = {9},
number = {5},
pages = {},
doi = {10.1128/mBio.01348-18},
pmid = {30206171},
issn = {2150-7511},
abstract = {Our knowledge of how the gut microbiome relates to mammalian evolution benefits from the identification of gut microbial taxa that are unexpectedly prevalent or unexpectedly conserved across mammals. Such taxa enable experimental determination of the traits needed for such microbes to succeed as gut generalists, as well as those traits that impact mammalian fitness. However, the punctuated resolution of microbial taxonomy may limit our ability to detect conserved gut microbes, especially in cases in which broadly related microbial lineages possess shared traits that drive their apparent ubiquity across mammals. To advance the discovery of conserved mammalian gut microbes, we developed a novel ecophylogenetic approach to taxonomy that groups microbes into taxonomic units based on their shared ancestry and their common distribution across mammals. Applying this approach to previously generated gut microbiome data uncovered monophyletic clades of gut bacteria that are conserved across mammals. It also resolved microbial clades exclusive to and conserved among particular mammalian lineages. Conserved clades often manifest phylogenetic patterns, such as cophylogeny with their host, that indicate that they are subject to selective processes, such as host filtering. Moreover, this analysis identified variation in the rate at which mammals acquire or lose conserved microbial clades and resolved a human-accelerated loss of conserved clades. Collectively, the data from this study reveal mammalian gut microbiota that possess traits linked to mammalian phylogeny, point to the existence of a core set of microbes that comprise the mammalian gut microbiome, and clarify potential evolutionary or ecologic mechanisms driving the gut microbiome's diversification throughout mammalian evolution.IMPORTANCE Our understanding of mammalian evolution has become microbiome-aware. While emerging research links mammalian biodiversity and the gut microbiome, we lack insight into which microbes potentially impact mammalian evolution. Microbes common to diverse mammalian species may be strong candidates, as their absence in the gut may affect how the microbiome functionally contributes to mammalian physiology to adversely affect fitness. Identifying such conserved gut microbes is thus important to ultimately assessing the microbiome's potential role in mammalian evolution. To advance their discovery, we developed an approach that identifies ancestrally related groups of microbes that distribute across mammals in a way that indicates their collective conservation. These conserved clades are presumed to have evolved a trait in their ancestor that matters to their distribution across mammals and which has been retained among clade members. We found not only that such clades do exist among mammals but also that they appear to be subject to natural selection and characterize human evolution.},
}