@article {pmid30448738,
year = {2018},
author = {Rehman, ZU and Ali, M and Iftikhar, H and Leiknes, T},
title = {Genome-resolved metagenomic analysis reveals roles of microbial community members in full-scale seawater reverse osmosis plant.},
journal = {Water research},
volume = {149},
number = {},
pages = {263-271},
doi = {10.1016/j.watres.2018.11.012},
pmid = {30448738},
issn = {1879-2448},
abstract = {Biofouling of Reverse Osmosis (RO) membrane is a significant issue for the water treatment industry. In this study, we apply the metagenomic shot-gun sequencing technology to characterise the composition and functional potential of the microbial community in a full-scale RO plant, at different stages of seawater treatment. We find Proteobacteria, Bacteroidetes and Planctomycetes to be the most abundant bacterial phyla. The genetic potential of the RO membrane microbial community shows the enrichment of genes involved in biofilm formation, representing the selective pressure of the biofilm formation process. We recover 31 metagenome-assembled genomes (MAGs) from intake (raw seawater), fouled RO membranes (leading and middle RO module) and brine reject water. A total of 25 MAGs are recovered from the biofilm samples (leading and middle RO modules), with 9 of them (36%) belonging to Planctomycetes. We investigate all 25 MAGs for genes (pili, flagella, quorum sensing, quorum quenching and nitrate reduction) that play an important role in biofilm formation and sustenance of cells. We show that Planctomycetes contain genes for the formation of flagella and pili, and the reduction of nitrate. Although genes for quorum sensing are not detected, quorum quenching genes are identified in the biofilm MAGs. Our results show that Planctomycetes, along with other microbes, play an important role in the formation and sustenance of biofilms on seawater RO membranes.},
}

@article {pmid30447151,
year = {2018},
author = {Zhang, F and Shan, A and Luan, Y},
title = {A novel method to accurately calculate statistical significance of local similarity analysis for high-throughput time series.},
journal = {Statistical applications in genetics and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1515/sagmb-2018-0019},
pmid = {30447151},
issn = {1544-6115},
abstract = {In recent years, a large number of time series microbial community data has been produced in molecular biological studies, especially in metagenomics. Among the statistical methods for time series, local similarity analysis is used in a wide range of environments to capture potential local and time-shifted associations that cannot be distinguished by traditional correlation analysis. Initially, the permutation test is popularly applied to obtain the statistical significance of local similarity analysis. More recently, a theoretical method has also been developed to achieve this aim. However, all these methods require the assumption that the time series are independent and identically distributed. In this paper, we propose a new approach based on moving block bootstrap to approximate the statistical significance of local similarity scores for dependent time series. Simulations show that our method can control the type I error rate reasonably, while theoretical approximation and the permutation test perform less well. Finally, our method is applied to human and marine microbial community datasets, indicating that it can identify potential relationship among operational taxonomic units (OTUs) and significantly decrease the rate of false positives.},
}

@article {pmid30445993,
year = {2018},
author = {Breitwieser, FP and Baker, DN and Salzberg, SL},
title = {KrakenUniq: confident and fast metagenomics classification using unique k-mer counts.},
journal = {Genome biology},
volume = {19},
number = {1},
pages = {198},
doi = {10.1186/s13059-018-1568-0},
pmid = {30445993},
issn = {1474-760X},
support = {W911NF-14-1-0490//Army Research Office (US)/ ; R01-HG006677//National Human Genome Research Institute (US)/ ; R01-GM083873//National Institute of General Medical Sciences/ ; R01-GM118568//National Institute of General Medical Sciences/ ; },
abstract = {False-positive identifications are a significant problem in metagenomics classification. We present KrakenUniq, a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory. KrakenUniq is freely available at https://github.com/fbreitwieser/krakenuniq .},
}

@article {pmid30445181,
year = {2018},
author = {Starke, R and Jehmlich, N and Bastida, F},
title = {Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jprot.2018.11.011},
pmid = {30445181},
issn = {1876-7737},
abstract = {Metaproteomics was established to analyse both the structure and the function of microbial communities and, particularly in soils, their contribution to ecosystem services. In this review, we provide an overview on how the study of the soil metaproteome can provide fundamental information on the role of microbial communities in soil ecosystem services. We further discuss the strengths and weaknesses of soil metaproteomics in comparison to other culture-independent OMIC techniques. We critically review its bottlenecks but also provide strategies to mitigate and possible directions for future research as the direct link of structure and function is advantageous and complementary to metagenomics, metatranscriptomics and metametabolomics.},
}

@article {pmid30444087,
year = {2018},
author = {Tokarz-Deptuła, B and Czupryńska, P and Poniewierska-Baran, A and Deptuła, W},
title = {Characteristics of virophages and giant viruses.},
journal = {Acta biochimica Polonica},
volume = {},
number = {},
pages = {},
doi = {10.18388/abp.2018_2631},
pmid = {30444087},
issn = {1734-154X},
abstract = {Five years after being discovered in 2003, some giant viruses were demonstrated to play a role of the hosts for virophages, their parasites, setting out a novel and yet unknown regulatory mechanism of the giant viruses presence in an aqueous. So far, 20 virophages have been registered and 13 of them have been described as a metagenomic material, which indirectly impacts the number of single- and multi-cell organisms, the environment where giant viruses replicate.},
}

@article {pmid30443861,
year = {2018},
author = {Zhang, QY and Gui, JF},
title = {Diversity, evolutionary contribution and ecological roles of aquatic viruses.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11427-018-9414-7},
pmid = {30443861},
issn = {1869-1889},
abstract = {Aquatic viruses include infected viruses in aquatic animals, plants and microorganisms, and free-floating viruses (virioplankton) in water environments. In the last three decades, a huge number of aquatic viruses, especially diverse free-floating viruses, including cyanophages, phycoviruses, archaea viruses, giant viruses, and even virophages, have been identified by virological experiments and metagenomic analyses. Based on a comprehensive introduction of aquatic virus classification and their morphological and genetic diversity, here, we summarize and outline main virus species, their evolutionary contribution to aquatic communities through horizontal gene transfer, and their ecological roles for cyanobacterial bloom termination and global biogeochemical cycling in freshwater and marine ecosystems. Thereby, some novel insights of aquatic viruses and virus-host interactions, especially their evolutionary contribution and ecological rolesin diverse aquatic communities and ecosystems, are highlighted in this review.},
}

@article {pmid30443602,
year = {2018},
author = {Hillmann, B and Al-Ghalith, GA and Shields-Cutler, RR and Zhu, Q and Gohl, DM and Beckman, KB and Knight, R and Knights, D},
title = {Evaluating the Information Content of Shallow Shotgun Metagenomics.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00069-18},
pmid = {30443602},
issn = {2379-5077},
abstract = {Although microbial communities are associated with human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes in such communities. While deep whole-metagenome shotgun (WMS) sequencing provides high taxonomic and functional resolution, it is often prohibitively expensive for large-scale studies. The prevailing alternative, 16S rRNA gene amplicon (16S) sequencing, often does not resolve taxonomy past the genus level and provides only moderately accurate predictions of the functional profile; thus, there is currently no widely accepted approach to affordable, high-resolution, taxonomic, and functional microbiome analysis. To address this technology gap, we evaluated the information content of shallow shotgun sequencing with as low as 0.5 million sequences per sample as an alternative to 16S sequencing for large human microbiome studies. We describe a library preparation protocol enabling shallow shotgun sequencing at approximately the same per-sample cost as 16S sequencing. We analyzed multiple real and simulated biological data sets, including two novel human stool samples with ultradeep sequencing of 2.5 billion sequences per sample, and found that shallow shotgun sequencing recovers more-accurate species-level taxonomic and functional profiles of the human microbiome than 16S sequencing. We discuss the inherent limitations of shallow shotgun sequencing and note that 16S sequencing remains a valuable and important method for taxonomic profiling of novel environments. Although deep WMS sequencing remains the gold standard for high-resolution microbiome analysis, we recommend that researchers consider shallow shotgun sequencing as a useful alternative to 16S sequencing for large-scale human microbiome research studies where WMS sequencing may be cost-prohibitive. IMPORTANCE A common refrain in recent microbiome-related academic meetings is that the field needs to move away from broad taxonomic surveys using 16S sequencing and toward more powerful longitudinal studies using shotgun sequencing. However, performing deep shotgun sequencing in large longitudinal studies remains prohibitively expensive for all but the most well-funded research labs and consortia, which leads many researchers to choose 16S sequencing for large studies, followed by deep shotgun sequencing on a subset of targeted samples. Here, we show that shallow- or moderate-depth shotgun sequencing may be used by researchers to obtain species-level taxonomic and functional data at approximately the same cost as amplicon sequencing. While shallow shotgun sequencing is not intended to replace deep shotgun sequencing for strain-level characterization, we recommend that microbiome scientists consider using shallow shotgun sequencing instead of 16S sequencing for large-scale human microbiome studies.},
}

@article {pmid30442907,
year = {2018},
author = {Zhou, W and Chow, KH and Fleming, E and Oh, J},
title = {Selective colonization ability of human fecal microbes in different mouse gut environments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0312-9},
pmid = {30442907},
issn = {1751-7370},
support = {1 DP2 GM126893-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; ACS-RSG-16-255-01-MPC//American Cancer Society (American Cancer Society, Inc.)/ ; },
abstract = {Mammalian hosts constantly interact with diverse exogenous microbes, but only a subset of the microbes manage to colonize due to selective colonization resistance exerted by host genetic factors as well as the native microbiota of the host. An important question in microbial ecology and medical science is if such colonization resistance can discriminate closely related microbial species, or even closely related strains of the same species. Using human-mouse fecal microbiota transplantation and metagenomic shotgun sequencing, we reconstructed colonization patterns of human fecal microbes in mice with different genotypes (C57BL6/J vs. NSG) and with or without an intact gut microbiota. We found that mouse genotypes and the native mouse gut microbiota both exerted different selective pressures on exogenous colonizers: human fecal Bacteroides successfully established in the mice gut, however, different species of Bacteroides selectively enriched under different gut conditions, potentially due to a multitude of functional differences, ranging from versatility in nutrient acquisition to stress responses. Additionally, different clades of Bacteroides cellulosilyticus strains were selectively enriched in different gut conditions, suggesting that the fitness of conspecific microbial strains in a novel host environment could differ.},
}

@article {pmid30441786,
year = {2018},
author = {Bal, A and Sarkozy, C and Josset, L and Cheynet, V and Oriol, G and Becker, J and Vilchez, G and Sesques, P and Mallet, F and Pachot, A and Morfin, F and Lina, B and Salles, G and Reynier, F and Trouillet-Assant, S and Brengel-Pesce, K},
title = {Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management.},
journal = {Viruses},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/v10110633},
pmid = {30441786},
issn = {1999-4915},
abstract = {Over recent years, there has been increasing interest in the use of the anelloviruses, the major component of the human virome, for the prediction of post-transplant complications such as severe infections. Due to an important diversity, the comprehensive characterization of this viral family over time has been poorly studied. To overcome this challenge, we used a metagenomic next-generation sequencing (mNGS) approach with the aim of determining the individual anellovirus profile of autologous stem cell transplant (ASCT) patients. We conducted a prospective pilot study on a homogeneous patient cohort regarding the chemotherapy regimens that included 10 ASCT recipients. A validated viral mNGS workflow was used on 108 plasma samples collected at 11 time points from diagnosis to 90 days post-transplantation. A complex interindividual variability in terms of abundance and composition was noticed. In particular, a strong sex effect was found and confirmed using quantitative PCR targeting torque teno virus, the most abundant anellovirus. Interestingly, an important turnover in the anellovirus composition was observed during the course of the disease revealing a strong intra-individual variability. Although more studies are needed to better understand anellovirus dynamics, these findings are of prime importance for their future use as biomarkers of immune competence.},
}

@article {pmid30440884,
year = {2018},
author = {Gao, Z and Chen, KY and Mueller, O and Zhang, H and Rakhilin, N and Chen, J and Shen, X},
title = {Microbiota of Inflammatory Bowel Disease Models.},
journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference},
volume = {2018},
number = {},
pages = {2374-2377},
doi = {10.1109/EMBC.2018.8512848},
pmid = {30440884},
issn = {1557-170X},
abstract = {Gut microbiome plays an important role in inflammatory bowel disease (IBD), a group of intestinal chronic inflammation conditions that affect a large population. The animal models of IBD have long been established on basis of pathological features, but their ability to recapitulate patient gut microbiota is unknown. We investigated and compared the composition and biodiversity of bacterial population in the fecal samples from rat models of the two IBD subtypes, and compared them with patient samples. Our analyses revealed that inflammation reduces overall microbiome diversity and increased variation between individuals. We identified specific microbial signatures associated with the two IBD subtypes that were consistent between the animal models and human IBD patients, suggesting that the animal models can partially recapitulate the microbiota in human diseases. Furthermore, metagenome prediction analysis suggested microbial functions that were likely altered by host-microbiota interactions in IBD models.},
}

@article {pmid30440633,
year = {2018},
author = {Ariza-Jimenez, L and Quintero, OL and Pinel, N},
title = {Unsupervised fuzzy binning of metagenomic sequence fragments on three-dimensional Barnes-Hut t-Stochastic Neighbor Embeddings.},
journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference},
volume = {2018},
number = {},
pages = {1315-1318},
doi = {10.1109/EMBC.2018.8512529},
pmid = {30440633},
issn = {1557-170X},
abstract = {Shotgun metagenomic studies attempt to reconstruct population genome sequences from complex microbial communities. In some traditional genome demarcation approaches, high-dimensional sequence data are embedded into two-dimensional spaces and subsequently binned into candidate genomic populations. One such approach uses a combination of the Barnes-Hut approximation and the $t -$Stochastic Neighbor Embedding (BH-SNE) algorithm for dimensionality reduction of DNA sequence data pentamer profiles; and demarcation of groups based on Gaussian mixture models within humanimposed boundaries. We found that genome demarcation from three-dimensional BH-SNE embeddings consistently results in more accurate binnings than 2-D embeddings. We further addressed the lack of a priori population number information by developing an unsupervised binning approach based on the Subtractive and Fuzzy c-means (FCM) clustering algorithms combined with internal clustering validity indices. Lastly, we addressed the subject of shared membership of individual data objects in a mixed community by assigning a degree of membership to individual objects using the FCM algorithm, and discriminated between confidently binned and uncertain sequence data objects from the community for subsequent biological interpretation. The binning of metagenome sequence fragments according to thresholds in the degree of membership opens the door for the identification of horizontally transferred elements and other genomic regions of uncertain assignment in which biologically meaningful information resides. The reported approach improves the unsupervised genome demarcation of populations within complex communities, increases the confidence in the coherence of the binned elements, and enables the identification of evolutionary processes ignored in hard-binning approaches in shotgun metagenomic studies.},
}

@article {pmid29901703,
year = {2018},
author = {Simon, LM and Karg, S and Westermann, AJ and Engel, M and Elbehery, AHA and Hense, B and Heinig, M and Deng, L and Theis, FJ},
title = {MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.},
journal = {GigaScience},
volume = {7},
number = {6},
pages = {},
doi = {10.1093/gigascience/giy070},
pmid = {29901703},
issn = {2047-217X},
mesh = {Disease/*genetics ; Humans ; Lymphocytes/metabolism ; *Metagenomics ; *Sequence Analysis, RNA ; *Software ; Transcriptome/*genetics ; },
abstract = {Background: With the advent of the age of big data in bioinformatics, large volumes of data and high-performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts; however, its generic nature also enables the detection of microbial and viral transcripts.

Findings: We developed a bioinformatic pipeline to screen existing human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. We validated this approach by recapitulating outcomes from six independent, controlled infection experiments of cell line models and compared them with an alternative metatranscriptomic mapping strategy. We then applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from more than 17,000 samples from more than 400 studies relevant to human disease using state-of-the-art high-performance computing systems. The resulting data from this large-scale re-analysis are made available in the presented MetaMap resource.

Conclusions: Our results demonstrate that common human RNA-seq data, including those archived in public repositories, might contain valuable information to correlate microbial and viral detection patterns with diverse diseases. The presented MetaMap database thus provides a rich resource for hypothesis generation toward the role of the microbiome in human disease. Additionally, codes to process new datasets and perform statistical analyses are made available.},
}

Disease/*genetics
Humans
Lymphocytes/metabolism
*Metagenomics
*Sequence Analysis, RNA
*Software
Transcriptome/*genetics

@article {pmid29746643,
year = {2018},
author = {Metzler-Zebeli, BU and Lawlor, PG and Magowan, E and Zebeli, Q},
title = {Interactions between metabolically active bacteria and host gene expression at the cecal mucosa in pigs of diverging feed efficiency.},
journal = {Journal of animal science},
volume = {96},
number = {6},
pages = {2249-2264},
doi = {10.1093/jas/sky118},
pmid = {29746643},
issn = {1525-3163},
mesh = {Animal Feed ; Animals ; Bacteria/genetics/*metabolism ; Cecum/microbiology ; *Eating ; Female ; Gastrointestinal Microbiome/*physiology ; *Gene Expression Regulation ; High-Throughput Nucleotide Sequencing/veterinary ; Immunity, Innate ; Male ; *Metagenome ; Sequence Analysis, RNA/veterinary ; Swine/genetics/immunology/*microbiology ; },
abstract = {Little is known about the role of the gut mucosal microbiota and microbe-host signaling in the variation of pig's feed efficiency (FE). This study therefore aimed to investigate the FE-related differences in the metabolically active mucosal bacterial microbiota and expression of genes for innate immune response, barrier function, nutrient uptake, and incretins in the cecum of finishing pigs. Pigs (n = 72) were ranked for their residual feed intake (RFI; metric for FE) between days 42 and 91 postweaning and were stratified within litter and sex into high (HRFI; n = 8) and low RFI (LRFI; n = 8). Cecal mucosa and digesta were collected on day 137-141 of life. After isolating total RNA from the mucosa, the RNA was transcribed into cDNA which was used for gene expression analysis, total bacterial quantification, and high-throughput sequencing (Illumina MiSeq) of the hypervariable V3-V4 region of the 16S rRNA gene. The RFI differed by 2.1 kg between low RFI (LRFI; good FE) and high RFI (HRFI; poor FE) pigs (P < 0.001). The cecal mucosa was mainly colonized by Helicobacteraceae, Campylobacteraceae, Veillonellaceae, Lachnospiraceae, and Prevotellaceae. Despite the lack of differences in microbial diversity and absolute abundance, RFI-associated compositional differences were found. The predominant genus Campylobacter tended (P < 0.10) to be 0.4-fold more abundant in LRFI pigs, whereas low abundant Escherichia/Shigella (P < 0.05), Ruminobacter (P < 0.05), and Veillonella (P < 0.10) were 3.4-, 6.6-, and 4.4-fold less abundant at the cecal mucosa of LRFI compared to HRFI pigs. Moreover, mucin 2 and zona occludens-1 were less expressed (P < 0.05) in the cecal mucosa of LRFI compared to HRFI pigs. Cecal mucosal expression of monocarboxylate transporter-1, glucagon-like peptide-1, and peptide YY further tended (P < 0.10) to be downregulated in LRFI compared to HRFI pigs, indicating an enhanced VFA uptake and signaling in HRFI pigs. Sparse partial least square regression and relevance networking support the hypothesis that certain mucosal bacteria and luminal microbial metabolites were more associated than others with differences in RFI and cecal gene expression. However, present results do not allow the determination of whether mucosal bacterial changes contributed to variation in FE or were rather a consequence of FE-related changes in the pig's physiology or feeding behavior.},
}

Animal Feed
Animals
Bacteria/genetics/*metabolism
Cecum/microbiology
*Eating
Female
Gastrointestinal Microbiome/*physiology
*Gene Expression Regulation
High-Throughput Nucleotide Sequencing/veterinary
Immunity, Innate
Male
*Metagenome
Sequence Analysis, RNA/veterinary
Swine/genetics/immunology/*microbiology

@article {pmid29321640,
year = {2018},
author = {Ehsani, E and Hernandez-Sanabria, E and Kerckhof, FM and Props, R and Vilchez-Vargas, R and Vital, M and Pieper, DH and Boon, N},
title = {Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {340},
doi = {10.1038/s41598-017-18668-1},
pmid = {29321640},
issn = {2045-2322},
mesh = {*Biodiversity ; *Ecosystem ; Metagenome ; Metagenomics/methods ; *Microbiota ; Models, Theoretical ; Phenotype ; },
abstract = {The effect of initial evenness on the temporal trajectory of synthetic communities in comprehensive, low-volume microcosm studies remains unknown. We used flow cytometric fingerprinting and 16S rRNA gene amplicon sequencing to assess the impact of time on community structure in one hundred synthetic ecosystems of fixed richness but varying initial evenness. Both methodologies uncovered a similar reduction in diversity within synthetic communities of medium and high initial evenness classes. However, the results of amplicon sequencing showed that there were no significant differences between and within the communities in all evenness groups at the end of the experiment. Nevertheless, initial evenness significantly impacted the cell density of the community after five medium transfers. Highly even communities retained the highest cell densities at the end of the experiment. The relative abundances of individual species could be associated to particular evenness groups, suggesting that their presence was dependent on the initial evenness of the synthetic community. Our results reveal that using synthetic communities for testing ecological hypotheses requires prior assessment of initial evenness, as it impacts temporal dynamics.},
}

*Biodiversity
*Ecosystem
Metagenome
Metagenomics/methods
*Microbiota
Models, Theoretical
Phenotype

@article {pmid29311585,
year = {2018},
author = {Odamaki, T and Bottacini, F and Kato, K and Mitsuyama, E and Yoshida, K and Horigome, A and Xiao, JZ and van Sinderen, D},
title = {Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {85},
doi = {10.1038/s41598-017-18391-x},
pmid = {29311585},
issn = {2045-2322},
mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Bifidobacterium longum/*classification/*genetics ; Child ; Child, Preschool ; Gastrointestinal Microbiome ; Gene Order ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Infant ; Infant, Newborn ; Japan ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; Multigene Family ; Phylogeny ; Young Adult ; },
abstract = {Bifidobacterium longum subsp. longum represents one of the most prevalent bifidobacterial species in the infant, adult and elderly (human) gut. In the current study, we performed a comparative genome analysis involving 145 B. longum representatives, including 113 B. longum subsp. longum strains obtained from healthy Japanese subjects aged between 0 and 98 years. Although MCL clustering did not reveal any correlation between isolated strains and subject age, certain characteristics appear to be more prevalent among strains corresponding to specific host ages, such as genes involved in carbohydrate metabolism and environmental response. Remarkably, a substantial number of strains appeared to have been transmitted across family members, a phenomenon that was shown not to be confined to mother-infant pairs. This suggests that the ubiquitous distribution of B. longum subsp. longum across the human lifespan is at least partly due to extensive transmission between relatives. Our findings form a foundation for future research aimed at unraveling the mechanisms that allow B. longum strains to successfully transfer between human hosts, where they then colonize and persist in the gut environment throughout the host's lifespan.},
}

Adolescent
Adult
Age Factors
Aged
Aged, 80 and over
Bifidobacterium longum/*classification/*genetics
Child
Child, Preschool
Gastrointestinal Microbiome
Gene Order
*Genetic Variation
*Genome, Bacterial
Humans
Infant
Infant, Newborn
Japan
*Metagenome
*Metagenomics/methods
*Microbiota
Middle Aged
Multigene Family
Phylogeny
Young Adult

@article {pmid30440093,
year = {2018},
author = {Park, CH and Lee, AR and Lee, YR and Eun, CS and Lee, SK and Han, DS},
title = {Evaluation of gastric microbiome and metagenomic function in patients with intestinal metaplasia using 16S rRNA gene sequencing.},
journal = {Helicobacter},
volume = {},
number = {},
pages = {e12547},
doi = {10.1111/hel.12547},
pmid = {30440093},
issn = {1523-5378},
support = {//National Research Foundation of Korea (NRF)/ ; NRF-2017R1C1B5015928//Korea government (MSIP; Ministry of Science, ICT & Future Planning)/ ; },
abstract = {BACKGROUND: Despite recent advances in studies on the gastric microbiome, the role of the non-Helicobacter pylori gastric microbiome in gastric carcinogenesis remains unclear. We evaluated the characteristics of the gastric microbiome and metagenomic functions in patients with IM.

METHODS: Participants were classified into six groups according to disease status (chronic superficial gastritis [CSG], intestinal metaplasia [IM], and cancer) and H. pylori- infection status (H. pylori-positive and H. pylori-negative). The gastric microbiome was analyzed in mucosal tissues at the gastric antrum by 16S rRNA gene sequencing. Moreover, we assessed the metagenome including the type IV secretion system (T4SS) gene, as T4SS proteins are essential for transferring CagA from H. pylori- into the human gastric epithelium.

RESULTS: Among the 138 included patients, 48, 9, 23, 14, 12, and 32 were classified into the H. pylori-negative CSG, H. pylori-negative IM, H. pylori-negative cancer, H. pylori-positive CSG, H. pylori-positive IM, and H. pylori-positive cancer groups, respectively. Cyanobacteria were predominant in the H. pylori-negative CSG group compared to in the H. pylori-negative IM and H. pylori-negative cancer groups (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 14.0% vs 4.2% vs 0.04%, P < 0.001). In contrast, Rhizobiales were commonly observed in the H. pylori-negative IM group (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 1.9% vs 15.4% vs 2.8%, P < 0.001). The relative abundance of Rhizobiales increased as H. pylori-infected stomachs progressed from gastritis to IM. In the H. pylori-negative IM group, genes encoding T4SS were prevalent among the metagenome. Additionally, after H. pylori- eradication therapy, the gastric microbiome was similar to the microbiome observed after spontaneous clearance of H. pylori-.

CONCLUSIONS: The relative abundance of Rhizobiales was higher in patients with H. pylori-negative IM than in those with H. pylori-negative CSG or cancer. Additionally, T4SS genes were highly observed in the metagenome of patients with IM. Highly abundant T4SS proteins in these patients may promote gastric carcinogenesis.},
}

@article {pmid30430271,
year = {2018},
author = {Zhang, B and Xu, X and Zhu, L},
title = {Activated sludge bacterial communities of typical wastewater treatment plants: distinct genera identification and metabolic potential differential analysis.},
journal = {AMB Express},
volume = {8},
number = {1},
pages = {184},
doi = {10.1186/s13568-018-0714-0},
pmid = {30430271},
issn = {2191-0855},
support = {51478416//National Natural Science Foundation of China/ ; },
abstract = {To investigate the differences in activated sludge microbial communities of different wastewater treatment plants (WWTPs) and understand their metabolic potentials, we sampled sludge from every biological treatment unit of 5 full-scale waste water treatment systems in 3 typical Chinese municipal WWTPs. The microbial communities and overall metabolic patterns were not only affected by influent characteristics but also varied between different biological treatment units. Distinct genera in different wastewater treatment systems were identified. The important microorganisms in domestic sewage treatment systems were unclassified SHA-20, Caldilinea, Dechloromonas, and unclassified genera from Rhodospirilaceae and Caldilineaceae. The important microorganisms in dyeing wastewater treatment systems were Nitrospira, Sphingobacteriales, Thiobacillus, Sinobacteraceae and Comamonadaceae. Compared with the obvious differences in microbial community composition, the metabolic potential showed no significant differences.},
}

@article {pmid30429253,
year = {2018},
author = {Yan, Q and Wi, YM and Thoendel, MJ and Raval, YS and Greenwood-Quaintance, KE and Abdel, MP and Jeraldo, PR and Chia, N and Patel, R},
title = {Evaluation of the CosmosID Bioinformatics Platform for Prosthetic Joint-Associated Sonicate Fluid Shotgun Metagenomic Data Analysis.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JCM.01182-18},
pmid = {30429253},
issn = {1098-660X},
abstract = {We previously demonstrated that shotgun metagenomic sequencing can detect bacteria in sonicate fluid, providing a diagnosis of prosthetic joint infection (PJI). A limitation of the approach we used is that data analysis was time consuming and specialized bioinformatics expertise was required, both barriers to routine clinical use. Fortunately, automated commercial analytic platforms that can "interpret" shotgun metagenomic data are emerging. In this study, we evaluated the CosmosID bioinformatics platform using shotgun metagenomic sequencing data derived from 408 sonicate fluids from our prior study, with the goal of evaluating the platform vis-à-vis bacterial detection and antibiotic resistance gene detection for predicting staphylococcal antibacterial susceptibility. Samples were divided into a derivation set and a validation set, each consisting of 204 samples; results from the derivation set were used to establish cutoffs which were then tested in the validation set for identifying pathogens and predicting staphylococcal antibacterial resistance. Metagenomic analysis detected bacteria in 94.8% (109/115) of sonicate culture-positive PJIs and 37.8% (37/98) of sonicate culture-negative PJIs. Metagenomic analysis showed sensitivities ranging from 65.7 to 85.0% for predicting staphylococcal antibacterial resistance. In conclusion, the CosmosID platform has the potential to provide fast, reliable bacterial detection and identification from metagenomic shotgun sequencing data derived from sonicate fluid for diagnosis of PJI. Strategies for metagenomic detection of antibiotic resistance genes for predicting staphylococcal antibacterial resistance need further development.},
}

@article {pmid30249639,
year = {2018},
author = {Guellil, M and Kersten, O and Namouchi, A and Bauer, EL and Derrick, M and Jensen, AØ and Stenseth, NC and Bramanti, B},
title = {Genomic blueprint of a relapsing fever pathogen in 15th century Scandinavia.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {41},
pages = {10422-10427},
doi = {10.1073/pnas.1807266115},
pmid = {30249639},
issn = {1091-6490},
mesh = {Adult ; Animals ; Bacterial Proteins/*genetics ; Borrelia/classification/*genetics/pathogenicity ; Child ; Female ; *Genome, Bacterial ; History, 15th Century ; Humans ; *Metagenomics ; Phylogeny ; Relapsing Fever/*genetics/history/microbiology ; Scandinavian and Nordic Countries ; },
abstract = {Louse-borne relapsing fever (LBRF) is known to have killed millions of people over the course of European history and remains a major cause of mortality in parts of the world. Its pathogen, Borrelia recurrentis, shares a common vector with global killers such as typhus and plague and is known for its involvement in devastating historical epidemics such as the Irish potato famine. Here, we describe a European and historical genome of Brecurrentis, recovered from a 15th century skeleton from Oslo. Our distinct European lineage has a discrete genomic makeup, displaying an ancestral oppA-1 gene and gene loss in antigenic variation sites. Our results illustrate the potential of ancient DNA research to elucidate dynamics of reductive evolution in a specialized human pathogen and to uncover aspects of human health usually invisible to the archaeological record.},
}

Adult
Animals
Bacterial Proteins/*genetics
Borrelia/classification/*genetics/pathogenicity
Child
Female
*Genome, Bacterial
History, 15th Century
Humans
*Metagenomics
Phylogeny
Relapsing Fever/*genetics/history/microbiology
Scandinavian and Nordic Countries

@article {pmid30427852,
year = {2018},
author = {Brito, TL and Campos, AB and Bastiaan von Meijenfeldt, FA and Daniel, JP and Ribeiro, GB and Silva, GGZ and Wilke, DV and de Moraes, DT and Dutilh, BE and Meirelles, PM and Trindade-Silva, AE},
title = {The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0200437},
doi = {10.1371/journal.pone.0200437},
pmid = {30427852},
issn = {1932-6203},
abstract = {Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae "clade I" strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills' metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.},
}

@article {pmid30427574,
year = {2018},
author = {Barnes, RC and Kim, H and Fang, C and Bennett, W and Nemec, M and Sirven, MA and Suchodolski, JS and Deutz, N and Britton, RA and Mertens-Talcott, SU and Talcott, ST},
title = {Body Mass Index as a determinant of systemic exposures to gallotannin metabolites during six-week consumption of mango (Mangifera Indica L.) and modulation of intestinal microbiota in lean and obese individuals.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e1800512},
doi = {10.1002/mnfr.201800512},
pmid = {30427574},
issn = {1613-4133},
abstract = {SCOPE: This human clinical pilot trial investigated pharmacokinetics of gallotannin-metabolites and modulation of intestinal microbiota in healthy lean and obese individuals after 6 weeks of daily mango consumption.

METHODS AND RESULTS: Participants were divided into three groups: Lean Mango (LM: n = 12; BMI = 22.9 kg/m2), Obese Mango (OM: n = 9; BMI = 34.6 kg/m2), and Lean Control (LC: n = 11; BMI = 22.1 kg/m2). LM and OM consumed 400 g of mango/d for 6 weeks. LC consumed mango only on Days 0 and 42. After 6 weeks, LM experienced increased systemic exposure (AUC0-8h) to gallotannin-metabolites, 1.4-fold (p = 0.043). The greatest increase was 4-O-methyl-gallic acid, 3.3-fold (p = 0.0026). Cumulative urinary excretion of gallotannin-metabolites significantly increased in LM and OM, but not LC. For OM, qPCR data show increased levels of tannase-producing Lactococcus lactis and decreased levels of Clostridium leptum and Bacteroides thetaiotaomicron, bacteria associated with obesity. LM experienced an increased trend of fecal levels of butyric (1.3-fold; p = 0.09) and valeric acids (1.5-fold; p = 0.056). Plasma endotoxins showed a decreased trend in LM and OM.

CONCLUSION: Continuous mango intake significantly increased systemic exposure to gallotannin- metabolites and induced increased trend for fecal short-chain fatty acids in lean but not obese individuals. This pharmacokinetic discrepancy may result in BMI-associated reduced gallotannin-derived health benefits. This article is protected by copyright. All rights reserved.},
}

@article {pmid30425894,
year = {2018},
author = {Ornelas-García, P and Pajares, S and Sosa-Jiménez, VM and Rétaux, S and Miranda-Gamboa, RA},
title = {Microbiome differences between river-dwelling and cave-adapted populations of the fish Astyanax mexicanus (De Filippi, 1853).},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5906},
doi = {10.7717/peerj.5906},
pmid = {30425894},
issn = {2167-8359},
abstract = {Symbiotic relationships between host and microbiome can play a major role in local adaptation. Previous studies with freshwater organisms have shown that microbiome performs numerous important biochemical functions for the host, playing a key role in metabolism, physiology or health. Experimental studies in fish groups have found an effect of enzymatic activity of gut microbiota on a variety of metabolic processes. The goal of this study was to compare stomach microbiome from cave and surface Astyanax mexicanus, in order to evaluate the potential response of microbiota to contrasting environmental conditions and physiological adaptations of the host. Stomach microbiota was obtained from three different populations: Pachón cave, and two surface rivers (Rascón and Micos rivers). The stomach microbiome was analyzed using the Ion 16S Metagenomic kit considering seven variable regions: V2, V3, V4, V6-7, V8 and V9. A high diversity was observed across samples, including 16 phyla, 120 families and 178 genera. Gammaproteobacteria, Firmicutes, Bacteroidetes and Betaproteobacteria were the most abundant phyla across the samples. Although the relative abundance of the core OTUs at genus level were highly contrasting among populations, we did not recover differences in stomach microbiome between contrasting habitats (cave vs. surface rivers). Rather, we observed a consistent association between β-diversity and dissolved oxygen concentration in water. Therefore, and unexpectedly, the microbiota of A. mexicanus is not linked with the contrasting conditions of the habitat considered here but is related to water parameters.},
}

@article {pmid30425704,
year = {2018},
author = {Jäger, T and Hembach, N and Elpers, C and Wieland, A and Alexander, J and Hiller, C and Krauter, G and Schwartz, T},
title = {Reduction of Antibiotic Resistant Bacteria During Conventional and Advanced Wastewater Treatment, and the Disseminated Loads Released to the Environment.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2599},
doi = {10.3389/fmicb.2018.02599},
pmid = {30425704},
issn = {1664-302X},
abstract = {The occurrence of new chemical and microbiological contaminants in the aquatic environment has become an issue of increasing environmental concern. Thus, wastewater treatment plants (WWTPs) play an important part in the distribution of so-called new emerging pathogens and antibiotic resistances. Therefore, the daily loads released by the WWTP were calculated including a model system for the distribution of these loads within the receiving water body. UV-, as well as ozone-treatment in separate or in combination for wastewater treatment were under investigation aiming at the reduction of these loads. Here, the impact of these treatments on the DNA integrity via antibody staining and PCR efficiencies experiments were included. All three facultative pathogenic bacteria [enterococci (23S rRNA), Pseudomonas aeruginosa (ecfX), and Escherichia coli (yccT)] and seven clinically relevant antibiotic resistance genes (ARGs) (mecA (methicillin resistance gene), ctx-M32 (β- lactame resistance gene), ermB (erythromycine resistance gene), blaTEM (β- lactame resistance gene), sul1 (sulfonamide resistance gene), vanA (vancomycin resistance gene), and intI1 (Integrase1 gene) associated with mobile genetic elements were detected in wastewaters. Different reduction efficiencies were analyzed during advanced wastewater treatments. ARGs were still found to be present in the effluents under the parameters of 1.0 g ozone per g dissolved organic carbon (DOC) and 400 J/m2, like ctx-M32, ermB, blaTEM, sul1, and intI1. Especially UV radiation induced thymidine dimerization which was analyzed via antibody mediated detection in the metagenome of the natural wastewater population. These specific DNA alterations were not observed during ozone treatment and combinations of UV/ozone treatment. The dimerization or potential other DNA alterations during UV treatment might be responsible for a decreased PCR efficiency of the 16S rRNA amplicons (176, 490, and 880 bp fragments) from natural metagenomes compared to the untreated sample. This impact on PCR efficiencies was also observed for the combination of ozone and UV treatment.},
}

@article {pmid30425690,
year = {2018},
author = {Fang, X and Monk, JM and Nurk, S and Akseshina, M and Zhu, Q and Gemmell, C and Gianetto-Hill, C and Leung, N and Szubin, R and Sanders, J and Beck, PL and Li, W and Sandborn, WJ and Gray-Owen, SD and Knight, R and Allen-Vercoe, E and Palsson, BO and Smarr, L},
title = {Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2559},
doi = {10.3389/fmicb.2018.02559},
pmid = {30425690},
issn = {1664-302X},
abstract = {Dysbiosis of the gut microbiome, including elevated abundance of putative leading bacterial triggers such as E. coli in inflammatory bowel disease (IBD) patients, is of great interest. To date, most E. coli studies in IBD patients are focused on clinical isolates, overlooking their relative abundances and turnover over time. Metagenomics-based studies, on the other hand, are less focused on strain-level investigations. Here, using recently developed bioinformatic tools, we analyzed the abundance and properties of specific E. coli strains in a Crohns disease (CD) patient longitudinally, while also considering the composition of the entire community over time. In this report, we conducted a pilot study on metagenomic-based, strain-level analysis of a time-series of E. coli strains in a left-sided CD patient, who exhibited sustained levels of E. coli greater than 100X healthy controls. We: (1) mapped out the composition of the gut microbiome over time, particularly the presence of E. coli strains, and found that the abundance and dominance of specific E. coli strains in the community varied over time; (2) performed strain-level de novo assemblies of seven dominant E. coli strains, and illustrated disparity between these strains in both phylogenetic origin and genomic content; (3) observed that strain ST1 (recovered during peak inflammation) is highly similar to known pathogenic AIEC strains NC101 and LF82 in both virulence factors and metabolic functions, while other strains (ST2-ST7) that were collected during more stable states displayed diverse characteristics; (4) isolated, sequenced, experimentally characterized ST1, and confirmed the accuracy of the de novo assembly; and (5) assessed growth capability of ST1 with a newly reconstructed genome-scale metabolic model of the strain, and showed its potential to use substrates found abundantly in the human gut to outcompete other microbes. In conclusion, inflammation status (assessed by the blood C-reactive protein and stool calprotectin) is likely correlated with the abundance of a subgroup of E. coli strains with specific traits. Therefore, strain-level time-series analysis of dominant E. coli strains in a CD patient is highly informative, and motivates a study of a larger cohort of IBD patients.},
}

@article {pmid30425689,
year = {2018},
author = {Spini, G and Spina, F and Poli, A and Blieux, AL and Regnier, T and Gramellini, C and Varese, GC and Puglisi, E},
title = {Molecular and Microbiological Insights on the Enrichment Procedures for the Isolation of Petroleum Degrading Bacteria and Fungi.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2543},
doi = {10.3389/fmicb.2018.02543},
pmid = {30425689},
issn = {1664-302X},
abstract = {Autochthonous bioaugmentation, by exploiting the indigenous microorganisms of the contaminated environment to be treated, can represent a successful bioremediation strategy. In this perspective, we have assessed by molecular methods the evolution of bacterial and fungal communities during the selective enrichment on different pollutants of a soil strongly polluted by mixtures of aliphatic and polycyclic hydrocarbons. Three consecutive enrichments were carried out on soil samples from different soil depths (0-1, 1-2, 2-3 m), and analyzed at each step by means of high-throughput sequencing of bacterial and fungal amplicons biomarkers. At the end of the enrichments, bacterial and fungal contaminants degrading strains were isolated and identified in order to (i) compare the composition of enriched communities by culture-dependent and culture-independent molecular methods and to (ii) obtain a collection of hydrocarbon degrading microorganisms potentially exploitable for soil bioremediation. Molecular results highlighted that for both bacteria and fungi the pollutant had a partial shaping effect on the enriched communities, with paraffin creating distinct enriched bacterial community from oil, and polycyclic aromatic hydrocarbons generally overlapping; interestingly neither the soil depth or the enrichment step had significant effects on the composition of the final enriched communities. Molecular analyses well-agreed with culture-dependent analyses in terms of most abundant microbial genera. A total of 95 bacterial and 94 fungal strains were isolated after selective enrichment procedure on different pollutants. On the whole, isolated bacteria where manly ascribed to Pseudomonas genus followed by Sphingobacterium, Bacillus, Stenothrophomonas, Achromobacter, and Serratia. As for fungi, Fusarium was the most abundant genus followed by Trichoderma and Aspergillus. The species comprising more isolates, such as Pseudomonas putida, Achromobacter xylosoxidans and Ochromobactrum anthropi for bacteria, Fusarium oxysporum and Fusarium solani for fungi, were also the dominant OTUs assessed in Illumina.},
}

@article {pmid30424933,
year = {2018},
author = {Castillo-Álvarez, F and Marzo-Sola, ME},
title = {Disease of the holobiont, the example of multiple sclerosis.},
journal = {Medicina clinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.medcli.2018.08.019},
pmid = {30424933},
issn = {1578-8989},
abstract = {In recent years there has been a revolution regarding the role of the microbiota in different diseases, most of them within the spectrum of inflammatory and autoimmune diseases, associated with the development of metagenomics and the concept of holobiont, a large organism together with its microbiota. Specifically, in Multiple Sclerosis, multiple evidence points to the role of the microbiota in experimental autoimmune encephalomyelitis, animal model of the disease, and several articles have been published in recent years about differences in intestinal microbiota among patients with multiple sclerosis and control subjects. We review in this article the concept of holobiont and the gut microbiota functions, as well as the evidence accumulated about the role of the microbiota in experimental autoimmune encephalomyelitis and multiple sclerosis. Nowadays, there is a lot of evidence showing the role of the microbiota in the genesis, prevention and treatment of experimental autoimmune encephalomyelitis based mainly on three immunological pillars, the Th1-Th17 / Th2 balance, the Treg cells and the humoral immunity. It is also well documented that there are differences in the microbiota of patients with MS that are associated with a different expression of genes related to inflammation.},
}

@article {pmid30424821,
year = {2018},
author = {Singh, NK and Wood, JM and Karouia, F and Venkateswaran, K},
title = {Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {204},
doi = {10.1186/s40168-018-0585-2},
pmid = {30424821},
issn = {2049-2618},
support = {19-12829-26//2012 Space Biology NNH12ZTT001N/ ; },
abstract = {BACKGROUND: The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms.

RESULTS: The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii, and Aspergillus lentulus. Even though Rhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3. The AMR signatures associated with β-lactam, cationic antimicrobial peptide, and vancomycin were detected. Prominent virulence factors were cobalt-zinc-cadmium resistance and multidrug-resistance efflux pumps.

CONCLUSIONS: There was an increase in AMR and virulence gene factors detected over the period sampled, and metagenome sequences of human pathogens persisted over time. Comparative analysis of the microbial compositions of ISS with Earth analogs revealed that the ISS environmental surfaces were different in microbial composition. Metagenomics coupled with PMA treatment would help future space missions to estimate problematic risk group microbial pathogens. Cataloging AMR/virulence characteristics, succession, accumulation, and persistence of microorganisms would facilitate the development of suitable countermeasures to reduce their presence in the closed built environment.},
}

@article {pmid29040451,
year = {2018},
author = {Chen, J and King, E and Deek, R and Wei, Z and Yu, Y and Grill, D and Ballman, K and Stegle, O},
title = {An omnibus test for differential distribution analysis of microbiome sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {4},
pages = {643-651},
doi = {10.1093/bioinformatics/btx650},
pmid = {29040451},
issn = {1367-4811},
mesh = {Arthritis, Rheumatoid/microbiology ; Humans ; Inflammatory Bowel Diseases/microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; *Models, Statistical ; *Software ; },
abstract = {Motivation: One objective of human microbiome studies is to identify differentially abundant microbes across biological conditions. Previous statistical methods focus on detecting the shift in the abundance and/or prevalence of the microbes and treat the dispersion (spread of the data) as a nuisance. These methods also assume that the dispersion is the same across conditions, an assumption which may not hold in presence of sample heterogeneity. Moreover, the widespread outliers in the microbiome sequencing data make existing parametric models not overly robust. Therefore, a robust and powerful method that allows covariate-dependent dispersion and addresses outliers is still needed for differential abundance analysis.

Results: We introduce a novel test for differential distribution analysis of microbiome sequencing data by jointly testing the abundance, prevalence and dispersion. The test is built on a zero-inflated negative binomial regression model and winsorized count data to account for zero-inflation and outliers. Using simulated data and real microbiome sequencing datasets, we show that our test is robust across various biological conditions and overall more powerful than previous methods.

R package is available at https://github.com/jchen1981/MicrobiomeDDA.

Contact: chen.jun2@mayo.edu or zhiwei@njit.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.},
}

Arthritis, Rheumatoid/microbiology
Humans
Inflammatory Bowel Diseases/microbiology
Metagenomics/*methods
Microbiota/*genetics
*Models, Statistical
*Software

@article {pmid30423107,
year = {2018},
author = {García-Jiménez, B and de la Rosa, T and Wilkinson, MD},
title = {MDPbiome: microbiome engineering through prescriptive perturbations.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {17},
pages = {i838-i847},
doi = {10.1093/bioinformatics/bty562},
pmid = {30423107},
issn = {1367-4811},
abstract = {Motivation: Recent microbiome dynamics studies highlight the current inability to predict the effects of external perturbations on complex microbial populations. To do so would be particularly advantageous in fields such as medicine, bioremediation or industrial scenarios.

Results: MDPbiome statistically models longitudinal metagenomics samples undergoing perturbations as a Markov Decision Process (MDP). Given a starting microbial composition, our MDPbiome system suggests the sequence of external perturbation(s) that will engineer that microbiome to a goal state, for example, a healthier or more performant composition. It also estimates intermediate microbiome states along the path, thus making it possible to avoid particularly undesirable/unhealthy states. We demonstrate MDPbiome performance over three real and distinct datasets, proving its flexibility, and the reliability and universality of its output 'optimal perturbation policy'. For example, an MDP created using a vaginal microbiome time series, with a goal of recovering from bacterial vaginosis, suggested avoidance of perturbations such as lubricants or sex toys; while another MDP provided a quantitative explanation for why salmonella vaccine accelerates gut microbiome maturation in chicks. This novel analytical approach has clear applications in medicine, where it could suggest low-impact clinical interventions that will lead to achievement or maintenance of a healthy microbial population, or alternately, the sequence of interventions necessary to avoid strongly negative microbiome states.

Code (https://github.com/beatrizgj/MDPbiome) and result files (https://tomdelarosa.shinyapps.io/MDPbiome/) are available online.

Supplementary information: Supplementary data are available at Bioinformatics online.},
}

@article {pmid30423080,
year = {2018},
author = {Dadi, TH and Siragusa, E and Piro, VC and Andrusch, A and Seiler, E and Renard, BY and Reinert, K},
title = {DREAM-Yara: an exact read mapper for very large databases with short update time.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {17},
pages = {i766-i772},
doi = {10.1093/bioinformatics/bty567},
pmid = {30423080},
issn = {1367-4811},
abstract = {Motivation: Mapping-based approaches have become limited in their application to very large sets of references since computing an FM-index for very large databases (e.g. >10 GB) has become a bottleneck. This affects many analyses that need such index as an essential step for approximate matching of the NGS reads to reference databases. For instance, in typical metagenomics analysis, the size of the reference sequences has become prohibitive to compute a single full-text index on standard machines. Even on large memory machines, computing such index takes about 1 day of computing time. As a result, updates of indices are rarely performed. Hence, it is desirable to create an alternative way of indexing while preserving fast search times.

Results: To solve the index construction and update problem we propose the DREAM (Dynamic seaRchablE pArallel coMpressed index) framework and provide an implementation. The main contributions are the introduction of an approximate search distributor via a novel use of Bloom filters. We combine several Bloom filters to form an interleaved Bloom filter and use this new data structure to quickly exclude reads for parts of the databases where they cannot match. This allows us to keep the databases in several indices which can be easily rebuilt if parts are updated while maintaining a fast search time. The second main contribution is an implementation of DREAM-Yara a distributed version of a fully sensitive read mapper under the DREAM framework.

https://gitlab.com/pirovc/dream_yara/.},
}

@article {pmid30423069,
year = {2018},
author = {Andrusch, A and Dabrowski, PW and Klenner, J and Tausch, SH and Kohl, C and Osman, AA and Renard, BY and Nitsche, A},
title = {PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {17},
pages = {i715-i721},
doi = {10.1093/bioinformatics/bty595},
pmid = {30423069},
issn = {1367-4811},
abstract = {Motivation: Next generation sequencing (NGS) has provided researchers with a powerful tool to characterize metagenomic and clinical samples in research and diagnostic settings. NGS allows an open view into samples useful for pathogen detection in an unbiased fashion and without prior hypothesis about possible causative agents. However, NGS datasets for pathogen detection come with different obstacles, such as a very unfavorable ratio of pathogen to host reads. Alongside often appearing false positives and irrelevant organisms, such as contaminants, tools are often challenged by samples with low pathogen loads and might not report organisms present below a certain threshold. Furthermore, some metagenomic profiling tools are only focused on one particular set of pathogens, for example bacteria.

Results: We present PAIPline, a bioinformatics pipeline specifically designed to address problems associated with detecting pathogens in diagnostic samples. PAIPline particularly focuses on userfriendliness and encapsulates all necessary steps from preprocessing to resolution of ambiguous reads and filtering up to visualization in a single tool. In contrast to existing tools, PAIPline is more specific while maintaining sensitivity. This is shown in a comparative evaluation where PAIPline was benchmarked along other well-known metagenomic profiling tools on previously published well-characterized datasets. Additionally, as part of an international cooperation project, PAIPline was applied to an outbreak sample of hemorrhagic fevers of then unknown etiology. The presented results show that PAIPline can serve as a robust, reliable, user-friendly, adaptable and generalizable stand-alone software for diagnostics from NGS samples and as a stepping stone for further downstream analyses.

PAIPline is freely available under https://gitlab.com/rki_bioinformatics/paipline.},
}

@article {pmid30423048,
year = {2018},
author = {Miao, Q and Ma, Y and Wang, Q and Pan, J and Zhang, Y and Jin, W and Yao, Y and Su, Y and Huang, Y and Wang, M and Li, B and Li, H and Zhou, C and Li, C and Ye, M and Xu, X and Li, Y and Hu, B},
title = {Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {67},
number = {suppl_2},
pages = {S231-S240},
doi = {10.1093/cid/ciy693},
pmid = {30423048},
issn = {1537-6591},
abstract = {Background: Metagenomic next-generation sequencing (mNGS) was suggested to potentially replace traditional microbiological methodology because of its comprehensiveness. However, clinical experience with application of the test is relatively limited.

Methods: From April 2017 to December 2017, 511 specimens were collected, and their retrospective diagnoses were classified into infectious disease (347 [67.9%]), noninfectious disease (119 [23.3%]), and unknown cases (45 [8.8%]). The diagnostic performance of pathogens was compared between mNGS and culture. The effect of antibiotic exposure on detection rate was also assessed.

Results: The sensitivity and specificity of mNGS for diagnosing infectious disease were 50.7% and 85.7%, respectively, and these values outperformed those of culture, especially for Mycobacterium tuberculosis (odds ratio [OR], 4 [95% confidence interval {CI},
1.7-10.8]; P < .01), viruses (mNGS only; P < .01), anaerobes (OR, ∞ [95% CI, 1.71-∞]; P < .01) and fungi (OR, 4.0 [95% CI, 1.6-10.3]; P < .01). Importantly, for mNGS-positive cases where the conventional method was inconclusive, 43 (61%) cases led to diagnosis modification, and 41 (58%) cases were not covered by empirical antibiotics. For cases where viruses were identified, broad-spectrum antibiotics were commonly administered (14/27), and 10 of 27 of these cases were suspected to be inappropriate. Interestingly, the sensitivity of mNGS was superior to that of culture (52.5% vs 34.2%; P < .01) in cases with, but not without, antibiotic exposure.

Conclusions: mNGS could yield a higher sensitivity for pathogen identification and is less affected by prior antibiotic exposure, thereby emerging as a promising technology for detecting infectious diseases.},
}

@article {pmid30422704,
year = {2018},
author = {Yue, SJ and Liu, J and Wang, AT and Meng, XT and Yang, ZR and Peng, C and Guan, HS and Wang, CY and Yan, D},
title = {Berberine alleviates insulin resistance by reducing peripheral branched-chain amino acids.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpendo.00256.2018},
pmid = {30422704},
issn = {1522-1555},
abstract = {Increased circulating branched-chain amino acids (BCAAs) have been involved in the pathogenesis of obesity and insulin resistance (IR). However, evidence relating berberine (BBR), gut microbiota, BCAAs and IR is limited. Here, we showed that BBR could effectively rectify steatohepatitis and glucose intolerance in high-fat diet (HFD)-fed mice. BBR reorganized gut microbiota populations under both the normal chow diet (NCD) and HFD. Particularly, BBR noticeably decreased the relative abundance of BCAA-producing bacteria, including order Clostridiales, families Streptococcaceae, Clostridiaceae and Prevotellaceae, and genera Streptococcus and Prevotella. Compared with the HFD group, predictive metagenomics indicated a reduction in the proportion of gut microbiota genes involved in BCAA biosynthesis, but the enrichment genes for BCAA degradation and transport by BBR treatment. Accordingly, the elevated serum BCAAs of HFD group were significantly decreased by BBR. Furthermore, the Western blotting results implied that BBR could promote the BCAA catabolism in the liver and epididymal white adipose tissues of HFD-fed mice by activation of the multienzyme branched-chain α-ketoacid dehydrogenase complex (BCKDC), whereas by inhibition of the phosphorylation state of BCKDHA (E1α subunit) and branched-chain α-ketoacid dehydrogenase kinase (BCKDK). The ex vivo assay further confirmed that BBR could increase BCAA catabolism in both AML12 hepatocytes and 3T3-L1 adipocytes. Finally, data from healthy subjects and diabetics confirmed that BBR could improve glycemic control and modulate circulating BCAAs. Together, our findings clarified BBR improving IR associated not only with gut microbiota alteration in BCAA biosynthesis, but also with BCAA catabolism in liver and adipose tissues.},
}

@article {pmid30421297,
year = {2018},
author = {Shah, A and Morrison, M and Holtmann, GJ},
title = {Gastroduodenal "Dysbiosis": a New Clinical Entity.},
journal = {Current treatment options in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11938-018-0207-x},
pmid = {30421297},
issn = {1092-8472},
abstract = {PURPOSE OF REVIEW: Like the rest of the gastrointestinal tract, the small intestine is colonised by microbes, but how this "microbiome" affects the immune system and digestive functions has largely been overlooked, especially in the "omics" era. Here, we present recent findings that show that the diversity, density and interactions of these microbes in the small intestine can play an important role in the pathogenesis of a number of gastrointestinal and extraintestinal disorders.

RECENT FINDINGS: Changes in the small intestinal mucosa-associated microbiota (SI-MAM) have been shown to occur with inflammatory bowel diseases, functional gastrointestinal disorders, metabolic disorders such as obesity and type 2 diabetes. More recently, there is emerging evidence that small intestinal dysbiosis can be a driver for the progression of chronic liver disease. Initially believed that small intestinal dysbiosis (e.g. SIBO) is mainly due to alterations of luminal conditions (e.g. after surgical resections of the ileocecal valve), there is now enough evidence to conclude that small intestinal dysbiosis can occur without underlying structural abnormalities. Alterations of the SI-MAM appear to play a key role for the manifestation and progression of inflammatory and metabolic disorders.},
}

@article {pmid30420843,
year = {2018},
author = {Alves, LF and Meleiro, LP and Silva, RN and Westmann, CA and Guazzaroni, ME},
title = {Novel Ethanol- and 5-Hydroxymethyl Furfural-Stimulated β-Glucosidase Retrieved From a Brazilian Secondary Atlantic Forest Soil Metagenome.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2556},
doi = {10.3389/fmicb.2018.02556},
pmid = {30420843},
issn = {1664-302X},
abstract = {Beta-glucosidases are key enzymes involved in lignocellulosic biomass degradation for bioethanol production, which complete the final step during cellulose hydrolysis by converting cellobiose into glucose. Currently, industry requires enzymes with improved catalytic performance or tolerance to process-specific parameters. In this sense, metagenomics has become a powerful tool for accessing and exploring the biochemical biodiversity present in different natural environments. Here, we report the identification of a novel β-glucosidase from metagenomic DNA isolated from soil samples enriched with decaying plant matter from a Secondary Atlantic Forest region. For this, we employed a functional screening approach using an optimized and synthetic broad host-range vector for library production. The novel β-glucosidase - named Lfa2 - displays three GH3-family conserved domains and conserved catalytic amino acids D283 and E487. The purified enzyme was most active in pH 5.5 and at 50°C, and showed hydrolytic activity toward several pNP synthetic substrates containing β-glucose, β-galactose, β-xylose, β-fucose, and α-arabinopyranose, as well as toward cellobiose. Lfa2 showed considerable glucose tolerance, exhibiting an IC50 of 300 mM glucose and 30% of remaining activity in 600 mM glucose. In addition, Lfa2 retained full or slightly enhanced activity in the presence of several metal ions. Further, β-glucosidase activity was increased by 1.7-fold in the presence of 10% (v/v) ethanol, a concentration that can be reached in conventional fermentation processes. Similarly, Lfa2 showed 1.7-fold enhanced activity at high concentrations of 5-hydroxymethyl furfural, one of the most important cellulase inhibitors in pretreated sugarcane bagasse hydrolysates. Moreover, the synergistic effect of Lfa2 on Bacillus subtilis GH5-CBM3 endoglucanase activity was demonstrated by the increased production of glucose (1.6-fold). Together, these results indicate that β-glucosidase Lfa2 is a promissory enzyme candidate for utilization in diverse industrial applications, such as cellulosic biomass degradation or flavor enhancement in winemaking and grape processing.},
}

@article {pmid30420838,
year = {2018},
author = {Li, W and Yuan, Y and Xia, Y and Sun, Y and Miao, Y and Ma, S},
title = {A Cross-Scale Neutral Theory Approach to the Influence of Obesity on Community Assembly of Human Gut Microbiome.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2320},
doi = {10.3389/fmicb.2018.02320},
pmid = {30420838},
issn = {1664-302X},
abstract = {Background: The implications of gut microbiome to obesity have been extensively investigated in recent years although the exact mechanism is still unclear. The question whether or not obesity influences gut microbiome assembly has not been addressed. The question is significant because it is fundamental for investigating the diversity maintenance and stability of gut microbiome, and the latter should hold a key for understanding the etiological implications of gut microbiome to obesity. Methods: In this study, we adopt a dual neutral theory modeling strategy to address this question from both species and community perspectives, with both discrete and continuous neutral theory models. The first neutral theory model we apply is Hubbell's neutral theory of biodiversity that has been extensively tested in macro-ecology of plants and animals, and the second we apply is Sloan's neutral theory model that was developed particularly for microbial communities based on metagenomic sequencing data. Both the neutral models are complementary to each other and integrated together offering a comprehensive approach to more accurately revealing the possible influence of obesity on gut microbiome assembly. This is not only because the focus of both neutral theory models is different (community vs. species), but also because they adopted two different modeling strategies (discrete vs. continuous). Results: We test both the neutral theory models with datasets from Turnbaugh et al. (2009). Our tests showed that the species abundance distributions of more than ½ species (59-69%) in gut microbiome satisfied the prediction of Sloan's neutral theory, although at the community level, the number of communities satisfied the Hubbell's neutral theory was negligible (2 out of 278). Conclusion: The apparently contradictory findings above suggest that both stochastic neutral effects and deterministic environmental (host) factors play important roles in shaping the assembly and diversity of gut microbiome. Furthermore, obesity may just be one of the host factors, but its influence may not be strong enough to tip the balance between stochastic and deterministic forces that shape the community assembly. Finally, the apparent contradiction from both the neutral theories should not be surprising given that there are still near 30-40% species that do not obey the neutral law.},
}

@article {pmid30420687,
year = {2018},
author = {Gao, Y and Li, H},
title = {Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41592-018-0182-0},
pmid = {30420687},
issn = {1548-7105},
abstract = {The accurate quantification of microbial growth dynamics for species without complete genome sequences is biologically important, but computationally challenging in metagenomics. Here we present dynamic estimator of microbial communities (DEMIC; https://sourceforge.net/projects/demic/), a multi-sample algorithm based on contigs and coverage values, to infer the relative distances of contigs from the replication origin and to accurately compare bacterial growth rates between samples. We demonstrate robust performances of DEMIC for various sample sizes and assembly qualities using multiple synthetic and real datasets.},
}

@article {pmid30420263,
year = {2018},
author = {Lamprecht, P and Fischer, N and Huang, J and Burkhardt, L and Lütgehetmann, M and Arndt, F and Rolfs, I and Kerstein, A and Iking-Konert, C and Laudien, M},
title = {Changes in the composition of the upper respiratory tract microbial community in granulomatosis with polyangiitis.},
journal = {Journal of autoimmunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaut.2018.10.005},
pmid = {30420263},
issn = {1095-9157},
abstract = {Dysbiosis¸ i.e. changes in microbial composition at a mucosal interface, is implicated in the pathogenesis of many chronic inflammatory and autoimmune diseases. To assess the composition of the microbial upper respiratory tract (URT) community in patients with granulomatosis with polyangiitis (GPA), we used culture-independent high-throughput methods. In this prospective clinical study, nasal swabs were collected from patients with GPA, patients with rheumatoid arthritis (RA, disease control), and healthy controls. Nasal bacterial taxa were assessed using V3-V4 region 16S rRNA amplicon sequencing. Staphylococcus aureus, Haemophilus influenza, and entero- and rhinoviruses were detected using qPCR. Unbiased metagenomic RNA sequencing (UMERS) was performed in a subset of samples to determine the relative abundance of bacterial, fungal, and viral species. A trend toward reduced microbiome diversity was detected in GPA samples compared with healthy controls. The abundance of bacterial taxa and microbial richness were significantly decreased in GPA samples compared with RA samples. The relative abundance of bacterial families shifted, with increased Planococcaceae and decreased Moraxellaceae, Tissierellaceae, Staphylococcaceae, and Propionibacteriaceae in GPA and RA. Further, decreased abundance of Corynebacteriaceae, and Aerococcaceae was observed in GPA samples. Significantly more colonization of S. aureus was seen in the nasal microbiome of GPA compared with RA and healthy control samples. H. influenzae colonization was also observed in GPA samples. UMERS detected the presence of rhinoviral sequences in some GPA samples. Thus, our study uncovered changes in the URT microbial composition in patients with GPA and RA, suggesting that both immunosuppression and disease background affect the URT microbiome. Complex alterations of host-microbiome interactions in the URT could influence chronic endonasal inflammation in GPA.},
}

@article {pmid30419949,
year = {2018},
author = {Silverman, JD and Durand, HK and Bloom, RJ and Mukherjee, S and David, LA},
title = {Dynamic linear models guide design and analysis of microbiota studies within artificial human guts.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {202},
doi = {10.1186/s40168-018-0584-3},
pmid = {30419949},
issn = {2049-2618},
support = {1R01DK116187//National Institutes of Health/ ; IIS-1546331//National Science Foundation/ ; DMS-1418261//National Science Foundation/ ; IIS-1320357//National Science Foundation (US)/ ; DMS-1045153//National Science Foundation (US)/ ; DMS1613261//National Science Foundation (US)/ ; None//University of North Carolina Center for Gastrointestinal Biology and Disease/ ; None//Hartwell Foundation/ ; NNX16AO69A//Translational Research Institute/ ; },
abstract = {BACKGROUND: Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models' fundamental biology include the timescales on which microbiota vary and the factors that drive such change. Answering these questions though requires overcoming analytical obstacles like estimating the effects of technical variation on observed microbiota dynamics, as well as the lack of appropriate benchmark datasets.

RESULTS: To address these obstacles, we created a modeling framework based on multinomial logistic-normal dynamic linear models (MALLARDs) and performed dense longitudinal sampling of four replicate artificial human guts over the course of 1 month. The resulting analyses revealed how the ratio of biological variation to technical variation from sample processing depends on sampling frequency. In particular, we find that at hourly sampling frequencies, 76% of observed variation could be ascribed to technical sources, which could also skew the observed covariation between taxa. We also found that the artificial guts demonstrated replicable trajectories even after a recovery from a transient feed disruption. Additionally, we observed irregular sub-daily oscillatory dynamics associated with the bacterial family Enterobacteriaceae within all four replicate vessels.

CONCLUSIONS: Our analyses suggest that, beyond variation due to sequence counting, technical variation from sample processing can obscure temporal variation from biological sources in artificial gut studies. Our analyses also supported hypotheses that human gut microbiota fluctuates on sub-daily timescales in the absence of a host and that microbiota can follow replicable trajectories in the presence of environmental driving forces. Finally, multiple aspects of our approach are generalizable and could ultimately be used to facilitate the design and analysis of longitudinal microbiota studies in vivo.},
}

@article {pmid30419782,
year = {2018},
author = {Dąbkowski, D and Tabaszewski, P and Górecki, P},
title = {Minimizing the deep coalescence cost.},
journal = {Journal of bioinformatics and computational biology},
volume = {16},
number = {5},
pages = {1840021},
doi = {10.1142/S0219720018400218},
pmid = {30419782},
issn = {1757-6334},
abstract = {Metagenomic studies identify the species present in an environmental sample usually by using procedures that match molecular sequences, e.g. genes, with the species taxonomy. Here, we first formulate the problem of gene-species matching in the parsimony framework using binary phylogenetic gene and species trees under the deep coalescence cost and the assumption that each gene is paired uniquely with one species. In particular, we solve the problem in the cases when one of the trees is a caterpillar. Next, we propose a dynamic programming algorithm, which solves the problem exactly, however, its time and space complexity is exponential. Next, we generalize the problem to include non-binary trees and show the solution for caterpillar trees. We then propose time and space-efficient heuristic algorithms for solving the gene-species matching problem for any input trees. Finally, we present the results of computational experiments on simulated and empirical datasets consisting of binary tree pairs.},
}

@article {pmid30418610,
year = {2018},
author = {Huerta-Cepas, J and Szklarczyk, D and Heller, D and Hernández-Plaza, A and Forslund, SK and Cook, H and Mende, DR and Letunic, I and Rattei, T and Jensen, LJ and von Mering, C and Bork, P},
title = {eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gky1085},
pmid = {30418610},
issn = {1362-4962},
abstract = {eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. In total, 4.4M orthologous groups (OGs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, HMM models and functional descriptors. Precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each OG. Our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. All precomputed data are publicly available for downloading or via API queries at http://eggnog.embl.de.},
}

@article {pmid30418481,
year = {2018},
author = {Stewart, RD and Auffret, M and Snelling, TJ and Roehe, R and Watson, M},
title = {MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs).},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/bty905},
pmid = {30418481},
issn = {1367-4811},
abstract = {Motivation: Metagenomics is a powerful tool for assaying the DNA from every genome present in an environment. Recent advances in bioinformatics have enabled the rapid assembly of near complete metagenome-assembled genomes (MAGs), and there is a need for reproducible pipelines that can annotate and characterise thousands of genomes simultaneously, to enable identification and functional characterisation.

Results: Here we present MAGpy, a scalable and reproducible pipeline that takes multiple genome assemblies as FASTA and compares them to several public databases, checks quality, suggests a taxonomy and draws a phylogenetic tree.

Availability: MAGpy is available on github: https://github.com/WatsonLab/MAGpy.

Supplementary information: Supplementary data are available at Bioinformatics online.},
}

@article {pmid30417889,
year = {2018},
author = {Hyeon, JY and Mann, DA and Townsend, AM and Deng, X},
title = {Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {140},
pages = {},
doi = {10.3791/58612},
pmid = {30417889},
issn = {1940-087X},
abstract = {Quasi-metagenomics sequencing refers to the sequencing-based analysis of modified microbiomes of food and environmental samples. In this protocol, microbiome modification is designed to concentrate genomic DNA of a target foodborne pathogen contaminant to facilitate the detection and subtyping of the pathogen in a single workflow. Here, we explain and demonstrate the sample preparation steps for the quasi-metagenomics analysis of Salmonella enterica from representative food and environmental samples including alfalfa sprouts, ground black pepper, ground beef, chicken breast and environmental swabs. Samples are first subjected to the culture enrichment of Salmonella for a shortened and adjustable duration (4-24 h). Salmonella cells are then selectively captured from the enrichment culture by immunomagnetic separation (IMS). Finally, multiple displacement amplification (MDA) is performed to amplify DNA from IMS-captured cells. The DNA output of this protocol can be sequenced by high throughput sequencing platforms. An optional quantitative PCR analysis can be performed to replace sequencing for Salmonella detection or assess the concentration of Salmonella DNA before sequencing.},
}

@article {pmid30417114,
year = {2018},
author = {Huang, SK and Ye, KT and Huang, WF and Ying, BH and Su, X and Lin, LH and Li, JH and Chen, YP and Li, JL and Bao, XL and Hu, JZ},
title = {Influence of Feeding Type and Nosema ceranae Infection on the Gut Microbiota of Apis cerana Workers.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00177-18},
pmid = {30417114},
issn = {2379-5077},
abstract = {The gut microbiota plays an essential role in the health of bees. To elucidate the effect of feed and Nosema ceranae infection on the gut microbiota of honey bee (Apis cerana), we used 16S rRNA sequencing to survey the gut microbiota of honey bee workers fed with sugar water or beebread and inoculated with or without N. ceranae. The gut microbiota of A. cerana is dominated by Serratia, Snodgrassella, and Lactobacillus genera. The overall gut microbiota diversity was show to be significantly differential by feeding type. N. ceranae infection significantly affects the gut microbiota only in bees fed with sugar water. Higher abundances of Lactobacillus, Gluconacetobacter, and Snodgrassella and lower abundances of Serratia were found in bees fed with beebread than in those fed with sugar water. N. ceranae infection led to a higher abundance of Snodgrassella and a lower abundance of Serratia in sugar-fed bees. Imputed bacterial Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed the significant metagenomics functional differences by feeding and N. ceranae infections. Furthermore, A. cerana workers fed with sugar water showed lower N. ceranae spore loads but higher mortality than those fed with beebread. The cumulative mortality was strongly positive correlated (rho = 0.61) with the changes of overall microbiota dissimilarities by N. ceranae infection. Both feeding types and N. ceranae infection significantly affect the gut microbiota in A. cerana workers. Beebread not only provides better nutrition but also helps establish a more stable gut microbiota and therefore protects bees in response to N. ceranae infection. IMPORTANCE The gut microbiota plays an essential role in the health of bees. Scientific evidence suggests that diet and infection can affect the gut microbiota and modulate the health of the gut; however, the interplay between those two factors and the bee gut microbiota is not well known. In this study, we used a high-throughput sequencing method to monitor the changes of gut microbiota associated with both feeding types and Nosema ceranae infection. Our results showed that the gut microbiota composition and diversity of Asian honey bee were significantly associated with both feeding types and the N. ceranae infection. More interestingly, bees fed with beebread showed higher microbiota stability and lower mortality rates than those fed with sugar water when infected by N. ceranae. Those data suggest that beebread has the potential not only to provide better nutrition but also help to establish a more stable gut microbiota to protect bees against N. ceranae infection.},
}

@article {pmid30417110,
year = {2018},
author = {Wei, ST and Wu, YW and Lee, TH and Huang, YS and Yang, CY and Chen, YL and Chiang, YR},
title = {Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge.},
journal = {mSystems},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSystems.00113-18},
pmid = {30417110},
issn = {2379-5077},
abstract = {The 2,3-seco pathway, the pathway for anaerobic cholesterol degradation, has been established in the denitrifying betaproteobacterium Sterolibacterium denitrificans. However, knowledge of how microorganisms respond to cholesterol at the community level is elusive. Here, we applied mesocosm incubation and 16S rRNA sequencing to reveal that, in denitrifying sludge communities, three betaproteobacterial operational taxonomic units (OTUs) with low (94% to 95%) 16S rRNA sequence similarity to Stl. denitrificans are cholesterol degraders and members of the rare biosphere. Metatranscriptomic and metabolite analyses show that these degraders adopt the 2,3-seco pathway to sequentially catalyze the side chain and sterane of cholesterol and that two molybdoenzymes-steroid C25 dehydrogenase and 1-testosterone dehydrogenase/hydratase-are crucial for these bioprocesses, respectively. The metatranscriptome further suggests that these betaproteobacterial degraders display chemotaxis and motility toward cholesterol and that FadL-like transporters may be the key components for substrate uptake. Also, these betaproteobacteria are capable of transporting micronutrients and synthesizing cofactors essential for cellular metabolism and cholesterol degradation; however, the required cobalamin is possibly provided by cobalamin-de novo-synthesizing gamma-, delta-, and betaproteobacteria via the salvage pathway. Overall, our results indicate that the ability to degrade cholesterol in sludge communities is reserved for certain rare biosphere members and that C25 dehydrogenase can serve as a biomarker for sterol degradation in anoxic environments. IMPORTANCE Steroids are ubiquitous and abundant natural compounds that display recalcitrance. Biodegradation via sludge communities in wastewater treatment plants is the primary removal process for steroids. To date, compared to studies for aerobic steroid degradation, the knowledge of anaerobic degradation of steroids has been based on only a few model organisms. Due to the increase of anthropogenic impacts, steroid inputs may affect microbial diversity and functioning in ecosystems. Here, we first investigated microbial functional responses to cholesterol, the most abundant steroid in sludge, at the community level. Our metagenomic and metatranscriptomic analyses revealed that the capacities for cholesterol approach, uptake, and degradation are unique traits of certain low-abundance betaproteobacteria, indicating the importance of the rare biosphere in bioremediation. Apparent expression of genes involved in cofactor de novo synthesis and salvage pathways suggests that these micronutrients play important roles for cholesterol degradation in sludge communities.},
}

@article {pmid30417108,
year = {2018},
author = {Ren, L and Zhang, R and Rao, J and Xiao, Y and Zhang, Z and Yang, B and Cao, D and Zhong, H and Ning, P and Shang, Y and Li, M and Gao, Z and Wang, J},
title = {Transcriptionally Active Lung Microbiome and Its Association with Bacterial Biomass and Host Inflammatory Status.},
journal = {mSystems},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSystems.00199-18},
pmid = {30417108},
issn = {2379-5077},
abstract = {Alteration of the lung microbiome has been observed in several respiratory tract diseases. However, most previous studies were based on 16S ribosomal RNA and shotgun metagenome sequencing; the viability and functional activity of the microbiome, as well as its interaction with host immune systems, have not been well studied. To characterize the active lung microbiome and its associations with host immune response and clinical features, we applied metatranscriptome sequencing to bronchoalveolar lavage fluid (BALF) samples from 25 patients with chronic obstructive pulmonary disease (COPD) and from nine control cases without known pulmonary disease. Community structure analyses revealed three distinct microbial compositions, which were significantly correlated with bacterial biomass, human Th17 immune response, and COPD exacerbation frequency. Specifically, samples with transcriptionally active Streptococcus, Rothia, or Pseudomonas had bacterial loads 16 times higher than samples enriched for Escherichia and Ralstonia. These high-bacterial-load samples also tended to undergo a stronger Th17 immune response. Furthermore, an increased proportion of lymphocytes was found in samples with active Pseudomonas. In addition, COPD patients with active Streptococcus or Rothia infections tended to have lower rates of exacerbations than patients with active Pseudomonas and patients with lower bacterial biomass. Our results support the idea of a stratified structure of the active lung microbiome and a significant host-microbe interaction. We speculate that diverse lung microbiomes exist in the population and that their presence and activities could either influence or reflect different aspects of lung health. IMPORTANCE Recent studies of the microbiome proposed that resident microbes play a beneficial role in maintaining human health. Although lower respiratory tract disease is a leading cause of sickness and mortality, how the lung microbiome interacts with human health remains largely unknown. Here we assessed the association between the lung microbiome and host gene expression, cytokine concentration, and over 20 clinical features. Intriguingly, we found a stratified structure of the active lung microbiome which was significantly associated with bacterial biomass, lymphocyte proportion, human Th17 immune response, and COPD exacerbation frequency. These observations suggest that the microbiome plays a significant role in lung homeostasis. Not only microbial composition but also active functional elements and host immunity characteristics differed among different individuals. Such diversity may partially account for the variation in susceptibility to particular diseases.},
}

@article {pmid30416839,
year = {2018},
author = {Chu, H and Williams, B and Schnabl, B},
title = {Gut microbiota, fatty liver disease, and hepatocellular carcinoma.},
journal = {Liver research},
volume = {2},
number = {1},
pages = {43-51},
doi = {10.1016/j.livres.2017.11.005},
pmid = {30416839},
issn = {2096-2878},
abstract = {Intestinal bacteria contribute to the pathogenesis of non-alcoholic fatty liver disease (NAFLD). Recently developed microbial profiling techniques are beginning to shed light on the nature of the changes in the gut microbiota that accompany NAFLD and non-alcoholic steatohepatitis (NASH). In this review, we summarize the role of gut microbiota in the development of NAFLD, NASH, and hepatocellular carcinoma (HCC). We highlight the mechanisms by which gut microbiota contribute to NAFLD/NASH, including through alterations in gut epithelial permeability, choline metabolism, endogenous alcohol production, release of inflammatory cytokines, regulation of hepatic Toll-like receptor (TLR), and bile acid metabolism. In addition, we analyze possible mechanisms for enhanced hepatic carcinogenesis, including alterations in bile acid metabolism, release of inflammatory cytokines, and expression of TLR-4. Finally, we describe therapeutic approaches for NAFLD/NASH and preventive strategies for HCC involving modulation of the intestinal microbiota or affected host pathways. Although recent studies have provided useful information, large-scale prospective studies are required to better characterize the intestinal microbiota and metabolome, in order to demonstrate a causative role for changes in the gut microbiota in the etiology of NAFLD/NASH, to identify new therapeutic strategies for NAFLD/NASH, and to develop more effective methods of preventing HCC.},
}

@article {pmid30416642,
year = {2017},
author = {Thaker, VV},
title = {GENETIC AND EPIGENETIC CAUSES OF OBESITY.},
journal = {Adolescent medicine: state of the art reviews},
volume = {28},
number = {2},
pages = {379-405},
pmid = {30416642},
issn = {1934-4287},
abstract = {Obesity is a complex, heritable trait influenced by the interplay of genetics, epigenetics, metagenomics and the environment. With the increasing access to high precision diagnostic tools for genetic investigations, numerous genes influencing the phenotype have been identified, especially in early onset severe obesity. This review summarizes the current knowledge on the known genetic causes of obesity and the available therapeutic options. Furthermore, we discuss the role and potential mechanism of epigenetic changes that may be involved as mediators of the environmental influences and that may provide future opportunities for intervention.},
}

@article {pmid30416499,
year = {2018},
author = {Hendrickson, HL and Poole, AM},
title = {Manifold Routes to a Nucleus.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2604},
doi = {10.3389/fmicb.2018.02604},
pmid = {30416499},
issn = {1664-302X},
abstract = {It is widely assumed that there is a clear distinction between eukaryotes, with cell nuclei, and prokaryotes, which lack nuclei. This suggests the evolution of nuclear compartmentation is a singular event. However, emerging knowledge of the diversity of bacterial internal cell structures suggests the picture may not be as black-and-white as previously thought. For instance, some members of the bacterial PVC superphylum appear to have nucleus-like compartmentation, where transcription and translation are physically separated, and some jumbophages have recently been shown to create nucleus-like structures within their Pseudomonad hosts. Moreover, there is also tantalizing metagenomic identification of new Archaea that carry homologs of genes associated with internal cell membrane structure in eukaryotes. All these cases invite comparison with eukaryote cell biology. While the bacterial cases of genetic compartmentation are likely convergent, and thus viewed by many as not germane to the question of eukaryote origins, we argue here that, in addressing the broader question of the evolution of compartmentation, other instances are at least as important: they provide us with a point of comparison which is critical for a more general understanding of both the conditions favoring the emergence of intracellular compartmentation of DNA and the evolutionary consequences of such cellular architecture. Finally, we consider three classes of explanation for the emergence of compartmentation: physical protection, crosstalk avoidance and nonadaptive origins.},
}

@article {pmid30416492,
year = {2018},
author = {Annavajhala, MK and Kapoor, V and Santo-Domingo, J and Chandran, K},
title = {Structural and Functional Interrogation of Selected Biological Nitrogen Removal Systems in the United States, Denmark, and Singapore Using Shotgun Metagenomics.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2544},
doi = {10.3389/fmicb.2018.02544},
pmid = {30416492},
issn = {1664-302X},
abstract = {Conventional biological nitrogen removal (BNR), comprised of nitrification and denitrification, is traditionally employed in wastewater treatment plants (WWTPs) to prevent eutrophication in receiving water bodies. More recently, the combination of selective ammonia to nitrite oxidation (nitritation) and autotrophic anaerobic ammonia oxidation (anammox), collectively termed deammonification, has also emerged as a possible energy- and cost-effective BNR alternative. Herein, we analyzed microbial diversity and functional potential within 13 BNR processes in the United States, Denmark, and Singapore operated with varying reactor configuration, design, and operational parameters. Using next-generation sequencing and metagenomics, gene-coding regions were aligned against a custom protein database expanded to include all published aerobic ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB), anaerobic ammonia oxidizing bacteria (AMX), and complete ammonia oxidizing bacteria (CMX). Overall contributions of these N-cycle bacteria to the total functional potential of each reactor was determined, as well as that of several organisms associated with denitrification and/or structural integrity of microbial aggregates (biofilm or granules). The potential for these engineered processes to foster a broad spectrum of microbial catabolic, anabolic, and carbon assimilation transformations was elucidated. Seeded sidestream DEMON® deammonification systems and single-stage nitritation-anammox moving bed biofilm reactors (MBBRs) and a mainstream Cleargreen reactor designed to enrich in AOB and AMX showed lower enrichment in AMX functionality than an enriched two-stage nitritation-anammox MBBR system treating mainstream wastewater. Conventional BNR systems in Singapore and the United States had distinct metagenomes, especially relating to AOB. A hydrocyclone process designed to recycle biomass granules for mainstream BNR contained almost identical structural and functional characteristics in the overflow, underflow, and inflow of mixed liquor (ALT) rather than the expected selective enrichment of specific nitrifying or AMX organisms. Inoculum used to seed a sidestream deammonification process unexpectedly contained <10% of total coding regions assigned to AMX. These results suggest the operating conditions of engineered bioprocesses shape the resident microbial structure and function far more than the bioprocess configuration itself. We also highlight the advantage of a systems- and metagenomics-based interrogation of both the microbial structure and potential function therein over targeting of individual populations or specific genes.},
}

@article {pmid30416489,
year = {2018},
author = {Stamps, BW and Leddy, MB and Plumlee, MH and Hasan, NA and Colwell, RR and Spear, JR},
title = {Characterization of the Microbiome at the World's Largest Potable Water Reuse Facility.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2435},
doi = {10.3389/fmicb.2018.02435},
pmid = {30416489},
issn = {1664-302X},
abstract = {Conventional water resources are not sufficient in many regions to meet the needs of growing populations. Due to cyclical weather cycles, drought, and climate change, water stress has increased worldwide including in Southern California, which serves as a model for regions that integrate reuse of wastewater for both potable and non-potable use. The Orange County Water District (OCWD) Advanced Water Purification Facility (AWPF) is a highly engineered system designed to treat and produce up to 100 million gallons per day (MGD) of purified water from a municipal wastewater source for potable reuse. Routine facility microbial water quality analysis is limited to standard indicators at this and similar facilities. Given recent advances in high throughput DNA sequencing techniques, complete microbial profiling of communities in water samples is now possible. By using 16S/18S rRNA gene sequencing, metagenomic and metatranscriptomic sequencing coupled to a highly accurate identification method along with 16S rRNA gene qPCR, we describe a detailed view of the total microbial community throughout the facility. The total bacterial load of the water at stages of the treatment train ranged from 3.02 × 106 copies in source, unchlorinated wastewater feed to 5.49 × 101 copies of 16S rRNA gene/mL after treatment (consisting of microfiltration, reverse osmosis, and ultraviolet/advanced oxidation). Microbial diversity and load decreased by several orders of magnitude after microfiltration and reverse osmosis treatment, falling to almost non-detectable levels that more closely resembled controls of molecular grade laboratory water than the biomass detected in the source water. The presence of antibiotic resistance genes and viruses was also greatly reduced. Overall, system design performance was achieved, and comprehensive microbial community analysis was found to enable a more complete characterization of the water/wastewater microbial signature.},
}

@article {pmid30415264,
year = {2018},
author = {Samra, M and Nam, SK and Lim, DH and Kim, DH and Yang, J and Kim, YK and Kim, JH},
title = {Urine Bacteria-Derived Extracellular Vesicles and Allergic Airway Diseases in Children.},
journal = {International archives of allergy and immunology},
volume = {},
number = {},
pages = {1-9},
doi = {10.1159/000492677},
pmid = {30415264},
issn = {1423-0097},
abstract = {BACKGROUND: Microbiota and human allergic airway diseases have been proven to be interrelated. Bacteria-derived extracellular vesicle (EV)s are known to play important roles in interbacterial and human-bacteria communications, but their relationship with allergies has not been examined yet. Urine EVs were investigated to determine whether they could be used as biomarkers for monitoring allergic airway diseases in children.

METHODS: Subjects were 4 groups of chronic rhinitis (CR), allergic rhinitis (AR), atopic asthma (AS) and healthy controls. Single voided urine samples were collected. Urine EVs were isolated and their DNA was extracted for 16S-rDNA pyrosequencing.

RESULTS: A total of 118 children participated in this study; 27, 39, 19, and 33 were in the CR, AR, AS, and control group, respectively. The AR had a significantly high Chao-1 index than that of controls. Principal component analysis revealed dysbiosis in the CR, AR, and AS compared to the controls. One phylum and 19 families and genera were significantly enriched or depleted in the disease groups compared to the controls; the Actinobacteria phylum and the Sphingomonadaceae family were more abundant in the AS and CR, the Comamonadaceae family, the Propionibacteraceae family, Propionibacterium and Enhydrobacter were more enriched in the CR, and the Methylobacteriaceae family and Methylobacterium were more abundant in each disease group, while the Enterobacteriaceae family was depleted in each disease group.

CONCLUSIONS: CR, AR, and AS had a distinct composition of urine EVs. Urine EVs could be an indicator for assessing allergic airway diseases in children.},
}

@article {pmid30414312,
year = {2018},
author = {Magnusson, AO and Szekrenyi, A and Joosten, HJ and Finnigan, J and Charnock, S and Fessner, WD},
title = {nanoDSF as screening tool for enzyme libraries and biotechnology development.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.14696},
pmid = {30414312},
issn = {1742-4658},
abstract = {Enzymes are attractive tools for synthetic applications. To be viable for industrial use enzymes need sufficient stability towards the desired reaction conditions such as high substrate and cosolvent concentration, non-neutral pH and elevated temperatures. Thermal stability is an attractive feature not only because it allows for protein purification by thermal treatment and higher process temperatures, but also due to the associated higher stability against other destabilising factors. Therefore, high-throughput screening methods are desirable for the identification of thermostable biocatalysts by discovery from nature or by protein engineering but current methods have low throughput and require time-demanding purification of protein samples. We found that nanoscale differential scanning fluorimetry (nanoDSF) is a valuable tool to rapidly and reliably determine melting points of native proteins. To avoid intrinsic problems posed by crude protein extracts, hypotonic extraction of over-expressed protein from bacterial host cells resulted in higher sample quality and accurate manual determination of several hundred melting temperatures per day. We have probed the use of nanoDSF for high-throughput screening of a phylogenetically diverse aldolase library to identify novel thermostable enzymes from metagenomic sources and for the rapid measurements of variants from saturation mutagenesis. The feasibility of nanoDSF for the screening of synthetic reaction conditions was proved by studies of co-solvent tolerance, which showed protein melting temperature to decrease linearly with increasing cosolvent concentration for all combinations of six enzymes and eight water-miscible cosolvents investigated, and of substrate affinity, which showed stabilization of hexokinase by sugars in the absence of ATP cofactor. This article is protected by copyright. All rights reserved.},
}

@article {pmid30413677,
year = {2018},
author = {Franzo, G and Kekarainen, T and Llorens, A and Correa-Fiz, F and Segalés, J},
title = {Exploratory metagenomic analyses of periweaning failure-to-thrive syndrome-affected pigs.},
journal = {The Veterinary record},
volume = {},
number = {},
pages = {},
doi = {10.1136/vr.105125},
pmid = {30413677},
issn = {2042-7670},
abstract = {Modern pig farming is characterised by the emergence of several syndromes whose aetiology is unclear or has a multifactorial origin, including periweaning failure-to-thrive syndrome (PFTS). In fact, its specific aetiology remains elusive, although several causes have been investigated over time. The present study aimed to investigate the potential role of viral agents in PFTS-affected and healthy animals by evaluating the virome composition of different organs using a metagenomic approach. This analysis allowed demonstrating a higher abundance of Porcine parvovirus 6 (PPV6) in healthy subjects while Ungulate bocaparvovirus 2 (BoPV2), Ungulate protoparvovirus 1 (PPV) and Porcine circovirus 3 (PCV-3) were increased in pigs with PFTS. No differential abundance of RNA viruses was found between PFTS-affected and control pigs. Remarkably, this is the first molecular characterisation of PPV6 and BoPV2 in Spain and one of the few all around the world, supporting their apparent widespread circulation. Interestingly, PCV-3 has been recently identified in several clinical-pathological conditions as well as in healthy pigs, while BoPV2 pathogenic potential is unknown. Although obtained results must be taken as preliminary, they open the door for further studies on the potential role of these viruses or their combination as predisposing factor/s for PFTS occurrence.},
}

@article {pmid30412889,
year = {2018},
author = {Nathani, NM and Mootapally, C and Dave, BP},
title = {Antibiotic resistance genes allied to the pelagic sediment microbiome in the Gulf of Khambhat and Arabian Sea.},
journal = {The Science of the total environment},
volume = {653},
number = {},
pages = {446-454},
doi = {10.1016/j.scitotenv.2018.10.409},
pmid = {30412889},
issn = {1879-1026},
abstract = {Antibiotics have been widely spread in the environments, imposing profound stress on the resistome of the residing microbes. Marine microbiomes are well established large reservoirs of novel antibiotics and corresponding resistance genes. The Gulf of Khambhat is known for its extreme tides and complex sedimentation process. We performed high throughput sequencing and applied bioinformatics techniques on pelagic sediment microbiome across four coordinates of the Gulf of Khambhat to assess the marine resistome, its corresponding bacterial community and compared with the open Arabian Sea sample. We identified a total of 2354 unique types of resistance genes, with most abundant and diverse gene profile in the area that had anthropogenic activities being carried out on-shore. The genes with >1% abundance in all samples included carA, macB, sav1866, tlrC, srmB, taeA, tetA, oleC and bcrA which belonged to the macrolides, glycopeptides and peptide drug classes. ARG enriched phyla distribution was quite varying between all the sites, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes among the dominant phyla. Based on the outcomes, we also propose potential biomarker candidates Desulfovibrio, Thermotaga and Pelobacter for antibiotic monitoring in the two of the Gulf samples probable contamination prone environments, and genera Nitrosocccus, Marinobacter and Streptomyces in the rest of the three studied samples. Outcomes support the concept that ARGs naturally originate in environments and human activities contribute to the dissemination of antibiotic resistance.},
}

@article {pmid30412190,
year = {2018},
author = {Goordial, J and Ronholm, J},
title = {Metagenomics meets read clouds.},
journal = {Nature biotechnology},
volume = {36},
number = {11},
pages = {1049-1051},
doi = {10.1038/nbt.4284},
pmid = {30412190},
issn = {1546-1696},
}

@article {pmid30412047,
year = {2018},
author = {Charles, J and Tangudu, CS and Hurt, SL and Tumescheit, C and Firth, AE and Garcia-Rejon, JE and Machain-Williams, C and Blitvich, BJ},
title = {Detection of novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico using metagenomics and characterization of their in vitro host ranges.},
journal = {The Journal of general virology},
volume = {},
number = {},
pages = {},
doi = {10.1099/jgv.0.001165},
pmid = {30412047},
issn = {1465-2099},
abstract = {A metagenomics approach was used to detect novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico. A total of 1359 mosquitoes of 7 species and 5 genera (Aedes, Anopheles, Culex, Mansonia and Psorophora) were sorted into 37 pools, homogenized and inoculated onto monolayers of Aedes albopictus (C6/36) cells. A second blind passage was performed and then total RNA was extracted and analysed by RNA-seq. Two novel viruses, designated Uxmal virus and Mayapan virus, were identified. Uxmal virus was isolated from three pools of Aedes (Ochlerotatus) taeniorhynchus and phylogenetic data indicate that it should be classified within the recently proposed taxon Negevirus. Mayapan virus was recovered from two pools of Psorophora ferox and is most closely related to unclassified Nodaviridae-like viruses. Two recognized viruses were also detected: Culex flavivirus (family Flaviviridae) and Houston virus (family Mesoniviridae), with one and two isolates being recovered, respectively. The in vitro host ranges of all four viruses were determined by assessing their replicative abilities in cell lines of avian, human, monkey, hamster, murine, lepidopteran and mosquito (Aedes, Anopheles and Culex) origin, revealing that all viruses possess vertebrate replication-incompetent phenotypes. In conclusion, we report the isolation of both novel and recognized RNA viruses from mosquitoes collected in Mexico, and add to the growing plethora of viruses discovered recently through the use of metagenomics.},
}

@article {pmid30409177,
year = {2018},
author = {Zhu, Q and Dupont, CL and Jones, MB and Pham, KM and Jiang, ZD and DuPont, HL and Highlander, SK},
title = {Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {201},
doi = {10.1186/s40168-018-0579-0},
pmid = {30409177},
issn = {2049-2618},
support = {R21DK099573//National Institute of Diabetes and Digestive and Kidney Diseases/ ; },
abstract = {BACKGROUND: Travelers' diarrhea (TD) is often caused by enterotoxigenic Escherichia coli, enteroaggregative E. coli, other bacterial pathogens, Norovirus, and occasionally parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 40% of TD patients. It is predicted that new pathogens may be causative agents of the disease.

RESULTS: We performed a comprehensive amplicon and whole genome shotgun (WGS) metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers, all of which were negative for the known etiologic agents of TD based on standard microbiological and immunological assays. Abnormal and diverse taxonomic profiles in TD samples were revealed. WGS reads were assembled and the resulting contigs were visualized using multiple query types. A semi-manual workflow was applied to isolate independent genomes from metagenomic pools. A total of 565 genome bins were extracted, 320 of which were complete enough to be characterized as cellular genomes; 160 were viral genomes. We made predictions of the etiology of disease for many of the individual subjects based on the properties and features of the recovered genomes. Multiple patients with low-diversity metagenomes were predominated by one to several E. coli strains. Functional annotation allowed prediction of pathogenic type in many cases. Five patients were co-infected with E. coli and other members of Enterobacteriaceae, including Enterobacter, Klebsiella, and Citrobacter; these may represent blooms of organisms that appear following secretory diarrhea. New "dark matter" microbes were observed in multiple samples. In one, we identified a novel TM7 genome that phylogenetically clustered with a sludge isolate; it carries genes encoding potential virulence factors. In multiple samples, we observed high proportions of putative novel viral genomes, some of which form clusters with the ubiquitous gut virus, crAssphage. The total relative abundance of viruses was significantly higher in healthy travelers versus TD patients.

CONCLUSION: Our study highlights the strength of assembly-based metagenomics, especially the manually curated, visualization-assisted binning of contigs, in resolving unusual and under-characterized pathogenic profiles of human-associated microbiomes. Results show that TD may be polymicrobial, with multiple novel cellular and viral strains as potential players in the diarrheal disease.},
}

@article {pmid30408669,
year = {2018},
author = {You, Y and Wang, Z and Xu, W and Wang, C and Zhao, X and Su, Y},
title = {Phthalic acid esters disturbed the genetic information processing and improved the carbon metabolism in black soils.},
journal = {The Science of the total environment},
volume = {653},
number = {},
pages = {212-222},
doi = {10.1016/j.scitotenv.2018.10.355},
pmid = {30408669},
issn = {1879-1026},
abstract = {Phthalic acid esters (PAEs), such as dimethyl phthalate (DMP) and dibutyl phthalate (DBP), are widely distributed as environmental pollutants. In this study, the effects of these chemicals were investigated in black soils using a metagenomics approach. The results clearly showed that DMP or DBP increased the abundance of genes involved in transcription, replication and repair in black soils. In addition, the abundances of genes associated with metabolic functions was improved following treatment with DMP or DBP, including those involved in lipid transport and metabolism, carbohydrate transport and metabolism, and energy production and conversion. There could be many reasons for these observed changes. First, the DMP or DBP treatments increased the abundances of genes associated with the LuxR family, the UvrABC repair system, DNA replication pathways, the RNA polymerase complex and base excision repair. Second, the abundances of genes associated with isocitrate lyase regulator (IclR) family transcriptional regulators, lipid metabolism and carbohydrate active enzymes (CAZys) were altered by the DMP or DBP treatments. Finally, the DMP or DBP treatments also increased the emission load of CO2 and altered the fluorescence intensity of humic acid. Therefore, the results of this study suggested that DMP and DBP contamination altered the abundances of genes associated with genetic information processing and improved the carbon metabolism in black soils.},
}

@article {pmid30406643,
year = {2018},
author = {Gao, B and Chi, L and Tu, P and Gao, N and Lu, K},
title = {The carbamate aldicarb altered the gut microbiome, metabolome and lipidome of C57BL/6J mice.},
journal = {Chemical research in toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.chemrestox.8b00179},
pmid = {30406643},
issn = {1520-5010},
abstract = {The gut microbiome is highly involved in numerous aspects of host physiology, from energy harvest to stress response, and can confer many benefits to the host. The gut microbiome development could be affected by genetic and environmental factors, including the pesticides. The carbamate insecticide aldicarb has been extensively used in agriculture, which raises serious public health concern. However, the impact of aldicarb on the gut microbiome, host metabolome and lipidome has not been well studied yet. Herein, we use multi-omics approaches, including16S rRNA sequencing, shotgun metagenomics sequencing, metabolomics and lipidomics, to elucidate aldicarb-induced toxicity in the gut microbiome and the host metabolic homeostasis. We demonstrated that aldicarb perturbed the gut microbiome development trajectory, enhanced gut bacterial pathogenicity, altered complex lipid profile, induced oxidative stress, protein degradation and DNA damage. The brain metabolism was also disturbed by the aldicarb exposure. These findings may provide a novel understanding of the toxicity of carbamate insecticides.},
}

@article {pmid30406048,
year = {2018},
author = {Oechslin, CP and Lenz, N and Liechti, N and Ryter, S and Agyeman, P and Bruggmann, R and Leib, SL and Beuret, CM},
title = {Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {375},
doi = {10.3389/fcimb.2018.00375},
pmid = {30406048},
issn = {2235-2988},
abstract = {The etiologic cause of encephalitis, meningitis or meningo-encephalitis is unknown in up to 70% of cases. Clinical shotgun metagenomics combined with host depletion is a promising technique to identify infectious etiologies of central nervous system (CNS) infections. We developed a straightforward eukaryotic host nucleic acid depletion method that preserves intact viruses and bacteria for subsequent shotgun metagenomics screening of clinical samples, focusing on cerebrospinal fluid (CSF). A surrogate CSF sample for a CNS infection paradigm was used to evaluate the proposed depletion method consisting of selective host cell lysis, followed by enzymatic degradation of the liberated genomic DNA for final depletion with paramagnetic beads. Extractives were subjected to reverse transcription, followed by whole genome amplification and next generation sequencing. The effectiveness of the host depletion method was demonstrated in surrogate CSF samples spiked with three 1:100 dilutions of Influenza A H3N2 virus (qPCR Ct-values 20.7, 28.8, >42/negative). Compared to the native samples, host depletion increased the amount of the virus subtype reads by factor 7127 and 132, respectively, while in the qPCR negative sample zero vs. 31 (1.4E-4 %) virus subtype reads were detected (native vs. depleted). The workflow was applied to thirteen CSF samples of patients with meningo-/encephalitis (two bacterial, eleven viral etiologies), a serum of an Andes virus infection and a nose swab of a common cold patient. Unlike surrogate samples, host depletion of the thirteen human CSF samples and the nose swab did not result in more reads indicating presence of damaged pathogens due to, e.g., host immune response. Nevertheless, previously diagnosed pathogens in the human CSF samples (six viruses, two bacteria), the serum, and the nose swab (Human rhinovirus A31) were detected in the depleted and/or the native samples. Unbiased evaluation of the taxonomic profiles supported the diagnosed pathogen in two native CSF samples and the native and depleted serum and nose swab, while detecting various contaminations that interfered with pathogen identification at low concentration levels. In summary, damaged pathogens and contaminations complicated analysis and interpretation of clinical shotgun metagenomics data. Still, proper consideration of these issues may enable future application of metagenomics for clinical diagnostics.},
}

@article {pmid30406041,
year = {2018},
author = {Xiao, P and Li, C and Zhang, Y and Han, J and Guo, X and Xie, L and Tian, M and Li, Y and Wang, M and Liu, H and Ren, J and Zhou, H and Lu, H and Jin, N},
title = {Metagenomic Sequencing From Mosquitoes in China Reveals a Variety of Insect and Human Viruses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {364},
doi = {10.3389/fcimb.2018.00364},
pmid = {30406041},
issn = {2235-2988},
abstract = {We collected 8,700 mosquitoes in three sites in China, which belonged to seven species. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The abundant viral sequences were detected and annotated belonging to more than 50 viral taxonomic families. The results were verified by PCR, followed by phylogenetic analysis. In the present study, we identified partial viral genes of dengue virus (DENV), a novel circovirus (CCV), densovirus (DNV), Japanese encephalitis virus (JEV), and Wuhan mosquito virus (WMV) in mosquitoes. Metagenomic analysis and PCR amplification revealed three DENV sequences, which were as homologous to the NS3 gene of DENV from Singapore isolated in 2005, with at least 91% nucleotide (nt) identity. Seven fragments of JEV encoding structural proteins were identified belonging to genotype I. They all shared high homology with structural protein genes of JEV isolated from Laos in 2009. The production of infectious virus particles of the newly isolated virus YunnanJEV2017-4 increased after passage from the BHK-21 cell line to the Vero cell line. Novel circovirus-related genes were identified and as being related to an unnamed gene of a mosquito circovirus (MCCV) sequence from the USA isolated in 2011, with at least 41% nt identity: this distant relationship suggests that the parent virus might belong to a novel circovirus genus. Additionally, numerous known viruses and some unknown viruses were also detected in mosquitoes from Yunnan province, China, which will be tested for propagation.},
}

@article {pmid30406038,
year = {2018},
author = {Xiao, P and Han, J and Zhang, Y and Li, C and Guo, X and Wen, S and Tian, M and Li, Y and Wang, M and Liu, H and Ren, J and Zhou, H and Lu, H and Jin, N},
title = {Metagenomic Analysis of Flaviviridae in Mosquito Viromes Isolated From Yunnan Province in China Reveals Genes From Dengue and Zika Viruses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {359},
doi = {10.3389/fcimb.2018.00359},
pmid = {30406038},
issn = {2235-2988},
abstract = {More than 6,000 mosquitoes of six species from six sites were collected and tested for their virome using metagenomics sequencing and bioinformatic analysis. The identified viral sequences belonged to more than 50 viral families. The results were verified by PCR of selected viruses in all mosquitoes, followed by phylogenetic analysis. In the present study, we identified the partial dengue virus (DENV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV) sequences in mosquitoes. Metagenomic analysis and the PCR amplification revealed three DENV sequences, one of which encodes a partial envelope protein. Two ZIKV sequences both encoding partial nonstructural protein 3 and one JEV sequence encoding the complete envelope protein were identified. There was variability in the viral titers of the newly isolated virus JEV-China/YN2016-1 of different passage viruses. The newly identified Zika virus gene from ZIKV-China/YN2016-1 was an Asian genotype and shared the highest nucleotide sequence identity (97.1%) with a ZIKV sequence from Thailand isolated in 2004. Phylogenetic analysis of ZIKV-China/YN2016-1 and ZIKV-China/YN2016-2 with known Flavivirus genes indicated that ZIKV has propagated in Yunnan province, China.},
}

@article {pmid30405973,
year = {2018},
author = {Castro, JC and Rodriguez-R, LM and Harvey, WT and Weigand, MR and Hatt, JK and Carter, MQ and Konstantinidis, KT},
title = {imGLAD: accurate detection and quantification of target organisms in metagenomes.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5882},
doi = {10.7717/peerj.5882},
pmid = {30405973},
issn = {2167-8359},
abstract = {Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting from inadequate identification of regions of the genome that are either too highly conserved to be diagnostic (e.g., rRNA genes) or prone to frequent horizontal genetic exchange (e.g., mobile elements) remains unknown. To overcome these limitations, we introduce imGLAD, which aims to detect (target) genomic sequences in metagenomic datasets. imGLAD achieves high accuracy because it uses the sequence-discrete population concept for discriminating between metagenomic reads originating from the target organism compared to reads from co-occurring close relatives, masks regions of the genome that are not informative using the MyTaxa engine, and models both the sequencing breadth and depth to determine relative abundance and limit of detection. We validated imGLAD by analyzing metagenomic datasets derived from spinach leaves inoculated with the enteric pathogen Escherichia coli O157:H7 and showed that its limit of detection can be comparable to that of PCR-based approaches for these samples (∼1 cell/gram).},
}

@article {pmid30405597,
year = {2018},
author = {Goldbeck, O and Eck, AW and Seibold, GM},
title = {Real Time Monitoring of NADPH Concentrations in Corynebacterium glutamicum and Escherichia coli via the Genetically Encoded Sensor mBFP.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2564},
doi = {10.3389/fmicb.2018.02564},
pmid = {30405597},
issn = {1664-302X},
abstract = {Analyses of intracellular NADPH concentrations are prerequisites for the design of microbial production strains and process optimization. mBFP was described as metagenomics derived, blue fluorescent protein showing NADPH-dependent fluorescence. Characterization of mBFP showed a high specificity for binding of NADPH (KD 0.64 mM) and no binding of NADH, the protein exclusively amplified fluorescence of NADPH. mBFP catalyzed the NADPH-dependent reduction of benzaldehyde and further aldehydes, which fits to its classification as short chain dehydrogenase. For in vivo NADPH analyses a codon-optimized gene for mBFP was introduced into Corynebacterium glutamicum WT and the phosphoglucoisomerase-deficient strain C. glutamicum Δpgi, which accumulates high levels of NADPH. For determination of intracellular NADPH concentrations by mBFP a calibration method with permeabilized cells was developed. By this means an increase of intracellular NADPH concentrations within seconds after the addition of glucose to nutrient-starved cells of both C. glutamicum WT and C. glutamicum Δpgi was observed; as expected the internal NADPH concentration was significantly higher for C. glutamicum Δpgi (0.31 mM) when compared to C. glutamicum WT (0.19 mM). Addition of paraquat to E. coli cells carrying mBFP led as expected to an immediate decrease of intracellular NADPH concentrations, showing the versatile use of mBFP as intracellular sensor.},
}

@article {pmid30405589,
year = {2018},
author = {Jarvis, KG and Daquigan, N and White, JR and Morin, PM and Howard, LM and Manetas, JE and Ottesen, A and Ramachandran, P and Grim, CJ},
title = {Microbiomes Associated With Foods From Plant and Animal Sources.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2540},
doi = {10.3389/fmicb.2018.02540},
pmid = {30405589},
issn = {1664-302X},
abstract = {Food microbiome composition impacts food safety and quality. The resident microbiota of many food products is influenced throughout the farm to fork continuum by farming practices, environmental factors, and food manufacturing and processing procedures. Currently, most food microbiology studies rely on culture-dependent methods to identify bacteria. However, advances in high-throughput DNA sequencing technologies have enabled the use of targeted 16S rRNA gene sequencing to profile complex microbial communities including non-culturable members. In this study we used 16S rRNA gene sequencing to assess the microbiome profiles of plant and animal derived foods collected at two points in the manufacturing process; post-harvest/pre-retail (cilantro) and retail (cilantro, masala spice mixes, cucumbers, mung bean sprouts, and smoked salmon). Our findings revealed microbiome profiles, unique to each food, that were influenced by the moisture content (dry spices, fresh produce), packaging methods, such as modified atmospheric packaging (mung bean sprouts and smoked salmon), and manufacturing stage (cilantro prior to retail and at retail). The masala spice mixes and cucumbers were comprised mainly of Proteobacteria, Firmicutes, and Actinobacteria. Cilantro microbiome profiles consisted mainly of Proteobacteria, followed by Bacteroidetes, and low levels of Firmicutes and Actinobacteria. The two brands of mung bean sprouts and the three smoked salmon samples differed from one another in their microbiome composition, each predominated by either by Firmicutes or Proteobacteria. These data demonstrate diverse and highly variable resident microbial communities across food products, which is informative in the context of food safety, and spoilage where indigenous bacteria could hamper pathogen detection, and limit shelf life.},
}

@article {pmid30405577,
year = {2018},
author = {Bertelli, C and Courtois, S and Rosikiewicz, M and Piriou, P and Aeby, S and Robert, S and Loret, JF and Greub, G},
title = {Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2520},
doi = {10.3389/fmicb.2018.02520},
pmid = {30405577},
issn = {1664-302X},
abstract = {In drinking water distribution systems (DWDS), a disinfectant residual is usually applied to limit bacterial regrowth. However, delivering water with no or reduced chlorine residual could potentially decrease the selection for antimicrobial resistant microorganisms, favor bacterial regrowth and result in changes in bacterial populations. To evaluate the feasibility of water reduction in local DWDS while ensuring water safety, water quality was measured over 2 months in two different networks, each of them harboring sub-areas with normal and reduced chlorine. Water quality remained good in chlorine reduced samples, with limited development of total flora and absence of coliforms. Furthermore, 16S rRNA amplicon-based metagenomics was used to investigate the diversity and the composition of microbial communities in the sub-networks. Taxonomic classification of sequence reads showed a reduced bacterial diversity in sampling points with higher chlorine residuals. Chlorine disinfection created more homogeneous bacterial population, dominated by Pseudomonas, a genus that contains some major opportunistic pathogens such as P. aeruginosa. In the absence of chlorine, a larger and unknown biodiversity was unveiled, also highlighted by a decreased rate of taxonomic classification to the genus and species level. Overall, this experiment in a functional DWDS will facilitate the move toward potable water delivery systems without residual disinfectants and will improve water taste for consumers.},
}

@article {pmid30405551,
year = {2018},
author = {Sasaki, N and Katagiri, S and Komazaki, R and Watanabe, K and Maekawa, S and Shiba, T and Udagawa, S and Takeuchi, Y and Ohtsu, A and Kohda, T and Tohara, H and Miyasaka, N and Hirota, T and Tamari, M and Izumi, Y},
title = {Endotoxemia by Porphyromonas gingivalis Injection Aggravates Non-alcoholic Fatty Liver Disease, Disrupts Glucose/Lipid Metabolism, and Alters Gut Microbiota in Mice.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2470},
doi = {10.3389/fmicb.2018.02470},
pmid = {30405551},
issn = {1664-302X},
abstract = {Many risk factors related to the development of non-alcoholic fatty liver disease (NAFLD) have been proposed, including the most well-known of diabetes and obesity as well as periodontitis. As periodontal pathogenic bacteria produce endotoxins, periodontal treatment can result in endotoxemia. The aim of this study was to investigate the effects of intravenous, sonicated Porphyromonas gingivalis (Pg) injection on glucose/lipid metabolism, liver steatosis, and gut microbiota in mice. Endotoxemia was induced in C57BL/6J mice (8 weeks old) by intravenous injection of sonicated Pg; Pg was deactivated but its endotoxin remained. The mice were fed a high-fat diet and administered sonicated Pg (HFPg) or saline (HFco) injections for 12 weeks. Liver steatosis, glucose metabolism, and gene expression in the liver were evaluated. 16S rRNA gene sequencing with metagenome prediction was performed on the gut microbiota. Compared to HFco mice, HFPg mice exhibited impaired glucose tolerance and insulin resistance along with increased liver steatosis. Liver microarray analysis demonstrated that 1278 genes were differentially expressed between HFco and HFPg mice. Gene set enrichment analysis showed that fatty acid metabolism, hypoxia, and TNFα signaling via NFκB gene sets were enriched in HFPg mice. Although sonicated Pg did not directly reach the gut, it changed the gut microbiota and decreased bacterial diversity in HFPg mice. Metagenome prediction in the gut microbiota showed enriched citrate cycle and carbon fixation pathways in prokaryotes. Overall, intravenous injection of sonicated Pg caused impaired glucose tolerance, insulin resistance, and liver steatosis in mice fed high-fat diets. Thus, blood infusion of Pg contributes to NAFLD and alters the gut microbiota.},
}

@article {pmid30405201,
year = {2018},
author = {Wankhade, UD and Zhong, Y and Kang, P and Alfaro, M and Chintapalli, SV and Piccolo, BD and Mercer, KE and Andres, A and Thakali, KM and Shankar, K},
title = {Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16502},
doi = {10.1038/s41598-018-34453-0},
pmid = {30405201},
issn = {2045-2322},
support = {6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; },
abstract = {The contributions of maternal diet and obesity in shaping offspring microbiome remain unclear. Here we employed a mouse model of maternal diet-induced obesity via high-fat diet feeding (HFD, 45% fat calories) for 12 wk prior to conception on offspring gut microbial ecology. Male and female offspring were provided access to control or HFD from weaning until 17 wk of age. Maternal HFD-associated programming was sexually dimorphic, with male offspring from HFD dams showing hyper-responsive weight gain to postnatal HFD. Likewise, microbiome analysis of offspring cecal contents showed differences in α-diversity, β-diversity and higher Firmicutes in male compared to female mice. Weight gain in offspring was significantly associated with abundance of Lachnospiraceae and Clostridiaceae families and Adlercreutzia, Coprococcus and Lactococcus genera. Sex differences in metagenomic pathways relating to lipid metabolism, bile acid biosynthesis and immune response were also observed. HFD-fed male offspring from HFD dams also showed worse hepatic pathology, increased pro-inflammatory cytokines, altered expression of bile acid regulators (Cyp7a1, Cyp8b1 and Cyp39a1) and serum bile acid concentrations. These findings suggest that maternal HFD alters gut microbiota composition and weight gain of offspring in a sexually dimorphic manner, coincident with fatty liver and a pro-inflammatory state in male offspring.},
}

@article {pmid30405065,
year = {2018},
author = {Aučynaitė, A and Rutkienė, R and Tauraitė, D and Meškys, R and Urbonavičius, J},
title = {Identification of a 2'-O-Methyluridine Nucleoside Hydrolase Using the Metagenomic Libraries.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {11},
pages = {},
doi = {10.3390/molecules23112904},
pmid = {30405065},
issn = {1420-3049},
support = {SEN-07/2015//Lietuvos Mokslo Taryba/ ; },
abstract = {Ribose methylation is among the most ubiquitous modifications found in RNA. 2'-O-methyluridine is found in rRNA, snRNA, snoRNA and tRNA of Archaea, Bacteria, and Eukaryota. Moreover, 2'-O-methylribonucleosides are promising starting materials for the production of nucleic acid-based drugs. Despite the countless possibilities of practical use for the metabolic enzymes associated with methylated nucleosides, there are very few reports regarding the metabolic fate and enzymes involved in the metabolism of 2'-O-alkyl nucleosides. The presented work focuses on the cellular degradation of 2'-O-methyluridine. A novel enzyme was found using a screening strategy that employs Escherichia coli uracil auxotroph and the metagenomic libraries. A 2'-O-methyluridine hydrolase (RK9NH) has been identified together with an aldolase (RK9DPA)-forming a part of a probable gene cluster that is involved in the degradation of 2'-O-methylated nucleosides. The RK9NH is functional in E. coli uracil auxotroph and in vitro. The RK9NH nucleoside hydrolase could be engineered to enzymatically produce 2'-O-methylated nucleosides that are of great demand as raw materials for production of nucleic acid-based drugs. Moreover, RK9NH nucleoside hydrolase converts 5-fluorouridine, 5-fluoro-2'-deoxyuridine and 5-fluoro-2'-O-methyluridine into 5-fluorouracil, which suggests it could be employed in cancer therapy.},
}

@article {pmid30404941,
year = {2018},
author = {Morand, A and Cornu, F and Dufour, JC and Tsimaratos, M and Lagier, JC and Raoult, D},
title = {Human bacterial repertoire of the urinary tract: a potential paradigm shift.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JCM.00675-18},
pmid = {30404941},
issn = {1098-660X},
abstract = {The aim of this article is to review the human repertoire of bacteria already described by culture and metagenomic techniques in urine, and published in the literature. Our study led us to compare this repertoire with other human repertoires available.We followed automatic and manual bibliographical methods and found 562 bacterial species reported in the literature as part of the human urinary microbiota. Of the 562 species, 322 were described only by culture, 101 by both culture and metagenomics, and 139 only by metagenomic. Three hundred and fifty-two species (62.6%) have been associated with at least one case report of human infection, of which 225 (40.0%) have been described as causative agents of urinary tract infection. The urinary tract bacterial repertoire contains 21.4% of the known prokaryotic diversity associated with human beings (464 in common) and share 23.6% species with the human gut microbiota (350 in common, 62.3% of the urine species). Urinary repertoire shares a significant difference in aero-intolerant species compared with gut microbiota (100/562; 17.8% and 505/1484; 34.0% respectively; p<0.001; OR=9.0 [7.0-11.4]). Studies using high-throughput sequencing show a higher proportion of aero-intolerant bacteria in urine (74/240, 30.8%).Most pathogenic bacteria are part of the commensal human urinary tract bacteria and their pathogenicity may occur following any imbalance of this microbiota. The restoration of urinary tract health can occur following a fecal transplantation. The potential gut origin of the human bacterial microbiota has to be explored.},
}

@article {pmid30404810,
year = {2018},
author = {Harvey, E and Rose, K and Eden, JS and Lo, N and Abeyasuriya, T and Shi, M and Doggett, SL and Holmes, EC},
title = {Extensive Diversity of RNA Viruses in Australian Ticks.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JVI.01358-18},
pmid = {30404810},
issn = {1098-5514},
abstract = {Understanding the microbiome of ticks in Australia is of considerable interest given the ongoing debate over whether Lyme disease, and its causative agent the bacterium Borrelia burgdorferi sensu lato, are present in Australia. The diversity of bacteria infecting Australian ticks has been studied using both culture and metagenomics based techniques. However, little is known about the virome of Australian ticks, including whether this includes viruses with the potential to infect mammals. We used a meta-transcriptomics approach to reveal the diversity and evolution of viruses from Australian ticks collected from two locations on the central-east coast of Australia, including metropolitan Sydney. From this we identified 19 novel RNA viruses belonging to 12 families, as well as one previously described RNA virus. The majority of these viruses were related to arthropod-associated viruses suggesting that they do not utilize mammalian hosts. However, two novel viruses discovered in ticks feeding on bandicoot marsupials clustered closely within the mammalian-associated hepacivirus and pestivirus groups (family Flaviviridae). Another bandicoot tick yielded a novel coltivirus (family Reoviridae) - a group of largely tick-associated viruses containing the known human pathogen Colorado tick fever virus and its relative Eyach virus. Importantly, our transcriptomic data provided no evidence for the presence of B. burgdorferi s.l. in any tick sample, providing further evidence against the presence of Lyme Disease in Australia. In sum, this study reveals that Australian ticks harbor a diverse virome, including some viruses that merit additional screening in the context of emerging infectious disease.IMPORTANCE Each year a growing number of individuals along the east coast of Australia experience debilitating disease following tick bites. As there is no evidence for the presence of the causative agent of Lyme disease, Borrelia Burgdorferi sensu lato, in Australian ticks, the etiological basis of this disease syndrome remains controversial. To characterize the viruses associated with Australian ticks, particularly those that might be associated with mammalian infection, we performed unbiased RNA sequencing on 146 ticks collected across two locations along the coast of New South Wales, Australia. This revealed 19 novel RNA viruses from a diverse set of families. Notably, three of these viruses clustered with known mammalian viruses, including a novel coltivirus that was related to the human pathogen Colorado tick fever virus.},
}

@article {pmid30404694,
year = {2018},
author = {Ma, LK and Xue, Y and He, TC and Zhang, YM},
title = {[Associations of Socioeconomic Factors,Nutrients Intake,and Gut Microbiota of Healthy Pregnant Women in the Third Trimester with Gestational Weight Gain].},
journal = {Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae},
volume = {40},
number = {5},
pages = {630-636},
doi = {10.3881/j.issn.1000-503X.10505},
pmid = {30404694},
issn = {1000-503X},
abstract = {Objective To investigate the associations of socioeconomic factors,nutrients intake,and gut microbiota of healthy pregnant women in the third trimester with gestational weight gain (GWG).Methods We recruited 98 pregnant women in the third trimester who had received antenatal care in the Department of Obstetrics Gynecology,Peking Union Medical College Hospital from October,2015 to May,2016. We collected socioeconomic information through a structured questionnaire covering age,ethnicity,height,pre-pregnancy weight,and education. Nutritional status of these pregnant women was assessed by a 24-hour dietary intake recall. The participants were provided with collective tubes for faecal sample collection at home;their weight before the delivery was recorded. The pre-pregnancy weight and GWG were classified according to World Health Organization body mass index (BMI) standard for adults and the Institute of Medicine GWG guidelines (2009),respectively. The gut microbiota of the participants were analyzed using a whole-metagenome shotgun sequencing method.Results Insufficient and excessive GWG accounted for 15.3% and 50.0% of the cohort,respectively. Appropriate GWG level was associated with intakes of fat (F=3.113,P=0.049),carbohydrates (F=3.750,P=0.027),and dietary fiber (F=4.499,P=0.014) but not with age (F=2.495,P=0.088),ethnicity (Χ 2=0.065,P=0.968),education (Χ 2=0.827,P=0.661),or pre-pregnancy BMI (F=0.121,P=0.887). Compared with the participants with appropriate GWG,those with excessive GWG had significantly higher abundance of Akkermansia muciniphila,Atopobium parvulum,and Alistipes indistinctus as well as lower abundance of Lactobacillus rhamnosus,Weissella unclassified,Eubacterium ventriosum,Ruminococcus torques,and Bacteroides uniformis. Compared with the participants with appropriate GWG,those with insufficient GWG had significantly higher abundance of Dialister invisus,Alistipes unclassified,Peptoniphilus harei,Escherichia unclassified,Parvimonas unclassified,Campylobacter ureolyticus,Lactobacillus crispatus,and Fusobacterium nucleatum and lower abundance of Eubacterium ventriosum.Conclusions Abnormal GWG is common in pregnant women. GWG is significantly associated with gut microbiota as well as with nutritional factors including fat,carbohydrate,and dietary fiber intake.},
}

@article {pmid30400422,
year = {2017},
author = {Theodorou, E and Scanga, R and Twardowski, M and Snyder, MP and Brouzes, E},
title = {A Droplet Microfluidics Based Platform for Mining Metagenomic Libraries for Natural Compounds.},
journal = {Micromachines},
volume = {8},
number = {8},
pages = {},
doi = {10.3390/mi8080230},
pmid = {30400422},
issn = {2072-666X},
support = {1R43GM95227//National Institutes of Health/ ; //Elm Street Ventures/ ; },
abstract = {Historically, microbes from the environment have been a reliable source for novel bio-active compounds. Cloning and expression of metagenomic DNA in heterologous strains of bacteria has broadened the range of potential compounds accessible. However, such metagenomic libraries have been under-exploited for applications in mammalian cells because of a lack of integrated methods. We present an innovative platform to systematically mine natural resources for pro-apoptotic compounds that relies on the combination of bacterial delivery and droplet microfluidics. Using the violacein operon from C. violaceum as a model, we demonstrate that E. coli modified to be invasive can serve as an efficient delivery vehicle of natural compounds. This approach permits the seamless screening of metagenomic libraries with mammalian cell assays and alleviates the need for laborious extraction of natural compounds. In addition, we leverage the unique properties of droplet microfluidics to amplify bacterial clones and perform clonal screening at high-throughput in place of one-compound-per-well assays in multi-well format. We also use droplet microfluidics to establish a cell aggregate strategy that overcomes the issue of background apoptosis. Altogether, this work forms the foundation of a versatile platform to efficiently mine the metagenome for compounds with therapeutic potential.},
}

@article {pmid29256104,
year = {2018},
author = {Zhao, Y and Peng, W and Guo, H and Chen, B and Zhou, Z and Xu, J and Zhang, D and Xu, P},
title = {Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus).},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {20},
number = {1},
pages = {45-59},
doi = {10.1007/s10126-017-9786-0},
pmid = {29256104},
issn = {1436-2236},
support = {2015C006//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 20720160110//Fundamental Research Funds for the Central Universities, Xiamen University/ ; 31422057//National Natural Science Foundation of China/ ; 2017L3019//Local Science and Technology Development Project Guide by The Central Government/ ; },
mesh = {Adaptation, Physiological/genetics ; Animals ; Bass/*genetics ; Gene Flow ; *Genetics, Population ; *Metagenomics ; Pacific Ocean ; Phylogeography ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; },
abstract = {The marine species usually show high dispersal capabilities accompanied by high levels of gene flow. On the other hand, many physical barriers distribute along the continental marginal seas and may prevent dispersals and increase population divergence. These complexities along the continental margin generate serious challenges to population genetic studies of marine species. Chinese sea bass Lateolabrax maculatus distributes broad latitudinal gradient spanning from the tropical to the mid-temperate zones in the continental margin seas of the Northwest Pacific Ocean. Using the double digest restriction-site-associated DNA tag sequencing (ddRAD) approach, we genotyped 10,297 SNPs for 219 Chinese seabass individuals of 12 populations along the Chinese coast in the Northwest Pacific region. Genetic divergence among these populations was evaluated, and population structure was established. The results suggested that geographically distant populations in the Bohai Gulf and the Beibu Gulf retain significant genetic divergence, which are connected by a series of intermediate populations in between. The results also suggested that Leizhou Peninsula, Hainan Island, and Shandong Peninsula are major physical barriers and substantially block gene flow and genetic admixture of L. maculatus. We also investigated the potential genetic basis of local adaptation correlating with population differentiation of L. maculatus. The sea surface temperature is a significantly differentiated environmental factor for the distribution of L. maculatus. The correlation of water temperature and genetic variations in extensively distributed populations was investigated with Bayesian-based approaches. The candidate genes underlying the local selection in geographically divergent populations were identified and annotated, providing clues to understand the potential mechanisms of adaptive evolution. Overall, our genome scale population genetic analysis provided insight into population divergence and local adaptation of Chinese sea bass in the continental marginal seas along Chinese coast.},
}

Adaptation, Physiological/genetics
Animals
Bass/*genetics
Gene Flow
*Genetics, Population
*Metagenomics
Pacific Ocean
Phylogeography
Polymorphism, Single Nucleotide
Sequence Analysis, DNA

@article {pmid28348830,
year = {2016},
author = {Monteil, CL and Yahara, K and Studholme, DJ and Mageiros, L and Méric, G and Swingle, B and Morris, CE and Vinatzer, BA and Sheppard, SK},
title = {Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens.},
journal = {Microbial genomics},
volume = {2},
number = {10},
pages = {e000089},
doi = {10.1099/mgen.0.000089},
pmid = {28348830},
issn = {2057-5858},
support = {MR/L015080/1//Medical Research Council/United Kingdom ; 088786/C/09/Z//Wellcome Trust/United Kingdom ; },
mesh = {Bacterial Proteins/genetics ; Crops, Agricultural/*microbiology ; Genome, Bacterial/*genetics ; Genome-Wide Association Study ; *Metagenomics ; Phylogeny ; Plant Diseases/microbiology ; Pseudomonas syringae/*physiology ; Virulence/genetics ; },
abstract = {Many bacterial pathogens are well characterized but, in some cases, little is known about the populations from which they emerged. This limits understanding of the molecular mechanisms underlying disease. The crop pathogen Pseudomonas syringae sensu lato has been widely isolated from the environment, including wild plants and components of the water cycle, and causes disease in several economically important crops. Here, we compared genome sequences of 45 P. syringae crop pathogen outbreak strains with 69 closely related environmental isolates. Phylogenetic reconstruction revealed that crop pathogens emerged many times independently from environmental populations. Unexpectedly, differences in gene content between environmental populations and outbreak strains were minimal with most virulence genes present in both. However, a genome-wide association study identified a small number of genes, including the type III effector genes hopQ1 and hopD1, to be associated with crop pathogens, but not with environmental populations, suggesting that this small group of genes may play an important role in crop disease emergence. Intriguingly, genome-wide analysis of homologous recombination revealed that the locus Psyr 0346, predicted to encode a protein that confers antibiotic resistance, has been frequently exchanged among lineages and thus may contribute to pathogen fitness. Finally, we found that isolates from diseased crops and from components of the water cycle, collected during the same crop disease epidemic, form a single population. This provides the strongest evidence yet that precipitation and irrigation water are an overlooked inoculum source for disease epidemics caused by P. syringae.},
}

Bacterial Proteins/genetics
Crops, Agricultural/*microbiology
Genome, Bacterial/*genetics
Genome-Wide Association Study
*Metagenomics
Phylogeny
Plant Diseases/microbiology
Pseudomonas syringae/*physiology
Virulence/genetics

@article {pmid30403636,
year = {2018},
author = {Sokolovska, N and Permiakova, O and Forslund, K and Zucker, JD},
title = {Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1109/TCBB.2018.2879504},
pmid = {30403636},
issn = {1557-9964},
abstract = {An important question in microbiology is whether treatment causes changes in gut flora, and whether it also affects metabolism. The reconstruction of causal relations purely from non-temporal observational data is challenging. We address the problem of causal inference in a bivariate case, where the joint distribution of two variables is observed. In this contribution, we introduce a novel method of causality discovering which is based on the widely used assumption that if X causes Y, then P(X) and P(Y|X) are independent. We propose to explore a semi-supervised approach where P(Y|X) and P(X) are estimated from labeled and unlabeled data respectively, whereas the marginal probability is estimated potentially from much more unlabeled data than the conditional distribution. We illustrate by experiments on several benchmarks of biological network reconstruction that the proposed approach is very competitive in terms of computational time and accuracy compared to the state-of-the-art methods. Finally, we apply the proposed method to an original medical task where we study whether drugs confound human metagenome.},
}

@article {pmid30401779,
year = {2018},
author = {Bratburd, JR and Keller, C and Vivas, E and Gemperline, E and Li, L and Rey, FE and Currie, CR},
title = {Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans.},
journal = {mBio},
volume = {9},
number = {6},
pages = {},
doi = {10.1128/mBio.02032-18},
pmid = {30401779},
issn = {2150-7511},
abstract = {The gut microbiota confers resistance to pathogens of the intestinal ecosystem, yet the dynamics of pathogen-microbiome interactions and the metabolites involved in this process remain largely unknown. Here, we use gnotobiotic mice infected with the virulent pathogen Salmonella enterica serovar Typhimurium or the opportunistic pathogen Candida albicans in combination with metagenomics and discovery metabolomics to identify changes in the community and metabolome during infection. To isolate the role of the microbiota in response to pathogens, we compared mice monocolonized with the pathogen, uninfected mice "humanized" with a synthetic human microbiome, or infected humanized mice. In Salmonella-infected mice, by 3 days into infection, microbiome community structure and function changed substantially, with a rise in Enterobacteriaceae strains and a reduction in biosynthetic gene cluster potential. In contrast, Candida-infected mice had few microbiome changes. The LC-MS metabolomic fingerprint of the cecum differed between mice monocolonized with either pathogen and humanized infected mice. Specifically, we identified an increase in glutathione disulfide, glutathione cysteine disulfide, inosine 5'-monophosphate, and hydroxybutyrylcarnitine in mice infected with Salmonella in contrast to uninfected mice and mice monocolonized with Salmonella These metabolites potentially play a role in pathogen-induced oxidative stress. These results provide insight into how the microbiota community members interact with each other and with pathogens on a metabolic level.IMPORTANCE The gut microbiota is increasingly recognized for playing a critical role in human health and disease, especially in conferring resistance to both virulent pathogens such as Salmonella, which infects 1.2 million people in the United States every year (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, et al., Emerg Infect Dis 17:7-15, 2011, https://doi.org/10.3201/eid1701.P11101), and opportunistic pathogens like Candida, which causes an estimated 46,000 cases of invasive candidiasis each year in the United States (Centers for Disease Control and Prevention, Antibiotic Resistance Threats in the United States, 2013, 2013). Using a gnotobiotic mouse model, we investigate potential changes in gut microbial community structure and function during infection using metagenomics and metabolomics. We observe that changes in the community and in biosynthetic gene cluster potential occur within 3 days for the virulent Salmonella enterica serovar Typhimurium, but there are minimal changes with a poorly colonizing Candida albicans In addition, the metabolome shifts depending on infection status, including changes in glutathione metabolites in response to Salmonella infection, potentially in response to host oxidative stress.},
}

@article {pmid30401770,
year = {2018},
author = {Smith, GJ and Angle, JC and Solden, LM and Borton, MA and Morin, TH and Daly, RA and Johnston, MD and Stefanik, KC and Wolfe, R and Gil, B and Wrighton, KC},
title = {Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland.},
journal = {mBio},
volume = {9},
number = {6},
pages = {},
doi = {10.1128/mBio.00815-18},
pmid = {30401770},
issn = {2150-7511},
abstract = {Microbial carbon degradation and methanogenesis in wetland soils generate a large proportion of atmospheric methane, a highly potent greenhouse gas. Despite their potential to mitigate greenhouse gas emissions, knowledge about methane-consuming methanotrophs is often limited to lower-resolution single-gene surveys that fail to capture the taxonomic and metabolic diversity of these microorganisms in soils. Here our objective was to use genome-enabled approaches to investigate methanotroph membership, distribution, and in situ activity across spatial and seasonal gradients in a freshwater wetland near Lake Erie. 16S rRNA gene analyses demonstrated that members of the methanotrophic Methylococcales were dominant, with the dominance largely driven by the relative abundance of four taxa, and enriched in oxic surface soils. Three methanotroph genomes from assembled soil metagenomes were assigned to the genus Methylobacter and represented the most abundant methanotrophs across the wetland. Paired metatranscriptomes confirmed that these Old Woman Creek (OWC) Methylobacter members accounted for nearly all the aerobic methanotrophic activity across two seasons. In addition to having the capacity to couple methane oxidation to aerobic respiration, these new genomes encoded denitrification potential that may sustain energy generation in soils with lower dissolved oxygen concentrations. We further show that Methylobacter members that were closely related to the OWC members were present in many other high-methane-emitting freshwater and soil sites, suggesting that this lineage could participate in methane consumption in analogous ecosystems. This work contributes to the growing body of research suggesting that Methylobacter may represent critical mediators of methane fluxes in freshwater saturated sediments and soils worldwide.IMPORTANCE Here we used soil metagenomics and metatranscriptomics to uncover novel members within the genus Methylobacter We denote these closely related genomes as members of the lineage OWC Methylobacter Despite the incredibly high microbial diversity in soils, here we present findings that unexpectedly showed that methane cycling was primarily mediated by a single genus for both methane production ("Candidatus Methanothrix paradoxum") and methane consumption (OWC Methylobacter). Metatranscriptomic analyses revealed that decreased methanotrophic activity rather than increased methanogenic activity possibly contributed to the greater methane emissions that we had previously observed in summer months, findings important for biogeochemical methane models. Although members of this Methylococcales order have been cultivated for decades, multi-omic approaches continue to illuminate the methanotroph phylogenetic and metabolic diversity harbored in terrestrial and marine ecosystems.},
}

@article {pmid30400812,
year = {2018},
author = {Kumar, MS and Slud, EV and Okrah, K and Hicks, SC and Hannenhalli, S and Corrada Bravo, H},
title = {Analysis and correction of compositional bias in sparse sequencing count data.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {799},
doi = {10.1186/s12864-018-5160-5},
pmid = {30400812},
issn = {1471-2164},
support = {1564785//National Science Foundation (US)/ ; GM083084//National Institutes of Health/ ; GM114267//National Institutes of Health/ ; HG005220//National Institutes of Health/ ; },
abstract = {BACKGROUND: Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count data is compositional, measuring relative and not absolute abundances of the assayed features. This compositional bias confounds inference of absolute abundances. Commonly used count data normalization approaches like library size scaling/rarefaction/subsampling cannot correct for compositional or any other relevant technical bias that is uncorrelated with library size.

RESULTS: We demonstrate that existing techniques for estimating compositional bias fail with sparse metagenomic 16S count data and propose an empirical Bayes normalization approach to overcome this problem. In addition, we clarify the assumptions underlying frequently used scaling normalization methods in light of compositional bias, including scaling methods that were not designed directly to address it.

CONCLUSIONS: Compositional bias, induced by the sequencing machine, confounds inferences of absolute abundances. We present a normalization technique for compositional bias correction in sparse sequencing count data, and demonstrate its improved performance in metagenomic 16s survey data. Based on the distribution of technical bias estimates arising from several publicly available large scale 16s count datasets, we argue that detailed experiments specifically addressing the influence of compositional bias in metagenomics are needed.},
}

@article {pmid30399430,
year = {2018},
author = {Tang, P and Zhu, JC and Zheng, BY and Wei, SJ and Sharkey, M and Chen, XX and Vogler, AP},
title = {Mitochondrial phylogenomics of the Hymenoptera.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ympev.2018.10.040},
pmid = {30399430},
issn = {1095-9513},
abstract = {The insect order Hymenoptera presents marvelous morphological and ecological diversity. Higher-level hymenopteran relationships remain controversial, even after recent phylogenomic analyses, as their taxon sampling was limited. To shed light on the origin and diversification of Hymenoptera, in particular the poorly studied Parasitica, we undertook phylogenetic analyses of 40 newly and 43 previously sequenced mitochondrial genomes representing all major clades of Hymenoptera. Various Bayesian inferences using different data partitions and phylogenetic methods recovered similar phylogenetic trees with strong statistical support for almost all nodes. Novel findings of the mitogenomic phylogeny mainly affected the three infraorders Ichneumonomorpha, Proctotrupomorpha and Evaniomorpha, the latter of which was split into three clades. Basal relationships of Parasitica recovered Stephanoidea + (Gasteruptiidae + Aulacidae) as the sister group to Ichneumonomorpha + (Trigonalyoidea + Megalyroidea). This entire clade is sister to Proctotrupomorpha, and Ceraphronoidea + Evaniidae is sister to Aculeata (stinging wasps). Our divergence time analysis indicates that major hymenopteran lineages originated in the Mesozoic. The radiation of early apocritans may have been triggered by the Triassic-Jurassic mass extinction; all extant families were present by the Cretaceous.},
}

@article {pmid30398115,
year = {2018},
author = {Hazra, S and Patra, S},
title = {Alleviating the Neglected Tropical Diseases: Recent Developments in Diagnostics and Detection.},
journal = {Current topics in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/1568026618666181106124015},
pmid = {30398115},
issn = {1873-4294},
abstract = {Background Neglected tropical diseases (NTDs) are communicable diseases caused by a group of bacteria, viruses, protozoa and helminths prevalent in more than 145 countries that affect the world's poverty stricken populations. WHO enlists 18 NTDs amongst people living in endemic areas having inaccessibility to preventive measures. Steps to reduce the global disease burden of the NTDs need attention at multi-factorial levels. Control programmes, mass drug administrations, transmission checks, eradication surveillances and diagnoses are some of them. The foremost in this list is confirmatory diagnosis. A comprehensive summary of the innovative, high-impact, multiplexed, low-cost diagnostic tools developed in the last decade that helped to meet the needs of users can depict a holistic approach to further evaluate potential technologies and reagents currently in research. Major advancements A literature survey based on developing nano-biotechnological platforms to meet the diagnostic challenges in NTDs towards development of a useful point-of-care (POC) unit is reported. However, in order to pave the way for complete eradication more sensitive tools are required that are user-friendly and applicable for use in endemic and low-resource settings. There are various novel research progresses/advancements made for qualitative and quantitative measurement of infectious load in some diseases like dengue, Chagas disease and leishmaniasis; though further improvements on the specificity and sensitivity front are still awaited. Strategies to combat the problem of antimicrobial drug resistance in diagnosis of NTDs have also been put forward by various research groups and organizations. Moreover, the state-of-the-art "omics" approaches like metabolomics and metagenomics have also started to contribute constructively towards diagnosis and prevention of the NTDs. Conclusion A concrete solution towards a single specimen based common biomarker detection platform for NTDs is lacking. Identifying robust biomarkers and implementing them on simple diagnostic tools to ease the process of pathogen detection can help us understand the obstacles in current diagnostic measures of the NTDs.},
}

@article {pmid30398110,
year = {2018},
author = {Wang, L and Yu, X and Zhang, C and Zeng, T},
title = {Detecting personalized determinates during drug treatment from omics big data.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/1381612824666181106102111},
pmid = {30398110},
issn = {1873-4286},
abstract = {BACKGROUNDS: The targeted therapy is the foundation of personalized medicine in cancer, which is often understood as the right patient using the right drug. Thinking from the viewpoint of determinates during personalized drug treatment, the genetics, epigenetics and metagenomics would provide individual-specific biological elements to characterize the personalized responses for therapy.

METHODS: Such personalized determinates should be not extremely understood as specificity for only one person, while they should have certain replicate observations in a group of individuals but no all, which actually provide more credible and reproducible personalized biological features. And the requirement of detecting personalized determinates is well supported by novel high-throughput sequencing technologies and newly temporal-spatial experimental protocols, which quickly produce the omics big data.

RESULTS: In this mini-review, we would like to give a brief introduction firstly on the advanced drug or drug-like therapy with genetics, epigenetics and metagenomics respectively from the viewpoint of personalized determinates; then summarize the computational methods helpful to analyze the corresponding omics data under the consideration of personalized biological context; and particularly focus on the metagenomics to discuss current data, method, and opportunity for personalized medicine.

CONCLUSIONS: Totally, detecting personalized determinates during drug treatment from omics big data will bring the precision medicine or personalized medicine from concept to application. More and more inspiring bio-technologies, data resources, and analytic approaches will benefit All of US in the near future.},
}

@article {pmid30397794,
year = {2018},
author = {Lau, NS and Zarkasi, KZ and Md Sah, ASR and Shu-Chien, AC},
title = {Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1283-0},
pmid = {30397794},
issn = {1432-184X},
abstract = {Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.},
}

@article {pmid30397546,
year = {2018},
author = {Md Zoqratt, MZH and Eng, WWH and Thai, BT and Austin, CM and Gan, HM},
title = {Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5826},
doi = {10.7717/peerj.5826},
pmid = {30397546},
issn = {2167-8359},
abstract = {Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3-V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.},
}

@article {pmid30397357,
year = {2018},
author = {Tirosh, O and Conlan, S and Deming, C and Lee-Lin, SQ and Huang, X and , and Su, HC and Freeman, AF and Segre, JA and Kong, HH},
title = {Expanded skin virome in DOCK8-deficient patients.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-018-0211-7},
pmid = {30397357},
issn = {1546-170X},
abstract = {Human microbiome studies have revealed the intricate interplay of host immunity and bacterial communities to achieve homeostatic balance. Healthy skin microbial communities are dominated by bacteria with low viral representation1-3, mainly bacteriophage. Specific eukaryotic viruses have been implicated in both common and rare skin diseases, but cataloging skin viral communities has been limited. Alterations in host immunity provide an opportunity to expand our understanding of microbial-host interactions. Primary immunodeficient patients manifest with various viral, bacterial, fungal, and parasitic infections, including skin infections4. Dedicator of cytokinesis 8 (DOCK8) deficiency is a rare primary human immunodeficiency characterized by recurrent cutaneous and systemic infections, as well as atopy and cancer susceptibility5. DOCK8, encoding a guanine nucleotide exchange factor highly expressed in lymphocytes, regulates actin cytoskeleton, which is critical for migration through collagen-dense tissues such as skin6. Analyzing deep metagenomic sequencing data from DOCK8-deficient skin samples demonstrated a notable increase in eukaryotic viral representation and diversity compared with healthy volunteers. De novo assembly approaches identified hundreds of novel human papillomavirus genomes, illuminating microbial dark matter. Expansion of the skin virome in DOCK8-deficient patients underscores the importance of immune surveillance in controlling eukaryotic viral colonization and infection.},
}

@article {pmid30397356,
year = {2018},
author = {Sun, L and Xie, C and Wang, G and Wu, Y and Wu, Q and Wang, X and Liu, J and Deng, Y and Xia, J and Chen, B and Zhang, S and Yun, C and Lian, G and Zhang, X and Zhang, H and Bisson, WH and Shi, J and Gao, X and Ge, P and Liu, C and Krausz, KW and Nichols, RG and Cai, J and Rimal, B and Patterson, AD and Wang, X and Gonzalez, FJ and Jiang, C},
title = {Gut microbiota and intestinal FXR mediate the clinical benefits of metformin.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-018-0222-4},
pmid = {30397356},
issn = {1546-170X},
abstract = {The anti-hyperglycemic effect of metformin is believed to be caused by its direct action on signaling processes in hepatocytes, leading to lower hepatic gluconeogenesis. Recently, metformin was reported to alter the gut microbiota community in humans, suggesting that the hyperglycemia-lowering action of the drug could be the result of modulating the population of gut microbiota. However, the critical microbial signaling metabolites and the host targets associated with the metabolic benefits of metformin remained elusive. Here, we performed metagenomic and metabolomic analysis of samples from individuals with newly diagnosed type 2 diabetes (T2D) naively treated with metformin for 3 d, which revealed that Bacteroides fragilis was decreased and the bile acid glycoursodeoxycholic acid (GUDCA) was increased in the gut. These changes were accompanied by inhibition of intestinal farnesoid X receptor (FXR) signaling. We further found that high-fat-diet (HFD)-fed mice colonized with B. fragilis were predisposed to more severe glucose intolerance, and the metabolic benefits of metformin treatment on glucose intolerance were abrogated. GUDCA was further identified as an intestinal FXR antagonist that improved various metabolic endpoints in mice with established obesity. Thus, we conclude that metformin acts in part through a B. fragilis-GUDCA-intestinal FXR axis to improve metabolic dysfunction, including hyperglycemia.},
}

@article {pmid30397237,
year = {2018},
author = {Souza, WM and Fumagalli, MJ and Torres Carrasco, AO and Romeiro, MF and Modha, S and Seki, MC and Gheller, JM and Daffre, S and Nunes, MRT and Murcia, PR and Acrani, GO and Figueiredo, LTM},
title = {Viral diversity of Rhipicephalus microplus parasitizing cattle in southern Brazil.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16315},
doi = {10.1038/s41598-018-34630-1},
pmid = {30397237},
issn = {2045-2322},
support = {MC_UU_120/14/9//Medical Research Council (MRC)/ ; },
abstract = {Ticks are ectoparasites spread worldwide and are well known as vectors of many viruses of great importance to human and animal health. However, the viral diversity in ticks is still poorly understood, particularly in South America. Here we characterized the viral diversity present in Rhipicephalus microplus parasitizing cattle in the southern region of Brazil using metagenomics. Our study revealed the presence of viruses that had not been previously described in the region, including lihan tick virus (Phenuiviridae family) and wuhan tick virus 2 (Chuviridae family), as well as expands the biogeography of jingmen tick virus (Flaviviridae family) in Brazil. Also, we described three novel tymoviruses (Tymovirales order), named guarapuava tymovirus-like 1 to 3. We described the genomic and phylogenetic characterization of these viruses. Our study sheds light on the viral diversity of Rhipicephalus microplus in South America, and also expands the biogeography of tick viruses that were previously described only in Asia.},
}

@article {pmid30396371,
year = {2018},
author = {Meisel, JS and Nasko, DJ and Brubach, B and Cepeda-Espinoza, V and Chopyk, J and Corrada-Bravo, H and Fedarko, M and Ghurye, J and Javkar, K and Olson, ND and Shah, N and Allard, SM and Bazinet, AL and Bergman, NH and Brown, A and Caporaso, JG and Conlan, S and DiRuggiero, J and Forry, SP and Hasan, NA and Kralj, J and Luethy, PM and Milton, DK and Ondov, BD and Preheim, S and Ratnayake, S and Rogers, SM and Rosovitz, MJ and Sakowski, EG and Schliebs, NO and Sommer, DD and Ternus, KL and Uritskiy, G and Zhang, SX and Pop, M and Treangen, TJ},
title = {Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {197},
doi = {10.1186/s40168-018-0582-5},
pmid = {30396371},
issn = {2049-2618},
support = {R01-AI-100947//National Institutes of Health/ ; U54CA143924//National Institutes of Health/ ; U54CA143925//National Institutes of Health/ ; IIS-1513615//National Science Foundation (US)/ ; 1565100//National Science Foundation (US)/ ; DEB1556574//National Science Foundation (US)/ ; W911NF-17-2-0089//Intelligence Advanced Research Projects Activity (US)/ ; R01 GM114267//National Institutes of Health (US)/ ; HSHQDC-15-C-00064//Science and Technology Directorate/ ; },
abstract = {The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.},
}

@article {pmid29076296,
year = {2017},
author = {de la Calle, F},
title = {Marine microbiome as source of natural products.},
journal = {Microbial biotechnology},
volume = {10},
number = {6},
pages = {1293-1296},
doi = {10.1111/1751-7915.12882},
pmid = {29076296},
issn = {1751-7915},
mesh = {Biological Products/*metabolism ; Biotechnology/methods ; Data Mining/methods ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Seawater/*microbiology ; },
}

Biological Products/*metabolism
Biotechnology/methods
Data Mining/methods
Metabolic Networks and Pathways/genetics
Metagenomics
*Microbiota
Seawater/*microbiology

@article {pmid30396006,
year = {2018},
author = {Velikonja, A and Lipoglavšek, L and Zorec, M and Orel, R and Avguštin, G},
title = {Alterations in gut microbiota composition and metabolic parameters after dietary intervention with barley beta glucans in patients with high risk for metabolic syndrome development.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anaerobe.2018.11.002},
pmid = {30396006},
issn = {1095-8274},
abstract = {Metabolic syndrome is a complex disease that is exponentially increasing in the western world, and diet is one of the possible ways to improve the metabolic status of patients. Barley beta glucans are dietary fibres that show promise for improvement cholesterol levels and postprandial glucose response, but they have been rarely investigated in human trials with concurrent focus on gut microbiota. A double-blind, placebo-controlled, randomised clinical trial was conducted with 43 volunteers with high risk for metabolic syndrome development or with diagnosed metabolic syndrome. During a four-week intervention study, participants consumed experimental bread containing 6 g of barley beta glucans or equal bread but without beta glucans. After dietary intervention, total plasma cholesterol decreased in the test group (-0.26 ± 0.54, p = 0.019), but not in the control group. Short chain fatty acids (SCFA) composition in faeces significantly changed with increase of propionic acid in test group (43.2%, p = 0.045) and with decrease of acetic acid in control group (41.8%, p = 0.011). The microbiome analysis based on Illumina paired end sequencing of 16S rRNA genes showed a decrease in microbial diversity and richness in the test group. The pre-intervention gut microbiota composition showed higher abundance of health associated Bifidobacterium spp. and Akkermansia municiphila within cholesterol-responsive group, showing that diet-induced metabolic response is possibly dependent on individual gut microbiota composition.},
}

@article {pmid30395567,
year = {2018},
author = {Koehler, JW and Douglas, CE and Minogue, TD},
title = {A highly multiplexed broad pathogen detection assay for infectious disease diagnostics.},
journal = {PLoS neglected tropical diseases},
volume = {12},
number = {11},
pages = {e0006889},
doi = {10.1371/journal.pntd.0006889},
pmid = {30395567},
issn = {1935-2735},
abstract = {Rapid pathogen identification during an acute febrile illness is a critical first step for providing appropriate clinical care and patient isolation. Primary screening using sensitive and specific assays, such as real-time PCR and ELISAs, can rapidly test for known circulating infectious diseases. If the initial testing is negative, potentially due to a lack of developed diagnostic assays or an incomplete understanding of the pathogens circulating within a geographic region, additional testing would be required including highly multiplexed assays and metagenomic next generation sequencing. To bridge the gap between rapid point of care diagnostics and sequencing, we developed a highly multiplexed assay designed to detect 164 different viruses, bacteria, and parasites using the NanoString nCounter platform. Included in this assay were high consequence pathogens such as Ebola virus, highly endemic organisms including several Plasmodium species, and a large number of less prevalent pathogens to ensure a broad coverage of potential human pathogens. Evaluation of this panel resulted in positive detection of 113 (encompassing 98 different human pathogen types) of the 126 organisms available to us including the medically important Ebola virus, Lassa virus, dengue virus serotypes 1-4, Chikungunya virus, yellow fever virus, and Plasmodium falciparum. Overall, this assay could improve infectious disease diagnostics and biosurveillance efforts as a quick, highly multiplexed, and easy to use pathogen screening tool.},
}

@article {pmid30394652,
year = {2018},
author = {Borton, MA and Daly, RA and O'Banion, B and Hoyt, DW and Marcus, DN and Welch, S and Hastings, SS and Meulia, T and Wolfe, RA and Booker, AE and Sharma, S and Cole, DR and Wunch, K and Moore, JD and Darrah, TH and Wilkins, MJ and Wrighton, KC},
title = {Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14467},
pmid = {30394652},
issn = {1462-2920},
abstract = {About 60% of natural gas production in the United States comes from hydraulic fracturing of unconventional reservoirs, such as shales or organic-rich micrites. This process inoculates and enriches for halotolerant microorganisms in these reservoirs over time, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of methanogens across unconventional reservoirs, and report that members of genus Methanohalophilus are recovered from every hydraulically fractured unconventional reservoir sampled by metagenomics. We provide the first genomic sequencing of three isolate genomes, as well as two metagenome assembled genomes. Utilizing six other previously sequenced genomes, we perform comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in CRISPR-Cas systems of Methanohalophilus, with genomes from geographically distinct unconventional reservoirs sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic methane production in hydraulically fractured unconventional reservoirs. This article is protected by copyright. All rights reserved.},
}

@article {pmid30394313,
year = {2018},
author = {Wang, M and Zhou, J and He, F and Cai, C and Wang, H and Wang, Y and Lin, Y and Rong, H and Cheng, G and Xu, R and Zhou, W},
title = {Alteration of gut microbiota-associated epitopes in children with autism spectrum disorders.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2018.10.006},
pmid = {30394313},
issn = {1090-2139},
abstract = {BACKGROUND: Autism spectrum disorder (ASD) affects 1% of children and has no cure. Gastrointestinal (GI) problems are common in children with ASD, and although gut microbiota is known to play an important role in ASD through the gut-brain axis, the specific mechanism is unknown. Recent evidence suggests that gut microbiota may participate in the pathogenesis of ASD through immune- and inflammation-mediated pathways. Here, we identified potentially immunogenic epitopes derived from gut microbiota in stool samples from ASD children with and without GI problems and typically developing (TD) children.

METHODS: Candidate gut microbiota-associated epitopes (MEs) were identified by blast shotgun metagenomic sequencing of fecal samples from 43 ASD children (19 with and 24 without GI involvement) and 31 sex- and age-matched typically developing (TD) children. Potentially immunogenic epitopes were screened against a predictive human Immune Epitope Database. The composition and abundance of candidate MEs were compared between the three groups of children.

RESULTS: MEs identified in ASD children with GI problems were significantly more diverse than those in TD children. ME composition could discriminate between the three groups of children. We identified 34 MEs that were significantly more or less abundant in ASD children than TD children, most (29/34) of the differences in MEs were reduced in ASD and associated with abnormal gut IgA level and altered gut microbiota composition, these MEs were limited effected by clinical factors such as age, gender, and GI problems, of which eleven MEs were pathogenic microorganisms peptides with strong T or B cell response, nine MEs showed high homology to peptides from human self proteins associated with autoimmune disease occurrence, eliciting immune attack against hematopoietic stem cells and inhibition antigen binding. We also found that the abundance of five MEs were increased in ASD, including three human self proteins, gap junction alpha-1 (GJA1), paired box protein Pax-3 (PAX3) and eyes absent homolog 1 isoform 4 (EYA1) which associated with cancer, and a ME with homology to a Listeriolysin O peptide from the pathogenic bacterium Listeria monocytogenes was significantly increased in ASD children compared with TD children.

CONCLUSIONS: Our findings demonstrate the abnormal of MEs composition in the gut of children with ASD, moreover, the abnormality in MEs composition was associated with abnormal gut IgA levels and altered gut microbiota composition, this abnormality also suggests that there may be abnormalities in intestinal immunity in children with ASD; In all, thirty-four MEs identified were potential biomarker of ASD, andalterations in MEs may contribute to abnormalities in gut immunity and/or homeostasis in ASD children. Further study of the MEs identified here may advance our understanding of the pathogenesis of ASD.},
}

@article {pmid30392911,
year = {2018},
author = {Zhang, Y and Weng, Y and Gan, H and Zhao, X and Zhi, F},
title = {Streptococcus gallolyticus conspires myeloid cells to promote tumorigenesis of inflammatory bowel disease.},
journal = {Biochemical and biophysical research communications},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbrc.2018.10.136},
pmid = {30392911},
issn = {1090-2104},
abstract = {Metagenomic analyses indicate that streptococcus gallolyticus is enriched at carcinoma in colitis associated colorectal cancer compared with sporadic colorectal cancer. But the particular mechanism of streptococcus gallolyticus in Inflammatory Bowel Disease malignant progression remains undefined yet. We aim to explore the biological carcinogenesis efficacy of streptococcus gallolyticus and its potential mechanism in azoxymethane and dextran sodium sulphate-induced colitis associated colorectal cancer in mice. Oral pretreatment of streptococcus gallolyticus was adopted to evaluate its detrimental effect. The colorectums of experimental C57BL/6 mice were collected and examined for the degree of tumorigenesis. Comparative 16S rRNA sequencing was carried out to observe streptococcus gallolyticus alterations in abundance. We found that streptococcus gallolyticus are enriched in colonic carcinoma compared to adenoma and healthy mice. Pretreatment of Streptococcus gallolyticus aggravated tumor formation, with more colonic obstruction, larger number and diameter of tumor node. Furthermore, Streptococcus gallolyticus selectively recruits tumor-infiltrating myeloid cells but not mast cells, including marrow-derived suppressor cells, tumor-associated macrophages and dendritic cells, which can inhibit competence of T cells. Moreover, several myeloid-cell-derived proinflammatory cytokines (IL-6, IL-1β, IL-8, CCL2, COX-2, TNF-α) were increased with the formation of carcinoma in IBD. Collectively, these data suggest that, through recruitment of tumor-infiltrating immune cells, Streptococcus gallolyticus generate an immune suppressive microenvironment that is conducive for neoplasia progression of Inflammatory Bowel Disease.},
}

@article {pmid30392727,
year = {2018},
author = {Wang, L and Ravichandran, V and Yin, Y and Yin, J and Zhang, Y},
title = {Natural Products from Mammalian Gut Microbiota.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2018.10.003},
pmid = {30392727},
issn = {1879-3096},
abstract = {The mammalian gut has a remarkable abundance of microbes. These microbes have strong potential to biosynthesize distinct metabolites that are promising drugs, and many more bioactive compounds have yet to be explored as potential drug candidates. These small bioactive molecules often mediate important host-microbe and microbe-microbe interactions. In this review, we provide perspectives on and challenges associated with three mining strategies - culture-based, (meta)genomics-based, and metabolomics-based mining approaches - for discovering natural products derived from biosynthetic gene clusters (BGCs) in mammalian gut microbiota. In addition, we comprehensively summarize the structures, biological functions, and BGCs of these compounds. Improving these techniques, including by using combinatorial approaches, may accelerate drug discovery from gut microbes.},
}

@article {pmid30390805,
year = {2018},
author = {Wang, Q and Yang, F and Jia, H},
title = {Mining the Microbiome for Drug Targets.},
journal = {Methods in enzymology},
volume = {610},
number = {},
pages = {59-72},
doi = {10.1016/bs.mie.2018.09.014},
pmid = {30390805},
issn = {1557-7988},
abstract = {The human microbiome is our "other genome." Implicated in a growing list of complex diseases, for which genomic studies typically explain a portion of the disease susceptibility, the human gut microbiome has been at the spotlight for our understanding of human diseases. As the microbiome is intrinsically more variable than the human genome, it is important to take careful considerations at each step of a study. Here, we put forward our recommendations, which we envision would facilitate identification of true drug targets in the human microbiome in the colon as well as at other body sites.},
}

@article {pmid30390617,
year = {2018},
author = {Kwak, J and Park, J},
title = {What we can see from very small size sample of metagenomic sequences.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {399},
doi = {10.1186/s12859-018-2431-8},
pmid = {30390617},
issn = {1471-2105},
abstract = {BACKGROUND: Since the analysis of a large number of metagenomic sequences costs heavy computing resources and takes long time, we examined a selected small part of metagenomic sequences as "sample"s of the entire full sequences, both for a mock community and for 10 different existing metagenomics case studies. A mock community with 10 bacterial strains was prepared, and their mixed genome were sequenced by Hiseq. The hits of BLAST search for reference genome of each strain were counted. Each of 176 different small parts selected from these sequences were also searched by BLAST and their hits were also counted, in order to compare them to the original search results from the full sequences. We also prepared small parts of sequences which were selected from 10 publicly downloadable research data of MG-RAST service, and analyzed these samples with MG-RAST.

RESULTS: Both the BLAST search tests of the mock community and the results from the publicly downloadable researches of MG-RAST show that sampling an extremely small part from sequence data is useful to estimate brief taxonomic information of the original metagenomic sequences. For 9 cases out of 10, the most annotated classes from the MG-RAST analyses of the selected partial sample sequences are the same as the ones from the originals.

CONCLUSIONS: When a researcher wants to estimate brief information of a metagenome's taxonomic distribution with less computing resources and within shorter time, the researcher can analyze a selected small part of metagenomic sequences. With this approach, we can also build a strategy to monitor metagenome samples of wider geographic area, more frequently.},
}

@article {pmid30390509,
year = {2018},
author = {Leng, L and Nobu, MK and Narihiro, T and Yang, P and Amy Tan, GY and Lee, PH},
title = {Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: Pathways and mechanisms.},
journal = {Water research},
volume = {148},
number = {},
pages = {281-291},
doi = {10.1016/j.watres.2018.10.063},
pmid = {30390509},
issn = {1879-2448},
abstract = {Glycerol is presently being generated in surplus with the rapid growth of the biodiesel industry and seeks ways to be upcycled, rather than to be treated with costs. Glycerol for the co-production of 1,3-propanediol (1,3-PDO) and caproate has a great prospect. Yet, its technical difficulty lies in the enhancement of caproate productivity, which requires the presence of ethanol as a co-substrate and necessitates the co-existence of functional microbes for glycerol fermentation and chain elongation. This study successfully achieved 6.38 mM C 1,3-PDO d-1 and 2.95 mM C caproate d-1 in a 2-L mixed-cultured semi-continuous fermenter with a glycerol-ethanol-acetate stoichiometric ratio of 4:3:1. Such conversions were mainly facilitated by a microbial community of Eubacterium limosum, Clostridium kluyveri and Massilibacterium senegalense. With such a synergistic microbiome, the co-production of 1,3-PDO and caproate was achieved from glycerol without ethanol addition. Based on metagenomics, E. limosum is capable of converting glycerol to 1,3-PDO, ethanol and H2, and also redirecting the electron potential of H2 into acetate via the Wood-Ljungdahl pathway, which is then used for chain elongation. C. kluyveri worked synergistically with E. limosum by consuming ethanol and acetate for caproate production. M. senegalense encodes for ethanol oxidation to acetate and butyrate, facilitating the generation of these intermediates for C. kluyveri elongation to caproate. During the transition between fermentation and elongation, an unexpected observation of poly-β-hydroxybutyrate (PHB) formation and reutilization by M. senegalense may be associated with butyrate formation for further caproate generation. The knowledge gleaned from the substrate constitute, microbial consortium and their synergetic metabolism demonstrates a resource upgrade potential for crude glycerol or glycerol-containing wastewater generated from the biodiesel industry.},
}

@article {pmid30376898,
year = {2018},
author = {Leiby, JS and McCormick, K and Sherrill-Mix, S and Clarke, EL and Kessler, LR and Taylor, LJ and Hofstaedter, CE and Roche, AM and Mattei, LM and Bittinger, K and Elovitz, MA and Leite, R and Parry, S and Bushman, FD},
title = {Lack of detection of a human placenta microbiome in samples from preterm and term deliveries.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {196},
doi = {10.1186/s40168-018-0575-4},
pmid = {30376898},
issn = {2049-2618},
support = {P30 AI045008//National Institute of Allergy and Infectious Diseases/ ; T32 AI007632//National Institute of Allergy and Infectious Diseases/ ; T32 AI007324//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND: Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is colonized with bacteria. For example, analysis of DNA from placenta samples yielded small proportions of microbial sequences which were proposed to represent normal bacterial colonization. However, an analysis by our group showed no distinction between background negative controls and placenta samples. Also supporting the idea that the womb is sterile is the observation that germ-free mammals can be generated by sterile delivery of neonates into a sterile isolator, after which neonates remain germ-free, which would seem to provide strong data in support of sterility of the womb.

RESULTS: To probe this further and to investigate possible placental colonization associated with spontaneous preterm birth, we carried out another study comparing microbiota in placenta samples from 20 term and 20 spontaneous preterm deliveries. Both 16S rRNA marker gene sequencing and shotgun metagenomic sequencing were used to characterize placenta and control samples. We first quantified absolute amounts of bacterial 16S rRNA gene sequences using 16S rRNA gene quantitative PCR (qPCR). As in our previous study, levels were found to be low in the placenta samples and indistinguishable from negative controls. Analysis by DNA sequencing did not yield a placenta microbiome distinct from negative controls, either using marker gene sequencing as in our previous work, or with shotgun metagenomic sequencing. Several types of artifacts, including erroneous read classifications and barcode misattribution, needed to be identified and removed from the data to clarify this point.

CONCLUSIONS: Our findings do not support the existence of a consistent placental microbiome, in either placenta from term deliveries or spontaneous preterm births.},
}