@article {pmid30244151,
year = {2018},
author = {Schön, I and Kamiya, T and Van den Berghe, T and Van den Broecke, L and Martens, K},
title = {Novel Cardinium strains in non-marine ostracod (Crustacea) hosts from natural populations.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ympev.2018.09.008},
pmid = {30244151},
issn = {1095-9513},
abstract = {Endosymbiotic bacteria are known from many metazoan taxa, where they manipulate host biology and reproduction. Here, we used classic PCR amplification and direct DNA sequencing with universal primers for four different endosymbionts to test for their presence in more than 300 specimens of three recent non-marine ostracod superfamilies from different geographic areas and aquatic habitats. We verified these results with "high throughput" amplicon sequencing of 16S of nine selected specimens and evolutionary placement algorithms. The phylogenetic position of endosymbionts detected in ostracod hosts was compared to known endosymbionts from other metazoans. While Wolbachia, Spiroplasma and Ricketsia are absent, we find evidence for the general presence of Cardinium bacteria in natural populations of various non-marine ostracod species. Phylogenetic reconstructions based on Cardinium 16S data and estimates of genetic distances both indicate that Cardinium from ostracods are distantly related to Cardinium from Diptera and Nematoda but represent novel strains with a monophyletic origin. Cardinium bacteria from different ostracod hosts have genetic distances of up to 3.8%, providing evidence against recent and frequent horizontal transmissions amongst the three ostracod superfamilies. High throughput sequencing reveals more than 400 different 16S amplicon sequence variants in the investigated ostracods as well as the presence of different Cardinium strains within individual Eucypris virens and Heterocypris hosts. These results call for future, more in-depth investigations. Mapping Cardinium infections on COI trees of non-marine ostracod hosts shows that the occurrence of these endosymbionts is not linked to genetic species identity or phylogenetic host groups and, except for one ostracod morphospecies, prevalence never reaches 100%.},
}

@article {pmid30243649,
year = {2018},
author = {Wang, N and Zhu, F and Chen, L and Chen, K},
title = {Proteomics, metabolomics and metagenomics for type 2 diabetes and its complications.},
journal = {Life sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.lfs.2018.09.035},
pmid = {30243649},
issn = {1879-0631},
abstract = {Type 2 diabetes mellitus (T2DM) is one of the most common diseases of endocrine and metabolic disorders, whose mechanism is still largely unknown. Fortunately, various "omics" tools have been employed to better understand the progression pathologies of T2DM and its complications. More specifically, proteomics, metabolomics and metagenomics have played crucial roles in advancing deeper understanding of the physiological processes and regulatory mechanisms of T2DM, such as regulation of signaling pathways perturbed by glucose levels, intestinal microorganism, and inflammation and so on. By analyzing the dynamic change and modification of proteins, proteomics has become an important tool in biology and medicine. Metabolomic analysis can amplify and quantify metabolites in living organisms to reveal the relative relationship between metabolites and physiological and pathological changes. There are also increasing evidences that the human microbiome, specifically the gastrointestinal microbiome have a potential role in the etiology and pathological outcomes of T2DM and its complications. This article summarized and discussed the recent applications of these "omics" tools in finding biomarkers for T2DM and its complications. We also reviewed employing multiple "omics" to further advance our understanding of this pathology. This review will benefit deeper understanding in new therapeutic and/or diagnostic biological target for the discovery of T2DM and its complications.},
}

@article {pmid30242844,
year = {2018},
author = {Lee, JJ and Kim, SH and Lee, MJ and Kim, BK and Song, WJ and Park, HW and Cho, SH and Hong, SJ and Chang, YS and Kim, BS},
title = {Different Upper Airway Microbiome and Their Functional Genes Associated with Asthma in Young Adults and Elderly Individuals.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.13608},
pmid = {30242844},
issn = {1398-9995},
abstract = {BACKGROUND: Microbes in the airway has been shown to be associated with the pathogenesis of asthma. The upper airway microbiome influences the dysbiosis of the lower airway microbiome. However, to date, the influence of upper airway microbiome for adult and elderly asthma has not been fully elucidated. Here, the metagenome of upper airway microbiome of young adults and elderly was analyzed to identify their association with adult asthma.

METHODS: Nasopharyngeal swabs were collected from young-adult and elderly asthma patients and non-asthmatic subjects. The compositions and functional genes of airway microbiome were analyzed by high-throughput sequencing.

RESULTS: The composition of microbiota differed between young-adult and elderly, and it was different between asthmatics and non-asthmatics in each age group. Different bacteria were related to FEV1% predicted in each age group. Genes related to lysine degradation, N-glycan biosynthesis, caprolactam degradation, and PPAR signaling pathway, which could be related to the reduction of inflammation and degradation of air pollutants, were higher in non-asthmatics. Genes related to pentose phosphate pathway, lipopolysaccharide biosynthesis, flagella assembly, and bacterial chemotaxis - which may all be related to increased inflammation and colonization of pathogenic bacteria - were higher in young-adult asthmatic patients. However, the functional genes of airway microbiome in elderly patients were not significantly different according to asthma morbidity.

CONCLUSIONS: These results suggest that the composition and function of upper airway microbiome could influence asthma pathogenesis, and the microbiome could play various roles depending on the age group. This article is protected by copyright. All rights reserved.},
}

@article {pmid30242595,
year = {2018},
author = {Hemmat-Jou, MH and Safari-Sinegani, AA and Mirzaie-Asl, A and Tahmourespour, A},
title = {Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach.},
journal = {Ecotoxicology (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10646-018-1981-x},
pmid = {30242595},
issn = {1573-3017},
abstract = {Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.},
}

@article {pmid30240834,
year = {2018},
author = {Gofton, AW and Margos, G and Fingerle, V and Hepner, S and Loh, SM and Ryan, U and Irwin, P and Oskam, CL},
title = {Genome-wide analysis of Borrelia turcica and 'Candidatus Borrelia tachyglossi' shows relapsing fever-like genomes with unique genomic links to Lyme disease Borrelia.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.meegid.2018.09.013},
pmid = {30240834},
issn = {1567-7257},
abstract = {Borrelia are tick-borne bacteria that in humans are the aetiological agents of Lyme disease and relapsing fever. Here we present the first genomes of B. turcica and B. tachyglossi, members of a recently described and rapidly expanding Borrelia clade associated with reptile (B. turcica) or echidna (B. tachyglossi) hosts, transmitted by hard ticks, and of unknown pathogenicity. Borrelia tachyglossi and B. turcica genomes are similar to those of relapsing fever Borrelia species, containing a linear ~ 900 kb chromosome, a single long (> 70 kb) linear plasmid, and numerous short (< 40 kb) linear and circular plasmids, as well as a suite of housekeeping and macronutrient biosynthesis genes which are not found in Lyme disease Borrelia. Additionally, both B. tachyglossi and B. turcica contain paralogous vsp and vlp proteins homologous to those used in the multiphasic antigen-switching system used by relapsing fever Borrelia to evade vertebrate immune responses, although their number was greatly reduced compared to human-infectious species. However, B. tachyglossi and B. turcica chromosomes also contain numerous genes orthologous to Lyme disease Borrelia-specific genes, demonstrating a unique evolutionary, and potentially phenotypic link between these groups. Borrelia tachyglossi and B. turcica genomes also have unique genetic features, including degraded and deleted tRNA modification genes, and an expanded range of macronutrient salvage and biosynthesis genes compared to relapsing fever and Lyme disease Borrelia. These genomes and genomic comparisons provide an insight into the biology and evolutionary origin of these Borrelia, and provide a valuable resource for future work.},
}

@article {pmid30240703,
year = {2018},
author = {Kyburz, A and Fallegger, A and Zhang, X and Altobelli, A and Artola-Boran, M and Borbet, T and Urban, S and Paul, P and Münz, C and Floess, S and Huehn, J and Cover, TL and Blaser, MJ and Taube, C and Müller, A},
title = {Trans-maternal Helicobacter pylori exposure reduces allergic airway inflammation in offspring through regulatory T-cells.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2018.07.046},
pmid = {30240703},
issn = {1097-6825},
abstract = {BACKGROUND: The trans-maternal exposure to tobacco, microbes, nutrients and other environmental factors shapes the fetal immune system through epigenetic processes. The gastric microbe Helicobacter pylori represents an ancestral constituent of the human microbiota that causes gastric disorders on the one hand, and is inversely associated with allergies and chronic inflammatory conditions on the other.

OBJECTIVE: Here, we investigate the consequences of trans-maternal exposure to H. pylori, in utero and/or during lactation, for susceptibility to viral and bacterial infection, predisposition to allergic airway inflammation, and the development of immune cell populations in the lung and lymphoid organs.

METHODS: We use experimental models of house dust mite- or ovalbumin-induced airway inflammation and influenza A virus or Citrobacter infection along with metagenomics analyses, multi-color flow cytometry and bilsufite pyrosequencing to study the effects of H. pylori on allergy severity and immunological and microbiome correlates thereof.

RESULTS: Perinatal exposure to H. pylori extract, or its immunomodulator VacA, confers robust protective effects against allergic airway inflammation not only in the first, but also the second offspring generation, but does not increase susceptibility to viral or bacterial infection. Immune correlates of allergy protection include skewing of regulatory over effector T-cells, expansion of Treg subsets expressing CXCR3 or RORγt, and demethylation of the FOXP3 locus. The composition and diversity of the gastrointestinal microbiota is measurably affected by perinatal H. pylori exposure.

CONCLUSION: We conclude that exposure to H. pylori has consequences not only for the carrier, but also for subsequent generations that may be exploited for interventional purposes.},
}

@article {pmid30240699,
year = {2018},
author = {Harris, L and van Zyl, LJ and Kirby-McCullough, BM and Damelin, LH and Tiemessen, CT and Trindade, M},
title = {Identification and sequence analysis of two novel cryptic plasmids isolated from the vaginal mucosa of South African women.},
journal = {Plasmid},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.plasmid.2018.09.008},
pmid = {30240699},
issn = {1095-9890},
abstract = {The vaginal mucosa is dominated by Gram positive, rod shaped lactobacilli which serve as a natural barrier against infection. In both healthy- and bacterial vaginosis (BV)-infected women Lactobacillus crispatus and Lactobacillus jensenii have been found to be the predominant Lactobacillus species. Many studies have been conducted to assess factors influencing lactobacilli dominance in the vaginal microbiome. In the present study two plasmids, pLc4 and pLc17, isolated from vaginal Lactobacillus strains of both healthy and BV-infected women were characterized. The smaller plasmid, pLc4 (4224 bp in size), was detected in both L. crispatus and L. jensenii strains, while pLc17 was only detected in L. crispatus. Based on its nucleotide sequence pLc4 appears highly novel, with its replication protein having 44% identity to the replication initiation protein of pSMQ173b_03. Phylogenetic analysis with other Rolling Circle Replication plasmids confirmed that pLc4 shows a low degree of similarity to these plasmids. Plasmid pLc17 (16,663 bp in size) appears to carry both a RCR replicon and a theta replicon, which is rare in naturally occurring plasmids. pLc4 was maintained at a high copy number of 29, while pLc17 appears to be a medium copy number plasmid maintained at 11 copies per chromosome. While sequence analysis is a valuable tool to study cryptic plasmids, further function-based analysis will be required in order to fully elucidate the role of these plasmids within the vaginal milieu.},
}

@article {pmid30240114,
year = {2018},
author = {Bergner, LM and Orton, RJ and da Silva Filipe, A and Shaw, AE and Becker, DJ and Tello, C and Biek, R and Streicker, DG},
title = {Using non-invasive metagenomics to characterize viral communities from wildlife.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.12946},
pmid = {30240114},
issn = {1755-0998},
abstract = {Microbial communities play an important role in organismal and ecosystem health. While high throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses present and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from non-invasively collected fecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in fetal bovine serum, we recommend storing swabs in RNALater or another non-biological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNAse treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time. This article is protected by copyright. All rights reserved.},
}

@article {pmid30240049,
year = {2018},
author = {Wackett, LP},
title = {Global microbial metagenomics: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.},
journal = {Environmental microbiology},
volume = {20},
number = {8},
pages = {3127-3128},
doi = {10.1111/1462-2920.14402},
pmid = {30240049},
issn = {1462-2920},
}

@article {pmid30239621,
year = {2018},
author = {Zinter, MS and Dvorak, CC and Mayday, MY and Iwanaga, K and Ly, NP and McGarry, ME and Church, GD and Faricy, LE and Rowan, CM and Hume, JR and Steiner, ME and Crawford, ED and Langelier, C and Kalantar, K and Chow, ED and Miller, S and Shimano, K and Melton, A and Yanik, GA and Sapru, A and DeRisi, JL},
title = {Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciy802},
pmid = {30239621},
issn = {1537-6591},
abstract = {Background: Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next generation sequencing assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children.

Methods: We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at three children's hospitals from 2014-2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the NCBI nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort.

Results: We identified a rich cross-domain pulmonary microbiome containing bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median 0.61, IQR 0.33-0.72 vs. median 0.96, IQR 0.94-0.96, p<0.001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (p<0.001).

Conclusions: An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.},
}

@article {pmid30239587,
year = {2018},
author = {Zou, Q and Lin, G and Jiang, X and Liu, X and Zeng, X},
title = {Sequence clustering in bioinformatics: an empirical study.},
journal = {Briefings in bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bib/bby090},
pmid = {30239587},
issn = {1477-4054},
abstract = {Sequence clustering is a basic bioinformatics task that is attracting renewed attention with the development of metagenomics and microbiomics. The latest sequencing techniques have decreased costs and as a result, massive amounts of DNA/RNA sequences are being produced. The challenge is to cluster the sequence data using stable, quick and accurate methods. For microbiome sequencing data, 16S ribosomal RNA operational taxonomic units are typically used. However, there is often a gap between algorithm developers and bioinformatics users. Different software tools can produce diverse results and users can find them difficult to analyze. Understanding the different clustering mechanisms is crucial to understanding the results that they produce. In this review, we selected several popular clustering tools, briefly explained the key computing principles, analyzed their characters and compared them using two independent benchmark datasets. Our aim is to assist bioinformatics users in employing suitable clustering tools effectively to analyze big sequencing data. Related data, codes and software tools were accessible at the link http://lab.malab.cn/∼lg/clustering/.},
}

@article {pmid30237139,
year = {2018},
author = {Obbard, DJ},
title = {Expansion of the metazoan virosphere: progress, pitfalls, and prospects.},
journal = {Current opinion in virology},
volume = {31},
number = {},
pages = {17-23},
doi = {10.1016/j.coviro.2018.08.008},
pmid = {30237139},
issn = {1879-6265},
abstract = {Metagenomic sequencing has led to a recent and rapid expansion of the animal virome. It has uncovered a multitude of new virus lineages from under-sampled host groups, including many that break up long branches in the virus tree, and many that display unexpected genome sizes and structures. Although there are challenges to inferring the existence of a virus from a `virus-like sequence', in the absence of an isolate the analysis of nucleic acid (including small RNAs) and sequence data can provide considerable confidence. As a consequence, this period of molecular natural history is helping to reshape our views of deep virus evolution.},
}

@article {pmid30237098,
year = {2018},
author = {Varsani, A and Lefeuvre, P and Roumagnac, P and Martin, D},
title = {Notes on recombination and reassortment in multipartite/segmented viruses.},
journal = {Current opinion in virology},
volume = {33},
number = {},
pages = {156-166},
doi = {10.1016/j.coviro.2018.08.013},
pmid = {30237098},
issn = {1879-6265},
abstract = {Besides evolving through nucleotide substitution, viruses frequently also evolve by genetic recombination which can occur when related viral variants co-infect the same cells. Viruses with segmented or multipartite genomes can additionally evolve via the reassortment of genomic components. Various computational techniques are now available for identifying and characterizing recombination and reassortment. While these techniques have revealed both that all well studied segmented and multipartite virus species show some capacity for reassortment, and that recombination is common in many multipartite species, they have indicated that recombination is either rare or does not occur in species with segmented genomes. Reassortment and recombination can make it very difficult to study segmented/multipartite viruses using metagenomics-based approaches. Notable challenges include, both the accurate identification and assignment of genomic components to individual genomes, and the differentiation between natural 'real' recombination events and artifactual 'fake' recombination events arising from the inaccurate de novo assembly of genome component sequences determined using short read sequencing.},
}

@article {pmid30236898,
year = {2018},
author = {Pasin, F and Tseng, XA and Bedoya, LC and Heydarnejad, J and Deng, TC and García, JA and Chen, YR},
title = {Streamlined generation of plant virus infectious clones using the pLX mini binary vectors.},
journal = {Journal of virological methods},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jviromet.2018.09.007},
pmid = {30236898},
issn = {1879-0984},
abstract = {Recent metagenomic surveys have provided unprecedented amounts of data which have revolutionized our understanding of virus evolution and diversity. Infectious clones are powerful tools to aid the biological characterization of viruses. We have recently described the pLX vectors, a set of mini binary T-DNA vectors (~3 kb) that includes strong bacterial terminators and a minimal replicon from the broad-host-range plasmid pBBR1, which autonomously replicate in both Escherichia coli and Agrobacterium tumefaciens. In this study, a workflow that encompassed pLX binary vectors, overlap-based assembly strategies and sequencing-by-synthesis verification steps is described and applied for the streamlined generation of infectious clones suitable for Agrobacterium-mediated delivery. The pLX-based vectors herein assembled include the first infectious clone of Wasabi mottle virus, a crucifer-infecting tobamovirus, as well as binary clones of positive-single-stranded RNA and single- and double-stranded DNA viruses from the Potyviridae, Geminiviridae and Caulimoviridae families, respectively. Finally, the clones generated were used to agro-inoculate the model plant Arabidopsis thaliana and infections were confirmed by a multiplex RT-PCR assay. This workflow facilitated the rapid generation of infectious clones which, together with agro-infection scalability, would allow the pursuit of systematic insights into virus biology and physiology of plant infections and the design of novel biotechnological applications.},
}

@article {pmid30235593,
year = {2019},
author = {Shu, D and Guo, J and Zhang, B and He, Y and Wei, G},
title = {rDNA- and rRNA-derived communities present divergent assemblage patterns and functional traits throughout full-scale landfill leachate treatment process trains.},
journal = {The Science of the total environment},
volume = {646},
number = {},
pages = {1069-1079},
doi = {10.1016/j.scitotenv.2018.07.388},
pmid = {30235593},
issn = {1879-1026},
abstract = {Understanding the influences of microbial interactions and niche heterogeneities on microbial communities and functional traits is critical for determining its engineering and ecological significance. However, little is known about microbial community assemblage and functional gene expression throughout full-scale landfill leachate treatment plants. Here, we applied a combination of 16S rRNA and rDNA amplicon sequencing, shotgun metagenomic, and qPCR approaches to unveil the ecological associations between distinct communities, functional gene expression and nitrogen cycling processes. By comparing the rDNA and rRNA-derived communities, the rRNA/rDNA ratios suggested that 57.2% of rare taxa were active, and their abundance decreased as increasing of potential activities. In particular, rDNA- and rRNA-based communities exhibited divergent assemblage patterns, and stronger intra-associations among core taxa in the rRNA-based communities than in rDNA-based communities. Furthermore, results regarding both bacterial assemblage and functional traits indicated that the habitat filtering and niche differentiation (treatment units) exerted selection on microbial communities based on functional traits, particular for key ecological functions related to nitrogen cycling. Collectively, our findings provide insights into structure-function associations at the local level and shed light on ecological rules guiding rDNA- and rRNA-based community assembly in landfill leachate treatment systems.},
}

@article {pmid30233538,
year = {2018},
author = {Black, EM and Just, CL},
title = {The Genomic Potentials of NOB and Comammox Nitrospira in River Sediment Are Impacted by Native Freshwater Mussels.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2061},
doi = {10.3389/fmicb.2018.02061},
pmid = {30233538},
issn = {1664-302X},
abstract = {Freshwater mussel assemblages of the Upper Mississippi River (UMR) sequester tons of ammonia- and urea-based biodeposits each day and aerate sediment through burrowing activities, thus creating a unique niche for nitrogen (N) cycling microorganisms. This study explored how mussels impact the abundance of N-cycling species with an emphasis on Candidatus Nitrospira inopinata, the first microorganism known to completely oxidize ammonia (comammox) to nitrate. This study used metagenomic shotgun sequencing of genomic DNA to compare nitrogen cycling species in sediment under a well-established mussel assemblage and in nearby sediment without mussels. Metagenomic reads were aligned to the prokaryotic RefSeq non-redundant protein database using BLASTx, taxonomic binning was performed using the weighted lowest common ancestor algorithm, and protein-coding genes were categorized by metabolic function using the SEED subsystem. Linear discriminant analysis (LDA) effect sizes were used to determine which metagenomes and metabolic features explained the most differences between the mussel habitat sediment and sediment without mussels. Of the N-cycling species deemed differentially abundant, Nitrospira moscoviensis and "Candidatus Nitrospira inopinata" were responsible for creating a distinctive N-cycling microbiome in the mussel habitat sediment. Further investigation revealed that comammox Nitrospira had a large metabolic potential to degrade mussel biodeposits, as evidenced the top ten percent of protein-coding genes including the cytochrome c-type biogenesis protein required for hydroxylamine oxidation, ammonia monooxygenase, and urea decomposition SEED subsystems. Genetic marker analysis of these two Nitrospira taxons suggested that N. moscoviensis was most impacted by diverse carbon metabolic processes while "Candidatus Nitrospira inopinata" was most distinguished by multidrug efflux proteins (AcrB), NiFe hydrogenase (HypF) used in hydrogen oxidation and sulfur reduction coupled reactions, and a heme chaperone (CcmE). Furthermore, our research suggests that comammox and NOB Nitrospira likely coexisted by utilizing mixotrophic metabolisms. For example, "Candidatus Nitrospira inopinata" had the largest potentials for ammonia oxidation, nitrite reduction with NirK, and hydrogen oxidation, while NOB Nitrospira had the greatest potential for nitrite oxidation, and nitrate reduction possibly coupled with formate oxidation. Overall, our results suggest that this mussel habitat sediment harbors a niche for NOB and comammox Nitrospira, and ultimately impacts N-cycling in backwaters of the UMR.},
}

@article {pmid30233528,
year = {2018},
author = {Clerissi, C and Brunet, S and Vidal-Dupiol, J and Adjeroud, M and Lepage, P and Guillou, L and Escoubas, JM and Toulza, E},
title = {Protists Within Corals: The Hidden Diversity.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2043},
doi = {10.3389/fmicb.2018.02043},
pmid = {30233528},
issn = {1664-302X},
abstract = {Previous observations suggested that microbial communities contribute to coral health and the ecological resilience of coral reefs. However, most studies of coral microbiology focused on prokaryotes and the endosymbiotic algae Symbiodinium. In contrast, knowledge concerning diversity of other protists is still lacking, possibly due to methodological constraints. As most eukaryotic DNA in coral samples was derived from hosts, protist diversity was missed in metagenome analyses. To tackle this issue, we designed blocking primers for Scleractinia sequences amplified with two primer sets that targeted variable loops of the 18S rRNA gene (18SV1V2 and 18SV4). These blocking primers were used on environmental colonies of Pocillopora damicornis sensu lato from two regions with contrasting thermal regimes (Djibouti and New Caledonia). In addition to Symbiodinium clades A/C/D, Licnophora and unidentified coccidia genera were found in many samples. In particular, coccidian sequences formed a robust monophyletic clade with other protists identified in Agaricia, Favia, Montastraea, Mycetophyllia, Porites, and Siderastrea coral colonies. Moreover, Licnophora and coccidians had different distributions between the two geographic regions. A similar pattern was observed between Symbiodinium clades C and A/D. Although we were unable to identify factors responsible for this pattern, nor were we able to confirm that these taxa were closely associated with corals, we believe that these primer sets and the associated blocking primers offer new possibilities to describe the hidden diversity of protists within different coral species.},
}

@article {pmid30233525,
year = {2018},
author = {Guajardo-Leiva, S and Pedrós-Alió, C and Salgado, O and Pinto, F and Díez, B},
title = {Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2039},
doi = {10.3389/fmicb.2018.02039},
pmid = {30233525},
issn = {1664-302X},
abstract = {Cyanophages are viruses with a wide distribution in aquatic ecosystems, that specifically infect Cyanobacteria. These viruses can be readily isolated from marine and fresh waters environments; however, their presence in cosmopolitan thermophilic phototrophic mats remains largely unknown. This study investigates the morphological diversity (TEM), taxonomic composition (metagenomics), and active infectivity (metatranscriptomics) of viral communities over a thermal gradient in hot spring phototrophic mats from Northern Patagonia (Chile). The mats were dominated (up to 53%) by cosmopolitan thermophilic filamentous true-branching cyanobacteria from the genus Mastigocladus, the associated viral community was predominantly composed of Caudovirales (70%), with most of the active infections driven by cyanophages (up to 90% of Caudovirales transcripts). Metagenomic assembly lead to the first full genome description of a T7-like Thermophilic Cyanophage recovered from a hot spring (Porcelana Hot Spring, Chile), with a temperature of 58°C (TC-CHP58). This could potentially represent a world-wide thermophilic lineage of podoviruses that infect cyanobacteria. In the hot spring, TC-CHP58 was active over a temperature gradient from 48 to 66°C, showing a high population variability represented by 1979 single nucleotide variants (SNVs). TC-CHP58 was associated to the Mastigocladus spp. by CRISPR spacers. Marked differences in metagenomic CRISPR loci number and spacers diversity, as well as SNVs, in the TC-CHP58 proto-spacers at different temperatures, reinforce the theory of co-evolution between natural virus populations and cyanobacterial hosts. Considering the importance of cyanobacteria in hot spring biogeochemical cycles, the description of this new cyanopodovirus lineage may have global implications for the functioning of these extreme ecosystems.},
}

@article {pmid30233512,
year = {2018},
author = {Fernández, J and Moreno, FJ and Olano, A and Clemente, A and Villar, CJ and Lombó, F},
title = {A Galacto-Oligosaccharides Preparation Derived From Lactulose Protects Against Colorectal Cancer Development in an Animal Model.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2004},
doi = {10.3389/fmicb.2018.02004},
pmid = {30233512},
issn = {1664-302X},
abstract = {Colorectal cancer (CRC) is one of the most common neoplasias worldwide, and its incidence is increasing. Consumption of prebiotics is a useful strategy in order to prevent this important disease. These nutraceutical compounds might exert protective biological functions as antitumors. In order to test the chemopreventive effect of GOS-Lu (galacto-oligosaccharides derived from lactulose) prebiotic preparation against this cancer, an animal model (Rattus norvegicus F344) was used. In this model, two doses of azoxymethane (10 mg/kg) and two treatments with dextran sodium sulfate (DSS) were administered to the animals. Animals were fed for 20 weeks, and either control drinking water or drinking water containing 10% (w/w) GOS-Lu prebiotic preparation was provided to them. Animals were sacrificed after those 20 weeks, and their digestive tract tissues were analyzed. The results revealed a statistically significant reduction in the number of colon tumors in the GOS-Lu cohort with respect to control animals. Metagenomics sequencing was used for studying colon microbiota populations, revealing significant reductions in populations of pro-inflammatory bacteria families and species, and significant increases in interesting beneficial populations, such as Bifidobacterium. Therefore, oral administration of the prebiotic GOS-Lu preparation may be an effective strategy for preventing CRC.},
}

@article {pmid30232199,
year = {2018},
author = {Goltsman, DSA and Sun, CL and Proctor, DM and DiGiulio, DB and Robaczewska, A and Thomas, BC and Shaw, GM and Stevenson, DK and Holmes, SP and Banfield, JF and Relman, DA},
title = {Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.236000.118},
pmid = {30232199},
issn = {1549-5469},
abstract = {Recent studies suggest that the microbiome has an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an assembly-driven, metagenomics-based, longitudinal study of the vaginal, gut, and oral microbiomes in 292 samples from 10 subjects sampled every three weeks throughout pregnancy. Nonhuman sequences in the amount of 1.53 Gb were assembled into scaffolds, and functional genes were predicted for gene- and pathway-based analyses. Vaginal assemblies were binned into 97 draft quality genomes. Redundancy analysis (RDA) of microbial community composition at all three body sites revealed gestational age to be a significant source of variation in patterns of gene abundance. In addition, health complications were associated with variation in community functional gene composition in the mouth and gut. The diversity of Lactobacillus iners-dominated communities in the vagina, unlike most other vaginal community types, significantly increased with gestational age. The genomes of co-occurring Gardnerella vaginalis strains with predicted distinct functions were recovered in samples from two subjects. In seven subjects, gut samples contained strains of the same Lactobacillus species that dominated the vaginal community of that same subject and not other Lactobacillus species; however, these within-host strains were divergent. CRISPR spacer analysis suggested shared phage and plasmid populations across body sites and individuals. This work underscores the dynamic behavior of the microbiome during pregnancy and suggests the potential importance of understanding the sources of this behavior for fetal development and gestational outcome.},
}

@article {pmid30232167,
year = {2018},
author = {Ingala, MR and Simmons, NB and Perkins, SL},
title = {Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals.},
journal = {mSphere},
volume = {3},
number = {5},
pages = {},
doi = {10.1128/mSphere.00397-18},
pmid = {30232167},
issn = {2379-5042},
abstract = {Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome.},
}

@article {pmid30232133,
year = {2018},
author = {Wylie, KM and Wylie, TN and Buller, R and Herter, B and Cannella, MT and Storch, GA},
title = {Detection of Viruses in Clinical Samples Using Metagenomic Sequencing and Targeted Sequence Capture.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JCM.01123-18},
pmid = {30232133},
issn = {1098-660X},
abstract = {Metagenomic shotgun sequencing (MSS) is a revolutionary approach to viral diagnostic testing that allows simultaneous detection of a broad range of viruses, detailed taxonomic assignment, and detection of mutations associated with antiviral drug resistance. To enhance sensitivity for virus detection, we previously developed ViroCap, a targeted sequence capture panel designed to enrich nucleic acid from a comprehensive set of eukaryotic viruses prior to sequencing. To demonstrate the utility of MSS with targeted sequence capture for detecting clinically important viruses and characterizing clinically important viral features, we used ViroCap to analyze clinical samples from a diagnostic virology laboratory containing a broad range of medically relevant viruses. From 26 samples, MSS with ViroCap detected all of the expected viruses and 30 additional viruses. Comparing sequencing after capture enrichment with standard MSS, we detected 13 viruses only with capture enrichment and observed a consistent increase in number and percentage of viral sequence reads as well as breadth and depth of coverage of the viral genomes. Compared with clinical testing, MSS enhanced taxonomic assignment for 15 viruses, and codons associated with antiviral drug resistance in influenza A, HSV, HIV, and HCV could be analyzed. Overall, in clinical samples, MSS with targeted sequence capture provides enhanced virus detection and information of clinical and epidemiologic relevance compared with clinical testing and MSS without targeted sequence capture.},
}

@article {pmid30231979,
year = {2018},
author = {Hill, AA and Diehl, GE},
title = {Identifying the Patterns of Pattern Recognition Receptors.},
journal = {Immunity},
volume = {49},
number = {3},
pages = {389-391},
doi = {10.1016/j.immuni.2018.08.027},
pmid = {30231979},
issn = {1097-4180},
abstract = {Intestinal homeostasis requires microbial recognition that results in appropriate responses to commensals and pathogens. In this issue of Immunity, Price et al. (2018) map the in vivo expression of five toll-like receptors (TLR) in intestinal epithelia, revealing distinct spatio-temporal expression patterns that shape responses to TLR ligands.},
}

@article {pmid30231921,
year = {2018},
author = {Vavourakis, CD and Andrei, AS and Mehrshad, M and Ghai, R and Sorokin, DY and Muyzer, G},
title = {A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {168},
doi = {10.1186/s40168-018-0548-7},
pmid = {30231921},
issn = {2049-2618},
support = {322551//European Research Council/International ; 322551//European Research Council/International ; L200961651//Czech Academy of Science/ ; 16-14-00121//Russian Science Support Foundation/ ; 24002002//Dutch Ministry of Education and Science/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 17-04828S//Grant Agency of the Czech Republic/ ; },
abstract = {BACKGROUND: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.

RESULTS: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.

CONCLUSIONS: Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.},
}

@article {pmid30231528,
year = {2018},
author = {Claverie, JM and Abergel, C},
title = {Mimiviridae: An Expanding Family of Highly Diverse Large dsDNA Viruses Infecting a Wide Phylogenetic Range of Aquatic Eukaryotes.},
journal = {Viruses},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/v10090506},
pmid = {30231528},
issn = {1999-4915},
support = {10-INSB0009; ANR-11-INSB0013,//Agence Nationale de la Recherche/ ; OTP51251//Fondation Bettencourt Schueller/ ; },
abstract = {Since 1998, when Jim van Etten's team initiated its characterization, Paramecium bursaria Chlorella virus 1 (PBCV-1) had been the largest known DNA virus, both in terms of particle size and genome complexity. In 2003, the Acanthamoeba-infecting Mimivirus unexpectedly superseded PBCV-1, opening the era of giant viruses, i.e., with virions large enough to be visible by light microscopy and genomes encoding more proteins than many bacteria. During the following 15 years, the isolation of many Mimivirus relatives has made Mimiviridae one of the largest and most diverse families of eukaryotic viruses, most of which have been isolated from aquatic environments. Metagenomic studies of various ecosystems (including soils) suggest that many more remain to be isolated. As Mimiviridae members are found to infect an increasing range of phytoplankton species, their taxonomic position compared to the traditional Phycodnaviridae (i.e., etymologically "algal viruses") became a source of confusion in the literature. Following a quick historical review of the key discoveries that established the Mimiviridae family, we describe its current taxonomic structure and propose a set of operational criteria to help in the classification of future isolates.},
}

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

@article {pmid30230256,
year = {2018},
author = {Kenward, PA and Simister, RL and Morgan-Lang, C and Finke, N and Sturm, A and Hallam, SJ and Crowe, SA},
title = {Recovering cellular biomass from fluids using chemical flocculation.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12690},
pmid = {30230256},
issn = {1758-2229},
abstract = {We developed an efficient, scalable, and inexpensive method for recovering cellular biomass from complex fluid matrices that cannot be processed using conventional filtration methods. The method uses chemical flocculation with iron oxyhydroxides, is capable of recovering >90% of cellular biomass from fluids with more than 103 cells ml-1 , and was validated using both mock communities and field samples. High quality DNA can be readily extracted from iron flocs using standard soil extraction kits. We applied chemical flocculation to fracing fluids from British Columbia, Canada, and recovered a diversity of microbial taxa including abundant members of the Epsilon- and Deltaproteobacteria previously recovered from shale gas operations in the United States. Application of chemical flocculation presents new opportunities for scalable time-series monitoring and experimentation on complex fluid matrices including microbial community profiling and shotgun metagenomics over gas production well completion cycles. This article is protected by copyright. All rights reserved.},
}

@article {pmid30230202,
year = {2018},
author = {Schultz-Johansen, M and Cueff, M and Hardouin, K and Jam, M and Larocque, R and Glaring, MA and Hervé, C and Czjzek, M and Stougaard, P},
title = {Discovery and screening of novel metagenome-derived GH107 enzymes targeting sulfated fucans from brown algae.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.14662},
pmid = {30230202},
issn = {1742-4658},
abstract = {Sulfated fucans, often denoted fucoidans, are highly variable cell wall polysaccharides of brown algae, which possess a wide range of bioactive properties with potential pharmaceutical applications. Due to their complex architecture, the structures of algal fucans have until now only been partly determined. Enzymes capable of hydrolyzing sulfated fucans may allow specific release of defined bioactive oligosaccharides and may serve as a tool for structural elucidation of algal walls. Currently, such enzymes include only a few hydrolases belonging to the glycoside hydrolase family 107 (GH107), and little is known about their mechanistics and the substrates they degrade. In this study, we report the identification and recombinant production of three novel GH107 family proteins derived from a marine metagenome. Activity screening against a large substrate collection showed that all three enzymes degraded sulfated fucans from brown algae in the order Fucales. This is in accordance with a hydrolytic activity against α-1,4-fucosidic linkages in sulfated fucans as reported for previous GH107 members. Also, the activity screening gave new indications about the structural differences of brown algal cell walls. Finally, sequence analyses allowed identification of the proposed catalytic residues of the GH107 family. The findings presented here form a new basis for understanding the GH107 family of enzymes and investigating the complex sulfated fucans from brown algae. This article is protected by copyright. All rights reserved.},
}

@article {pmid30228802,
year = {2018},
author = {Gacesa, R and Baranasic, D and Starcevic, A and Diminic, J and Korlević, M and Najdek, M and Blažina, M and Oršolić, D and Kolesarić, D and Long, PF and Cullum, J and Hranueli, D and Orlic, S and Zucko, J},
title = {Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from 
Northern Adriatic Sea Sediments.},
journal = {Food technology and biotechnology},
volume = {56},
number = {2},
pages = {270-277},
doi = {10.17113/ftb.56.02.18.5393},
pmid = {30228802},
issn = {1330-9862},
abstract = {Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been enriched using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (http://redpet.bioinfo.pbf.hr/REDPET), which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. The use of this system for bioprospecting was exemplified using potential alkB and almA genes from this library.},
}

@article {pmid30228361,
year = {2018},
author = {Mangifesta, M and Mancabelli, L and Milani, C and Gaiani, F and de'Angelis, N and de'Angelis, GL and van Sinderen, D and Ventura, M and Turroni, F},
title = {Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13974},
doi = {10.1038/s41598-018-32413-2},
pmid = {30228361},
issn = {2045-2322},
abstract = {The human intestine retains a complex microbial ecosystem, which performs crucial functions that impact on host health. Several studies have indicated that intestinal dysbiosis may impact on the establishment of life-threatening intestinal diseases such as colorectal cancer. An adenomatous polyp is the result of abnormal tissue growth, which is benign but is considered to be associated with a high risk of developing colorectal cancer, based on its grade of dysplasia. Development of diagnostic tools that are based on surveying the gut microbiota and are aimed at early detection of colorectal cancer represent highly desirable target. For this purpose, we performed a pilot study in which we applied a metataxonomic analysis based on 16S rRNA gene sequencing approach to unveil the composition of microbial communities of intestinal polyps. Moreover, we performed a meta-analysis involving the reconstructed microbiota composition of adenomatous polyps and publicly available metagenomics datasets of colorectal cancer. These analyses allowed the identification of microbial taxa such as Faecalibacterium, Bacteroides and Romboutsia, which appear to be depleted in cancerogenic mucosa as well as in adenomatous polyps, thus representing novel microbial biomarkers associated with early tumor formation. Furthermore, an absolute quantification of Fusubacterium nucleatum in polyps further compounded the important role of this microorganism as a valuable putative microbial biomarker for early diagnosis of colorectal cancer.},
}

@article {pmid30228235,
year = {2018},
author = {Getz, EW and Tithi, SS and Zhang, L and Aylward, FO},
title = {Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum.},
journal = {mBio},
volume = {9},
number = {5},
pages = {},
doi = {10.1128/mBio.01089-18},
pmid = {30228235},
issn = {2150-7511},
abstract = {Diverse bacterial and archaeal lineages drive biogeochemical cycles in the global ocean, but the evolutionary processes that have shaped their genomic properties and physiological capabilities remain obscure. Here we track the genome evolution of the globally abundant marine bacterial phylum Marinimicrobia across its diversification into modern marine environments and demonstrate that extant lineages are partitioned between epipelagic and mesopelagic habitats. Moreover, we show that these habitat preferences are associated with fundamental differences in genomic organization, cellular bioenergetics, and metabolic modalities. Multiple lineages present in epipelagic niches independently acquired genes necessary for phototrophy and environmental stress mitigation, and their genomes convergently evolved key features associated with genome streamlining. In contrast, lineages residing in mesopelagic waters independently acquired nitrate respiratory machinery and a variety of cytochromes, consistent with the use of alternative terminal electron acceptors in oxygen minimum zones (OMZs). Further, while epipelagic clades have retained an ancestral Na+-pumping respiratory complex, mesopelagic lineages have largely replaced this complex with canonical H+-pumping respiratory complex I, potentially due to the increased efficiency of the latter together with the presence of the more energy-limiting environments deep in the ocean's interior. These parallel evolutionary trends indicate that key features of genomic streamlining and cellular bioenergetics have occurred repeatedly and congruently in disparate clades and underscore the importance of environmental conditions and nutrient dynamics in driving the evolution of diverse bacterioplankton lineages in similar ways throughout the global ocean.IMPORTANCE Understanding long-term patterns of microbial evolution is critical to advancing our knowledge of past and present role microbial life in driving global biogeochemical cycles. Historically, it has been challenging to study the evolution of environmental microbes due to difficulties in obtaining genome sequences from lineages that could not be cultivated, but recent advances in metagenomics and single-cell genomics have begun to obviate many of these hurdles. Here we present an evolutionary genomic analysis of the Marinimicrobia, a diverse bacterial group that is abundant in the global ocean. We demonstrate that distantly related Marinimicrobia species that reside in similar habitats have converged to assume similar genome architectures and cellular bioenergetics, suggesting that common factors shape the evolution of a broad array of marine lineages. These findings broaden our understanding of the evolutionary forces that have given rise to microbial life in the contemporary ocean.},
}

@article {pmid30227944,
year = {2018},
author = {Storci, G and De Carolis, S and Olivieri, F and Bonafè, M},
title = {Changes in the biochemical taste of cytoplasmic and cell-free DNA are major fuels for inflamm-aging.},
journal = {Seminars in immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.smim.2018.08.003},
pmid = {30227944},
issn = {1096-3618},
abstract = {Inflamm-aging depicts the progressive activation of the innate immune system that accompanies human aging. Its role as a disease-predisposing condition has been proposed, but its molecular basis is still poorly understood. A wealth of literature conveys that, particularly upon stress, nuclear and mitochondrial genomes are released into the cytoplasmic and extracellular compartments. Cytoplasmic (cy) and cell-free (cf) DNA pools trigger inflammation and innate immunity at local and systemic level. In particular, cyDNA plays a crucial role in the phenomenon of cell senescence and in the cognate pro-inflammatory secretome. Here we propose that changes in a variety of biochemical characteristics "tastes" of cy- and cf-DNA (e.g. the amount of 8-oxo-deoxy-guanosine and 5-methyl-deoxy-cytosine, the proportion of DNA hybridized with RNA) potentially affect the capability of these DNA pools to ignite the innate immune system. We also underpin that telomeric sequences are major components of the cy/cfDNA payload. Telomere shortening, a hallmark of aging, causes the depletion of telomeric sequences in cy/cfDNA pool, thus unleashing their potential to exert an age-related activation of the innate immune system. Finally, we posit that various sources of DNA (extracellular vesicles, the commensal metagenome and food) contribute to the cy/cfDNA payloads. We speculate that changes in the biochemical "taste" of cy/cfDNA are major modifiers of inflamm-aging.},
}

@article {pmid30227146,
year = {2018},
author = {Masuda, T and Sunaga, F and Naoi, Y and Ito, M and Takagi, H and Katayama, Y and Omatsu, T and Oba, M and Sakaguchi, S and Furuya, T and Yamasato, H and Shirai, J and Makino, S and Mizutani, T and Nagai, M},
title = {Whole genome analysis of a novel picornavirus related to the Enterovirus/Sapelovirus supergroup from porcine feces in Japan.},
journal = {Virus research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virusres.2018.09.003},
pmid = {30227146},
issn = {1872-7492},
abstract = {A novel virus related to the Enterovirus/Sapelovirus supergroup in the family Picornaviridae was identified in healthy porcine feces in Japan by using a metagenomics approach. The genome of the virus, named Sapelo-like porcine picornavirus Japan (SPPVJ) Pig/Isi-Im1/JPN/2016, had a type-IV internal ribosomal entry site and carried a 6,978-nucleotide-long single open reading frame encoding a 2,326 amino acids (aa) polyprotein precursor. The coding sequence region consisted of leader protein (68 aa), a structural protein region P1 (824 aa), and the non-structural protein regions P2 (672 aa) and P3 (762 aa). Among representative picornaviruses, the P1, 2C, and 3CD regions of SPPVJ had the highest aa identities of 64.4%, 61.9%, and 73.3%, respectively, with the corresponding regions of sapelo-like bat picornavirus BtVs-PicoV/SC2013. Sequencing analysis of the RT-PCR products derived from the 5' untranslated and 3D regions revealed the presence of SPPVJ in 17.8% (19/107) of the feces from healthy and diarrheal pigs in 12 farms in 2015-2016. Further studies are needed to determine the origin and pathogenic potential of SPPJV in pigs and other mammals.},
}

@article {pmid30225519,
year = {2018},
author = {Wang, Y and Yang, S and Liu, D and Zhou, C and Li, W and Lin, Y and Wang, X and Shen, Q and Wang, H and Li, C and Zong, M and Ding, Y and Song, Q and Deng, X and Qi, D and Zhang, W and Delwart, E},
title = {The fecal virome of red-crowned cranes.},
journal = {Archives of virology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00705-018-4037-x},
pmid = {30225519},
issn = {1432-8798},
support = {No. 2017YFC1200201//National Key Research and Development Programs of China/ ; No. 81741062//National Natural Science Foundation of China/ ; No. BE2017693//Jiangsu Provincial Key Research and Development Projects/ ; No. 12JDG085//the Professional Research Foundation for Advanced Talents of Jiangsu University/ ; No. 13JDG087//the Professional Research Foundation for Advanced Talents of Jiangsu University/ ; No. 1302058C//the Postdoctoral Foundation of Jiangsu Province/ ; No. 1302057C//the Postdoctoral Foundation of Jiangsu Province/ ; No. 2014M561597//Postdoctoral Research Foundation of China/ ; },
abstract = {The red-crowned crane is one of the rarest crane species, and its population is decreasing due to loss of habitat, poisoning, and infections. Using a viral metagenomics approach, we analyzed the virome of feces from wild and captive red-crowned cranes, which were pooled separately. Vertebrate viruses belonging to the families Picornaviridae, Parvoviridae, Circoviridae, and Caliciviridae were detected. Among the members of the family Picornaviridae, we found three that appear to represent new genera. Six nearly complete genomes from members of the family Parvoviridae were also obtained, including four new members of the proposed genus "Chapparvovirus", and two members of the genus Aveparvovirus. Six small circular DNA genomes were also characterized. One nearly complete genome showing a low level of sequence identity to caliciviruses was also characterized. Numerous viruses believed to infect insects, plants, and crustaceans were also identified, which were probably derived from the diet of red-crowned cranes. This study increases our understanding of the enteric virome of red-crowned cranes and provides a baseline for comparison to those of other birds or following disease outbreaks.},
}

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

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

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

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

@article {pmid29404836,
year = {2018},
author = {Boers, SA and de Zeeuw, M and Jansen, R and van der Schroeff, MP and van Rossum, AMC and Hays, JP and Verhaegh, SJC},
title = {Characterization of the nasopharyngeal and middle ear microbiota in gastroesophageal reflux-prone versus gastroesophageal reflux non-prone children.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {37},
number = {5},
pages = {851-857},
doi = {10.1007/s10096-017-3178-2},
pmid = {29404836},
issn = {1435-4373},
mesh = {Bacterial Typing Techniques ; Biodiversity ; Child ; Child, Preschool ; Ear, Middle/*microbiology ; Female ; Gastroesophageal Reflux/*complications ; Humans ; Infant ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Nasopharyngitis/diagnosis/*etiology ; Nasopharynx/*microbiology ; Otitis Media/diagnosis/*etiology ; RNA, Ribosomal, 16S ; },
abstract = {Otitis media (OM) is one of the most common pediatric infections worldwide, but the complex microbiology associated with OM is poorly understood. Previous studies have shown an association between OM and gastroesophageal reflux (GER) in children. Therefore, in order to bridge the gap in our current understanding of the interaction between GER and OM, we investigated the nasopharyngeal and middle ear microbiota of children suffering from GER-associated OM and OM only, using culture-independent 16S rRNA gene sequencing. Middle ear fluid, nasopharyngeal swabs, and clinical data were collected as part of a prospective pilot study conducted at the Department of Otorhinolaryngology of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands. A total of 30 children up to 12 years of age who suffered from recurrent acute otitis media (AOM) (5), chronic otitis media with effusion (OME) (23), or both (2), and who were listed for tympanostomy tube placement, were included in the study. Nine children were included in the GER-associated OM cohort and 21 in the OM-only cohort. We found no obvious effect of GER on the nasopharyngeal and middle ear microbiota between the two groups of children. However, our results highlight the need to assess the true role of Alloiococcus spp. and Turicella spp. in children presenting with a high prevalence of recurrent AOM and chronic OME.},
}

Bacterial Typing Techniques
Biodiversity
Child
Child, Preschool
Ear, Middle/*microbiology
Female
Gastroesophageal Reflux/*complications
Humans
Infant
Male
Metagenome
Metagenomics/methods
*Microbiota
Nasopharyngitis/diagnosis/*etiology
Nasopharynx/*microbiology
Otitis Media/diagnosis/*etiology
RNA, Ribosomal, 16S

@article {pmid29340898,
year = {2018},
author = {Mirande, C and Bizine, I and Giannetti, A and Picot, N and van Belkum, A},
title = {Epidemiological aspects of healthcare-associated infections and microbial genomics.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {37},
number = {5},
pages = {823-831},
doi = {10.1007/s10096-017-3170-x},
pmid = {29340898},
issn = {1435-4373},
mesh = {Bacteria/classification/genetics ; Bacterial Typing Techniques/methods ; Cross Infection/*epidemiology/*microbiology/prevention & control ; Disease Outbreaks ; Genome, Bacterial ; Humans ; *Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; Molecular Epidemiology ; Whole Genome Sequencing ; },
abstract = {Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determinants. This renders correct and rapid species identification and antibiotic susceptibility testing (AST) important and underscores the relevance of bacterial epidemiological typing. The latter is needed for the sensitive detection and exact tracing of nosocomial spread of these potentially multidrug-resistant microorganisms (MDRO). Many microbial typing technologies have been developed and put to some level of executive practice, but it seems that the continued evolution in methodology has currently reached an apex: there is likely to be scientific and practical consensus on the ultimate typing potential of bacterial whole-genome sequencing (WGS). The possibility to perform pan-genomic nucleotide-to-nucleotide comparisons between strains belonging to a single species and to detect even minute changes in nucleotide order will identify closely related organisms, while upon accumulation of such mutations, independent descend can be assumed. Calibration of difference levels [i.e. number of single nucleotide polymorphisms (SNPs)] into categories of inter-strain relatedness needs to be performed in order to generate robust, portable typing schemes. Here, we will briefly discuss the state of affairs regarding bacterial epidemiology based upon WGS, its relatedness with the nomenclature of former typing approaches and the continuing need for a global typing language.},
}

Bacteria/classification/genetics
Bacterial Typing Techniques/methods
Cross Infection/*epidemiology/*microbiology/prevention & control
Disease Outbreaks
Genome, Bacterial
Humans
*Metagenome
*Metagenomics/methods
Microbiota/*genetics
Molecular Epidemiology
Whole Genome Sequencing

@article {pmid28442730,
year = {2017},
author = {Wang, S and Hou, X and Su, H},
title = {Exploration of the relationship between biogas production and microbial community under high salinity conditions.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {1149},
doi = {10.1038/s41598-017-01298-y},
pmid = {28442730},
issn = {2045-2322},
mesh = {Biofuels/*microbiology ; Biota/*drug effects ; Carbon Dioxide/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Metagenomics ; Methane/*metabolism ; *Salinity ; Sewage/*microbiology ; Sodium Chloride/metabolism ; },
abstract = {High salinity frequently causes inhibition and even failure in anaerobic digestion. To explore the impact of increasing NaCl concentrations on biogas production, and reveal the microbial community variations in response to high salinity stress, the Illumina high-throughput sequencing technology was employed. The results showed that a NaCl concentration of 20 g/L (H group) exhibited a similar level of VFAs and specific CO2 production rate with that in the blank group, thus indicating that the bacterial activity in acidogenesis might not be inhibited. However, the methanogenic activity in the H group was significantly affected compared with that in the blank group, causing a 42.2% decrease in CH4 production, a 37.12% reduction in the specific CH4 generation rate and a lower pH value. Illumina sequencing revealed that microbial communities between the blank and H groups were significantly different. Bacteroides, Clostridium and BA021 uncultured were the dominant species in the blank group while some halotolerant genera, such as Thermovirga, Soehngenia and Actinomyces, dominated and complemented the hydrolytic and acidogenetic abilities in the H group. Additionally, the most abundant archaeal species included Methanosaeta, Methanolinea, Methanospirillum and Methanoculleus in both groups, but hydrogenotrophic methanogens showed a lower resistance to high salinity than aceticlastic methanogens.},
}

Biofuels/*microbiology
Biota/*drug effects
Carbon Dioxide/metabolism
High-Throughput Nucleotide Sequencing
Hydrogen-Ion Concentration
Metagenomics
Methane/*metabolism
*Salinity
Sewage/*microbiology
Sodium Chloride/metabolism

@article {pmid30223126,
year = {2018},
author = {Phandanouvong-Lozano, V and Sun, W and Sanders, JM and Hay, AG},
title = {Biochar does not attenuate triclosan's impact on soil bacterial communities.},
journal = {Chemosphere},
volume = {213},
number = {},
pages = {215-225},
doi = {10.1016/j.chemosphere.2018.08.132},
pmid = {30223126},
issn = {1879-1298},
abstract = {Triclosan, a broad-spectrum antimicrobial, has been widely used in pharmaceutical and personal care products. It undergoes limited degradation during wastewater treatment and is present in biosolids, most of which are land applied in the United States. This study assessed the impact of triclosan (0-100 mg kg-1) with and without biochar on soil bacterial communities. Very little 14C-triclosan was mineralized to 14CO2 (<7%) over the course of the study (42 days). While biochar (1%) significantly lowered mineralization of triclosan, analysis of 16S rRNA gene sequences revealed that biochar impacted very few OTUs and did not alter the overall structure of the community. Triclosan, on the other hand, significantly affected bacterial diversity and community structure (alpha diversity, ANOVA, p < 0.001; beta diversity, AMOVA, p < 0.01). Dirichlet multinomial mixtures (DMM) modeling and complete linkage clustering (CLC) revealed a dose-dependent impact of triclosan. Non-Parametric Metastats (NPM) analysis showed that 150 of 734 OTUs from seven main phyla were significantly impacted by triclosan (adjusted p < 0.05). Genera harboring opportunistic pathogens such as Flavobacterium were enriched in the presence of triclosan, as was Stenotrophomonas. The latter has previously been implicated in triclosan degradation via stable isotope probing. Surprisingly, Sphingomonads, which include well-characterized triclosan degraders were negatively impacted by even low doses of triclosan. Analyses of published genomes showed that triclosan resistance determinants were rare in Sphingomonads which may explain why they were negatively impacted by triclosan in our soil.},
}

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

@article {pmid30221538,
year = {2018},
author = {Venkataraman, A and Parlov, M and Hu, P and Schnell, D and Wei, X and Tiesman, JP},
title = {Spike-in genomic DNA for validating performance of metagenomics workflows.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {},
doi = {10.2144/btn-2018-0089},
pmid = {30221538},
issn = {1940-9818},
abstract = {Shotgun metagenomics is a powerful platform to characterize human microbiomes. However, to translate such survey data into consumer-relevant products or services, it is critical to have a robust metagenomics workflow. We present a tool - spike-in DNA - to assess performance of metagenomics workflows. The spike-in is DNA from two organisms - Alivibrio fischeri and Rhodopseudomonas palustris, in a ratio of 4:1 added to samples before DNA extraction. With a valid workflow, the output ratio of relative abundances of these organisms should be close to 4. This expectation was tested in samples of varying diversities (n = 110), and the mean ratio was 4.73 (99% CI [4.0, 5.24]). We anticipate this tool to be a relevant community resource for assessing the quality of shotgun metagenomics workflows and thereby enable robust characterization of microbiomes.},
}

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

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

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

@article {pmid30220458,
year = {2018},
author = {Roediger, B and Lee, Q and Tikoo, S and Cobbin, JCA and Henderson, JM and Jormakka, M and O'Rourke, MB and Padula, MP and Pinello, N and Henry, M and Wynne, M and Santagostino, SF and Brayton, CF and Rasmussen, L and Lisowski, L and Tay, SS and Harris, DC and Bertram, JF and Dowling, JP and Bertolino, P and Lai, JH and Wu, W and Bachovchin, WW and Wong, JJ and Gorrell, MD and Shaban, B and Holmes, EC and Jolly, CJ and Monette, S and Weninger, W},
title = {An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2018.08.013},
pmid = {30220458},
issn = {1097-4172},
abstract = {The occurrence of a spontaneous nephropathy with intranuclear inclusions in laboratory mice has puzzled pathologists for over 4 decades, because its etiology remains elusive. The condition is more severe in immunodeficient animals, suggesting an infectious cause. Using metagenomics, we identify the causative agent as an atypical virus, termed "mouse kidney parvovirus" (MKPV), belonging to a divergent genus of Parvoviridae. MKPV was identified in animal facilities in Australia and North America, is transmitted via a fecal-oral or urinary-oral route, and is controlled by the adaptive immune system. Detailed analysis of the clinical course and histopathological features demonstrated a stepwise progression of pathology ranging from sporadic tubular inclusions to tubular degeneration and interstitial fibrosis and culminating in renal failure. In summary, we identify a widely distributed pathogen in laboratory mice and establish MKPV-induced nephropathy as a new tool for elucidating mechanisms of tubulointerstitial fibrosis that shares molecular features with chronic kidney disease in humans.},
}

@article {pmid30220037,
year = {2018},
author = {Richet, C and Kraberger, S and Filloux, D and Bernardo, P and Harkins, GW and Martin, DP and Roumagnac, P and Varsani, A},
title = {Novel circular DNA viruses associated with Apiaceae and Poaceae from South Africa and New Zealand.},
journal = {Archives of virology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00705-018-4031-3},
pmid = {30220037},
issn = {1432-8798},
support = {TTK1207122745//National Research Foundation/ ; TTK1207122745//National Research Foundation/ ; TTK1207122745//National Research Foundation/ ; PIOF-GA-2013-622571//FP7-PEOPLE-2013-IOF/ ; internal//Direction Générale de l'Armement, MEM INRA Metaprogram, the Fondation pour la Recherche/ ; },
abstract = {Advances in molecular techniques used in viral metagenomics coupled with high throughput sequencing is rapidly expanding our knowledge of plant-associated virus diversity. Applying such approaches, we have identified five novel circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses from Poaceae and Apiaceae plant from South Africa and New Zealand. These viruses have a simple genomic organization, including two open reading frames that likely encode a Rep and a capsid protein (CP), a conserved nonanucleotide motif on the apex of a putative stem loop structure, and conserved rolling-circle replication and helicase motifs within their likely Rep: all suggesting that they replicate through rolling-circle replication. The Reps and the CPs putatively encoded by these five novel viruses share low to moderate degrees of similarity (22.1 - 44.6%) with other CRESS DNA viruses.},
}

@article {pmid30220035,
year = {2018},
author = {Namonyo, S and Wagacha, M and Maina, S and Wambua, L and Agaba, M},
title = {A metagenomic study of the rumen virome in domestic caprids.},
journal = {Archives of virology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00705-018-4022-4},
pmid = {30220035},
issn = {1432-8798},
abstract = {This project sought to investigate the domestic caprid rumen virome by developing a robust viral DNA isolation and enrichment protocol (utilizing membrane filtration, ultra-centrifugation, overnight PEG treatment and nuclease treatment) and using RSD-PCR and high throughput sequencing (HTS) techniques. 3.53% of the reads obtained were analogous to those of viruses denoting Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, Microviridae, Poxviridae, Tectiviridae and Marseillevirus. Most of the sequenced reads from the rumen were similar to those of phages, which are critical in maintaining the rumen microbial populations under its carrying capacity. Though identified in the rumen, most of these viruses have been reported in other environments as well. Improvements in the viral DNA enrichment and isolation protocol are required to obtain data that are more representative of the rumen virome. The 102,130 unknown reads (92.31%) for the goat and 36,241 unknown reads (93.86%) for the sheep obtained may represent novel genomes that need further study.},
}

@article {pmid30219103,
year = {2018},
author = {Uritskiy, GV and DiRuggiero, J and Taylor, J},
title = {MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {158},
doi = {10.1186/s40168-018-0541-1},
pmid = {30219103},
issn = {2049-2618},
support = {NNX15AP18G//National Aeronautics and Space Administration/ ; NNX15AK57G//National Aeronautics and Space Administration/ ; DEB1556574//National Science Foundation/ ; HG006620//National Human Genome Research Institute/ ; },
abstract = {BACKGROUND: The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization.

RESULTS: To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP's hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization.

CONCLUSIONS: MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP .},
}

@article {pmid30218379,
year = {2018},
author = {Matsutani, M and Yakushi, T},
title = {Pyrroloquinoline quinone-dependent dehydrogenases of acetic acid bacteria.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-018-9360-3},
pmid = {30218379},
issn = {1432-0614},
support = {26830126//Japan Society for the Promotion of Science/ ; 17K07722//Japan Society for the Promotion of Science/ ; },
abstract = {Pyrroloquinoline quinone (PQQ)-dependent dehydrogenases (quinoproteins) of acetic acid bacteria (AAB), such as the membrane-bound alcohol dehydrogenase (ADH) and the membrane-bound glucose dehydrogenase, contain PQQ as the prosthetic group. Most of them are located on the periplasmic surface of the cytoplasmic membrane, and function as primary dehydrogenases in cognate substance-oxidizing respiratory chains. Here, we have provided an overview on the function and molecular architecture of AAB quinoproteins, which can be categorized into six groups according to the primary amino acid sequences. Based on the genomic data, we discuss the types of quinoproteins found in AAB genome and how they are distributed. Our analyses indicate that a significant number of uncharacterized orphan quinoproteins are present in AAB. By reviewing recent experimental developments, we discuss how to characterize the as-yet-unknown enzymes. Moreover, our bioinformatics studies also provide insights on how quinoproteins have developed into intricate enzymes. ADH comprises at least two subunits: the quinoprotein dehydrogenase subunit encoded by adhA and the cytochrome subunit encoded by adhB, and the genes are located in a polycistronic transcriptional unit. Findings on stand-alone derivatives of adhA encourage us to speculate on a possible route for ADH development in the evolutional history of AAB. A combination of bioinformatics studies on big genome sequencing data and wet studies assisted with genetic engineering would unravel biochemical functions and physiological role of uncharacterized quinoproteins in AAB, or even in unculturable metagenome.},
}

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

@article {pmid30217078,
year = {2018},
author = {Li, Y and Hingamp, P and Watai, H and Endo, H and Yoshida, T and Ogata, H},
title = {Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters.},
journal = {Viruses},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/v10090496},
pmid = {30217078},
issn = {1999-4915},
support = {203143100025//Canon Foundation for Scientific Research/ ; 16KT0020//Japan Society for the Promotion of Science/ ; 17H03850//Japan Society for the Promotion of Science/ ; 26430184//Japan Society for the Promotion of Science/ ; 2016-28//Institute for Chemical Research, Kyoto University/ ; 2017-25//Institute for Chemical Research, Kyoto University/ ; ANR-11-BTBR-0008//French Investments for the Future program/ ; },
abstract = {"Megaviridae" is a proposed family of giant viruses infecting unicellular eukaryotes. These viruses are ubiquitous in the sea and have impact on marine microbial community structure and dynamics through their lytic infection cycle. However, their diversity and biogeography have been poorly characterized due to the scarce detection of Megaviridae sequences in metagenomes, as well as the limitation of reference sequences used to design specific primers for this viral group. Here, we propose a set of 82 degenerated primers (referred to as MEGAPRIMER), targeting DNA polymerase genes (polBs) of Megaviridae. MEGAPRIMER was designed based on 921 Megaviridae polBs from sequenced genomes and metagenomes. By applying this primer set to environmental DNA meta-barcoding of a coastal seawater sample, we report 5595 non-singleton operational taxonomic units (OTUs) of Megaviridae at 97% nucleotide sequence identity. The majority of the OTUs were found to form diverse clades, which were phylogenetically distantly phylogenetically related to known viruses such as Mimivirus. The Megaviridae OTUs detected in this study outnumber the giant virus OTUs identified in previous individual studies by more than an order of magnitude. Hence, MEGAPRIMER represents a useful tool to study the diversity of Megaviridae at the population level in natural environments.},
}

@article {pmid30213965,
year = {2018},
author = {Couto, N and Schuele, L and Raangs, EC and Machado, MP and Mendes, CI and Jesus, TF and Chlebowicz, M and Rosema, S and Ramirez, M and Carriço, JA and Autenrieth, IB and Friedrich, AW and Peter, S and Rossen, JW},
title = {Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13767},
doi = {10.1038/s41598-018-31873-w},
pmid = {30213965},
issn = {2045-2322},
abstract = {High throughput sequencing has been proposed as a one-stop solution for diagnostics and molecular typing directly from patient samples, allowing timely and appropriate implementation of measures for treatment, infection prevention and control. However, it is unclear how the variety of available methods impacts the end results. We applied shotgun metagenomics on diverse types of patient samples using three different methods to deplete human DNA prior to DNA extraction. Libraries were prepared and sequenced with Illumina chemistry. Data was analyzed using methods likely to be available in clinical microbiology laboratories using genomics. The results of microbial identification were compared to standard culture-based microbiological methods. On average, 75% of the reads corresponded to human DNA, being a major determinant in the analysis outcome. None of the kits was clearly superior suggesting that the initial ratio between host and microbial DNA or other sample characteristics were the major determinants of the proportion of microbial reads. Most pathogens identified by culture were also identified through metagenomics, but substantial differences were noted between the taxonomic classification tools. In two cases the high number of human reads resulted in insufficient sequencing depth of bacterial DNA for identification. In three samples, we could infer the probable multilocus sequence type of the most abundant species. The tools and databases used for taxonomic classification and antimicrobial resistance identification had a key impact on the results, recommending that efforts need to be aimed at standardization of the analysis methods if metagenomics is to be used routinely in clinical microbiology.},
}

@article {pmid30213145,
year = {2018},
author = {Gómez-Villegas, P and Vigara, J and León, R},
title = {Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain).},
journal = {Marine drugs},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/md16090332},
pmid = {30213145},
issn = {1660-3397},
support = {0055_ALGARED_PLUS_5_E//INTERREG VA España-Portugal (POCTEP) 2014-2020 Cooperation Program/ ; },
abstract = {The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown.},
}

@article {pmid27739535,
year = {2016},
author = {Koch, L},
title = {Population genomics: Off the beaten track.},
journal = {Nature reviews. Genetics},
volume = {17},
number = {11},
pages = {657},
doi = {10.1038/nrg.2016.135},
pmid = {27739535},
issn = {1471-0064},
mesh = {Genetic Variation/*genetics ; Genome, Human/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; },
}

Genetic Variation/*genetics
Genome, Human/*genetics
High-Throughput Nucleotide Sequencing/methods
Humans
Metagenomics/methods

@article {pmid30212909,
year = {2018},
author = {Marks, PC and Bigler, M and Alsop, EB and Vigneron, A and Lomans, BP and De Paula, R and Geissler, B and Tsesmetzis, N},
title = {MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources.},
journal = {Database : the journal of biological databases and curation},
volume = {2018},
number = {},
pages = {1-10},
doi = {10.1093/database/bay087},
pmid = {30212909},
issn = {1758-0463},
abstract = {The ever-increasing metagenomic data necessitate appropriate cataloguing in a way that facilitates the comparison and better contextualization of the underlying investigations. To this extent, information associated with the sequencing data as well as the original sample and the environment where it was obtained from is crucial. To date, there are not any publicly available repositories able to capture environmental metadata pertaining to hydrocarbon-rich environments. As such, contextualization and comparative analysis among sequencing datasets derived from these environments is to a certain degree hindered or cannot be fully evaluated. The metagenomics data management system for hydrocarbon resources (MetaHCRs) enables the capturing of marker gene and whole metagenome sequencing data as well as over 300 contextual attributes associated with samples, organisms, environments and geological properties, among others. Moreover, MetaHCR implements the Minimum Information about any Sequence-hydrocarbon resource specification from the Genomic Standards Consortium; it integrates a user-friendly web interface and relational database model, and it enables the generation of complex custom search. MetaHCR has been tested with 36 publicly available metagenomic studies, and its modular architecture can be easily customized for other types of environmental and metagenomics studies.},
}

@article {pmid30212773,
year = {2018},
author = {Gu, Z and Li, Y and Yang, Y and Xia, S and Hermanowicz, SW and Alvarez-Cohen, L},
title = {Inhibition of anammox by sludge thermal hydrolysis and metagenomic insights.},
journal = {Bioresource technology},
volume = {270},
number = {},
pages = {46-54},
doi = {10.1016/j.biortech.2018.08.132},
pmid = {30212773},
issn = {1873-2976},
abstract = {Anaerobic ammonium oxidation (anammox) would be a feasible treatment method for thermal hydrolysis processed sidestream (THPS). Short-term study revealed that the 1/20 diluted THPS caused a 28% decrease of specific anammox activity. The MBR achieved a volumetric nitrogen loading rate of 3.64 kg/(m3·d) with undiluted regular sidestream (RS) fed, while the reactor crashed with 70% diluted THPS as feed. The ratio of produced NO3--N to consumed NH4+-N also decreased compared with RS feeding. Candidatus brocadia was the major anammox bacteria species with the average abundance of 33.3% (synthetic wastewater), 6.42% (RS) and 2.51% (THPS). The abundances of metagenome bins for dissimilatory nitrate reduction to ammonium (DNRA) increased in the system with THPS compared with RS. The reason for the inhibition of anammox by THPS could be the high content of organic carbon in THPS, which caused the over-population of heterotrophic bacteria, i.e. DNRA bacteria, leading to anammox bacteria washout.},
}

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

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

@article {pmid30210471,
year = {2018},
author = {Momper, L and Aronson, HS and Amend, JP},
title = {Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1993},
doi = {10.3389/fmicb.2018.01993},
pmid = {30210471},
issn = {1664-302X},
abstract = {The subsurface biosphere is a massive repository of fixed carbon, harboring approximately 90% of Earth's microbial biomass. These microbial communities drive transformations central to Earth's biogeochemical cycles. However, there is still much we do not understand about how complex subterranean microbial communities survive and how they interact with these cycles. Recent metagenomic investigation of deeply circulating terrestrial subsurface fluids revealed the presence of several novel lineages of bacteria. In one particular example, phylogenomic analyses do not converge on any one previously identified taxon; here we describe the first full genomic sequences of a new bacterial lineage within the candidate phylum Hydrogenedentes, 'Candidatus Abyssubacteria.' A global survey revealed that members of this proposed lineage are widely distributed in both marine and terrestrial subsurface environments, but their physiological and ecological roles have remained unexplored. Two high quality metagenome assembled genomes (SURF_5: 97%, 4%; SURF_17: 91% and 4% completeness and contamination, respectively) were reconstructed from fluids collected 1.5 kilometers below surface in the former Homestake gold mine-now the Sanford Underground Research Facility (SURF)-in Lead, South Dakota, United States. Metabolic reconstruction suggests versatile metabolic capability, including possible nitrogen reduction, sulfite oxidation, sulfate reduction and homoacetogenesis. This first glimpse into the metabolic capabilities of these cosmopolitan bacteria suggests that they are involved in key geochemical processes, including sulfur, nitrogen, and carbon cycling, and that they are adapted to survival in the dark, often anoxic, subsurface biosphere.},
}

@article {pmid30210468,
year = {2018},
author = {Nguyen, NL and Yu, WJ and Gwak, JH and Kim, SJ and Park, SJ and Herbold, CW and Kim, JG and Jung, MY and Rhee, SK},
title = {Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1982},
doi = {10.3389/fmicb.2018.01982},
pmid = {30210468},
issn = {1664-302X},
abstract = {Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.},
}

@article {pmid30210461,
year = {2018},
author = {Sukul, P and Lupilov, N and Leichert, LI},
title = {Characterization of ML-005, a Novel Metaproteomics-Derived Esterase.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1925},
doi = {10.3389/fmicb.2018.01925},
pmid = {30210461},
issn = {1664-302X},
abstract = {A novel gene encoding for a lipolytic enzyme, designated ML-005, was recently identified using a functional metaproteomics approach. We heterologously expressed this protein in Escherichia coli and biochemically characterized it. ML-005 exhibited lipolytic activity toward short-chained substrates with the preferred substrate being p-nitrophenyl-butyrate, suggesting that ML-005 is an esterase. According to homology analysis and site-directed mutagenesis, the catalytic triad of the enzyme was identified as Ser-99, Asp-164, and His-191. Its optimal pH was determined to be at pH 8. Optimal activity was observed at 45°C. It also exhibited temperature, pH and salt tolerance. Residual relative activity after incubating at 50-60°C for 360 min was above 80% of its initial activity. It showed tolerance over a broad range of pH (5-12) and retained most of its initial activity. Furthermore, incubating ML-005 in 1 - 5M NaCl solution had negligible effect on its activity. DTT, EDTA, and ß-mercaptoethanol had no significant effect on ML-005's activity. However, addition of PMSF led to almost complete inactivation consistent with ML-005 being a serine hydrolase. ML-005 remains stable in the presence of a range of metal ions, but addition of Cu2+ significantly reduces its relative activity. Organic solvents have an inhibitory effect on ML-005, but it retained 21% of activity in 10% methanol. SDS had the most pronounced inhibitory effect on ML-005 among all detergents tested and completely inactivated it. Furthermore, the Vmax of ML-005 was determined to be 59.8 μM/min along with a Km of 137.9 μM. The kcat of ML-005 is 26 s-1 and kcat/Km is 1.88 × 105 M-1 s-1.},
}

@article {pmid30210456,
year = {2018},
author = {Hily, JM and Candresse, T and Garcia, S and Vigne, E and Tannière, M and Komar, V and Barnabé, G and Alliaume, A and Gilg, S and Hommay, G and Beuve, M and Marais, A and Lemaire, O},
title = {High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1782},
doi = {10.3389/fmicb.2018.01782},
pmid = {30210456},
issn = {1664-302X},
abstract = {In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more "reductionist" view focusing on one or a few known agents, HTS-based approaches are able to give a "holistic snapshot" of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species. In the present study, a total RNAseq-based approach was used to determine the full genome sequences of various grapevine fanleaf virus (GFLV) isolates and to analyze the eventual presence of other viral agents. From four RNAseq datasets, a few complete grapevine-infecting virus and viroid genomes were de-novo assembled: (a) three GFLV genomes, 11 grapevine rupestris stem-pitting associated virus (GRSPaV) and six viroids. In addition, a novel viral genome was detected in all four datasets, consisting of a single-stranded, positive-sense RNA molecule of 6033 nucleotides. This genome displays an organization similar to Tymoviridae family members in the Tymovirales order. Nonetheless, the new virus shows enough differences to be considered as a new species defining a new genus. Detection of this new agent in the original grapevines proved very erratic and was only consistent at the end of the growing season. This virus was never detected in the spring period, raising the possibility that it might not be a grapevine-infecting virus, but rather a virus infecting a grapevine-associated organism that may be transiently present on grapevine samples at some periods of the year. Indeed, the Tymoviridae family comprises isometric viruses infecting a wide range of hosts in different kingdoms (Plantae, Fungi, and Animalia). The present work highlights the fact that even though HTS technologies produce invaluable data for the description of the sanitary status of a plant, in-depth biological studies are necessary before assigning a new virus to a particular host in such metagenomic approaches.},
}

@article {pmid30209883,
year = {2018},
author = {Chase, AB and Gomez-Lunar, Z and Lopez, AE and Li, J and Allison, SD and Martiny, AC and Martiny, JBH},
title = {Emergence of Soil Bacterial Ecotypes Along a Climate Gradient.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14405},
pmid = {30209883},
issn = {1462-2920},
abstract = {The high diversity of soil bacteria is attributed to the spatial complexity of soil systems, where habitat heterogeneity promotes niche partitioning among bacterial taxa. This premise remains challenging to test, however, as it requires quantifying the traits of closely-related soil bacteria and relating these traits to bacterial abundances and geographic distributions. Here, we sought to investigate whether the widespread soil taxon Curtobacterium consists of multiple coexisting ecotypes with differential geographic distributions. We isolated Curtobacterium strains from six sites along a climate gradient and assayed four functional traits that may contribute to niche partitioning in leaf litter, the top layer of soil. Our results revealed that cultured isolates separated into fine-scale genetic clusters that reflected distinct suites of phenotypic traits, denoting the existence of multiple ecotypes. We then quantified the distribution of Curtobacterium by analyzing metagenomic data collected across the gradient over 18 months. Six abundant ecotypes were observed with differential abundances along the gradient, suggesting fine-scale niche partitioning. However, we could not clearly explain observed geographic distributions of ecotypes by relating their traits to environmental variables. Thus, while we can resolve soil bacterial ecotypes, the traits delineating their distinct niches in the environment remains unclear. This article is protected by copyright. All rights reserved.},
}

@article {pmid30209867,
year = {2018},
author = {Zhuang, GC and Peña-Montenegro, TD and Montgomery, A and Hunter, KS and Joye, SB},
title = {Microbial metabolism of methanol and methylamine in the Gulf of Mexico: insight into marine carbon and nitrogen cycling.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14406},
pmid = {30209867},
issn = {1462-2920},
abstract = {One carbon (C1) metabolism plays an important role in marine carbon cycling but the dynamics and modes of C1 transformations are not fully understood. We made contemporaneous measurements of methylamine and methanol metabolism to elucidate the role of C1 compounds as sources of carbon, energy, and nitrogen. Methanol and methylamine were predominantly used as an energy source in offshore waters (oxidation rate constant: kmethanol : 0.02 d-1 -0.10 d-1 ; kmethylamine : 0.01 d-1 -0.18 d-1), but were also important sources of biomass carbon in coastal waters (assimilation rate constant: kmethanol : 0.01 d-1 -0.10 d-1 ; kmethylamine : 0.01 d-1 -0.05 d-1). The relative extent of assimilation versus oxidation for these substrates correlated positively with chlorophyll, nutrients, and heterotrophic bacterial production. Methanol oxidation and assimilation were stimulated significantly by nutrient addition. In contrast, methylamine metabolism was inhibited by ammonium or nitrate, suggesting that methylamine served as a nitrogen source. A preliminary metagenomic survey revealed a diverse population of putative C1-utilizing microorganisms. These results show that the remineralization of methylamine could provide both C and N sources for microbes. Both methanol and methylamine contribute to microbial energetic and carbon substrate demands with a distinctly different signature in nearshore versus offshore environments. This article is protected by copyright. All rights reserved.},
}

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

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

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

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

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

@article {pmid29325632,
year = {2018},
author = {Aminoff, MJ and Boller, F and Swaab, DF},
title = {Foreword.},
journal = {Handbook of clinical neurology},
volume = {147},
number = {},
pages = {vii},
doi = {10.1016/B978-0-444-63233-3.09990-5},
pmid = {29325632},
issn = {0072-9752},
mesh = {*Guidelines as Topic ; Humans ; Metagenomics ; *Molecular Biology/methods ; Publications ; },
}

*Guidelines as Topic
Humans
Metagenomics
*Molecular Biology/methods
Publications

@article {pmid30207899,
year = {2018},
author = {Filloux, D and Fernandez, E and Comstock, JC and Mollov, D and Roumagnac, P and Rott, P},
title = {Viral Metagenomic-Based Screening of Sugarcane from Florida Reveals Occurrence of Six Sugarcane-Infecting Viruses and High Prevalence of Sugarcane yellow leaf virus.},
journal = {Plant disease},
volume = {},
number = {},
pages = {PDIS04180581RE},
doi = {10.1094/PDIS-04-18-0581-RE},
pmid = {30207899},
issn = {1943-7692},
abstract = {A viral metagenomics study of the sugarcane virome in Florida was carried out in 2013 to 2014 to analyze occurrence of known and potentially new viruses. In total, 214 sugarcane leaf samples were collected from different commercial sugarcane (Saccharum interspecific hybrids) fields in Florida and from other Saccharum and related species taken from two local germplasm collections. Virion-associated nucleic acids (VANA) metagenomics was used for detection and identification of viruses present within the collected leaf samples. VANA sequence reads were obtained for 204 leaf samples and all four previously reported sugarcane viruses occurring in Florida were detected: Sugarcane yellow leaf virus (SCYLV, 150 infected samples out of 204), Sugarcane mosaic virus (1 of 204), Sugarcane mild mosaic virus (13 of 204), and Sugarcane bacilliform virus (54 of 204). High prevalence of SCYLV in Florida commercial fields and germplasm collections was confirmed by reverse-transcription polymerase chain reaction. Sequence analyses revealed the presence of SCYLV isolates belonging to two different phylogenetic clades (I and II), including a new genotype of this virus. This viral metagenomics approach also resulted in the detection of a new sugarcane-infecting mastrevirus (recently described and named Sugarcane striate virus), and two potential new viruses in the genera Chrysovirus and Umbravirus.},
}

@article {pmid30207068,
year = {2018},
author = {Dunon, V and Bers, K and Lavigne, R and Top, EM and Springael, D},
title = {Targeted metagenomics demonstrates the ecological role of IS1071 in bacterial community adaptation to pesticide degradation.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14404},
pmid = {30207068},
issn = {1462-2920},
abstract = {IS1071, an insertion element that primarily flanks organic xenobiotic degradation genes of cultured isolates, is suggested to play a key role in the formation and distribution of bacterial catabolic pathway gene clusters. However, in environmental settings the identity of the IS1071 genetic cargo and its correspondence to the local selective conditions remain unknown. To respond, we developed a long-range PCR approach amplifying accessory genes between two IS1071 copies from community DNA followed by amplicon sequencing. We applied this method to pesticide exposed environments, i.e., linuron-treated agricultural soil and on-farm biopurification systems (BPS) treating complex agricultural wastewater, as to non-treated controls. Amplicons were mainly recovered from the pesticide exposed environments and the BPS matrix showed a higher size diversity compared to the agricultural soil. Retrieved gene functions mirrored the main selection pressure as (i) a large fraction of the BPS amplicons contained genes/gene clusters related to the degradation of organics including herbicides present in the wastewater and (ii) in the agricultural soil, recovered genes were associated with linuron degradation. Our metagenomic analysis extends observations from cultured isolates and provides evidence that IS1071 is a carrier of catabolic genes in xenobiotica stressed environments and contributes to community level adaptation towards pesticide biodegradation. This article is protected by copyright. All rights reserved.},
}

@article {pmid30206424,
year = {2018},
author = {Jameson, E and Stephenson, J and Jones, H and Millard, A and Kaster, AK and Purdy, KJ and Airs, R and Murrell, JC and Chen, Y},
title = {Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0269-8},
pmid = {30206424},
issn = {1751-7370},
abstract = {Coastal saltmarsh sediments represent an important source of natural methane emissions, much of which originates from quaternary and methylated amines, such as choline and trimethylamine. In this study, we combine DNA stable isotope probing with high throughput sequencing of 16S rRNA genes and 13C2-choline enriched metagenomes, followed by metagenome data assembly, to identify the key microbes responsible for methanogenesis from choline. Microcosm incubation with 13C2-choline leads to the formation of trimethylamine and subsequent methane production, suggesting that choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate. Amplicon sequencing analysis identifies Deltaproteobacteria of the genera Pelobacter as the major choline utilizers. Methanogenic Archaea of the genera Methanococcoides become enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of metagenomic DNA results in the identification of bins classified as Pelobacter and Methanococcoides. Analyses of these bins reveal that Pelobacter have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway. Together, our data provide a new insight on the diversity of choline utilizing organisms in coastal sediments and support a syntrophic relationship between Bacteria and Archaea as the dominant route for methanogenesis from choline in this environment.},
}

@article {pmid30206336,
year = {2018},
author = {Seck, EH and Senghor, B and Merhej, V and Bachar, D and Cadoret, F and Robert, C and Azhar, EI and Yasir, M and Bibi, F and Jiman-Fatani, AA and Konate, DS and Musso, D and Doumbo, O and Sokhna, C and Levasseur, A and Lagier, JC and Khelaifia, S and Million, M and Raoult, D},
title = {Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41366-018-0201-3},
pmid = {30206336},
issn = {1476-5497},
abstract = {BACKGROUND/OBJECTIVES: High salt intake has been linked to several diseases including obesity and an increased risk of death; however, fecal salinity and the ability of salt to alter the gut microbiota, which was recently identified as an instrumental factor for health and disease, remains poorly explored.

METHODS/SUBJECTS: We analyzed the fecal samples of 1326 human individuals for salinity by refractometry, 572 for gut microbiota by culturomics, and 164 by 16S rRNA-targeted metagenomics. Geographical origin, age, gender, and obesity were tested as predictors of fecal salinity and halophilic diversity. All halophilic isolates were characterized by taxonogenomics and their genome sequenced.

RESULTS: Fecal salinity was associated with obesity independently of geographical origin, gender, and age. The first 2 human-associated halophilic archaeal members were isolated along with 64 distinct halophilic species, including 21 new species and 41 known in the environment but not in humans. No halophiles grow in less than 1.5% salinity. Above this threshold, the richness of the halophilic microbiota was correlated with fecal salinity (r = 0.58, p < 0.0001). 16S metagenomics linked high fecal salinity to decreased diversity (linear regression, p < .035) and a depletion in anti-obesity Akkermansia muciniphila and Bifidobacterium, specifically B. longum and B. adolescentis. Genomics analysis suggested that halophilic microbes are not only transient passengers but may be residents of the human gut.

CONCLUSIONS: High salt levels are associated with alteration of the gut microbial ecosystem and halophilic microbiota, as discovered during this study. Further studies should clarify if the gut microbiota alterations associated with high salt levels and the human halophilic microbiota could be causally related to human disease, such as obesity.},
}

@article {pmid30205462,
year = {2018},
author = {Hidalgo-Cantabrana, C and Sanozky-Dawes, R and Barrangou, R},
title = {Insights into the Human Virome Using CRISPR Spacers from Microbiomes.},
journal = {Viruses},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/v10090479},
pmid = {30205462},
issn = {1999-4915},
support = {support//North Carolina Agricultural Foundation/ ; internal support//North Carolina State University/ ; },
abstract = {Due to recent advances in next-generation sequencing over the past decade, our understanding of the human microbiome and its relationship to health and disease has increased dramatically. Yet, our insights into the human virome, and its interplay with important microbes that impact human health, is relatively limited. Prokaryotic and eukaryotic viruses are present throughout the human body, comprising a large and diverse population which influences several niches and impacts our health at various body sites. The presence of prokaryotic viruses like phages, has been documented at many different body sites, with the human gut being the richest ecological niche. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated proteins constitute the adaptive immune system of bacteria, which prevents attack by invasive nucleic acid. CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing.},
}

@article {pmid29433650,
year = {2018},
author = {Koonin, EV and Dolja, VV},
title = {Metaviromics: a tectonic shift in understanding virus evolution.},
journal = {Virus research},
volume = {246},
number = {},
pages = {A1-A3},
doi = {10.1016/j.virusres.2018.02.001},
pmid = {29433650},
issn = {1872-7492},
mesh = {Animals ; *Evolution, Molecular ; Humans ; Metagenomics/methods/*trends ; Phylogeny ; Plants/virology ; Prokaryotic Cells/virology ; Virology/methods/*trends ; Viruses/classification/*genetics/isolation & purification ; },
}

Animals
*Evolution, Molecular
Humans
Metagenomics/methods/*trends
Phylogeny
Plants/virology
Prokaryotic Cells/virology
Virology/methods/*trends
Viruses/classification/*genetics/isolation & purification

@article {pmid30204767,
year = {2018},
author = {Lee, JZ and Everroad, RC and Karaoz, U and Detweiler, AM and Pett-Ridge, J and Weber, PK and Prufert-Bebout, L and Bebout, BM},
title = {Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0202792},
doi = {10.1371/journal.pone.0202792},
pmid = {30204767},
issn = {1932-6203},
abstract = {Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.},
}

@article {pmid30203997,
year = {2018},
author = {Dadwal, SS and Kontoyiannis, DP},
title = {Recent advances in the molecular diagnosis of mucormycosis.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2018.1522250},
pmid = {30203997},
issn = {1744-8352},
abstract = {INTRODUCTION: Fungal infection burden related to Mucorales has been on the rise with significant associated morbidity and mortality. The major obstacle in the management has been lack of a non-invasive rapid and a reliable diagnostic test. Developing a culture-independent biomarker for the early diagnosis of mucormycosis is a major unmet need in modern mycology. Several approaches have been developed, such as immunohistochemistry that can confirm the histopathologic diagnosis of the invasive mold infection, polymerase chain reaction (PCR) on formalin fixed paraffin embedded (FFPE) or fresh tissue, body fluids such as bronchoalveolar fluid (BAL), and detection directly from serum/blood. Serologic tests, matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS), metabolomics and metagenomic shotgun sequencing are other evolving technologies. Area covered: In this review paper, we report the current status of the molecular diagnostics in the diagnosis of mucormycosis: serologic tests, immunohistochemistry, PCR, protein based with MALDI-TOF, metabolomics and metagenomic sequencing. Expert commentary: This review will conclude with an expert commentary on the potential uses/challenges of the currently available tests and the future of molecular diagnostics for mucormycosis.},
}

@article {pmid30203917,
year = {2018},
author = {Abbas, AA and Young, JC and Clarke, EL and Diamond, JM and Imai, I and Haas, AR and Cantu, E and Lederer, DJ and Meyer, K and Milewski, RK and Olthoff, KM and Shaked, A and Christie, JD and Bushman, FD and Collman, RG},
title = {Bidirectional transfer of anelloviridae lineages between graft and host during lung transplantation.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1111/ajt.15116},
pmid = {30203917},
issn = {1600-6143},
abstract = {Solid organ transplantation disrupts virus-host relationships, potentially resulting in viral transfer from donor to recipient, reactivation of latent viruses, and new viral infections. Viral transfer, colonization, and reactivation are typically monitored using assays for specific viruses, leaving the behavior of full viral populations (the "virome") understudied. Here we sought to investigate the temporal behavior of viruses from donor lungs and transplant recipients comprehensively. We interrogated the bronchoalveolar lavage (BAL) and blood viromes during the peri-transplant period and 6-16 months post-transplant in 13 donor-recipient pairs using shotgun metagenomic sequencing. Anelloviridae, ubiquitous human commensal viruses, were the most abundant human viruses identified. Herpesviruses, parvoviruses, polyomaviruses and bacteriophages were also detected. Anelloviridae populations were complex, with some donor organs and hosts harboring multiple contemporaneous lineages. We identified transfer of Anelloviridae lineages from donor organ to recipient serum in 4 of 7 cases that could be queried, and immigration of lineages from recipient serum into the allograft in 6 of 10 such cases. Thus, metagenomic analyses revealed that viral populations move between graft and host in both directions, showing that organ transplantation involves implantation of both the allograft and commensal viral communities. This article is protected by copyright. All rights reserved.},
}

@article {pmid30203072,
year = {2018},
author = {Graells, T and Ishak, H and Larsson, M and Guy, L},
title = {The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fiy185},
pmid = {30203072},
issn = {1574-6941},
abstract = {Legionellales is an order of the Gammaproteobacteria, only composed of host-adapted, intracellular bacteria, including the accidental human pathogens Legionella pneumophila and Coxiella burnetii. Although the diversity in terms of lifestyle is large across the order, only a few genera have been sequenced, owing to the difficulty to grow intracellular bacteria in pure culture. In particular, we know little about their global distribution and abundance.Here, we analyze 16/18S rDNA amplicons both from tens of thousands of published studies and from two separate sampling campaigns in and around ponds and in a silver mine. We demonstrate that the diversity of the order is much larger than previously thought, with over 450 uncultured genera. We show that Legionellales are found in about half of the samples from freshwater, soil and marine environments, and quasi-ubiquitous in man-made environments. Their abundance is low, typically 0.1%, with few samples up to 1%. Most Legionellales OTUs are globally distributed, while many do not belong to a previously identified species.This study sheds a new light on the ubiquity and diversity of one major group of host-adapted bacteria. It also emphasizes the need to use metagenomics to better understand the role of host-adapted bacteria in all environments.},
}

@article {pmid30203066,
year = {2018},
author = {Corinne, BP and Najwa, T and Hélène, G and Corentin, H and Didier, D},
title = {New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiy183},
pmid = {30203066},
issn = {1574-6941},
abstract = {Advances in metagenomics have given rise to the possibility of obtaining genome sequences from uncultured microorganisms, even for those poorly represented in microbial community, thereby providing important means to study their ecology and evolution. In this study, metagenomic sequencing was carried out at four sampling depths having different oxygen concentrations or environmental conditions in the water column of Lake Pavin. By analyzing the sequenced reads and matching the contigs to the proxy genomes of the closest cultivated relatives, we evaluated the metabolic potential of the dominant planktonic species involved in the methane cycle. We demonstrated that methane-producing communities were dominated by the genus Methanoregula while methane-consuming communities were dominated by the genus Methylobacter, thus confirming prior observations. Our work allowed the reconstruction of a draft of their core metabolic pathways. Although hydrogenotrophs, the presence of the genes required for acetate activation in the methanogen genome were also detected. Regarding methanotrophy, Methylobacter was present in the same areas as the non-methanotrophic, methylotrophic Methylotenera, which could suggest a relationship between these two groups. Furthermore, the presence of a large gene inventory for nitrogen metabolism (nitrate transport, denitrification, nitrite assimilation and nitrogen fixation, for instance) was detected in the Methylobacter genome.},
}

@article {pmid30202970,
year = {2018},
author = {Taylor-Brown, A and Pillonel, T and Greub, G and Vaughan, L and Nowak, B and Polkinghorne, A},
title = {Metagenomic analysis of fish-associated Ca. Parilichlamydiaceae reveals striking metabolic similarities to the terrestrial Chlamydiaceae.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evy195},
pmid = {30202970},
issn = {1759-6653},
abstract = {Chlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.0 to 3.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesise themselves. The Chlamydiae is a phylum with a very wide host range spanning mammals, birds, fish, invertebrates and unicellular protists. This ecological and phylogenetic diversity offers ongoing opportunities to study intracellular survival and metabolic pathways and adaptations. Of particular evolutionary significance are Chlamydiae from the recently proposed Ca. Parilichlamydiaceae, the earliest diverging clade in this phylum, species of which are found only in aquatic vertebrates.Gill extracts from three Chlamydiales-positive Australian aquaculture species (Yellowtail kingfish, Striped trumpeter and Barramundi) were subject to DNA preparation to deplete host DNA and enrich microbial DNA, prior to metagenome sequencing. We assembled chlamydial genomes corresponding to three Ca. Parilichlamydiaceae species from gill metagenomes, and conducted functional genomics comparisons with diverse members of the phylum.This revealed highly reduced genomes more similar in size to the terrestrial Chlamydiaceae, standing in contrast to members of the Chlamydiae with a demonstrated cosmopolitan host range. We describe a reduction in genes encoding synthesis of nucleotides and amino acids, among other nutrients, and an enrichment of predicted transport proteins. Ca. Parilichlamydiaceae share 342 orthologs with other chlamydial families. We hypothesise that the genome reduction exhibited by Ca. Parilichlamydiaceae and Chlamydiaceae is an example of within-phylum convergent evolution. The factors driving these events remain to be elucidated.},
}

@article {pmid30202961,
year = {2018},
author = {Kohl, KD and Oakeson, KF and Orr, TJ and Miller, AW and Forbey, JS and Phillips, CD and Dale, C and Weiss, RB and Dearing, MD},
title = {Metagenomic sequencing provides insights into microbial detoxification in the guts of small mammalian herbivores (Neotoma spp.).},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiy184},
pmid = {30202961},
issn = {1574-6941},
abstract = {Microbial detoxification of plant toxins influences the use ofplants as food sources by herbivores. Stephen's woodrats (Neotoma stephensi) specialize on juniper, which is defended by oxalate, phenolics, and monoterpenes, while closely related N. albigula specialize on cactus, which only contains oxalate. Woodrats maintain two gut chambers harboring dense microbial communities: a foregut chamber proximal to the major site of toxin absorption, and a cecal chamber in their hindgut. We performed several experiments to investigate the location and nature of microbial detoxification in the woodrat gut. First, we measured toxin concentrations across gut chambers of N. stephensi. Compared to food material, oxalate concentrations were immediately lower in the foregut, while concentrations of terpenes remained high in the foregut, and were lowest in the cecal chamber. We conducted metagenomic sequencing of the foregut chambers of both woodrat species and and cecal chambers of N. stephensi to compare microbial functions. We found that most genes associated with detoxification were more abundant in the cecal chambers of N. stephensi. However, some genes associated with degradation of oxalate and phenolic compounds were more abundant in the foregut chambers. Thus, microbial detoxification may take place in various chambers depending on the class of chemical compound.},
}

@article {pmid30202918,
year = {2018},
author = {Zhang, Y and Bernau, C and Parmigiani, G and Waldron, L},
title = {The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models.},
journal = {Biostatistics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/biostatistics/kxy044},
pmid = {30202918},
issn = {1468-4357},
abstract = {Cross-study validation (CSV) of prediction models is an alternative to traditional cross-validation (CV) in domains where multiple comparable datasets are available. Although many studies have noted potential sources of heterogeneity in genomic studies, to our knowledge none have systematically investigated their intertwined impacts on prediction accuracy across studies. We employ a hybrid parametric/non-parametric bootstrap method to realistically simulate publicly available compendia of microarray, RNA-seq, and whole metagenome shotgun microbiome studies of health outcomes. Three types of heterogeneity between studies are manipulated and studied: (i) imbalances in the prevalence of clinical and pathological covariates, (ii) differences in gene covariance that could be caused by batch, platform, or tumor purity effects, and (iii) differences in the "true" model that associates gene expression and clinical factors to outcome. We assess model accuracy, while altering these factors. Lower accuracy is seen in CSV than in CV. Surprisingly, heterogeneity in known clinical covariates and differences in gene covariance structure have very limited contributions in the loss of accuracy when validating in new studies. However, forcing identical generative models greatly reduces the within/across study difference. These results, observed consistently for multiple disease outcomes and omics platforms, suggest that the most easily identifiable sources of study heterogeneity are not necessarily the primary ones that undermine the ability to accurately replicate the accuracy of omics prediction models in new studies. Unidentified heterogeneity, such as could arise from unmeasured confounding, may be more important.},
}

@article {pmid30202438,
year = {2018},
author = {Liang, X and Whitham, JM and Holwerda, EK and Shao, X and Tian, L and Wu, YW and Lombard, V and Henrissat, B and Klingeman, DM and Yang, ZK and Podar, M and Richard, TL and Elkins, JG and Brown, SD and Lynd, LR},
title = {Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times.},
journal = {Biotechnology for biofuels},
volume = {11},
number = {},
pages = {243},
doi = {10.1186/s13068-018-1238-1},
pmid = {30202438},
issn = {1754-6834},
abstract = {Background: Anaerobic fermentation of lignocellulose occurs in both natural and managed environments, and is an essential part of the carbon cycle as well as a promising route to sustainable production of fuels and chemicals. Lignocellulose solubilization by mixed microbiomes is important in these contexts.

Results: Here, we report the development of stable switchgrass-fermenting enrichment cultures maintained at various residence times and moderately high (55 °C) temperatures. Anaerobic microbiomes derived from a digester inoculum were incubated at 55 °C and fed semi-continuously with medium containing 30 g/L mid-season harvested switchgrass to achieve residence times (RT) of 20, 10, 5, and 3.3 days. Stable, time-invariant cellulolytic methanogenic cultures with minimal accumulation of organic acids were achieved for all RTs. Fractional carbohydrate solubilization was 0.711, 0.654, 0.581 and 0.538 at RT = 20, 10, 5 and 3.3 days, respectively, and glucan solubilization was proportional to xylan solubilization at all RTs. The rate of solubilization was described well by the equation r = k(C - C0fr), where C represents the concentration of unutilized carbohydrate, C0 is the concentration of carbohydrate (cellulose and hemicellulose) entering the bioreactor and fr is the extrapolated fraction of entering carbohydrate that is recalcitrant at infinite residence time. The 3.3 day RT is among the shortest RT reported for stable thermophilic, methanogenic digestion of a lignocellulosic feedstock. 16S rDNA phylotyping and metagenomic analyses were conducted to characterize the effect of RT on community dynamics and to infer functional roles in the switchgrass to biogas conversion to the various microbial taxa. Firmicutes were the dominant phylum, increasing in relative abundance from 54 to 96% as RT decreased. A Clostridium clariflavum strain with genetic markers for xylose metabolism was the most abundant lignocellulose-solubilizing bacterium. A Thermotogae (Defluviitoga tunisiensis) was the most abundant bacterium in switchgrass digesters at RT = 20 days but decreased in abundance at lower RTs as did multiple Chloroflexi. Synergistetes and Euryarchaeota were present at roughly constant levels over the range of RTs examined.

Conclusions: A system was developed in which stable methanogenic steady-states were readily obtained with a particulate biomass feedstock, mid-season switchgrass, at laboratory (1 L) scale. Characterization of the extent and rate of carbohydrate solubilization in combination with 16S rDNA and metagenomic sequencing provides a multi-dimensional view of performance, species composition, glycoside hydrolases, and metabolic function with varying residence time. These results provide a point of reference and guidance for future studies and organism development efforts involving defined cultures.},
}

@article {pmid30201528,
year = {2018},
author = {Kadnikov, VV and Mardanov, AV and Beletsky, AV and Rakitin, AL and Frank, YA and Karnachuk, OV and Ravin, NV},
title = {Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer.},
journal = {Systematic and applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.syapm.2018.08.013},
pmid = {30201528},
issn = {1618-0984},
abstract = {Candidate bacterial phylum BRC1 has been identified in a broad range of mostly organic-rich oxic and anoxic environments through molecular analysis of microbial communities. None of the members of BRC1 have been cultivated and only a few draft genome sequences have been obtained from metagenomes or as a result of single-cell sequencing. We have reconstructed complete genome of BRC1 bacterium, BY40, from metagenome of the microbial community of a deep subsurface thermal aquifer in the Tomsk Region of the Western Siberia, Russia, and used it for metabolic reconstruction and comparison with existing genomic data. Analysis of 3.3Mb genome of BY40 bacterium revealed numerous glycoside hydrolases that could enable utilization of carbohydrates, including enzymes of chitin-degradation pathway. The bacterium lacks flagellar machinery but the twitching motility is encoded. The reconstructed central metabolism revealed pathways enabling the fermentation of organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Phylogenetic analysis using BY40 genome supported the phylum level classification of BRC1 lineage. Based on phylogenetic and genomic analyses, the novel bacterium is proposed to be classified as Candidatus Sumerlaea chitinivorans, within a candidate phylum Sumerlaeota.},
}

@article {pmid30201501,
year = {2018},
author = {Sauvage, V and Gomez, J and Barray, A and Vandenbogaert, M and Boizeau, L and Tagny, CT and Rakoto, O and Bizimana, P and Guitteye, H and Ciré, BB and Soumana, H and Tchomba, JS and Caro, V and Laperche, S},
title = {High prevalence of cyclovirus Vietnam (CyCV-VN) in plasma samples from Madagascan healthy blood donors.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.meegid.2018.09.002},
pmid = {30201501},
issn = {1567-7257},
abstract = {Cycloviruses, small ssDNA viruses belonging to the Circoviridae family, have been suggested as possible causes of enteric, respiratory and neurological disorders in human patients. One of these species, cyclovirus-Vietnam (CyCV-VN), initially isolated from cerebrospinal fluid samples of patients with unexplained neurological disorders, has since been reported in serum samples from chronically patients infected with HBV, HCV or HIV, in Italy. On the other hand, CyCV-VN was not detected in serum samples from healthy individuals. Here, we report on a high prevalence of 43.4% (40/92) of CyCV-VN in plasma samples from asymptomatic blood donors from Madagascar. Interestingly, this virus was not detected by metagenomics and PCR in six other African countries, suggesting regional differences in CyCV-VN prevalence across Africa. Phylogenetic analysis based on the complete genomes showed that CyCV-VN sequences isolated from blood were most closely related to sequences previously reported from human stool in Madagascar. Further investigations using larger cohorts are required to determine the global epidemiology, the natural history and the pathological significance, if any, of CyCV-VN infection in humans.},
}

@article {pmid30200636,
year = {2018},
author = {Pratas, D and Hosseini, M and Grilo, G and Pinho, AJ and Silva, RM and Caetano, T and Carneiro, J and Pereira, F},
title = {Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard.},
journal = {Genes},
volume = {9},
number = {9},
pages = {},
doi = {10.3390/genes9090445},
pmid = {30200636},
issn = {2073-4425},
support = {PD/BD/113969/2015//Fundação para a Ciência e a Tecnologia/ ; SFRH/BPD/111148/2015//Fundação para a Ciência e a Tecnologia/ ; SFRH/BPD/77900/2011//Fundação para a Ciência e a Tecnologia/ ; SFRH/BPD/100912/2014//Fundação para a Ciência e a Tecnologia/ ; IF/01356/2012//Fundação para a Ciência e a Tecnologia/ ; UID/BIM/04501/2013//Fundação para a Ciência e a Tecnologia/ ; UID/CEC/00127/2013//Fundação para a Ciência e a Tecnologia/ ; UID/AMB/50017//Fundação para a Ciência e a Tecnologia/ ; PTCD/EEI-SII/6608/2014//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of assemblies and subsequent data analysis. More importantly, such analysis allows extinct and extant species to be identified without requiring a specific or new sequencing run. However, the identification of exogenous organisms is a complex task, given the nature and degradation of the samples, and the evident necessity of using efficient computational tools, which rely on algorithms that are both fast and highly sensitive. In this work, we relied on a fast and highly sensitive tool, FALCON-meta, which measures similarity against whole-genome reference databases, to analyse the metagenomic composition of an ancient polar bear (Ursus maritimus) jawbone fossil. The fossil was collected in Svalbard, Norway, and has an estimated age of 110,000 to 130,000 years. The FASTQ samples contained 349 GB of nonamplified shotgun sequencing data. We identified and localized, relative to the FASTQ samples, the genomes with significant similarities to reference microbial genomes, including those of viruses, bacteria, and archaea, and to fungal, mitochondrial, and plastidial sequences. Among other striking features, we found significant similarities between modern-human, some bacterial and viral sequences (contamination) and the organelle sequences of wild carrot and tomato relative to the whole samples. For each exogenous candidate, we ran a damage pattern analysis, which in addition to revealing shallow levels of damage in the plant candidates, identified the source as contamination.},
}

@article {pmid30200350,
year = {2018},
author = {Ferrari, G and Lischer, HEL and Neukamm, J and Rayo, E and Borel, N and Pospischil, A and Rühli, F and Bouwman, AS and Campana, MG},
title = {Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf.},
journal = {Genes},
volume = {9},
number = {9},
pages = {},
doi = {10.3390/genes9090436},
pmid = {30200350},
issn = {2073-4425},
support = {URPP Evolution in Action: from Genomes to Ecosystems//Universität Zürich/ ; n/a//Mäxi Foundation Zurich/ ; n/a//Smithsonian Institution/ ; },
abstract = {The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies. However, as for all ancient DNA (aDNA) studies, environmental and laboratory contamination need to be specifically addressed. Here we attempted to reconstruct the tissue-specific metagenomes of a 42,000-year-old, permafrost-preserved woolly mammoth calf through shotgun high-throughput sequencing. We analyzed the taxonomic composition of all tissue samples together with environmental and non-template experimental controls and compared them to metagenomes obtained from permafrost and elephant fecal samples. Preliminary results suggested the presence of tissue-specific metagenomic signals. We identified bacterial species that were present in only one experimental sample, absent from controls, and consistent with the nature of the samples. However, we failed to further authenticate any of these signals and conclude that, even when experimental samples are distinct from environmental and laboratory controls, this does not necessarily indicate endogenous presence of ancient host-associated microbiomic signals.},
}

@article {pmid30200218,
year = {2018},
author = {Hernández-García, JA and Gonzalez-Escobedo, R and Briones-Roblero, CI and Cano-Ramírez, C and Rivera-Orduña, FN and Zúñiga, G},
title = {Gut Bacterial Communities of Dendroctonus valens and D. mexicanus (Curculionidae: Scolytinae): A Metagenomic Analysis across Different Geographical Locations in Mexico.},
journal = {International journal of molecular sciences},
volume = {19},
number = {9},
pages = {},
doi = {10.3390/ijms19092578},
pmid = {30200218},
issn = {1422-0067},
support = {CONACyT 169494/CB2011//Consejo Nacional de Ciencia y Tecnología/ ; ICyTDF 45/2012//Instituto de Ciencia y Tecnología del Distrito Federal/ ; },
abstract = {Dendroctonus bark beetles are a worldwide significant pest of conifers. This genus comprises 20 species found in North and Central America, and Eurasia. Several studies have documented the microbiota associated with these bark beetles, but little is known regarding how the gut bacterial communities change across host range distribution. We use pyrosequencing to characterize the gut bacterial communities associated with six populations of Dendroctonus valens and D. mexicanus each across Mexico, determine the core bacteriome of both insects and infer the metabolic pathways of these communities with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to evaluate whether these routes are conserved across geographical locations. Our results show that the β-diversity with UniFrac unweighted varies among locations of both bark beetles mainly due to absence/presence of some rare taxa. No association is found between the pairwise phylogenetic distance of bacterial communities and geographic distance. A strict intraspecific core bacteriome is determined for each bark beetle species, but these cores are different in composition and abundance. However, both bark beetles share the interspecific core bacteriome recorded previously for the Dendroctonus genus consisting of Enterobacter, Pantoea, Providencia, Pseudomonas, Rahnella, and Serratia. The predictions of metabolic pathways are the same in the different localities, suggesting that they are conserved through the geographical locations.},
}

@article {pmid28686571,
year = {2017},
author = {Chistoserdova, L},
title = {Application of Omics Approaches to Studying Methylotrophs and Methylotroph Comunities.},
journal = {Current issues in molecular biology},
volume = {24},
number = {},
pages = {119-142},
doi = {10.21775/cimb.024.119},
pmid = {28686571},
issn = {1467-3045},
mesh = {Aerobiosis ; Anaerobiosis ; Bacteria/*metabolism ; Metabolomics/methods ; Metagenomics/*methods ; Methane/chemistry/*metabolism ; Methanol/chemistry/*metabolism ; *Microbial Consortia ; Proteomics/methods ; },
abstract = {This review covers some recent advances in application of omics technologies to studying methylotrophs, with special reference to their activities in natural environments. Some of the developments highlighted in this review are the new outlook at the role of the XoxF-type, lanthanum-dependent methanol dehydrogenase in natural habitats, new mechanistic details of methane oxidation through the reverse methanogenesis pathway, propensity of 'aerobic' methanotrophs to thrive in hypoxic environments and potential connection of this process to denitrification, and a novel outlook at methane oxidation as a community function.},
}

Aerobiosis
Anaerobiosis
Bacteria/*metabolism
Metabolomics/methods
Metagenomics/*methods
Methane/chemistry/*metabolism
Methanol/chemistry/*metabolism
*Microbial Consortia
Proteomics/methods

@article {pmid27572648,
year = {2016},
author = {Jansson, JK and Baker, ES},
title = {A multi-omic future for microbiome studies.},
journal = {Nature microbiology},
volume = {1},
number = {},
pages = {16049},
doi = {10.1038/nmicrobiol.2016.49},
pmid = {27572648},
issn = {2058-5276},
mesh = {*Gene Expression Profiling ; Humans ; *Metabolomics ; *Metagenomics ; *Microbiota ; *Proteomics ; },
}

*Gene Expression Profiling
Humans
*Metabolomics
*Metagenomics
*Microbiota
*Proteomics

@article {pmid30199629,
year = {2018},
author = {Zhao, Y and Liu, S and Jiang, B and Feng, Y and Zhu, T and Tao, HC and Tang, X and Liu, S},
title = {Genome-centered metagenomics analysis reveals the symbiotic organisms possessing ability to cross-feed with anammox bacteria in anammox consortia.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.8b02599},
pmid = {30199629},
issn = {1520-5851},
abstract = {Although using anammox communities for efficient wastewater treatment has attracted much attention, the pure anammox bacteria are difficult to obtain, and the potential roles of symbiotic bacteria in anammox performance are still elusive. Here, we combined long-term reactor operation, genome-centered metagenomics, community functional structure, and metabolic pathway reconstruction to reveal multiple potential cross-feedings during anammox reactor start-up according to the 37 recovered metagenome-assembled genomes (MAGs). We found Armatimonadetes and Proteobacteria could contribute the secondary metabolites molybdopterin cofactor and folate for anammox bacteria to benefit their activity and growth. Chloroflexi-affiliated bacteria encoded the function of biosynthesizing exopolysaccharides for anammox consortium aggregation, based on the partial nucleotide sugars produced by anammox bacteria. Chlorobi-affiliated bacteria had the ability to degrade extracellular proteins produced by anammox bacteria to amino acids to affect consortium aggregation. Additionally, the Chloroflexi-affiliated bacteria harbored genes for a nitrite loop and could have a dual role in anammox performance during reactor start-up. Cross-feeding in anammox community adds a different dimension for understanding microbial interactions and emphasizes the importance of symbiotic bacteria in the anammox process for wastewater treatment.},
}

@article {pmid30198719,
year = {2018},
author = {Kaleda, A and Haleva, L and Sarusi, G and Pinsky, T and Mangiagalli, M and Bar-Dolev, M and Lotti, M and Nardini, M and Braslavsky, I},
title = {Saturn-shaped ice burst pattern and fast basal binding of an ice-binding protein from an Antarctic bacterial consortium.},
journal = {Langmuir : the ACS journal of surfaces and colloids},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.langmuir.8b01914},
pmid = {30198719},
issn = {1520-5827},
abstract = {Ice-binding Proteins (IBPs) bind to ice crystals and control their growth, enabling host organisms to adapt to sub-zero temperatures. By binding to ice, IBPs can affect the shape and recrystallization of ice crystals. The shape of ice crystals produced by IBPs varies, and is partially due to which ice planes the IBPs are bound. Previously we have described a bacterial IBP found in the metagenome of the symbionts of Euplotes focardii (EfcIBP). EfcIBP shows remarkable ice recrystallization inhibition activity. As recrystallization inhibition of IBPs and other materials are important to the cryopreservation of cells and tissues, we speculate that the EfcIBP can play a future role as an ice recrystallization inhibitor in cryopreservation applications. Here we show that EfcIBP results in a Saturn-shaped ice burst pattern, which may be due to the unique ice-plane affinity of the protein that we elucidated using the fluorescent-based ice-plane affinity analysis. EfcIBP binds to ice at a speed similar to that of other moderate IBPs (5 ± 2 mM-1 s-1); however, it is unique in that it binds to the basal and a previously unobserved pyramidal near-basal planes, while other moderate IBPs typically bind to the prism and pyramidal planes, however not basal or near-basal planes. These insights into EfcIBP allow a better understanding of the recrystallization inhibition for this unique protein.},
}

@article {pmid30198178,
year = {2018},
author = {Koonin, EV},
title = {Environmental microbiology and metagenomics: the Brave New World is here, what's next?.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14403},
pmid = {30198178},
issn = {1462-2920},
}

@article {pmid30197785,
year = {2018},
author = {Hu, T and Gallins, P and Zhou, YH},
title = {A Zero-inflated Beta-binomial Model for Microbiome Data Analysis.},
journal = {Stat (International Statistical Institute)},
volume = {7},
number = {1},
pages = {},
doi = {10.1002/sta4.185},
pmid = {30197785},
issn = {2049-1573},
abstract = {The microbiome is increasingly recognized as an important aspect of the health of host species, involved in many biological pathways and processes and potentially useful as health biomarkers. Taking advantage of high-throughput sequencing technologies, modern bacterial microbiome studies are metagenomic, interrogating thousands of taxa simultaneously. Several data analysis frameworks have been proposed for microbiome sequence read count data and determining the most significant features. However, there is still room for improvement. We introduce a zero-inflated beta-binomial (ZIBB) to model the distribution of microbiome count data and to determine association with a continuous or categorical phenotype of interest. The approach can exploit mean-variance relationships to improve power and adjust for covariates. The proposed method is a mixture model with two components: (i) a zero model accounting for excess zeros and (ii) a count model to capture the remaining component by beta-binomial regression, allowing for overdispersion effects. Simulation studies show that our proposed method effectively controls type I error and has higher power than competing methods to detect taxa associated with phenotype. An R package ZIBBSeqDiscovery is available on R CRAN.},
}

@article {pmid30197212,
year = {2018},
author = {Overmann, J and Huang, S and Nübel, U and Hahnke, RL and Tindall, BJ},
title = {Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms.},
journal = {Systematic and applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.syapm.2018.08.009},
pmid = {30197212},
issn = {1618-0984},
abstract = {To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and their names validly published. Aside from these quantitative limitations, our understanding of phenotypic and functional diversity of prokaryotes is also highly biased as not a single species has been described for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal genome sequences become available at a faster rate than newly described species. The growing gap between the diversity of Bacteria and Archaea held in pure culture and that detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet-cultured taxa primarily based on sequence information. According to this proposal, the concept of Candidatus species would be extended to groups of closely related genome sequences and their names validly published following established rules of bacterial nomenclature. The corresponding sequences would be deposited in public databases as the type. The suggested alterations of the International Code of Nomenclature of Prokaryotes raise concerns regarding (1) the reliability and stability of nomenclature, (2) the technological and conceptual limitations as well as availability of reference genomes, (3) the information content of in silico functional predictions, and (4) the recognition of evolutionary units of microbial diversity. These challenges need to be overcome to arrive at a meaningful taxonomy of not-yet-cultured prokaryotes with so far poorly understood phenotypes.},
}

@article {pmid29946026,
year = {2018},
author = {Bunnefeld, L and Hearn, J and Stone, GN and Lohse, K},
title = {Whole-genome data reveal the complex history of a diverse ecological community.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {28},
pages = {E6507-E6515},
doi = {10.1073/pnas.1800334115},
pmid = {29946026},
issn = {1091-6490},
mesh = {*Ecosystem ; *Metagenome ; *Models, Biological ; },
abstract = {How widespread ecological communities assemble remains a key question in ecology. Trophic interactions between widespread species may reflect a shared population history or ecological fitting of local pools of species with very different population histories. Which scenario applies is central to the stability of trophic associations and the potential for coevolution between species. Here we show how alternative community assembly hypotheses can be discriminated using whole-genome data for component species and provide a likelihood framework that overcomes current limitations in formal comparison of multispecies histories. We illustrate our approach by inferring the assembly history of a Western Palearctic community of insect herbivores and parasitoid natural enemies, trophic groups that together comprise 50% of terrestrial species. We reject models of codispersal from a shared origin and of delayed enemy pursuit of their herbivore hosts, arguing against herbivore attainment of "enemy-free space." The community-wide distribution of species expansion times is also incompatible with a random, neutral model of assembly. Instead, we reveal a complex assembly history of single- and multispecies range expansions through the Pleistocene from different directions and over a range of timescales. Our results suggest substantial turnover in species associations and argue against tight coevolution in this system. The approach we illustrate is widely applicable to natural communities of nonmodel species and makes it possible to reveal the historical backdrop against which natural selection acts.},
}

*Ecosystem
*Metagenome
*Models, Biological

@article {pmid29486256,
year = {2018},
author = {Reid, T and Chaganti, SR and Droppo, IG and Weisener, CG},
title = {Novel insights into freshwater hydrocarbon-rich sediments using metatranscriptomics: Opening the black box.},
journal = {Water research},
volume = {136},
number = {},
pages = {1-11},
doi = {10.1016/j.watres.2018.02.039},
pmid = {29486256},
issn = {1879-2448},
mesh = {Bacteria/genetics/isolation & purification/*metabolism ; Biodegradation, Environmental ; Ecosystem ; Fresh Water/*analysis/microbiology ; Geologic Sediments/*chemistry/microbiology ; Hydrocarbons/*analysis/metabolism ; Metagenome ; Methane/metabolism ; Mining ; Petroleum/metabolism ; },
abstract = {Baseline biogeochemical surveys of natural environments is an often overlooked field of environmental studies. Too often research begins once contamination has occurred, with a knowledge gap as to how the affected area behaved prior to outside (often anthropogenic) influences. These baseline characterizations can provide insight into proposed bioremediation strategies crucial in cleaning up chemical spill sites or heavily mined regions. Hence, this study was conducted to survey the in-situ microbial activity within freshwater hydrocarbon-rich environments cutting through the McMurray formation - the geologic strata constituting the oil sands. We are the first to report in-situ functional variations among these freshwater microbial ecosystems using metatranscriptomics, providing insight into the in-situ gene expression within these naturally hydrocarbon-rich sites. Key genes involved in energy metabolism (nitrogen, sulfur and methane) and hydrocarbon degradation, including transcripts relating to the observed expression of methane oxidation are reported. This information provides better linkages between hydrocarbon impacted environments, closing knowledge gaps for optimizing not only oil sands mine reclamation but also enhancing microbial reclamation strategies in various freshwater environments. These finding can also be applied to existing contaminated environments, in need of efficient reclamation efforts.},
}

Bacteria/genetics/isolation & purification/*metabolism
Biodegradation, Environmental
Ecosystem
Fresh Water/*analysis/microbiology
Geologic Sediments/*chemistry/microbiology
Hydrocarbons/*analysis/metabolism
Metagenome
Methane/metabolism
Mining
Petroleum/metabolism

@article {pmid30196241,
year = {2018},
author = {Schiwitza, S and Arndt, H and Nitsche, F},
title = {Four new choanoflagellate species from extreme saline environments: Indication for isolation-driven speciation exemplified by highly adapted Craspedida from salt flats in the Atacama Desert (Northern Chile).},
journal = {European journal of protistology},
volume = {66},
number = {},
pages = {86-96},
doi = {10.1016/j.ejop.2018.08.001},
pmid = {30196241},
issn = {1618-0429},
abstract = {With this study we aim to extend the knowledge on the biogeography of craspedid choanoflagellates with additional data from extreme environments. Up to now, very little is known about choanoflagellates from extreme saline environments, as most studies have focused on marine and freshwater habitats. Though previously investigated high saline ice biota communities have indicated a possible adaptation to environments with high salt concentrations. Hypersaline endorheic basins, so-called salt flats or salares from the Atacama Desert in Northern Chile provide an intense environment regarding fluctuating and extreme salinities, which allow for studies on evolutionary adaptations of protists to hypersaline conditions. This study focused on choanoflagellate species isolated from different salt flats, their morphological characteristics using light and electron microscopy, molecular marker genes (SSU and LSU rDNA) and their salinity tolerance. Here, we described four new craspedid choanoflagellate species, highly adapted to the hypersaline environment of the Atacama Desert. This study extends our knowledge on choanoflagellate phylogeny and ecology and can become the basis for further molecular studies to understand the mechanisms of adaptations. Additionally, we emphasize the need of adding additional data such as autecological characteristics to amend species definitions, which is only possible from cultivated strains. This data would support the use of molecular data originating from metagenomic analyses also in an ecological context.},
}

@article {pmid30195168,
year = {2018},
author = {Gu, M and Yin, Q and Wang, Z and He, K and Wu, G},
title = {Color and nitrogen removal from synthetic dye wastewater in an integrated mesophilic hydrolysis/acidification and multiple anoxic/aerobic process.},
journal = {Chemosphere},
volume = {212},
number = {},
pages = {881-889},
doi = {10.1016/j.chemosphere.2018.08.162},
pmid = {30195168},
issn = {1879-1298},
abstract = {Dye wastewater is one kind of refractory pollutant and it is commonly treated by the integrated anaerobic and aerobic process. A new integrated hydrolysis/acidification and multiple anoxic/aerobic (AO) process was proposed for the removal of color and nitrogen from azo dye wastewater. System performance, the degradation pathway of azo dye and nitrogen metabolic pathway were investigated with quadrupole-time-of-flight and metagenomic analyses. The proposed process removed color and nitrogen efficiently, with the removal percentages of 89.4% and 54.0%, respectively. A colorful intermediate C16H11N3O7S2 during the degradation of azo dye was detected. Controlling a low dissolved oxygen concentration in the multiple AO process could enhance nitrogen removal. The detected bacteria possessing azoreductase for the azo dye degradation included Desulfovibrio aminophilus, Thermoanaerobacter, Lactococcus raffinolactis, Ruminiclostridium and Rhodopirellula. The nitrifying genes of amo and hao were mainly detected in Nitrosomonas, while the denitrifying genes were detected in Thauera, Candidatus Accumulibacter and Rhodothermus marinus.},
}

@article {pmid30195162,
year = {2018},
author = {Saleem, M and Lavagnolo, MC and Campanaro, S and Squartini, A},
title = {Dynamic membrane bioreactor (DMBR) for the treatment of landfill leachate; bioreactor's performance and metagenomic insights into microbial community evolution.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {243},
number = {Pt A},
pages = {326-335},
doi = {10.1016/j.envpol.2018.08.090},
pmid = {30195162},
issn = {1873-6424},
abstract = {The use of dynamic membranes as a low-cost alternative for conventional membrane for the treatment of landfill leachate (LFL) was investigated in this study. For this purpose a lab-scale, submerged pre-anoxic and post-aerobic bioreactor configuration was used with nylon mesh as dynamic membrane support. The study was conducted at ambient temperature and LFL was fed to the bioreactor in gradually increasing concentration mixed with tap water (from 20% to 100%). The results of this study demonstrated that lower mesh pore size of 52 μm achieved better results in terms of solid-liquid separation performance (turbidity <10 NTU) of the formed dynamic membrane layer as compared to 200 and 85 μm meshes while treating LFL. Consistently high NH4+-N conversion efficiency of more than 98% was achieved under all nitrogen loading conditions, showing effectiveness of the formed dynamic membrane in retaining slow growing nitrifying species. Total nitrogen removal reached more than 90% however, the denitrification activity showed a fluctuating profile and found to be inhibited by elevated concentrations of free nitrous acid and NO2--N at low pH values inside the anoxic bioreactor. A detailed metagenomic analysis allowed a taxonomic investigation over time and revealed the potential biochemical pathways involved in NH4+-N conversion. This study led to the identification of a dynamic system in which nitrite concentration is determined by the contribution of NH4+ oxidizers (Nitrosomonas), and by a competition between nitrite oxidizers (Nitrospira and Nitrobacter) and reducers (Thauera).},
}

@article {pmid30194429,
year = {2018},
author = {Beulig, F and Røy, H and McGlynn, SE and Jørgensen, BB},
title = {Cryptic CH4 cycling in the sulfate-methane transition of marine sediments apparently mediated by ANME-1 archaea.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0273-z},
pmid = {30194429},
issn = {1751-7370},
support = {DNRF104//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; Advanced Grant 294200//EC | European Research Council (ERC)/ ; DFF - 7014-00196//Det Frie Forskningsråd (Danish Council for Independent Research)/ ; },
abstract = {Methane in the seabed is mostly oxidized to CO2 with sulfate as the oxidant before it reaches the overlying water column. This microbial oxidation takes place within the sulfate-methane transition (SMT), a sediment horizon where the downward diffusive flux of sulfate encounters an upward flux of methane. Across multiple sites in the Baltic Sea, we identified a systematic discrepancy between the opposing fluxes, such that more sulfate was consumed than expected from the 1:1 stoichiometry of methane oxidation with sulfate. The flux discrepancy was consistent with an oxidation of buried organic matter within the SMT, as corroborated by stable carbon isotope budgets. Detailed radiotracer experiments showed that up to 60% of the organic matter oxidation within the SMT first produced methane, which was concurrently oxidized to CO2 by sulfate reduction. This previously unrecognized "cryptic" methane cycling in the SMT is not discernible from geochemical profiles due to overall net methane consumption. Sedimentary gene pools suggested that nearly all potential methanogens within and beneath the SMT belonged to ANME-1 archaea, which are typically associated with anaerobic methane oxidation. Analysis of a metagenome-assembled genome suggests that predominant ANME-1 do indeed have the enzymatic potential to catalyze both methane production and consumption.},
}