@article {pmid30886779, year = {2019}, author = {Eisenhofer, R and Weyrich, LS}, title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6594}, doi = {10.7717/peerj.6594}, pmid = {30886779}, issn = {2167-8359}, abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.}, }
@article {pmid30690359, year = {2019}, author = {Qiao, R and Sheng, C and Lu, Y and Zhang, Y and Ren, H and Lemos, B}, title = {Microplastics induce intestinal inflammation, oxidative stress, and disorders of metabolome and microbiome in zebrafish.}, journal = {The Science of the total environment}, volume = {662}, number = {}, pages = {246-253}, doi = {10.1016/j.scitotenv.2019.01.245}, pmid = {30690359}, issn = {1879-1026}, mesh = {Animals ; Dose-Response Relationship, Drug ; Dysbiosis/chemically induced/immunology/*physiopathology ; Fish Diseases/chemically induced/*immunology/physiopathology ; Gastrointestinal Microbiome/drug effects ; Inflammation/chemically induced/*immunology ; Intestines/immunology/physiology ; Metabolome/drug effects ; Metagenomics ; Oxidative Stress/drug effects ; Polystyrenes/*adverse effects/metabolism ; Random Allocation ; Toxicity Tests, Chronic ; Water Pollutants, Chemical/*adverse effects/metabolism ; *Zebrafish/metabolism/microbiology ; }, abstract = {Microplastics (MPs) can be ingested by a variety of species and mainly accumulate in the gut. However, the consequences of MPs exposure in the gut are largely unknown. Here we evaluated the impacts of MPs exposure in zebrafish gut. Animals were experimentally exposed to polystyrene MPs (5-μm beads; 50 μg/L and 500 μg/L) for 21 days and monitored for alterations in tissue histology, enzymatic biomarkers, gut microbiome and metabolomic responses. Inflammation and oxidative stress were observed in the zebrafish gut after exposed to MPs. Furthermore, significant alterations in the gut microbiome and tissue metabolic profiles were observed, with most of these were associated with oxidative stress, inflammation and lipid metabolism. This study provides evidence that MPs exposure causes gut damage as well as alterations in gut metabolome and microbiome, yielding novel insights into the consequences of MPs exposure.}, }
@article {pmid30482830, year = {2018}, author = {Espinoza, JL and Harkins, DM and Torralba, M and Gomez, A and Highlander, SK and Jones, MB and Leong, P and Saffery, R and Bockmann, M and Kuelbs, C and Inman, JM and Hughes, T and Craig, JM and Nelson, KE and Dupont, CL}, title = {Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30482830}, issn = {2150-7511}, support = {R01 DE019665/DE/NIDCR NIH HHS/United States ; R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Australia ; Bacteria/*classification/*genetics ; Child ; Child, Preschool ; Dental Caries/*microbiology ; Dental Plaque/*microbiology ; Humans ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {To address the question of how microbial diversity and function in the oral cavities of children relates to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. Caries phenotypes contained statistically significant enrichments in specific genome abundances and distinct community composition profiles, including strain-level changes. Metabolic pathways that are statistically associated with caries include several sugar-associated phosphotransferase systems, antimicrobial resistance, and metal transport. Numerous closely related previously uncharacterized microbes had substantial variation in central metabolism, including the loss of biosynthetic pathways resulting in auxotrophy, changing the ecological role. We also describe the first complete Gracilibacteria genomes from the human microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.IMPORTANCE Oral health has substantial economic importance, with over $100 billion spent on dental care in the United States annually. The microbiome plays a critical role in oral health, yet remains poorly classified. To address the question of how microbial diversity and function in the oral cavities of children relate to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. This unveiled several new previously uncharacterized but ubiquitous microbial lineages in the oral microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.}, }
@article {pmid29695035, year = {2018}, author = {Yuan, QS and Yang, P and Wu, AB and Zuo, DY and He, WJ and Guo, MW and Huang, T and Li, HP and Liao, YC}, title = {Variation in the Microbiome, Trichothecenes, and Aflatoxins in Stored Wheat Grains in Wuhan, China.}, journal = {Toxins}, volume = {10}, number = {5}, pages = {}, pmid = {29695035}, issn = {2072-6651}, mesh = {Aflatoxins/*analysis ; Agriculture/methods ; Bacteria/genetics/isolation &amp; purification ; China ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; Edible Grain/*chemistry/*microbiology ; Environmental Monitoring ; Food Contamination/*analysis ; Fungi/genetics/isolation &amp; purification ; Microbiota ; Trichothecenes/*analysis ; Triticum/*chemistry/*microbiology ; }, abstract = {Contamination by fungal and bacterial species and their metabolites can affect grain quality and health of wheat consumers. In this study, sequence analyses of conserved DNA regions of fungi and bacteria combined with determination of trichothecenes and aflatoxins revealed the microbiome and mycotoxins of wheat from different silo positions (top, middle, and bottom) and storage times (3, 6, 9, and 12 months). The fungal community in wheat on the first day of storage (T₀) included 105 classified species (81 genera) and 41 unclassified species. Four species had over 10% of the relative abundance: Alternaria alternata (12%), Filobasidium floriforme (27%), Fusarium graminearum (12%), and Wallemia sebi (12%). Fungal diversity and relative abundance of Fusarium in wheat from top silo positions were significantly lower than at other silo positions during storage. Nivalenol and deoxynivalenol in wheat were 13⁻34% higher in all positions at 3 months compared to T₀, and mycotoxins in wheat from middle and bottom positions at 6 to 12 months were 24⁻57% higher than at T₀. The relative abundance of toxigenic Aspergillus and aflatoxins were low at T₀ and during storage. This study provides information on implementation and design of fungus and mycotoxin management strategies as well as prediction models.}, }
@article {pmid30759613, year = {2019}, author = {Wang, X and Li, X and Yu, L and Huang, L and Xiu, J and Lin, W and Zhang, Y}, title = {Characterizing the microbiome in petroleum reservoir flooded by different water sources.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {872-885}, doi = {10.1016/j.scitotenv.2018.10.410}, pmid = {30759613}, issn = {1879-1026}, mesh = {Betaproteobacteria/genetics/*metabolism ; China ; Environmental Monitoring ; Gammaproteobacteria/genetics/*metabolism ; Metagenomics ; *Microbiota/genetics ; Oil and Gas Fields/*microbiology ; Petroleum/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; Water Microbiology ; *Water Resources/supply &amp; distribution ; }, abstract = {Petroleum reservoir is an unusual subsurface biosphere, where indigenous microbes lived and evolved for million years. However, continual water injection changed the situation by introduction of new electron acceptors, donors and exogenous microbes. In this study, 16S-rRNA gene sequencing, comparative metagenomics and genomic bins reconstruction were employed to investigate the microbial community and metabolic potential in three typical water-flooded blocks of the Shen84 oil reservoir in Liaohe oil field, China. The results showed significant difference of microbial community compositions and metabolic characteristics existed between the injected water and the produced water/oil mixtures; however, there was considerable uniformity between the produced samples in different blocks. Microbial communities in the produced fluids were dominated by exogenous facultative microbes such as Pseudomonas and Thauera members from Proteobacteria phylum. Metabolic potentials for O2-dependent hydrocarbon degradation, dissimilarly nitrate reduction, and thiosulfate‑sulfur oxidation were much more abundant, whereas genes involved in dissimilatory sulfate reduction, anaerobic hydrocarbon degradation and methanogenesis were less abundant in the oil reservoir. Statistical analysis indicated the water composition had an obvious influence on microbial community composition and metabolic potential. The water-flooding process accompanied with introduction of nitrate or nitrite, and dissolved oxygen promoted the alteration of microbiome in oil reservoir from slow-growing anaerobic indigenous microbes (such as Thermotoga, Clostridia, and Syntrophobacter) to fast-growing opportunists as Beta- and Gama- Proteobacteria. The findings of this study shed light on the microbial ecology change in water flooded petroleum reservoir.}, }
@article {pmid29274958, year = {2018}, author = {Li, F and Neves, ALA and Ghoshal, B and Guan, LL}, title = {Symposium review: Mining metagenomic and metatranscriptomic data for clues about microbial metabolic functions in ruminants.}, journal = {Journal of dairy science}, volume = {101}, number = {6}, pages = {5605-5618}, doi = {10.3168/jds.2017-13356}, pmid = {29274958}, issn = {1525-3198}, mesh = {Animals ; Gene Expression Profiling ; *Metagenomics ; Methane/metabolism ; Microbiota ; Rumen/*microbiology ; *Ruminants ; Transcriptome ; }, abstract = {Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption. To date, hundreds to thousands of microbial phylotypes have been identified in the rumen using culture-independent molecular-based approaches, and genomic information of rumen microorganisms is rapidly accumulating through the single genome sequencing. However, functional characteristics of the rumen microbiome have not been well described because there are numerous uncultivable microorganisms in the rumen. The advent of metagenomics and metatranscriptomics along with advanced bioinformatics methods can help us better understand mechanisms of the rumen fermentation, which is vital for improving nutrient utilization and animal productivity. Therefore, in this review, we summarize a general workflow to conduct rumen metagenomics and metatranscriptomics and discuss how the data can be interpreted to be useful information. Moreover, we review recent literatures studying associations between the rumen microbiome and host phenotypes (e.g., feed efficiency and methane emissions) using these approaches, aiming to provide a useful guide to include studying the rumen microbiome as one of the research objectives using these 2 approaches.}, }
@article {pmid30871459, year = {2019}, author = {Thrash, A and Arick, M and Barbato, RA and Jones, RM and Douglas, TA and Esdale, J and Perkins, EJ and Garcia-Reyero, N}, title = {Keanu: a novel visualization tool to explore biodiversity in metagenomes.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {103}, doi = {10.1186/s12859-019-2629-4}, pmid = {30871459}, issn = {1471-2105}, abstract = {BACKGROUND: One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, especially with metagenomics data or data suspected to be contaminated. Here, we describe the development and application of a command-line tool, Keanu, for visualizing and exploring sample content in metagenomics data. We developed Keanu as an interactive tool to make viewing complex data easier.<br><br>RESULTS: Keanu, a tool for exploring sequence content, helps a user to understand the presence and abundance of organisms in a sample by analyzing alignments against a database that contains taxonomy data and displaying them in an interactive web page. The content of a sample can be presented either as a collapsible tree, with node size indicating abundance, or as a bilevel partition graph, with arc size indicating abundance. Here, we illustrate how Keanu works by exploring shotgun metagenomics data from a sample collected from a bluff that contained paleosols and a krotovina in an alpine site in Ft. Greely, Alaska.<br><br>CONCLUSIONS: Keanu provides a simple means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu .}, }
@article {pmid30623233, year = {2019}, author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS}, title = {Chinese liver fluke Clonorchis sinensis infection changes the gut microbiome and increases probiotic Lactobacillus in mice.}, journal = {Parasitology research}, volume = {118}, number = {2}, pages = {693-699}, doi = {10.1007/s00436-018-6179-x}, pmid = {30623233}, issn = {1432-1955}, support = {NRF-2016R1A2B4016194//National Research Foundation of Korea/ ; 2011-0012166//National Research Foundation of Korea/ ; }, mesh = {Animals ; Clonorchiasis/*immunology/parasitology ; Clonorchis sinensis/growth &amp; development/*immunology ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing ; Lactobacillus/classification/cytology/*growth &amp; development ; Metacercariae/cytology ; Mice ; Mice, Inbred C57BL ; Probiotics/*analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Chinese liver fluke Clonorchis sinensis changes the host's immune system. Recently, it has been reported that helminths including C. sinensis can ameliorate immune-related diseases such as allergy. In addition, recent studies showed that helminth infection can alleviate immune-mediated disorders by altering the gut microbiome. However, changes in the gut microbiome due to C. sinensis have not been reported yet. In this study, changes in the gut microbiome of C57BL/6 mice infected with C. sinensis metacercariae were evaluated over time. Stool was analyzed by 16S rRNA amplicon analysis using high-throughput sequencing technology. There was no apparent difference in species richness and diversity between the infected and control groups. However, the composition of the microbiome was different between the infected and control groups at 20 days and 30 days post-infection, and the difference disappeared at 50 days post-infection. In particular, this microbiome alteration was associated with a change in the relative abundance of genus Lactobacillus and the probiotic Lactobacillus species that are known to have an immune-modulation role in immune-mediated diseases.}, }
@article {pmid30609875, year = {2019}, author = {Waseem, H and Jameel, S and Ali, J and Saleem Ur Rehman, H and Tauseef, I and Farooq, U and Jamal, A and Ali, MI}, title = {Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {1}, pages = {}, doi = {10.3390/molecules24010163}, pmid = {30609875}, issn = {1420-3049}, mesh = {Anti-Infective Agents/*pharmacology ; Computational Biology/methods ; Data Analysis ; *Drug Resistance, Microbial ; *Environmental Microbiology ; Gastrointestinal Microbiome ; Genes, Bacterial ; *High-Throughput Screening Assays ; Humans ; Metagenome ; Metagenomics/methods ; Quality Control ; *Real-Time Polymerase Chain Reaction ; }, abstract = {Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGenTM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.}, }
@article {pmid29611114, year = {2018}, author = {Wang, J and Chen, L and Zhao, N and Xu, X and Xu, Y and Zhu, B}, title = {Of genes and microbes: solving the intricacies in host genomes.}, journal = {Protein &amp; cell}, volume = {9}, number = {5}, pages = {446-461}, pmid = {29611114}, issn = {1674-8018}, mesh = {Animals ; Biomedical Research ; *Genes ; *Genetic Variation ; *Genome ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a &quot;hologenome&quot;, that is, the organized, closely interacting genome of the host and the microbiome.}, }
@article {pmid29482661, year = {2018}, author = {Han, M and Hao, L and Lin, Y and Li, F and Wang, J and Yang, H and Xiao, L and Kristiansen, K and Jia, H and Li, J}, title = {A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {43}, pmid = {29482661}, issn = {2049-2618}, support = {2017YFC0909700//National Key Research and Development Program of China/International ; 31601073//National Natural Science Foundation of China/International ; JSGG20160229172752028//Shenzhen Municipal Government of China/International ; JCYJ20160229172757249//Shenzhen Municipal Government of China/International ; }, mesh = {Bacteria/*genetics/metabolism ; Bromides/*chemistry ; DNA, Bacterial/*genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenomics ; Pyridinium Compounds/*chemistry ; Specimen Handling/*methods ; Temperature ; }, abstract = {BACKGROUND: The number of large-scale studies on the gut microbiota in human cohorts is rapidly increasing. However, the few and expensive options for storage of fecal samples at room temperature have been an obstacle for large-scale metagenomic studies and the development of clinical/commercial personal metagenomic sequencing.<br><br>RESULTS: In this study, we systematically tested a novel N-octylpyridinium bromide-based fecal sample preservation method and compared it with other currently used storage methods. We found that the N-octylpyridinium bromide-based method enabled preservation of the bacterial composition in fecal samples transported and stored at room temperature for up to at least 14 days.<br><br>CONCLUSIONS: We describe a novel chemical stabilizer that allows cost-effective transportation and storage at room temperature for several days with preservation of bacterial composition. This method will facilitate sample collection even in remote area and also enable transport via normal commercial transportation routes.}, }
@article {pmid28827532, year = {2017}, author = {Jiang, J and Song, Z and Yang, X and Mao, Z and Nie, X and Guo, H and Peng, X}, title = {Microbial community analysis of apple rhizosphere around Bohai Gulf.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8918}, pmid = {28827532}, issn = {2045-2322}, mesh = {Biodiversity ; Environment ; Malus/*microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Plant Roots/microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Bohai Gulf is the main area for apple tree cultivation in China. Consecutive replanting significantly affects the yield and quality of apple trees in this area. Microecological imbalance in apple trees' rhizospheres caused by variation in the soil microbial community is considered the primary cause of apple replant disease (ARD). This study analysed the microbial communities of the rhizospheres of perennial apple trees (PAT) and apple tree saplings under replanting (ATS) around Bohai Gulf using high-throughput sequencing. The results revealed increased populations of typical pathogenic fungi Verticillium and bacteria Xanthomonadaceae, and decreased populations of beneficial bacterial populations Pseudomonas and Bacillus with replanting, suggesting that competition between pathogens and beneficial microbes varies according to the ratio of pathogens to beneficial microbes in rhizosphere soil under the replanting system. Meanwhile, replanting was accompanied by an increase in the antagonistic bacteria Arthrobacter and fungus Chaetomium, suggesting that increased numbers of pathogens can lead to more instances of antagonism. Redundancy analysis (RDA) revealed site position and the main soil properties (pH, organic matter, available N, available K, available P, and moisture) affected the microbial community composition. It found clear differences in soil microbial communities and demonstrated a better understanding of the causes for ARD.}, }
@article {pmid28821872, year = {2017}, author = {Nakagawa, S and Saito, H and Tame, A and Hirai, M and Yamaguchi, H and Sunata, T and Aida, M and Muto, H and Sawayama, S and Takaki, Y}, title = {Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8764}, pmid = {28821872}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; Fish Diseases/microbiology ; Helicobacter/*classification/*genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Starfish/*microbiology ; }, abstract = {Marine invertebrates associate with diverse microorganisms. Microorganisms even inhabit coelomic fluid (CF), namely, the fluid filling the main body cavity of echinoderms. The CF microbiota potentially impacts host health and disease. Here, we analysed the CF microbiota in two common coastal starfish species, Patiria pectinifera and Asterias amurensis. Although microbial community structures were highly variable among individual starfish, those of P. pectinifera were compositionally similar to those in the surrounding seawater. By contrast, many A. amurensis individuals harboured unique microbes in the CF, which was dominated by the unclassified Thiotrichales or previously unknown Helicobacter-related taxon. In some individuals, the Helicobacter-related taxon was the most abundant genus-level taxon, accounting for up to 97.3% of reads obtained from the CF microbial community. Fluorescence in situ hybridization using a Helicobacter-related-taxon-specific probe suggested that probe-reactive cells in A. amurensis were spiral-shaped, morphologically similar to known Helicobacter species. Electron microscopy revealed that the spiral cells had a prosthecate-like polar appendage that has never been reported in Helicobacter species. Although culture of Helicobacter-related taxon was unsuccessful, this is the first report of the dominance of a Helicobacter-related taxon in invertebrates and non-digestive organs, reshaping our knowledge of the phylogeography of Helicobacter-related taxa.}, }
@article {pmid28821814, year = {2017}, author = {Fang, D and Shi, D and Lv, L and Gu, S and Wu, W and Chen, Y and Guo, J and Li, A and Hu, X and Guo, F and Ye, J and Li, Y and Li, L}, title = {Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8770}, pmid = {28821814}, issn = {2045-2322}, mesh = {Animals ; Bifidobacterium/*physiology ; Bifidobacterium pseudocatenulatum/*physiology ; Cytokines/blood/metabolism ; Galactosamine/*adverse effects ; Gastrointestinal Microbiome/*drug effects ; Inflammation Mediators/blood/metabolism ; Intestinal Mucosa/drug effects/metabolism/pathology ; Liver Diseases/*etiology/metabolism/pathology ; Male ; Metagenome ; Metagenomics ; Models, Biological ; Rats ; }, abstract = {The gut microbiota is altered in liver diseases, and several probiotics have been shown to reduce the degree of liver damage. We hypothesized that oral administration of specific Bifidobacterium strains isolated from healthy guts could attenuate liver injury. Five strains were tested in this study. Acute liver injury was induced by D-galactosamine after pretreating Sprague-Dawley rats with the Bifidobacterium strains, and liver function, liver and ileum histology, plasma cytokines, bacterial translocation and the gut microbiome were assessed. Two strains, Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10, conferred liver protection, as well as alleviated the increase in plasma M-CSF, MIP-1α and MCP-1 and bacterial translocation. They also ameliorated ileal mucosal injury and gut flora dysbiosis, especially the enrichment of the opportunistic pathogen Parasutterella and the depletion of the SCFA-producing bacteria Anaerostipes, Coprococcus and Clostridium XI. Negative correlations were found between MIP-1α / MCP-1 and Odoribacter (LI09 group) and MIP-1α / M-CSF and Flavonifractor (LI10 group). Our results indicate that the liver protection effects might be mediated through gut microbiota modification, which thus affect the host immune profile. The desirable characteristics of these two strains may enable them to serve as potential probiotics for the prevention or adjuvant treatment of liver injury.}, }
@article {pmid28821731, year = {2017}, author = {Glymenaki, M and Barnes, A and O'Hagan, S and Warhurst, G and McBain, AJ and Wilson, ID and Kell, DB and Else, KJ and Cruickshank, SM}, title = {Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8836}, pmid = {28821731}, issn = {2045-2322}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Chromatography, High Pressure Liquid ; Colitis/*etiology/*metabolism ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; Genotype ; Inflammatory Bowel Diseases/etiology/metabolism ; Male ; Mass Spectrometry ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics ; Mice ; Mice, Knockout ; *Phenotype ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Inflammatory bowel disease (IBD) is associated with altered microbiota composition and metabolism, but it is unclear whether these changes precede inflammation or are the result of it since current studies have mainly focused on changes after the onset of disease. We previously showed differences in mucus gut microbiota composition preceded colitis-induced inflammation and stool microbial differences only became apparent at colitis onset. In the present study, we aimed to investigate whether microbial dysbiosis was associated with differences in both predicted microbial gene content and endogenous metabolite profiles. We examined the functional potential of mucus and stool microbial communities in the mdr1a -/- mouse model of colitis and littermate controls using PICRUSt on 16S rRNA sequencing data. Our findings indicate that despite changes in microbial composition, microbial functional pathways were stable before and during the development of mucosal inflammation. LC-MS-based metabolic phenotyping (metabotyping) in urine samples confirmed that metabolite profiles in mdr1a -/- mice were remarkably unaffected by development of intestinal inflammation and there were no differences in previously published metabolic markers of IBD. Metabolic profiles did, however, discriminate the colitis-prone mdr1a -/- genotype from controls. Our results indicate resilience of the metabolic network irrespective of inflammation. Importantly as metabolites differentiated genotype, genotype-differentiating metabolites could potentially predict IBD risk.}, }
@article {pmid30868805, year = {2019}, author = {Liu, ZX and Xu, J and Sun, W and Shi, YH and Chen, SL}, title = {[Application of DNA metabarcoding in species identification of Chinese herbal medicines].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {44}, number = {1}, pages = {1-8}, doi = {10.19540/j.cnki.cjcmm.2019.0001}, pmid = {30868805}, issn = {1001-5302}, abstract = {DNA metabarcoding,one rapid and robust method using specific standard DNA fragments,has been widely used for rapid species identification of a bulk sample through high-throughput sequencing technologies.While it has been widely used in the studies of metagenomics,animal and plant biodiversity,it has gradually come to be used as a profitable method in species identification of mixed Chinese herbal medicines.In this paper,we mainly summarize the current studies of the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines.Moreover,high-throughput sequencing technologies adopted in those studies,such as Sanger,the next-generation,and third-generation sequencing technologies,are discussed.It is conducted to provide a theoretical guidance for the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines and in more other biodiversity studies.}, }
@article {pmid30594064, year = {2019}, author = {Procopio, N and Ghignone, S and Williams, A and Chamberlain, A and Mello, A and Buckley, M}, title = {Metabarcoding to investigate changes in soil microbial communities within forensic burial contexts.}, journal = {Forensic science international. Genetics}, volume = {39}, number = {}, pages = {73-85}, doi = {10.1016/j.fsigen.2018.12.002}, pmid = {30594064}, issn = {1878-0326}, mesh = {Animals ; Burial ; DNA Barcoding, Taxonomic/*methods ; Forensic Sciences ; Metagenomics/methods ; Microbiota/*genetics ; Models, Animal ; Polymerase Chain Reaction ; *Postmortem Changes ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Swine ; }, abstract = {The estimation of the time elapsed since death (post-mortem interval, or PMI) is one of the key themes that forensic scientists have to address frequently. However, the estimation of PMI still suffers from poor accuracy and biases especially when decomposition stages are prolonged, so further improvements in methods for PMI estimation are desirable. Soil microbial communities associated with decomposing bodies have been shown to be good candidates for the estimation of the PMI of exposed bodies. Nevertheless, further research is required to better understand the bacterial succession associated with decomposition of buried carcasses in order to test its reliability and applicability for the estimation of PMI and to better understand the dynamics involved with decomposition within this particular scenario. Therefore we explored the succession of soil microbial communities associated with four decomposing pig carcasses (from one to six months PMI) using a metabarcoding approach. The sequencing of the bacterial 16S rRNA variable region 4 (V4) revealed trends linking particular microbial taxa with specific PMIs, and notably an increase in Proteobacteria, Firmicutes and Bacteroidetes at specific PMIs as well as a decrease in Acidobacteria. Our results, in accordance with previous studies conducted on exposed bodies of different mammalian species (including humans), also showed a general reduction of the taxonomic richness from two months PMI onwards, as well as an incomplete re-establishment of the starting soil microbial conditions after six months PMI. We also found specific mammal-derived taxa, such as Bacteroides spp., being still present in the soil after six months PMI. As such, this study serves as a baseline for additional research to allow the characterisation of biomarkers associated with specific PMIs. Due to the similarity between the results presented here and those reported in other types of decomposition studies we believe that the metabarcoding approach has considerable potential in the estimation of the PMI, particularly to clarify cases involving heavily skeletonised bodies or for the investigation of clandestine graves in which the carcass has been moved from its original place of deposition.}, }
@article {pmid30010734, year = {2018}, author = {Geng, S and Cheng, S and Li, Y and Wen, Z and Ma, X and Jiang, X and Wang, Y and Han, X}, title = {Faecal Microbiota Transplantation Reduces Susceptibility to Epithelial Injury and Modulates Tryptophan Metabolism of the Microbial Community in a Piglet Model.}, journal = {Journal of Crohn's &amp; colitis}, volume = {12}, number = {11}, pages = {1359-1374}, doi = {10.1093/ecco-jcc/jjy103}, pmid = {30010734}, issn = {1876-4479}, mesh = {Animals ; Colitis/chemically induced/pathology/*prevention &amp; control ; *Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*physiology ; Homeostasis ; Indoleacetic Acids/metabolism ; Interleukins/metabolism ; Intestinal Mucosa/metabolism/*pathology ; Lipopolysaccharides ; Mass Spectrometry ; Metabolome ; RNA, Ribosomal, 16S/analysis ; Receptors, Aryl Hydrocarbon/metabolism ; Swine ; Tryptophan/*metabolism ; }, abstract = {Background and Aims: Faecal microbiota transplantation [FMT] has shown promise as a treatment for inflammatory bowel disease [IBD]. Using a piglet model, our previous study indicated that exogenous faecal microbiota can increase the expressions of tight junction proteins, mucin and antimicrobial peptide in the intestinal mucosa, suggesting a beneficial effect of FMT on gut barrier and gastrointestinal health. However, specific connections between FMT-induced microbial changes and modulation of the intestinal barrier remain to be fully illustrated. Here, we aimed to determine the potential role of metabolic function of gut microbiota in the beneficial effects of FMT.<br><br>Methods: The influence of FMT on the maintenance of intestinal homeostasis was assessed by early-life gut microbiota intervention on newborn piglets and subsequent lipopolysaccharide [LPS] challenge. Analysis of the gut microbiome and metabolome was carried out by 16S rRNA gene sequencing and multiple mass spectrometry platforms.<br><br>Results: FMT modulated the diversity and composition of colonic microbiota and reduced the susceptibility to LPS-induced destruction of epithelial integrity and severe inflammatory response. Metabolomic analysis revealed functional changes of the gut metabolome along with a significant increase of the typical microbiota-derived tryptophan catabolite indole-3-acetic acid in the colonic lumen. In concordance with the metabolome data, metagenomics prediction analysis based on 16S rRNA gene sequencing also demonstrated that FMT modulated the metabolic functions of gut microbiota associated with indole alkaloid biosynthesis, cytochrome P450 and intestinal homeostasis, which coincided with up-regulation of cytokine interleukin-22 and enhanced activation of aryl hydrocarbon receptor in the recipient colon.<br><br>Conclusions: Our data reveal a regulatory effect of FMT on tryptophan metabolism of gut microbiota in the recipient colon, which may play a potential role in maintenance of the intestinal barrier.}, }
@article {pmid29786880, year = {2018}, author = {Sánchez-Sanhueza, G and Bello-Toledo, H and González-Rocha, G and Gonçalves, AT and Valenzuela, V and Gallardo-Escárate, C}, title = {Metagenomic study of bacterial microbiota in persistent endodontic infections using Next-generation sequencing.}, journal = {International endodontic journal}, volume = {51}, number = {12}, pages = {1336-1348}, doi = {10.1111/iej.12953}, pmid = {29786880}, issn = {1365-2591}, support = {folio 21130022//CONICYT-PCHA/Doctorado Nacional/2013/ ; N°214.102.016-1 IN//VRID UDEC/ ; }, mesh = {Adult ; Bacteria/*classification/*genetics/*pathogenicity ; Biodiversity ; Chile ; DNA, Bacterial/analysis ; Dental Pulp Cavity/*microbiology ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; Periapical Periodontitis/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Canal Therapy ; }, abstract = {AIM: To determine the bacterial microbiota in root canals associated with persistent apical periodontitis and their relationship with the clinical characteristics of patients using next-generation sequencing (NGS).<br><br>METHODOLOGY: Bacterial samples from root canals associated with teeth having persistent apical periodontitis were taken from 24 patients undergoing root canal retreatment. Bacterial DNA was extracted, and V3-V4 variable regions of the 16S rRNA gene were amplified. The amplification was deep sequenced by Illumina technology to establish the metagenetic relationships among the bacterial species identified. The composition and diversity of microbial communities in the root canal and their relationships with clinical features were analysed. Parametric and nonparametric tests were used to analyse differences between patient characteristics and microbial data.<br><br>RESULTS: A total of 86 different operational taxonomic units (OTUs) were identified and Good's nonparametric coverage estimator method indicated that 99.9 ± 0.00001% diversity was recovered per sample. The largest number of bacteria belonged to the phylum Proteobacteria. According to the medical history from the American Society of Anesthesiologists (ASA) Classification System, ASA II-III had higher richness estimates and distinct phylogenetic relationships compared to ASA I individuals (P < 0.05). Periapical index (PAI) score 5 was associated with increased microbiota diversity in comparison to PAI score 4, and this index was reduced in symptomatic patients.<br><br>CONCLUSIONS: Based on the findings of this study, it is possible to suggest a close relationship between several clinical features and greater microbiota diversity with persistent endodontic infections. This work provides a better understanding on how microbial communities interact with their host and vice versa.}, }
@article {pmid29524500, year = {2018}, author = {Ruppé, E and Schrenzel, J}, title = {Messages from the second International Conference on Clinical Metagenomics (ICCMg2).}, journal = {Microbes and infection}, volume = {20}, number = {4}, pages = {222-227}, doi = {10.1016/j.micinf.2018.02.005}, pmid = {29524500}, issn = {1769-714X}, mesh = {Bacteria/genetics/isolation &amp; purification/pathogenicity ; Clinical Laboratory Techniques/standards/trends ; Computational Biology ; Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/standards/trends ; Humans ; Metagenome/genetics ; *Metagenomics/standards/trends ; Microbiota/genetics ; }, abstract = {Clinical metagenomics (CMg) refers to as the application of metagenomic sequencing of clinical samples in order to recover clinically-relevant information. Due to the increasing access to next-generation sequencing (NGS) facilities, CMg is a gast-growing field. In this context, we held the second International Conference on Clinical Metagenomics (ICCMg2) in Geneva in October 2017. During the two days of the conference, several aspects of CMg were addressed, which we propose to summarize in the present manuscript. Besides, we also discuss the evolution of CMg from the last conference held in 2016. In brief, many technical issues related to CMg are expected to be successfully addressed in the coming years. Conversely, assessing the clinical value of CMg, implementing a quality process, storage of data and the ethics of CMg are emerging challenges.}, }
@article {pmid30359379, year = {2018}, author = {Bidot, WA and Ericsson, AC and Franklin, CL}, title = {Effects of water decontamination methods and bedding material on the gut microbiota.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0198305}, pmid = {30359379}, issn = {1932-6203}, support = {K01 OD019924/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Cecum/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Housing, Animal ; Mice, Inbred ICR ; *Water Microbiology ; Water Purification/*methods ; }, abstract = {Rodent models are invaluable to understanding health and disease in many areas of biomedical research. Unfortunately, many models suffer from lack of phenotype reproducibility. Our laboratory has shown that differences in gut microbiota (GM) can modulate phenotypes of models of colon cancer and inflammatory bowel disease. We and others have also shown that a number of factors associated with rodent research, including vendor, cage system, and bedding can alter GM. The objective of this study was to expand these studies to examine the effect of additional bedding materials and methods of water decontamination on GM diversity and composition. To this end, Crl:CD1 (ICR) mice were housed on corn cob or compressed paper chip bedding and provided water that was decontaminated by four different methods: autoclaving with reverse osmosis, autoclaving with hydrochloric acid, autoclaving with sulfuric acid, and autoclaving alone. Feces was collected at day 0, and at day 28 (endpoint), fecal and cecal samples were collected. DNA was extracted from samples, amplified by PCR using conserved bacterial primer sets and subjected to next generation sequencing. Sequence data were analyzed using Qiime and groups were compared using principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA). Two factor PERMANOVA of cecal GM data revealed significant changes when comparing bedding and water decontamination methods, while no significant effects were noted in the fecal GM data. Subsequent PERMANOVA and PCoA of cecal data revealed that several combinations of bedding and water decontamination methods resulted in differing GM, highlighting the complexity by which environmental factors interact to modulate GM.}, }
@article {pmid29906449, year = {2018}, author = {Tropini, C and Moss, EL and Merrill, BD and Ng, KM and Higginbottom, SK and Casavant, EP and Gonzalez, CG and Fremin, B and Bouley, DM and Elias, JE and Bhatt, AS and Huang, KC and Sonnenburg, JL}, title = {Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota.}, journal = {Cell}, volume = {173}, number = {7}, pages = {1742-1754.e17}, pmid = {29906449}, issn = {1097-4172}, support = {K08 CA184420/CA/NCI NIH HHS/United States ; P50 GM107615/GM/NIGMS NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteroidetes/drug effects/genetics/isolation &amp; purification ; Cecum/chemistry/metabolism/microbiology/pathology ; Colon/chemistry/microbiology/pathology ; Cytokines/metabolism ; Diarrhea/immunology/microbiology/*pathology/veterinary ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Glycoside Hydrolases/metabolism ; Humans ; Immunity, Humoral/drug effects ; Immunoglobulin G/metabolism ; Intestinal Mucosa/microbiology/pathology ; Metagenomics ; Mice ; Osmolar Concentration ; Polyethylene Glycols/metabolism/*pharmacology ; Proteome/analysis ; RNA, Ribosomal, 16S/chemistry/genetics ; Verrucomicrobia/drug effects/genetics/isolation &amp; purification ; }, abstract = {Osmotic diarrhea is a prevalent condition in humans caused by food intolerance, malabsorption, and widespread laxative use. Here, we assess the resilience of the gut ecosystem to osmotic perturbation at multiple length and timescales using mice as model hosts. Osmotic stress caused reproducible extinction of highly abundant taxa and expansion of less prevalent members in human and mouse microbiotas. Quantitative imaging revealed decimation of the mucus barrier during osmotic perturbation, followed by recovery. The immune system exhibited temporary changes in cytokine levels and a lasting IgG response against commensal bacteria. Increased osmolality prevented growth of commensal strains in vitro, revealing one mechanism contributing to extinction. Environmental availability of microbiota members mitigated extinction events, demonstrating how species reintroduction can affect community resilience. Our findings (1) demonstrate that even mild osmotic diarrhea can cause lasting changes to the microbiota and host and (2) lay the foundation for interventions that increase system-wide resilience.}, }
@article {pmid28940049, year = {2018}, author = {Tremlett, H and Waubant, E}, title = {The Gut Microbiota and Pediatric Multiple Sclerosis: Recent Findings.}, journal = {Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics}, volume = {15}, number = {1}, pages = {102-108}, pmid = {28940049}, issn = {1878-7479}, mesh = {Biomarkers ; Child ; *Gastrointestinal Microbiome ; Humans ; Multiple Sclerosis/immunology/*microbiology ; Recurrence ; }, abstract = {Pediatric multiple sclerosis (MS) is a chronic, life-long neurological condition associated with inflammation and degeneration in the brain and spinal cord. Fortunately, < 5% of people with MS have their onset in childhood years. However, studying these very-early-onset cases of MS offers key advantages. In particular, with fewer years lived, children have had a limited range of exposures, potentially enhancing our ability to identify what might cause MS. Further, as the actual timing of the biological MS onset is unknown, the possibility to study these children much closer to the real onset of disease is far greater than in the typical adult with MS. Whether MS (in children or adults) can be prevented is unknown and the available drugs are only modestly effective in modifying the disease course and are not without risk. Emerging evidence is providing insight into the gut microbiota's potential role in triggering and shaping neurological conditions such as MS. The limited number of studies in humans with MS and absence of prior work in pediatric MS motivated the following 3 fundamental questions, addressed in 2 cross-sectional and 1 longitudinal investigation in children with and without MS: 1) Does the gut microbiota composition differ between children with and without MS? 2) Is there an association between the gut microbiota and host immune markers in children with and without MS? 3) Is the gut microbiota associated with the future risk of a MS relapse?}, }
@article {pmid30075203, year = {2018}, author = {Kumar, M and Ji, B and Babaei, P and Das, P and Lappa, D and Ramakrishnan, G and Fox, TE and Haque, R and Petri, WA and Bäckhed, F and Nielsen, J}, title = {Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling.}, journal = {Metabolic engineering}, volume = {49}, number = {}, pages = {128-142}, doi = {10.1016/j.ymben.2018.07.018}, pmid = {30075203}, issn = {1096-7184}, mesh = {Amino Acids/*blood ; Child ; *Child Nutrition Disorders/blood/genetics/microbiology ; Child, Preschool ; *Dysbiosis/blood/genetics/microbiology ; Female ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; Humans ; Male ; }, abstract = {Malnutrition is a severe non-communicable disease, which is prevalent in children from low-income countries. Recently, a number of metagenomics studies have illustrated associations between the altered gut microbiota and child malnutrition. However, these studies did not examine metabolic functions and interactions between individual species in the gut microbiota during health and malnutrition. Here, we applied genome-scale metabolic modeling to model the gut microbial species, which were selected from healthy and malnourished children from three countries. Our analysis showed reduced metabolite production capabilities in children from two low-income countries compared with a high-income country. Additionally, the models were also used to predict the community-level metabolic potentials of gut microbes and the patterns of pairwise interactions among species. Hereby we found that due to bacterial interactions there may be reduced production of certain amino acids in malnourished children compared with healthy children from the same communities. To gain insight into alterations in the metabolism of malnourished (stunted) children, we also performed targeted plasma metabolic profiling in the first 2 years of life of 25 healthy and 25 stunted children. Plasma metabolic profiling further revealed that stunted children had reduced plasma levels of essential amino acids compared to healthy controls. Our analyses provide a framework for future efforts towards further characterization of gut microbial metabolic capabilities and their contribution to malnutrition.}, }
@article {pmid30037148, year = {2018}, author = {Cross, ST and Kapuscinski, ML and Perino, J and Maertens, BL and Weger-Lucarelli, J and Ebel, GD and Stenglein, MD}, title = {Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms.}, journal = {Viruses}, volume = {10}, number = {7}, pages = {}, pmid = {30037148}, issn = {1999-4915}, support = {UL1 TR002535/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Borrelia burgdorferi/genetics/isolation &amp; purification ; Coinfection/epidemiology/*microbiology/*virology ; Eukaryota/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Ixodes/genetics/*microbiology/*virology ; Lyme Disease ; Microbiota/genetics ; Orthobunyavirus/genetics/isolation &amp; purification ; Phlebovirus/genetics/isolation &amp; purification ; Prevalence ; Symbiosis ; Tick Infestations/epidemiology/microbiology/virology ; Tick-Borne Diseases/*epidemiology/microbiology/virology ; Viruses/genetics/isolation &amp; purification ; Wisconsin/epidemiology ; }, abstract = {Ixodes scapularis ticks harbor a variety of microorganisms, including eukaryotes, bacteria and viruses. Some of these can be transmitted to and cause disease in humans and other vertebrates. Others are not pathogenic, but may impact the ability of the tick to harbor and transmit pathogens. A growing number of studies have examined the influence of bacteria on tick vector competence but the influence of the tick virome remains less clear, despite a surge in the discovery of tick-associated viruses. In this study, we performed shotgun RNA sequencing on 112 individual adult I. scapularis collected in Wisconsin, USA. We characterized the abundance, prevalence and co-infection rates of viruses, bacteria and eukaryotic microorganisms. We identified pairs of tick-infecting microorganisms whose observed co-infection rates were higher or lower than would be expected, or whose RNA levels were positively correlated in co-infected ticks. Many of these co-occurrence and correlation relationships involved two bunyaviruses, South Bay virus and blacklegged tick phlebovirus-1. These viruses were also the most prevalent microorganisms in the ticks we sampled, and had the highest average RNA levels. Evidence of associations between microbes included a positive correlation between RNA levels of South Bay virus and Borrelia burgdorferi, the Lyme disease agent. These findings contribute to the rationale for experimental studies on the impact of viruses on tick biology and vector competence.}, }
@article {pmid29600282, year = {2018}, author = {Auchtung, TA and Fofanova, TY and Stewart, CJ and Nash, AK and Wong, MC and Gesell, JR and Auchtung, JM and Ajami, NJ and Petrosino, JF}, title = {Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi.}, journal = {mSphere}, volume = {3}, number = {2}, pages = {}, pmid = {29600282}, issn = {2379-5042}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; }, mesh = {Adult ; Candida albicans/genetics/isolation &amp; purification ; DNA, Ribosomal Spacer/genetics ; Diet ; Feces/microbiology ; Food Microbiology ; Fungi/*classification/isolation &amp; purification ; Gastrointestinal Tract/*microbiology/physiology ; Healthy Volunteers ; Humans ; Mouth/microbiology ; Mycobiome/*physiology ; RNA, Ribosomal, 18S/genetics ; Saccharomyces cerevisiae/genetics/isolation &amp; purification ; Saliva/microbiology ; Sequence Analysis, DNA ; }, abstract = {A wide diversity of fungi have been detected in the human gastrointestinal (GI) tract with the potential to provide or influence important functions. However, many of the fungi most commonly detected in stool samples are also present in food or the oral cavity. Therefore, to recognize which gut fungi are likely to have a sustained influence on human health, there is a need to separate transient members of the GI tract from true colonizers. To identify colonizing fungi, the eukaryotic rRNA operon's second internal transcribed spacer (ITS2) was sequenced from the stool, saliva, and food of healthy adults following consumption of different controlled diets. Unlike most bacterial 16S rRNA genes, the only fungal ITS2 operational taxonomic units (OTUs) detected in stool DNA across multiple diets were also present in saliva and/or food. Additional analyses, including culture-based approaches and sequencing of the 18S rRNA gene, ITS2 cDNA, and DNA extracted using alternative methods, failed to detect additional fungi. Two abundant fungi, Saccharomyces cerevisiae and Candida albicans, were examined further in healthy volunteers. Saccharomyces became undetectable in stool when a S. cerevisiae-free diet was consumed, and the levels of C. albicans in stool were dramatically reduced by more frequent cleaning of teeth. Extremely low fungal abundance, the inability of fungi to grow under conditions mimicking the distal gut, and evidence from analysis of other public datasets further support the hypothesis that fungi do not routinely colonize the GI tracts of healthy adults. IMPORTANCE We sought to identify the fungi that colonize healthy GI tracts and that have a sustained influence on the diverse functions of the gut microbiome. Instead, we found that all fungi in the stool of healthy volunteers could be explained by their presence in oral and dietary sources and that our results, together with those from other analyses, support the model that there is little or no gastrointestinal colonization by fungi. This may be due to Westernization, primate evolution, fungal ecology, and/or the strong defenses of a healthy immune system. Importantly, fungal colonization of the GI tract may often be indicative of disease. As fungi can cause serious infections in immunocompromised individuals and are found at increased abundance in multiple disorders of the GI tract, understanding normal fungal colonization is essential for proper treatment and prevention of fungal pathogenesis.}, }
@article {pmid30518125, year = {2018}, author = {Raimundo, I and Silva, SG and Costa, R and Keller-Costa, T}, title = {Bioactive Secondary Metabolites from Octocoral-Associated Microbes-New Chances for Blue Growth.}, journal = {Marine drugs}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/md16120485}, pmid = {30518125}, issn = {1660-3397}, support = {EXPL/MAR-EST/1664/2013//Fundação para a Ciência e a Tecnologia/ ; PTDC/MAR-BIO/1547/2014//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/genetics/*metabolism ; Biological Products/isolation &amp; purification/metabolism/*pharmacology ; Biosynthetic Pathways/*genetics ; Fungi/genetics/*metabolism ; Industrial Microbiology/methods ; Microbiota/physiology ; Multigene Family ; Symbiosis ; Technology, Pharmaceutical/methods ; }, abstract = {Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. However, mechanistic understanding of the contribution of microbial symbionts to the chemical diversity of octocorals is yet to be achieved. This review inventories the natural products so-far described for octocoral-derived bacteria and fungi, uncovering a true chemical arsenal of terpenes, steroids, alkaloids, and polyketides with antibacterial, antifungal, antiviral, antifouling, anticancer, anti-inflammatory, and antimalarial activities of enormous potential for blue growth. Genome mining of 15 bacterial associates (spanning 12 genera) cultivated from Eunicella spp. resulted in the identification of 440 putative and classifiable secondary metabolite biosynthetic gene clusters (BGCs), encompassing varied terpene-, polyketide-, bacteriocin-, and nonribosomal peptide-synthase BGCs. This points towards a widespread yet uncharted capacity of octocoral-associated bacteria to synthetize a broad range of natural products. However, to extend our knowledge and foster the near-future laboratory production of bioactive compounds from (cultivatable and currently uncultivatable) octocoral symbionts, optimal blending between targeted metagenomics, DNA recombinant technologies, improved symbiont cultivation, functional genomics, and analytical chemistry are required. Such a multidisciplinary undertaking is key to achieving a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties.}, }
@article {pmid30479272, year = {2018}, author = {Glover, AG and Wiklund, H and Chen, C and Dahlgren, TG}, title = {Managing a sustainable deep-sea 'blue economy' requires knowledge of what actually lives there.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30479272}, issn = {2050-084X}, mesh = {*Biodiversity ; Conservation of Energy Resources/*methods ; *Ecosystem ; Metagenomics/*methods ; *Oceans and Seas ; }, abstract = {Ensuring that the wealth of resources contained in our oceans are managed and developed in a sustainable manner is a priority for the emerging 'blue economy'. However, modern ecosystem-based management approaches do not translate well to regions where we know almost nothing about the individual species found in the ecosystem. Here, we propose a new taxon-focused approach to deep-sea conservation that includes regulatory oversight to set targets for the delivery of taxonomic data. For example, a five-year plan to deliver taxonomic and genomic knowledge on a thousand species in regions of the ocean earmarked for industrial activity is an achievable target. High-throughput, integrative taxonomy can, therefore, provide the data that is needed to monitor various ecosystem services (such as the natural history, connectivity, value and function of species) and to help break the regulatory deadlock of high-seas conservation.}, }
@article {pmid30108167, year = {2018}, author = {Peura, S and Buck, M and Aalto, SL and Morales, SE and Nykänen, H and Eiler, A}, title = {Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake.}, journal = {mBio}, volume = {9}, number = {4}, pages = {}, pmid = {30108167}, issn = {2150-7511}, mesh = {Anaerobiosis ; *Autotrophic Processes ; *Biota ; Carbon/*metabolism ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Finland ; Lakes/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Oxygen-stratified lakes are typical for the boreal zone and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study, we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome-assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in an oxygen-depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, potentially deriving their energy from reactions related to sulfur, iron, and nitrogen transformations. The community, as well as the functions, was stratified along the redox gradient. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing toward a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change-associated fluctuations in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole-lake metabolism even beyond the impact to the phototrophic community.IMPORTANCE Autotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into the organic form, facilitating the survival of all other organisms. In certain environments, the autotrophic production is limited by environmental conditions and the food web is supported by external carbon inputs. One such environment is stratified boreal lakes, which are one of the biggest natural sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of utmost importance for the future climate. Here, we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the anoxic, poorly illuminated layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics.}, }
@article {pmid30042197, year = {2018}, author = {Murray, AK and Zhang, L and Yin, X and Zhang, T and Buckling, A and Snape, J and Gaze, WH}, title = {Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities.}, journal = {mBio}, volume = {9}, number = {4}, pages = {}, pmid = {30042197}, issn = {2150-7511}, support = {BB/L502509/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Cefotaxime/*pharmacology ; *Cephalosporin Resistance ; Cephalosporinase/genetics/metabolism ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; Microbiota/*drug effects ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Selection, Genetic ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Recent research has demonstrated that selection for antibiotic resistance occurs at very low antibiotic concentrations in single-species experiments, but the relevance of these findings when species are embedded in complex microbial communities is unclear. We show that the strength of selection for naturally occurring resistance alleles in a complex community remains constant from low subinhibitory to above clinically relevant concentrations. Selection increases with antibiotic concentration before reaching a plateau where selection remains constant over a 2-order-magnitude concentration range. This is likely to be due to cross protection of the susceptible bacteria in the community following rapid extracellular antibiotic degradation by the resistant population, shown experimentally through a combination of chemical quantification and bacterial growth experiments. Metagenome and 16S rRNA analyses of sewage-derived bacterial communities evolved under cefotaxime exposure show preferential enrichment for blaCTX-M genes over all other beta-lactamase genes, as well as positive selection and co-selection for antibiotic resistant, opportunistic pathogens. These findings have far-reaching implications for our understanding of the evolution of antibiotic resistance, by challenging the long-standing assumption that selection occurs in a dose-dependent manner.IMPORTANCE Antibiotic resistance is one of the greatest global issues facing society. Still, comparatively little is known about selection for resistance at very low antibiotic concentrations. We show that the strength of selection for clinically important resistance genes within a complex bacterial community can remain constant across a large antibiotic concentration range (wide selective space). Therefore, largely understudied ecological compartments could be just as important as clinical environments for selection of antibiotic resistance.}, }
@article {pmid29621980, year = {2018}, author = {Pace, RM and Prince, AL and Ma, J and Belfort, BDW and Harvey, AS and Hu, M and Baquero, K and Blundell, P and Takahashi, D and Dean, T and Kievit, P and Sullivan, EL and Friedman, JE and Grove, K and Aagaard, KM}, title = {Modulations in the offspring gut microbiome are refractory to postnatal synbiotic supplementation among juvenile primates.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {28}, pmid = {29621980}, issn = {1471-2180}, support = {F32 HD082969/HD/NICHD NIH HHS/United States ; R01 MH107508/MH/NIMH NIH HHS/United States ; K12 GM084897/GM/NIGMS NIH HHS/United States ; R24DK090964//National Institute of Child Health and Human Development/International ; 1RO1DK089201//National Institute of Child Health and Human Development/International ; DP2 OD001500/OD/NIH HHS/United States ; F32HD082969//National Institute of Child Health and Human Development/International ; DP21DP2OD001500//NIH Director New Innovator Pioneer Award/International ; R01 DK089201/DK/NIDDK NIH HHS/United States ; K12GM084897/NH/NIH HHS/United States ; R24 DK090964/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics/*metabolism ; *Diet, High-Fat ; Dysbiosis/microbiology ; Enterococcus/physiology ; Faecalibacterium ; Feces/microbiology ; Female ; Firmicutes ; Gastrointestinal Microbiome/genetics/*physiology ; Lactobacillus/physiology ; Lipids/blood ; Macaca/microbiology ; Male ; Metabolic Networks and Pathways ; Metagenomics ; Primates/*microbiology ; Probiotics ; Psyllium ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; *Synbiotics ; Triglycerides/blood ; }, abstract = {BACKGROUND: We and others have previously shown that alterations in the mammalian gut microbiome are associated with diet, notably early life exposure to a maternal high fat diet (HFD). Here, we aimed to further these studies by examining alterations in the gut microbiome of juvenile Japanese macaques (Macaca fuscata) that were exposed to a maternal HFD, weaned onto a control diet, and later supplemented with a synbiotic comprised of psyllium seed and Enterococcus and Lactobacillus species.<br><br>RESULTS: Eighteen month old offspring (n = 7) of 36% HFD fed dams were fed a control (14% fat) diet post weaning, then were synbiotic supplemented for 75 days and longitudinal stool and serum samples were obtained. All stool samples were subjected to 16S rRNA metagenomic sequencing, and microbiome profiles and serum lipids and triglycerides were compared to untreated, healthy age matched and diet matched controls (n = 7). Overall, 16S-based metagenomic analysis revealed that supplementation exerted minimal alterations to the gut microbiome including transient increased abundance of Lactobacillus species and decreased abundance of few bacterial genera, including Faecalibacterium and Anaerovibrio. However, serum lipid analysis revealed significant decreases in triglycerides, cholesterol, and LDL (p < 0.05). Nevertheless, supplemented juveniles challenged 4 months later were not protected from HFD-induced gut dysbiosis.<br><br>CONCLUSIONS: Synbiotic supplementation is temporally associated with alterations in the gut microbiome and host lipid profiles of juvenile Japanese macaques that were previously exposed to a maternal HFD. Despite these presumptive temporal benefits, a protective effect against later HFD-challenge gut dysbiosis was not observed.}, }
@article {pmid28819272, year = {2017}, author = {Concheri, G and Stevanato, P and Zaccone, C and Shotyk, W and D'Orazio, V and Miano, T and Piffanelli, P and Rizzi, V and Ferrandi, C and Squartini, A}, title = {Rapid peat accumulation favours the occurrence of both fen and bog microbial communities within a Mediterranean, free-floating peat island.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8511}, pmid = {28819272}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; DNA, Fungal/chemistry/genetics/isolation &amp; purification ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/genetics ; *Islands ; Italy ; Metagenomics ; *Microbiota ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Wetlands ; }, abstract = {The unique environment of a 4m-thick, free-floating peat island within the Posta Fibreno lake (Central Italy) was analyzed using DNA-based techniques to assess bacterial and fungal community members identity and abundance. Two depths were sampled at 41 and 279 cm from the surface, the former corresponding to an emerged portion of Sphagnum residues accumulated less than 30 yrs ago, and the latter mainly consisting of silty peat belonging to the deeply submerged part of the island, dating back to 1520-1660 AD. The corresponding communities were very diverse, each of them dominated by a different member of the Delta-proteobacteria class for prokaryotes. Among Eukaryotes, Ascomycota prevailed in the shallow layer while Basidiomycota were abundant in the deep sample. The identity of taxa partitioning between acidic surface layer and neutral core is very reminiscent of the differences reported between bogs and fens respectively, supporting the view of Posta Fibreno as a relic transitional floating mire. Moreover, some microbial taxa show an unusual concurrent species convergence between this sub-Mediterranean site and far Nordic or circumpolar environments. This study represents the first report describing the biotic assemblages of such a peculiar environment, and provides some insights into the possible mechanisms of its evolution.}, }
@article {pmid28819242, year = {2017}, author = {Lim, Y and Totsika, M and Morrison, M and Punyadeera, C}, title = {The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8523}, pmid = {28819242}, issn = {2045-2322}, mesh = {Adult ; Bacteria/classification/genetics ; Cluster Analysis ; DNA, Bacterial/analysis/genetics/*isolation &amp; purification ; DNA, Ribosomal/chemistry/genetics ; Healthy Volunteers ; Humans ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Saliva/*microbiology ; Sequence Analysis, DNA ; Specimen Handling/*methods ; Young Adult ; beta-Globins/analysis/genetics ; }, abstract = {Saliva has attracted attention as a diagnostic fluid due to the association of oral microbiota with systemic diseases. However, the lack of standardised methods for saliva collection has led to the slow uptake of saliva in microbiome research. The aim of this study was to systematically evaluate the potential effects on salivary microbiome profiles using different methods of saliva collection, storage and gDNA extraction. Three types of saliva fractions were collected from healthy individuals with or without the gDNA stabilising buffer. Subsequently, three types of gDNA extraction methods were evaluated to determine the gDNA extraction efficiencies from saliva samples. The purity of total bacterial gDNA was evaluated using the ratio of human β-globin to bacterial 16S rRNA PCR while 16S rRNA gene amplicon sequencing was carried out to identify the bacterial profiles present in these samples. The quantity and quality of extracted gDNA were similar among all three gDNA extraction methods and there were no statistically significant differences in the bacterial profiles among different saliva fractions at the genus-level of taxonomic classification. In conclusion, saliva sampling, processing and gDNA preparation do not have major influence on microbiome profiles.}, }
@article {pmid29543557, year = {2018}, author = {Kiely, CJ and Pavli, P and O'Brien, CL}, title = {The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome.}, journal = {Gut microbes}, volume = {9}, number = {6}, pages = {477-485}, pmid = {29543557}, issn = {1949-0984}, mesh = {Adult ; Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; Colitis, Ulcerative/microbiology/pathology ; Crohn Disease/microbiology/pathology ; Endoscopy, Gastrointestinal ; *Gastrointestinal Microbiome ; Humans ; Inflammation/pathology ; Inflammatory Bowel Diseases/*microbiology/*pathology ; Intestinal Mucosa/*microbiology/*pathology ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Time Factors ; }, abstract = {Studies of the human intestinal microbiome in patients with inflammatory bowel disease (IBD) consistently show that there are differences (an abnormal or unbalanced microbiome, &quot;dysbiosis&quot;) when compared to healthy subjects. We sought to describe changes in the microbiome in individual patients over time, and determine the clinical factors that are associated with significant alteration. Forty-two mucosal biopsies were collected from 20 patients that were spaced an average of 2.4 years apart. These were analysed using bacterial 16S rRNA gene high-throughput sequencing methods. Presence of active inflammation was determined endoscopically and histologically. Inferred metagenomics analysis was conducted using the PICRUSt package. We found that the differences in the microbiome over time in individual patients were greatest in the presence of ongoing intestinal inflammation, as determined by the Yue and Clayton theta distance between sample pairs (adjusted p = 0.00031). Samples from patients with previous abdominal surgery had lower alpha (within sample) diversity compared with those with no prior operations (mean Shannon index 2.083, 2.510 respectively, p = 0.017). There were no changes in the inferred bacterial metagenomic profile. The microbiome in IBD undergoes considerable fluctuation over time. These changes are greatest when there is histologically confirmed inflammation at both time-points.}, }
@article {pmid29980437, year = {2018}, author = {Kim, M and Galan, C and Hill, AA and Wu, WJ and Fehlner-Peach, H and Song, HW and Schady, D and Bettini, ML and Simpson, KW and Longman, RS and Littman, DR and Diehl, GE}, title = {Critical Role for the Microbiota in CX3CR1+ Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses.}, journal = {Immunity}, volume = {49}, number = {1}, pages = {151-163.e5}, pmid = {29980437}, issn = {1097-4180}, support = {R21 AI123945/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; T32 AI053831/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 AI036211/AI/NIAID NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 AI125264/AI/NIAID NIH HHS/United States ; R01 DK114252/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Antigen Presentation ; Bacterial Adhesion/immunology ; CX3C Chemokine Receptor 1/*metabolism ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*immunology ; Homeostasis ; Immune Tolerance ; Immunity, Mucosal ; Inflammation/immunology ; Inflammatory Bowel Diseases/immunology ; Interleukin-10/immunology/metabolism ; Intestinal Mucosa/*immunology/microbiology ; Male ; Mice ; Mononuclear Phagocyte System/*immunology ; RAW 264.7 Cells ; T-Lymphocytes, Regulatory/*immunology ; Th1 Cells/*immunology ; }, abstract = {The intestinal barrier is vulnerable to damage by microbiota-induced inflammation that is normally restrained through mechanisms promoting homeostasis. Such disruptions contribute to autoimmune and inflammatory diseases including inflammatory bowel disease. We identified a regulatory loop whereby, in the presence of the normal microbiota, intestinal antigen-presenting cells (APCs) expressing the chemokine receptor CX3CR1 reduced expansion of intestinal microbe-specific T helper 1 (Th1) cells and promoted generation of regulatory T cells responsive to food antigens and the microbiota itself. We identified that disruption of the microbiota resulted in CX3CR1+ APC-dependent inflammatory Th1 cell responses with increased pathology after pathogen infection. Colonization with microbes that can adhere to the epithelium was able to compensate for intestinal microbiota loss, indicating that although microbial interactions with the epithelium can be pathogenic, they can also activate homeostatic regulatory mechanisms. Our results identify a cellular mechanism by which the microbiota limits intestinal inflammation and promotes tissue homeostasis.}, }
@article {pmid28811583, year = {2017}, author = {Chen, CH and Lin, YL and Chen, KH and Chen, WP and Chen, ZF and Kuo, HY and Hung, HF and Tang, CY and Liou, ML}, title = {Bacterial diversity among four healthcare-associated institutes in Taiwan.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8230}, pmid = {28811583}, issn = {2045-2322}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Cross Infection/epidemiology/microbiology ; *Environmental Microbiology ; *Health Facilities ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Taiwan/epidemiology ; }, abstract = {Indoor microbial communities have important implications for human health, especially in health-care institutes (HCIs). The factors that determine the diversity and composition of microbiomes in a built environment remain unclear. Herein, we used 16S rRNA amplicon sequencing to investigate the relationships between building attributes and surface bacterial communities among four HCIs located in three buildings. We examined the surface bacterial communities and environmental parameters in the buildings supplied with different ventilation types and compared the results using a Dirichlet multinomial mixture (DMM)-based approach. A total of 203 samples from the four HCIs were analyzed. Four bacterial communities were grouped using the DMM-based approach, which were highly similar to those in the 4 HCIs. The α-diversity and β-diversity in the naturally ventilated building were different from the conditioner-ventilated building. The bacterial source composition varied across each building. Nine genera were found as the core microbiota shared by all the areas, of which Acinetobacter, Enterobacter, Pseudomonas, and Staphylococcus are regarded as healthcare-associated pathogens (HAPs). The observed relationship between environmental parameters such as core microbiota and surface bacterial diversity suggests that we might manage indoor environments by creating new sanitation protocols, adjusting the ventilation design, and further understanding the transmission routes of HAPs.}, }
@article {pmid30589606, year = {2019}, author = {Yasir, M and Qureshi, AK and Khan, I and Bibi, F and Rehan, M and Khan, SB and Azhar, EI}, title = {Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {1}, pages = {17-27}, doi = {10.1089/omi.2018.0176}, pmid = {30589606}, issn = {1557-8100}, mesh = {Bacteria/*genetics ; Biodiversity ; Hot Springs/*microbiology ; Hot Temperature ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Saudi Arabia ; Sequence Analysis, DNA/methods ; }, abstract = {Hot springs are natural habitats for thermophilic microorganisms and provide a significant opportunity for bioprospecting thermostable biomolecules. However, the scientific community has only a fragmented understanding of the microbial diversity and composition in these biotopes. In this study, bacterial diversity in sediment samples from six hot springs of Saudi Arabia was investigated using an improved culture-dependent approach. High-throughput MALDI-TOF MS (matrix assisted laser desorption/ionization mass spectrometry) and 16S rRNA genes sequencing were used for the identification of purified isolates. Most of the hot springs had a neutral pH and a temperature range of 45-89°C. Relatively higher colony-forming units (1.9 ± 0.45 × 104) were observed with 60°C incubation of an 89°C sediment sample from the hot spring at Ain al Harra1. Among the 536 purified isolates, 6 novel candidate species were found, and the remaining isolates represented 139 distinct species. Several species, such as Bacillus cereus, Bacillus subtilis, and Bacillus schlegelii, were ubiquitous in the hot springs sampled, but 102 of the identified species were uniquely distributed among the hot springs. Sixteen of the isolated thermophilic bacteria, including Geobacillus kaustophilus, Thermus oshimai, and Brevibacillus thermoruber, grew at ≥60°C. In addition, 21 species exhibited hydrolytic enzymatic activity. Most of these species belonged to Bacillus and Brevibacillus. Overall, this study contributes to global knowledgebase on bacterial communities by comprehensively profiling culture-based bacterial diversity in the hot springs of Saudi Arabia. Further studies are required for investigating bacteria from hot springs by a metagenomic approach.}, }
@article {pmid30486439, year = {2018}, author = {Yi, X and Yuan, J and Zhu, Y and Yi, X and Zhao, Q and Fang, K and Cao, L}, title = {Comparison of the Abundance and Community Structure of N-Cycling Bacteria in Paddy Rhizosphere Soil under Different Rice Cultivation Patterns.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19123772}, pmid = {30486439}, issn = {1422-0067}, mesh = {Bacteria/*classification/genetics/metabolism ; *Biodiversity ; Enzymes/genetics/metabolism ; Metagenome ; Metagenomics/methods ; Nitrogen ; Oryza/*microbiology ; Phylogeny ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Eco-agricultural systems aim to reduce the use of chemical fertilizers in order to improve sustainable production and maintain a healthy ecosystem. The aim of this study was to explore the effects of rice-frog farming on the bacterial community and N-cycling microbes in paddy rhizosphere soil. This experiment involved three rice cultivation patterns: Conventionally cultivated rice (CR), green rice-frog farming (GR), and organic rice-frog farming (OR). The rice yield, paddy soil enzyme activities, physicochemical variables and bacterial and N-cycling bacterial abundances were quantitatively analyzed. Rice-frog cultivations significantly increased soil protease, nitrate and reductase activity. Additionally, the nirS gene copy number and the relative abundance of denitrifying bacteria also increased, however urease activity and the relative abundance of nitrifying bacteria significantly decreased. The bacterial community richness and diversity of OR soil was significantly higher than that of the GR or CR soil. Nitrogen use efficiency (NUE) of GR was highest. The N-cycling bacterial community was positively correlated with the total carbon (TC), total nitrogren (TN) and carbon to nitrogen (C:N) ratio. The present work strengthens our current understanding of the soil bacterial community structure and its functions under rice-frog farming. The present work also provides certain theoretical support for the selection of rational rice cultivation patterns.}, }
@article {pmid30486338, year = {2018}, author = {Amedei, A and Boem, F}, title = {I've Gut A Feeling: Microbiota Impacting the Conceptual and Experimental Perspectives of Personalized Medicine.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19123756}, pmid = {30486338}, issn = {1422-0067}, support = {FAS SALUTE 2014//Regione Toscana/ ; P2016.0808//Ente Cassa di Risparmio di Firenze/ ; }, mesh = {Animals ; Biodiversity ; Biological Therapy ; Disease Susceptibility ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genomics/methods ; Humans ; Metagenomics/methods ; Microbiota ; Organ Specificity ; *Precision Medicine/methods ; Research ; Symbiosis ; }, abstract = {In recent years, the human microbiota has gained increasing relevance both in research and clinical fields. Increasing studies seem to suggest the centrality of the microbiota and its composition both in the development and maintenance of what we call &quot;health&quot; and in generating and/or favoring (those cases in which the microbiota's complex relational architecture is dysregulated) the onset of pathological conditions. The complex relationships between the microbiota and human beings, which invest core notions of biomedicine such as &quot;health&quot; and &quot;individual,&quot; do concern not only problems of an empirical nature but seem to require the need to adopt new concepts and new perspectives in order to be properly analysed and utilized, especially for their therapeutic implementation. In this contribution we report and discuss some of the theoretical proposals and innovations (from the ecological component to the notion of polygenomic organism) aimed at producing this change of perspective. In conclusion, we summarily analyze what impact and what new challenges these new approaches might have on personalized/person centred/precision medicine.}, }
@article {pmid30248115, year = {2018}, author = {Kurobe, T and Lehman, PW and Hammock, BG and Bolotaolo, MB and Lesmeister, S and Teh, SJ}, title = {Biodiversity of cyanobacteria and other aquatic microorganisms across a freshwater to brackish water gradient determined by shotgun metagenomic sequencing analysis in the San Francisco Estuary, USA.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0203953}, pmid = {30248115}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Chlorophyta/classification/genetics ; Cyanobacteria/classification/*genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Diatoms/classification/genetics/isolation &amp; purification ; Estuaries ; Fresh Water/microbiology ; Genotype ; Harmful Algal Bloom ; Metagenomics ; Microcystis/genetics/isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction ; Saline Waters ; Salinity ; San Francisco ; Spatio-Temporal Analysis ; *Water Microbiology ; }, abstract = {Blooms of Microcystis and other harmful cyanobacteria can degrade water quality by producing cyanotoxins or other toxic compounds. The goals of this study were (1) to facilitate understanding of community structure for various aquatic microorganisms in brackish water and freshwater regions with emphasis on cyanobacteria, and (2) to test a hypothesis that Microcystis genotypes that tolerate higher salinity were blooming in brackish water environments during the severe drought, 2014. Shotgun metagenomic analysis revealed that cyanobacteria dominated the brackish water region while bacteria dominated the freshwater region. A group of cyanobacteria (e.g., Aphanizomenon, Microcystis, Planktothrix, Pseudanabaena), bacteria (e.g., Bacillus, Porphyrobacter), and diatoms (Phaeodactylum and Thalassiosira) were abundant in the brackish water region. In contrast, Hassallia (cyanobacteria) and green algae (Nannochloropsis, Chlamydomonas, and Volvox) were abundant in the landward freshwater region. Station variation was also apparent. One landward sampling station located downstream of an urbanized area differed substantially from the other stations in terms of both water chemistry and community structure, with a higher percentage of arthropods, green algae, and eukaryotes. Screening of the Microcystis internal transcribed spacer region revealed six representative genotypes, and two of which were successfully quantified using qPCR (Genotypes I and VI). Both genotypes occurred predominantly in the freshwater region, so the data from this study did not support the hypothesis that salinity tolerant Microcystis genotypes bloomed in the brackish water region in 2014.}, }
@article {pmid29459499, year = {2018}, author = {Kato, S and Sakai, S and Hirai, M and Tasumi, E and Nishizawa, M and Suzuki, K and Takai, K}, title = {Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle.}, journal = {Microbes and environments}, volume = {33}, number = {1}, pages = {107-110}, pmid = {29459499}, issn = {1347-4405}, mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics/metabolism ; *Bacterial Physiological Phenomena ; Biodiversity ; Denitrification ; Ecosystem ; Hot Springs/microbiology ; Metagenome ; *Metagenomics ; Nitrification ; Nitrogen/metabolism ; *Nitrogen Cycle ; Soil Microbiology ; }, abstract = {Many thermophiles thriving in a natural high-temperature environment remain uncultivated, and their ecophysiological functions in the biogeochemical cycle remain unclear. In the present study, we performed long-term continuous cultivation at 65°C and 70°C using a microbial mat sample, collected from a subsurface geothermal stream, as the inoculum, and reconstructed the whole genome of the maintained populations using metagenomics. Some metagenome-assembled genomes (MAGs), affiliated into phylum-level bacterial and archaeal clades without cultivated representatives, contained genes involved in nitrogen metabolism including nitrification and denitrification. Our results show genetic components and their potential interactions for the biogeochemical nitrogen cycle in a subsurface geothermal environment.}, }
@article {pmid30701707, year = {2019}, author = {Jerde, CL and Wilson, EA and Dressler, TL}, title = {Measuring global fish species richness with eDNA metabarcoding.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {19-22}, doi = {10.1111/1755-0998.12929}, pmid = {30701707}, issn = {1755-0998}, support = {AID-OAA-A-16-00057//United States Agency for International Development/ ; }, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA/chemistry/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification/*genetics ; French Guiana ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Water/chemistry ; }, abstract = {Despite mounting threats to global freshwater and marine biodiversity, including climate change, habitat alteration, overharvesting and pollution, we struggle to know which species are present below the water's surface that are suffering from these stressors. However, the idea that a water sample containing environmental DNA (eDNA) can be screened using high-throughput sequencing and bioinformatics to reveal the identity of aquatic species is a revolutionary advance for studying the patterns of species extirpation, invasive species establishment and the dynamics of species richness. To date, many of the critical tests of fisheries diversity using this metabarcoding approach have been conducted in lower diversity systems (<40 fish species), but in this issue of Molecular Ecology Resources, Cilleros et al. (2018) described their eDNA application in the species-rich French Guiana fishery (>200 fish species) and showed the greater potential and some limitations of using eDNA in species-rich environments.}, }
@article {pmid30642268, year = {2019}, author = {Aiemjoy, K and Altan, E and Aragie, S and Fry, DM and Phan, TG and Deng, X and Chanyalew, M and Tadesse, Z and Callahan, EK and Delwart, E and Keenan, JD}, title = {Viral species richness and composition in young children with loose or watery stool in Ethiopia.}, journal = {BMC infectious diseases}, volume = {19}, number = {1}, pages = {53}, doi = {10.1186/s12879-019-3674-3}, pmid = {30642268}, issn = {1471-2334}, support = {F31 HD088070-01A1//National Institute of Child Health and Human Development/ ; U10 EY016214//National Eye Institute/ ; R01 HL105770//National Heart, Lung, and Blood Institute/ ; }, mesh = {Biodiversity ; Caliciviridae Infections/virology ; Child, Preschool ; Diarrhea/epidemiology/*virology ; Ethiopia/epidemiology ; Feces/*virology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics ; Norovirus/genetics/isolation &amp; purification ; Picornaviridae/genetics/isolation &amp; purification ; Picornaviridae Infections/virology ; Prevalence ; Viruses/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: Stool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease.<br><br>METHODS: We examine the pediatric enteric virome across stool consistencies to evaluate differences in richness and community composition using fecal samples collected from children aged 0 to 5 years participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling.<br><br>RESULTS: Of 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The median age of children with stool samples was 36 months. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman's r = - 0.45, p = 0.013). The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95%CI 3.9, 7.7).<br><br>CONCLUSIONS: In conclusion, we documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition.}, }
@article {pmid30358106, year = {2019}, author = {Siegenthaler, A and Wangensteen, OS and Soto, AZ and Benvenuto, C and Corrigan, L and Mariani, S}, title = {Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {206-220}, doi = {10.1111/1755-0998.12956}, pmid = {30358106}, issn = {1755-0998}, support = {//Santander Advantage Fund/ ; //University of Salford Manchester/ ; NE/N005759/1//Natural Environment Research Council/ ; //Mersey Gateway Environmental Trust/ ; }, mesh = {Animals ; *Biodiversity ; Crangonidae/*physiology ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV ; Estuaries ; Europe ; Feeding Behavior ; Fishes/*classification/*genetics ; *Gastrointestinal Contents ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; RNA, Ribosomal/genetics ; }, abstract = {Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time is one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity. Here, we evaluate the application of a novel, high-throughput DNA-based monitoring tool to assess fish diversity, based on the analysis of the gut contents of a generalist predator/scavenger, the European brown shrimp, Crangon crangon. Sediment and shrimp samples were collected from eight European estuaries, and DNA metabarcoding (using both 12S and COI markers) was carried out to infer fish assemblage composition. We detected 32 teleost species (16 and 20, for 12S and COI, respectively). Twice as many species were recovered using metabarcoding than by traditional net surveys. By comparing and interweaving trophic, environmental DNA and traditional survey-based techniques, we show that the DNA-assisted gut content analysis of a ubiquitous, easily accessible, generalist species may serve as a powerful, rapid and cost-effective tool for large-scale, routine estuarine biodiversity monitoring.}, }
@article {pmid30336790, year = {2018}, author = {Liu, YR and Delgado-Baquerizo, M and Bi, L and Zhu, J and He, JZ}, title = {Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {183}, pmid = {30336790}, issn = {2049-2618}, mesh = {Bacteroidetes/classification/genetics/*growth &amp; development ; Biodiversity ; China ; Environmental Monitoring ; Environmental Pollution/*analysis ; Firmicutes/classification/genetics/*growth &amp; development ; Mercury/*analysis ; Metagenome/genetics ; Methylmercury Compounds/*analysis ; Microbiota/genetics ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {BACKGROUND: The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulating bacterial abundance, diversity, and co-occurrence network. We also investigated the associations between Hg contents and the relative abundance of microbial functional genes by analyzing the soil metagenomes from a subset of those sites.<br><br>RESULTS: We found that soil Hg largely influenced the taxonomic and functional attributes of microbial communities in the two studied regions. In general, Hg pollution was negatively related to bacterial abundance, but positively related to the diversity of bacteria in two separate regions. We also found some consistent associations between soil Hg contents and the community composition of bacteria. For example, soil total Hg content was positively related to the relative abundance of Firmicutes and Bacteroidetes in both paddy and upland soils. In contrast, the methylmercury (MeHg) concentration was negatively correlated to the relative abundance of Nitrospirae in the two types of soils. Increases in soil Hg pollution correlated with drastic changes in the relative abundance of ecological clusters within the co-occurrence network of bacterial communities for the two regions. Using metagenomic data, we were also able to detect the effect of Hg pollution on multiple functional genes relevant to key soil processes such as element cycles and Hg transformations (e.g., methylation and reduction).<br><br>CONCLUSIONS: Together, our study provides solid evidence that Hg pollution has predictable and significant effects on multiple taxonomic and functional attributes including bacterial abundance, diversity, and the relative abundance of ecological clusters and functional genes. Our results suggest an increase in soil Hg pollution linked to human activities will lead to predictable shifts in the taxonomic and functional attributes in the Hg-impacted areas, with potential implications for sustainable management of agricultural ecosystems and elsewhere.}, }
@article {pmid30326954, year = {2018}, author = {Korpela, K and Salonen, A and Vepsäläinen, O and Suomalainen, M and Kolmeder, C and Varjosalo, M and Miettinen, S and Kukkonen, K and Savilahti, E and Kuitunen, M and de Vos, WM}, title = {Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {182}, pmid = {30326954}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage ; Bifidobacterium/*classification ; Breast Feeding ; Cesarean Section ; Clostridium/isolation &amp; purification ; Dietary Supplements ; Double-Blind Method ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Infant ; Lactobacillus rhamnosus/*classification ; Male ; Pregnancy ; Probiotics/*administration &amp; dosage ; Propionibacterium/*classification ; Proteobacteria/isolation &amp; purification ; }, abstract = {BACKGROUND: Infants born by caesarean section or receiving antibiotics are at increased risk of developing metabolic, inflammatory and immunological diseases, potentially due to disruption of normal gut microbiota at a critical developmental time window. We investigated whether probiotic supplementation could ameliorate the effects of antibiotic use or caesarean birth on infant microbiota in a double blind, placebo-controlled randomized clinical trial. Mothers were given a multispecies probiotic, consisting of Bifidobacterium breve Bb99 (Bp99 2 × 108 cfu) Propionibacterium freundenreichii subsp. shermanii JS (2 × 109cfu), Lactobacillus rhamnosus Lc705 (5 × 109 cfu) and Lactobacillus rhamnosus GG (5 × 109 cfu) (N = 168 breastfed and 31 formula-fed), or placebo supplement (N = 201 breastfed and 22 formula-fed) during pregnancy, and the infants were given the same supplement. Faecal samples of the infants were collected at 3 months and analyzed using taxonomic, metagenomic and metaproteomic approaches.<br><br>RESULTS: The probiotic supplement had a strong overall impact on the microbiota composition, but the effect depended on the infant's diet. Only breastfed infants showed the expected increase in bifidobacteria and reduction in Proteobacteria and Clostridia. In the placebo group, both birth mode and antibiotic use were significantly associated with altered microbiota composition and function, particularly reduced Bifidobacterium abundance. In the probiotic group, the effects of antibiotics and birth mode were either completely eliminated or reduced.<br><br>CONCLUSIONS: The results indicate that it is possible to correct undesired changes in microbiota composition and function caused by antibiotic treatments or caesarean birth by supplementing infants with a probiotic mixture together with at least partial breastfeeding.<br><br>TRIAL REGISTRATION: clinicaltrials.gov NCT00298337 . Registered March 2, 2006.}, }
@article {pmid30305166, year = {2018}, author = {Guyomar, C and Legeai, F and Jousselin, E and Mougel, C and Lemaitre, C and Simon, JC}, title = {Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {181}, pmid = {30305166}, issn = {2049-2618}, mesh = {Animals ; Aphids/*microbiology ; Buchnera/classification/genetics/*isolation &amp; purification ; Genome, Bacterial/genetics ; Metagenome/genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rickettsia/classification/genetics/*isolation &amp; purification ; Symbiosis/*physiology ; }, abstract = {BACKGROUND: Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact.<br><br>RESULTS: We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host.<br><br>CONCLUSIONS: We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.}, }
@article {pmid30285861, year = {2018}, author = {O'Neill, AM and Gallo, RL}, title = {Host-microbiome interactions and recent progress into understanding the biology of acne vulgaris.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {177}, pmid = {30285861}, issn = {2049-2618}, support = {R01 AR069653/AR/NIAMS NIH HHS/United States ; U19 AI117673/AI/NIAID NIH HHS/United States ; R01 AR064781/AR/NIAMS NIH HHS/United States ; R01 AI116576/AI/NIAID NIH HHS/United States ; }, mesh = {Acne Vulgaris/drug therapy/*microbiology ; Dysbiosis/microbiology ; Hair Follicle/*microbiology ; Humans ; Metagenome/genetics ; Microbiota/genetics ; Propionibacterium acnes/*genetics/isolation &amp; purification ; Sebaceous Glands/*microbiology ; Staphylococcus epidermidis/*genetics/isolation &amp; purification ; }, abstract = {Acne is one of the most common skin diseases worldwide and results in major health care costs and significant morbidity to severely affected individuals. However, the pathophysiology of this disorder is not well understood. Host-microbiome interactions that affect both innate and adaptive immune homeostasis appear to be a central factor in this disease, with recent observations suggesting that the composition and activities of the microbiota in acne is perturbed. Staphylococcus epidermidis and Cutibacterium acnes (C. acnes; formerly Propionibacterium acnes) are two major inhabitants of the skin that are thought to contribute to the disease but are also known to promote health by inhibiting the growth and invasion of pathogens. Because C. acnes is ubiquitous in sebaceous-rich skin, it is typically labeled as the etiological agent of acne yet it fails to fulfill all of Koch's postulates. The outdated model of acne progression proposes that increased sebum production promotes over-proliferation of C. acnes in a plugged hair follicle, thereby driving inflammation. In contrast, growing evidence indicates that C. acnes is equally abundant in both unaffected and acne-affected follicles. Moreover, recent advances in metagenomic sequencing of the acne microbiome have revealed a diverse population structure distinct from healthy individuals, uncovering new lineage-specific virulence determinants. In this article, we review recent developments in the interactions of skin microbes with host immunity, discussing the contribution of dysbiosis to the immunobiology of acne and newly emerging skin microbiome-based therapeutics to treat acne.}, }
@article {pmid30281913, year = {2019}, author = {Jusino, MA and Banik, MT and Palmer, JM and Wray, AK and Xiao, L and Pelton, E and Barber, JR and Kawahara, AY and Gratton, C and Peery, MZ and Lindner, DL}, title = {An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {176-190}, doi = {10.1111/1755-0998.12951}, pmid = {30281913}, issn = {1755-0998}, support = {//United States Forest Service, Northern Research Station/ ; Hatch Formula Funds//University of Wisconsin-Madison, Wisconsin Agricultural Experiment Station/ ; IOS-1121739//National Science Foundation/ ; IOS-1121807//National Science Foundation/ ; }, mesh = {Animals ; *Chiroptera ; Computational Biology/*methods ; DNA/chemistry/genetics/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Feces/chemistry ; *Feeding Behavior ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; }, abstract = {DNA analysis of predator faeces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To better characterize insectivorous animal diets, we used DNA from a diverse set of arthropods to assess PCR biases of commonly used and novel primer pairs for the mitochondrial gene, cytochrome oxidase C subunit 1 (COI). We compared diversity recovered from HTS of bat guano samples using a commonly used primer pair &quot;ZBJ&quot; to results using the novel primer pair &quot;ANML.&quot; To parameterize our bioinformatics pipeline, we created an arthropod mock community consisting of single-copy (cloned) COI sequences. To examine biases associated with both PCR and HTS, mock community members were combined in equimolar amounts both pre- and post-PCR. We validated our system using guano from bats fed known diets and using composite samples of morphologically identified insects collected in pitfall traps. In PCR tests, the ANML primer pair amplified 58 of 59 arthropod taxa (98%), whereas ZBJ amplified 24-40 of 59 taxa (41%-68%). Furthermore, in an HTS comparison of field-collected samples, the ANML primers detected nearly fourfold more arthropod taxa than the ZBJ primers. The additional arthropods detected include medically and economically relevant insect groups such as mosquitoes. Results revealed biases at both the PCR and sequencing levels, demonstrating the pitfalls associated with using HTS read numbers as proxies for abundance. The use of an arthropod mock community allowed for improved bioinformatics pipeline parameterization.}, }
@article {pmid30267472, year = {2019}, author = {Suchan, T and Talavera, G and Sáez, L and Ronikier, M and Vila, R}, title = {Pollen metabarcoding as a tool for tracking long-distance insect migrations.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {149-162}, doi = {10.1111/1755-0998.12948}, pmid = {30267472}, issn = {1755-0998}, support = {CGL2016-76322//AEI/FEDER, UE/ ; IJCI-2016-29083//MINECO programme Juan de la Cierva Incorporación/ ; LRB16/1015//British Ecological Society/ ; //Polish Academy of Sciences statutory fund/ ; 622716//FP7/ ; WW1-300R-18//National Geographic Society/ ; }, mesh = {Africa ; *Animal Migration ; Animals ; Arabia ; Butterflies/*physiology ; DNA Barcoding, Taxonomic/*methods ; Entomology/*methods ; Mediterranean Region ; Metagenomics/*methods ; Pollen/*genetics ; Spain ; }, abstract = {Insects account for a large portion of Earth's biodiversity and are key players for ecosystems, notably as pollinators. While insect migration is suspected to represent a natural phenomenon of major importance, remarkably little is known about it, except for a few flagship species. The reason for this situation is mainly due to technical limitations in the study of insect movement. Here, we propose using metabarcoding of pollen carried by insects as a method for tracking their migrations. We developed a flexible and simple protocol allowing efficient multiplexing and not requiring DNA extraction, one of the most time-consuming part of metabarcoding protocols, and apply this method to the study of the long-distance migration of the butterfly Vanessa cardui, an emerging model for insect migration. We collected 47 butterfly samples along the Mediterranean coast of Spain in spring and performed metabarcoding of pollen collected from their bodies to test for potential arrivals from the African continent. In total, we detected 157 plant species from 23 orders, most of which (82.8%) were insect-pollinated. Taxa present in Africa-Arabia represented 73.2% of our data set, and 19.1% were endemic to this region, strongly supporting the hypothesis that migratory butterflies colonize southern Europe from Africa in spring. Moreover, our data suggest that a northwards trans-Saharan migration in spring is plausible for early arrivals (February) into Europe, as shown by the presence of Saharan floristic elements. Our results demonstrate the possibility of regular insect-mediated transcontinental pollination, with potential implications for ecosystem functioning, agriculture and plant phylogeography.}, }
@article {pmid30266101, year = {2018}, author = {Alneberg, J and Karlsson, CMG and Divne, AM and Bergin, C and Homa, F and Lindh, MV and Hugerth, LW and Ettema, TJG and Bertilsson, S and Andersson, AF and Pinhassi, J}, title = {Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {173}, pmid = {30266101}, issn = {2049-2618}, support = {310039//European Research Council/International ; }, mesh = {Bacteria/classification/*genetics ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Microbiota/*genetics ; *Nucleic Acid Amplification Techniques ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sweden ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.<br><br>RESULTS: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.<br><br>CONCLUSIONS: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.}, }
@article {pmid30225935, year = {2019}, author = {Drinkwater, R and Schnell, IB and Bohmann, K and Bernard, H and Veron, G and Clare, E and Gilbert, MTP and Rossiter, SJ}, title = {Using metabarcoding to compare the suitability of two blood-feeding leech species for sampling mammalian diversity in North Borneo.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {105-117}, doi = {10.1111/1755-0998.12943}, pmid = {30225935}, issn = {1755-0998}, support = {SAS-2016-100//The Leverhulme Trust/ ; NE/K016148/1//Natural Environment Research Council/ ; DFF 5051-00140//The Danish Council for Independent Research/ ; }, mesh = {Animals ; Borneo ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/chemistry/genetics ; *Feeding Behavior ; High-Throughput Nucleotide Sequencing ; *Host Specificity ; Leeches/*physiology ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. To address these questions, we collected spatially matched samples of two congeneric leech species Haemadipsa picta and Haemadipsa sumatrana from lowland rainforest in Borneo. For each species, we pooled ~500 leeches into batches of 10 individuals, performed PCR to target a section of the mammalian 16S rRNA locus and undertook sequencing of amplicon libraries using an Illumina MiSeq. In total, we identified sequences from 14 mammalian genera, spanning nine families and five orders. We found greater numbers of detections, and higher diversity of OTUs, in H. picta compared with H. sumatrana, with rodents only present in the former leech species. However, comparison of samples from across the landscape revealed no significant difference in mammal community composition between the leech species. We therefore suggest that H. picta is the more suitable iDNA sampler in this degraded Bornean forest. We conclude that the choice of invertebrate sampler can influence the detectability of different mammal groups and that this should be accounted for when designing iDNA studies.}, }
@article {pmid29768738, year = {2019}, author = {Cilleros, K and Valentini, A and Allard, L and Dejean, T and Etienne, R and Grenouillet, G and Iribar, A and Taberlet, P and Vigouroux, R and Brosse, S}, title = {Unlocking biodiversity and conservation studies in high-diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {27-46}, doi = {10.1111/1755-0998.12900}, pmid = {29768738}, issn = {1755-0998}, mesh = {Animals ; *Biodiversity ; DNA/chemistry/*genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification/genetics ; Fresh Water/*chemistry ; Guyana ; Metagenomics/*methods ; }, abstract = {Determining the species compositions of local assemblages is a prerequisite to understanding how anthropogenic disturbances affect biodiversity. However, biodiversity measurements often remain incomplete due to the limited efficiency of sampling methods. This is particularly true in freshwater tropical environments that host rich fish assemblages, for which assessments are uncertain and often rely on destructive methods. Developing an efficient and nondestructive method to assess biodiversity in tropical freshwaters is highly important. In this study, we tested the efficiency of environmental DNA (eDNA) metabarcoding to assess the fish diversity of 39 Guianese sites. We compared the diversity and composition of assemblages obtained using traditional and metabarcoding methods. More than 7,000 individual fish belonging to 203 Guianese fish species were collected by traditional sampling methods, and ~17 million reads were produced by metabarcoding, among which ~8 million reads were assigned to 148 fish taxonomic units, including 132 fish species. The two methods detected a similar number of species at each site, but the species identities partially matched. The assemblage compositions from the different drainage basins were better discriminated using metabarcoding, revealing that while traditional methods provide a more complete but spatially limited inventory of fish assemblages, metabarcoding provides a more partial but spatially extensive inventory. eDNA metabarcoding can therefore be used for rapid and large-scale biodiversity assessments, while at a local scale, the two approaches are complementary and enable an understanding of realistic fish biodiversity.}, }
@article {pmid29253074, year = {2018}, author = {Huang, L and Krüger, J and Sczyrba, A}, title = {Analyzing large scale genomic data on the cloud with Sparkhit.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {9}, pages = {1457-1465}, pmid = {29253074}, issn = {1367-4811}, mesh = {Algorithms ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {Motivation: The increasing amount of next-generation sequencing data poses a fundamental challenge on large scale genomic analytics. Existing tools use different distributed computational platforms to scale-out bioinformatics workloads. However, the scalability of these tools is not efficient. Moreover, they have heavy run time overheads when pre-processing large amounts of data. To address these limitations, we have developed Sparkhit: a distributed bioinformatics framework built on top of the Apache Spark platform.<br><br>Results: Sparkhit integrates a variety of analytical methods. It is implemented in the Spark extended MapReduce model. It runs 92-157 times faster than MetaSpark on metagenomic fragment recruitment and 18-32 times faster than Crossbow on data pre-processing. We analyzed 100 terabytes of data across four genomic projects in the cloud in 21 h, which includes the run times of cluster deployment and data downloading. Furthermore, our application on the entire Human Microbiome Project shotgun sequencing data was completed in 2 h, presenting an approach to easily associate large amounts of public datasets with reference data.<br><br>Sparkhit is freely available at: https://rhinempi.github.io/sparkhit/.<br><br>Contact: asczyrba@cebitec.uni-bielefeld.de.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid29211828, year = {2018}, author = {Orakov, AN and Sakenova, NK and Sorokin, A and Goryanin, II}, title = {ASAR: visual analysis of metagenomes in R.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {8}, pages = {1404-1405}, pmid = {29211828}, issn = {1367-4811}, mesh = {Metagenomics/*methods ; Microbiota/*genetics ; *Software ; }, abstract = {Motivation: Functional and taxonomic analyses are critical steps in understanding interspecific interactions within microbial communities. Currently, such analyses are run separately, which complicates interpretation of results. Here we present the ASAR interactive tool for simultaneous analysis of metagenomic data in three dimensions: taxonomy, function, metagenome.<br><br>Results: An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.<br><br>Source code of the ASAR is accessible at GitHub (https://github.com/Askarbek-orakov/ASAR).<br><br>Contact: askarbek.orakov@nu.edu.kz or goryanin@gmail.com.}, }
@article {pmid29028892, year = {2018}, author = {Weber, N and Liou, D and Dommer, J and MacMenamin, P and Quiñones, M and Misner, I and Oler, AJ and Wan, J and Kim, L and Coakley McCarthy, M and Ezeji, S and Noble, K and Hurt, DE}, title = {Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {8}, pages = {1411-1413}, pmid = {29028892}, issn = {1367-4811}, mesh = {*Cloud Computing ; Computational Biology/*methods ; Humans ; Metagenomics/methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA ; *Software ; }, abstract = {Motivation: Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools.<br><br>Results: The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights. Nephele integrates common microbiome analysis tools as well as valuable reference datasets like the healthy human subjects cohort of the Human Microbiome Project (HMP). Nephele is built on the Amazon Web Services cloud, which provides centralized and automated storage and compute capacity, thereby reducing the burden on researchers and their institutions.<br><br>https://nephele.niaid.nih.gov and https://github.com/niaid/Nephele.<br><br>Contact: darrell.hurt@nih.gov.}, }
@article {pmid30446169, year = {2019}, author = {Kosek, K and Kozioł, K and Luczkiewicz, A and Jankowska, K and Chmiel, S and Polkowska, Ż}, title = {Environmental characteristics of a tundra river system in Svalbard. Part 2: Chemical stress factors.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {1585-1596}, doi = {10.1016/j.scitotenv.2018.11.012}, pmid = {30446169}, issn = {1879-1026}, mesh = {Bacteria/classification/*drug effects ; *Environmental Monitoring ; Formaldehyde/analysis ; Metagenomics ; Metals/analysis ; Microbiota/*drug effects ; Phenols/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; Rivers/*chemistry/*microbiology ; Svalbard ; Tundra ; Water Pollutants, Chemical/*analysis ; }, abstract = {Bacterial communities in the Arctic environment are subject to multiple stress factors, including contaminants, although typically their concentrations are small. The Arctic contamination research has focused on persistent organic pollutants (POPs) because they are bioaccumulative, resistant to degradation and toxic for all organisms. Pollutants have entered the Arctic predominantly by atmospheric and oceanic long-range transport, and this was facilitated by their volatile or semi-volatile properties, while their chemical stability extended their lifetimes following emission. Chemicals present in the Arctic at detectable and quantifiable concentrations testify to their global impact. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. In this study, the abundance and the types of bacteria in the Arctic freshwater were examined and the microbial characteristics were compared to the amount of potentially harmful chemical compounds in particular elements of the Arctic catchment. The highest concentrations of all determined PAHs were observed in two samples in the vicinity of the estuary both in June and September 2016 and were 1964 ng L-1 (R12) and 3901 ng L-1 (R13) in June, and 2179 ng L-1 (R12) and 1349 ng L-1 (R13) in September. Remarkable concentrations of the sum of phenols and formaldehyde were detected also at the outflow of the Revelva river into the sea (R12) and were 0.24 mg L-1 in June and 0.35 mg L-1 in September 2016. The elevated concentrations of chemical compounds near the estuary suggest a potential impact of the water from the lower tributaries (including the glacier-fed stream measured at R13) or the sea currents and the sea aerosol as pollutant sources. The POPs' degradation at low temperature is not well understood but bacteria capable to degrading such compounds were noted in each sampling point.}, }
@article {pmid30412889, year = {2019}, author = {Nathani, NM and Mootapally, C and Dave, BP}, title = {Antibiotic resistance genes allied to the pelagic sediment microbiome in the Gulf of Khambhat and Arabian Sea.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {446-454}, doi = {10.1016/j.scitotenv.2018.10.409}, pmid = {30412889}, issn = {1879-1026}, mesh = {Bacteria/classification/drug effects/*genetics/*isolation &amp; purification ; *Drug Resistance, Microbial ; Genes, Bacterial/*drug effects ; Geologic Sediments/*microbiology ; Indian Ocean ; *Microbiota ; }, abstract = {Antibiotics have been widely spread in the environments, imposing profound stress on the resistome of the residing microbes. Marine microbiomes are well established large reservoirs of novel antibiotics and corresponding resistance genes. The Gulf of Khambhat is known for its extreme tides and complex sedimentation process. We performed high throughput sequencing and applied bioinformatics techniques on pelagic sediment microbiome across four coordinates of the Gulf of Khambhat to assess the marine resistome, its corresponding bacterial community and compared with the open Arabian Sea sample. We identified a total of 2354 unique types of resistance genes, with most abundant and diverse gene profile in the area that had anthropogenic activities being carried out on-shore. The genes with >1% abundance in all samples included carA, macB, sav1866, tlrC, srmB, taeA, tetA, oleC and bcrA which belonged to the macrolides, glycopeptides and peptide drug classes. ARG enriched phyla distribution was quite varying between all the sites, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes among the dominant phyla. Based on the outcomes, we also propose potential biomarker candidates Desulfovibrio, Thermotaga and Pelobacter for antibiotic monitoring in the two of the Gulf samples probable contamination prone environments, and genera Nitrosocccus, Marinobacter and Streptomyces in the rest of the three studied samples. Outcomes support the concept that ARGs naturally originate in environments and human activities contribute to the dissemination of antibiotic resistance.}, }
@article {pmid30382616, year = {2019}, author = {Ganuza, M and Pastor, N and Boccolini, M and Erazo, J and Palacios, S and Oddino, C and Reynoso, MM and Rovera, M and Torres, AM}, title = {Evaluating the impact of the biocontrol agent Trichoderma harzianum ITEM 3636 on indigenous microbial communities from field soils.}, journal = {Journal of applied microbiology}, volume = {126}, number = {2}, pages = {608-623}, doi = {10.1111/jam.14147}, pmid = {30382616}, issn = {1365-2672}, support = {//Agencia Nacional de Promoción Científica y Tecnológica (MINCyT)/ ; }, mesh = {Agriculture ; Arachis ; Argentina ; Bacteria/genetics/isolation &amp; purification ; *Biological Control Agents ; Denaturing Gradient Gel Electrophoresis ; Fungi/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Microbiota ; Polymerase Chain Reaction ; Seeds ; Soil/chemistry ; *Soil Microbiology ; *Trichoderma ; }, abstract = {AIM: To investigate the impact of inoculating peanut seeds with the biocontrol agent Trichoderma harzianum ITEM 3636 on the structure of bacterial and fungal communities from agricultural soils.<br><br>METHODS AND RESULTS: Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing (NGS) of amplicons (or marker gene amplification metagenomics) were performed to investigate potential changes in the structure of microbial communities from fields located in a peanut-producing area in the province of Córdoba, Argentina. Fields had history of peanut smut (caused by Thecaphora frezii) incidence. The Shannon indexes (H'), which estimate diversity, obtained from the PCR-DGGE assays did not show significant differences neither for bacterial nor for fungal communities between control and inoculation treatments. On the other hand, the number of operational taxonomic units obtained after NGS was similar between all the analysed samples. Moreover, results of alpha and beta diversity showed that there were no significant variations between the relative abundances of the most representative bacterial and fungal phyla and genera, in both fields.<br><br>CONCLUSIONS: Trichoderma harzianum ITEM 3636 decreases the incidence and severity of agriculturally relevant diseases without causing significant changes in the microbial communities of agricultural soils.<br><br>Our investigations provide information on the structure of bacterial and fungal communities in peanut-producing fields after inoculation of seeds with a biocontrol agent.}, }
@article {pmid30362648, year = {2019}, author = {Larivière-Gauthier, G and Thibodeau, A and Letellier, A and Yergeau, É and Fravalo, P}, title = {Salmonella shedding status of the sow affects the microbiota of their piglets at weaning.}, journal = {Journal of applied microbiology}, volume = {126}, number = {2}, pages = {411-423}, doi = {10.1111/jam.14139}, pmid = {30362648}, issn = {1365-2672}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Bacterial Shedding ; Female ; *Microbiota ; Pregnancy ; Salmonella/*isolation &amp; purification ; Swine/growth &amp; development/*microbiology ; Weaning ; }, abstract = {AIM: To observe the transfer of the digestive microbiota from sow to piglet, describe the impact of the sow's Salmonella shedding on this transfer and identify transferred populations that could be associated with the future Salmonella status of the piglets.<br><br>METHODS AND RESULTS: Salmonella shedding status of 19 sows was determined at the beginning and end of gestation. Four piglets were randomly selected from each sow. Using MiSeq, the microbiotas of the sows at the end of gestation and of their piglets 1 day before weaning were described. Results showed that the Salmonella shedding of the sows, the birth mother, the lairage room, the parity and the contamination of the lairage environment were associated to the microbiota of the piglets (permanova P < 0·05). Several genera were associated with piglets born from negative or positive sows.<br><br>CONCLUSION: There is a link between the microbiota of the sows at the end of gestation and the microbiota of their piglets at weaning, and the Salmonella shedding of the sow is associated with the microbiota of the piglets.<br><br>Salmonella status of the sows affects the microbiota of their piglets and could affect the long-term Salmonella colonization resistance of these animals and their health.}, }
@article {pmid29920461, year = {2018}, author = {Graham, EB and Crump, AR and Kennedy, DW and Arntzen, E and Fansler, S and Purvine, SO and Nicora, CD and Nelson, W and Tfaily, MM and Stegen, JC}, title = {Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone.}, journal = {The Science of the total environment}, volume = {642}, number = {}, pages = {742-753}, doi = {10.1016/j.scitotenv.2018.05.256}, pmid = {29920461}, issn = {1879-1026}, mesh = {Carbon ; Environmental Monitoring/*methods ; Groundwater ; Metabolome/*physiology ; Microbiota ; Rivers ; }, abstract = {Biogeochemical hotspots are pervasive at terrestrial-aquatic interfaces, particularly within groundwater-surface water mixing zones (hyporheic zones), and they are critical to understanding spatiotemporal variation in biogeochemical cycling. Here, we use multi 'omic comparisons of hotspots to low-activity sediments to gain mechanistic insight into hyporheic zone organic matter processing. We hypothesized that microbiome structure and function, as described by metagenomics and metaproteomics, would distinguish hotspots from low-activity sediments by shifting metabolism towards carbohydrate-utilizing pathways and elucidate discrete mechanisms governing organic matter processing in each location. We also expected these differences to be reflected in the metabolome, whereby hotspot carbon (C) pools and metabolite transformations therein would be enriched in sugar-associated compounds. In contrast to expectations, we found pronounced phenotypic plasticity in the hyporheic zone microbiome that was denoted by similar microbiome structure, functional potential, and expression across sediments with dissimilar metabolic rates. Instead, diverse nitrogenous metabolites and biochemical transformations characterized hotspots. Metabolomes also corresponded more strongly to aerobic metabolism than bulk C or N content only (explaining 67% vs. 42% and 37% of variation respectively), and bulk C and N did not improve statistical models based on metabolome composition alone. These results point to organic nitrogen as a significant regulatory factor influencing hyporheic zone organic matter processing. Based on our findings, we propose incorporating knowledge of metabolic pathways associated with different chemical fractions of C pools into ecosystem models will enhance prediction accuracy.}, }
@article {pmid29667371, year = {2019}, author = {Han, Z and Sun, J and Lv, A and Wang, A}, title = {Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi.}, journal = {MicrobiologyOpen}, volume = {8}, number = {1}, pages = {e00626}, doi = {10.1002/mbo3.626}, pmid = {29667371}, issn = {2045-8827}, mesh = {Animals ; Carps/microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics/*isolation &amp; purification ; DNA, Ribosomal/chemistry/genetics/*isolation &amp; purification ; *Gastrointestinal Microbiome ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {This study examined the technical bias associated with different DNA extraction methods used in microbiome research. Three methods were used to extract genomic DNA from the same intestinal microbiota sample that was taken from the koi carp Cyprinus carpio var. koi, after which their microbial diversity and community structure were investigated on the basis of a 16S rDNA high-throughput sequencing analysis. Biased results were observed in relation to the number of reads, alpha diversity indexes and taxonomic composition among the three DNA extraction protocols. A total of 1,381 OTUs from the intestinal bacteria were obtained, with 852, 759, and 698 OTUs acquired, using the Lysozyme and Ultrasonic Lysis method, Zirmil-beating Cell Disruption method, and a QIAamp Fast DNA Stool Mini Kit, respectively. Additionally, 336 OTUs were commonly acquired, using the three methods. The results showed that the alpha diversity indexes (Rarefaction, Shannon, and Chao1) of the community that were determined using the Lysozyme and Ultrasonic Lysis method were higher than those obtained with the Zirmil-beating Cell Disruption method, while the Zirmil method results were higher than those measured, using the QIAamp Fast DNA Stool Mini Kit. Moreover, all the major phyla (ratio>1%) could be identified with all three DNA extraction methods, but the phyla present at a lower abundance (ratio <1%) could not. Similar findings were observed at the genus level. Taken together, these findings indicated that the bias observed in the results about the community structure occurred primarily in OTUs with a lower abundance. The results of this study demonstrate that possible bias exists in community analyses, and researchers should therefore be conservative when drawing conclusions about community structures based on the currently available DNA extraction methods.}, }
@article {pmid28798374, year = {2017}, author = {Patel, SH and Vaidya, YH and Patel, RJ and Pandit, RJ and Joshi, CG and Kunjadiya, AP}, title = {Culture independent assessment of human milk microbial community in lactational mastitis.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7804}, pmid = {28798374}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; Case-Control Studies ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Gene Regulatory Networks ; Humans ; Lactation ; Mastitis/*microbiology ; Metagenomics/*methods ; Microbiota ; Milk, Human/*microbiology ; Odds Ratio ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Breastfeeding undoubtedly provides important benefits to the mother-infant dyad and should be encouraged. Mastitis, one of the common but major cause of premature weaning among lactating women, is an inflammation of connective tissue within the mammary gland. This study reports the influence of mastitis on human milk microbiota by utilizing 16 S rRNA gene sequencing approach. We sampled and sequenced microbiome from 50 human milk samples, including 16 subacute mastitis (SAM), 16 acute mastitis (AM) and 18 healthy-controls. Compared to controls, SAM and AM microbiota were quite distinct and drastically reduced. Genera including, Aeromonas, Staphylococcus, Ralstonia, Klebsiella, Serratia, Enterococcus and Pseudomonas were significantly enriched in SAM and AM samples, while Acinetobacter, Ruminococcus, Clostridium, Faecalibacterium and Eubacterium were consistently depleted. Further analysis of our samples revealed positive aerotolerant odds ratio, indicating dramatic depletion of obligate anaerobes and enrichment of aerotolerant bacteria during the course of mastitis. In addition, predicted functional metagenomics identified several gene pathways related to bacterial proliferation and colonization (e.g. two-component system, bacterial secretion system and motility proteins) in SAM and AM samples. In conclusion, our study confirmed previous hypothesis that mastitis women have lower microbial diversity, increased abundance of opportunistic pathogens and depletion of commensal obligate anaerobes.}, }
@article {pmid29931479, year = {2018}, author = {Philips, CA and Phadke, N and Ganesan, K and Ranade, S and Augustine, P}, title = {Corticosteroids, nutrition, pentoxifylline, or fecal microbiota transplantation for severe alcoholic hepatitis.}, journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology}, volume = {37}, number = {3}, pages = {215-225}, pmid = {29931479}, issn = {0975-0711}, mesh = {Administration, Oral ; Adult ; Aged ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Hepatitis, Alcoholic/microbiology/*therapy ; Humans ; Male ; Middle Aged ; *Nutrition Therapy ; Pentoxifylline/*therapeutic use ; Prednisolone/*administration &amp; dosage ; Severity of Illness Index ; Treatment Outcome ; }, abstract = {INTRODUCTION: Alcohol-induced intestinal dysbiosis is central to the development of the severe alcoholic liver disease. We present the first study to compare outcomes in patients of severe alcoholic hepatitis (SAH) on nutritional therapy, corticosteroids, pentoxifylline, and healthy donor fecal transplantation (FMT) and discuss distinct microbial community and microbiome metabolic functional changes after FMT.<br><br>METHODS: Out of 1271 liver disease patients, 809 (63.7%) were diagnosed to have the alcoholic liver disease, of which 51 patients (8 treated with corticosteroids, 17 with nutritional support only, 10 with pentoxifylline, 16 receiving FMT) were included. Clinical, biochemical parameters, liver disease, and alcoholic hepatitis severity scores at baseline and mortality at the end of 1 and 3 months were analyzed between groups. Stool microbiota (SM) analysis was performed for healthy controls (HC) and respective recipients after FMT.<br><br>RESULTS: All the patients were male. The proportions of patients surviving at the end of 1 and 3 months in the steroids, nutrition, pentoxifylline, and FMT group were 63%, 47%, 40% and 75% [p = 0.179] and 38%, 29%, 30%, and 75% [p = 0.036], respectively. When compared with FMT, relative risk and hazard ratios for death were higher in all the other groups. Following FMT, distinct and beneficial modulation of SM and pathways of dysregulated metabolism, infections, inflammation, and oxidative stress in SAH patients were noted in tandem with improved clinical outcomes.<br><br>CONCLUSIONS: Healthy donor FMT for SAH improves survival beyond what is offered by current therapies and can function as a cost-effective bridge to liver transplant (LT) or for improving transplant-free survival. Larger studies and randomized trials are unmet needs.}, }
@article {pmid30612183, year = {2019}, author = {Ding, W and Zhang, W and Alikunhi, NM and Batang, Z and Pei, B and Wang, R and Chen, L and Al-Suwailem, A and Qian, PY}, title = {Metagenomic Analysis of Zinc Surface-Associated Marine Biofilms.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {406-416}, doi = {10.1007/s00248-018-01313-3}, pmid = {30612183}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; *Biofilms ; Indian Ocean ; Metagenomics ; Phylogeny ; Seawater/analysis/*microbiology ; Zinc/analysis/*metabolism ; }, abstract = {Biofilms are a significant source of marine biofouling. Marine biofilm communities are established when microorganisms adhere to immersed surfaces. Despite the microbe-inhibiting effect of zinc surfaces, microbes can still attach to the surface and form biofilms. However, the diversity of biofilm-forming microbes that can attach to zinc surfaces and their common functional features remain elusive. Here, by analyzing 9,000,000 16S rRNA gene amplicon sequences and 270 Gb of metagenomic data, we comprehensively explored the taxa and functions related to biofilm formation in subtidal zones of the Red Sea. A clear difference was observed between the biofilm and adjacent seawater microbial communities in terms of the taxonomic structure at phylum and genus levels, and a huge number of genera were only present in the biofilms. Saturated alpha-diversity curves suggested the existence of more than 14,000 operational taxonomic units in one biofilm sample, which is much higher than previous estimates. Remarkably, the biofilms contained abundant and diverse transposase genes, which were localized along microbial chromosomal segments and co-existed with genes related to metal ion transport and resistance. Genomic analyses of two cyanobacterial strains that were abundant in the biofilms revealed a variety of metal ion transporters and transposases. Our analyses revealed the high diversity of biofilm-forming microbes that can attach to zinc surfaces and the ubiquitous role of transposase genes in microbial adaptation to toxic metal surfaces.}, }
@article {pmid30177353, year = {2018}, author = {Rhoads, JM and Collins, J and Fatheree, NY and Hashmi, SS and Taylor, CM and Luo, M and Hoang, TK and Gleason, WA and Van Arsdall, MR and Navarro, F and Liu, Y}, title = {Infant Colic Represents Gut Inflammation and Dysbiosis.}, journal = {The Journal of pediatrics}, volume = {203}, number = {}, pages = {55-61.e3}, doi = {10.1016/j.jpeds.2018.07.042}, pmid = {30177353}, issn = {1097-6833}, mesh = {Acinetobacter/isolation &amp; purification ; Breast Feeding ; Case-Control Studies ; Colic/*complications ; Dysbiosis/*diagnosis ; Feces/*chemistry/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Infant Formula ; Infant, Newborn ; Inflammation/*diagnosis ; Lactobacillus/isolation &amp; purification ; Leukocyte L1 Antigen Complex/*analysis ; Male ; }, abstract = {OBJECTIVE: To dissect potential confounding effects of breast milk and formula feeding on crying + fussing, fecal calprotectin, and gut microbiota in babies with colic. We hypothesized that infant colic is associated with gut inflammation linked to intestinal dysbiosis.<br><br>STUDY DESIGN: A nested case-control design of 3 of our studies was used to analyze clinical and laboratory data at presentation, comparing babies with colic with controls. All investigators other than the biostatistician were blinded during data analysis. Subjects were recruited based on their age and crying + fussy time. We screened 65 infants, 37 with colic, as defined by Barr diary (crying + fussing time >3 hours daily), who were compared with 28 noncolicky infants.<br><br>RESULTS: Fecal calprotectin was elevated in babies with colic. For each mode of infant feeding (breast milk, formula, or breast + formula), infants' fecal calprotectin was higher in babies with colic. Infants with colic had similar levels of fecal alpha diversity (richness) when compared with controls, and alpha diversity was lower in breast-fed babies. Beta diversity at the phylum level revealed significant differences in microbial population. A phylum difference resulted from reduced Actinobacteria (95% of which are Bifidobacilli) in babies with colic. Species significantly associated with colic were Acinetobacter and Lactobacillus iners.<br><br>CONCLUSIONS: Colic is linked with gut inflammation (as determined by fecal calprotectin) and dysbiosis, independent of mode of feeding, with fewer Bifidobacilli.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov: NCT01279265 and NCT01849991.}, }
@article {pmid29956164, year = {2018}, author = {Tang, MS and Bowcutt, R and Loke, P}, title = {Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1799}, number = {}, pages = {359-370}, doi = {10.1007/978-1-4939-7896-0_26}, pmid = {29956164}, issn = {1940-6029}, mesh = {Animals ; Gastrointestinal Microbiome/*immunology ; Helminthiasis/diagnosis/immunology/parasitology ; Helminths/immunology ; Host-Pathogen Interactions ; *Immunity ; Metagenome ; Metagenomics/methods ; Mice ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The microbial communities that reside within the mammalian host play important roles in the development of a robust host immune system. With the advent of sequencing technology and barcoding strategy of the bacterial 16S ribosomal RNA (rRNA) gene, microbiota studies are becoming more economical but also more important in many immunology studies. Here, we described a representative study protocol to characterize how the microbiota changes during an intestinal helminth infection, with emphasis on subtle aspects of the experimental design that are critical for data interpretation.}, }
@article {pmid29371652, year = {2018}, author = {Fernández, L and Rodríguez, A and García, P}, title = {Phage or foe: an insight into the impact of viral predation on microbial communities.}, journal = {The ISME journal}, volume = {12}, number = {5}, pages = {1171-1179}, pmid = {29371652}, issn = {1751-7370}, mesh = {Bacteria/genetics/*metabolism/pathogenicity ; Bacteriophages/*physiology ; Biological Evolution ; Genomics ; Metagenomics ; *Microbial Interactions ; Microbiota ; Proteomics ; }, abstract = {Since their discovery, bacteriophages have been traditionally regarded as the natural enemies of bacteria. However, recent advances in molecular biology techniques, especially data from &quot;omics&quot; analyses, have revealed that the interplay between bacterial viruses and their hosts is far more intricate than initially thought. On the one hand, we have become more aware of the impact of viral predation on the composition and genetic makeup of microbial communities thanks to genomic and metagenomic approaches. Moreover, data obtained from transcriptomic, proteomic, and metabolomic studies have shown that responses to phage predation are complex and diverse, varying greatly depending on the bacterial host, phage, and multiplicity of infection. Interestingly, phage exposure may alter different phenotypes, including virulence and biofilm formation. The complexity of the interactions between microbes and their viral predators is also evidenced by the link between quorum-sensing signaling pathways and bacteriophage resistance. Overall, new data increasingly suggests that both temperate and virulent phages have a positive effect on the evolution and adaptation of microbial populations. From this perspective, further research is still necessary to fully understand the interactions between phage and host under conditions that allow co-existence of both populations, reflecting more accurately the dynamics in natural microbial communities.}, }
@article {pmid30543873, year = {2019}, author = {Lima, DA and Cibulski, SP and Tochetto, C and Varela, APM and Finkler, F and Teixeira, TF and Loiko, MR and Cerva, C and Junqueira, DM and Mayer, FQ and Roehe, PM}, title = {The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics.}, journal = {Virus research}, volume = {261}, number = {}, pages = {9-20}, doi = {10.1016/j.virusres.2018.12.005}, pmid = {30543873}, issn = {1872-7492}, mesh = {Animals ; Chickens ; Feces/*virology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Malabsorption Syndromes/*veterinary/virology ; Metagenomics ; Poultry Diseases/*virology ; Viruses/*classification/*genetics ; }, abstract = {Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated. Through analysis of de novo assembled contigs, 144 contigs > 1000 nt were identified with hits to eukaryotic viral sequences, as determined by GenBank database. A number of known and unknown representatives of Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, as well as novel uncharacterized CRESS-DNA viruses, were identified. However, the distribution of sequence reads of viral genomes identified in diseased or healthy birds revealed no statistically significant differences. These findings indicate no association between the occurrence of MAS and enteric viruses. The viral genomes reported in the present study, including a variety of novel viruses, seem part of the normal intestinal microbiota of chickens.}, }
@article {pmid30152883, year = {2018}, author = {Toivonen, L and Hasegawa, K and Ajami, NJ and Celedón, JC and Mansbach, JM and Petrosino, JF and Camargo, CA}, title = {Circulating 25-hydroxyvitamin D, nasopharyngeal microbiota, and bronchiolitis severity.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {29}, number = {8}, pages = {877-880}, pmid = {30152883}, issn = {1399-3038}, support = {//Päivikki ja Sakari Sohlbergin Säätiö/International ; R01 AI134940/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; R01 AI137091/AI/NIAID NIH HHS/United States ; //Suomen Lääketieteen Säätiö/International ; UG3 OD023253/OD/NIH HHS/United States ; }, mesh = {Bronchiolitis/*etiology ; Cohort Studies ; Female ; Humans ; Infant ; Male ; Microbiota/genetics/*immunology ; Nasopharynx/*microbiology ; Prospective Studies ; Risk Factors ; United States ; Vitamin D/*analogs &amp; derivatives/blood ; }, }
@article {pmid29729376, year = {2018}, author = {Li, M and Zhou, M and Tian, X and Tan, C and McDaniel, CT and Hassett, DJ and Gu, T}, title = {Microbial fuel cell (MFC) power performance improvement through enhanced microbial electrogenicity.}, journal = {Biotechnology advances}, volume = {36}, number = {4}, pages = {1316-1327}, doi = {10.1016/j.biotechadv.2018.04.010}, pmid = {29729376}, issn = {1873-1899}, mesh = {*Bioelectric Energy Sources ; *Biofilms ; *Microbial Consortia ; Oxidation-Reduction ; Synthetic Biology ; }, abstract = {Within the past 5 years, tremendous advances have been made to maximize the performance of microbial fuel cells (MFCs) for both &quot;clean&quot; bioenergy production and bioremediation. Most research efforts have focused on parameters including (i) optimizing reactor configuration, (ii) electrode construction, (iii) addition of redox-active, electron donating mediators, (iv) biofilm acclimation and feed nutrient adjustment, as well as (v) other parameters that contribute to enhanced MFC performance. To date, tremendous advances have been made, but further improvements are needed for MFCs to be economically practical. In this review, the diversity of electrogenic microorganisms and microbial community changes in mixed cultures are discussed. More importantly, different approaches including chemical/genetic modifications and gene regulation of exoelectrogens, synthetic biology approaches and bacterial community cooperation are reviewed. Advances in recent years in metagenomics and microbiomes have allowed researchers to improve bacterial electrogenicity of robust biofilms in MFCs using novel, unconventional approaches. Taken together, this review provides some important and timely information to researchers who are examining additional means to enhance power production of MFCs.}, }
@article {pmid29575679, year = {2018}, author = {Zhou, Y and Zhu, H and Yao, Q}, title = {Contrasting P acquisition strategies of the bacterial communities associated with legume and grass in subtropical orchard soil.}, journal = {Environmental microbiology reports}, volume = {10}, number = {3}, pages = {310-319}, doi = {10.1111/1758-2229.12641}, pmid = {29575679}, issn = {1758-2229}, mesh = {Bacteria/*classification/isolation &amp; purification/metabolism ; Metagenomics ; Microbiota ; Paspalum/metabolism/*microbiology ; Phosphorus/*metabolism ; Pterocarpus/metabolism/*microbiology ; *Soil Microbiology ; Turkey ; }, abstract = {Phosphorus (P) cycling is a fundamental process driven by microorganisms, and plants can regulate P cycling directly or via their influence on the soil microbial community. However, the differential P cycling patterns associated with legumes and grass are largely unknown. Therefore, we investigated the microbial community involved in P cycling in subtropical soil grown with stylo (Stylosanthes guianensis, legume) or bahiagrass (Paspalum notatum, grass) using metagenomic sequencing. P fractionation indicated that sparingly soluble inorganic P (Pi) accounted for approximately 75% of P pool. Bacteria involved in sparingly soluble Pi solubilization (pqq, gad, JEN) were more abundant in bahiagrass soil, with Candidatus Pelagibacter, Trichodesmium, Neorickettsia, Nitrobacter, Paraburkholderia, Candidatus Solibacter, Burkholderia as major contributors. In contrast, bacteria involved in organic P (Po) mineralization (php, glpQ, phn) were more abundant in stylo soil, consistent with phosphatase activity and Frankia, Kyrpidia, Thermobispora, Streptomyces, Rhodococcus were major contributors. Bacteria taking up low molecular-weight Po were more abundant in stylo soil than in bahiagrass soil, while those taking up Pi were less abundant. These data suggest that bacterial communities associated with legumes and grass develop contrasting P acquisition strategies, highlighting the possibility of intercropping with legumes and grass for better P cycling.}, }
@article {pmid29515974, year = {2018}, author = {Ewan, VC and Reid, WDK and Shirley, M and Simpson, AJ and Rushton, SP and Wade, WG}, title = {Oropharyngeal Microbiota in Frail Older Patients Unaffected by Time in Hospital.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {42}, pmid = {29515974}, issn = {2235-2988}, support = {G0800440//Medical Research Council/United Kingdom ; }, mesh = {Aged ; Aged, 80 and over ; Biodiversity ; Carrier State/*epidemiology ; Cross Infection/epidemiology/microbiology ; Female ; *Geriatric Assessment ; *Hospitalization ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Oropharynx/*microbiology ; Pharyngitis/epidemiology/microbiology ; Time Factors ; }, abstract = {Respiratory tract infections are the commonest nosocomial infections, and occur predominantly in frailer, older patients with multiple comorbidities. The oropharyngeal microbiota is the major reservoir of infection. This study explored the relative contributions of time in hospital and patient demographics to the community structure of the oropharyngeal microbiota in older patients with lower limb fracture. We collected 167 throat swabs from 53 patients (mean age 83) over 14 days after hospitalization, and analyzed these using 16S rRNA gene sequencing. We calculated frailty/comorbidity indices, undertook dental examinations and collected data on respiratory tract infections. We analyzed microbial community composition using correspondence (CA) and canonical correspondence analysis. Ten patients were treated for respiratory tract infection. Microbial community structure was related to frailty, number of teeth and comorbidity on admission, with comorbidity exerting the largest effect. Time in hospital neither significantly changed alpha (t = -0.910, p = 0.365) nor beta diversity (CA1 t = 0.022, p = 0.982; CA2 t = -0.513, p = 0.609) of microbial communities in patient samples. Incidence of respiratory pathogens were not associated with time in hospital (t = -0.207, p = 0.837), nor with alpha diversity of the oral microbiota (t = -1.599, p = 0.113). Patient characteristics at admission, rather than time in hospital, influenced the community structure of the oral microbiota.}, }
@article {pmid29488349, year = {2018}, author = {Lang-Yona, N and Maier, S and Macholdt, DS and Müller-Germann, I and Yordanova, P and Rodriguez-Caballero, E and Jochum, KP and Al-Amri, A and Andreae, MO and Fröhlich-Nowoisky, J and Weber, B}, title = {Insights into microbial involvement in desert varnish formation retrieved from metagenomic analysis.}, journal = {Environmental microbiology reports}, volume = {10}, number = {3}, pages = {264-271}, doi = {10.1111/1758-2229.12634}, pmid = {29488349}, issn = {1758-2229}, mesh = {Actinobacteria/*classification/genetics/isolation &amp; purification/metabolism ; Clay/*microbiology ; Cyanobacteria/*classification/genetics/isolation &amp; purification/metabolism ; Ferric Compounds/*metabolism ; Manganese Compounds/*metabolism ; Metagenomics/methods ; Microbiota/genetics ; Oxides/*metabolism ; Proteobacteria/*classification/genetics/isolation &amp; purification/metabolism ; Sequence Analysis, DNA/methods ; *Soil Microbiology ; }, abstract = {Desert varnishes are dark rock coatings observed in arid environments and might resemble Mn-rich coatings found on Martian rocks. Their formation mechanism is not fully understood and the possible microbial involvement is under debate. In this study, we applied DNA metagenomic Shotgun sequencing of varnish and surrounding soil to evaluate the composition of the microbial community and its potential metabolic function. We found that the α diversity was lower in varnish compared to soil samples (p value < 0.05), suggesting distinct populations with significantly higher abundance of Actinobacteria, Proteobacteria and Cyanobacteria within the varnish. Additionally, we observed increased levels of transition metal metabolic processes in varnish compared to soil samples. Nevertheless, potentially relevant enzymes for varnish formation were detected at low to insignificant levels in both niches, indicating no current direct microbial involvement in Mn oxidation. This finding is supported by quantitative genomic analysis, elemental analysis, fluorescence imaging and scanning transmission X-ray microscopy. We thus conclude that the distinct microbial communities detected in desert varnish originate from settled Aeolian microbes, which colonized this nutrient-enriched niche, and discuss possible indirect contributions of microorganisms to the formation of desert varnish.}, }
@article {pmid29368406, year = {2018}, author = {Chai, ZY and He, ZL and Deng, YY and Yang, YF and Tang, YZ}, title = {Cultivation of seaweed Gracilaria lemaneiformis enhanced biodiversity in a eukaryotic plankton community as revealed via metagenomic analyses.}, journal = {Molecular ecology}, volume = {27}, number = {4}, pages = {1081-1093}, doi = {10.1111/mec.14496}, pmid = {29368406}, issn = {1365-294X}, mesh = {*Biodiversity ; Biomass ; China ; Geography ; Gracilaria/*growth &amp; development ; *Metagenomics ; Phylogeny ; Plankton/*genetics ; Principal Component Analysis ; RNA, Ribosomal, 28S/genetics ; Seaweed/*growth &amp; development ; }, abstract = {Plankton diversity reflects the quality and health of waters and should be monitored as a critical feature of marine ecosystems. This study applied a pair of 28S rRNA gene-specific primers and pyrosequencing to assess the effects of large-scale cultivation of the seaweed Gracilaria lemaneiformis on the biodiversity of eukaryotic plankton community in the coastal water of Guangdong, China. With 1 million sequences (2,221 operational taxonomic units [OTUs]) obtained from 51 samples, we found that the biodiversity of eukaryotic plankton community was significantly higher in the seaweed cultivation area than that in the nearby control area as reflected in OTU richness, evenness (Shannon-Wiener index) and dominance (Simpson index) for total plankton community and its four subcategories when Gracilaria biomass reached the maximum, while no such a significant difference was observed before seaweed inoculation. Our laboratory experiment using an artificial phytoplankton community of nine species observed the same effects of Gracilaria exposure. Principal component analysis and principal coordinates analysis showed the plankton community structure in cultivation area markedly differed from the control area when Gracilaria biomass reached its maximum. Redundancy analysis showed that G. lemaneiformis was the critical factor in controlling the dynamics of eukaryotic plankton communities in the studied coastal ecosystem. Our results explicitly demonstrated G. lemaneiformis cultivation could enhance biodiversity of plankton community via allelopathy, which prevents one or several plankton species from blooming and consequently maintains a relatively higher biodiversity. Our study provided further support for using large-scale G. lemaneiformis cultivation as an effective approach for improving costal ecosystem health.}, }
@article {pmid28607352, year = {2017}, author = {Zhou, J and Jiang, X and Wei, D and Zhao, B and Ma, M and Chen, S and Cao, F and Shen, D and Guan, D and Li, J}, title = {Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3267}, pmid = {28607352}, issn = {2045-2322}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; China ; Crops, Agricultural ; Fertilizers/*analysis ; Metagenome ; Metagenomics/methods ; Nitrogen/*analysis ; RNA, Ribosomal, 16S ; *Seasons ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.}, }
@article {pmid30793504, year = {2019}, author = {Kwon, YM and Patra, AK and Chiura, HX and Kim, SJ}, title = {Production of extracellular vesicles with light-induced proton pump activity by proteorhodopsin-containing marine bacteria.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e808}, doi = {10.1002/mbo3.808}, pmid = {30793504}, issn = {2045-8827}, support = {2019M00700//MABIK/ ; }, abstract = {The production and release of extracellular vesicles (EVs) is a common process occurring in various types of bacteria. However, little is known regarding the functions of EVs derived from marine bacteria. We observed that during cell growth, Sediminicola sp. YIK13, a proteorhodopsin (PR)-containing marine flavobacterium, produces EVs (S13EVs). Transmission electron microscopy showed that Sediminicola sp. YIK13 released two spherical vesicle types, with mono- and/or bi-layered membranes, in the culture. Interestingly, the S13EVs have an orange pigment, indicating the presence of putative carotenoid and PR pigments ascribed to the parental cells. The S13EVs demonstrated the same PR-derived absorption peak spectrum and light-induced proton pump activity as the parental cells. Western blot (immunoblot) analysis of the S13EVs revealed the presence of PR. We confirmed the 16S rRNA gene, pro gene, and genes required for chromophore retinal synthesis, namely blh and crtI, in the DNA packaged into these vesicles. In addition, by metagenomic sequencing, we found microbial rhodopsin-related genes in vesicles derived from natural aquatic environments. Our results suggest that EVs as well potentially pursue horizontal gene transfer of diverse microbial rhodopsin genes in marine ecosystems.}, }
@article {pmid30625669, year = {2019}, author = {Costeira, R and Doherty, R and Allen, CCR and Larkin, MJ and Kulakov, LA}, title = {Analysis of viral and bacterial communities in groundwater associated with contaminated land.}, journal = {The Science of the total environment}, volume = {656}, number = {}, pages = {1413-1426}, doi = {10.1016/j.scitotenv.2018.11.429}, pmid = {30625669}, issn = {1879-1026}, mesh = {Bacteria/classification/*genetics ; Groundwater/*microbiology/virology ; *Metagenome ; *Microbiota ; Northern Ireland ; Soil Pollutants/*analysis ; Viruses/classification/*genetics ; }, abstract = {This work aimed at the comprehensive analysis of total microbial communities inhabiting a typical hydrocarbon-polluted site, where chemical characteristics of the groundwater were readily available. To achieve this, a joint metagenomic characterization of bacteria and viruses surrounding a contaminant plume was performed over a one-year period. The results presented demonstrated that both potential hydrocarbon degraders and their bacteriophages were dominant around the plume, and that the viral and bacterial diversities found at the site were probably influenced by the pH of the groundwater. Niche-specific and dispersed associations between phages and bacteria were identified. The niche phage-host associations were found at the edge of the site and at the core of the plume where pH was the highest (9.52). The identified host populations included several classes of bacteria (e.g. Clostridia and Proteobacteria). Thirty-six viral generalists were also discovered, with BGW-G9 having the broadest host range across 23 taxa, including Pseudomonas, Polycyclovorans, Methylocaldum and Candidatus Magnetobacterium species. The phages with broad host ranges are presumed to have significant effects on prokaryotic production and horizontal gene transfer, and therefore impact the biodegradation processes conducted by various bacteria of the environment studied. This study for the first time characterized the phages and their bacterial hosts associated with a contaminant plume.}, }
@article {pmid30537931, year = {2018}, author = {Benavides, A and Isaza, JP and Niño-García, JP and Alzate, JF and Cabarcas, F}, title = {CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 8}, pages = {858}, pmid = {30537931}, issn = {1471-2164}, mesh = {*Algorithms ; Colombia ; Genes, Bacterial ; Genetic Markers ; *Genome, Bacterial ; *Metagenomics ; Microbiota ; Phylogeny ; Sequence Analysis, DNA/*methods ; Xanthomonadaceae/*classification/*genetics ; }, abstract = {BACKGROUND: Hot spring bacteria have unique biological adaptations to survive the extreme conditions of these environments; these bacteria produce thermostable enzymes that can be used in biotechnological and industrial applications. However, sequencing these bacteria is complex, since it is not possible to culture them. As an alternative, genome shotgun sequencing of whole microbial communities can be used. The problem is that the classification of sequences within a metagenomic dataset is very challenging particularly when they include unknown microorganisms since they lack genomic reference. We failed to recover a bacterium genome from a hot spring metagenome using the available software tools, so we develop a new tool that allowed us to recover most of this genome.<br><br>RESULTS: We present a proteobacteria draft genome reconstructed from a Colombian's Andes hot spring metagenome. The genome seems to be from a new lineage within the family Rhodanobacteraceae of the class Gammaproteobacteria, closely related to the genus Dokdonella. We were able to generate this genome thanks to CLAME. CLAME, from Spanish &quot;CLAsificador MEtagenomico&quot;, is a tool to group reads in bins. We show that most reads from each bin belong to a single chromosome. CLAME is very effective recovering most of the reads belonging to the predominant species within a metagenome.<br><br>CONCLUSIONS: We developed a tool that can be used to extract genomes (or parts of them) from a complex metagenome.}, }
@article {pmid30338752, year = {2018}, author = {Abranches, J and Zeng, L and Kajfasz, JK and Palmer, SR and Chakraborty, B and Wen, ZT and Richards, VP and Brady, LJ and Lemos, JA}, title = {Biology of Oral Streptococci.}, journal = {Microbiology spectrum}, volume = {6}, number = {5}, pages = {}, pmid = {30338752}, issn = {2165-0497}, support = {R01 DE022559/DE/NIDCR NIH HHS/United States ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; }, mesh = {Carbohydrate Metabolism ; Dental Caries/microbiology ; Endocarditis/microbiology ; Fermentation ; Humans ; Hydrogen Peroxide/metabolism ; Metagenomics ; Microbiota/physiology ; Mouth/*microbiology ; Phylogeny ; Streptococcus/classification/genetics/pathogenicity/*physiology ; Streptococcus gordonii/metabolism ; Streptococcus mutans ; Streptococcus salivarius/metabolism ; }, abstract = {Bacteria belonging to the genus Streptococcus are the first inhabitants of the oral cavity, which can be acquired right after birth and thus play an important role in the assembly of the oral microbiota. In this article, we discuss the different oral environments inhabited by streptococci and the species that occupy each niche. Special attention is given to the taxonomy of Streptococcus, because this genus is now divided into eight distinct groups, and oral species are found in six of them. Oral streptococci produce an arsenal of adhesive molecules that allow them to efficiently colonize different tissues in the mouth. Also, they have a remarkable ability to metabolize carbohydrates via fermentation, thereby generating acids as byproducts. Excessive acidification of the oral environment by aciduric species such as Streptococcus mutans is directly associated with the development of dental caries. However, less acid-tolerant species such as Streptococcus salivarius and Streptococcus gordonii produce large amounts of alkali, displaying an important role in the acid-base physiology of the oral cavity. Another important characteristic of certain oral streptococci is their ability to generate hydrogen peroxide that can inhibit the growth of S. mutans. Thus, oral streptococci can also be beneficial to the host by producing molecules that are inhibitory to pathogenic species. Lastly, commensal and pathogenic streptococci residing in the oral cavity can eventually gain access to the bloodstream and cause systemic infections such as infective endocarditis.}, }
@article {pmid30192933, year = {2018}, author = {Li, F and Chen, C and Wei, W and Wang, Z and Dai, J and Hao, L and Song, L and Zhang, X and Zeng, L and Du, H and Tang, H and Liu, N and Yang, H and Wang, J and Madsen, L and Brix, S and Kristiansen, K and Xu, X and Li, J and Wu, R and Jia, H}, title = {The metagenome of the female upper reproductive tract.}, journal = {GigaScience}, volume = {7}, number = {10}, pages = {}, pmid = {30192933}, issn = {2047-217X}, mesh = {Biodiversity ; Computational Biology/methods ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Reproductive Tract Infections/*microbiology ; Vagina/microbiology ; }, abstract = {Background: The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking.<br><br>Results: We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. Direct annotation of sequencing reads identified the taxonomy of bacteria, archaea, fungi and viruses, confirming and extending the results from our previous study. We replicated our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of the 20GB raw data. After filtering, vaginal microorganisms were well covered in the generated reproductive tract gene catalogue, while the more diverse upper reproductive tract microbiota would require greater depth of sequencing and more samples to meet the full coverage scale.<br><br>Conclusions: We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.}, }
@article {pmid30168288, year = {2018}, author = {Minich, JJ and Zhu, Q and Xu, ZZ and Amir, A and Ngochera, M and Simwaka, M and Allen, EE and Zidana, H and Knight, R}, title = {Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus).}, journal = {MicrobiologyOpen}, volume = {7}, number = {6}, pages = {e00716}, doi = {10.1002/mbo3.716}, pmid = {30168288}, issn = {2045-8827}, mesh = {Animal Feed/analysis/microbiology ; Animals ; Aquaculture ; Bacteria/classification/genetics/*isolation &amp; purification ; Catfishes/*growth &amp; development/metabolism ; Cattle ; Livestock ; Manure/analysis/*microbiology ; Microbiota ; Ponds/analysis/*microbiology ; Poultry ; Swine ; Tilapia/*growth &amp; development/metabolism ; }, abstract = {The majority of seafood is farmed, with most finfish coming from freshwater ponds. Ponds are often fertilized to promote microbial productivity as a natural feed source to fish. To understand if pond fertilization with livestock manure induces a probiotic or prebiotic effect, we communally reared tilapia (Oreochromis shiranus), and North African catfish (Clarias gariepinus), for 4 weeks under seven manure treatments including layer chicken, broiler chicken, guinea fowl, quail, pig, cow, vs. commercial feed to evaluate microbial community dynamics of the manure, pond water, and fish feces using 16S and 18S rRNA marker genes along with metagenome sequencing. Catfish growth, but not tilapia, was positively associated with plankton abundance (p = 0.0006, R2 = 0.4887) and greatest in ponds fertilized with quail manure (ANOVA, p < 0.05). Manure was unique and influenced the 16S microbiome in pond water, tilapia gut, and catfish gut and 18S community in pond water and catfish guts (PERMANOVA, p = 0.001). On average, 18.5%, 18.6%, and 45.3% of manure bacteria sOTUs, (sub-operational taxonomic units), were present in the water column, catfish feces, and tilapia feces which comprised 3.7%, 12.8%, and 10.9% of the total microbial richness of the communities, respectively. Antibiotic resistance genes were highest in the manure and water samples followed by tilapia feces and lowest in catfish feces (p < 0.0001). In this study, we demonstrate how the bacterial and eukaryotic microbial composition of fish ponds are influenced by specific livestock manure inputs and that the gut microbiome of tilapia is more sensitive and responsive than catfish to these changes. We conclude that animal manure used as fertilizer induces a primarily prebiotic effect on the pond ecosystem rather than a direct probiotic effect on fish.}, }
@article {pmid29652573, year = {2018}, author = {Laudadio, I and Fulci, V and Palone, F and Stronati, L and Cucchiara, S and Carissimi, C}, title = {Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome.}, journal = {Omics : a journal of integrative biology}, volume = {22}, number = {4}, pages = {248-254}, doi = {10.1089/omi.2018.0013}, pmid = {29652573}, issn = {1557-8100}, mesh = {Adolescent ; Child ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The analysis of microbiota composition in humans, animals, and built environments is important because of emerging roles and applications in a broad range of disease and ecological phenotypes. Next Generation Sequencing is the current method of choice to characterize microbial community composition. The taxonomic profile of a microbial community can be obtained either by shotgun analysis of random DNA fragments or through 16S ribosomal RNA gene (rDNA) amplicon sequencing. It has been previously shown that the 16S rDNA amplicon sequencing approach yields quantitatively and qualitatively different results compared to shotgun metagenomics when the two techniques are used to assess microbial community composition on the same samples. However, most of such comparisons were either based on the recovery of 16S rDNA sequences in the shotgun metagenomics data or limited to a single microbiome or synthetic samples. Direct comparison of shotgun metagenomics and 16S rDNA amplicon sequencing on the same samples was performed only once in the recent literature, suggesting that the two methods yield comparable results. Here, we set out to compare the outcome of these two alternative approaches to the microbiome characterization in human gut microbiomes from stool samples. To this end, we processed six different samples with both techniques. We report here that shotgun next generation sequencing metagenomics allows much deeper characterization of the microbiome complexity, allowing identification of a larger number of species for each sample, compared to 16S rDNA amplicon sequencing. Further comparative studies in independent samples are called for.}, }
@article {pmid30777011, year = {2019}, author = {Feng, Y and Ramnarine, VR and Bell, R and Volik, S and Davicioni, E and Hayes, VM and Ren, S and Collins, CC}, title = {Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {146}, doi = {10.1186/s12864-019-5457-z}, pmid = {30777011}, issn = {1471-2164}, support = {CSC201606325044//China Scholarship Council/ ; 201012TFF//Terry Fox Foundation/ ; T2013-01//Prostate Cancer Canada/ ; 81472397//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Prostate cancer (PCa) is the most common malignant neoplasm among men in many countries. Since most precancerous and cancerous tissues show signs of inflammation, chronic bacterial prostatitis has been hypothesized to be a possible etiology. However, establishing a causal relationship between microbial inflammation and PCa requires a comprehensive analysis of the prostate microbiome. The aim of this study was to characterize the microbiome in prostate tissue of PCa patients and investigate its association with tumour clinical characteristics as well as host expression profiles.<br><br>RESULTS: The metagenome and metatranscriptome of tumour and the adjacent benign tissues were assessed in 65 Chinese radical prostatectomy specimens. Escherichia, Propionibacterium, Acinetobacter and Pseudomonas were abundant in both metagenome and metatranscriptome, thus constituting the core of the prostate microbiome. The biodiversity of the microbiomes could not be differentiated between the matched tumour/benign specimens or between the tumour specimens of low and high Gleason Scores. The expression profile of ten Pseudomonas genes was strongly correlated with that of eight host small RNA genes; three of the RNA genes may negatively associate with metastasis. Few viruses could be identified from the prostate microbiomes.<br><br>CONCLUSIONS: This is the first study of the human prostate microbiome employing an integrated metagenomics and metatranscriptomics approach. In this Chinese cohort, both metagenome and metatranscriptome analyses showed a non-sterile microenvironment in the prostate of PCa patients, but we did not find links between the microbiome and local progression of PCa. However, the correlated expression of Pseudomonas genes and human small RNA genes may provide tantalizing preliminary evidence that Pseudomonas infection may impede metastasis.}, }
@article {pmid30031771, year = {2018}, author = {Wade, RM and Sherwood, AR}, title = {Updating Plakobranchus cf. ianthobapsus (Gastropoda, Sacoglossa) host use: Diverse algal-animal interactions revealed by NGS with implications for invasive species management.}, journal = {Molecular phylogenetics and evolution}, volume = {128}, number = {}, pages = {172-181}, doi = {10.1016/j.ympev.2018.07.010}, pmid = {30031771}, issn = {1095-9513}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; Gastropoda/*genetics/*parasitology ; Hawaii ; *High-Throughput Nucleotide Sequencing ; *Host-Parasite Interactions ; *Introduced Species ; Likelihood Functions ; Metagenomics ; Phylogeny ; Principal Component Analysis ; }, abstract = {Sacoglossa, the &quot;sap sucking&quot; sea slugs, are highly specialized herbivores and the only metazoans that exhibit kleptoplasty, the sequestration and retention of chloroplasts from algae. Plakobranchus is one of the most generalistic herbivores within this order, with as many as 12 reported &quot;algal host&quot; (i.e. kleptoplast source) species. However, kleptoplast diversity studies conducted on Plakobranchus to date most likely underestimated the full diversity of kleptoplast sources within the studied populations due to limitations of the molecular techniques employed. Here, we apply a high throughput sequencing technique to assess kleptoplast diversity of Plakobranchus cf. ianthobapsus' from 10 sites across the Main Hawaiian Islands during winter and summer seasons. In so doing, we effectively used P. cf. ianthobapsus as a novel sampling tool to explore diminutive algal communities, including the current distribution of the invasive alga &quot;Avrainvillea amadelpha.&quot; Our results show that P. cf. ianthobapsus sequesters chloroplasts from 23 algal species from across the siphonous green algal order Bryopsidales. We identified &quot;Avrainvillea amadelpha&quot; and Codium edule as new host species for P. cf. ianthobapusus, but their rarity among the data suggests they were most likely less preferential as hosts and were possibly utilized due to low abundance or unavailability of more preferable species, and therefore a response to starvation risk. Additionally, the identification of the highly invasive siphonous green alga &quot;A. amadelpha&quot; as a kleptoplast source provides new fine-scale range and distribution data for this problematic species. Overall kleptoplast diversity does not differ among sites, except in a coral-dominated, (i.e. not algal dominated) environment, suggesting that siphonous algal assemblages are common in algal-dominated ecosystems in the Hawaiian Islands. Diversity dissimilarity among seasons was recovered from the majority of sites sampled, supporting the need for seasonal data collection in algal diversity assessments. This case study using metabarcoding of sacoglossan kleptoplasts provides deeper insights into these plant-animal interactions with a better understanding of host use than previous studies using traditional molecular methods and illustrates how algal diversity studies on the scale of plastids can have implications for understanding algal community structure and invasive species dynamics.}, }
@article {pmid29165844, year = {2018}, author = {Lassalle, F and Spagnoletti, M and Fumagalli, M and Shaw, L and Dyble, M and Walker, C and Thomas, MG and Bamberg Migliano, A and Balloux, F}, title = {Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet.}, journal = {Molecular ecology}, volume = {27}, number = {1}, pages = {182-195}, doi = {10.1111/mec.14435}, pmid = {29165844}, issn = {1365-294X}, support = {BB/H008802/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Department of Health/United Kingdom ; MR/N010760/1//Medical Research Council/United Kingdom ; }, mesh = {Biodiversity ; *Diet, Paleolithic ; *Farmers ; Genetics, Population ; Geography ; *Host-Pathogen Interactions ; Humans ; *Microbiota/genetics ; Mouth/*microbiology ; Philippines ; Principal Component Analysis ; Species Specificity ; }, abstract = {Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in close proximity in the Philippines. Deep shotgun sequencing of salivary DNA generated high-coverage microbiomes along with human genomes. Comparing these microbiomes with publicly available data from individuals living on a Western diet revealed that abundance ratios of core species were significantly correlated with subsistence strategy, with hunter-gatherers and Westerners occupying either end of a gradient of Neisseria against Haemophilus, and traditional farmers falling in between. Species found preferentially in hunter-gatherers included microbes often considered as oral pathogens, despite their hosts' apparent good oral health. Discriminant analysis of gene functions revealed vitamin B5 autotrophy and urease-mediated pH regulation as candidate adaptations of the microbiome to the hunter-gatherer and Western diets, respectively. These results suggest that major transitions in diet selected for different communities of commensals and likely played a role in the emergence of modern oral pathogens.}, }
@article {pmid29113023, year = {2018}, author = {Andújar, C and Arribas, P and Gray, C and Bruce, C and Woodward, G and Yu, DW and Vogler, AP}, title = {Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill.}, journal = {Molecular ecology}, volume = {27}, number = {1}, pages = {146-166}, doi = {10.1111/mec.14410}, pmid = {29113023}, issn = {1365-294X}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; *Environmental Monitoring ; *Fresh Water ; High-Throughput Nucleotide Sequencing ; Invertebrates/*drug effects ; *Metagenomics ; Pesticides/*toxicity ; Species Specificity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species-level resolution is difficult to obtain. Next-generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 &quot;barcode&quot; and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in the River Kennet (southern England). Operational taxonomic unit (OTU) recovery was tested under 72 parameters (read denoising, filtering, pair merging and clustering). Similar taxonomic profiles were obtained under a broad range of parameters. The SSU marker recovered Platyhelminthes and Nematoda, missed by cox1, while Rotifera were only amplified with cox1. A reference set was created from all available barcode entries for Arthropoda in the BOLD database and clustered into OTUs. The River Kennet metabarcoding produced matches to 207 of these reference OTUs, five times the number of species recognized with morphological monitoring. The increase was due to the following: greater taxonomic resolution (e.g., splitting a single morphotaxon &quot;Chironomidae&quot; into 55 named OTUs); splitting of Linnaean binomials into multiple molecular OTUs; and the use of a filtration-flotation protocol for extraction of minute specimens (meiofauna). Community analyses revealed strong differences between &quot;impacted&quot; vs. &quot;control&quot; samples, detectable with each gene marker, for each major taxonomic group, and for meio- and macrofaunal samples separately. Thus, highly resolved taxonomic data can be extracted at a fraction of the time and cost of traditional nonmolecular methods, opening new avenues for freshwater invertebrate biodiversity monitoring and molecular ecology.}, }
@article {pmid28779076, year = {2017}, author = {Yin, D and Du, E and Yuan, J and Gao, J and Wang, Y and Aggrey, SE and Guo, Y}, title = {Supplemental thymol and carvacrol increases ileum Lactobacillus population and reduces effect of necrotic enteritis caused by Clostridium perfringes in chickens.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7334}, pmid = {28779076}, issn = {2045-2322}, mesh = {Animals ; Chickens ; Clostridium Infections/*veterinary ; Clostridium perfringens/*drug effects ; Dietary Supplements ; Enterocolitis, Necrotizing/*veterinary ; Gastrointestinal Microbiome ; Ileum/microbiology ; Lactobacillus/*drug effects/genetics ; Male ; Metagenome ; Metagenomics/methods ; Monoterpenes/*pharmacology ; Poultry Diseases/*drug therapy/*microbiology/mortality/pathology ; Thymol/*pharmacology ; }, abstract = {Necrotic enteritis (NE) caused by Clostridium perfringens is one of the most detrimental infectious diseases in poultry. This study examined the effect of blends of essential oils (BEOs) (25% thymol and 25% carvacrol) on NE and bacterial dynamics and functions in chicks challenged with C. perfringens. Chicks were assigned to a Control diet and BEOs diet (Control diet + 120 mg/kg BEOs), were challenged with C. perfringens from days 14 to 20 and were killed on day 21 for assessment. Supplementation with BEOs decreased the mortality, alleviated gut lesions, and decreased the virulence factors of pathogenic bacteria (VF 0073-ClpE, VF0124-LPS, and VF0350-BSH). Lack of supplementation also changed the nutrient and immunological dynamics of host microbiota in responding to C. perfringens infection. Adding BEOs changed the host ileum microbial population by increasing the numbers of Lactobacillus crispatus and Lactobacillus agilis, and decreasing Lactobacillus salivarius and Lactobacillus johnsonii. The functional roles of these changing host bacterial populations coupled with the putative reduced pathogenicity of C. perfringens by BEOs contributed to the reduction in gut lesions and mortality in infected chickens. It suggests that dietary supplementation with BEOs could significantly reduce the impact of NE caused by C. perfringens on broilers.}, }
@article {pmid28775301, year = {2017}, author = {Erwin, PM and Rhodes, RG and Kiser, KB and Keenan-Bateman, TF and McLellan, WA and Pabst, DA}, title = {High diversity and unique composition of gut microbiomes in pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7205}, pmid = {28775301}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Sperm Whale ; Symbiosis ; *Whales ; }, abstract = {Mammals host diverse bacterial and archaeal symbiont communities (i.e. microbiomes) that play important roles in digestive and immune system functioning, yet cetacean microbiomes remain largely unexplored, in part due to sample collection difficulties. Here, fecal samples from stranded pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales were used to characterize the gut microbiomes of two closely-related species with similar diets. 16S rRNA gene sequencing revealed diverse microbial communities in kogiid whales dominated by Firmicutes and Bacteroidetes. Core symbiont taxa were affiliated with phylogenetic lineages capable of fermentative metabolism and sulfate respiration, indicating potential symbiont contributions to energy acquisition during prey digestion. The diversity and phylum-level composition of kogiid microbiomes differed from those previously reported in toothed whales, which exhibited low diversity communities dominated by Proteobacteria and Actinobacteria. Community structure analyses revealed distinct gut microbiomes in K. breviceps and K. sima, driven by differential relative abundances of shared taxa, and unique microbiomes in kogiid hosts compared to other toothed and baleen whales, driven by differences in symbiont membership. These results provide insight into the diversity, composition and structure of kogiid gut microbiomes and indicate that host identity plays an important role in structuring cetacean microbiomes, even at fine-scale taxonomic levels.}, }
@article {pmid28720895, year = {2017}, author = {Liu, J and Techtmann, SM and Woo, HL and Ning, D and Fortney, JL and Hazen, TC}, title = {Rapid Response of Eastern Mediterranean Deep Sea Microbial Communities to Oil.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5762}, pmid = {28720895}, issn = {2045-2322}, mesh = {Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; Biodiversity ; Geography ; Mediterranean Sea ; Metagenomics/methods ; Microbiota/*drug effects/genetics ; Petroleum/*toxicity ; Petroleum Pollution/*analysis ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Deep marine oil spills like the Deepwater Horizon (DWH) in the Gulf of Mexico have the potential to drastically impact marine systems. Crude oil contamination in marine systems remains a concern, especially for countries around the Mediterranean Sea with off shore oil production. The goal of this study was to investigate the response of indigenous microbial communities to crude oil in the deep Eastern Mediterranean Sea (E. Med.) water column and to minimize potential bias associated with storage and shifts in microbial community structure from sample storage. 16S rRNA amplicon sequencing was combined with GeoChip metagenomic analysis to monitor the microbial community changes to the crude oil and dispersant in on-ship microcosms set up immediately after water collection. After 3 days of incubation at 14 °C, the microbial communities from two different water depths: 824 m and 1210 m became dominated by well-known oil degrading bacteria. The archaeal population and the overall microbial community diversity drastically decreased. Similarly, GeoChip metagenomic analysis revealed a tremendous enrichment of genes related to oil biodegradation, which was consistent with the results from the DWH oil spill. These results highlight a rapid microbial adaption to oil contamination in the deep E. Med., and indicate strong oil biodegradation potential.}, }
@article {pmid30504145, year = {2018}, author = {Tokuda, G and Mikaelyan, A and Fukui, C and Matsuura, Y and Watanabe, H and Fujishima, M and Brune, A}, title = {Fiber-associated spirochetes are major agents of hemicellulose degradation in the hindgut of wood-feeding higher termites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {51}, pages = {E11996-E12004}, doi = {10.1073/pnas.1810550115}, pmid = {30504145}, issn = {1091-6490}, mesh = {Animals ; Cellulases/genetics/metabolism ; Cellulose/metabolism ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Glycoside Hydrolases/genetics/metabolism ; Isoptera/*microbiology ; Metagenome/genetics ; Metagenomics ; Phylogeny ; Polysaccharides/*metabolism ; Sequence Analysis, DNA ; Spirochaetales/*enzymology/*genetics/*metabolism ; Symbiosis ; Wood/*metabolism ; Xylans/metabolism ; Xylosidases/classification/genetics/metabolism ; }, abstract = {Symbiotic digestion of lignocellulose in wood-feeding higher termites (family Termitidae) is a two-step process that involves endogenous host cellulases secreted in the midgut and a dense bacterial community in the hindgut compartment. The genomes of the bacterial gut microbiota encode diverse cellulolytic and hemicellulolytic enzymes, but the contributions of host and bacterial symbionts to lignocellulose degradation remain ambiguous. Our previous studies of Nasutitermes spp. documented that the wood fibers in the hindgut paunch are consistently colonized not only by uncultured members of Fibrobacteres, which have been implicated in cellulose degradation, but also by unique lineages of Spirochaetes. Here, we demonstrate that the degradation of xylan, the major component of hemicellulose, is restricted to the hindgut compartment, where it is preferentially hydrolyzed over cellulose. Metatranscriptomic analysis documented that the majority of glycoside hydrolase (GH) transcripts expressed by the fiber-associated bacterial community belong to family GH11, which consists exclusively of xylanases. The substrate specificity was further confirmed by heterologous expression of the gene encoding the predominant homolog. Although the most abundant transcripts of GH11 in Nasutitermes takasagoensis were phylogenetically placed among their homologs of Firmicutes, immunofluorescence microscopy, compositional binning of metagenomics contigs, and the genomic context of the homologs indicated that they are encoded by Spirochaetes and were most likely obtained by horizontal gene transfer among the intestinal microbiota. The major role of spirochetes in xylan degradation is unprecedented and assigns the fiber-associated Treponema clades in the hindgut of wood-feeding higher termites a prominent part in the breakdown of hemicelluloses.}, }
@article {pmid29272453, year = {2018}, author = {Pérez-Brocal, V and Andremont, A and Moya, A}, title = {Isolation in small populations of Wayampi Amerindians promotes endemicity and homogenisation of their faecal virome, but its distribution is not entirely random.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {2}, pages = {}, doi = {10.1093/femsec/fix184}, pmid = {29272453}, issn = {1574-6941}, mesh = {Adult ; Anti-Bacterial Agents/therapeutic use ; DNA Viruses/classification/*genetics/isolation &amp; purification ; Enterobacteriaceae/genetics/metabolism ; Feces/*virology ; Female ; French Guiana ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; Prophages/classification/*genetics/isolation &amp; purification ; beta-Lactamases/*genetics ; }, abstract = {The isolated community of the Wayampi Amerindians has been extensively studied for the presence of beta lactamase-producing enterobacteria and their gut microbiota. However, no information about their virome was available. This study tries to establish potential associations between the virome and diverse epidemiological data, through the metagenomic study of the faecal prophages and DNA viruses from 31 samples collected in 2010. Taxonomic assignments, composition, abundance and diversity analyses were obtained to characterise the virome and were compared between groups according to several demographic, environmental and medical data. Prophages outnumbered viruses. Composition and abundance of virome indicated relatively low variability. Diversity within samples showed no significant differences, regardless of the group comparison. Significant differences were observed in the beta diversity among samples according to hospitalisation and gender, but not by extended spectrum β-lactamase carriage, antibiotic intake or possession of pets, although some viruses differed in some cases (e.g. immunodeficiency-associated stool virus associated with antibiotic intake). The faecal virome of adult Wayampi is more homogeneous than that from western populations. Not a single factor analysed can explain alone the observed distribution of the virome, but differences by gender (fewer variability in females than males) may reflect differences in life habits and work.}, }
@article {pmid29228244, year = {2018}, author = {Cleary, DFR and Polónia, ARM and de Voogd, NJ}, title = {Prokaryote composition and predicted metagenomic content of two Cinachyrella Morphospecies and water from West Papuan Marine Lakes.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {2}, pages = {}, doi = {10.1093/femsec/fix175}, pmid = {29228244}, issn = {1574-6941}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biodiversity ; Indonesia ; Lakes/microbiology ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Porifera/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Certain sponge species are difficult to identify using classical taxonomic characters, and other techniques are often necessary. Here we used 454-pyrosequencing of the 16S rRNA gene to investigate bacterial and archaeal communities of two distinct Cinachyrella morphospecies collected from two Indonesian marine lakes with differing degrees of connection to the surrounding sea. Our main goal was to assess whether these morphospecies hosted distinct bacterial and archaeal communities and to what extent these differed from those found in lake water. A recently developed bioinformatic tool (PICRUSt) was used to predict metagenomic gene content of the studied communities. Compositionally, sponge samples clustered according to morphospecies as opposed to marine lake indicating that each morphospecies hosted distinct bacterial and archaeal communities. There were, however, also differences in higher taxon abundance among lakes. In the less connected lake, for example, both Cinachyrella morphospecies had higher levels of the order Synechococcales. With respect to metabolic gene content, although there were pronounced differences in predicted enrichment between both morphospecies, both were putatively enriched for KOs involved in pathways related to stress response, energy metabolism, environmental information processing and the production of secondary metabolites compared to prokaryote communities in water. These morphospecies may thus prove to be interesting sources of novel compounds of potential pharmaceutical and/or biotechnological importance.}, }
@article {pmid30761108, year = {2019}, author = {Ulloa, R and Moya-Beltrán, A and Rojas-Villalobos, C and Nuñez, H and Chiacchiarini, P and Donati, E and Giaveno, A and Quatrini, R}, title = {Domestication of Local Microbial Consortia for Efficient Recovery of Gold Through Top-Down Selection in Airlift Bioreactors.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {60}, doi = {10.3389/fmicb.2019.00060}, pmid = {30761108}, issn = {1664-302X}, abstract = {Extreme acidophiles play central roles in the geochemical cycling of diverse elements in low pH environments. This has been harnessed in biotechnologies such as biomining, where microorganisms facilitate the recovery of economically important metals such as gold. By generating both extreme acidity and a chemical oxidant (ferric iron) many species of prokaryotes that thrive in low pH environments not only catalyze mineral dissolution but also trigger both community and individual level adaptive changes. These changes vary in extent and direction depending on the ore mineralogy, water availability and local climate. The use of indigenous versus introduced microbial consortia in biomining practices is still a matter of debate. Yet, indigenous microbial consortia colonizing sulfidic ores that have been domesticated, i.e., selected for their ability to survive under specific polyextreme conditions, are claimed to outperform un-adapted foreign consortia. Despite this, little is known on the domestication of acidic microbial communities and the changes elicited in their members. In this study, high resolution targeted metagenomic techniques were used to analyze the changes occurring in the community structure of local microbial consortia acclimated to growing under extreme acidic conditions and adapted to endure the conditions imposed by the target mineral during biooxidation of a gold concentrate in an airlift reactor over a period of 2 years. The results indicated that operative conditions evolving through biooxidation of the mineral concentrate exerted strong selective pressures that, early on, purge biodiversity in favor of a few Acidithiobacillus spp. over other iron oxidizing acidophiles. Metagenomic analysis of the domesticated consortium present at the end of the adaptation experiment enabled reconstruction of the RVS1-MAG, a novel representative of Acidithiobacillus ferrooxidans from the Andacollo gold mineral district. Comparative genomic analysis performed with this genome draft revealed a net enrichment of gene functions related to heavy metal transport and stress management that are likely to play a significant role in adaptation and survival to adverse conditions experienced by these acidophiles during growth in presence of gold concentrates.}, }
@article {pmid30759800, year = {2019}, author = {Tremblay, ÉD and Kimoto, T and Bérubé, JA and Bilodeau, GJ}, title = {High-Throughput Sequencing to Investigate Phytopathogenic Fungal Propagules Caught in Baited Insect Traps.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {5}, number = {1}, pages = {}, doi = {10.3390/jof5010015}, pmid = {30759800}, issn = {2309-608X}, support = {OLF-P-1304, GRDI, QIS and CFIA OFL-P-1411, Genome Canada, and Genome BC (LSARP2112), CFIA-RPS and CFIA-TD and GRDI-CFIA mandated//Canadian Food Inspection Agency/ ; }, abstract = {Studying the means of dispersal of plant pathogens is crucial to better understand the dynamic interactions involved in plant infections. On one hand, entomologists rely mostly on both traditional molecular methods and morphological characteristics, to identify pests. On the other hand, high-throughput sequencing (HTS) is becoming the go-to avenue for scientists studying phytopathogens. These organisms sometimes infect plants, together with insects. Considering the growing number of exotic insect introductions in Canada, forest pest-management efforts would benefit from the development of a high-throughput strategy to investigate the phytopathogenic fungal and oomycete species interacting with wood-boring insects. We recycled formerly discarded preservative fluids from the Canadian Food Inspection Agency annual survey using insect traps and analysed more than one hundred samples originating from across Canada. Using the Ion Torrent Personal Genome Machine (PGM) HTS technology and fusion primers, we performed metabarcoding to screen unwanted fungi and oomycetes species, including Phytophthora spp. Community profiling was conducted on the four different wood-boring, insect-attracting semiochemicals; although the preservative (contained ethanol) also attracted other insects. Phytopathogenic fungi (e.g., Leptographium spp. and Merialaricis in the pine sawyer semiochemical) and oomycetes (mainly Peronospora spp. and Pythium aff. hypogynum in the General Longhorn semiochemical), solely associated with one of the four types of semiochemicals, were detected. This project demonstrated that the insect traps' semiochemical microbiome represents a new and powerful matrix for screening phytopathogens. Compared to traditional diagnostic techniques, the fluids allowed for a faster and higher throughput assessment of the biodiversity contained within. Additionally, minimal modifications to this approach would allow it to be used in other phytopathology fields.}, }
@article {pmid30755506, year = {2019}, author = {Hausmann, B and Pelikan, C and Rattei, T and Loy, A and Pester, M}, title = {Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02189-18}, pmid = {30755506}, issn = {2150-7511}, abstract = {Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize &quot;Candidatus Desulfosporosinus infrequens,&quot; a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 106 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of &quot;Ca. Desulfosporosinus infrequens&quot; increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days.IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.}, }
@article {pmid30740092, year = {2019}, author = {Grządziel, J and Gałązka, A}, title = {Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {6}, doi = {10.3389/fmicb.2019.00006}, pmid = {30740092}, issn = {1664-302X}, abstract = {The aim of the study was to investigate fungal genetic diversity in eight different types of soil in a long-term microplot experiment founded in 1881 in Puławy, Poland. The experiment consists of eight plots (14 m2), each 1 m deep with concrete walls, filled with profiles of different soils. The soils represent the most common Polish soil types (Cambic Leptosol, Fluvic Cambisol, Gleyic Chernozem, Cambisol and Haplic Cambisol, two Brunic Arenosols and Haplic Luvisol). Each soil was characterized by different pH (from 4.0 to 7.5) and organic carbon content (4.5-21.3 g kg-1). The soil structure was not destroyed by compaction because the soils had always been cultivated by hand. The same plant species were always grown in all plots at the same time and the soils received the same fertilization. Moreover, the soils were always under the same weather conditions. Ascomycota was the most abundant phylum in all samples, ranging from 70 to 90% of total fungi. Some genera (Mortierella, Solicoccozyma, and Mycosphaerella) were found to be adapted to a wide range of pH. Acidic soils were dominated by Talaromyces, Cladophialophora, Devriesia, and Saitozyma, while good quality soils primarily consisted of Plectosphaerella, Tetracladium, and Mortierella. The study confirmed previous reports that pH has a decisive influence on soil fungal diversity, but also indicated the strong impact of soil type itself. These studies have launched a new cycle of research in these historical soil profiles.}, }
@article {pmid30717665, year = {2019}, author = {Jayasundara, D and Herath, D and Senanayake, D and Saeed, I and Yang, CY and Sun, Y and Chang, BC and Tang, SL and Halgamuge, SK}, title = {ENVirT: inference of ecological characteristics of viruses from metagenomic data.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 13}, pages = {377}, doi = {10.1186/s12859-018-2398-5}, pmid = {30717665}, issn = {1471-2105}, support = {LP140100670//Australian Research Council/ ; DP150103512//Australian Research Council/ ; }, abstract = {BACKGROUND: Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databases to first estimate an average genome length of a viral community before being able to estimate other parameters, such as viral richness. Although this approach has been widely used, it can adversely skew results since the majority of viruses are yet to be catalogued in databases.<br><br>RESULTS: In this paper, we present ENVirT, a method for estimating the richness of novel viral mixtures, and for the first time we also show that it is possible to simultaneously estimate the average genome length without a priori information. This is shown to be a significant improvement over database-dependent methods, since we can now robustly analyze samples that may include novel viral types under-represented in current databases. We demonstrate that the viral richness estimates produced by ENVirT are several orders of magnitude higher in accuracy than the estimates produced by existing methods named PHACCS and CatchAll when benchmarked against simulated data. We repeated the analysis of 20 metavirome samples using ENVirT, which produced results in close agreement with complementary in virto analyses.<br><br>CONCLUSIONS: These insights were previously not captured by existing computational methods. As such, ENVirT is shown to be an essential tool for enhancing our understanding of novel viral populations.}, }
@article {pmid30715365, year = {2019}, author = {Goss-Souza, D and Mendes, LW and Borges, CD and Rodrigues, JLM and Tsai, SM}, title = {Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz009}, pmid = {30715365}, issn = {1574-6941}, abstract = {The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due liming and fertilization in long-term no-till cropping. Data revealed that long-term no-till culminated with decrease in Acidobacteria, Actinobacteria and Proteobacteria abundances. However, α- and β-Proteobacteria abundances were higher in rhizosphere than in bulk soil, regardless time after forest-to-agriculture conversion. Changes in functional potential occurred predominantly in bulk soil, with decreases in functions related to potassium metabolism and virulence, disease and defense while functions related to nucleic acids metabolism increased. Functions in soybean rhizosphere remained stable, except for those related to potassium metabolism, which decreased after 20-year no-till cropping. Together, our results show that soybean root system selects microbial taxa via trade-offs, to keep functional resilience in the rhizosphere microbiome along time.}, }
@article {pmid30712189, year = {2019}, author = {Brito, EMS and Romero-Núñez, VM and Caretta, CA and Bertin, P and Valerdi-Negreros, JC and Guyoneaud, R and Goñi-Urriza, M}, title = {The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {2}, pages = {249-263}, doi = {10.1007/s00792-019-01078-8}, pmid = {30712189}, issn = {1433-4909}, support = {0627/15//Convocatoria de Apoyo a la Investigacion de la UG (DAIP)/ ; ANR-CONACyT-188775//Biometal Project/ ; }, abstract = {Vapor steam vents are prevailing structures on geothermal sites in which local geochemical conditions allow the development of extremophilic microorganisms. We describe the structure of the prokaryotic community able to grow on the walls and rocks of such microecosystems in two terrestrial Mexican volcanoes: Paricutín (PI and PII samples) and its satellite Sapichu (S sample). The investigated samples showed similar diversity indices, with few dominant OTUs (abundance > 1%): 21, 16 and 23, respectively for PI, PII and S. However, each steam vent showed a particular community profile: PI was dominated by photosynthetic bacteria (Cyanobacteria and Chloroflexia class), PII by Actinobacteria and Proteobacteria, and S by Ktedonobacteria class, Acidobacteria and Cyanobacteria phyla. Concerning the predicted metabolic potential, we found a dominance of cellular pathways, especially the ones for energy generation with metabolisms for sulfur respiration, nitrogen fixation, methanogenesis, carbon fixation, photosynthesis, and metals, among others. We suggest a different maturity stage for the three studied fumaroles, from the youngest (PI) to the oldest (S and PII), also influenced by the temperature and other geochemical parameters. Furthermore, four anaerobic strains were isolated, belonging to Clostridia class (Clostridium sphenoides, C. swellfunanium and Anaerocolumna cellulosilytica) and to Bacilli class (Paenibacillus azoreducens).}, }
@article {pmid30683856, year = {2019}, author = {Ellegaard, KM and Engel, P}, title = {Genomic diversity landscape of the honey bee gut microbiota.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {446}, doi = {10.1038/s41467-019-08303-0}, pmid = {30683856}, issn = {2041-1723}, mesh = {Age Factors ; Animals ; Bees/*microbiology ; Bifidobacterium/classification/*genetics/isolation &amp; purification ; *Biological Variation, Individual ; DNA, Bacterial/genetics ; Firmicutes/classification/*genetics/isolation &amp; purification ; Gammaproteobacteria/classification/*genetics/isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Metagenomics ; Microbial Consortia/genetics ; Phylogeny ; Symbiosis/physiology ; }, abstract = {The structure and distribution of genomic diversity in natural microbial communities is largely unexplored. Here, we used shotgun metagenomics to assess the diversity of the honey bee gut microbiota, a community consisting of few bacterial phylotypes. Our results show that most phylotypes are composed of sequence-discrete populations, which co-exist in individual bees and show age-specific abundance profiles. In contrast, strains present within these sequence-discrete populations were found to segregate into individual bees. Consequently, despite a conserved phylotype composition, each honey bee harbors a distinct community at the functional level. While ecological differentiation seems to facilitate coexistence at higher taxonomic levels, our findings suggest that, at the level of strains, priority effects during community assembly result in individualized profiles, despite the social lifestyle of the host. Our study underscores the need to move beyond phylotype-level characterizations to understand the function of this community, and illustrates its potential for strain-level analysis.}, }
@article {pmid30680877, year = {2019}, author = {Alessandri, G and Milani, C and Mancabelli, L and Mangifesta, M and Lugli, GA and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14540}, pmid = {30680877}, issn = {1462-2920}, abstract = {Domestication of dogs from wolves is the oldest known example of ongoing animal selection, responsible for generating more than 300 dog breeds worldwide. In order to investigate the taxonomic and functional evolution of the canine gut microbiota, a multi-omics approach was applied to six wild wolves and 169 dog fecal samples, the latter encompassing 51 breeds, which fully covers currently known canine genetic biodiversity. Specifically, 16S rRNA gene and bifidobacterial Internally Transcribed Spacer (ITS) profiling were employed to reconstruct and then compare the canine core gut microbiota to those of wolves and humans, revealing that artificial selection and subsequent cohabitation of dogs with their owners influenced the microbial population of canine gut through loss and acquisition of specific bacterial taxa. Moreover, comparative analysis of the intestinal bacterial population of dogs fed on Bones and Raw Food (BARF) or commercial food (CF) diet, coupled with shotgun metagenomics, highlighted that both bacterial composition and metabolic repertoire of the canine gut microbiota have evolved to adapt to high-protein or high-carbohydrates intake. Altogether, these data indicate that artificial selection and domestication not only affected the canine genome, but also shaped extensively the bacterial population harbored by the canine gut. This article is protected by copyright. All rights reserved.}, }
@article {pmid30680143, year = {2019}, author = {Rytkönen, S and Vesterinen, EJ and Westerduin, C and Leviäkangas, T and Vatka, E and Mutanen, M and Välimäki, P and Hukkanen, M and Suokas, M and Orell, M}, title = {From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web.}, journal = {Ecology and evolution}, volume = {9}, number = {1}, pages = {631-639}, doi = {10.1002/ece3.4787}, pmid = {30680143}, issn = {2045-7758}, abstract = {Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits Poecile montanus, Siberian tits Poecile cinctus, great tits Parus major and blue tits Cyanistes caeruleus) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (Betula spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.}, }
@article {pmid30649062, year = {2019}, author = {Sessa, L and Reddel, S and Manno, E and Quagliariello, A and Cotugno, N and Del Chierico, F and Amodio, D and Capponi, C and Leone, F and Bernardi, S and Rossi, P and Putignani, L and Palma, P}, title = {Distinct gut microbiota profile in ART-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.}, journal = {AIDS (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1097/QAD.0000000000002131}, pmid = {30649062}, issn = {1473-5571}, abstract = {OBJECTIVE: Persistent inflammation and higher risk to develop cardiovascular diseases (CVDs) still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota (GM) profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART.<br><br>DESIGN: Cross-sectional study including sixty-one ART-treated PHIV (age range 3-30 years old) and seventy-one age-matched healthy controls (CTRL). Blood and stool sample were collected at the same time and analyzed for GM composition and plasma biomarkers.<br><br>METHODS: GM composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, SI and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4+ and CD8+T-cells.<br><br>RESULTS: We identified two distinct GM profiles (group A and B) among PHIV. No different clinical parameters (age, sex, ethnicity, clinical class), dietary and sexual habits were found between the groups. The group A showed a relative dominance of Akkermansia muciniphila (A.muciniphila), whereas GM of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of sE-selectin (p = 0.0296), ICAM-1 (p = 0.0028), VCAM-1 (p = 0.0230), IL-6 (p = 0.0247) and sCD14 (p = 0.0142) in group A compared to group B.<br><br>CONCLUSIONS: Distinctive GM profiles are differently associated with inflammation, MT and VEA. Future studies are needed in order to understand the role of A.muciniphila and risk to develop CVDs in PHIV.}, }
@article {pmid30648011, year = {2019}, author = {Susi, H and Filloux, D and Frilander, MJ and Roumagnac, P and Laine, AL}, title = {Diverse and variable virus communities in wild plant populations revealed by metagenomic tools.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6140}, doi = {10.7717/peerj.6140}, pmid = {30648011}, issn = {2167-8359}, abstract = {Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.}, }
@article {pmid30619130, year = {2018}, author = {Timmers, PHA and Vavourakis, CD and Kleerebezem, R and Damsté, JSS and Muyzer, G and Stams, AJM and Sorokin, DY and Plugge, CM}, title = {Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3039}, doi = {10.3389/fmicb.2018.03039}, pmid = {30619130}, issn = {1664-302X}, support = {322551//European Research Council/International ; 323009//European Research Council/International ; }, abstract = {Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H2 and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was 'Candidatus Syntrophonatronum acetioxidans,' and a near-complete draft genome of this SAOB was reconstructed. 'Ca. S. acetioxidans' has all genes necessary for operating the Wood-Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na+-dependent ATP synthase and marker genes for 'salt-out' strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of 'Ca. S. acetioxidans' showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA gene amplicon datasets of the soda lake sediments showed a high similarity of reads to 'Ca. S. acetioxidans' with abundance as high as 1.3% of all reads, whereas aceticlastic methanogens and acetate oxidizing sulfate-reducers were not abundant (≤0.1%) or could not be detected. These combined results indicate that SAO is the primary anaerobic acetate oxidizing pathway at extreme haloalkaline conditions performed by haloalkaliphilic syntrophic consortia.}, }
@article {pmid30606162, year = {2019}, author = {Xue, F and Nan, X and Li, Y and Pan, X and Guo, Y and Jiang, L and Xiong, B}, title = {Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows.}, journal = {BMC veterinary research}, volume = {15}, number = {1}, pages = {7}, doi = {10.1186/s12917-018-1745-0}, pmid = {30606162}, issn = {1746-6148}, support = {Grant No. 31572435//Project of National Nature Science Foundation of China/ ; 2016YFD0700205//National Key Research and Development Plan/ ; }, mesh = {Animal Feed ; Animals ; Archaea/*drug effects/genetics ; Cattle ; Diet/*veterinary ; *Dietary Supplements ; Eating/drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Hydrogen-Ion Concentration ; Lactation/drug effects ; Metagenomics ; Rumen/chemistry/*microbiology ; Thiamine/analysis/*pharmacology ; }, abstract = {BACKGROUND: Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows' production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear. The objective of the present study was therefore to investigate the effects of thiamine supplementation on ruminal archaea, especially non-methanogens in HC induced SARA cows.<br><br>RESULTS: HC feeding significantly decreased dry matter intake, milk production, milk fat content, ruminal pH and the concentrations of thiamine and acetate in rumen fluid compared with control diet (CON) (P < 0.05), while the concentrations of propionate and ammonia-nitrogen (NH3-N) were significantly increased compared with CON (P < 0.05). These changes caused by HC were inversed by thiamine supplementation (P < 0.05). The taxonomy results showed that ruminal archaea ranged from 0.37 to 0.47% of the whole microbiota. Four characterized phyla, a number of Candidatus archaea and almost 660 species were identified in the present study. In which Euryarchaeota occupied the largest proportion of the whole archaea. Furthermore, thiamine supplementation treatment significantly increased the relative abundance of non-methanogens compared with CON and HC treatments. Thaumarchaeota was increased in HC compared with CON. Thiamine supplementation significantly increased Crenarchaeota, Nanoarchaeota and the Candidatus phyla, however decreased Thaumarchaeota compared with HC treatment.<br><br>CONCLUSIONS: HC feeding significantly decreased ruminal pH and increased the content of NH3-N which led to N loss and the increase of the relative abundance of Thaumarchaeota. Thiamine supplementation increased ruminal pH, improved the activity of ammonia utilizing bacteria, and decreased Thaumarchaeota abundance to reduce the ruminal NH3 content and finally reduced N loss. Overall, these findings contributed to the understanding of thiamine's function in dairy cows and provided new strategies to improve dairy cows' health under high-concentrate feeding regime.}, }
@article {pmid30597002, year = {2019}, author = {Choi, I and Ponsero, AJ and Bomhoff, M and Youens-Clark, K and Hartman, JH and Hurwitz, BL}, title = {Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons.}, journal = {GigaScience}, volume = {8}, number = {2}, pages = {}, doi = {10.1093/gigascience/giy165}, pmid = {30597002}, issn = {2047-217X}, abstract = {Background: Shotgun metagenomics provides powerful insights into microbial community biodiversity and function. Yet, inferences from metagenomic studies are often limited by dataset size and complexity and are restricted by the availability and completeness of existing databases. De novo comparative metagenomics enables the comparison of metagenomes based on their total genetic content.<br><br>Results: We developed a tool called Libra that performs an all-vs-all comparison of metagenomes for precise clustering based on their k-mer content. Libra uses a scalable Hadoop framework for massive metagenome comparisons, Cosine Similarity for calculating the distance using sequence composition and abundance while normalizing for sequencing depth, and a web-based implementation in iMicrobe (http://imicrobe.us) that uses the CyVerse advanced cyberinfrastructure to promote broad use of the tool by the scientific community.<br><br>Conclusions: A comparison of Libra to equivalent tools using both simulated and real metagenomic datasets, ranging from 80 million to 4.2 billion reads, reveals that methods commonly implemented to reduce compute time for large datasets, such as data reduction, read count normalization, and presence/absence distance metrics, greatly diminish the resolution of large-scale comparative analyses. In contrast, Libra uses all of the reads to calculate k-mer abundance in a Hadoop architecture that can scale to any size dataset to enable global-scale analyses and link microbial signatures to biological processes.}, }
@article {pmid30581574, year = {2019}, author = {Angelakis, E and Bachar, D and Yasir, M and Musso, D and Djossou, F and Melenotte, C and Robert, C and Davoust, B and Gaborit, B and Azhar, EI and Bibi, F and Dutour, A and Raoult, D}, title = {Comparison of the gut microbiota of obese individuals from different geographic origins.}, journal = {New microbes and new infections}, volume = {27}, number = {}, pages = {40-47}, doi = {10.1016/j.nmni.2018.11.005}, pmid = {30581574}, issn = {2052-2975}, abstract = {Few studies have examined the interaction of human geography, microbial community structure and obesity. We tested obese adult volunteers from France, Saudi Arabia, French Polynesia and from a traditional population in the village of Trois-Sauts in French Guiana by sequencing the V3-V4 region. We also sequenced homemade fermented cachiri beers that were obtained from the traditional Amazonian population and are highly consumed by this population. We found that French and Saudis had significantly less richness and biodiversity in their gut microbiota than Amazonians and Polynesians (p <0.05). Principle coordinate analysis of the overall composition of the genera communities revealed that the microbiomes of Amazonians clustered independently from the other obese individuals. Moreover, we found that Amazonians presented significantly stricter anaerobic genera than the Saudis, French and Polynesians (p < 0.001). Polynesians presented significantly lower relative abundance of Lactobacillus sp. than French (p 0.01) and Saudis (p 0.05). Treponema berlinense and Treponema succinifaciens were only present in the gut microbiome of Amazonians. The cachiri beers presented significantly more bacterial species in common with the gut microbiome of Amazonians (p < 0.005). Obese individuals with different origins present modifications in their gut microbiota, and we provide evidence that the cachiri beers influenced the gut microbiome of Amazonians.}, }
@article {pmid30579193, year = {2019}, author = {Deng, Y and Wang, Y and Xia, Y and Zhang, AN and Zhao, Y and Zhang, T}, title = {Genomic resolution of bacterial populations in saccharin and cyclamate degradation.}, journal = {The Science of the total environment}, volume = {658}, number = {}, pages = {357-366}, doi = {10.1016/j.scitotenv.2018.12.162}, pmid = {30579193}, issn = {1879-1026}, mesh = {Alphaproteobacteria/genetics/isolation &amp; purification/metabolism ; *Biodegradation, Environmental ; Biodiversity ; Cyclamates/*metabolism ; *Genome, Bacterial ; Metagenomics/methods ; Methylobacteriaceae/genetics/isolation &amp; purification/metabolism ; Rhodocyclaceae/genetics/isolation &amp; purification/metabolism ; Saccharin/*metabolism ; Sphingomonadaceae/genetics/isolation &amp; purification/metabolism ; Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The benefits of extensive artificial sweeteners use come at a cost of their ubiquitous occurrence in the aquatic environment. Biodegradation is crucial for the removal of artificial sweeteners in the environment, yet comprehensive characterizations of the degradation consortia that degrade these compounds have not been initiated. Here, we performed metagenomic analysis of microbial communities fulfilling complete mineralization of two typical artificial sweeteners, i.e. saccharin and cyclamate. Genome-resolved metagenomics enabled the recovery and metabolic characterization of total 23 population genomes from 8 phyla in the two consortia, most of which represented novel species. The saccharin-degrading consortia was notably dominated by a betaproteobacterial genome from the family Rhodocyclaceae, accounting for 15.5% of total sequences. For the cyclamate enrichment, 28.1% of the total sequences were assigned to three similarly abundant Alphaproteobacteria population genomes belonging to the family Sphingomonadaceae and Methylobacteriaceae. The metabolic potential of these population genomes were examined to potentially identify the roles of these populations in biodegradation of artificial sweeteners, and focusing on the energy and nutrient metabolisms.}, }
@article {pmid30577803, year = {2018}, author = {Chappell, T and Geva, S and Hogan, JM and Huygens, F and Rathnayake, IU and Rudd, S and Kelly, W and Perrin, D}, title = {Rapid analysis of metagenomic data using signature-based clustering.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 20}, pages = {509}, doi = {10.1186/s12859-018-2540-4}, pmid = {30577803}, issn = {1471-2105}, mesh = {Algorithms ; Cluster Analysis ; *Data Analysis ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; }, abstract = {BACKGROUND: Sequencing highly-variable 16S regions is a common and often effective approach to the study of microbial communities, and next-generation sequencing (NGS) technologies provide abundant quantities of data for analysis. However, the speed of existing analysis pipelines may limit our ability to work with these quantities of data. Furthermore, the limited coverage of existing 16S databases may hamper our ability to characterise these communities, particularly in the context of complex or poorly studied environments.<br><br>RESULTS: In this article we present the SigClust algorithm, a novel clustering method involving the transformation of sequence reads into binary signatures. When compared to other published methods, SigClust yields superior cluster coherence and separation of metagenomic read data, while operating within substantially reduced timeframes. We demonstrate its utility on published Illumina datasets and on a large collection of labelled wound reads sourced from patients in a wound clinic. The temporal analysis is based on tracking the dominant clusters of wound samples over time. The analysis can identify markers of both healing and non-healing wounds in response to treatment. Prominent clusters are found, corresponding to bacterial species known to be associated with unfavourable healing outcomes, including a number of strains of Staphylococcus aureus.<br><br>CONCLUSIONS: SigClust identifies clusters rapidly and supports an improved understanding of the wound microbiome without reliance on a reference database. The results indicate a promising use for a SigClust-based pipeline in wound analysis and prediction, and a possible novel method for wound management and treatment.}, }
@article {pmid30559737, year = {2018}, author = {Gong, Z and Liang, Y and Wang, M and Jiang, Y and Yang, Q and Xia, J and Zhou, X and You, S and Gao, C and Wang, J and He, J and Shao, H and McMinn, A}, title = {Viral Diversity and Its Relationship With Environmental Factors at the Surface and Deep Sea of Prydz Bay, Antarctica.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2981}, doi = {10.3389/fmicb.2018.02981}, pmid = {30559737}, issn = {1664-302X}, abstract = {A viral metagenomic analysis of five surface and two bottom water (878 meters below surface, mbs, and 3,357 mbs) samples from Prydz Bay, was conducted during February-March 2015. The results demonstrated that most of the DNA viruses were dsDNA viruses (79.73-94.06%, except at PBI1, 37.51%). Of these, Caudovirales (Siphoviridae, Myoviridae, and Podoviridae) phages were most abundant in surface seawater (67.67-71.99%), while nucleocytoplasmic large DNA viruses (NCLDVs) (Phycodnaviridae, Mimiviridae, and Pandoraviridae accounted for >30% of dsDNA viruses) were most abundant in the bottom water (3,357 mbs). Of the ssDNA viruses, Microviridae was the dominant family in PBI2, PBI3, PBOs, and PBI4b (57.09-87.55%), while Inoviridae (58.16%) was the dominant family in PBI1. Cellulophaga phages (phi38:1 and phi10:1) and Flavobacterium phage 11b, infecting the possible host strains affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, were abundant in surface water dsDNA viromes. The long contig (PBI2_1_C) from the viral metagenomes were most similar to the genome architectures of Cellulophaga phage phi10:1 and Flavobacterium phage 11b from the Arctic Ocean. Comparative analysis showed that the surface viral community of Prydz Bay could be clearly separated from other marine and freshwater environments. The deep sea viral community was similar to the deep sea viral metagenome at A Long-term Oligotrophic Habitat Assessment Station (ALOHA, at 22°45'N, 158°00'W). The multivariable analysis indicated that nutrients probably played an important role in shaping the local viral community structure. This study revealed the preliminary characteristics of the viral community in Prydz Bay, from both the surface and the deep sea. It provided evidence of the relationships between the virome and the environment in Prydz Bay and provided the first data from the deep sea viral community of the Southern Ocean.}, }
@article {pmid30522530, year = {2018}, author = {Edlund, A and Yang, Y and Yooseph, S and He, X and Shi, W and McLean, JS}, title = {Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {217}, pmid = {30522530}, issn = {2049-2618}, support = {R00DE024543//National Institute of Dental and Craniofacial Research/ ; K99DE024543//National Institute of Dental and Craniofacial Research/ ; 1R01DE023810//National Institute of Dental and Craniofacial Research/ ; 1R01DE023810//National Institute of Dental and Craniofacial Research/ ; 1R01DE023810//National Institute of Dental and Craniofacial Research/ ; 1R01DE020102//National Institute of Dental and Craniofacial Research/ ; 1R01DE020102//National Institute of Dental and Craniofacial Research/ ; 1R01DE020102//National Institute of Dental and Craniofacial Research/ ; 1R01DE026186//National Institute of Dental and Craniofacial Research/ ; 1R01DE026186//National Institute of Dental and Craniofacial Research/ ; 1R01DE026186//National Institute of Dental and Craniofacial Research/ ; R01GM095373//National Institute of General Medical Sciences/ ; }, abstract = {BACKGROUND: Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processes such as co-aggregation, competition for space and resources, and by bacterially produced reactive agents. Knowledge on the dynamics of assembly within complex communities is very limited and derives mainly from studies composed of a limited number of bacterial species. To fill current knowledge gaps, we applied parallel metagenomic and metatranscriptomic analyses during assembly and maturation of an in vitro oral biofilm. This model system has previously demonstrated remarkable reproducibility in taxonomic composition across replicate samples during maturation.<br><br>RESULTS: Time course analysis of the biofilm maturation was performed by parallel sampling every 2-3 h for 24 h for both DNA and RNA. Metagenomic analyses revealed that community taxonomy changed most dramatically between three and six hours of growth when pH dropped from 6.5 to 5.5. By applying comparative metatranscriptome analysis we could identify major shifts in overall community activities between six and nine hours of growth when pH dropped below 5.5, as 29,015 genes were significantly up- or down- expressed. Several of the differentially expressed genes showed unique activities for individual bacterial genomes and were associated with pyruvate and lactate metabolism, two-component signaling pathways, production of antibacterial molecules, iron sequestration, pH neutralization, protein hydrolysis, and surface attachment. Our analysis also revealed several mechanisms responsible for the niche expansion of the cariogenic pathogen Lactobacillus fermentum.<br><br>CONCLUSION: It is highly regarded that acidic conditions in dental plaque cause a net loss of enamel from teeth. Here, as pH drops below 5.5 pH to 4.7, we observe blooms of cariogenic lactobacilli, and a transition point of many bacterial gene expression activities within the community. To our knowledge, this represents the first study of the assembly and maturation of a complex oral bacterial biofilm community that addresses gene level functional responses over time.}, }
@article {pmid30532085, year = {2018}, author = {Chen, B and Yu, T and Xie, S and Du, K and Liang, X and Lan, Y and Sun, C and Lu, X and Shao, Y}, title = {Comparative shotgun metagenomic data of the silkworm Bombyx mori gut microbiome.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180285}, pmid = {30532085}, issn = {2052-4463}, abstract = {Lepidoptera (butterflies and moths) is a major insect order including important pollinators and agricultural pests, however their microbiomes are little studied. Here, using next-generation sequencing (NGS)-based shotgun metagenomics, we characterize both the biodiversity and functional potential of gut microbiota of a lepidopteran model insect, the silkworm Bombyx mori. Two metagenomes, including the standard inbred strain Dazao (P50) and an improved hybrid strain Qiufeng × Baiyu (QB) widely used in commercial silk production, were generated, containing 45,505,084 and 69,127,002 raw reads, respectively. Taxonomic analysis revealed that a total of 663 bacterial species were identified in P50 silkworms, while 322 unique species in QB silkworms. Notably, Enterobacter, Acinetobacter and Enterococcus were dominated in both strains. The further functional annotation was performed by both BlastP and MG-RAST against various databases including Nr, COG, KEGG, CAZy and SignalP, which revealed >5 × 106 protein-coding genes. These datasets not only provide first insights into all bacterial genes in silkworm guts, but also help to generate hypotheses for subsequently testing functional traits of gut microbiota in an important insect group.}, }
@article {pmid30528276, year = {2019}, author = {Ramos-Barbero, MD and Martin-Cuadrado, AB and Viver, T and Santos, F and Martinez-Garcia, M and Antón, J}, title = {Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {1}, pages = {30-40}, doi = {10.1016/j.syapm.2018.11.001}, pmid = {30528276}, issn = {1618-0984}, mesh = {Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; *Genome, Microbial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; *Salinity ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next generation sequencing, are democratizing this powerful approach that is spreading from specialized research groups to the general public. Using metagenomes from hypersaline environments, as well as mock metagenomes composed of Archaea and Bacteria frequently found in these systems, we have analyzed the advantages and difficulties of the binning process in these extreme environments to tackle microbial population diversity. These extreme systems harbor relatively low species diversity but high intraspecific diversity, which can compromise metagenome assembly and therefore the whole binning process. The main goal is to compare the output of the binning process with what is previously known from the analyzed samples, based on years of study using different approaches. Several scenarios have been analyzed in detail: (i) a good quality bin from a species highly abundant in the environment; (ii) an intermediate quality bin with incongruences that can be solved by further analyses and manual curation, and (iii) a low-quality bin to investigate the failure to recover a very abundant microbial genome as well as some possible solutions. The latter can be considered the &quot;great metagenomics anomaly&quot; and is mainly due to assembly problems derived from the microdiversity of naturally co-existing populations in nature.}, }
@article {pmid30518356, year = {2018}, author = {Bin, P and Tang, Z and Liu, S and Chen, S and Xia, Y and Liu, J and Wu, H and Zhu, G}, title = {Intestinal microbiota mediates Enterotoxigenic Escherichia coli-induced diarrhea in piglets.}, journal = {BMC veterinary research}, volume = {14}, number = {1}, pages = {385}, pmid = {30518356}, issn = {1746-6148}, mesh = {Animals ; Bacteria/classification/genetics ; Diarrhea/microbiology/*veterinary ; Dysbiosis/immunology/microbiology/*veterinary ; Enterotoxigenic Escherichia coli/immunology/physiology ; Escherichia coli Infections/veterinary ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*genetics/*immunology ; Intestinal Diseases/immunology/microbiology/*veterinary ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Swine ; Swine Diseases/immunology/*microbiology ; }, abstract = {BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) causes diarrhea in humans, cows, and pigs. The gut microbiota underlies pathology of several infectious diseases yet the role of the gut microbiota in the pathogenesis of ETEC-induced diarrhea is unknown.<br><br>RESULTS: By using an ETEC induced diarrheal model in piglet, we profiled the jejunal and fecal microbiota using metagenomics and 16S rRNA sequencing. A jejunal microbiota transplantation experiment was conducted to determine the role of the gut microbiota in ETEC-induced diarrhea. ETEC-induced diarrhea influenced the structure and function of gut microbiota. Diarrheal piglets had lower Bacteroidetes: Firmicutes ratio and microbiota diversity in the jejunum and feces, and lower percentage of Prevotella in the feces, but higher Lactococcus in the jejunum and higher Escherichia-Shigella in the feces. The transplantation of the jejunal microbiota from diarrheal piglets to uninfected piglets leaded to diarrhea after transplantation. Microbiota transplantation experiments also supported the notion that dysbiosis of gut microbiota is involved in the immune responses in ETEC-induced diarrhea.<br><br>CONCLUSION: We conclude that ETEC infection influences the gut microbiota and the dysbiosis of gut microbiota after ETEC infection mediates the immune responses in ETEC infection.}, }
@article {pmid30507071, year = {2018}, author = {Alsammar, HF and Naseeb, S and Brancia, LB and Gilman, RT and Wang, P and Delneri, D}, title = {Targeted metagenomics approach to capture the biodiversity of Saccharomyces genus in wild environments.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12724}, pmid = {30507071}, issn = {1758-2229}, support = {//Kuwait University/ ; BB/L021471/1//BBSRC/ ; 767015//European Union's Horizon 2020 research and innovation programme/ ; }, abstract = {The species of the genus Saccharomyces are commonly inhabiting tree bark and the surrounding soil, but their abundance have likely been underestimated due to biases in culturing methods. Metagenomic studies have so far been unable to detect Saccharomyces species in wild environments. Here, we sequenced the mycobiome of soils surrounding different trees at various altitudes in the Italian Alps. To survey for yeasts species belonging to Saccharomyces genus rather than other fungal species, we performed a selectivity step involving the isolation of the internal transcribed spacer (ITS) region that is specific to this yeast group. Reads mapping to Saccharomyces species were detected in all soil samples, including reads for S. mikatae and for S. eubayanus. ITS1 alignment of the S. cerevisiae, S. paradoxus and S. kudriavzevii sequences showed up to three base pair polymorphisms with other known strains, indicating possible new lineages. Basidiomycetous fungi were still the dominant species, compared to the Ascomycota, but the selectivity step allowed for the first time the detection and study of the biodiversity of the Saccharomyces species in their natural environment.}, }
@article {pmid30504906, year = {2018}, author = {Wampach, L and Heintz-Buschart, A and Fritz, JV and Ramiro-Garcia, J and Habier, J and Herold, M and Narayanasamy, S and Kaysen, A and Hogan, AH and Bindl, L and Bottu, J and Halder, R and Sjöqvist, C and May, P and Andersson, AF and de Beaufort, C and Wilmes, P}, title = {Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5091}, doi = {10.1038/s41467-018-07631-x}, pmid = {30504906}, issn = {2041-1723}, mesh = {Cesarean Section ; Delivery, Obstetric ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; In Vitro Techniques ; Infant, Newborn ; Infectious Disease Transmission, Vertical ; Interleukin-18/metabolism ; Lipopolysaccharides/metabolism ; Metagenomics/methods ; Pregnancy ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {The rate of caesarean section delivery (CSD) is increasing worldwide. It remains unclear whether disruption of mother-to-neonate transmission of microbiota through CSD occurs and whether it affects human physiology. Here we perform metagenomic analysis of earliest gut microbial community structures and functions. We identify differences in encoded functions between microbiomes of vaginally delivered (VD) and CSD neonates. Several functional pathways are over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis. We link these enriched functions to individual-specific strains, which are transmitted from mothers to neonates in case of VD. The stimulation of primary human immune cells with LPS isolated from early stool samples of VD neonates results in higher levels of tumour necrosis factor (TNF-α) and interleukin 18 (IL-18). Accordingly, the observed levels of TNF-α and IL-18 in neonatal blood plasma are higher after VD. Taken together, our results support that CSD disrupts mother-to-neonate transmission of specific microbial strains, linked functional repertoires and immune-stimulatory potential during a critical window for neonatal immune system priming.}, }
@article {pmid30503454, year = {2018}, author = {Hwang, J and Park, SY and Lee, S and Lee, TK}, title = {High diversity and potential translocation of DNA viruses in ballast water.}, journal = {Marine pollution bulletin}, volume = {137}, number = {}, pages = {449-455}, doi = {10.1016/j.marpolbul.2018.10.053}, pmid = {30503454}, issn = {1879-3363}, mesh = {Animals ; DNA Viruses/*genetics/*isolation &amp; purification ; Introduced Species ; Metagenomics ; Mexico ; New York ; Panama ; Republic of Korea ; Saudi Arabia ; *Ships ; Water/*analysis/chemistry ; Water Microbiology ; }, abstract = {Ballast water is a common vector for the transport of invasive species to new marine and aquatic environments. We used a metagenomics approach to examine the composition and diversity of viral communities in ballast water from ships originating in Mexico, Saudi Arabia, New York, and Panama, and in water from the port of their destination in Busan, Korea. Myoviridae was the most abundant virus family in ballast water, followed Podoviridae and Siphoviridae. We also identified viruses that infect invertebrates, amoebas, and algae in ballast water and in the Busan port water. Interestingly, there were several viruses that infect humans or other animals (Swinepox virus, Raccoonpox virus, Suid herpesvirus, and Human endogenous retrovirus) in the samples from New York and Panama. In addition, there were giant viruses in all the ballast water samples, especially, identified Megavirus chilensis in New York and Panama, and Pandoravirus salinus in Mexico and Saudi Arabia. These results provide detailed descriptions of the characteristics of the viruses present in ballast water, document significant viral diversity, and indicate the potential translocation of viruses via ballast water.}, }
@article {pmid30513942, year = {2018}, author = {Pinho, CJ and Santos, B and Mata, VA and Seguro, M and Romeiras, MM and Lopes, RJ and Vasconcelos, R}, title = {What Is the Giant Wall Gecko Having for Dinner? Conservation Genetics for Guiding Reserve Management in Cabo Verde.}, journal = {Genes}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/genes9120599}, pmid = {30513942}, issn = {2073-4425}, support = {MP/EAM/2016/06//Fondation Ensemble/ ; NA//Club 300 Foundation for Bird Protection/ ; NA//Monaco Explorations/ ; Fellowships PD/BD/106055/2015 (to BS), PD/BD/113462/2015 (to VAM), SFRH/BPD/84141/2012 (to RJL), and SFRH/BPD/79913/2011 (to RV) were funded by FCT/MEC and POPH/QREN/FSE//Fundação para a Ciência e a Tecnologia/ ; (NORTE-01-0145-FEDER-AGRIGEN)//NORTE2020/PORTUGAL/ ; VAM by ERA Chair in Environmental Metagenomics (EU Horizon 2020 Research and Innovation Programme Grant agreement No 668981)//Horizon 2020/ ; MACDIV-FCT-PTDC/BIABIC/0054/2014, and CVAgrobiodiversity/333111699 (to MMR)//Aga Khan Development Network (AKDN) and FCT/ ; }, abstract = {Knowledge on diet composition of a species is an important step to unveil its ecology and guide conservation actions. This is especially important for species that inhabit remote areas within biodiversity hotspots, with little information about their ecological roles. The emblematic giant wall gecko of Cabo Verde, Tarentola gigas, is restricted to the uninhabited Branco and Raso islets, and presents two subspecies. It is classified as Endangered, and locally Extinct on Santa Luzia Island; however, little information is known about its diet and behaviour. In this study, we identified the main plant, arthropods, and vertebrates consumed by both gecko subspecies using next generation sequencing (NGS) (metabarcoding of faecal pellets), and compared them with the species known to occur on Santa Luzia. Results showed that plants have a significant role as diet items and identified vertebrate and invertebrate taxa with higher taxonomic resolution than traditional methods. With this study, we now have data on the diet of both subspecies for evaluating the reintroduction of this threatened gecko on Santa Luzia as potentially successful, considering the generalist character of both populations. The information revealed by these ecological networks is important for the development of conservation plans by governmental authorities, and reinforces the essential and commonly neglected role of reptiles on island systems.}, }
@article {pmid30509257, year = {2018}, author = {He, F and Liu, D and Zhang, L and Zhai, J and Ma, Y and Xu, Y and Jiang, G and Rong, K and Ma, J}, title = {Metagenomic analysis of captive Amur tiger faecal microbiome.}, journal = {BMC veterinary research}, volume = {14}, number = {1}, pages = {379}, pmid = {30509257}, issn = {1746-6148}, support = {31372209//National Natural Science Foundation of China/ ; 2572017AA20//The Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Animals, Zoo/*microbiology ; Bacteria/*classification/genetics/metabolism ; Endangered Species ; Feces/*microbiology ; *Gastrointestinal Microbiome ; *Metagenome ; Tigers/*microbiology ; }, abstract = {BACKGROUND: The gastrointestinal tracts of animals are home to large, complex communities of microbes. The compositions of these communities ultimately reflect the coevolution of microorganisms with their animal host and are influenced by the living environment, diet and immune status of the host. Gut microbes have been shown to be important for human disease and health, but little research exists in the gut microbiome of the Amur tiger, which is one of the most endangered species in the world.<br><br>RESULTS: In this study, we present the use of whole-metagenome shotgun sequencing to analyze the composition and functional structures of the gut microbiota in captive Amur tigers. Our results showed a high abundance of four major phyla in captive Amur tigers, including Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. Moreover, at the genus level, Escherichia, Collinsella and Fusobacterium were most abundant in the captive Amur tiger fecal metagenome. At the species level, Escherichia coli, Fusobacterium ulcerans and Fusobacterium varium were the species with highest abundances in the captive Amur tiger gut microbiota. The primary functional categories of the Amur tiger faecal metagenome were associated mainly with Carbohydrate metabolism, Membrane transport and Amino acid metabolism based on the KEGG pathway database. The comparative metagenomic analyses showed that the captive Amur tiger fecal metagenome had a lower abundance of Spirochaetes, Cyanobacteria and Ascomycota than other animals, and the primary functional categories were primarily associated with carbohydrate metabolism subsystems, clustering-based subsystems and protein metabolism.<br><br>CONCLUSIONS: We presented here for the first time the use of the shotgun metagenomic sequencing approach to study the composition and functional structures of the gut microbiota in captive Amur tiger.}, }
@article {pmid30486388, year = {2018}, author = {Labbé, M and Raymond, F and Lévesque, A and Thaler, M and Mohit, V and Audet, M and Corbeil, J and Culley, A}, title = {Communities of Phytoplankton Viruses across the Transition Zone of the St. Lawrence Estuary.}, journal = {Viruses}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/v10120672}, pmid = {30486388}, issn = {1999-4915}, mesh = {Biodiversity ; Ecosystem ; Environment ; *Estuaries ; Evolution, Molecular ; Geography ; Metagenome ; Metagenomics/methods ; Phycodnaviridae/classification/genetics ; Phylogeny ; Phytoplankton/*virology ; RNA, Ribosomal, 18S ; *Water Microbiology ; }, abstract = {The St. Lawrence hydrographic system includes freshwater, brackish, and marine habitats, and is the largest waterway in North America by volume. The food-webs in these habitats are ultimately dependent on phytoplankton. Viral lysis is believed to be responsible for a major part of phytoplankton mortality. To better understand their role, we characterized the diversity and distribution of two viral taxa infecting phytoplankton: the picornaviruses and phycodnaviruses. Our study focused on the estuary transition zone, which is an important nursery for invertebrates and fishes. Both viral taxa were investigated by PCR amplification of conserved molecular markers and next-generation sequencing at six sites, ranging from freshwater to marine. Our results revealed few shared viral phylotypes between saltwater and freshwater sites. Salinity appeared to be the primary determinant of viral community composition. Moreover, our analysis indicated that the viruses identified in this region of the St. Lawrence diverge from classified viruses and homologous published environmental virotypes. These results suggest that DNA and RNA viruses infecting phytoplankton are likely active in the estuary transition zone, and that this region harbors its own unique viral assemblages.}, }
@article {pmid30479342, year = {2018}, author = {Ramani, S and Stewart, CJ and Laucirica, DR and Ajami, NJ and Robertson, B and Autran, CA and Shinge, D and Rani, S and Anandan, S and Hu, L and Ferreon, JC and Kuruvilla, KA and Petrosino, JF and Venkataram Prasad, BV and Bode, L and Kang, G and Estes, MK}, title = {Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5010}, pmid = {30479342}, issn = {2041-1723}, support = {R01 AI036040/AI/NIAID NIH HHS/United States ; R01 AI105101/AI/NIAID NIH HHS/United States ; R37 AI036040/AI/NIAID NIH HHS/United States ; }, mesh = {Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Milk, Human/*chemistry/*microbiology ; Oligosaccharides/*metabolism ; Rotavirus/pathogenicity ; Rotavirus Infections/immunology/*microbiology ; Rotavirus Vaccines/immunology ; }, abstract = {Neonatal rotavirus infections are predominantly asymptomatic. While an association with gastrointestinal symptoms has been described in some settings, factors influencing differences in clinical presentation are not well understood. Using multidisciplinary approaches, we show that a complex interplay between human milk oligosaccharides (HMOs), milk microbiome, and infant gut microbiome impacts neonatal rotavirus infections. Validating in vitro studies where HMOs are not decoy receptors for neonatal strain G10P[11], population studies show significantly higher levels of Lacto-N-tetraose (LNT), 2'-fucosyllactose (2'FL), and 6'-siallylactose (6'SL) in milk from mothers of rotavirus-positive neonates with gastrointestinal symptoms. Further, these HMOs correlate with abundance of Enterobacter/Klebsiella in maternal milk and infant stool. Specific HMOs also improve the infectivity of a neonatal strain-derived rotavirus vaccine. This study provides molecular and translational insight into host factors influencing neonatal rotavirus infections and identifies maternal components that could promote the performance of live, attenuated rotavirus vaccines.}, }
@article {pmid30478343, year = {2018}, author = {Regan, T and Barnett, MW and Laetsch, DR and Bush, SJ and Wragg, D and Budge, GE and Highet, F and Dainat, B and de Miranda, JR and Watson, M and Blaxter, M and Freeman, TC}, title = {Characterisation of the British honey bee metagenome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4995}, pmid = {30478343}, issn = {2041-1723}, mesh = {Animals ; Bees/*genetics/microbiology ; Contig Mapping ; Genetic Variation ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; Symbiosis/genetics ; United Kingdom ; }, abstract = {The European honey bee (Apis mellifera) plays a major role in pollination and food production. Honey bee health is a complex product of the environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of these factors will help manage modern challenges to bee health. Here we used DNA sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from across Britain. Low heterozygosity was observed in many Scottish colonies which had high similarity to the native dark bee. Colonies exhibited high diversity in composition and relative abundance of individual microbiome taxa. Most non-bee sequences were derived from known honey bee commensal bacteria or pathogens. However, DNA was also detected from additional fungal, protozoan and metazoan species. To classify cobionts lacking genomic information, we developed a novel network analysis approach for clustering orphan DNA contigs. Our analyses shed light on microbial communities associated with honey bees and demonstrate the power of high-throughput, directed metagenomics for identifying novel biological threats in agroecosystems.}, }
@article {pmid30463925, year = {2018}, author = {Bulow, C and Langdon, A and Hink, T and Wallace, M and Reske, KA and Patel, S and Sun, X and Seiler, S and Jones, S and Kwon, JH and Burnham, CA and Dantas, G and Dubberke, ER}, title = {Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential.}, journal = {mSphere}, volume = {3}, number = {6}, pages = {}, pmid = {30463925}, issn = {2379-5042}, support = {KL2 TR002346/TR/NCATS NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; TL1 TR000449/TR/NCATS NIH HHS/United States ; TL1 TR002344/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Amoxicillin-Potassium Clavulanate Combination/*administration &amp; dosage ; Anti-Bacterial Agents/*administration &amp; dosage ; Enema ; Fecal Microbiota Transplantation/*methods ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; *Metabolism ; *Microbiota ; Middle Aged ; Treatment Outcome ; Young Adult ; beta-Lactamase Inhibitors/*administration &amp; dosage ; }, abstract = {Strategies to prevent multidrug-resistant organism (MDRO) infections are scarce, but autologous fecal microbiota transplantation (autoFMT) may limit gastrointestinal MDRO expansion. AutoFMT involves banking one's feces during a healthy state for later use in restoring gut microbiota following perturbation. This pilot study evaluated the effect of autoFMT on gastrointestinal microbiome taxonomic composition, resistance gene content, and metabolic capacity after exposure to amoxicillin-clavulanic acid (Amox-Clav). Ten healthy participants were enrolled. All received 5 days of Amox-Clav. Half were randomized to autoFMT, derived from stool collected pre-antimicrobial exposure, by enema, and half to saline enema. Participants submitted stool samples pre- and post-Amox-Clav and enema and during a 90-day follow-up period. Shotgun metagenomic sequencing revealed taxonomic composition, resistance gene content, and metabolic capacity. Amox-Clav significantly altered gut taxonomic composition in all participants (n = 10, P < 0.01); however, only three participants exhibited major changes at the phylum level following exposure. In the cohort as a whole, beta-lactamase genes were enriched following Amox-Clav (P < 0.05), and predicted metabolic capacity was significantly altered (P < 0.01). Species composition, metabolic capacity, and beta-lactamase abundance returned to pre-antimicrobial exposure state 7 days after either autoFMT or saline enema (P > 0.05, compared to enrollment). Alterations to microbial metabolic capacity occurred following antimicrobial exposure even in participants without substantial taxonomic disruption, potentially creating open niches for pathogen colonization. Our findings suggest that metabolic potential is an important consideration for complete assessment of antimicrobial impact on the microbiome. AutoFMT was well tolerated and may have contributed to phylogenetic recovery. (This study has been registered at ClinicalTrials.gov under identifier NCT02046525.)IMPORTANCE The spread of multidrug resistance among pathogenic organisms threatens the efficacy of antimicrobial treatment options. The human gut serves as a reservoir for many drug-resistant organisms and their resistance genes, and perturbation of the gut microbiome by antimicrobial exposure can open metabolic niches to resistant pathogens. Once established in the gut, antimicrobial-resistant bacteria can persist even after antimicrobial exposure ceases. Strategies to prevent multidrug-resistant organism (MDRO) infections are scarce, but autologous fecal microbiota transplantation (autoFMT) may limit gastrointestinal MDRO expansion. AutoFMT involves banking one's feces during a healthy state for later use in restoring gut microbiota following perturbation. This pilot study evaluated the effect of amoxicillin-clavulanic acid (Amox-Clav) exposure and autoFMT on gastrointestinal microbiome taxonomic composition, resistance gene content, and metabolic capacity. Importantly, we found that metabolic capacity was perturbed even in cases where gross phylogeny remained unchanged and that autoFMT was safe and well tolerated.}, }
@article {pmid30459421, year = {2018}, author = {Xu, J and Zhang, Y and Zhang, P and Trivedi, P and Riera, N and Wang, Y and Liu, X and Fan, G and Tang, J and Coletta-Filho, HD and Cubero, J and Deng, X and Ancona, V and Lu, Z and Zhong, B and Roper, MC and Capote, N and Catara, V and Pietersen, G and Vernière, C and Al-Sadi, AM and Li, L and Yang, F and Xu, X and Wang, J and Yang, H and Jin, T and Wang, N}, title = {The structure and function of the global citrus rhizosphere microbiome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4894}, pmid = {30459421}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics ; Citrus/*microbiology ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/genetics ; Metagenome/genetics ; Metagenomics/classification/methods ; Microbiota/*genetics ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.}, }
@article {pmid30458701, year = {2018}, author = {Banos, S and Lentendu, G and Kopf, A and Wubet, T and Glöckner, FO and Reich, M}, title = {A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {190}, pmid = {30458701}, issn = {1471-2180}, abstract = {BACKGROUND: Several fungi-specific primers target the 18S rRNA gene sequence, one of the prominent markers for fungal classification. The design of most primers goes back to the last decades. Since then, the number of sequences in public databases increased leading to the discovery of new fungal groups and changes in fungal taxonomy. However, no reevaluation of primers was carried out and relevant information on most primers is missing. With this study, we aimed to develop an 18S rRNA gene sequence primer toolkit allowing an easy selection of the best primer pair appropriate for different sequencing platforms, research aims (biodiversity assessment versus isolate classification) and target groups.<br><br>RESULTS: We performed an intensive literature research, reshuffled existing primers into new pairs, designed new Illumina-primers, and annealing blocking oligonucleotides. A final number of 439 primer pairs were subjected to in silico PCRs. Best primer pairs were selected and experimentally tested. The most promising primer pair with a small amplicon size, nu-SSU-1333-5'/nu-SSU-1647-3' (FF390/FR-1), was successful in describing fungal communities by Illumina sequencing. Results were confirmed by a simultaneous metagenomics and eukaryote-specific primer approach. Co-amplification occurred in all sample types but was effectively reduced by blocking oligonucleotides.<br><br>CONCLUSIONS: The compiled data revealed the presence of an enormous diversity of fungal 18S rRNA gene primer pairs in terms of fungal coverage, phylum spectrum and co-amplification. Therefore, the primer pair has to be carefully selected to fulfill the requirements of the individual research projects. The presented primer toolkit offers comprehensive lists of 164 primers, 439 primer combinations, 4 blocking oligonucleotides, and top primer pairs holding all relevant information including primer's characteristics and performance to facilitate primer pair selection.}, }
@article {pmid30447983, year = {2019}, author = {Vasquez, AK and Ganda, EK and Capel, MB and Eicker, S and Virkler, PD and Bicalho, RC and Nydam, DV}, title = {The microbiome of Escherichia coli and culture-negative nonsevere clinical mastitis: Characterization and associations with linear score and milk production.}, journal = {Journal of dairy science}, volume = {102}, number = {1}, pages = {578-594}, doi = {10.3168/jds.2018-15062}, pmid = {30447983}, issn = {1525-3198}, mesh = {Animals ; Anti-Infective Agents/therapeutic use ; Bacteria/classification/genetics ; Biodiversity ; Cattle ; Escherichia coli/*isolation &amp; purification ; Female ; Lactation/*physiology ; Mastitis, Bovine/*microbiology ; Metagenomics ; Microbiota/*physiology ; Milk/microbiology ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Culture-negative and Escherichia coli cases are uncommonly treated in pathogen-based protocols for nonsevere mastitis. High-throughput 16S rRNA sequencing might reveal the presence of other pathogens and can provide information on microbial diversity. The objective was to explore the milk microbiome at the time of the mastitis event (enrollment) and its association with survival in the herd, milk production, and postevent linear score (LS) for cows with clinical mastitis characterized as negative or E. coli by culture. Fifty E. coli-positive and 35 culture-negative samples from cases were enrolled. No cases were treated with antimicrobials. All E. coli-positive quarters were characterized as transient; microbiological culture of samples taken 15 d postmastitis were negative for this organism. However, a difference in α-diversity (Shannon index) was present between enrollment and follow-up samples (3.8 vs. 5.1). When α-diversity was explored for enrollment E. coli samples, no relationship was observed between the Shannon indices of these samples and postmastitis LS. Alpha-diversity of the enrollment samples was lower for E. coli-positive cows that subsequently had greater losses in milk production. This difference was explained by a greater relative abundance of the family Enterobacteriaceae (67.8 vs. 38.4%) for cows that dropped in production. Analysis of composition of the microbiome identified one phylum, Proteobacteria, that differed between E. coli-positive cows that dropped in production and those that did not. Evaluation of β -diversity found no statistical relationship between postmastitis LS and the microbiome. When evaluating α- and β-diversities and composition of the microbiomes for culture-negative quarters, no associations were found for milk production changes and postmastitis LS. Three cows did not remain in the herd, limiting the ability to analyze survival. The findings suggest that a contributing factor to negative outcomes in E. coli-positive cows is relative abundance of this pathogen, and that no single or collective group of bacterial families is associated with milk production changes or postmastitis LS in culture-negative quarters. Although additional studies should be performed, the absence of associations between outcomes explored and microbial profiles in this study suggests that we are not missing opportunities by not treating nonsevere E. coli or culture-negative mastitis cases.}, }
@article {pmid30420843, year = {2018}, author = {Alves, LF and Meleiro, LP and Silva, RN and Westmann, CA and Guazzaroni, ME}, title = {Novel Ethanol- and 5-Hydroxymethyl Furfural-Stimulated β-Glucosidase Retrieved From a Brazilian Secondary Atlantic Forest Soil Metagenome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2556}, pmid = {30420843}, issn = {1664-302X}, abstract = {Beta-glucosidases are key enzymes involved in lignocellulosic biomass degradation for bioethanol production, which complete the final step during cellulose hydrolysis by converting cellobiose into glucose. Currently, industry requires enzymes with improved catalytic performance or tolerance to process-specific parameters. In this sense, metagenomics has become a powerful tool for accessing and exploring the biochemical biodiversity present in different natural environments. Here, we report the identification of a novel β-glucosidase from metagenomic DNA isolated from soil samples enriched with decaying plant matter from a Secondary Atlantic Forest region. For this, we employed a functional screening approach using an optimized and synthetic broad host-range vector for library production. The novel β-glucosidase - named Lfa2 - displays three GH3-family conserved domains and conserved catalytic amino acids D283 and E487. The purified enzyme was most active in pH 5.5 and at 50°C, and showed hydrolytic activity toward several pNP synthetic substrates containing β-glucose, β-galactose, β-xylose, β-fucose, and α-arabinopyranose, as well as toward cellobiose. Lfa2 showed considerable glucose tolerance, exhibiting an IC50 of 300 mM glucose and 30% of remaining activity in 600 mM glucose. In addition, Lfa2 retained full or slightly enhanced activity in the presence of several metal ions. Further, β-glucosidase activity was increased by 1.7-fold in the presence of 10% (v/v) ethanol, a concentration that can be reached in conventional fermentation processes. Similarly, Lfa2 showed 1.7-fold enhanced activity at high concentrations of 5-hydroxymethyl furfural, one of the most important cellulase inhibitors in pretreated sugarcane bagasse hydrolysates. Moreover, the synergistic effect of Lfa2 on Bacillus subtilis GH5-CBM3 endoglucanase activity was demonstrated by the increased production of glucose (1.6-fold). Together, these results indicate that β-glucosidase Lfa2 is a promissory enzyme candidate for utilization in diverse industrial applications, such as cellulosic biomass degradation or flavor enhancement in winemaking and grape processing.}, }
@article {pmid30413473, year = {2019}, author = {Coscolín, C and Katzke, N and García-Moyano, A and Navarro-Fernández, J and Almendral, D and Martínez-Martínez, M and Bollinger, A and Bargiela, R and Gertler, C and Chernikova, TN and Rojo, D and Barbas, C and Tran, H and Golyshina, OV and Koch, R and Yakimov, MM and Bjerga, GEK and Golyshin, PN and Jaeger, KE and Ferrer, M}, title = {Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {2}, pages = {}, doi = {10.1128/AEM.02404-18}, pmid = {30413473}, issn = {1098-5336}, abstract = {Amination of bulky ketones, particularly in (R) configuration, is an attractive chemical conversion; however, known ω-transaminases (ω-TAs) show insufficient levels of performance. By applying two screening methods, we discovered 10 amine transaminases from the class III ω-TA family that were 38% to 76% identical to homologues. We present examples of such enzymes preferring bulky ketones over keto acids and aldehydes with stringent (S) selectivity. We also report representatives from the class III ω-TAs capable of converting (R) and (S) amines and bulky ketones and one that can convert amines with longer alkyl substituents. The preference for bulky ketones was associated with the presence of a hairpin region proximal to the conserved Arg414 and residues conforming and close to it. The outward orientation of Arg414 additionally favored the conversion of (R) amines. This configuration was also found to favor the utilization of putrescine as an amine donor, so that class III ω-TAs with Arg414 in outward orientation may participate in vivo in the catabolism of putrescine. The positioning of the conserved Ser231 also contributes to the preference for amines with longer alkyl substituents. Optimal temperatures for activity ranged from 45 to 65°C, and a few enzymes retained ≥50% of their activity in water-soluble solvents (up to 50% [vol/vol]). Hence, our results will pave the way to design, in the future, new class III ω-TAs converting bulky ketones and (R) amines for the production of high-value products and to screen for those converting putrescine.IMPORTANCE Amine transaminases of the class III ω-TAs are key enzymes for modification of chemical building blocks, but finding those capable of converting bulky ketones and (R) amines is still challenging. Here, by an extensive analysis of the substrate spectra of 10 class III ω-TAs, we identified a number of residues playing a role in determining the access and positioning of bulky ketones, bulky amines, and (R)- and (S) amines, as well as of environmentally relevant polyamines, particularly putrescine. The results presented can significantly expand future opportunities for designing (R)-specific class III ω-TAs to convert valuable bulky ketones and amines, as well as for deepening the knowledge into the polyamine catabolic pathways.}, }
@article {pmid30405577, year = {2018}, author = {Bertelli, C and Courtois, S and Rosikiewicz, M and Piriou, P and Aeby, S and Robert, S and Loret, JF and Greub, G}, title = {Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2520}, pmid = {30405577}, issn = {1664-302X}, abstract = {In drinking water distribution systems (DWDS), a disinfectant residual is usually applied to limit bacterial regrowth. However, delivering water with no or reduced chlorine residual could potentially decrease the selection for antimicrobial resistant microorganisms, favor bacterial regrowth and result in changes in bacterial populations. To evaluate the feasibility of water reduction in local DWDS while ensuring water safety, water quality was measured over 2 months in two different networks, each of them harboring sub-areas with normal and reduced chlorine. Water quality remained good in chlorine reduced samples, with limited development of total flora and absence of coliforms. Furthermore, 16S rRNA amplicon-based metagenomics was used to investigate the diversity and the composition of microbial communities in the sub-networks. Taxonomic classification of sequence reads showed a reduced bacterial diversity in sampling points with higher chlorine residuals. Chlorine disinfection created more homogeneous bacterial population, dominated by Pseudomonas, a genus that contains some major opportunistic pathogens such as P. aeruginosa. In the absence of chlorine, a larger and unknown biodiversity was unveiled, also highlighted by a decreased rate of taxonomic classification to the genus and species level. Overall, this experiment in a functional DWDS will facilitate the move toward potable water delivery systems without residual disinfectants and will improve water taste for consumers.}, }
@article {pmid30400812, year = {2018}, author = {Kumar, MS and Slud, EV and Okrah, K and Hicks, SC and Hannenhalli, S and Corrada Bravo, H}, title = {Analysis and correction of compositional bias in sparse sequencing count data.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {799}, pmid = {30400812}, issn = {1471-2164}, support = {K99 HG009007/HG/NHGRI NIH HHS/United States ; R01 RR021967/RR/NCRR NIH HHS/United States ; GM114267//National Institutes of Health/ ; R01 GM083084/GM/NIGMS NIH HHS/United States ; HG005220//National Institutes of Health/ ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R21 GM107683/GM/NIGMS NIH HHS/United States ; 1564785//National Science Foundation (US)/ ; R01 GM114267/GM/NIGMS NIH HHS/United States ; GM083084//National Institutes of Health/ ; R01 GM103552/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Bayes Theorem ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count data is compositional, measuring relative and not absolute abundances of the assayed features. This compositional bias confounds inference of absolute abundances. Commonly used count data normalization approaches like library size scaling/rarefaction/subsampling cannot correct for compositional or any other relevant technical bias that is uncorrelated with library size.<br><br>RESULTS: We demonstrate that existing techniques for estimating compositional bias fail with sparse metagenomic 16S count data and propose an empirical Bayes normalization approach to overcome this problem. In addition, we clarify the assumptions underlying frequently used scaling normalization methods in light of compositional bias, including scaling methods that were not designed directly to address it.<br><br>CONCLUSIONS: Compositional bias, induced by the sequencing machine, confounds inferences of absolute abundances. We present a normalization technique for compositional bias correction in sparse sequencing count data, and demonstrate its improved performance in metagenomic 16s survey data. Based on the distribution of technical bias estimates arising from several publicly available large scale 16s count datasets, we argue that detailed experiments specifically addressing the influence of compositional bias in metagenomics are needed.}, }
@article {pmid30394652, year = {2018}, author = {Borton, MA and Daly, RA and O'Banion, B and Hoyt, DW and Marcus, DN and Welch, S and Hastings, SS and Meulia, T and Wolfe, RA and Booker, AE and Sharma, S and Cole, DR and Wunch, K and Moore, JD and Darrah, TH and Wilkins, MJ and Wrighton, KC}, title = {Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale.}, journal = {Environmental microbiology}, volume = {20}, number = {12}, pages = {4596-4611}, doi = {10.1111/1462-2920.14467}, pmid = {30394652}, issn = {1462-2920}, support = {1342701//National Science Foundation Dimensions of Biodiversity/ ; FE0024297//Department of Energy's National Energy Technology Laboratory/ ; //U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//Office of Science of the U.S. Department of Energy/ ; }, abstract = {About 60% of natural gas production in the United States comes from hydraulic fracturing of unconventional reservoirs, such as shales or organic-rich micrites. This process inoculates and enriches for halotolerant microorganisms in these reservoirs over time, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of methanogens across unconventional reservoirs, and report that members of genus Methanohalophilus are recovered from every hydraulically fractured unconventional reservoir sampled by metagenomics. We provide the first genomic sequencing of three isolate genomes, as well as two metagenome assembled genomes (MAGs). Utilizing six other previously sequenced isolate genomes and MAGs, we perform comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in CRISPR-Cas systems of Methanohalophilus, with genomes from geographically distinct unconventional reservoirs sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic methane production in hydraulically fractured unconventional reservoirs.}, }
@article {pmid30384903, year = {2018}, author = {Huang, X and Zhu, J and Cai, Z and Lao, Y and Jin, H and Yu, K and Zhang, B and Zhou, J}, title = {Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach.}, journal = {Microbiological research}, volume = {217}, number = {}, pages = {1-13}, doi = {10.1016/j.micres.2018.08.015}, pmid = {30384903}, issn = {1618-0623}, mesh = {Acyltransferases/genetics/metabolism ; Bacteria/classification/*genetics/*metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Carbon-Sulfur Lyases/genetics/metabolism ; China ; Dinoflagellida/growth &amp; development/*microbiology ; Eutrophication/physiology ; Marine Biology ; Metagenomics/*methods ; Microbiota/*genetics/*physiology ; Phylogeny ; Proteobacteria/genetics/metabolism ; Quorum Sensing/*genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis ; Sequence Analysis, Protein ; Sequence Homology ; Symbiosis ; Transcription Factors/genetics/metabolism ; }, abstract = {The complicated relationships among environmental microorganisms are regulated by quorum sensing (QS). Understanding QS-based signals could shed light on the interactions between microbial communities in certain environments. Although QS characteristics have been widely discussed, few studies have been conducted on the role of QS in phycospheric microorganisms. Here, we used metagenomics to examine the profile of AI-1 (AinS, HdtS, LuxI) and AI-2 (LuxS) autoinducers from a deeply sequenced microbial database, obtained from a complete dinoflagellate bloom. A total of 3001 putative AI-1 homologs and 130 AI-2 homologs were identified. The predominant member among the AI groups was HdtS. The abundance of HdtS, AinS, and LuxS increased as the bloom developed, whereas the abundance of LuxI showed the opposite trend. Phylogenetic analysis suggested that HdtS and LuxI synthase originated mainly from alpha-, beta-, and gamma-Proteobacteria, whereas AinS synthase originated solely from Vibrionales. In comparison to AI-1, the sequences related to AI-2 (LuxS) demonstrated a much wider taxonomic coverage. Some significant correlations were found between dominant species and QS signals. In addition to the QS, we also performed parallel analysis of the quorum quenching (QQ) sequences. In comparison to QS, the relative abundance of QQ signals was lower; however, an obvious frequency correlation was observed. These results suggested that QS and QQ signals co-participate in regulating microbial communities during an algal bloom. These data helped to reveal the characteristic behavior of algal symbiotic bacteria, and facilitated a better understanding of microbial dynamics during an algal bloom event from a chemical ecological perspective.}, }
@article {pmid30372979, year = {2019}, author = {Park, SE and Seo, SH and Kim, EJ and Byun, S and Na, CS and Son, HS}, title = {Changes of microbial community and metabolite in kimchi inoculated with different microbial community starters.}, journal = {Food chemistry}, volume = {274}, number = {}, pages = {558-565}, doi = {10.1016/j.foodchem.2018.09.032}, pmid = {30372979}, issn = {1873-7072}, mesh = {Bacteria/metabolism ; Brassica/metabolism/*microbiology ; *Fermentation ; Fermented Foods/*microbiology ; *Food Microbiology ; *Microbiota ; }, abstract = {Gas chromatography mass spectrometry-based metabolomics and next generation sequencing-based metagenomics were applied to investigate the effect of different microbial community starters (MCSs) on kimchi fermentation. Profiles of metabolites and microbial community in kimchi were remarkably different from those on the first day of fermentation according to MCS used. Kimchi inoculated with MCS5 or MCS10 had relatively higher levels of lactic acid, leucine, propanedioic acid, serine, glycerol, erythritol, and sorbitol but lower levels of butanedioic acid, glyceric acid, myo-inositol, xylose, fructose, and talose compared to control kimchi or kimchi inoculated with MCS1. Microbial communities of kimchi inoculated with MCS1, MCS5, and MCS10 were characterized by high ratios of Leuconostoc, Lactobacillus plantarum, and Lactobacillus brevis, respectively. The microbial community of kimchi formed on the first day of fermentation was stable for 50 days, suggesting that microbial communities containing multiple microorganisms can be used as starters to obtain desired quality of kimchi.}, }
@article {pmid30356699, year = {2018}, author = {Weißbecker, C and Wubet, T and Lentendu, G and Kühn, P and Scholten, T and Bruelheide, H and Buscot, F}, title = {Experimental Evidence of Functional Group-Dependent Effects of Tree Diversity on Soil Fungi in Subtropical Forests.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2312}, pmid = {30356699}, issn = {1664-302X}, abstract = {Deconvoluting the relative contributions made by specific biotic and abiotic drivers to soil fungal community compositions facilitates predictions about the functional responses of ecosystems to environmental changes, such as losses of plant diversity, but it is hindered by the complex interactions involved. Experimental assembly of tree species allows separation of the respective effects of plant community composition (biotic components) and soil properties (abiotic components), enabling much greater statistical power than can be achieved in observational studies. We therefore analyzed these contributions by assessing, via pyrotag sequencing of the internal transcribed spacer (ITS2) rDNA region, fungal communities in young subtropical forest plots included in a large experiment on the effects of tree species richness. Spatial variables and soil properties were the main drivers of soil fungal alpha and beta-diversity, implying strong early-stage environmental filtering and dispersal limitation. Tree related variables, such as tree community composition, significantly affected arbuscular mycorrhizal and pathogen fungal community structure, while differences in tree host species and host abundance affected ectomycorrhizal fungal community composition. At this early stage of the experiment, only a limited amount of carbon inputs (rhizodeposits and leaf litter) was being provided to the ecosystem due to the size of the tree saplings, and persisting legacy effects were observed. We thus expect to find increasing tree related effects on fungal community composition as forest development proceeds.}, }
@article {pmid30353943, year = {2018}, author = {Sonoda, A and Kamiyama, N and Ozaka, S and Gendo, Y and Ozaki, T and Hirose, H and Noguchi, K and Saechue, B and Sachi, N and Sakai, K and Mizukami, K and Hidano, S and Murakami, K and Kobayashi, T}, title = {Oral administration of antibiotics results in fecal occult bleeding due to metabolic disorders and defective proliferation of the gut epithelial cell in mice.}, journal = {Genes to cells : devoted to molecular &amp; cellular mechanisms}, volume = {23}, number = {12}, pages = {1043-1055}, doi = {10.1111/gtc.12649}, pmid = {30353943}, issn = {1365-2443}, support = {//Suzuken Memorial Foundation/ ; 15K08953//Japan Society for the Promotion of Science/ ; 15K19577//Japan Society for the Promotion of Science/ ; 16K01872//Japan Society for the Promotion of Science/ ; 17H04649//Japan Society for the Promotion of Science/ ; 17H17104//Japan Society for the Promotion of Science/ ; 17K08695//Japan Society for the Promotion of Science/ ; 17K08889//Japan Society for the Promotion of Science/ ; 17K15954//Japan Society for the Promotion of Science/ ; 17K16346//Japan Society for the Promotion of Science/ ; //GlaxoSmithKline/ ; }, mesh = {Administration, Oral ; Ampicillin/administration &amp; dosage/pharmacology ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage/*adverse effects ; Antimicrobial Cationic Peptides/metabolism ; Butyric Acid/pharmacology ; Carbohydrate Metabolism/drug effects ; Cecum/microbiology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Colon/*pathology ; Colonic Neoplasms/pathology ; Cytokines/metabolism ; Epithelial Cells/*pathology ; Glutamine/administration &amp; dosage ; Lipid Metabolism/drug effects ; Macrophages/drug effects/metabolism ; Metabolic Diseases/*complications ; Metabolome/drug effects ; Metagenomics ; Mice ; Microbiota/drug effects/genetics ; *Occult Blood ; RAW 264.7 Cells ; Regeneration/drug effects ; Sodium Glutamate/administration &amp; dosage ; Species Specificity ; Vancomycin/administration &amp; dosage/pharmacology ; }, abstract = {Antibiotics sometimes exert adverse effects on the pathogenesis of colitis due to the dysbiosis resulting from the disruption of gut homeostasis. However, the precise mechanisms underlying colitogenic effects of antibiotic-induced colitis are largely unknown. Here, we show a novel murine fecal occult bleeding model induced by the combinatorial treatment of ampicillin and vancomycin, which is accompanied by an enlarged cecum, upregulation of pro-inflammatory cytokines IL-6 and IL-12, a reduction in Ki-67-positive epithelial cell number and an increase in the apoptotic cell number in the colon. Moreover, gas chromatography-tandem mass analysis showed that various kinds of metabolites, including glutamic acid and butyric acid, were significantly decreased in the cecal contents. In addition, abundance of butyric acid producer Clostridiales was dramatically reduced in the enlarged cecum. Interestingly, supplementation of monosodium glutamate or its precursor glutamine suppressed colonic IL-6 and IL-12, protected from cell apoptosis and prevented fecal occult blood indicating that the reduced level of glutamic acid is a possible mechanism of antibiotic-induced fecal occult bleeding. Our data showed a novel mechanism of antibiotic-induced fecal occult bleeding providing a new insight into the clinical application of glutamic acid for the treatment of antibiotic-induced colitis.}, }
@article {pmid30346155, year = {2018}, author = {Pérez-Burillo, S and Pastoriza, S and Jiménez-Hernández, N and D'Auria, G and Francino, MP and Rufián-Henares, JA}, title = {Effect of Food Thermal Processing on the Composition of the Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {43}, pages = {11500-11509}, doi = {10.1021/acs.jafc.8b04077}, pmid = {30346155}, issn = {1520-5118}, mesh = {Bacteria/classification ; *Cooking ; Edible Grain ; Fabaceae ; Fatty Acids, Volatile/analysis ; Fermentation ; Fruit ; Furaldehyde/analogs &amp; derivatives/analysis ; *Gastrointestinal Microbiome ; *Hot Temperature ; Humans ; Lysine/analogs &amp; derivatives/analysis ; Maillard Reaction ; Meat ; RNA, Ribosomal, 16S/genetics ; Vegetables ; }, abstract = {Cooking modifies food composition due to chemical reactions. Additionally, food composition shapes the human gut microbiota. Thus, the objective of this research was to unravel the effect of different food cooking methods on the structure and functionality of the gut microbiota. Common culinary techniques were applied to five foods, which were submitted to in vitro digestion-fermentation. Furosine, 5-(hydroxymethyl)furfural, and furfural were used as Maillard reaction indicators to control the heat treatment. Short-chain fatty acids production was quantified as indicator of healthy metabolic output. Gut microbial community structure was analyzed through 16S rRNA. Both food composition and cooking methods modified the microbiota composition and released short-chain fatty acids. In general, intense cooking technologies (roasting and grilling) increased the abundance of beneficial bacteria like Ruminococcus spp. or Bifidobacterium spp. compared to milder treatments (boiling). However, for some foods (banana or bread), intense cooking decreased the levels of healthy bacteria.}, }
@article {pmid30342053, year = {2018}, author = {Vallianou, NG and Stratigou, T and Tsagarakis, S}, title = {Microbiome and diabetes: Where are we now?.}, journal = {Diabetes research and clinical practice}, volume = {146}, number = {}, pages = {111-118}, doi = {10.1016/j.diabres.2018.10.008}, pmid = {30342053}, issn = {1872-8227}, mesh = {Animals ; Diabetes Mellitus, Type 2/*microbiology ; Dysbiosis/*microbiology ; Fecal Microbiota Transplantation/*methods ; Gastrointestinal Microbiome/*genetics ; Humans ; Mice ; Prebiotics/*microbiology ; Probiotics/*metabolism ; }, abstract = {Alterations in the diversity or structure of gut microbiota known as dysbiosis, may affect metabolic activities, resulting in metabolic disorders, such as obesity and diabetes. The development of more sophisticated methods, such as metagenomics sequencing, PCR-denaturing gradient gel electrophoresis, microarrays and fluorescence in situ hybridization, has expanded our knowledge on gut microbiome. Dysbiosis has been related to increased plasma concentrations of gut microbiota-derived lipopolysaccharide (LPS), which triggers the production of a variety of cytokines and the recruitment of inflammatory cells. Metabolomics have demonstrated that butyrate and propionate suppress weight gain in mice with high fat diet-induced obesity, and acetate has been proven to reduce food intake in healthy mice. The role of prebiotics, probiotics, genetically modified bacteria and fecal microbiota transplantation, as potential therapeutic challenges for type 2 diabetes will be discussed in this review.}, }
@article {pmid30325092, year = {2019}, author = {Zhang, SY and Tsementzi, D and Hatt, JK and Bivins, A and Khelurkar, N and Brown, J and Tripathi, SN and Konstantinidis, KT}, title = {Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics.}, journal = {Environmental microbiology}, volume = {21}, number = {1}, pages = {182-196}, doi = {10.1111/1462-2920.14439}, pmid = {30325092}, issn = {1462-2920}, support = {//Georgia Institute of Technology/ ; DEB 1241046//National Science Foundation/ ; }, abstract = {Little is known about microbial communities in the Ganges River, India and how they respond to intensive anthropogenic inputs. Here we applied shotgun metagenomics sequencing to study microbial community dynamics and function in planktonic samples collected along an approximately 700 km river transect, including urban cities and rural settings in upstream waters, before and after the monsoon rainy season. Our results showed that 11%-32% of the microbes represented terrestrial, sewage and human inputs (allochthonous). Sewage inputs significantly contributed to the higher abundance, by 13-fold of human gut microbiome (HG) associated sequences and 2-fold of antibiotic resistance genes (ARGs) in the Ganges relative to other riverine ecosystems in Europe, North and South America. Metagenome-assembled genome sequences (MAGs) representing allochthonous populations were detectable and tractable across the river after 1-2 days of (downstream) transport (> 200 km apart). Only approximately 8% of these MAGs were abundant in U.S. freshwater ecosystems, revealing distinct biodiversity for the Ganges. Microbial communities in the rainy season exhibited increased alpha-diversity and spatial heterogeneity and showed significantly weaker distance-decay patterns compared with the dry season. These results advance our understanding of the Ganges microbial communities and how they respond to anthropogenic pollution.}, }
@article {pmid30309375, year = {2018}, author = {Zepeda Mendoza, ML and Roggenbuck, M and Manzano Vargas, K and Hansen, LH and Brunak, S and Gilbert, MTP and Sicheritz-Pontén, T}, title = {Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.}, journal = {Acta veterinaria Scandinavica}, volume = {60}, number = {1}, pages = {61}, pmid = {30309375}, issn = {1751-0147}, support = {R52-A5062//Lundbeckfonden/ ; }, mesh = {Adaptation, Biological ; Animals ; Animals, Wild/microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Falconiformes/*microbiology/physiology ; *Feeding Behavior ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Skin/*microbiology ; }, abstract = {BACKGROUND: Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut.<br><br>RESULTS: We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut.<br><br>CONCLUSIONS: Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.}, }
@article {pmid30308944, year = {2018}, author = {Fehlbaum, S and Prudence, K and Kieboom, J and Heerikhuisen, M and van den Broek, T and Schuren, FHJ and Steinert, RE and Raederstorff, D}, title = {In Vitro Fermentation of Selected Prebiotics and Their Effects on the Composition and Activity of the Adult Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {19}, number = {10}, pages = {}, pmid = {30308944}, issn = {1422-0067}, mesh = {*Biodiversity ; Dietary Fiber ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; *Prebiotics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recently, the concept of prebiotics has been revisited to expand beyond non-digestible oligosaccharides, and the requirements for selective stimulation were extended to include microbial groups other than, and additional to, bifidobacteria and lactobacilli. Here, the gut microbiota-modulating effects of well-known and novel prebiotics were studied. An in vitro fermentation screening platform (i-screen) was inoculated with adult fecal microbiota, exposed to different dietary fibers that had a range of concentrations (inulin, alpha-linked galacto-oligosaccharides (alpha-GOS), beta-linked GOS, xylo-oligosaccharides (XOS) from corn cobs and high-fiber sugar cane, and beta-glucan from oats), and compared to a positive fructo-oligosaccharide (FOS) control and a negative control (no fiber addition). All dietary fibers displayed prebiotic activity, with beta-glucan showing more distinct effects on the microbial composition and metabolism compared to the other fibers. Beta-glucan induced the growth of Prevotella and Roseburia with a concomitant increase in propionate production. Inulin and both forms of GOS and XOS had a strong bifidogenic effect on the microbial composition. A dose-response effect was observed for butyrate when exposed to beta-glucan and inulin. The findings of this study support the potential for alpha-GOS, XOS, and oat beta-glucan to serve as novel prebiotics, due to their association with the positive shifts in microbiome composition and short-chain fatty acid production that point to potential health benefits.}, }
@article {pmid30308887, year = {2019}, author = {Coble, AA and Flinders, CA and Homyack, JA and Penaluna, BE and Cronn, RC and Weitemier, K}, title = {eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications.}, journal = {The Science of the total environment}, volume = {649}, number = {}, pages = {1157-1170}, doi = {10.1016/j.scitotenv.2018.08.370}, pmid = {30308887}, issn = {1879-1026}, mesh = {Aquatic Organisms/*chemistry ; DNA/*analysis ; *Environment ; Environmental Monitoring/*methods ; *Forestry ; Fresh Water ; Hydrobiology/*methods ; }, abstract = {Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our objectives are to describe potential applications of eDNA across the wood products supply chain extending from regenerating forests, harvesting, and wood transport, to manufacturing facilities, and to review the current state of the science in this context. To meet our second objective, we summarize the taxa examined with targeted (PCR, qPCR or ddPCR) or metagenomic eDNA methods (eDNA metabarcoding), evaluate how estimated species richness compares between traditional field sampling and eDNA metabarcoding approaches, and compare the geographical representation of prior eDNA studies in freshwater ecosystems to global wood baskets. Potential applications of eDNA include evaluating the effects of forestry and forest manufacturing activities on aquatic biota, delineating fish-bearing versus non fish-bearing reaches, evaluating effectiveness of constructed road crossings for freshwater organism passage, and determining the presence of at-risk species. Studies using targeted eDNA approaches focused on fish, amphibians, and invertebrates, while metagenomic studies focused on fish, invertebrates, and microorganisms. Rare, threatened, or endangered species received the least attention in targeted eDNA research, but are arguably of greatest interest to sustainable forestry and forest manufacturing that seek to preserve freshwater biodiversity. Ultimately, using eDNA methods will enable forestry and forest manufacturing managers to have data-driven prioritization for conservation actions for all freshwater species.}, }
@article {pmid30308248, year = {2018}, author = {Hessler, T and Harrison, STL and Huddy, RJ}, title = {Stratification of microbial communities throughout a biological sulphate reducing up-flow anaerobic packed bed reactor, revealed through 16S metagenomics.}, journal = {Research in microbiology}, volume = {169}, number = {10}, pages = {543-551}, doi = {10.1016/j.resmic.2018.09.003}, pmid = {30308248}, issn = {1769-7123}, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Bioreactors/*microbiology ; DNA, Bacterial/genetics ; Genome, Bacterial ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sulfur Compounds/*metabolism ; }, abstract = {Biological sulphate reduction (BSR) is a promising low-cost treatment of acid rock drainage effluents. In this paper, the system performance and microbial ecology of a lactate supplemented BSR up-flow anaerobic packed bed reactor (UAPBR) are evaluated across reactor height and compared to a continuous stirred tank reactor (CSTR). The biomass concentrations of planktonic and biofilm communities were quantified and subsequently characterised by 16S rRNA gene amplicon sequencing. The defined microbial communities were shown to correlate with differing availability of lactate, volatile fatty acids produced from lactate degradation and sulphate concentration. The UAPBR was able to achieve near complete sulphate conversion at a 4-day hydraulic residence time (HRT) at a sulphate feed concentration of 10.41 mM (1 g/L). The high volumetric sulphate reduction rate of 0.184 mM/L.h achieved in the first third of the reactor was attributed to OTUs present in the planktonic and biofilm communities. While the scavenging of sulphate within the final third of the UAPBR was attributed to an acetate oxidising genus of SRB which was not detected in the lactate-fed CSTR. The detailed analyses of the microbial communities throughout the UAPBR and CSTR contribute to the growing understanding of the impact of the microbial communities of BSR reactors on system performance.}, }
@article {pmid30301312, year = {2018}, author = {Yu, YC and Yum, SJ and Jeon, DY and Jeong, HG}, title = {Analysis of the Microbiota on Lettuce (Lactuca sativa L.) Cultivated in South Korea to Identify Foodborne Pathogens.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {8}, pages = {1318-1331}, doi = {10.4014/jmb.1803.03007}, pmid = {30301312}, issn = {1738-8872}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; *Food Microbiology ; Foodborne Diseases/*microbiology ; Geography ; Lettuce/*microbiology ; Metagenomics ; Microbial Interactions ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; }, abstract = {Lettuce (Lactuca sativa L.) is a major ingredient used in many food recipes in South Korea. Lettuce samples were collected during their maximum production period between April and July in order to investigate the microbiota of lettuce during different seasons. 16S rRNA gene-based sequencing was conducted using Illumina MiSeq, and real-time PCR was performed for quantification. The number of total bacterial was greater in lettuce collected in July than in that collected in April, albeit with reduced diversity. The bacterial compositions varied according to the site and season of sample collection. Potential pathogenic species such as Bacillus spp., Enterococcus casseliflavus, Klebsiella pneumoniae, and Pseudomonas aeruginosa showed season-specific differences. Results of the network co-occurrence analysis with core genera correlations showed characteristics of bacterial species in lettuce, and provided clues regarding the role of different microbes, including potential pathogens, in this microbiota. Although further studies are needed to determine the specific effects of regional and seasonal characteristics on the lettuce microbiota, our results imply that the 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria in lettuce.}, }
@article {pmid30272305, year = {2018}, author = {Zhou, S and Cai, Y and Wang, M and Yang, WD and Duan, N}, title = {Oral microbial flora of patients with Sicca syndrome.}, journal = {Molecular medicine reports}, volume = {18}, number = {6}, pages = {4895-4903}, pmid = {30272305}, issn = {1791-3004}, mesh = {Biodiversity ; Case-Control Studies ; Computational Biology/methods ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Sjogren's Syndrome/*etiology ; }, abstract = {Primary sicca syndrome (pSS) is a systemic autoimmune disease. However, its exact etiology and pathogenesis remain elusive. Various infectious factors have been identified to be closely associated with the occurrence and development of PSS. The present study aimed to assess the composition of the oral microbial flora of patients with pSS in China in order to provide guidance for treatment. The microbial flora of nine patients with pSS and five healthy controls from East China was evaluated in saliva samples using high‑throughput sequencing. A high microbial diversity was detected in the pSS and control groups, with bacteroidetes, firmicutes and proteobacteria constituting the largest phyla in the two groups. Compared with the control group, bacteroidetes and actinobacteria were significantly more abundant in the pSS group, whereas proteobacteria were significantly less abundant. However, no significant differences in bacterial richness and diversity were observed between the two groups. According to a Kyoto Encyclopedia of Genes and Genomes linear discriminant analysis, genes regulating cell apoptosis and the immune and digestive systems were significantly upregulated in the pSS group compared with those in the control group. In conclusion, the present study provided basic data on the flora of the oral cavity in patients with pSS from East China and may serve as a reference for the treatment of this condition.}, }
@article {pmid30271256, year = {2018}, author = {Anslan, S and Nilsson, RH and Wurzbacher, C and Baldrian, P and Leho Tedersoo,  and Bahram, M}, title = {Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding.}, journal = {MycoKeys}, volume = {}, number = {39}, pages = {29-40}, pmid = {30271256}, issn = {1314-4049}, abstract = {Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.}, }
@article {pmid30267313, year = {2018}, author = {Song, EJ and Lee, ES and Nam, YD}, title = {Progress of analytical tools and techniques for human gut microbiome research.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {56}, number = {10}, pages = {693-705}, pmid = {30267313}, issn = {1976-3794}, mesh = {Computational Biology/*trends ; Data Analysis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*trends ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Massive DNA sequencing studies have expanded our insights and understanding of the ecological and functional characteristics of the gut microbiome. Advanced sequencing technologies allow us to understand the close association of the gut microbiome with human health and critical illnesses. In the future, analyses of the gut microbiome will provide key information associating with human individual health, which will help provide personalized health care for diseases. Numerous molecular biological analysis tools have been rapidly developed and employed for the gut microbiome researches; however, methodological differences among researchers lead to inconsistent data, limiting extensive share of data. It is therefore very essential to standardize the current methodologies and establish appropriate pipelines for human gut microbiome research. Herein, we review the methods and procedures currently available for studying the human gut microbiome, including fecal sample collection, metagenomic DNA extraction, massive DNA sequencing, and data analyses with bioinformatics. We believe that this review will contribute to the progress of gut microbiome research in the clinical and practical aspects of human health.}, }
@article {pmid30261940, year = {2018}, author = {Denman, SE and Morgavi, DP and McSweeney, CS}, title = {Review: The application of omics to rumen microbiota function.}, journal = {Animal : an international journal of animal bioscience}, volume = {12}, number = {s2}, pages = {s233-s245}, doi = {10.1017/S175173111800229X}, pmid = {30261940}, issn = {1751-732X}, mesh = {Animals ; Bacteria/*classification/genetics ; Gastrointestinal Microbiome/*genetics ; Gene Expression Profiling/veterinary ; *Genomics ; Livestock ; *Metagenome ; Metagenomics ; Methane/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/metabolism ; }, abstract = {Rumen microbiome profiling uses 16S rRNA (18S rRNA, internal transcribed spacer) gene sequencing, a method that usually sequences a small portion of a single gene and is often biased and varies between different laboratories. Functional information can be inferred from this data, but only for those that are closely related to known annotated species, and even then may not truly reflect the function performed within the environment being studied. Genome sequencing of isolates and metagenome-assembled genomes has now reached a stage where representation of the majority of rumen bacterial genera are covered, but this still only represents a portion of rumen microbial species. The creation of a microbial genome (bins) database with associated functional annotations will provide a consistent reference to allow mapping of RNA-Seq reads for functional gene analysis from within the rumen microbiome. The integration of multiple omic analytics is linking functional gene activity, metabolic pathways and rumen metabolites with the responsible microbiota, supporting our biological understanding of the rumen system. The application of these techniques has advanced our understanding of the major microbial populations and functional pathways that are used in relation to lower methane emissions, higher feed efficiencies and responses to different feeding regimes. Continued and more precise use of these tools will lead to a detailed and comprehensive understanding of compositional and functional capacity and design of techniques for the directed intervention and manipulation of the rumen microbiota towards a desired state.}, }
@article {pmid30260956, year = {2018}, author = {Hunt, KA and Jennings, RM and Inskeep, WP and Carlson, RP}, title = {Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community.}, journal = {PLoS computational biology}, volume = {14}, number = {9}, pages = {e1006431}, pmid = {30260956}, issn = {1553-7358}, support = {U01 EB019416/EB/NIBIB NIH HHS/United States ; }, mesh = {Autotrophic Processes ; Biomass ; Carbon/chemistry ; Computer Simulation ; Electron Transport ; Electrons ; Ferric Compounds/*chemistry ; Genome, Archaeal ; Heterotrophic Processes ; Hot Temperature ; Iron/chemistry ; Metagenomics ; *Microbiota ; Oxygen/chemistry ; Phylogeny ; Sulfides/chemistry ; Sulfolobaceae/*metabolism ; Transcriptome ; }, abstract = {Interactions among microbial community members can lead to emergent properties, such as enhanced productivity, stability, and robustness. Iron-oxide mats in acidic (pH 2-4), high-temperature (> 65 °C) springs of Yellowstone National Park contain relatively simple microbial communities and are well-characterized geochemically. Consequently, these communities are excellent model systems for studying the metabolic activity of individual populations and key microbial interactions. The primary goals of the current study were to integrate data collected in situ with in silico calculations across process-scales encompassing enzymatic activity, cellular metabolism, community interactions, and ecosystem biogeochemistry, as well as to predict and quantify the functional limits of autotroph-heterotroph interactions. Metagenomic and transcriptomic data were used to reconstruct carbon and energy metabolisms of an important autotroph (Metallosphaera yellowstonensis) and heterotroph (Geoarchaeum sp. OSPB) from the studied Fe(III)-oxide mat communities. Standard and hybrid elementary flux mode and flux balance analyses of metabolic models predicted cellular- and community-level metabolic acclimations to simulated environmental stresses, respectively. In situ geochemical analyses, including oxygen depth-profiles, Fe(III)-oxide deposition rates, stable carbon isotopes and mat biomass concentrations, were combined with cellular models to explore autotroph-heterotroph interactions important to community structure-function. Integration of metabolic modeling with in situ measurements, including the relative population abundance of autotrophs to heterotrophs, demonstrated that Fe(III)-oxide mat communities operate at their maximum total community growth rate (i.e. sum of autotroph and heterotroph growth rates), as opposed to net community growth rate (i.e. total community growth rate subtracting autotroph consumed by heterotroph), as predicted from the maximum power principle. Integration of multiscale data with ecological theory provides a basis for predicting autotroph-heterotroph interactions and community-level cellular organization.}, }
@article {pmid30258040, year = {2018}, author = {Taft, DH and Liu, J and Maldonado-Gomez, MX and Akre, S and Huda, MN and Ahmad, SM and Stephensen, CB and Mills, DA}, title = {Bifidobacterial Dominance of the Gut in Early Life and Acquisition of Antimicrobial Resistance.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30258040}, issn = {2379-5042}, support = {S10 RR029668/RR/NCRR NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; F32 HD093185/HD/NICHD NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; R01 AT007079/AT/NCCIH NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bangladesh ; Bifidobacterium/genetics/*physiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; Probiotics/therapeutic use ; Regression Analysis ; }, abstract = {Bifidobacterium species are important commensals capable of dominating the infant gut microbiome, in part by producing acids that suppress growth of other taxa. Bifidobacterium species are less prone to possessing antimicrobial resistance (AMR) genes (ARGs) than other taxa that may colonize infants. Given that AMR is a growing public health crisis and ARGs are present in the gut microbiome of humans from early life, this study examines the correlation between a Bifidobacterium-dominated infant gut microbiome and AMR levels, measured by a culture-independent metagenomic approach both in early life and as infants become toddlers. In general, Bifidobacterium dominance is associated with a significant reduction in AMR in a Bangladeshi cohort, both in the number of acquired AMR genes present and in the abundance of AMR genes. However, by year 2, Bangladeshi infants had no significant differences in AMR related to their early-life Bifidobacterium levels. A generalized linear model including all infants in a previously published Swedish cohort found a significant negative association between log-transformed total AMR and Bifidobacterium levels, thus confirming the relationship between Bifidobacterium levels and AMR. In both cohorts, there was no change between early-life and later-life AMR abundance in high-Bifidobacterium infants but a significant reduction in AMR abundance in low-Bifidobacterium infants. These results support the hypothesis that early Bifidobacterium dominance of the infant gut microbiome may help reduce colonization by taxa containing ARGs.IMPORTANCE Infants are vulnerable to an array of infectious diseases, and as the gut microbiome may serve as a reservoir of AMR for pathogens, reducing the levels of AMR in infants is important to infant health. This study demonstrates that high levels of Bifidobacterium are associated with reduced levels of AMR in early life and suggests that probiotic interventions to increase infant Bifidobacterium levels have the potential to reduce AMR in infants. However, this effect is not sustained at year 2 of age in Bangladeshi infants, underscoring the need for more detailed studies of the biogeography and timing of infant AMR acquisition.}, }
@article {pmid30250208, year = {2018}, author = {Pärnänen, K and Karkman, A and Hultman, J and Lyra, C and Bengtsson-Palme, J and Larsson, DGJ and Rautava, S and Isolauri, E and Salminen, S and Kumar, H and Satokari, R and Virta, M}, title = {Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3891}, pmid = {30250208}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/*adverse effects ; Antibiotic Prophylaxis/adverse effects ; Breast Feeding ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Humans ; Infant ; Interspersed Repetitive Sequences/*genetics ; Maternal Inheritance ; Metagenomics ; Milk, Human/*microbiology ; Phylogeny ; Time Factors ; }, abstract = {The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers. MGEs in mothers' breast milk are also shared with their own infants. Termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers, which have the potential to affect microbial community composition, are associated with higher abundances of specific ARGs, the composition of which is largely shaped by bacterial phylogeny in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but microbiota composition still strongly impacts the overall resistance load.}, }
@article {pmid30249182, year = {2018}, author = {Cavalcanti, GS and Shukla, P and Morris, M and Ribeiro, B and Foley, M and Doane, MP and Thompson, CC and Edwards, MS and Dinsdale, EA and Thompson, FL}, title = {Rhodoliths holobionts in a changing ocean: host-microbes interactions mediate coralline algae resilience under ocean acidification.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {701}, pmid = {30249182}, issn = {1471-2164}, mesh = {Biodiversity ; Hydrogen-Ion Concentration ; Metagenome ; *Microbiota/genetics ; Oceans and Seas ; Photosynthesis ; Rhodophyta/metabolism/*microbiology/physiology ; Seawater/chemistry/microbiology ; Stress, Physiological ; }, abstract = {BACKGROUND: Life in the ocean will increasingly have to contend with a complex matrix of concurrent shifts in environmental properties that impact their physiology and control their life histories. Rhodoliths are coralline red algae (Corallinales, Rhodophyta) that are photosynthesizers, calcifiers, and ecosystem engineers and therefore represent important targets for ocean acidification (OA) research. Here, we exposed live rhodoliths to near-future OA conditions to investigate responses in their photosynthetic capacity, calcium carbonate production, and associated microbiome using carbon uptake, decalcification assays, and whole genome shotgun sequencing metagenomic analysis, respectively. The results from our live rhodolith assays were compared to similar manipulations on dead rhodolith (calcareous skeleton) biofilms and water column microbial communities, thereby enabling the assessment of host-microbiome interaction under climate-driven environmental perturbations.<br><br>RESULTS: Under high pCO2 conditions, live rhodoliths exhibited positive physiological responses, i.e. increased photosynthetic activity, and no calcium carbonate biomass loss over time. Further, whereas the microbiome associated with live rhodoliths remained stable and resembled a healthy holobiont, the microbial community associated with the water column changed after exposure to elevated pCO2.<br><br>CONCLUSIONS: Our results suggest that a tightly regulated microbial-host interaction, as evidenced by the stability of the rhodolith microbiome recorded here under OA-like conditions, is important for host resilience to environmental stress. This study extends the scarce comprehension of microbes associated with rhodolith beds and their reaction to increased pCO2, providing a more comprehensive approach to OA studies by assessing the host holobiont.}, }
@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 = {27}, number = {9}, pages = {1281-1291}, pmid = {30242595}, issn = {1573-3017}, mesh = {Environmental Monitoring/*methods ; Metagenome ; *Metagenomics ; Metals, Heavy/*toxicity ; Soil ; *Soil Microbiology ; Soil Pollutants/*toxicity ; }, 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 {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 = {98}, number = {}, pages = {56-62}, doi = {10.1016/j.plasmid.2018.09.008}, pmid = {30240699}, issn = {1095-9890}, mesh = {DNA, Bacterial/*genetics ; Female ; Humans ; Lactobacillus/classification/*genetics/*isolation &amp; purification/metabolism ; Microbiota ; Mucous Membrane/*microbiology ; Phylogeny ; Plasmids/chemistry/*genetics ; Sequence Analysis, DNA ; South Africa/epidemiology ; Vagina/*microbiology ; Vaginosis, Bacterial/epidemiology/*microbiology ; }, 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), 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) 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 = {2019}, 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 noninvasive metagenomics to characterize viral communities from wildlife.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {128-143}, doi = {10.1111/1755-0998.12946}, pmid = {30240114}, issn = {1755-0998}, support = {102507/Z/13/Z//Sir Henry Dale Fellowship, jointly funded by the Wellcome Trust and Royal Society/ ; 102507/Z/13/A//Wellcome-Beit Prize/ ; MC_UU_12014/12//Medical Research Council/United Kingdom ; }, 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 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 noninvasively collected faecal 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 foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological 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.}, }
@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 = {}, pmid = {30232167}, issn = {2379-5042}, mesh = {Animals ; Chiroptera/*microbiology ; *Diet ; Ecology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; *Metagenomics ; Phylogeny ; }, 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 {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}, pmid = {30231921}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; Carbon Cycle ; Genetic Variation ; Genome, Bacterial ; Geologic Sediments/analysis/*microbiology ; Lakes/analysis/*microbiology ; Metagenome ; Metagenomics ; Microbiota ; Nitrogen Cycle ; Phylogeny ; Sodium Chloride/analysis ; }, 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.<br><br>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.<br><br>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 {pmid30227897, year = {2018}, author = {Arora-Williams, K and Olesen, SW and Scandella, BP and Delwiche, K and Spencer, SJ and Myers, EM and Abraham, S and Sooklal, A and Preheim, SP}, title = {Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {165}, pmid = {30227897}, issn = {2049-2618}, mesh = {Bacteria/classification/isolation &amp; purification/metabolism ; Carbon/chemistry/metabolism ; Ecosystem ; Lakes/*chemistry/*microbiology ; Metagenome ; Metagenomics ; Methane/chemistry/metabolism ; *Microbiota ; Oxidation-Reduction ; Oxygen/chemistry/metabolism ; }, abstract = {BACKGROUND: Microbial processes are intricately linked to the depletion of oxygen in in-land and coastal water bodies, with devastating economic and ecological consequences. Microorganisms deplete oxygen during biomass decomposition, degrading the habitat of many economically important aquatic animals. Microbes then turn to alternative electron acceptors, which alter nutrient cycling and generate potent greenhouse gases. As oxygen depletion is expected to worsen with altered land use and climate change, understanding how chemical and microbial dynamics impact dead zones will aid modeling efforts to guide remediation strategies. More work is needed to understand the complex interplay between microbial genes, populations, and biogeochemistry during oxygen depletion.<br><br>RESULTS: Here, we used 16S rRNA gene surveys, shotgun metagenomic sequencing, and a previously developed biogeochemical model to identify genes and microbial populations implicated in major biogeochemical transformations in a model lake ecosystem. Shotgun metagenomic sequencing was done for one time point in Aug., 2013, and 16S rRNA gene sequencing was done for a 5-month time series (Mar.-Aug., 2013) to capture the spatiotemporal dynamics of genes and microorganisms mediating the modeled processes. Metagenomic binning analysis resulted in many metagenome-assembled genomes (MAGs) that are implicated in the modeled processes through gene content similarity to cultured organism and the presence of key genes involved in these pathways. The MAGs suggested some populations are capable of methane and sulfide oxidation coupled to nitrate reduction. Using the model, we observe that modulating these processes has a substantial impact on overall lake biogeochemistry. Additionally, 16S rRNA gene sequences from the metagenomic and amplicon libraries were linked to processes through the MAGs. We compared the dynamics of microbial populations in the water column to the model predictions. Many microbial populations involved in primary carbon oxidation had dynamics similar to the model, while those associated with secondary oxidation processes deviated substantially.<br><br>CONCLUSIONS: This work demonstrates that the unique capabilities of resident microbial populations will substantially impact the concentration and speciation of chemicals in the water column, unless other microbial processes adjust to compensate for these differences. It further highlights the importance of the biological aspects of biogeochemical processes, such as fluctuations in microbial population dynamics. Integrating gene and population dynamics into biogeochemical models has the potential to improve predictions of the community response under altered scenarios to guide remediation efforts.}, }
@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}, pmid = {30219103}, issn = {2049-2618}, support = {T32 GM007231/GM/NIGMS NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/genetics/isolation &amp; purification ; Data Analysis ; Data Mining ; Gastrointestinal Microbiome ; *Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; *Software ; }, 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.<br><br>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.<br><br>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 {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 = {}, pmid = {30217078}, issn = {1999-4915}, support = {203143100025//Canon Foundation for Scientific Research/International ; 16KT0020//Japan Society for the Promotion of Science/International ; 17H03850//Japan Society for the Promotion of Science/International ; 26430184//Japan Society for the Promotion of Science/International ; 2016-28//Institute for Chemical Research, Kyoto University/International ; 2017-25//Institute for Chemical Research, Kyoto University/International ; ANR-11-BTBR-0008//French Investments for the Future program/International ; }, mesh = {*Biodiversity ; Computational Biology/methods ; Genome, Viral ; Giant Viruses/*classification/*genetics ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Polymerase Chain Reaction/methods ; Seawater/*virology ; *Water Microbiology ; }, abstract = {&quot;Megaviridae&quot; 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 {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 = {}, pmid = {30213145}, issn = {1660-3397}, support = {0055_ALGARED_PLUS_5_E//INTERREG VA España-Portugal (POCTEP) 2014-2020 Cooperation Program/ ; }, mesh = {Bacteroidetes/*genetics/isolation &amp; purification ; Biodiversity ; Biotechnology/methods ; DNA, Bacterial/isolation &amp; purification ; Genetic Variation ; Halobacteriales/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; Spain ; *Water Microbiology ; Wetlands ; }, 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 {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 &amp; evolution}, volume = {33}, number = {10}, pages = {731-744}, 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 {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 = {}, pmid = {30205462}, issn = {1999-4915}, support = {support//North Carolina Agricultural Foundation/International ; internal support//North Carolina State University/International ; }, mesh = {*Biodiversity ; Clustered Regularly Interspaced Short Palindromic Repeats ; Humans ; Metagenomics ; *Microbiota ; Viruses/*classification/genetics/*isolation &amp; purification ; }, 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 {pmid30185512, year = {2018}, author = {Rohwer, RR and Hamilton, JJ and Newton, RJ and McMahon, KD}, title = {TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30185512}, issn = {2379-5042}, mesh = {Algorithms ; Animals ; Bacteria/*classification ; DNA, Bacterial/genetics ; Databases as Topic ; *Databases, Genetic ; Ecosystem ; Fresh Water/*microbiology ; *Metagenomics ; Mice ; *Microbial Consortia ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set's sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at https://www.github.com/McMahonLab/TaxAssIMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.}, }
@article {pmid30177919, year = {2018}, author = {Lin, JD and Lemay, MA and Parfrey, LW}, title = {Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1914}, pmid = {30177919}, issn = {1664-302X}, abstract = {Bacteria are integral to marine carbon cycling. They transfer organic carbon to higher trophic levels and remineralise it into inorganic forms. Kelp forests are among the most productive ecosystems within the global oceans, yet the diversity and metabolic capacity of bacteria that transform kelp carbon is poorly understood. Here, we use 16S amplicon and metagenomic shotgun sequencing to survey bacterial communities associated with the surfaces of the giant kelp Macrocystis pyrifera and assess the capacity of these bacteria for carbohydrate metabolism. We find that Macrocystis-associated communities are distinct from the water column, and that they become more diverse and shift in composition with blade depth, which is a proxy for tissue age. These patterns are also observed in metagenomic functional profiles, though the broader functional groups-carbohydrate active enzyme families-are largely consistent across samples and depths. Additionally, we assayed more than 250 isolates cultured from Macrocystis blades and the surrounding water column for the ability to utilize alginate, the primary polysaccharide in Macrocystis tissue. The majority of cultured bacteria (66%) demonstrated this capacity; we find that alginate utilization is patchily distributed across diverse genera in the Bacteroidetes and Proteobacteria, yet can also vary between isolates with identical 16S rRNA sequences. The genes encoding enzymes involved in alginate metabolism were detected in metagenomic data across taxonomically diverse bacterial communities, further indicating this capacity is likely widespread amongst bacteria in kelp forests. Overall, the M. pyrifera epibiota shifts across a depth gradient, demonstrating a connection between bacterial assemblage and host tissue state.}, }
@article {pmid30177915, year = {2018}, author = {Wu, YT and Yang, CY and Chiang, PW and Tseng, CH and Chiu, HH and Saeed, I and Baatar, B and Rogozin, D and Halgamuge, S and Degermendzhi, A and Tang, SL}, title = {Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1763}, pmid = {30177915}, issn = {1664-302X}, abstract = {Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2-5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.}, }
@article {pmid30173738, year = {2018}, author = {Stroebel, C and Alexander, T and Workentine, ML and Timsit, E}, title = {Effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of recently weaned beef cattle.}, journal = {Veterinary microbiology}, volume = {223}, number = {}, pages = {126-133}, doi = {10.1016/j.vetmic.2018.08.007}, pmid = {30173738}, issn = {1873-2542}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; Bovine Respiratory Disease Complex/*microbiology ; Cattle ; DNA, Bacterial/chemistry/genetics ; Female ; *Metagenomics ; *Microbiota ; Moraxella/genetics/isolation &amp; purification ; Mycoplasma/genetics/isolation &amp; purification ; Nasopharynx/microbiology ; RNA, Ribosomal, 16S/chemistry/genetics ; Trachea/microbiology ; Transportation ; Weaning ; }, abstract = {The objective was to study effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of feedlot cattle. Two groups of 30 Angus-cross heifers were studied from weaning to 28 d after arrival at a feedlot. For each group, half the heifers were either transported directly to a feedlot after weaning (RANC) or transported to and co-mingled at an auction market for 24 h before being placed in a feedlot (AUCT). Deep nasal swabs (DNS) and trans-tracheal aspirates (TTA) were collected at weaning (d0) and at on-arrival processing at the feedlot (d2). At 7 (d9) and 28 d (d30) after arrival, DNS were repeated. The DNA was extracted from DNS and TTA and the V4 region of the 16S rRNA gene sequenced (MiSeq). Alpha diversity analysis did not reveal differences between AUCT and RANC. However, bacterial diversity decreased over time in the nasopharynx, especially at d9. Although beta-diversity was not different between AUCT and RANC, interval after arrival and feedlot where heifers were placed affected composition of the nasopharyngeal bacterial communities. In both groups, a large increase in Mycoplasma was observed after arrival; in one group, Mycoplasma bovis was dominant at d9 and remained dominant until d30. However, in the other group, Mycoplasma dispar dominated at d9 and was replaced by Moraxella at d30. We concluded that transportation to and co-mingling at an auction market for 24 h did not significantly influence diversity or composition of nasopharyngeal or tracheal bacterial communities.}, }
@article {pmid30166168, year = {2018}, author = {Li, Z and Feng, C and Luo, X and Yao, H and Zhang, D and Zhang, T}, title = {Revealing the influence of microbiota on the quality of Pu-erh tea during fermentation process by shotgun metagenomic and metabolomic analysis.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {405-415}, doi = {10.1016/j.fm.2018.07.001}, pmid = {30166168}, issn = {1095-9998}, mesh = {Aspergillus/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Camellia sinensis/chemistry/*microbiology ; Fermentation ; Flavoring Agents/chemistry/metabolism ; Metabolomics ; Metagenomics ; *Microbiota ; Phenols/chemistry/metabolism ; Quality Control ; Tea/*chemistry/microbiology ; }, abstract = {Multispecies microbial community in natural solid-state fermentation (SSF) is crucial for the formation of Chinese Pu-erh tea's unique quality. However, the association between microbiota and tea quality are still poorly understood. Herein, shotgun metagenomic and metabolomic analysis showed that significant variations in composition of microbiota, collective functional genes, and flavour compounds occurred during SSF process. Furthermore, the formation pathways of the dominant flavours including theabrownin, methoxy-phenolic compound, alcohol and carvone were proposed. Moreover, biological interaction networks analysis among functional core microbiota, functional genes, and dominant flavours indicated Aspergillus was the main flavour-producing microorganism in the early SSF, while many other genera including Bacillus, Rasamsonia, Lichtheimia, Debaryomyces were determined as the functional core microorganism for flavours production in the late SSF. This study provides a perspective for bridging the gap between the microbiota and quality in Pu-erh tea, and benefited for further optimizing production efficiency and product quality.}, }
@article {pmid30166158, year = {2018}, author = {Bouju-Albert, A and Pilet, MF and Guillou, S}, title = {Influence of lactate and acetate removal on the microbiota of French fresh pork sausages.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {328-336}, doi = {10.1016/j.fm.2018.06.011}, pmid = {30166158}, issn = {1095-9998}, mesh = {Acetates/*pharmacology ; Animals ; Brochothrix/drug effects/genetics/isolation &amp; purification ; Colony Count, Microbial ; Food Microbiology/methods ; Food Packaging/methods ; Food Preservation/methods ; Food Preservatives/chemistry/*pharmacology ; Hydrogen-Ion Concentration ; Lactic Acid/*pharmacology ; Lactobacillus/drug effects/genetics/isolation &amp; purification ; Leuconostoc/drug effects/genetics/isolation &amp; purification ; Meat Products/analysis/*microbiology ; Metagenomics ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S ; Red Meat/*microbiology ; Swine ; Vacuum ; }, abstract = {The microbiota of fresh French pork sausages were characterised in five batches of comminuted pork meat that were equally divided into two formulations either containing the acid-based preservatives lactate and acetate, or no preservatives. Conventional microbiological analysis and high-throughput 16S rDNA amplicon sequencing methods were performed on meat batches packed under modified atmosphere (70% oxygen and 30% carbon dioxide) during chilled storage. In addition, meat pH and colour, and gas composition of the packages were monitored until the end of the shelf-life. During storage, the population of mesophilic and lactic acid bacteria increased from 4 log CFU/g to 8 log CFU/g after 15 days of chilled storage, both with and without preservatives. Despite similar changes of the physical and chemical parameters, such as pH and package gas composition, spoilage was delayed in the meat containing the preservatives, suggesting that lactate and acetate are effective against spoilage. Metagenetic analysis showed that at the end of the shelf-life, the species distribution differed between both the formulations and the batches. Lactic acid bacteria were shown to dominate both with and without preservatives; however, samples containing no preservatives were characterised by the presence of an increased population of Brochothrix spp. and Pseudomonas spp. whereas, Leuconostoc mesenteroides/pseudomesenteroides and Lactobacillus curvatus/graminis were more abundant in the meat with preservatives.}, }
@article {pmid30166157, year = {2018}, author = {Jung, MJ and Kim, MS and Yun, JH and Lee, JY and Kim, PS and Lee, HW and Ha, JH and Roh, SW and Bae, JW}, title = {Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {319-327}, doi = {10.1016/j.fm.2018.06.010}, pmid = {30166157}, issn = {1095-9998}, mesh = {Bacteria/genetics/isolation &amp; purification/virology ; Bacteriophages/genetics/isolation &amp; purification ; Brassica/microbiology ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Fermented Foods/*microbiology/*virology ; Food Microbiology ; Geography ; High-Throughput Nucleotide Sequencing ; Humans ; Lactobacillales/genetics/isolation &amp; purification/virology ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vegetables/*microbiology/*virology ; }, abstract = {Fermented foods are considered as an integral part of the global human diet. Fermented foods also have unique microbial communities such as bacteria, archaea, fungi, and viruses that are essential to the fermentation process and affect final product characteristics. Despite the ecological importance of virus, little is known about the diversity and ecological role of virus in the food ecosystem. In this study, the viral and host bacterial communities from 10 representative samples of Korean and Chinese kimchi were analyzed in triplicate using next-generation sequencing technology. The overall structures of bacterial and viral communities were dominated by lactic acid bacteria in phylum Firmicutes and bacteriophages in order Caudovirales, respectively. For the single-stranded DNA (ssDNA) viruses, bacteriophage in family Microviridae were dominant in Korean kimchi. After correction for multiple comparisons using false discovery rate (FDR, P < 0.05), the relative abundances of 6 bacterial taxa and 33 viral host taxa at the genus level were significantly different between Korean and Chinese kimchi. Notably, in beta-diversity analysis, viral communities were much more clearly separated according to their geographical origin (PERMANOVA pseudo-F = 11.57, P < 0.001 in Bray-Curtis PCoA) than bacterial communities (pseudo-F = 4.75, P < 0.001 in unweighted UniFrac PCoA). Thus, viral metagenomics represents a potentially useful in-depth analytical method for determining the geographical origins of fermented foods.}, }
@article {pmid30166151, year = {2018}, author = {Mataragas, M and Alessandria, V and Ferrocino, I and Rantsiou, K and Cocolin, L}, title = {A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {279-286}, doi = {10.1016/j.fm.2018.05.009}, pmid = {30166151}, issn = {1095-9998}, mesh = {Algorithms ; Cheese/microbiology ; *Computational Biology ; DNA, Ribosomal ; Food Microbiology/methods ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Microbial Consortia/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Sequence Analysis, DNA ; Software ; }, abstract = {The recent advances in molecular biology, such as the advent of next-generation sequencing (NGS) platforms, have paved the way to new exciting tools which rapidly transform food microbiology. Nowadays, NGS methods such as 16S rDNA/rRNA metagenomics or amplicon sequencing are used for the taxonomic profiling of the food microbial communities. Although 16S rDNA/rRNA NGS-based microbial data are not suited for the investigation of the functional potential of the identified operational taxonomic units as compared to shotgun metagenomics, advances in the bioinformatics discipline allow now the performance of such studies. In this paper, a bioinformatics workflow is described integrating predictive metagenomics profiling with specific application to food microbiology data. Bioinformatics tools pertinent to each sub-module of the pipeline are suggested as well. The published 16S rDNA/rRNA amplicon data originated from an Italian Grana-type cheese, using an NGS platform, was employed to demonstrate the predictive metagenomics profiling approach. The pipeline identified the microbial community and the changes that occurred in the microbial profile during manufacture of the food product studied (taxonomic profiling). The workflow also indicated significant changes in the functional profiling of the community. The tool may help to investigate the functional potential, alterations, and interactions of a microbial community. The proposed workflow may also find an application in the investigation of the ecology of foodborne pathogens encountered in various food products.}, }
@article {pmid30165813, year = {2018}, author = {Rotimi, AM and Pierneef, R and Reva, ON}, title = {Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {309}, pmid = {30165813}, issn = {1471-2105}, support = {93664//National Research Foundation/ ; }, mesh = {Algorithms ; Bacteria/*genetics ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; *Genes, Bacterial ; Genetic Markers ; Humans ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; ROC Curve ; Reproducibility of Results ; Sample Size ; *Software ; Species Specificity ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant level of genetic heterogeneity on the species level. It has become apparent that patterns of superior bioactivity of bacteria applicable in biotechnology as well as the enhanced virulence of pathogens often requires distinguishing between closely related species or sub-species. Current methods for binning of metagenomic reads usually do not allow for identification below the genus level and generally stops at the family level.<br><br>RESULTS: In this work, an attempt was made to improve metagenomic binning resolution by creating genome specific barcodes based on the core and accessory genomes. This protocol was implemented in novel software tools available for use and download from http://bargene.bi.up.ac.za /. The most abundant barcode genes from the core genomes were found to encode for ribosomal proteins, certain central metabolic genes and ABC transporters. Performance of metabarcode sequences created by this package was evaluated using artificially generated and publically available metagenomic datasets. Furthermore, a program (Barcoding 2.0) was developed to align reads against barcode sequences and thereafter calculate various parameters to score the alignments and the individual barcodes. Taxonomic units were identified in metagenomic samples by comparison of the calculated barcode scores to set cut-off values. In this study, it was found that varying sample sizes, i.e. number of reads in a metagenome and metabarcode lengths, had no significant effect on the sensitivity and specificity of the algorithm. Receiver operating characteristics (ROC) curves were calculated for different taxonomic groups based on the results of identification of the corresponding genomes in artificial metagenomic datasets. The reliability of distinguishing between species of the same genus or family by the program was nearly perfect.<br><br>CONCLUSIONS: The results showed that the novel online tool BarcodeGenerator (http://bargene.bi.up.ac.za /) is an efficient approach for generating barcode sequences from a set of complete genomes provided by users. Another program, Barcoder 2.0 is available from the same resource to enable an efficient and practical use of metabarcodes for visualization of the distribution of organisms of interest in environmental and clinical samples.}, }
@article {pmid30158489, year = {2018}, author = {Garcia, R and La Clair, JJ and Müller, R}, title = {Future Directions of Marine Myxobacterial Natural Product Discovery Inferred from Metagenomics.}, journal = {Marine drugs}, volume = {16}, number = {9}, pages = {}, pmid = {30158489}, issn = {1660-3397}, support = {German Center for Infection Research//Deutsches Zentrum für Infektionsforschung/ ; X//Xenobe Research Institute/ ; }, mesh = {Aquatic Organisms/*genetics/metabolism ; Biodiversity ; Biological Products/metabolism/*pharmacology ; DNA, Bacterial/genetics ; *Metagenomics ; Myxococcales/*genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Salt Tolerance/genetics ; Sequence Analysis, DNA ; }, abstract = {Over the last two decades, halophilic (organisms that thrive at high salt concentrations) and halotolerant (organisms that have adapted to high salt concentrations) myxobacteria emerged as an important source of structurally diverse secondary metabolites from the marine environment. This review explores the advance of metagenomics analysis and 16S rRNA gene phylogeny of the cultured and uncultured myxobacteria from marine and other salt-environments up to July 2018. The diversity of novel groups of myxobacteria in these environments appears unprecedented, especially in the Sorangiineae and Nannocystineae suborders. The Sandaracinaceae related clade in the Sorangiineae suborder seems more widely distributed compared to the exclusively marine myxobacterial cluster. Some of the previously identified clones from metagenomic studies were found to be related to the Nannocystineae suborder. This understanding provides the foundation for a vital, unexplored resource. Understanding the conditions required to cultivate these yet &quot;uncultured&quot; myxobacteria in the laboratory, while a key next step, offers a significant potential to further expand access to diverse secondary metabolites.}, }
@article {pmid30155977, year = {2018}, author = {Bálint, M and Nowak, C and Márton, O and Pauls, SU and Wittwer, C and Aramayo, JL and Schulze, A and Chambert, T and Cocchiararo, B and Jansen, M}, title = {Accuracy, limitations and cost efficiency of eDNA-based community survey in tropical frogs.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1415-1426}, doi = {10.1111/1755-0998.12934}, pmid = {30155977}, issn = {1755-0998}, support = {//USGS Amphibian Research and Monitoring Initiative/ ; //Globetrotter/ ; //Erika and Walter Datz-Stiftung/ ; LOEWE - Landes-Offensive zur Entwicklung Wissens//Hessisches Ministerium für Wissenschaft und Kunst/ ; //Ministry of Higher Education/ ; }, mesh = {Amphibians/*classification/*genetics ; Animals ; *Biota ; Bolivia ; Costs and Cost Analysis ; DNA Barcoding, Taxonomic/economics/*methods ; Metagenomics/economics/*methods ; Tropical Climate ; }, abstract = {Rapid environmental change in highly biodiverse tropical regions demands efficient biomonitoring programmes. While existing metrics of species diversity and community composition rely on encounter-based survey data, eDNA recently emerged as alternative approach. Costs and ecological value of eDNA-based methods have rarely been evaluated in tropical regions, where high species richness is accompanied by high functional diversity (e.g., the use of different microhabitats by different species and life stages). We first tested whether estimation of tropical frogs' community structure derived from eDNA data is compatible with expert field assessments. Next, we evaluated whether eDNA is a financially viable solution for biodiversity monitoring in tropical regions. We applied eDNA metabarcoding to investigate frog species occurrence in five ponds in the Chiquitano dry forest region in Bolivia and compared our data with a simultaneous visual and audio encounter survey (VAES). We found that taxon lists and community structure generated with eDNA and VAES correspond closely, and most deviations are attributable to different species' life histories. Cost efficiency of eDNA surveys was mostly influenced by the richness of local fauna and the number of surveyed sites: VAES may be less costly in low-diversity regions, but eDNA quickly becomes more cost-efficient in high-diversity regions with many sites sampled. The results highlight that eDNA is suitable for large-scale biodiversity surveys in high-diversity areas if life history is considered, and certain precautions in sampling, genetic analyses and data interpretation are taken. We anticipate that spatially extensive, standardized eDNA biodiversity surveys will quickly emerge in the future.}, }
@article {pmid30153857, year = {2018}, author = {Ugarte, A and Vicedomini, R and Bernardes, J and Carbone, A}, title = {A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {149}, pmid = {30153857}, issn = {2049-2618}, mesh = {Algorithms ; Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Proteins/*chemistry/*genetics/metabolism ; Databases, Genetic ; Environmental Microbiology ; Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/*methods ; Molecular Sequence Annotation/*methods ; Protein Domains ; }, abstract = {BACKGROUND: Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism and one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires the reconstruction of biochemical and regulatory pathways at the community level in a given environment. In order to understand how environmental factors affect the genetic material and the dynamics of the expression from one environment to another, we want to evaluate the quantity of gene protein sequences or transcripts associated to a given pathway by precisely estimating the abundance of protein domains, their weak presence or absence in environmental samples.<br><br>RESULTS: MetaCLADE is a novel profile-based domain annotation pipeline based on a multi-source domain annotation strategy. It applies directly to reads and improves identification of the catalog of functions in microbiomes. MetaCLADE is applied to simulated data and to more than ten metagenomic and metatranscriptomic datasets from different environments where it outperforms InterProScan in the number of annotated domains. It is compared to the state-of-the-art non-profile-based and profile-based methods, UProC and HMM-GRASPx, showing complementary predictions to UProC. A combination of MetaCLADE and UProC improves even further the functional annotation of environmental samples.<br><br>CONCLUSIONS: Learning about the functional activity of environmental microbial communities is a crucial step to understand microbial interactions and large-scale environmental impact. MetaCLADE has been explicitly designed for metagenomic and metatranscriptomic data and allows for the discovery of patterns in divergent sequences, thanks to its multi-source strategy. MetaCLADE highly improves current domain annotation methods and reaches a fine degree of accuracy in annotation of very different environments such as soil and marine ecosystems, ancient metagenomes and human tissues.}, }
@article {pmid30149004, year = {2018}, author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS}, title = {Intestinal fluke Metagonimus yokogawai infection increases probiotic Lactobacillus in mouse cecum.}, journal = {Experimental parasitology}, volume = {193}, number = {}, pages = {45-50}, doi = {10.1016/j.exppara.2018.08.002}, pmid = {30149004}, issn = {1090-2449}, mesh = {Animals ; Bacteria/classification/growth &amp; development ; Cecum/*microbiology ; Fish Diseases/parasitology ; Gastrointestinal Microbiome ; Heterophyidae/*physiology ; *Lactobacillus ; Mice ; Mice, Inbred ICR ; Osmeriformes/parasitology ; *Probiotics ; Trematode Infections/*microbiology ; }, abstract = {Helminth infection can alleviate immune-mediated disorders such as allergies and autoimmune diseases, by altering the gut microbiome. However, changes in gut microbiome due to intestinal trematodes remain unelucidated. Here, we evaluated the changes in the gut microbiome of ICR mice infected with Metagonimus yokogawai, a hypo-virulent intestinal trematode. Four weeks after infection, mouse cecal content was analyzed by 16S rRNA amplicon analysis. Although there was no apparent difference in species richness and diversity, the microbiome composition was different in the infected and control groups. Furthermore, several Lactobacillus species with known immunomodulatory role in immune-mediated diseases were increased in the infected group.}, }
@article {pmid30143202, year = {2018}, author = {Shikata, A and Sermsathanaswadi, J and Thianheng, P and Baramee, S and Tachaapaikoon, C and Waeonukul, R and Pason, P and Ratanakhanokchai, K and Kosugi, A}, title = {Characterization of an Anaerobic, Thermophilic, Alkaliphilic, High Lignocellulosic Biomass-Degrading Bacterial Community, ISHI-3, Isolated from Biocompost.}, journal = {Enzyme and microbial technology}, volume = {118}, number = {}, pages = {66-75}, doi = {10.1016/j.enzmictec.2018.07.001}, pmid = {30143202}, issn = {1879-0909}, mesh = {Alkalies/chemistry ; Animals ; Bacteria, Anaerobic/growth &amp; development ; *Biomass ; Cattle ; *Composting ; Lignin/*metabolism ; Metagenome ; *Microbial Consortia ; Oryza/*metabolism/microbiology ; Phylogeny ; Temperature ; Zea mays/*metabolism/microbiology ; }, abstract = {The generation of a complex microbial consortium is a promising approach for efficient biomass decomposition. An anaerobic thermophilic alkaliphilic microbial consortium with efficient degradation ability was screened from bovine manure compost using non-pretreated milling corn stover (CS) and rice straw (RS). A stable microbial consortium ISHI-3 with high degradation ability for CS and RS was isolated by the roll tube technique. ISHI-3 comprised Herbivorax saccincola and bacteria belonging to the classes Pelotomaculum, Tepidanaerobacter, and Tepidimicrobium, as determined by DGGE of the PCR-generated 16S rRNA genes. Furthermore, metagenomics analysis using a 16S rRNA library was carried out to determine the bacterial distribution during degradation of CS and RS. H. saccincola and bacteria belonging to Pelotomaculum were relatively abundant in the beginning to middle periods of culture with CS and RS whereas bacteria belonging to Tepidanaerobacter and Tepidimicrobium gradually increased in the population during the later stages. To understand the role of non-cellulolytic bacteria in the consortium, novel strains ET1 and GL4, which were most closely related to Tepidimicrobium ferriphilum and Tepidanaerobacter acetatoxydans, were isolated from ISHI-3. Based on their carbon source usage, morphology, and phylogenetic analysis, we propose that strains ET1 and GL4 should be classified as a novel genus or species. Bacteria ET1 and GL4 can utilize different organic compounds as carbon and energy sources such as organic acids, alcohols, sugars, and amino acids, showing a preference for organic acids and alcohols rather than sugars such as glucose and cellobiose. These results indicated that ET1 and GL4 help to accelerate efficient lignocellulose degradation of H. saccincola.}, }
@article {pmid30143055, year = {2018}, author = {Chiarello, M and Auguet, JC and Bettarel, Y and Bouvier, C and Claverie, T and Graham, NAJ and Rieuvilleneuve, F and Sucré, E and Bouvier, T and Villéger, S}, title = {Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {147}, pmid = {30143055}, issn = {2049-2618}, mesh = {Animal Feed ; Animals ; Bacteria/*classification/genetics ; Biodiversity ; Coral Reefs ; Fishes/classification/*microbiology ; Humans ; Metagenomics/*methods ; Microbiota ; Phylogeny ; Plankton/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Skin/microbiology ; Species Specificity ; }, abstract = {BACKGROUND: The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host. While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area.<br><br>RESULTS: Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits.<br><br>CONCLUSIONS: These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.}, }
@article {pmid30141128, year = {2019}, author = {Li, H and Mishra, M and Ding, S and Miyamoto, MM}, title = {Diversity and Dynamics of &quot;Candidatus Endobugula&quot; and Other Symbiotic Bacteria in Chinese Populations of the Bryozoan, Bugula neritina.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {243-256}, doi = {10.1007/s00248-018-1233-x}, pmid = {30141128}, issn = {1432-184X}, support = {201205024-2//Public Welfare Project of the State Oceanic Administration/ ; 2013FY110700//National Basic Research Foundation of China/ ; }, mesh = {Animals ; Biodiversity ; Bryostatins/metabolism ; Bryozoa/growth &amp; development/*microbiology ; China ; DNA, Bacterial/isolation &amp; purification ; Ecology ; Gammaproteobacteria/*classification/genetics/*isolation &amp; purification/*metabolism ; Geography ; Larva/microbiology ; Life Cycle Stages ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Bugula neritina is a common invasive cosmopolitan bryozoan that harbors (like many sessile marine invertebrates) a symbiotic bacterial (SB) community. Among the SB of B. neritina, &quot;Candidatus Endobugula sertula&quot; continues to receive the greatest attention, because it is the source of bryostatins. The bryostatins are potent bioactive polyketides, which have been investigated for their therapeutic potential to treat various cancers, Alzheimer's disease, and AIDS. In this study, we compare the metagenomics sequences for the 16S ribosomal RNA gene of the SB communities from different geographic and life cycle samples of Chinese B. neritina. Using a variety of approaches for estimating alpha/beta diversity and taxonomic abundance, we find that the SB communities vary geographically with invertebrate and fish mariculture and with latitude and environmental temperature. During the B. neritina life cycle, we find that the diversity and taxonomic abundances of the SB communities change with the onset of host metamorphosis, filter feeding, colony formation, reproduction, and increased bryostatin production. &quot;Ca. Endobugula sertula&quot; is confirmed as the symbiont of the Chinese &quot;Ca. Endobugula&quot;/B. neritina symbiosis. Our study extends our knowledge about B. neritina symbiosis from the New to the Old World and offers new insights into the environmental and life cycle factors that can influence its SB communities, &quot;Ca. Endobugula,&quot; and bryostatins more globally.}, }
@article {pmid30138419, year = {2018}, author = {Oliveira, JL and Cury, JC and Gurgel-Gonçalves, R and Bahia, AC and Monteiro, FA}, title = {Field-collected Triatoma sordida from central Brazil display high microbiota diversity that varies with regard to developmental stage and intestinal segmentation.}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {8}, pages = {e0006709}, pmid = {30138419}, issn = {1935-2735}, mesh = {Animals ; Bacteria/*classification ; Brazil ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Male ; Nymph ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Triatoma/growth &amp; development/*microbiology ; }, abstract = {BACKGROUND/METHODOLOGY: Triatomine bugs are the vectors of Trypanosoma cruzi, the agent of Chagas disease. Vector control has for decades relied upon insecticide spraying, but insecticide resistance has recently emerged in several triatomine populations. One alternative strategy to reduce T. cruzi transmission is paratransgenesis, whereby symbiotic bacteria are genetically engineered to produce T. cruzi-killing proteins in the vector's gut. This approach requires in-depth knowledge of the vectors' natural gut microbiota. Here, we use metagenomics (16S rRNA 454 pyrosequencing) to describe the gut microbiota of field-caught Triatoma sordida-likely the most common peridomestic triatomine in Brazil. For large nymphs (4th and 5th stage) and adults, we also studied separately the three main digestive-tract segments-anterior midgut, posterior midgut, and hindgut.<br><br>PRINCIPAL FINDINGS: Bacteria of four phyla (12 genera) were present in both nymphs (all five stages) and adults, thus defining T. sordida's 'bacterial core': Actinobacteria (Brevibacterium, Corynebacterium, Dietzia, Gordonia, Nitriliruptor, Nocardia, Nocardiopsis, Rhodococcus, and Williamsia), Proteobacteria (Pseudomonas and Sphingobium), and Firmicutes (Staphylococcus). We found some clear differences in bacterial composition and relative abundance among development stages; overall, Firmicutes and Proteobacteria increased, but Actinobacteria decreased, through development. Finally, the bacterial microbiotas of the bugs' anterior midgut, posterior midgut, and hindgut were sharply distinct.<br><br>CONCLUSIONS/SIGNIFICANCE: Our results identify the 'bacterial core set' of T. sordida and reveal important gut microbiota differences among development stages-particularly between 1st-3rd stage nymphs and adults. Further, we show that, within any given development stage, the vectors' gut cannot be regarded as a single homogeneous environment. Cultivable, non-pathogenic 'core' bacterial species may now be tested as candidates for paratransgenic control of T. cruzi transmission by T. sordida.}, }
@article {pmid30138339, year = {2018}, author = {Whitfield-Cargile, CM and Chamoun-Emanuelli, AM and Cohen, ND and Richardson, LM and Ajami, NJ and Dockery, HJ}, title = {Differential effects of selective and non-selective cyclooxygenase inhibitors on fecal microbiota in adult horses.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0202527}, pmid = {30138339}, issn = {1932-6203}, mesh = {4-Butyrolactone/administration &amp; dosage/adverse effects/analogs &amp; derivatives ; Adult ; Animals ; Anti-Inflammatory Agents, Non-Steroidal/*administration &amp; dosage/adverse effects ; Cyclooxygenase 2/genetics ; Cyclooxygenase 2 Inhibitors/*administration &amp; dosage/adverse effects ; Feces/microbiology ; Horses/microbiology ; Humans ; Metagenome/drug effects ; Microbiota/*drug effects ; Phenylbutazone/administration &amp; dosage/adverse effects ; RNA, Ribosomal, 16S/*genetics ; Sulfones/administration &amp; dosage/adverse effects ; }, abstract = {Non-steroidal anti-inflammatory drugs (NSAIDs) are routinely used in both veterinary and human medicine. Gastrointestinal injury is a frequent adverse event associated with NSAID use and evidence suggests that NSAIDs induce gastrointestinal microbial imbalance (i.e., dysbiosis) in both animals and people. It is unknown, however, whether cyclooxygenase (COX)-2-selective NSAIDs induce dysbiosis, or if this phenomenon occurs in horses administered any class of NSAIDs. Therefore, our objectives were to determine whether the composition and diversity of the fecal microbiota of adult horses were altered by NSAID use, and whether these effects differed between non-selective and COX-2-selective NSAIDs. Twenty-five adult horses were randomly assigned to 1 of 3 groups: control (n = 5); phenylbutazone (n = 10); or, firocoxib (n = 10). Treatments were administered for 10 days. Fecal samples were collected every 5 days for 25 days. DNA was extracted from feces and the 16S rRNA gene amplified and sequenced to determine the composition of the microbiota and the inferred metagenome. While the fecal microbiota profile of the control group remained stable over time, the phenylbutazone and firocoxib groups had decreased diversity, and alteration of their microbiota profiles was most pronounced at day 10. Similarly, there were clear alterations of the inferred metagenome at day 10 compared to all other days, indicating that use of both non-selective and selective COX inhibitors resulted in temporary alterations of the fecal microbiota and inferred metagenome. Dysbiosis associated with NSAID administration is clinically relevant because dysbiosis has been associated with several important diseases of horses including abdominal pain (colic), colitis, enteric infections, and laminitis.}, }
@article {pmid30137571, year = {2019}, author = {Chen, WL and Tang, SGH and Jahromi, MF and Candyrine, SCL and Idrus, Z and Abdullah, N and Liang, JB}, title = {Metagenomics analysis reveals significant modulation of cecal microbiota of broilers fed palm kernel expeller diets.}, journal = {Poultry science}, volume = {98}, number = {1}, pages = {56-68}, doi = {10.3382/ps/pey366}, pmid = {30137571}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Arecaceae/chemistry ; Cecum/*microbiology ; Chickens/*microbiology ; Diet/veterinary ; Firmicutes/isolation &amp; purification ; Gastrointestinal Microbiome/*drug effects/genetics ; Lactobacillus/isolation &amp; purification ; Male ; *Metagenome ; Oligosaccharides/pharmacology ; RNA, Ribosomal, 16S ; }, abstract = {The potential use of palm kernel expeller (PKE) as an alternative energy source in broiler diets is limited by the high fiber content. Although enzymatic treatment could alleviate the fiber component and increase the nutritive value of PKE, this apparent improvement is not reflected in the growth response of birds fed with the treated-PKE. As chicken's ceca are the most heavily populated with microflora within their gastrointestinal tract, it was hypothesized that any modulation of the intestinal environment by dietary treatments should be reflected by the composition and activities of the cecal microflora. There is a correlation between cecal microbiota composition and the efficiency of the host to extract energy from the diet and to deposit that energy into improved feed conversion ratio. At present, little is known about the changes on cecal microflora of broilers fed with PKE diets. Hence, this study was designed to assess the effects of feeding different forms of PKE; namely untreated PKE (UPKE), enzyme-treated PKE (EPKE), and oligosaccharides extracted from PKE (OligoPKE), on the cecal microbiota of broiler chickens at 14 d old (day 14) and 28 d old (day 28) using 16S rRNA gene high-throughput next-generation sequencing method. The results showed that temporal changes in cecal microbiota of broiler chickens were evident on day 14 and day 28. The relative abundance of phylum Firmicutes, known to be involved in nutrient uptake and absorption in both age groups was higher in the UPKE as compared to EPKE group. In addition, supplementation of OligoPKE increased (P < 0.05) the relative abundance of Lactobacillus on both D14 and D28, signifying its effect as prebiotics in enhancing growth of indigenous Lactobacillus. Our results showed that cecal microbiota was significantly modulated by dietary treatments and that the lower relative abundance of phylum Firmicutes in chickens fed with EPKE could be a reason why broiler chickens fed with EPKE of higher metabolizable energy (ME) content did not show improvement in their growth performance.}, }
@article {pmid30134786, year = {2018}, author = {Denning, NL and Prince, JM}, title = {Neonatal intestinal dysbiosis in necrotizing enterocolitis.}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {24}, number = {1}, pages = {4}, pmid = {30134786}, issn = {1528-3658}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; *Dysbiosis/chemically induced ; *Enterocolitis, Necrotizing/immunology/microbiology ; *Gastrointestinal Microbiome ; Histamine H2 Antagonists/therapeutic use ; Humans ; Infant, Newborn ; Toll-Like Receptors/immunology ; }, abstract = {Necrotizing Enterocolitis (NEC) is one of the most devastating gastrointestinal diseases in neonates, particularly among preterm infants in whom surgical NEC is the leading cause of morbidity. NEC pathophysiology occurs in the hyper-reactive milieu of the premature gut after bacterial colonization. The resultant activation of the TLR4 pathway appears to be a strongly contributing factor. Advancements in metagenomics may yield new clarity to the relationship between the neonatal intestinal microbiome and the development of NEC. After a century without effective directed treatments, microbiome manipulation offers a promising therapeutic target for the prevention and treatment of this devastating disease.}, }
@article {pmid30131068, year = {2018}, author = {Jiao, S and Chen, W and Wang, J and Du, N and Li, Q and Wei, G}, title = {Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {146}, pmid = {30131068}, issn = {2049-2618}, mesh = {Archaea/*classification/genetics/isolation &amp; purification/metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Biodiversity ; Fungi/*classification/genetics/isolation &amp; purification/metabolism ; Metagenomics ; Nutrients/metabolism ; Phylogeny ; Plant Roots/microbiology ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; Trees/*growth &amp; development/microbiology ; }, abstract = {BACKGROUND: Soil microbiomes play an important role in the services and functioning of terrestrial ecosystems. However, little is known of their vertical responses to restoration process and their contributions to soil nutrient cycling in the subsurface profiles. Here, we investigated the community assembly of soil bacteria, archaea, and fungi along vertical (i.e., soil depths of 0-300 cm) and horizontal (i.e., distance from trees of 30-90 cm) profiles in a chronosequence of reforestation sites that represent over 30 years of restoration.<br><br>RESULTS: In the superficial layers (0-80 cm), bacterial and fungal diversity decreased, whereas archaeal diversity increased with increasing soil depth. As reforestation proceeded over time, the vertical spatial variation in bacterial communities decreased, while that in archaeal and fungal communities increased. Vertical distributions of the soil microbiomes were more related to the variation in soil properties, while their horizontal distributions may be driven by a gradient effect of roots extending from the tree. Bacterial and archaeal beta-diversity were strongly related to multi-nutrient cycling in the soil, respectively, playing major roles in deep and superficial layers.<br><br>CONCLUSIONS: Taken together, these results reveal a new perspective on the vertical and horizontal spatial variation in soil microbiomes at the fine scale of single trees. Distinct response patterns underpinned the contributions of soil bacteria, archaea, and fungi as a function of subsurface nutrient cycling during the reforestation of ex-arable land.}, }
@article {pmid30129704, year = {2018}, author = {Macher, JN and Vivancos, A and Piggott, JJ and Centeno, FC and Matthaei, CD and Leese, F}, title = {Comparison of environmental DNA and bulk-sample metabarcoding using highly degenerate cytochrome c oxidase I primers.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1456-1468}, doi = {10.1111/1755-0998.12940}, pmid = {30129704}, issn = {1755-0998}, mesh = {Aquatic Organisms/classification/*genetics ; DNA/chemistry/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; Electron Transport Complex IV/*genetics ; *Fresh Water ; Metagenomics/*methods ; New Zealand ; Rivers ; }, abstract = {Freshwater biodiversity provides important ecosystem services and is at the core of water quality monitoring worldwide. To assess freshwater biodiversity, genetic methods such as metabarcoding are increasingly used as they are faster and allow better taxonomic resolution than manual identification methods. Either sampled organisms are used directly for &quot;bulk metabarcoding,&quot; or water is filtered and the extracted environmental DNA serves as a proxy for biodiversity via &quot;eDNA metabarcoding.&quot; Despite the advantages of both methods, questions remain regarding their comparability and applicability for routine biomonitoring and stressor impact assessment. Therefore, we compared metabarcoding results from bulk and eDNA samples taken from 19 streams spanning a wide gradient of farming intensities in New Zealand. We performed PCR with highly degenerate cytochrome c oxidase I primers and sequenced libraries on an Illumina MiSeq. The inferred community composition differed strongly between the two methods. More taxa were captured by eDNA than bulk-sample metabarcoding (5,819 vs. 1,483), but more of the commonly used invertebrate bioindicator taxa (mayflies, stoneflies and caddisflies) were found in bulk (47) than eDNA samples (37). Catchment-wide and local land use impacts on communities were detected better by eDNA metabarcoding, especially for non-metazoan taxa. Our findings imply that bulk-sample metabarcoding resembles classical freshwater biomonitoring approaches better, as more indicator macroinvertebrate taxa are captured. However, eDNA metabarcoding might be better suited to infer the impact of stressors on stream ecosystems at larger scales, as many new and potentially more informative taxa are registered. We therefore suggest exploring both methods in future assessments of stream biodiversity.}, }
@article {pmid30128756, year = {2018}, author = {Mukhtar, S and Mirza, BS and Mehnaz, S and Mirza, MS and Mclean, J and Malik, KA}, title = {Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {34}, number = {9}, pages = {136}, pmid = {30128756}, issn = {1573-0972}, support = {Project # HEC (FD/2012/1843)//Higher Education Commission, Pakistan/ ; Project # 5-9/PAS/2012/969//Pakistan Academy of Sciences/ ; }, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Bacterial ; Ecosystem ; Metagenomics ; Microbiota/genetics/*physiology ; Pakistan ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Salinity ; Salt-Tolerant Plants/classification/*microbiology ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The rhizosphere microbiome plays a significant role in the life of plants in promoting plant survival under adverse conditions. However, limited information is available about microbial diversity in saline environments. In the current study, we compared the composition of the rhizosphere microbiomes of the halophytes Urochloa, Kochia, Salsola, and Atriplex living in moderate and high salinity environments (Khewra salt mines; Pakistan) with that of the non-halophyte Triticum. Soil microbiomes analysis using pyrosequencing of 16S rRNA gene indicated that Actinobacteria were dominant in saline soil samples whereas Proteobacteria predominated in non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes and Thaumarchaeota were predominant phyla in saline and non-saline soils, whereas Cyanobacteria, Verrucomicrobia, Gemmatimonadetes and the unclassified WPS-2 were less abundant. Sequences from Euryarchaeota, Ignavibacteriae, and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes gp4, Halalkalicoccus, Haloferula and Halobacterium. Our analysis showed that increases in soil salinity correlated with significant differences in the alpha and beta diversity of the microbial communities across saline and non-saline soil samples. Having a complete inventory of the soil bacteria from different saline environments in Pakistan will help in the discovery of potential inoculants for crops growing on salt-affected land.}, }
@article {pmid30126456, year = {2018}, author = {Milani, C and Casey, E and Lugli, GA and Moore, R and Kaczorowska, J and Feehily, C and Mangifesta, M and Mancabelli, L and Duranti, S and Turroni, F and Bottacini, F and Mahony, J and Cotter, PD and McAuliffe, FM and van Sinderen, D and Ventura, M}, title = {Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {145}, pmid = {30126456}, issn = {2049-2618}, mesh = {Bacteriophages/*classification/genetics/isolation &amp; purification ; Computational Biology/*methods/standards ; Feces/*virology ; Female ; Gastrointestinal Microbiome ; Genotype ; Humans ; Infant, Newborn ; Male ; Metagenomics/*methods/standards ; Mothers ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {BACKGROUND: Despite the relevance of viral populations, our knowledge of (bacterio) phage populations, i.e., the phageome, suffers from the absence of a &quot;gold standard&quot; protocol for viral DNA extraction with associated in silico sequence processing analyses. To overcome this apparent hiatus, we present here a comprehensive performance evaluation of various protocols and propose an optimized pipeline that covers DNA extraction, sequencing, and bioinformatic analysis of phageome data.<br><br>RESULTS: Five widely used protocols for viral DNA extraction from fecal samples were tested for their performance in removal of non-viral DNA. Moreover, we developed a novel bioinformatic platform, METAnnotatorX, for metagenomic dataset analysis. This in silico tool facilitates a range of read- and assembly-based analyses, including taxonomic profiling using an iterative multi-database pipeline, classification of contigs at genus and species level, as well as functional characterizations of reads and assembled data. Performances of METAnnotatorX were assessed through investigation of seven mother-newborn pairs, leading to the identification of shared phage genotypes, of which two were genomically decoded and characterized. METAnnotatorX was furthermore employed to evaluate a protocol for the identification of contaminant non-viral DNA in sequenced datasets and was exploited to determine the amount of metagenomic data needed for robust evaluation of human adult-derived (fecal) phageomes.<br><br>CONCLUSIONS: Results obtained in this study demonstrate that a comprehensive pipeline for analysis of phageomes will be pivotal for future explorations of the ecology of phages in the gut environment as well as for understanding their impact on the physiology and bacterial community kinetics as players of dysbiosis and homeostasis in the gut microbiota.}, }
@article {pmid30124863, year = {2018}, author = {McGrath, C}, title = {Up in the Air: The Emerging Science of Dust and Sandstorm Microbes.}, journal = {Genome biology and evolution}, volume = {10}, number = {8}, pages = {2008-2009}, pmid = {30124863}, issn = {1759-6653}, mesh = {*Dust ; Health ; Humans ; Metagenomics ; *Microbiota ; Soil Microbiology ; }, }
@article {pmid30123190, year = {2018}, author = {Roscini, L and Tristezza, M and Corte, L and Colabella, C and Perrotta, C and Rampino, P and Robert, V and Vu, D and Cardinali, G and Grieco, F}, title = {Early Ongoing Speciation of Ogataea uvarum Sp. Nov. Within the Grape Ecosystem Revealed by the Internal Variability Among the rDNA Operon Repeats.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1687}, pmid = {30123190}, issn = {1664-302X}, abstract = {A yeast strain was isolated during a study on vineyard-associated yeast strains from Apulia in Southern Italy. ITS and LSU D1/D2 rDNA sequences showed this strain not to belong to any known species and was described as the type strain of Ogataea uvarum sp. nov., a close relative of O. philodendri. Several secondary peaks appeared in the sequences, suggesting internal heterogeneity among the copies of the rDNA. This hypothesis was tested by sequencing single clones of the marker region. The analyses showed different levels of variability throughout the operon with differences between the rRNA encoding genes and the internally transcribed regions. O. uvarum and O. philodendri share high frequency variants, i.e., variants frequently found in many clones, whereas there is a large variability of the low frequency polymorphisms, suggesting that the mechanism of homogenization is more active with the former than with the latter type of variation. These findings indicate that low frequency variants are detected in Sanger sequencing as secondary peaks whereas in Next Generation Sequencing (NGS) of metagenomics DNA would lead to an overestimate of the alpha diversity. For the first time in our knowledge, this investigation shed light on the variation of the copy number of the rDNA cistron during the yeast speciation process. These polymorphisms can be used to investigate on the processes occurring in these taxonomic markers during the separation of fungal species, it being a genetic process highly frequent in the complex microbial ecosystem existing in grape, must and wine.}, }
@article {pmid30122883, year = {2018}, author = {Zhao, Y and Mao, YF and Tang, YS and Ni, MZ and Liu, QH and Wang, Y and Feng, Q and Peng, JH and Hu, YY}, title = {Altered oral microbiota in chronic hepatitis B patients with different tongue coatings.}, journal = {World journal of gastroenterology}, volume = {24}, number = {30}, pages = {3448-3461}, pmid = {30122883}, issn = {2219-2840}, mesh = {Adult ; Bacteria/genetics/*isolation &amp; purification/metabolism ; Case-Control Studies ; DNA, Viral/isolation &amp; purification ; Female ; Gastrointestinal Microbiome/*physiology ; Healthy Volunteers ; Hepatitis B virus/genetics/*isolation &amp; purification ; Hepatitis B, Chronic/diagnosis/metabolism/*microbiology ; Humans ; Male ; Medicine, Chinese Traditional/methods ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Tongue/*microbiology ; }, abstract = {AIM: To elucidate tongue coating microbiota and metabolic differences in chronic hepatitis B (CHB) patients with yellow or white tongue coatings.<br><br>METHODS: Tongue coating samples were collected from 53 CHB patients (28 CHB yellow tongue coating patients and 25 CHB white tongue coating patients) and 22 healthy controls. Microbial DNA was extracted from the tongue samples, and the bacterial 16S ribosomal RNA gene V3 region was amplified from all samples and sequenced with the Ion Torrent PGM™ sequencing platform according to the standard protocols. The metabolites in the tongue coatings were evaluated using a liquid chromatography-mass spectrometry (LC-MS) platform. Statistical analyses were then performed.<br><br>RESULTS: The relative compositions of the tongue coating microbiotas and metabolites in the CHB patients were significantly different from those of the healthy controls, but the tongue coating microbiota abundances and diversity levels were not significantly different. Compared with the CHB white tongue coating patients, the CHB yellow tongue coating patients had higher hepatitis B viral DNA (HBV-DNA) titers (median 21210 vs 500, respectively, P = 0.03) and a significantly lower level of Bacteroidetes (20.14% vs 27.93%, respectively, P = 0.013) and higher level of Proteobacteria (25.99% vs 18.17%, respectively, P = 0.045) in the microbial compositions at the phylum level. The inferred metagenomic pathways enriched in the CHB yellow tongue coating patients were mainly those involved in amino acid metabolism, which was consistent with the metabolic disorder. The abundances of bacteria from Bacteroidales at the order level were higher in the CHB white tongue coating patients (19.2% vs 27.22%, respectively, P = 0.011), whereas Neisseriales were enriched in the yellow tongue coating patients (21.85% vs 13.83%, respectively, P = 0.029). At the family level, the abundance of Neisseriaceae in the yellow tongue patients was positively correlated with the HBV-DNA level but negatively correlated with the S-adenosyl-L-methionine level.<br><br>CONCLUSION: This research illustrates specific clinical features and bacterial structures in CHB patients with different tongue coatings, which facilitates understanding of the traditional tongue diagnosis.}, }
@article {pmid30121535, year = {2019}, author = {Bedoya, K and Coltell, O and Cabarcas, F and Alzate, JF}, title = {Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia.}, journal = {The Science of the total environment}, volume = {648}, number = {}, pages = {572-581}, doi = {10.1016/j.scitotenv.2018.08.119}, pmid = {30121535}, issn = {1879-1026}, mesh = {Colombia ; *Metagenome ; Methane/*biosynthesis ; *Microbiota/genetics ; Solid Waste/*analysis ; *Waste Disposal, Fluid ; Waste Water/*microbiology ; }, abstract = {Abundance and diversity of microbial communities in biosolids are variable and poorly studied in the tropics, and it is known that rainfall is one of the events that could affect the phylogenetic and functional microbial structure. In the present study, using NGS technics, we studied the microbial diversity as well as the methanogenesis pathway in one of the largest WWTP in Colombia. Besides, we sampled and analyzed biosolids from rainy season and dry season. Phylogenetic classification showed a predominance of bacteria in both samples and difference in the dominant groups depending on the rainfall season. Whereas Pseudomonas was the dominant bacteria in the dry season, Coprothermobacter was in the rainy season. Archaea abundance was higher in the rainy season (11.5%) doubling dry season proportion. The bioreactor biogas production and total solids content showed similar results between rainy and dry season at the sampling dates. The most abundant Archaea related with methanogenesis was Methanosaeta, which is a methanogenic microorganism that exclusively uses acetate to produce methane. Moreover, annotation of the methanogenic pathway in the metagenome showed abundance in genes encoding Acetyl-CoA synthetases (ACSS), an enzyme that catalyzes acetate activation. Our results suggest that the microbial diversity was stable among the two time points tested, rainy season and dry season; and, although there were changes in the microbial abundance of dominant bacterial species, anaerobic digester performance is not affected.}, }
@article {pmid30110928, year = {2018}, author = {Wu, L and Wang, J and Wu, H and Chen, J and Xiao, Z and Qin, X and Zhang, Z and Lin, W}, title = {Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture.}, journal = {International journal of molecular sciences}, volume = {19}, number = {8}, pages = {}, pmid = {30110928}, issn = {1422-0067}, mesh = {*Bacteria/classification/genetics/growth &amp; development ; *Metagenome ; Microbial Consortia/*physiology ; Rehmannia/*microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Consecutive monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive monoculture. The results showed R. glutinosa monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive monoculture.}, }
@article {pmid30106226, year = {2018}, author = {Heeger, F and Bourne, EC and Baschien, C and Yurkov, A and Bunk, B and Spröer, C and Overmann, J and Mazzoni, CJ and Monaghan, MT}, title = {Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1500-1514}, doi = {10.1111/1755-0998.12937}, pmid = {30106226}, issn = {1755-0998}, support = {SAW-2014-IGB-1//Leibniz Association/ ; }, mesh = {Aquatic Organisms/classification/genetics ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/*genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Fungal/*genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {DNA metabarcoding is widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints limit most studies to marker lengths below 600 base pairs (bp). Longer sequencing reads of several thousand bp are now possible with third-generation sequencing. Increased marker lengths provide greater taxonomic resolution and allow for phylogenetic methods of classification, but longer reads may be subject to higher rates of sequencing error and chimera formation. In addition, most bioinformatics tools for DNA metabarcoding were designed for short reads and are therefore unsuitable. Here, we used Pacific Biosciences circular consensus sequencing (CCS) to DNA-metabarcode environmental samples using a ca. 4,500 bp marker that included most of the eukaryote SSU and LSU rRNA genes and the complete ITS region. We developed an analysis pipeline that reduced error rates to levels comparable to short-read platforms. Validation using a mock community indicated that our pipeline detected 98% of chimeras de novo. We recovered 947 OTUs from water and sediment samples from a natural lake, 848 of which could be classified to phylum, 397 to genus and 330 to species. By allowing for the simultaneous use of three databases (Unite, SILVA and RDP LSU), long-read DNA metabarcoding provided better taxonomic resolution than any single marker. We foresee the use of long reads enabling the cross-validation of reference sequences and the synthesis of ribosomal rRNA gene databases. The universal nature of the rRNA operon and our recovery of >100 nonfungal OTUs indicate that long-read DNA metabarcoding holds promise for studies of eukaryotic diversity more broadly.}, }
@article {pmid30102711, year = {2018}, author = {Watanabe, K and Igarashi, M and Li, X and Nakatani, A and Miyamoto, J and Inaba, Y and Sutou, A and Saito, T and Sato, T and Tachibana, N and Inoue, H and Kimura, I}, title = {Dietary soybean protein ameliorates high-fat diet-induced obesity by modifying the gut microbiota-dependent biotransformation of bile acids.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0202083}, pmid = {30102711}, issn = {1932-6203}, mesh = {Animals ; Bile Acids and Salts/*metabolism ; Biodiversity ; Diet, High-Fat/adverse effects ; Dietary Supplements ; Gastrointestinal Microbiome/*drug effects ; Glucagon-Like Peptide 1/metabolism ; Intestinal Mucosa/drug effects/metabolism/microbiology ; Male ; Metabolic Networks and Pathways/*drug effects ; Metagenome ; Metagenomics/methods ; Mice ; Obesity/*etiology/*metabolism ; Soybean Proteins/*pharmacology ; }, abstract = {The consumption of soybean protein has well-known favorable metabolic effects (e.g., reduced body weight, body fat, hyperglycemia, insulin resistance, hepatic steatosis, and lipogenesis). These effects of soy protein have been linked to modulation by the gut microbiota; however, the dynamic interplay among these factors remains unclear. Accordingly, we examined the metabolic phenotype, intestinal BA pool, and the gut microbiome of male C57BL/6 mice that were randomized to receive either a regular high-fat diet (HFD) or HFD that contained soybean protein isolate (SPI) in place of dairy protein. The intake of SPI significantly reduced the HFD-induced weight gain and adipose tissue mass accumulation and attenuated hepatic steatosis. Along with an enhancement in the secretion of intestinal Glucagon-like peptide-1 (GLP-1), an enlarged cecal BA pool with an elevated secondary/primary BA ratio was observed in the mice that consumed SPI, while fecal BA excretion remained unaltered. SPI also elicited dramatic changes in the gut microbiome, characterized by an expansion of taxa that may be involved in the biotransformation of BAs. The observed effects were abolished in germ-free (GF) mice, indicating that they were dependent on the microbiota. These findings collectively indicate that the metabolic benefits of SPI under the HFD regime may arise from a microbiota-driven increase in BA transformation and increase in GLP-1 secretion.}, }
@article {pmid30092815, year = {2018}, author = {Murali, A and Bhargava, A and Wright, ES}, title = {IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {140}, pmid = {30092815}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Machine Learning ; Metagenomics/*methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Software ; }, abstract = {BACKGROUND: Microbiome studies often involve sequencing a marker gene to identify the microorganisms in samples of interest. Sequence classification is a critical component of this process, whereby sequences are assigned to a reference taxonomy containing known sequence representatives of many microbial groups. Previous studies have shown that existing classification programs often assign sequences to reference groups even if they belong to novel taxonomic groups that are absent from the reference taxonomy. This high rate of &quot;over classification&quot; is particularly detrimental in microbiome studies because reference taxonomies are far from comprehensive.<br><br>RESULTS: Here, we introduce IDTAXA, a novel approach to taxonomic classification that employs principles from machine learning to reduce over classification errors. Using multiple reference taxonomies, we demonstrate that IDTAXA has higher accuracy than popular classifiers such as BLAST, MAPSeq, QIIME, SINTAX, SPINGO, and the RDP Classifier. Similarly, IDTAXA yields far fewer over classifications on Illumina mock microbial community data when the expected taxa are absent from the training set. Furthermore, IDTAXA offers many practical advantages over other classifiers, such as maintaining low error rates across varying input sequence lengths and withholding classifications from input sequences composed of random nucleotides or repeats.<br><br>CONCLUSIONS: IDTAXA's classifications may lead to different conclusions in microbiome studies because of the substantially reduced number of taxa that are incorrectly identified through over classification. Although misclassification error is relatively minor, we believe that many remaining misclassifications are likely caused by errors in the reference taxonomy. We describe how IDTAXA is able to identify many putative mislabeling errors in reference taxonomies, enabling training sets to be automatically corrected by eliminating spurious sequences. IDTAXA is part of the DECIPHER package for the R programming language, available through the Bioconductor repository or accessible online (http://DECIPHER.codes).}, }
@article {pmid30091981, year = {2018}, author = {Bradley, PH and Nayfach, S and Pollard, KS}, title = {Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.}, journal = {PLoS computational biology}, volume = {14}, number = {8}, pages = {e1006242}, pmid = {30091981}, issn = {1553-7358}, support = {T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Gastrointestinal Microbiome/*genetics/physiology ; Gene Expression Regulation, Bacterial/genetics ; Genes, Microbial/genetics ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; }, abstract = {The mechanisms by which different microbes colonize the healthy human gut versus other body sites, the gut in disease states, or other environments remain largely unknown. Identifying microbial genes influencing fitness in the gut could lead to new ways to engineer probiotics or disrupt pathogenesis. We approach this problem by measuring the statistical association between a species having a gene and the probability that the species is present in the gut microbiome. The challenge is that closely related species tend to be jointly present or absent in the microbiome and also share many genes, only a subset of which are involved in gut adaptation. We show that this phylogenetic correlation indeed leads to many false discoveries and propose phylogenetic linear regression as a powerful solution. To apply this method across the bacterial tree of life, where most species have not been experimentally phenotyped, we use metagenomes from hundreds of people to quantify each species' prevalence in and specificity for the gut microbiome. This analysis reveals thousands of genes potentially involved in adaptation to the gut across species, including many novel candidates as well as processes known to contribute to fitness of gut bacteria, such as acid tolerance in Bacteroidetes and sporulation in Firmicutes. We also find microbial genes associated with a preference for the gut over other body sites, which are significantly enriched for genes linked to fitness in an in vivo competition experiment. Finally, we identify gene families associated with higher prevalence in patients with Crohn's disease, including Proteobacterial genes involved in conjugation and fimbria regulation, processes previously linked to inflammation. These gene targets may represent new avenues for modulating host colonization and disease. Our strategy of combining metagenomics with phylogenetic modeling is general and can be used to identify genes associated with adaptation to any environment.}, }
@article {pmid30086347, year = {2018}, author = {Miró-Abella, E and Torrell, H and Herrero, P and Canela, N and Arola, L and Borrull, F and Ras, R and Fontanals, N}, title = {Monitoring and evaluation of the interaction between deoxynivalenol and gut microbiota in Wistar rats by mass spectrometry-based metabolomics and next-generation sequencing.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {121}, number = {}, pages = {124-130}, doi = {10.1016/j.fct.2018.08.006}, pmid = {30086347}, issn = {1873-6351}, mesh = {Animals ; Chromatography, High Pressure Liquid/methods ; Feces/chemistry ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing/*methods ; Metabolomics/*methods ; Metagenomics ; Mycotoxins/analysis/*toxicity ; No-Observed-Adverse-Effect Level ; RNA, Ribosomal, 16S/metabolism ; Rats ; Rats, Wistar ; Tandem Mass Spectrometry/*methods ; Trichothecenes/analysis/*toxicity ; }, abstract = {Published evidence has demonstrated the several toxic characteristics of mycotoxins and their considerable risk to human and animal health. One of the most common uncertainties regards whether if very low concentrations of the mycotoxin deoxynivalenol (DON), easily consumed within the Mediterranean Diet, can cause metabolic alterations; some of them produced by the interaction between DON and gut microbiota. Accordingly, faecal samples were collected from Wistar rats that had consumed the mycotoxin DON at low levels (60 and 120 μg kg-1 body weight of DON per day), and were analysed by ultra-high performance liquid chromatography coupled with tandem mass spectrometry detection, in order to monitor the mycotoxin DON and its metabolite de-epoxy deoxynivalenol (DOM-1). The obtained results showed an evolution in DON excretion and the metabolite DOM-1 which has less toxic properties, over the course of the days of the study. To elucidate whether intestinal microbiota had a role in the observed detoxification process, the changes in microbial gut biodiversity were explored through 16s rRNA high throughput sequencing. No main changes were detected but significant increase in Coprococcus genus relative abundance was found. Further studies are needed to confirm if intestinal microbiota composition and function are affected by low mycotoxin concentrations.}, }
@article {pmid30081953, year = {2018}, author = {Zhu, J and Liao, M and Yao, Z and Liang, W and Li, Q and Liu, J and Yang, H and Ji, Y and Wei, W and Tan, A and Liang, S and Chen, Y and Lin, H and Zhu, X and Huang, S and Tian, J and Tang, R and Wang, Q and Mo, Z}, title = {Breast cancer in postmenopausal women is associated with an altered gut metagenome.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {136}, pmid = {30081953}, issn = {2049-2618}, mesh = {Adult ; Bacteria/*classification/genetics ; Bacterial Proteins/genetics ; Breast Neoplasms/metabolism/*microbiology ; C-Reactive Protein/metabolism ; Case-Control Studies ; Estradiol/metabolism ; Female ; *Gastrointestinal Microbiome ; Gene Regulatory Networks ; Humans ; Metagenomics/*methods ; Middle Aged ; Phylogeny ; Postmenopause/metabolism ; Premenopause/metabolism ; }, abstract = {BACKGROUND: Increasing evidence suggests that gut microbiota play a role in the pathogenesis of breast cancer. The composition and functional capacity of gut microbiota associated with breast cancer have not been studied systematically.<br><br>METHODS: We performed a comprehensive shotgun metagenomic analysis of 18 premenopausal breast cancer patients, 25 premenopausal healthy controls, 44 postmenopausal breast cancer patients, and 46 postmenopausal healthy controls.<br><br>RESULTS: Microbial diversity was higher in breast cancer patients than in controls. Relative species abundance in gut microbiota did not differ significantly between premenopausal breast cancer patients and premenopausal controls. In contrast, relative abundance of 45 species differed significantly between postmenopausal patients and postmenopausal controls: 38 species were enriched in postmenopausal patients, including Escherichia coli, Klebsiella sp_1_1_55, Prevotella amnii, Enterococcus gallinarum, Actinomyces sp. HPA0247, Shewanella putrefaciens, and Erwinia amylovora, and 7 species were less abundant in postmenopausal patients, including Eubacterium eligens and Lactobacillus vaginalis. Acinetobacter radioresistens and Enterococcus gallinarum were positively but weakly associated with expression of high-sensitivity C-reactive protein; Shewanella putrefaciens and Erwinia amylovora were positively but weakly associated with estradiol levels. Actinomyces sp. HPA0247 negatively but weakly correlated with CD3+CD8+ T cell numbers. Further characterization of metagenome functional capacity indicated that the gut metagenomes of postmenopausal breast cancer patients were enriched in genes encoding lipopolysaccharide biosynthesis, iron complex transport system, PTS system, secretion system, and beta-oxidation.<br><br>CONCLUSION: The composition and functions of the gut microbial community differ between postmenopausal breast cancer patients and healthy controls. The gut microbiota may regulate or respond to host immunity and metabolic balance. Thus, while cause and effect cannot be determined, there is a reproducible change in the microbiota of treatment-naive patients relative to matched controls.}, }
@article {pmid30077182, year = {2018}, author = {Ye, Z and Zhang, N and Wu, C and Zhang, X and Wang, Q and Huang, X and Du, L and Cao, Q and Tang, J and Zhou, C and Hou, S and He, Y and Xu, Q and Xiong, X and Kijlstra, A and Qin, N and Yang, P}, title = {A metagenomic study of the gut microbiome in Behcet's disease.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {135}, pmid = {30077182}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Capsules/genetics ; Behcet Syndrome/*microbiology ; Case-Control Studies ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Humans ; Male ; Metagenomics/*methods ; Mice ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Saliva/microbiology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Behcet's disease (BD) is a recalcitrant, multisystemic inflammatory disease that can lead to irreversible blindness. Microbial agents have been considered to contribute to the pathogenesis of this disease, but the underlying mechanisms remain unclear. In this study, we investigated the association of gut microbiome composition with BD as well as its possible roles in the development of this disease.<br><br>METHODS: Fecal and saliva samples were collected from 32 active BD patients and 74 healthy controls. DNA extracted from fecal samples was subjected to metagenomic analysis, whereas DNA extracted from saliva samples was subjected to 16S rRNA gene sequencing analysis. The results were used to compare the composition and biological function of the microbiome between patients and healthy controls. Lastly, transplantation of pooled fecal samples from active BD patients into B10RIII mice undergoing experimental autoimmune uveitis (EAU) was performed to determine the causal relationship between the gut microbiome and BD.<br><br>RESULTS: Fecal samples from active BD patients were shown to be enriched in Bilophila spp., a sulfate-reducing bacteria (SRB) and several opportunistic pathogens (e.g., Parabacteroides spp. and Paraprevotella spp.) along with a lower level of butyrate-producing bacteria (BPB) Clostridium spp. and methanogens (Methanoculleus spp. Methanomethylophilus spp.). Analysis of microbial functions revealed that capsular polysaccharide transport system, oxidation-reduction process, type III, and type IV secretion systems were also increased in active BD patients. Network analysis showed that the BD-enriched SRB and opportunistic pathogens were positively correlated with each other, but they were negatively associated with the BPB and methanogens. Animal experiments revealed that fecal microbiota transplantation with feces from BD patients significantly exacerbated EAU activity and increased the production of inflammatory cytokines including IL-17 and IFN-γ.<br><br>CONCLUSIONS: Our findings revealed that BD is associated with considerable gut microbiome changes, which is corroborated by a mouse study of fecal microbiota transplants. A model explaining the association of the gut microbiome composition with BD pathogenesis is proposed.}, }
@article {pmid30072968, year = {2018}, author = {Dittberner, H and Ohlmann, N and Acquisti, C}, title = {Stoichio-Metagenomics of Ocean Waters: A Molecular Evolution Approach to Trace the Dynamics of Nitrogen Conservation in Natural Communities.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1590}, pmid = {30072968}, issn = {1664-302X}, abstract = {Nitrogen is crucially limiting in ocean surface waters, and its availability varies substantially with coastal regions typically richer in nutrients than open oceans. In a biological stoichiometry framework, a parsimonious strategy of nitrogen allocation predicts nitrogen content of proteins to be lower in communities adapted to open ocean than to coastal regions. To test this hypothesis we have directly interrogated marine microbial communities, using a series of metagenomics datasets with a broad geographical distribution from the Global Ocean Sampling Expedition. Analyzing over 20 million proteins, we document a ubiquitous signal of nitrogen conservation in open ocean communities, both in membrane and non-membrane proteins. Efficient nitrogen allocation is expected to specifically target proteins that are expressed at high rate in response to nitrogen starvation. Furthermore, in order to preserve protein functional efficiency, economic nitrogen allocation is predicted to target primarily the least functionally constrained regions of proteins. Contrasting the NtcA-induced pathway, typically up-regulated in response to nitrogen starvation, with the arginine anabolic pathway, which is instead up-regulated in response to nitrogen abundance, we show how both these predictions are fulfilled. Using evolutionary rates as an informative proxy of functional constraints, we show that variation in nitrogen allocation between open ocean and coastal communities is primarily localized in the least functionally constrained regions of the genes triggered by NtcA. As expected, such a pattern is not detectable in the genes involved in the arginine anabolic pathway. These results directly link environmental nitrogen availability to different adaptive strategies of genome evolution, and emphasize the relevance of the material costs of evolutionary change in natural ecosystems.}, }
@article {pmid30069051, year = {2018}, author = {Bahram, M and Hildebrand, F and Forslund, SK and Anderson, JL and Soudzilovskaia, NA and Bodegom, PM and Bengtsson-Palme, J and Anslan, S and Coelho, LP and Harend, H and Huerta-Cepas, J and Medema, MH and Maltz, MR and Mundra, S and Olsson, PA and Pent, M and Põlme, S and Sunagawa, S and Ryberg, M and Tedersoo, L and Bork, P}, title = {Structure and function of the global topsoil microbiome.}, journal = {Nature}, volume = {560}, number = {7717}, pages = {233-237}, doi = {10.1038/s41586-018-0386-6}, pmid = {30069051}, issn = {1476-4687}, abstract = {Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.}, }
@article {pmid30055354, year = {2018}, author = {Linard, B and Crampton-Platt, A and Moriniere, J and Timmermans, MJTN and Andújar, C and Arribas, P and Miller, KE and Lipecki, J and Favreau, E and Hunter, A and Gómez-Rodríguez, C and Barton, C and Nie, R and Gillett, CPDT and Breeschoten, T and Bocak, L and Vogler, AP}, title = {The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera.}, journal = {Molecular phylogenetics and evolution}, volume = {128}, number = {}, pages = {1-11}, doi = {10.1016/j.ympev.2018.07.008}, pmid = {30055354}, issn = {1095-9513}, abstract = {A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.}, }
@article {pmid30048915, year = {2018}, author = {Milanović, V and Osimani, A and Garofalo, C and De Filippis, F and Ercolini, D and Cardinali, F and Taccari, M and Aquilanti, L and Clementi, F}, title = {Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE.}, journal = {International journal of food microbiology}, volume = {286}, number = {}, pages = {66-74}, doi = {10.1016/j.ijfoodmicro.2018.07.022}, pmid = {30048915}, issn = {1879-3460}, mesh = {Acetic Acid/*analysis ; Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; Fermentation ; Metagenomics ; Microbiota/genetics ; Molecular Typing ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Wine/*microbiology ; }, abstract = {The production of traditional vinegar is usually carried out using the so-called &quot;seed vinegar&quot; or &quot;mother of vinegar&quot; that is composed of an undefined and complex pool of microorganisms deriving from a previous vinegar production. To date, there have been relatively few studies on the microbiota of seed vinegars. The present study was carried out to discover the bacterial biota of seed vinegar samples used in the homemade production of local vinegars obtained from the acetic fermentation of white wine. The seed vinegar samples were subjected to viable counting and advanced molecular analyses, namely, Illumina sequencing and PCR-DGGE. The adopted polyphasic approach allowed the bacterial diversity of the analyzed samples to be profiled, thus revealing the presence of acetic acid bacteria ascribed to the genera Acetobacter, Gluconacetobacter, Gluconobacter and Komagataeibacter. Moreover, other microbial genera as Pseudomonas, Bacillus and Clostridium were abundantly found in almost all the samples, together with other minority genera. The results of viable counting confirmed the well-acknowledged limitations inherent with acetic acid bacteria recovery on plate growth media. The overall results confirmed that seed vinegars have a complex and heterogeneous biodiversity, thus encouraging their exploitation for the isolation and future technological characterization of cultures to be selected for the manufacture of mixed starter cultures.}, }
@article {pmid30041354, year = {2018}, author = {Tiralerdpanich, P and Sonthiphand, P and Luepromchai, E and Pinyakong, O and Pokethitiyook, P}, title = {Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis.}, journal = {Marine pollution bulletin}, volume = {133}, number = {}, pages = {595-605}, doi = {10.1016/j.marpolbul.2018.06.015}, pmid = {30041354}, issn = {1879-3363}, mesh = {Alkanes/*metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Gasoline ; Geologic Sediments/*microbiology ; Metagenomics/methods ; Microbial Consortia/genetics/*physiology ; Phenanthrenes/*metabolism ; RNA, Ribosomal, 16S/metabolism ; Thailand ; Wetlands ; }, abstract = {Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg-1 sediment day-1, respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.}, }
@article {pmid30036363, year = {2018}, author = {Chai, H and Jiang, H and Lin, L and Liu, L}, title = {A marginalized two-part Beta regression model for microbiome compositional data.}, journal = {PLoS computational biology}, volume = {14}, number = {7}, pages = {e1006329}, pmid = {30036363}, issn = {1553-7358}, mesh = {Animals ; Colony Count, Microbial ; Likelihood Functions ; *Logistic Models ; Metagenomics ; Mice ; *Microbiota ; Skin/*microbiology ; }, abstract = {In microbiome studies, an important goal is to detect differential abundance of microbes across clinical conditions and treatment options. However, the microbiome compositional data (quantified by relative abundance) are highly skewed, bounded in [0, 1), and often have many zeros. A two-part model is commonly used to separate zeros and positive values explicitly by two submodels: a logistic model for the probability of a specie being present in Part I, and a Beta regression model for the relative abundance conditional on the presence of the specie in Part II. However, the regression coefficients in Part II cannot provide a marginal (unconditional) interpretation of covariate effects on the microbial abundance, which is of great interest in many applications. In this paper, we propose a marginalized two-part Beta regression model which captures the zero-inflation and skewness of microbiome data and also allows investigators to examine covariate effects on the marginal (unconditional) mean. We demonstrate its practical performance using simulation studies and apply the model to a real metagenomic dataset on mouse skin microbiota. We find that under the proposed marginalized model, without loss in power, the likelihood ratio test performs better in controlling the type I error than those under conventional methods.}, }
@article {pmid30033973, year = {2018}, author = {Choi, HJ and Jeong, TY and Yoon, H and Oh, BY and Han, YS and Hur, MJ and Kang, S and Kim, JG}, title = {Comparative microbial communities in tidal flats sediment on Incheon, South Korea.}, journal = {The Journal of general and applied microbiology}, volume = {64}, number = {5}, pages = {232-239}, doi = {10.2323/jgam.2017.12.007}, pmid = {30033973}, issn = {1349-8037}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; *Environmental Microbiology ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Republic of Korea ; Seawater/microbiology ; }, abstract = {Coastal ecosystems, play critical ecological roles of which tidal flats are a significant component of coastal wetlands, such as habitat and nutrient cycling in aquatic biology. Microbial communities in tidal flats are known to play vital roles of self-purification. And the microbial ecology of the sediment is easily affected by human activities and pollution. In this paper, we applied pyrosequencing technology to investigate microbial communities in three different tidal flats (Ganghwa Island, Ongnyeon land region and Yeongjong Island) on the Incheon, Korea peninsula. A total of 16,906 sequences were obtained. We used these sequences to identify the dominant phyla in the three tidal flats: Proteobacteria, Chloroflexi, Actinobacteria, and Bacteroidetes. The composition of the bacterial community of Ganghwa Island and the Ongnyeon region were more similar to each other than they were to the bacterial community of Yeongjong Island. Simpson's dominance index of Yeongjong Island was higher than that of the other regions, and the Shannon diversity index of this region was the lowest. Previous research of samples in these regions indicated that the three tidal flats had similar geochemical characteristics. However, their bacterial communities were rather distinct. This might be because the analysis of microbial communities and physiochemical analysis have different perspectives. Therefore, the pyrosequencing of a bacterial community with physiochemical analysis is recommended as an effective monitoring tool for the comprehensive management of tidal flats.}, }
@article {pmid30033505, year = {2018}, author = {Edouard, S and Million, M and Bachar, D and Dubourg, G and Michelle, C and Ninove, L and Charrel, R and Raoult, D}, title = {The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {37}, number = {9}, pages = {1725-1733}, pmid = {30033505}, issn = {1435-4373}, support = {10-IAHU-03//IHU Méditerranée Infection/ ; }, mesh = {Acute Disease/epidemiology ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteria/genetics/isolation &amp; purification/*pathogenicity ; Case-Control Studies ; Child ; Child, Preschool ; Coinfection/microbiology/virology ; Disease Susceptibility/virology ; Female ; Haemophilus influenzae/genetics/isolation &amp; purification/pathogenicity ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics ; Microbiota/*genetics ; Middle Aged ; Nasopharynx/*microbiology/virology ; RNA, Ribosomal, 16S/genetics ; Respiratory Tract Infections/epidemiology/*microbiology/*virology ; Staphylococcus aureus/genetics/isolation &amp; purification/pathogenicity ; Streptococcus pneumoniae/genetics/isolation &amp; purification/pathogenicity ; Virus Diseases/*microbiology/virology ; Young Adult ; }, abstract = {The nasopharynx is the primary site of colonization by respiratory pathogen that constitutes the port of entrance in the respiratory tract. The role of mucosal respiratory microbiota in infection has been recently emphasized; therefore, we aimed to assess if a specific respiratory microbiota profile was associated with symptomatic infection and/or with presence of respiratory viruses. We performed a case-control study to characterize the healthy respiratory microbiota and its alteration during acute viral infections. Next-generation sequencing of the 16S rRNA gene was applied to 225 nasopharyngeal samples from 177 patients with viral respiratory infection and 48 matched healthy controls. We evidenced an important decrease of bacterial alpha-diversity in patients with symptomatic respiratory infection and a loss of the healthy core microbiota, specifically anaerobes and Prevotella spp. Moreover, eight respiratory pathogens were enriched in these patients, including Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, Dol osigranulum pigrum and Corynebacterium propinquum/pseudodiphtheriticum, whose role in respiratory infection is unclear. The asymptomatic carrier of influenza harbors a microbiota similar to healthy subjects, suggesting a critical role of microbiota in the clinical expression of viruses. These data suggest that the commensal microbiota plays a significant role in susceptibility to viral infection. The frequent co-detection of virus and bacteria raises the question of a strategy to prevent bacterial disease, focusing on the prevention of nasopharyngeal colonization through effective antibiotic treatment. In addition to antibiotics, further studies should test preventive or therapeutic interventions for maintaining or restoring a healthy nasopharyngeal microbiota.}, }
@article {pmid30021874, year = {2018}, author = {Glassman, SI and Martiny, JBH}, title = {Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units.}, journal = {mSphere}, volume = {3}, number = {4}, pages = {}, pmid = {30021874}, issn = {2379-5042}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Environmental Microbiology ; Fungi/*classification/*genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Recent discussion focuses on the best method for delineating microbial taxa, based on either exact sequence variants (ESVs) or traditional operational taxonomic units (OTUs) of marker gene sequences. We sought to test if the binning approach (ESVs versus 97% OTUs) affected the ecological conclusions of a large field study. The data set included sequences targeting all bacteria (16S rRNA) and fungi (internal transcribed spacer [ITS]), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all α and β diversity metrics were highly positively correlated (r > 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Furthermore, ESVs only moderately increased the genetic resolution of fungal and bacterial diversity (1.3 and 2.1 times OTU richness, respectively). We conclude that for broadscale (e.g., all bacteria or all fungi) α and β diversity analyses, ESV or OTU methods will often reveal similar ecological results. Thus, while there are good reasons to employ ESVs, we need not question the validity of results based on OTUs.IMPORTANCE Microbial ecologists have made exceptional improvements in our understanding of microbiomes in the last decade due to breakthroughs in sequencing technologies. These advances have wide-ranging implications for fields ranging from agriculture to human health. Due to limitations in databases, the majority of microbial ecology studies use a binning approach to approximate taxonomy based on DNA sequence similarity. There remains extensive debate on the best way to bin and approximate this taxonomy. Here we examine two popular approaches using a large field-based data set examining both bacteria and fungi and conclude that there are not major differences in the ecological outcomes. Thus, it appears that standard microbial community analyses are not overly sensitive to the particulars of binning approaches.}, }
@article {pmid30018874, year = {2018}, author = {Colabella, C and Corte, L and Roscini, L and Bassetti, M and Tascini, C and Mellor, JC and Meyer, W and Robert, V and Vu, D and Cardinali, G}, title = {NGS barcode sequencing in taxonomy and diagnostics, an application in &quot;Candida&quot; pathogenic yeasts with a metagenomic perspective.}, journal = {IMA fungus}, volume = {9}, number = {1}, pages = {91-105}, pmid = {30018874}, issn = {2210-6340}, abstract = {Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected.}, }
@article {pmid30017197, year = {2018}, author = {He, F and Liu, D and Zhai, J and Zhang, L and Ma, Y and Xu, Y and Rong, K and Ma, J}, title = {Metagenomic analysis revealed the effects of goat milk feeding and breast feeding on the gut microbiome of Amur tiger cubs.}, journal = {Biochemical and biophysical research communications}, volume = {503}, number = {4}, pages = {2590-2596}, doi = {10.1016/j.bbrc.2018.07.020}, pmid = {30017197}, issn = {1090-2104}, mesh = {Animals ; Animals, Newborn ; Bacteria/isolation &amp; purification ; Feeding Behavior ; *Gastrointestinal Microbiome ; *Goats/microbiology ; Metagenomics/*methods ; *Milk ; *Tigers/microbiology ; }, abstract = {BACKGROUND: Ingredients in breast milk can help establish a healthy community of microorganisms in the infant gut, but no research exists regarding the effects of goat milk feeding and breast feeding on the gut microbiome of the Amur tiger, which is one of the most endangered species in the world.<br><br>METHODS: In this study, we used whole-metagenome shotgun sequencing to analyze the effects of two different feeding patterns, goat milk feeding and breast feeding, on the composition and functional structures of gut microbiota in Amur tiger cubs.<br><br>RESULTS: Goat milk-fed cubs have fewer beneficial bacteria and more pathogenic bacteria and a higher microbial diversity in their gut than breastfed cubs. A total of 15 genera showed statistically significant differences; the relative abundances of Streptomyces scabiei, Streptomyces avermitilis and Streptomyces davawensis were significantly decreased, whereas those of Niabella soli, Aeromonas media and Brochothrix thermosphacta were significantly increased in the goat milk-fed group compared with those in the breastfed group. At the functional level, carbohydrate metabolism, translation and replication and repair decreased, and amino acid metabolism, membrane transport and metabolism of cofactors and vitamins increased in the gut microbiota of goat milk-fed cubs compared with breastfed cubs.<br><br>CONCLUSION: Our results indicate for the first time that the different milk feeding patterns of goat milk feeding and breast feeding can change the composition and functional structures of gut microbiota in Amur tiger cubs and that breastfed tiger cubs and goat milk-fed tiger cubs have distinct microbiotas in their guts.}, }
@article {pmid30014577, year = {2018}, author = {Cordier, T and Forster, D and Dufresne, Y and Martins, CIM and Stoeck, T and Pawlowski, J}, title = {Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1381-1391}, doi = {10.1111/1755-0998.12926}, pmid = {30014577}, issn = {1755-0998}, support = {316030_150817//Swiss Network for International Studies/ ; 31003A_179125//Swiss National Science Foundation/ ; STO414/15-1//Deutsche Forschungsgemeinschaft/ ; //Carl Zeiss Foundation/ ; //NVIDIA GPU grant program/ ; }, mesh = {Bacteria/*classification ; *Biodiversity ; Biomarkers/analysis ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring/*methods ; Eukaryota/*classification ; Metagenomics/*methods ; RNA, Ribosomal/genetics ; *Supervised Machine Learning ; }, abstract = {Biodiversity monitoring is the standard for environmental impact assessment of anthropogenic activities. Several recent studies showed that high-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) could overcome many limitations of the traditional morphotaxonomy-based bioassessment. Recently, we demonstrated that supervised machine learning (SML) can be used to predict accurate biotic indices values from eDNA metabarcoding data, regardless of the taxonomic affiliation of the sequences. However, it is unknown to which extent the accuracy of such models depends on taxonomic resolution of molecular markers or how SML compares with metabarcoding approaches targeting well-established bioindicator species. In this study, we address these issues by training predictive models upon five different ribosomal bacterial and eukaryotic markers and measuring their performance to assess the environmental impact of marine aquaculture on independent data sets. Our results show that all tested markers are yielding accurate predictive models and that they all outperform the assessment relying solely on taxonomically assigned sequences. Remarkably, we did not find any significant difference in the performance of the models built using universal eukaryotic or prokaryotic markers. Using any molecular marker with a taxonomic range broad enough to comprise different potential bioindicator taxa, SML approach can overcome the limits of taxonomy-based eDNA bioassessment.}, }
@article {pmid30003485, year = {2018}, author = {Li, M and Zhang, X and Yang, H and Li, X and Cui, Z}, title = {Soil sustainable utilization technology: mechanism of flavonols in resistance process of heavy metal.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {26}, pages = {26669-26681}, pmid = {30003485}, issn = {1614-7499}, abstract = {The soil ecosystem is critical for agricultural production, affecting many aspects of human health. Soil has more unknown biodiversity and edaphic parameters than any other ecosystem especially when polluted. Metagenomics and metatranscriptomics were applied to research on toxicological characteristics of Pb and resistance mechanism of flavonols. Rhizosphere microorganisms-plants system, a unified system closely related to soil environment was taken as research object. Results emphasize gene expression changes in different test groups. Gene ontology enrichment and eggNOG showed that Pb has a toxic effect on gene and protein function which concentrated on ATPase and ATP-dependent activity. Differentially expressed genes in the flavonols group indicated that flavonols regulate amino acid transport and other transportation process related to Pb stress. Kegg analysis represents that Pb interferences energy production process via not only the upstream like glycolysis and tricarboxylic acid (TCA) circle but also oxidative phosphorylation process, which can also produce reactive oxygen species and impact the eliminating process. Flavonols have shown the ability in alleviating toxic effect of Pb and improving the resistance of plants. Flavonols can recover the electronic transmission and other process in TCA and oxidative phosphorylation via ascorbic acid-glutathione metabolism. Flavonols activated antioxidative process and non-specific immunity via vitamins B2-B6 metabolism.}, }
@article {pmid30001517, year = {2018}, author = {Yassour, M and Jason, E and Hogstrom, LJ and Arthur, TD and Tripathi, S and Siljander, H and Selvenius, J and Oikarinen, S and Hyöty, H and Virtanen, SM and Ilonen, J and Ferretti, P and Pasolli, E and Tett, A and Asnicar, F and Segata, N and Vlamakis, H and Lander, ES and Huttenhower, C and Knip, M and Xavier, RJ}, title = {Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.}, journal = {Cell host &amp; microbe}, volume = {24}, number = {1}, pages = {146-154.e4}, pmid = {30001517}, issn = {1934-6069}, support = {DP3 DK094338/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Bacteroides/*genetics ; Cohort Studies ; DNA, Bacterial/*genetics ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Male ; Meconium/microbiology ; Metagenomics ; *Mother-Child Relations ; Prospective Studies ; }, abstract = {Bacterial community acquisition in the infant gut impacts immune education and disease susceptibility. We compared bacterial strains across and within families in a prospective birth cohort of 44 infants and their mothers, sampled longitudinally in the first months of each child's life. We identified mother-to-child bacterial transmission events and describe the incidence of family-specific antibiotic resistance genes. We observed two inheritance patterns across multiple species, where often the mother's dominant strain is transmitted to the child, but occasionally her secondary strains colonize the infant gut. In families where the secondary strain of B. uniformis was inherited, a starch utilization gene cluster that was absent in the mother's dominant strain was identified in the child, suggesting the selective advantage of a mother's secondary strain in the infant gut. Our findings reveal mother-to-child bacterial transmission events at high resolution and give insights into early colonization of the infant gut.}, }
@article {pmid30001516, year = {2018}, author = {Ferretti, P and Pasolli, E and Tett, A and Asnicar, F and Gorfer, V and Fedi, S and Armanini, F and Truong, DT and Manara, S and Zolfo, M and Beghini, F and Bertorelli, R and De Sanctis, V and Bariletti, I and Canto, R and Clementi, R and Cologna, M and Crifò, T and Cusumano, G and Gottardi, S and Innamorati, C and Masè, C and Postai, D and Savoi, D and Duranti, S and Lugli, GA and Mancabelli, L and Turroni, F and Ferrario, C and Milani, C and Mangifesta, M and Anzalone, R and Viappiani, A and Yassour, M and Vlamakis, H and Xavier, R and Collado, CM and Koren, O and Tateo, S and Soffiati, M and Pedrotti, A and Ventura, M and Huttenhower, C and Bork, P and Segata, N}, title = {Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.}, journal = {Cell host &amp; microbe}, volume = {24}, number = {1}, pages = {133-145.e5}, doi = {10.1016/j.chom.2018.06.005}, pmid = {30001516}, issn = {1934-6069}, support = {//European Research Council/International ; }, mesh = {Adult ; DNA, Bacterial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Longitudinal Studies ; Metagenomics ; Middle Aged ; *Mother-Child Relations ; Mouth/microbiology ; Skin/microbiology ; Time Factors ; Vagina/microbiology ; }, abstract = {The acquisition and development of the infant microbiome are key to establishing a healthy host-microbiome symbiosis. The maternal microbial reservoir is thought to play a crucial role in this process. However, the source and transmission routes of the infant pioneering microbes are poorly understood. To address this, we longitudinally sampled the microbiome of 25 mother-infant pairs across multiple body sites from birth up to 4 months postpartum. Strain-level metagenomic profiling showed a rapid influx of microbes at birth followed by strong selection during the first few days of life. Maternal skin and vaginal strains colonize only transiently, and the infant continues to acquire microbes from distinct maternal sources after birth. Maternal gut strains proved more persistent in the infant gut and ecologically better adapted than those acquired from other sources. Together, these data describe the mother-to-infant microbiome transmission routes that are integral in the development of the infant microbiome.}, }
@article {pmid29992707, year = {2018}, author = {Ostrensky, A and Horodesky, A and Faoro, H and Balsanelli, E and Sfeir, MZT and Cozer, N and Pie, MR and Dal Pont, G and Castilho-Westphal, GG}, title = {Metagenomic evaluation of the effects of storage conditions on the bacterial microbiota of oysters Crassostrea gasar (Adanson, 1757).}, journal = {Journal of applied microbiology}, volume = {125}, number = {5}, pages = {1435-1443}, doi = {10.1111/jam.14045}, pmid = {29992707}, issn = {1365-2672}, support = {//Serviço Brasileiro de Apoio às Micro e Pequenas Empresas - Sebrae/ ; }, mesh = {Animals ; Brazil ; Crassostrea/*microbiology ; Food Safety ; Food Storage/*methods ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Seafood ; Temperature ; }, abstract = {AIMS: To evaluate the influence of storage conditions on the composition of the bacterial microbiota of living oysters Crassostrea gasar.<br><br>METHODS AND RESULTS: The oysters used in this study came from marine farms (Guaratuba Bay, Brazil) and were exposed to two conditions that simulated different storage situations: immersion in water (group I) and exposure to air (group II). The animals were subjected to five different temperatures (5-25°C), for 10 days. The 16S rRNA gene from oysters was amplified and sequenced to determine the taxonomic units and bacterial strains present in the samples. Group I showed higher diversity of bacteria (163 genera) rather than group II (104 genera). In all, 59 bacterial genera potentially pathogenic to humans were identified (n = 56 in group I and n = 45 in group II).<br><br>CONCLUSIONS: The storage conditions having a direct influence on the oyster microbiota. Live C. gasar should be stored exposed to air at 5-25°C, because it favours a lower prevalence of bacteria potentially pathogenic to humans.<br><br>During the oyster commercialization process, some conditions of storage, time and temperature must be followed in order to reduce the prevalence of bacteria potentially pathogenic to humans.}, }
@article {pmid29991350, year = {2018}, author = {Haro-Moreno, JM and López-Pérez, M and de la Torre, JR and Picazo, A and Camacho, A and Rodriguez-Valera, F}, title = {Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {128}, pmid = {29991350}, issn = {2049-2618}, mesh = {Archaea/*classification/isolation &amp; purification ; Bacteria/*classification/isolation &amp; purification ; Mediterranean Sea ; Metagenomics/*methods ; Phylogeny ; Seasons ; Water Microbiology ; }, abstract = {BACKGROUND: The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment.<br><br>RESULTS: Our results showed significant differences in the microbial composition of different layers within the stratified photic water column. The majority of microorganisms were confined to discreet horizontal layers of no more than 30 m (stenobathic). Only a few such as members of the SAR11 clade appeared at all depths (eurybathic). During the winter mixing period, only some groups of bloomers such as Pseudomonas were favored. Although most microbes appeared in both seasons, some groups like the SAR116 clade and some Bacteroidetes and Verrucomicrobia seemed to disappear during the mixing period. Furthermore, we found that some microbes previously considered seasonal (e.g., Archaea or Actinobacteria) were living in deeper layers within the photic zone during the stratification period. A strong depth-related specialization was detected, not only at the taxonomic level but also at the functional level, even within the different clades, for the manipulation and uptake of specific polysaccharides. Rhodopsin sequences (green or blue) also showed narrow depth distributions that correlated with the taxonomy of the microbe in which they were found but not with depth.<br><br>CONCLUSIONS: Although limited to a single location in the Mediterranean, this study has profound implications for our understanding of how marine microbial communities vary with depth within the photic zone when stratified. Our results highlight the importance of collecting samples at different depths in the water column when comparing seasonal variations and have important ramifications for global marine studies that most often take samples from only one single depth. Furthermore, our perspective and approaches (metagenomic assembly and recruitment) are broadly applicable to other metagenomic studies.}, }
@article {pmid29988102, year = {2018}, author = {Sfanos, KS and Markowski, MC and Peiffer, LB and Ernst, SE and White, JR and Pienta, KJ and Antonarakis, ES and Ross, AE}, title = {Compositional differences in gastrointestinal microbiota in prostate cancer patients treated with androgen axis-targeted therapies.}, journal = {Prostate cancer and prostatic diseases}, volume = {21}, number = {4}, pages = {539-548}, pmid = {29988102}, issn = {1476-5608}, support = {16CHAL13//Prostate Cancer Foundation (PCF)/International ; 16CHAL13//Prostate Cancer Foundation (PCF)/International ; 16CHAL13//Prostate Cancer Foundation (PCF)/International ; W81XWH-13-PCRP-CCA//U.S. Department of Defense (DOD)/International ; }, mesh = {Aged ; Aged, 80 and over ; Androgen Antagonists/*pharmacology/therapeutic use ; Androgens/*metabolism ; Antineoplastic Agents, Hormonal/*pharmacology/therapeutic use ; Biodiversity ; Cross-Sectional Studies ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Molecular Targeted Therapy ; Prostatic Neoplasms/drug therapy/metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: It is well known that the gastrointestinal (GI) microbiota can influence the metabolism, pharmacokinetics, and toxicity of cancer therapies. Conversely, the effect of cancer treatments on the composition of the GI microbiota is poorly understood. We hypothesized that oral androgen receptor axis-targeted therapies (ATT), including bicalutamide, enzalutamide, and abiraterone acetate, may be associated with compositional differences in the GI microbiota.<br><br>METHODS: We profiled the fecal microbiota in a cross-sectional study of 30 patients that included healthy male volunteers and men with different clinical states of prostate cancer (i.e., localized, biochemically recurrent, and metastatic disease) using 16S rDNA amplicon sequencing. Functional inference of identified taxa was performed using PICRUSt.<br><br>RESULTS: We report a significant difference in alpha diversity in GI microbiota among men with versus without a prostate cancer diagnosis. Further analysis identified significant compositional differences in the GI microbiota of men taking ATT, including a greater abundance of species previously linked to response to anti-PD-1 immunotherapy such as Akkermansia muciniphila and Ruminococcaceae spp. In functional analyses, we found an enriched representation of bacterial gene pathways involved in steroid biosynthesis and steroid hormone biosynthesis in the fecal microbiota of men taking oral ATT.<br><br>CONCLUSIONS: There are measurable differences in the GI microbiota of men receiving oral ATT. We speculate that oral hormonal therapies for prostate cancer may alter the GI microbiota, influence clinical responses to ATT, and/or potentially modulate the antitumor effects of future therapies including immunotherapy. Given our findings, larger, longitudinal studies are warranted.}, }
@article {pmid29980232, year = {2018}, author = {Hani, J and Abdel Nour, G and Matta, J and Jazzar, B and Pfaffl, MW and Hanna-Wakim, L and Abdel Nour, AM}, title = {Shisha microbiota: the good, the bad and the not so ugly.}, journal = {BMC research notes}, volume = {11}, number = {1}, pages = {446}, pmid = {29980232}, issn = {1756-0500}, mesh = {Adult ; Bacteria/genetics/*isolation &amp; purification ; Equipment Contamination ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S ; Smoking ; Smoking Water Pipes/*microbiology ; Tobacco ; }, abstract = {OBJECTIVE: Over the last decade, there has been a rapid expansion of the trendy water pipe smoking around the world especially among younger adults. The initial objective of this study was to identify the microbiota of the shisha, which may either be of no harm for the smoker or enhance the threat on his well-being. The total DNA for the metagenomics study was conducted on three different shishas from three different delivery shops in Jounieh, Lebanon. The microbiota in two solid parts of the shisha, shaft and hose, were analysed including the fresh tobacco and the water in the bowl. All samples were analysed using high-throughput sequencing of 16S rRNA gene amplicons.<br><br>RESULTS: Overall, more than 40 bacterial genera were found in the three investigated shishas, some are commensal others are pathogenic. All three shishas showed similar microbial content regarding the bacteria inhabiting in water, shaft, or hose. From the results of this study it appears that a very large quantity of bacteria was found in the water pipes, some are harmful and others beneficial. We assume that the presence of gut dependent microbiota is related to the loose hygienic conditions in which the shisha is prepared.}, }
@article {pmid29979780, year = {2018}, author = {Segura-Wang, M and Görzer, I and Jaksch, P and Puchhammer-Stöckl, E}, title = {Temporal dynamics of the lung and plasma viromes in lung transplant recipients.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0200428}, pmid = {29979780}, issn = {1932-6203}, mesh = {Adult ; Biodiversity ; Bronchoalveolar Lavage Fluid/virology ; Female ; Follow-Up Studies ; Humans ; Lung/*virology ; *Lung Transplantation ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Phylogeny ; Plasma/*virology ; Retrospective Studies ; Time Factors ; Transplant Recipients ; Young Adult ; }, abstract = {The human virome plays an important role for the clinical outcome of lung transplant recipients (LTRs). While pathogenic viruses may cause severe infections, non-pathogenic viruses may serve as potential markers for the level of immunosuppression. However, neither the complexity of the virome in different compartments nor the dynamics of the virus populations posttransplantation are yet understood. Therefore, in this study the virome was analyzed by metagenomic sequencing in simultaneously withdrawn bronchoalveolar lavage (BAL) and plasma samples of 15 LTRs. In seven patients, also follow-up samples were investigated for abundance and dynamics of virus populations posttransplantation. Five eukaryotic and two prokaryotic virus families were identified in BAL, and nine eukaryotic and two prokaryotic families in plasma. Anelloviruses were the most abundant in both compartments, followed by Herpes- and Coronaviruses. Virus abundance was significantly higher in LTRs than in healthy controls (Kruskal-Wallis test, p<0.001). Up to 48 different anellovirus strains were identified within a single LTR. Analyses in the follow-up patients revealed for the first time a highly complex and unique dynamics of individual anellovirus strains in the posttransplantation period. The abundance of anelloviruses in plasma was inversely correlated with that of other eukaryotic viruses (Pearson correlation coefficient r = -0.605; p<0.05). A broad spectrum of virus strains co-exists in BAL and plasma of LTRs. Especially for the anelloviruses, a high degree of co-infections and a highly individual and complex dynamics after transplantation was observed. The biological impact of these findings and their relation to clinical variables remain to be elucidated by future analyses.}, }
@article {pmid29978606, year = {2018}, author = {Xiong, W and Zhan, A}, title = {Testing clustering strategies for metabarcoding-based investigation of community-environment interactions.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1326-1338}, doi = {10.1111/1755-0998.12922}, pmid = {29978606}, issn = {1755-0998}, support = {31572228//National Natural Science Foundation of China/ ; ZDRW-ZS-2016-5-6//The Key Research Program of the Chinese Academy of Sciences/ ; 2015//The Innovation in Cross-functional Team Program of the Chinese Academy of Sciences/ ; 2015ZX07201-008-09//Water Pollution Control and Treatment Special Project/ ; 15K01ESPCR//The State Key Joint Laboratory of Environment Simulation and Pollution Control (RCEES, Chinese Academy of Sciences)/ ; 2017M620927//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; China ; *Cluster Analysis ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; *Environmental Exposure ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Rivers ; Water Pollutants/toxicity ; Zooplankton/drug effects ; }, abstract = {The degradation of freshwater ecosystems has become a common ecological and environmental problem globally. Owing to the complexity of biological communities, there remain tremendous technical challenges for investigating influence of environmental stressors (e.g., chemical pollution) on biological communities. High-throughput sequencing-based metabarcoding provides a powerful tool to reveal complex interactions between environments and biological communities. Among many technical issues, the clustering strategies for operational taxonomic units (OTUs) which are crucial for assessing biodiversity of communities, may affect final conclusions. Here, we used zooplankton communities along an environmental pollution gradient in the Chaobai River in Northern China to test different clustering strategies, including nonclustering and clustering with varied thresholds. Our results showed that though the number of OTUs estimated by nonclustering strategies and clustering strategies with divergence thresholds of 99%-97% largely varied, they were able to identify the same set of significant environmental and spatial variables responsible for geographical distributions of zooplankton communities. In addition, the ecological conclusions obtained by clustering thresholds of 99%-97% were consistent with nonclustering strategies, where for all eight clustering scenarios we detected that species sorting predicted by environmental variables overrode dispersal as the dominant factor in structuring zooplankton communities. However, clustering with the divergence thresholds of <95% affected the environmental and spatial variables identified. We conclude that both newly developed nonclustering methods and traditional clustering methods with divergence thresholds ≥97% were reliable to reveal mechanisms of complex community-environment interactions, although different clustering strategies could lead to largely varied biodiversity estimates such as those for α-diversity.}, }
@article {pmid29976643, year = {2018}, author = {Chaudhary, A and Kauser, I and Ray, A and Poretsky, R}, title = {Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community.}, journal = {mSphere}, volume = {3}, number = {4}, pages = {}, pmid = {29976643}, issn = {2379-5042}, mesh = {*Biota ; Chicago ; Cluster Analysis ; *Cyclonic Storms ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Urban streams are susceptible to stormwater and sewage inputs that can impact their ecological health and water quality. Microbial communities in streams play important functional roles, and their composition and metabolic potential can help assess ecological state and water quality. Although these environments are highly heterogenous, little is known about the influence of isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, we examined the microbial community composition and diversity in an urban stream during dry and wet weather conditions with both 16S rRNA gene sequencing across multiple years and shotgun metagenomics to more deeply analyze a single storm flow event. Metagenomics was used to assess population-level dynamics as well as shifts in the microbial community taxonomic profile and functional potential before and after a substantial rainfall. The results demonstrated general trends present in the stream under storm flow versus base flow conditions and also highlighted the influence of increased effluent flow following rain in shifting the stream microbial community from abundant freshwater taxa to those more associated with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to changes in functional gene content, particularly for transmembrane transport and organic substance biosynthesis. We also observed an increase in relative abundance of genes encoding degradation of organic pollutants and antibiotic resistance after rain. Overall, this study highlighted some differences in the microbial community of an urban stream under storm flow conditions and showed the impact of a storm flow event on the microbiome from an environmental and public health perspective.IMPORTANCE Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced storm flow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high-rainfall event, with potential environment and public health implications. Previous work in this area has focused on specific genes/organisms or has not assessed immediate storm flow impact.}, }
@article {pmid29976249, year = {2018}, author = {Kayani, MUR and Doyle, SM and Sangwan, N and Wang, G and Gilbert, JA and Christner, BC and Zhu, TF}, title = {Metagenomic analysis of basal ice from an Alaskan glacier.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {123}, pmid = {29976249}, issn = {2049-2618}, mesh = {Alaska ; Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Base Sequence ; Biodiversity ; Ecosystem ; Genome, Bacterial/*genetics ; Geologic Sediments/*microbiology ; Ice Cover/*microbiology ; *Metagenomics ; Microbiota/*genetics ; Nitrification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfur/metabolism ; }, abstract = {BACKGROUND: Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on the microbial community structures and their metabolic potential is very limited. Here, we provide insights into the microbial lifestyle present at the base of the Matanuska Glacier, Alaska.<br><br>RESULTS: DNA and RNA were extracted from samples of the Matanuska Glacier basal ice. Using Illumina MiSeq and HiSeq sequencing, we investigated the microbial diversity with the metagenomic shotgun reads and 16S ribosomal RNA data. We further assembled 9 partial and draft bacterial genomes from the metagenomic assembly, and identified key metabolic pathways such as sulfur oxidation and nitrification. Collectively, our analyses suggest a prevalence of lithotrophic and heterotrophic metabolisms in the subglacial microbiome.<br><br>CONCLUSION: Our results present the first metagenomic assembly and bacterial draft genomes for a subglacial environment. These results extend our understanding of the chemical and biological processes in subglacial environments critically influenced by global climate change.}, }
@article {pmid29974156, year = {2018}, author = {Sharma, S and Grewal, S and Vakhlu, J}, title = {Phylogenetic diversity and metabolic potential of microbiome of natural healing clay from Chamliyal (J&amp;K).}, journal = {Archives of microbiology}, volume = {200}, number = {9}, pages = {1333-1343}, doi = {10.1007/s00203-018-1549-4}, pmid = {29974156}, issn = {1432-072X}, support = {38(1269)/10/EMR-II//Council of Scientific and Industrial Research/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Clay/*analysis/*chemistry ; Fungi/classification/*isolation &amp; purification/*metabolism ; Humans ; India ; Iron/metabolism ; Metagenome ; Microbiota/*physiology ; Molecular Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Skin Diseases/therapy ; Sulfur/metabolism ; }, abstract = {Clay therapy for skin disease treatment is an ancient practice popular worldwide as a cheap alternative to pharmaceutical products. Effectiveness of clay against skin problems has been linked to its mineral composition and to microbial activity. The clay-water paste of a holy shrine Chamliyal in the Jammu region of J&amp;K, India is used as an ointment to treat different skin disorders particularly psoriasis. Using the 16 SrDNA amplicon pyrosequencing and whole-metagenome direct shotgun Illumina sequencing, microbial phylogeny and potential metabolic functions were catalogued for Chamliyal's clay. Microbial diversity profile of the Chamliyal's clay is similar to other medicinal clays, particularly Dead Sea; there is some uniqueness as well. Although Proteobacteria, Actinomycetes and Firmicutes are common inhabitants of all the clay types, sulphur- and iron-reducing bacteria like Deferribacterales are particular to clays used for skin healing. In the present study it is proposed that healing properties of clay may be due to the microbes and microbial genes associated with metabolism of minerals like iron and sulphur, that lead to mineral acquisition in the Chamliyal's clay.}, }
@article {pmid29964641, year = {2017}, author = {Wang, BQ and Li, CY and Lu, W and Fan, H and Zhang, DZ and Wang, Z and Lü, C and Shen, FD}, title = {[Shift of Microbial Communities During the CO2-Brine-Sandstone Interaction Process].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {38}, number = {7}, pages = {2978-2987}, doi = {10.13227/j.hjkx.201612067}, pmid = {29964641}, issn = {0250-3301}, mesh = {Bacteria/*classification ; *Carbon Dioxide ; *Salts ; Solubility ; }, abstract = {In this study, the dynamic variation of the structure, functionality and biodiversity of indigenous microorganism during the CO2-brine-sandstone interaction process was investigated using MiSeq sequencing techniques. The results indicated that some kinds of indigenous microorganisms could grow well under the extreme condition induced by CO2-injection. After injection of CO2, the species of indigenous microorganisms tended to be single and the relative abundance of Proteobacteria reached up to 99.77% after 6 months. The dominant species varied as follows:Pseudomonas sp., Citrobacter sp. and Brevundimonas sp.. Meanwhile, some special genera such as Bacillus sp., Hydrogenophaga sp. and Rhizobium sp. with functionality of iron-reducing and denitrification were found in this study, which may have a potential effect on the capture and storage of CO2. In addition, the Shannon index decreased from 5.3302 to 1.9465 after injection of CO2, suggesting that the biodiversity reduced significantly. Function and main metabolites analysis of bacteria in the CO2-brine-sandstone interaction process showed that bacteria like Bacillus sp., Citrobacter sp. and Pseudomonas sp. could enhance CO2 solubility-trapping process. Bacteria metabolisms could accelerate the dissolution of feldspar and chlorites, and facilitate the formation of transition-state calcite and siderite. Otherwise, the great variation was mainly attributed to the change of condition driven by CO2-brine-sandstone interactions, such as pH and the chemical composition of brine water(anion and cation), etc.}, }
@article {pmid29961874, year = {2018}, author = {Behzad, H and Mineta, K and Gojobori, T}, title = {Global Ramifications of Dust and Sandstorm Microbiota.}, journal = {Genome biology and evolution}, volume = {10}, number = {8}, pages = {1970-1987}, pmid = {29961874}, issn = {1759-6653}, mesh = {Agriculture ; *Dust ; Ecosystem ; Geography ; Humans ; *Internationality ; Metagenomics ; *Microbiota ; }, abstract = {Dust and sandstorm events inject substantial quantities of foreign microorganisms into global ecosystems, with the ability to impact distant environments. The majority of these microorganisms originate from deserts and drylands where the soil is laden with highly stress-resistant microbes capable of thriving under extreme environmental conditions, and a substantial portion of them survive long journeys through the atmosphere. This large-scale transmission of highly resilient alien microbial contaminants raises concerns with regards to the invasion of sensitive and/or pristine sink environments, and to human health-concerns exacerbated by increases in the rate of desertification. Further increases in the transport of dust-associated microbiota could extend the spread of foreign microbes to new ecosystems, increase their load in present sink environments, disrupt ecosystem balance, and potentially introduce new pathogens. Our present understanding of these microorganisms, their phylogenic affiliations and functional significance, is insufficient to determine their impact. The purpose of this review is to provide an overview of available data regarding dust and sandstorm microbiota and their potential ramifications on human and ecosystem health. We conclude by discussing current gaps in dust and sandstorm microbiota research, and the need for collaborative studies involving high-resolution meta-omic approaches in conjunction with extensive ecological time-series studies to advance the field towards an improved and sufficient understanding of these invisible atmospheric travelers and their global ramifications.}, }
@article {pmid29954453, year = {2018}, author = {Parras-Moltó, M and Rodríguez-Galet, A and Suárez-Rodríguez, P and López-Bueno, A}, title = {Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {119}, pmid = {29954453}, issn = {2049-2618}, mesh = {Base Composition/genetics ; DNA Viruses/*genetics ; Genetic Markers/genetics ; Genome, Viral/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/genetics ; Nucleic Acid Amplification Techniques/*methods ; Polymerase Chain Reaction ; Saliva/*virology ; }, abstract = {BACKGROUND: Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology and discovering new viruses. Unfortunately, several sources of bias lead to the misrepresentation of certain viruses within metagenomics workflows, hindering the shift from merely descriptive studies towards quantitative comparisons of communities. Therefore, benchmark studies on virus enrichment and random amplification protocols are required to better understand the sources of bias.<br><br>RESULTS: We assessed the bias introduced by viral enrichment on mock assemblages composed of seven DNA viruses, and the bias from random amplification methods on human saliva DNA viromes, using qPCR and deep sequencing, respectively. While iodixanol cushions and 0.45 μm filtration preserved the original composition of nuclease-protected viral genomes, low-force centrifugation and 0.22 μm filtration removed large viruses. Comparison of unamplified and randomly amplified saliva viromes revealed that multiple displacement amplification (MDA) induced stochastic bias from picograms of DNA template. However, the type of bias shifted to systematic using 1 ng, with only a marginal influence by amplification time. Systematic bias consisted of over-amplification of small circular genomes, and under-amplification of those with extreme GC content, a negative bias that was shared with the PCR-based sequence-independent, single-primer amplification (SISPA) method. MDA based on random priming provided by a DNA primase activity slightly outperformed those based on random hexamers and SISPA, which may reflect differences in ability to handle sequences with extreme GC content. SISPA viromes showed uneven coverage profiles, with high coverage peaks in regions with low linguistic sequence complexity. Despite misrepresentation of certain viruses after random amplification, ordination plots based on dissimilarities among contig profiles showed perfect overlapping of related amplified and unamplified saliva viromes and strong separation from unrelated saliva viromes. This result suggests that random amplification bias has a minor impact on beta diversity studies.<br><br>CONCLUSIONS: Benchmark analyses of mock and natural communities of viruses improve understanding and mitigate bias in metagenomics surveys. Bias induced by random amplification methods has only a minor impact on beta diversity studies of human saliva viromes.}, }
@article {pmid29950381, year = {2018}, author = {Jenior, ML and Leslie, JL and Young, VB and Schloss, PD}, title = {Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, pmid = {29950381}, issn = {2379-5042}, mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage/adverse effects ; Cecum/*chemistry/*microbiology ; Clostridium Infections/*microbiology ; Clostridium difficile/*growth &amp; development ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Metabolomics ; Metagenomics ; Mice ; }, abstract = {Susceptibility to Clostridium difficile infection (CDI) is primarily associated with previous exposure to antibiotics, which compromise the structure and function of the gut bacterial community. Specific antibiotic classes correlate more strongly with recurrent or persistent C. difficile infection. As such, we utilized a mouse model of infection to explore the effect of distinct antibiotic classes on the impact that infection has on community-level transcription and metabolic signatures shortly following pathogen colonization and how those changes may associate with persistence of C. difficile Untargeted metabolomic analysis revealed that C. difficile infection had significantly larger impacts on the metabolic environment across cefoperazone- and streptomycin-pretreated mice, which became persistently colonized compared to clindamycin-pretreated mice, where infection quickly became undetectable. Through metagenome-enabled metatranscriptomics, we observed that transcripts for genes associated with carbon and energy acquisition were greatly reduced in infected animals, suggesting that those niches were instead occupied by C. difficile Furthermore, the largest changes in transcription were seen in the least abundant species, indicating that C. difficile may &quot;attack the loser&quot; in gut environments where sustained infection occurs more readily. Overall, our results suggest that C. difficile is able to restructure the nutrient-niche landscape in the gut to promote persistent infection.IMPORTANCEClostridium difficile has become the most common single cause of hospital-acquired infection over the last decade in the United States. Colonization resistance to the nosocomial pathogen is primarily provided by the gut microbiota, which is also involved in clearing the infection as the community recovers from perturbation. As distinct antibiotics are associated with different risk levels for CDI, we utilized a mouse model of infection with 3 separate antibiotic pretreatment regimens to generate alternative gut microbiomes that each allowed for C. difficile colonization but varied in clearance rate. To assess community-level dynamics, we implemented an integrative multi-omics approach that revealed that infection significantly changed many aspects of the gut community. The degree to which the community changed was inversely correlated with clearance during the first 6 days of infection, suggesting that C. difficile differentially modifies the gut environment to promote persistence. This is the first time that metagenome-enabled metatranscriptomics have been employed to study the behavior of a host-associated microbiota in response to an infection. Our results allow for a previously unseen understanding of the ecology associated with C. difficile infection and provide the groundwork for identification of context-specific probiotic therapies.}, }
@article {pmid29941576, year = {2018}, author = {Borton, MA and Hoyt, DW and Roux, S and Daly, RA and Welch, SA and Nicora, CD and Purvine, S and Eder, EK and Hanson, AJ and Sheets, JM and Morgan, DM and Wolfe, RA and Sharma, S and Carr, TR and Cole, DR and Mouser, PJ and Lipton, MS and Wilkins, MJ and Wrighton, KC}, title = {Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {28}, pages = {E6585-E6594}, pmid = {29941576}, issn = {1091-6490}, mesh = {Bacteria/classification/*metabolism ; *Hydraulic Fracking ; Microbial Consortia/*physiology ; Natural Gas/*microbiology ; United States ; }, abstract = {Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth's surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and metabolite findings from the laboratory were then corroborated using regression-based modeling performed on metagenomic and metabolite data from more than 40 produced fluids from five hydraulically fractured shale wells. Collectively, our findings show that Halanaerobium, Geotoga, and Methanohalophilus strain abundances predict a significant fraction of nitrogen and carbon metabolites in the field. Our laboratory findings also exposed cryptic predatory, cooperative, and competitive interactions that impact microorganisms across fractured shales. Scaling these results from the laboratory to the field identified mechanisms underpinning biogeochemical reactions, yielding knowledge that can be harnessed to potentially increase energy yields and inform management practices in hydraulically fractured shales.}, }
@article {pmid29940835, year = {2018}, author = {Devlin, JC and Battaglia, T and Blaser, MJ and Ruggles, KV}, title = {WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {493}, pmid = {29940835}, issn = {1471-2164}, support = {U01 AI22285//Foundation for the National Institutes of Health/ ; }, mesh = {Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research.<br><br>RESULTS: We developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics.<br><br>CONCLUSIONS: WHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets.}, }
@article {pmid29934497, year = {2018}, author = {Ji, Y and Zhang, F and Zhang, R and Shen, Y and Liu, L and Wang, J and Yang, J and Tang, Q and Xun, J and Qi, T and Wang, Z and Song, W and Tang, Y and Chen, J and Lu, H}, title = {Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count.}, journal = {Emerging microbes &amp; infections}, volume = {7}, number = {1}, pages = {113}, pmid = {29934497}, issn = {2222-1751}, support = {81571977//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Adult ; Antiretroviral Therapy, Highly Active ; Biodiversity ; Biomarkers ; *CD4 Lymphocyte Count ; CD4-CD8 Ratio ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome/drug effects ; HIV Infections/drug therapy/*immunology/virology ; HIV-1/*immunology ; Humans ; Male ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Viral Load ; }, abstract = {The roles of immunodeficiency and combined antiretroviral therapy (cART) in shaping the gut microbiota in HIV-1-infected subjects (HISs) have not been described thoroughly by time-series investigations. In this study, 36 antiretroviral-naïve HISs were enrolled to prospectively assess alterations in the fecal microbiota and plasma markers of microbial translocation and inflammation with cART. At baseline, the species α-diversity of the fecal microbiota was significantly lower in HISs with a CD4+ T cell count <300/mm3 than in HISs with a CD4+ T cell count >300/mm3 (Shannon index: Median 2.557 vs. 2.981, P = 0.006; Simpson index: Median 0.168 vs. 0.096, P = 0.004). Additionally, the baseline α-diversity indices correlated with CD4+ T cell counts (Shannon index: r = 0.474, P = 0.004; Simpson index: r = -0.467, P = 0.004) and the specific plasma biomarkers for microbial translocation and inflammation. After cART introduction, the species α-diversity of fecal microbiota in HISs with CD4+ T cell counts <300/mm3 was significantly restored (Shannon index: Median 2.557 vs. 2.791, P = 0.007; Simpson index: Median 0.168 vs. 0.112, P = 0.004), while the variances were insignificant among HISs with CD4+ T cell counts >300/mm3 (Shannon index: Median 2.981 vs. 2.934, P = 0.179; Simpson index: Median 0.096 vs. 0.119, P = 0.082). Meanwhile, with cART introduction, alterations in the gut microbial composition were more significant in the subgroup with CD4+ T cell counts >300/mm3, corresponding to increases in the specific plasma inflammatory markers. These findings implicated the interactive roles of immunodeficiency and cART for affecting gut microbiota in HIV-1-infected individuals, providing new insights into intestinal microbiome dysbiosis related to HIV-1 infection.}, }
@article {pmid29925429, year = {2018}, author = {Tschitschko, B and Erdmann, S and DeMaere, MZ and Roux, S and Panwar, P and Allen, MA and Williams, TJ and Brazendale, S and Hancock, AM and Eloe-Fadrosh, EA and Cavicchioli, R}, title = {Genomic variation and biogeography of Antarctic haloarchaea.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {113}, pmid = {29925429}, issn = {2049-2618}, mesh = {Antarctic Regions ; Archaeal Viruses/*genetics/isolation &amp; purification ; Base Sequence ; Genetic Variation/genetics ; Genome, Archaeal/*genetics ; Genomic Islands/genetics ; Geography ; Halorubrum/classification/*genetics/isolation &amp; purification ; Lakes/microbiology ; Metagenome/genetics ; Microbiota/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands). To assess variation in haloarchaeal populations, including the presence of genomic islands, metagenomes from six hypersaline Antarctic lakes were characterised.<br><br>RESULTS: The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strains' two smaller replicons (secondary replicons) were highly variable. Intergenera gene exchange was identified, including the sharing of a type I-B CRISPR system. Evaluation of infectivity of an Antarctic halovirus provided experimental evidence for the differential susceptibility of the strains, bolstering inferences that strain variation is important for modulating interactions with viruses. A relationship was found between genomic structuring and the location of variation within replicons and genomic islands, demonstrating that the way in which haloarchaea accommodate genomic variability relates to replicon structuring. Metagenome read and contig mapping and clustering and scaling analyses demonstrated biogeographical patterning of variation consistent with environment and distance effects. The metagenome data also demonstrated that specific haloarchaeal species dominated the hypersaline systems indicating they are endemic to Antarctica.<br><br>CONCLUSION: The study describes how genomic variation manifests in Antarctic-lake haloarchaeal communities and provides the basis for future assessments of Antarctic regional and global biogeography of haloarchaea.}, }
@article {pmid29925423, year = {2018}, author = {Brooks, B and Olm, MR and Firek, BA and Baker, R and Geller-McGrath, D and Reimer, SR and Soenjoyo, KR and Yip, JS and Dahan, D and Thomas, BC and Morowitz, MJ and Banfield, JF}, title = {The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {112}, pmid = {29925423}, issn = {2049-2618}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Aerosols ; Bacteria/*classification/genetics/*isolation &amp; purification ; Base Sequence ; Dust ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Very Low Birth Weight ; *Intensive Care Units, Neonatal ; Premature Birth ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {BACKGROUND: The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it has been previously shown that the gut microbiomes of these infants often resemble the microbes found in the NICU. Little is known, however, about the identity, persistence, and absolute abundance of NICU room-associated bacteria over long stretches of time. Here, we couple droplet digital PCR (ddPCR), 16S rRNA gene surveys, and recently published metagenomics data from infant gut samples to infer the extent to which the NICU microbiome is shaped by its room occupants.<br><br>RESULTS: Over 2832 swabs, wipes, and air samples were collected from 16 private-style NICU rooms housing very low birth weight (< 1500 g), premature (< 31 weeks' gestation) infants. For each infant, room samples were collected daily, Monday through Friday, for 1 month. The first samples from the first infant and the last samples from the last infant were collected 383 days apart. Twenty-two NICU locations spanning room surfaces, hands, electronics, sink basins, and air were collected. Results point to an incredibly simple room community where 5-10 taxa, mostly skin-associated, account for over 50% of the amplicon reads. Biomass estimates reveal four to five orders of magnitude difference between the least to the most dense microbial communities, air, and sink basins, respectively. Biomass trends from bioaerosol samples and petri dish dust collectors suggest occupancy to be a main driver of suspended biological particles within the NICU. Using a machine learning algorithm to classify the origin of room samples, we show that each room has a unique microbial fingerprint. Several important taxa driving this model were dominant gut colonizers of infants housed within each room.<br><br>CONCLUSIONS: Despite regular cleaning of hospital surfaces, bacterial biomass was detectable at varying densities. A room-specific microbiome signature was detected, suggesting microbes seeding NICU surfaces are sourced from reservoirs within the room and that these reservoirs contain actively dividing cells. Collectively, the data suggests that hospitalized infants, in combination with their caregivers, shape the microbiome of NICU rooms.}, }
@article {pmid29921329, year = {2018}, author = {Call, L and Stoll, B and Oosterloo, B and Ajami, N and Sheikh, F and Wittke, A and Waworuntu, R and Berg, B and Petrosino, J and Olutoye, O and Burrin, D}, title = {Metabolomic signatures distinguish the impact of formula carbohydrates on disease outcome in a preterm piglet model of NEC.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {111}, pmid = {29921329}, issn = {2049-2618}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; T32 GM088129/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Feed/analysis ; Animals ; Bacillus/classification/genetics/*isolation &amp; purification ; Clostridium/classification/genetics/*isolation &amp; purification ; *Dietary Carbohydrates ; *Enteral Nutrition ; Enterocolitis, Necrotizing/etiology/microbiology ; Female ; Gammaproteobacteria/classification/genetics/*isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; High Fructose Corn Syrup/*administration &amp; dosage ; Lactose/*administration &amp; dosage ; Pregnancy ; Premature Birth ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Swine ; }, abstract = {BACKGROUND: Major risk factors for necrotizing enterocolitis (NEC) include premature birth and formula feeding in the context of microbial colonization of the gastrointestinal tract. We previously showed that feeding formula composed of lactose vs. corn syrup solids protects against NEC in preterm pigs; however, the microbial and metabolic effects of these different carbohydrates used in infant formula has not been explored.<br><br>OBJECTIVE: Our objective was to characterize the effects of lactose- and corn syrup solid-based formulas on the metabolic and microbial profiles of preterm piglets and to determine whether unique metabolomic or microbiome signatures correlate with severity or incidence of NEC.<br><br>DESIGN/METHODS: Preterm piglets (103 days gestation) were given total parenteral nutrition (2 days) followed by gradual (5 days) advancement of enteral feeding of formulas matched in nutrient content but containing either lactose (LAC), corn syrup solids (CSS), or 1:1 mix (MIX). Gut contents and mucosal samples were collected and analyzed for microbial profiles by sequencing the V4 region of the 16S rRNA gene. Metabolomic profiles of cecal contents and plasma were analyzed by LC/GC mass spectrometry.<br><br>RESULTS: NEC incidence was 14, 50, and 44% in the LAC, MIX, and CSS groups, respectively. The dominant classes of bacteria were Bacilli, Clostridia, and Gammaproteobacteria. The number of observed OTUs was lowest in colon contents of CSS-fed pigs. CSS-based formula was associated with higher Bacilli and lower Clostridium from clusters XIVa and XI in the colon. NEC was associated with decreased Gammaproteobacteria in the stomach and increased Clostridium sensu stricto in the ileum. Plasma from NEC piglets was enriched with metabolites of purine metabolism, aromatic amino acid metabolism, and bile acids. Markers of glycolysis, e.g., lactate, were increased in the cecal contents of CSS-fed pigs and in plasma of pigs which developed NEC.<br><br>CONCLUSIONS: Feeding formula containing lactose is not completely protective against NEC, yet selects for greater microbial richness associated with changes in Bacilli and Clostridium and lower NEC incidence. We conclude that feeding preterm piglets a corn syrup solid vs. lactose-based formula increases the incidence of NEC and produces distinct metabolomic signatures despite modest changes in microbiome profiles.}, }
@article {pmid29915700, year = {2018}, author = {Carew, ME and Coleman, RA and Hoffmann, AA}, title = {Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4980}, pmid = {29915700}, issn = {2167-8359}, abstract = {Background: High throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens identified by taxonomists are needed. This can be achieved through using DNA extraction methods that are not only suitable for metabarcoding but also for building reference DNA barcode libraries.<br><br>Methods: In this study, we test the suitability of a rapid non-destructive DNA extraction method for metabarcoding of freshwater invertebrate samples.<br><br>Results: This method resulted in detection of taxa from many taxonomic groups, comparable to results obtained with two other tissue-based extraction methods. Most taxa could also be successfully used for subsequent individual-based DNA barcoding and taxonomic identification. The method was successfully applied to field-collected invertebrate samples stored for taxonomic studies in 70% ethanol at room temperature, a commonly used storage method for freshwater samples.<br><br>Discussion: With further refinement and testing, non-destructive extraction has the potential to rapidly characterise species biodiversity in invertebrate samples, while preserving specimens for taxonomic investigation.}, }
@article {pmid29911322, year = {2018}, author = {Moon, CD and Young, W and Maclean, PH and Cookson, AL and Bermingham, EN}, title = {Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats.}, journal = {MicrobiologyOpen}, volume = {7}, number = {5}, pages = {e00677}, pmid = {29911322}, issn = {2045-8827}, mesh = {Animals ; Bacteria/*classification/*genetics ; Cats ; Dogs ; Feces/*microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {Interests in the impact of the gastrointestinal microbiota on health and wellbeing have extended from humans to that of companion animals. While relatively fewer studies to date have examined canine and feline gut microbiomes, analysis of the metagenomic DNA from fecal communities using next-generation sequencing technologies have provided insights into the microbes that are present, their function, and potential to contribute to overall host nutrition and health. As carnivores, healthy dogs and cats possess fecal microbiomes that reflect the generally higher concentrations of protein and fat in their diets, relative to omnivores and herbivores. The phyla Firmicutes and Bacteroidetes are highly abundant, and Fusobacteria, Actinobacteria, and Proteobacteria also feature prominently. Proteobacteria is the most diverse bacterial phylum and commonly features in the fecal microbiota of healthy dogs and cats, although its reputation is often sullied as its members include a number of well-known opportunistic pathogens, such as Escherichia coli, Salmonella, and Campylobacter, which may impact the health of the host and its owner. Furthermore, in other host species, high abundances of Proteobacteria have been associated with dysbiosis in hosts with metabolic or inflammatory disorders. In this review, we seek to gain further insight into the prevalence and roles of the Proteobacteria within the gastrointestinal microbiomes of healthy dogs and cats. We draw upon the growing number of metagenomic DNA sequence-based studies which now allow us take a culture-independent approach to examine the functions that this more minor, yet important, group contribute to normal microbiome function.}, }
@article {pmid29908593, year = {2018}, author = {Rastrojo, A and Alcamí, A}, title = {Viruses in Polar Lake and Soil Ecosystems.}, journal = {Advances in virus research}, volume = {101}, number = {}, pages = {39-54}, doi = {10.1016/bs.aivir.2018.02.002}, pmid = {29908593}, issn = {1557-8399}, mesh = {Antarctic Regions ; Arctic Regions ; Biological Evolution ; *Ecosystem ; Genetic Variation ; Lakes/*virology ; Metagenomics ; *Soil Microbiology ; Virus Physiological Phenomena ; Viruses/classification/*genetics ; }, abstract = {Viruses play an important role in the control of microbial communities, and it has been suggested that the influence of viruses in polar ecosystems, with low nutrients and under extreme environmental conditions, may be greater. Viral metagenomics allows the genetic characterization of complex viral communities without the need to isolate and grow viruses. Recent investigations in Antarctica and the Arctic are uncovering a great diversity of DNA viruses, including bacteriophages, circular single-stranded DNA viruses, algal-infecting phycodnaviruses, and virophages, adapted to these extreme environments. The limited sequence similarity between viruses in Antarctica and the Arctic suggests that viral communities in the two polar regions have evolved independently since the formation of the Antarctic continent, estimated to occur 25 million years ago. The community of RNA viruses in Antarctica is dominated by the order Picornavirales and their quasispecies composition suggests that higher genetic variability may correlate with viral adaptation to new environmental conditions.}, }
@article {pmid29902438, year = {2018}, author = {Milshteyn, A and Colosimo, DA and Brady, SF}, title = {Accessing Bioactive Natural Products from the Human Microbiome.}, journal = {Cell host &amp; microbe}, volume = {23}, number = {6}, pages = {725-736}, doi = {10.1016/j.chom.2018.05.013}, pmid = {29902438}, issn = {1934-6069}, support = {R01 AT009562/AT/NCCIH NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/metabolism ; Bacteria/genetics/metabolism ; Biological Products/*metabolism/*pharmacology ; Humans ; Indoles/metabolism ; Metabolomics ; Metagenomics ; Microbial Interactions ; Microbiota/genetics/*physiology ; Multigene Family ; Peptides, Cyclic/metabolism ; Pyrrolidonecarboxylic Acid/metabolism ; Thiazolidines/metabolism ; }, abstract = {Natural products have long played a pivotal role in the development of therapeutics for a variety of diseases. Traditionally, soil and marine environments have provided a rich reservoir from which diverse chemical scaffolds could be discovered. Recently, the human microbiome has been recognized as a promising niche from which secondary metabolites with therapeutic potential have begun to be isolated. In this Review, we address how the expansive history of identifying bacterial natural products in other environments is informing the approaches being brought to bear on the study of the human microbiota. We also touch on how these tools can lead to insights about microbe-microbe and host-microbe interactions and help generate biological hypotheses that may lead to developments of new therapeutic modalities.}, }
@article {pmid29902201, year = {2018}, author = {Li, X and Naser, SA and Khaled, A and Hu, H and Li, X}, title = {When old metagenomic data meet newly sequenced genomes, a case study.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0198773}, pmid = {29902201}, issn = {1932-6203}, support = {R15 GM123407/GM/NIGMS NIH HHS/United States ; }, mesh = {Colitis/genetics/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; *Metagenomics ; *Whole Genome Sequencing ; }, abstract = {Dozens of computational methods are developed to identify species present in a metagenomic dataset. Many of these computational methods depend on available sequenced microbial species, which are still far from being representative. To see how newly sequenced genomes affect the analysis results, we re-analyzed a shotgun metagenomic dataset composed of twelve colitis free metagenomic samples and ten colitis-related metagenomic samples. Unexpectedly, we identified at least two new phyla that may relate to colitis development in patients, together with the phylum identified previously. Compared with the previously identified phylum that differed between the two types of samples, the differences associated with the two new phyla are statistically more significant. Moreover, the abundance of the two new phyla correlates more with the severity of colitis. Surprisingly, even by repeating the analyses implemented in the previous study, we found that at least one main conclusion in the previous study is not supported. Our study indicates the importance of re-analysis of the generated metagenomic datasets and the necessity of considering multiple updated tools in metagenomic studies. It also sheds light on the limitations of the popular tools used currently and the importance to infer the presence of taxa without relying upon available sequenced genomes.}, }
@article {pmid29899109, year = {2018}, author = {Russo, AG and Eden, JS and Enosi Tuipulotu, D and Shi, M and Selechnik, D and Shine, R and Rollins, LA and Holmes, EC and White, PA}, title = {Viral Discovery in the Invasive Australian Cane Toad (Rhinella marina) Using Metatranscriptomic and Genomic Approaches.}, journal = {Journal of virology}, volume = {92}, number = {17}, pages = {}, pmid = {29899109}, issn = {1098-5514}, mesh = {Animals ; Bufo marinus/*virology ; Gene Expression Profiling ; Metagenomics ; Proviruses/*classification/genetics/*isolation &amp; purification ; Viruses/*classification/genetics/*isolation &amp; purification ; Western Australia ; }, abstract = {Cane toads are a notorious invasive species, inhabiting over 1.2 million km2 of Australia and threatening native biodiversity. The release of pathogenic cane toad viruses is one possible biocontrol strategy yet is currently hindered by the poorly described cane toad virome. Metatranscriptomic analysis of 16 cane toad livers revealed the presence of a novel and full-length picornavirus, Rhimavirus A (RhiV-A), a member of a reptile- and amphibian-specific cluster of the Picornaviridae basal to the Kobuvirus-like group. In the combined liver transcriptome, we also identified a complete genome sequence of a distinct epsilonretrovirus, Rhinella marina endogenous retrovirus (RMERV). The recently sequenced cane toad genome contains 8 complete RMERV proviruses as well as 21 additional truncated insertions. The oldest full-length RMERV provirus was estimated to have inserted 1.9 million years ago (MYA). To screen for these viral sequences in additional toads, we analyzed publicly available transcriptomes from six diverse Australian locations. RhiV-A transcripts were identified in toads sampled from three locations across 1,000 km of Australia, stretching to the current Western Australia (WA) invasion front, while RMERV transcripts were observed at all six sites. Finally, we scanned the cane toad genome for nonretroviral endogenous viral elements, finding three sequences related to small DNA viruses in the family Circoviridae This shows ancestral circoviral infection with subsequent genomic integration. The identification of these current and past viral infections enriches our knowledge of the cane toad virome, an understanding of which will facilitate future work on infection and disease in this important invasive species.IMPORTANCE Cane toads are poisonous amphibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study samples cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol.}, }
@article {pmid29899081, year = {2019}, author = {Aron-Wisnewsky, J and Prifti, E and Belda, E and Ichou, F and Kayser, BD and Dao, MC and Verger, EO and Hedjazi, L and Bouillot, JL and Chevallier, JM and Pons, N and Le Chatelier, E and Levenez, F and Ehrlich, SD and Dore, J and Zucker, JD and Clément, K}, title = {Major microbiota dysbiosis in severe obesity: fate after bariatric surgery.}, journal = {Gut}, volume = {68}, number = {1}, pages = {70-82}, doi = {10.1136/gutjnl-2018-316103}, pmid = {29899081}, issn = {1468-3288}, mesh = {Adult ; *Bariatric Surgery ; Biomarkers/blood ; Chromatography, Liquid ; Comorbidity ; Dysbiosis/*etiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Mass Spectrometry ; Metagenomics ; Obesity, Morbid/*microbiology/*surgery ; Phenotype ; Prospective Studies ; Risk Factors ; }, abstract = {OBJECTIVES: Decreased gut microbial gene richness (MGR) and compositional changes are associated with adverse metabolism in overweight or moderate obesity, but lack characterisation in severe obesity. Bariatric surgery (BS) improves metabolism and inflammation in severe obesity and is associated with gut microbiota modifications. Here, we characterised severe obesity-associated dysbiosis (ie, MGR, microbiota composition and functional characteristics) and assessed whether BS would rescue these changes.<br><br>DESIGN: Sixty-one severely obese subjects, candidates for adjustable gastric banding (AGB, n=20) or Roux-en-Y-gastric bypass (RYGB, n=41), were enrolled. Twenty-four subjects were followed at 1, 3 and 12 months post-BS. Gut microbiota and serum metabolome were analysed using shotgun metagenomics and liquid chromatography mass spectrometry (LC-MS). Confirmation groups were included.<br><br>RESULTS: Low gene richness (LGC) was present in 75% of patients and correlated with increased trunk-fat mass and comorbidities (type 2 diabetes, hypertension and severity). Seventy-eight metagenomic species were altered with LGC, among which 50% were associated with adverse body composition and metabolic phenotypes. Nine serum metabolites (including glutarate, 3-methoxyphenylacetic acid and L-histidine) and functional modules containing protein families involved in their metabolism were strongly associated with low MGR. BS increased MGR 1 year postsurgery, but most RYGB patients remained with low MGR 1 year post-BS, despite greater metabolic improvement than AGB patients.<br><br>CONCLUSIONS: We identified major gut microbiota alterations in severe obesity, which include decreased MGR and related functional pathways linked with metabolic deteriorations. The lack of full rescue post-BS calls for additional strategies to improve the gut microbiota ecosystem and microbiome-host interactions in severe obesity.<br><br>TRIAL REGISTRATION NUMBER: NCT01454232.}, }
@article {pmid29898983, year = {2018}, author = {Zhu, L and Yang, Z and Yao, R and Xu, L and Chen, H and Gu, X and Wu, T and Yang, X}, title = {Potential Mechanism of Detoxification of Cyanide Compounds by Gut Microbiomes of Bamboo-Eating Pandas.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, pmid = {29898983}, issn = {2379-5042}, mesh = {Ailuridae/*microbiology/*physiology ; Animals ; Bacteria/classification/genetics/metabolism ; Biotransformation ; Cyanides/*metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; Ursidae/*microbiology/*physiology ; }, abstract = {Gut microbes can enhance the ability of hosts to consume secondary plant compounds and, therefore, expand the dietary niche breadth of mammalian herbivores. The giant and red pandas are bamboo-eating specialists within the mammalian order Carnivora. Bamboo contains abundant plant secondary metabolites (e.g., cyanide-containing compounds). However, Carnivora species, including the giant panda, have deficient levels of rhodanese (one of the essential cyanide detoxification enzymes) in their tissues compared with the same tissues of herbivores. Here, we make a comparative analysis of 94 gut metagenomes, including 25 from bamboo-eating pandas (19 from giant pandas and 6 from red pandas), 30 from Père David's deer, and 39 from published data for other mammals. The bamboo-eating pandas' gut microbiomes had some common features, such as high proportions of Pseudomonas bacteria. The results revealed that bamboo-eating pandas' gut microbiomes were significantly enriched in putative genes coding for enzymes related to cyanide degradation (e.g., rhodanese) compared with the gut microbiomes of typical herbivorous mammals, which might have coevolved with their special bamboo diets. The enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet.IMPORTANCE The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), two obligate bamboo feeders, have distinct phylogenetic positions in the order Carnivora. Bamboo is extraordinarily rich in plant secondary metabolites, such as allied phenolic and polyphenolic compounds and even toxic cyanide compounds. Here, the enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet. Thus, here is another story of diet-driven gut microbiota in nature.}, }
@article {pmid29890228, year = {2018}, author = {Poussin, C and Sierro, N and Boué, S and Battey, J and Scotti, E and Belcastro, V and Peitsch, MC and Ivanov, NV and Hoeng, J}, title = {Interrogating the microbiome: experimental and computational considerations in support of study reproducibility.}, journal = {Drug discovery today}, volume = {23}, number = {9}, pages = {1644-1657}, doi = {10.1016/j.drudis.2018.06.005}, pmid = {29890228}, issn = {1878-5832}, mesh = {Animals ; Computational Biology/*methods ; Crowdsourcing ; Data Accuracy ; Humans ; *Metagenome/genetics ; Metagenomics/*methods ; *Microbiota/genetics ; Reproducibility of Results ; *Research Design ; Workflow ; }, abstract = {The microbiome is an important factor in human health and disease and is investigated to develop novel therapeutics. Metagenomics leverages advances in sequencing technologies and computational analysis to identify and quantify the microorganisms present in a sample. This field has, however, not yet reached maturity and the international metagenomics community, aware of the current limitations and of the necessity for standardization, has started investigating sources of variability in experimental and computational workflows. The first studies have already resulted in the identification of crucial steps and factors affecting metagenomics data quality, quantification and interpretation. This review summarizes experimental and computational considerations for interrogating the microbiome and establishing reproducible and robust analysis workflows.}, }
@article {pmid29882154, year = {2019}, author = {Kerfahi, D and Tripathi, BM and Dong, K and Kim, M and Kim, H and Ferry Slik, JW and Go, R and Adams, JM}, title = {From the High Arctic to the Equator: Do Soil Metagenomes Differ According to Our Expectations?.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {168-185}, doi = {10.1007/s00248-018-1215-z}, pmid = {29882154}, issn = {1432-184X}, support = {0409-20140091//Korea Polar Research Institute/ ; NRF-0409-20150076//National Research Foundation of Korea/ ; }, mesh = {Arctic Regions ; Bacteria/genetics/metabolism ; Biodiversity ; Biota/*genetics/*physiology ; Brunei ; Canada ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Barcoding, Taxonomic ; Ecosystem ; Eukaryota/genetics/metabolism ; Greenland ; Hydrogen-Ion Concentration ; Malaysia ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics/*physiology ; Metagenomics/methods ; Microbiota/genetics/physiology ; Rainforest ; Secondary Metabolism/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Stress, Physiological ; Svalbard ; }, abstract = {Comparing the functional gene composition of soils at opposite extremes of environmental gradients may allow testing of hypotheses about community and ecosystem function. Here, we were interested in comparing how tropical microbial ecosystems differ from those of polar climates. We sampled several sites in the equatorial rainforest of Malaysia and Brunei, and the high Arctic of Svalbard, Canada, and Greenland, comparing the composition and the functional attributes of soil biota between the two extremes of latitude, using shotgun metagenomic Illumina HiSeq2000 sequencing. Based upon &quot;classical&quot; views of how tropical and higher latitude ecosystems differ, we made a series of predictions as to how various gene function categories would differ in relative abundance between tropical and polar environments. Results showed that in some respects our predictions were correct: the polar samples had higher relative abundance of dormancy related genes, and lower relative abundance of genes associated with respiration, and with metabolism of aromatic compounds. The network complexity of the Arctic was also lower than the tropics. However, in various other respects, the pattern was not as predicted; there were no differences in relative abundance of stress response genes or in genes associated with secondary metabolism. Conversely, CRISPR genes, phage-related genes, and virulence disease and defense genes, were unexpectedly more abundant in the Arctic, suggesting more intense biotic interaction. Also, eukaryote diversity and bacterial diversity were higher in the Arctic of Svalbard compared to tropical Brunei, which is consistent with what may expected from amplicon studies in terms of the higher pH of the Svalbard soil. Our results in some respects confirm expectations of how tropical versus polar nature may differ, and in other respects challenge them.}, }
@article {pmid29877042, year = {2018}, author = {Schnell, IB and Bohmann, K and Schultze, SE and Richter, SR and Murray, DC and Sinding, MS and Bass, D and Cadle, JE and Campbell, MJ and Dolch, R and Edwards, DP and Gray, TNE and Hansen, T and Hoa, ANQ and Noer, CL and Heise-Pavlov, S and Sander Pedersen, AF and Ramamonjisoa, JC and Siddall, ME and Tilker, A and Traeholt, C and Wilkinson, N and Woodcock, P and Yu, DW and Bertelsen, MF and Bunce, M and Gilbert, MTP}, title = {Debugging diversity - a pan-continental exploration of the potential of terrestrial blood-feeding leeches as a vertebrate monitoring tool.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1282-1298}, doi = {10.1111/1755-0998.12912}, pmid = {29877042}, issn = {1755-0998}, support = {DNRF94//Danish National Research Foundation/ ; //University of Copenhagen/ ; FT0991741//Australian Research Council Future Fellowship/ ; //KfW Bankengruppe/ ; //WWF Germany/ ; DFF-5051-00140//The Danish Council for Independent Research/ ; 31400470//National Natural Science Foundation of China/ ; 41661144002//National Natural Science Foundation of China/ ; 2012FY110800//Ministry of Science and Technology of China/ ; GREKF13-13//State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology/ ; GREKF14-13//State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology/ ; GREKF16-09//State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology/ ; }, mesh = {Amphibians/parasitology ; Animals ; Birds/parasitology ; Blood Chemical Analysis/*methods ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring/*methods ; High-Throughput Nucleotide Sequencing/methods ; Leeches/*growth &amp; development ; Mammals/parasitology ; Metagenomics/*methods ; Reptiles/parasitology ; }, abstract = {The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and amphibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate biodiversity.}, }
@article {pmid29874232, year = {2018}, author = {Higashi, K and Suzuki, S and Kurosawa, S and Mori, H and Kurokawa, K}, title = {Latent environment allocation of microbial community data.}, journal = {PLoS computational biology}, volume = {14}, number = {6}, pages = {e1006143}, pmid = {29874232}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; Databases, Genetic ; Environmental Microbiology ; Humans ; Metagenomics ; *Microbiota/genetics/physiology ; Models, Statistical ; Rivers/microbiology ; }, abstract = {As data for microbial community structures found in various environments has increased, studies have examined the relationship between environmental labels given to retrieved microbial samples and their community structures. However, because environments continuously change over time and space, mixed states of some environments and its effects on community formation should be considered, instead of evaluating effects of discrete environmental categories. Here we applied a hierarchical Bayesian model to paired datasets containing more than 30,000 samples of microbial community structures and sample description documents. From the training results, we extracted latent environmental topics that associate co-occurring microbes with co-occurring word sets among samples. Topics are the core elements of environmental mixtures and the visualization of topic-based samples clarifies the connections of various environments. Based on the model training results, we developed a web application, LEA (Latent Environment Allocation), which provides the way to evaluate typicality and heterogeneity of microbial communities in newly obtained samples without confining environmental categories to be compared. Because topics link words and microbes, LEA also enables to search samples semantically related to the query out of 30,000 microbiome samples.}, }
@article {pmid29866485, year = {2018}, author = {Garin-Fernandez, A and Pereira-Flores, E and Glöckner, FO and Wichels, A}, title = {The North Sea goes viral: Occurrence and distribution of North Sea bacteriophages.}, journal = {Marine genomics}, volume = {41}, number = {}, pages = {31-41}, doi = {10.1016/j.margen.2018.05.004}, pmid = {29866485}, issn = {1876-7478}, mesh = {Bacteriophages/classification/*physiology ; *Biodiversity ; Metagenomics ; North Sea ; Water Movements ; }, abstract = {Marine viruses are dominated by phages and have an enormous influence on microbial population dynamics, due to lysis and horizontal gene transfer. The aim of this study is to analyze the occurrence and diversity of phages in the North Sea, considering the virus-host interactions and biogeographic factors. The virus community of four sampling stations were described using virus metagenomics (viromes). The results show that the virus community was not evenly distributed throughout the North Sea. The dominant phage members were identified as unclassified phage group, followed by Caudovirales order. Myoviridae was the dominant phage family in the North Sea, which occurrence decreased from the coast to the open sea. In contrast, the occurrence of Podoviridae increased and the occurrence of Siphoviridae was low throughout the North Sea. The occurrence of other groups such as Phycodnaviridae decreased from the coast to the open sea. The coastal virus community was genetically more diverse than the open sea community. The influence of riverine inflow and currents, for instance the English Channel flow affects the genetic virus diversity with the community carrying genes from a variety of metabolic pathways and other functions. The present study offers the first insights in the virus community in the North Sea using viromes and shows the variation in virus diversity and the genetic information moved from coastal to open sea areas.}, }
@article {pmid29860637, year = {2019}, author = {Torres, PJ and Thompson, J and McLean, JS and Kelley, ST and Edlund, A}, title = {Discovery of a Novel Periodontal Disease-Associated Bacterium.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {267-276}, pmid = {29860637}, issn = {1432-184X}, support = {R00 DE024543/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; U26IHS300292//National Institutes of Health/ ; }, mesh = {Alaska Natives ; Bacteroidetes/*classification/genetics/*isolation &amp; purification/*pathogenicity ; California ; Dental Plaque/microbiology ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Humans ; Indians, North American ; Metagenomics ; Microbiota ; Multigene Family ; Periodontal Diseases/*microbiology ; Periodontitis/microbiology ; *Phylogeny ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {One of the world's most common infectious disease, periodontitis (PD), derives from largely uncharacterized communities of oral bacteria growing as biofilms (a.k.a. plaque) on teeth and gum surfaces in periodontal pockets. Bacteria associated with periodontal disease trigger inflammatory responses in immune cells, which in later stages of the disease cause loss of both soft and hard tissue structures supporting teeth. Thus far, only a handful of bacteria have been characterized as infectious agents of PD. Although deep sequencing technologies, such as whole community shotgun sequencing have the potential to capture a detailed picture of highly complex bacterial communities in any given environment, we still lack major reference genomes for the oral microbiome associated with PD and other diseases. In recent work, by using a combination of supervised machine learning and genome assembly, we identified a genome from a novel member of the Bacteroidetes phylum in periodontal samples. Here, by applying a comparative metagenomics read-classification approach, including 272 metagenomes from various human body sites, and our previously assembled draft genome of the uncultivated Candidatus Bacteroides periocalifornicus (CBP) bacterium, we show CBP's ubiquitous distribution in dental plaque, as well as its strong association with the well-known pathogenic &quot;red complex&quot; that resides in deep periodontal pockets.}, }
@article {pmid29858829, year = {2018}, author = {Gupta, SK and Shin, H and Han, D and Hur, HG and Unno, T}, title = {Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {56}, number = {6}, pages = {408-415}, pmid = {29858829}, issn = {1976-3794}, mesh = {Anti-Bacterial Agents/*toxicity ; Bacteria/*classification/drug effects/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Metals, Heavy/*toxicity ; Microbial Consortia/genetics ; Phylogeny ; Republic of Korea ; Sequence Analysis ; Sewage/microbiology ; Waste Water/*microbiology ; Water Purification ; }, abstract = {The increased antibiotic resistance among microorganisms has resulted into growing interest for investigating the wastewater treatment plants (WWTPs) as they are reported to be the major source in the dissemination of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment. In this study, we investigated the prevalence and persistence of ARGs and HMRGs as well as bacterial diversity and mobile genetic elements (MGEs) in influent and effluent at the WWTP in Gwangju, South Korea, using high-throughput sequencing based metagenomic approach. A good number of broad-spectrum of resistance genes (both ARG and HMRG) were prevalent and likely persistent, although large portion of them were successfully removed at the wastewater treatment process. The relative abundance of ARGs and MGEs was higher in effluent as compared to that of influent. Our results suggest that the resistance genes with high abundance and bacteria harbouring ARGs and MGEs are likely to persist more through the treatment process. On analyzing the microbial community, the phylum Proteobacteria, especially potentially pathogenic species belonging to the genus Acinetobacter, dominated in WWTP. Overall, our study demonstrates that many ARGs and HMRGs may persist the treatment processes in WWTPs and their association to MGEs may contribute to the dissemination of resistance genes among microorganisms in the environment.}, }
@article {pmid29850933, year = {2019}, author = {Gołębiewski, M and Tarasek, A and Sikora, M and Deja-Sikora, E and Tretyn, A and Niklińska, M}, title = {Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {56-75}, doi = {10.1007/s00248-018-1209-x}, pmid = {29850933}, issn = {1432-184X}, support = {UMO-2012/05/NZ8/001362//Narodowe Centrum Nauki/ ; DS758//Uniwersytet Jagielloński w Krakowie/ ; DS759//Uniwersytet Jagielloński w Krakowie/ ; DSC//Uniwersytet Jagielloński w Krakowie/ ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics/metabolism ; *Biodiversity ; DNA/isolation &amp; purification ; DNA, Ribosomal/genetics ; *Decompression ; Ecosystem ; Eukaryota/classification/genetics ; Fungi/classification/genetics ; Metagenomics ; *Microbiota/genetics/physiology ; Pinus/*microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; *Soil Microbiology ; Trees/microbiology ; }, abstract = {Plant litter decomposition is a process enabling biogeochemical cycles closing in ecosystems, and decomposition in forests constitutes the largest part of this process taking place in terrestrial biomes. Microbial communities during litter decomposition were studied mainly with low-throughput techniques not allowing detailed insight, particularly into coniferous litter, as it is more difficult to obtain high quality DNA required for analyses. Motivated by these problems, we analyzed archaeal, bacterial, and eukaryotic communities at three decomposition stages: fresh, 3- and 8-month-old litter by 16/18S rDNA pyrosequencing, aiming at detailed insight into early stages of pine litter decomposition. Archaea were absent from our libraries. Bacterial and eukaryotic diversity was greatest in 8-month-old litter and the same applied to bacterial and fungal rDNA content. Community structure was different at various stages of decomposition, and phyllospheric organisms (bacteria: Acetobacteraceae and Pseudomonadaceae members, fungi: Lophodermium, Phoma) were replaced by communities with metabolic capabilities adapted to the particular stage of decomposition. Sphingomonadaceae and Xanthomonadaceae and fungal genera Sistotrema, Ceuthospora, and Athelia were characteristic for 3-month-old samples, while 8-month-old ones were characterized by Bradyrhizobiaceae and nematodes (Plectus). We suggest that bacterial and eukaryotic decomposer communities change at different stages of pine litter decomposition in a way similar to that in broadleaf litter. Interactions between bacteria and eukaryotes appear to be one of the key drivers of microbial community structure.}, }
@article {pmid29848762, year = {2018}, author = {Garcia, SL and Buck, M and Hamilton, JJ and Wurzbacher, C and Grossart, HP and McMahon, KD and Eiler, A}, title = {Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, pmid = {29848762}, issn = {2379-5042}, mesh = {Bacteria/*metabolism ; Fresh Water/*microbiology ; *Metabolism ; *Microbial Consortia ; Microbial Interactions ; }, abstract = {Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.}, }
@article {pmid29806626, year = {2018}, author = {Mihara, T and Koyano, H and Hingamp, P and Grimsley, N and Goto, S and Ogata, H}, title = {Taxon Richness of &quot;Megaviridae&quot; Exceeds those of Bacteria and Archaea in the Ocean.}, journal = {Microbes and environments}, volume = {33}, number = {2}, pages = {162-171}, pmid = {29806626}, issn = {1347-4405}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; Databases, Genetic ; Evolution, Molecular ; Giant Viruses/*classification/genetics ; Metagenomics ; *Oceans and Seas ; *Phylogeny ; RNA Polymerase II/genetics ; }, abstract = {Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family &quot;Megaviridae&quot;, suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean. In the present study, we compared the taxon richness and phylogenetic diversity of Megaviridae, Bacteria, and Archaea using DNA-dependent RNA polymerase as a common marker gene. By leveraging existing microbial metagenomic data, we found higher richness and phylogenetic diversity in this single viral family than in the two prokaryotic domains. We also obtained results showing that the evolutionary rate alone cannot account for the observed high diversity of Megaviridae lineages. These results suggest that the Megaviridae family has a deep co-evolutionary history with diverse marine protists since the early &quot;Big-Bang&quot; radiation of the eukaryotic tree of life.}, }
@article {pmid29803114, year = {2018}, author = {Wilcox, JJS and Hollocher, H}, title = {Unprecedented Symbiont Eukaryote Diversity Is Governed by Internal Trophic Webs in a Wild Non-Human Primate.}, journal = {Protist}, volume = {169}, number = {3}, pages = {307-320}, doi = {10.1016/j.protis.2018.03.001}, pmid = {29803114}, issn = {1618-0941}, mesh = {Animals ; *Biota ; DNA Barcoding, Taxonomic ; Feces/*parasitology ; Food Chain ; High-Throughput Nucleotide Sequencing ; Macaca fascicularis/*parasitology ; Metagenomics ; Parasites/*classification/*genetics ; Symbiosis ; }, abstract = {Research on host-associated microbiomes has highlighted major divisions between the role of eukaryotes in free-living and symbiont systems. These trends call into question the relevance of macroecological processes to host-associated systems and the relative importance of parasitism, commensalism, and mutualism as evolutionary patterns across the domains of life. However, it is unclear as to whether these apparent differences reflect biological realities or methodologies in community characterization: free-living eukaryotes tend to be characterized using metabarcoding whereas symbiont eukaryotes are typically characterized with microscopy. Here, we utilize an Illumina high-throughput metabarcoding approach to characterize the diversity and dynamics of eukaryotic symbiont communities in the feces of a wild non-human primate, Macaca fascicularis, revealing functionally and taxonomically diverse communities of eukaryotes hitherto unreported from any vertebrate. Importantly, community assembly was consistent with top-down and bottom-up trophic food web dynamics, highlighting the applicability of macroecological principles to these communities. Ultimately, our findings highlight vertebrate-associated symbiont communities of the gut that are much more similar to free-living systems than previously realized. Additionally, our results support a role for symbiosis as a major recurrent life strategy among eukaryotes and highlight the potential for vertebrates to host vast reservoirs of unexplored eukaryotic diversity.}, }
@article {pmid29800679, year = {2018}, author = {Feranchuk, S and Belkova, N and Potapova, U and Kuzmin, D and Belikov, S}, title = {Evaluating the use of diversity indices to distinguish between microbial communities with different traits.}, journal = {Research in microbiology}, volume = {169}, number = {4-5}, pages = {254-261}, doi = {10.1016/j.resmic.2018.03.004}, pmid = {29800679}, issn = {1769-7123}, mesh = {*Algorithms ; Bacteria/*classification/*genetics ; *Biodiversity ; Coral Reefs ; DNA, Bacterial/genetics ; Ecosystem ; Metagenomics/*methods ; Microbial Consortia/*genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Several measures of biodiversity are commonly used to describe microbial communities, analyzed using 16S gene sequencing. A wide range of available experiments on 16S gene sequencing allows us to present a framework for a comparison of various diversity indices. The criterion for the comparison is the statistical significance of the difference in index values for microbial communities with different traits, within the same experiment. The results of the evaluation indicate that Shannon diversity is the most effective measure among the commonly used diversity indices. The results also indicate that, within the present framework, the Gini coefficient as a diversity index is comparable to Shannon diversity, despite the fact that the Gini coefficient, as a diversity estimator, is far less popular in microbiology than several other measures.}, }
@article {pmid29800328, year = {2018}, author = {Birkl, P and Bharwani, A and Kjaer, JB and Kunze, W and McBride, P and Forsythe, P and Harlander-Matauschek, A}, title = {Differences in cecal microbiome of selected high and low feather-pecking laying hens.}, journal = {Poultry science}, volume = {97}, number = {9}, pages = {3009-3014}, pmid = {29800328}, issn = {1525-3171}, mesh = {*Aggression ; Animals ; Bacteria/classification ; Cecum/*microbiology ; Chickens/genetics/*microbiology/*physiology ; Feathers ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Selection, Genetic ; Sequence Analysis, RNA/veterinary ; }, abstract = {In mammals, it has become increasingly clear that the gut microbiota influences not only gastrointestinal physiology but also modulates behavior. In domestic birds, ceca have the greatest gastrointestinal microbial population. Feather-pecking (FP) behavior in laying hens is one of the most important unsolved behavioral issues in modern agriculture. The aim of the present study was to assess the cecal microbial community of divergently selected high (HFP; n = 20) and low (LFP; n = 20) feather-pecking birds at 60 wk of age. The cecal samples were subjected to community profiling of 16S rRNA and in silico metagenomics using a modified bar-coded Illumina sequencing method on a MiSeq Illumina sequencer. Our results revealed that compared to HFP birds, LFP birds are characterized by an increased overall microbial diversity (beta diversity) shown by a difference in the Bray-Curtis index (R2 = 0.171, P < 0.05). Furthermore, operational taxonomic unit comparisons showed an increased presence of Clostridiae and decreased presence of Lactobaccillacae in HFP birds when compared to LFP birds (False Discovery Rate < 0.05, Mann-Whitney comparisons). Our data indicate that there may be differences in the cecal profile between these 2 lines of laying hens. More research, building on this first study using sequencing technology for profiling the chicken cecal microbiome, will be needed in order to reveal if and how there exists a functional link between the performance of FP and the cecal microbial community.}, }
@article {pmid29794413, year = {2018}, author = {Hu, Y and Bai, C and Cai, J and Dai, J and Shao, K and Tang, X and Gao, G}, title = {Co-occurrence Network Reveals the Higher Fragmentation of the Bacterial Community in Kaidu River Than Its Tributaries in Northwestern China.}, journal = {Microbes and environments}, volume = {33}, number = {2}, pages = {127-134}, pmid = {29794413}, issn = {1347-4405}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; China ; Computational Biology ; DNA, Bacterial ; Ecosystem ; Metagenomics ; *Microbial Interactions ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; *Water Microbiology ; }, abstract = {Rivers and their tributaries sculpt the earth's surface, and play an important role in substance circulation and energy flow. Bacteria are involved in most biogeochemical processes in the fluvial ecosystem; however, their pattern distribution in a river and its tributaries has not yet been investigated in detail. In the present study, high-throughput sequencing was employed to examine bacterial communities and their co-occurrence networks between Kaidu River and its nine tributaries in northwestern China. The results obtained demonstrated that both bacterial communities shared a similar dominant sub-community, mainly consisting of Actinobacteria, Bacteroidetes, and Proteobacteria, with Limnohabitans and Variovorax as the dominant genera. In spite of these commonalities, bacterial community structures still significantly differed between these two habitats, which may be related to the distance-related dispersal limitation. Their co-occurrence networks were generally both positively structured. The structural analysis showed that OTUs from the same phyla were more likely to co-occur. Although the keystone genera were taxonomically different between Kaidu River and its tributaries, they both shared common trophic properties in exploiting niches under oligotrophic conditions. We noted that their relative abundances were less than 1%, indicating the over-proportional roles of rare genera in the bacterial community. In addition, the inferred networks showed less nodes and edges, but higher modularity in Kaidu River than its tributaries, suggesting the higher fragmentation of the bacterial community in the mainstream.}, }
@article {pmid29793542, year = {2018}, author = {Li, LG and Yin, X and Zhang, T}, title = {Tracking antibiotic resistance gene pollution from different sources using machine-learning classification.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {93}, pmid = {29793542}, issn = {2049-2618}, support = {172099/14E//Hong Kong General Research Fund/International ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; China ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Machine Learning ; Metagenomics ; Sewage/*microbiology ; Soil Microbiology ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) has been a worldwide public health concern. Current widespread AMR pollution has posed a big challenge in accurately disentangling source-sink relationship, which has been further confounded by point and non-point sources, as well as endogenous and exogenous cross-reactivity under complicated environmental conditions. Because of insufficient capability in identifying source-sink relationship within a quantitative framework, traditional antibiotic resistance gene (ARG) signatures-based source-tracking methods would hardly be a practical solution.<br><br>RESULTS: By combining broad-spectrum ARG profiling with machine-learning classification SourceTracker, here we present a novel way to address the question in the era of high-throughput sequencing. Its potential in extensive application was firstly validated by 656 global-scale samples covering diverse environmental types (e.g., human/animal gut, wastewater, soil, ocean) and broad geographical regions (e.g., China, USA, Europe, Peru). Its potential and limitations in source prediction as well as effect of parameter adjustment were then rigorously evaluated by artificial configurations with representative source proportions. When applying SourceTracker in region-specific analysis, excellent performance was achieved by ARG profiles in two sample types with obvious different source compositions, i.e., influent and effluent of wastewater treatment plant. Two environmental metagenomic datasets of anthropogenic interference gradient further supported its potential in practical application. To complement general-profile-based source tracking in distinguishing continuous gradient pollution, a few generalist and specialist indicator ARGs across ecotypes were identified in this study.<br><br>CONCLUSION: We demonstrated for the first time that the developed source-tracking platform when coupling with proper experiment design and efficient metagenomic analysis tools will have significant implications for assessing AMR pollution. Following predicted source contribution status, risk ranking of different sources in ARG dissemination will be possible, thereby paving the way for establishing priority in mitigating ARG spread and designing effective control strategies.}, }
@article {pmid29793532, year = {2018}, author = {Bilen, M and Dufour, JC and Lagier, JC and Cadoret, F and Daoud, Z and Dubourg, G and Raoult, D}, title = {The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {94}, pmid = {29793532}, issn = {2049-2618}, mesh = {Actinobacteria/isolation &amp; purification ; Archaea/*classification/genetics/*isolation &amp; purification ; Bacteria/*classification/genetics/*isolation &amp; purification ; Bacteroidetes/isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Firmicutes/isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics ; Proteobacteria/isolation &amp; purification ; }, abstract = {After a decade of research and metagenomic analyses, our knowledge of the human microbiota appears to have reached a plateau despite promising results. In many studies, culture has proven to be essential in describing new prokaryotic species and filling metagenomic gaps. In 2015, only 2172 different prokaryotic species were reported to have been isolated at least once from the human body as pathogens or commensals. In this review, we update the previous repertoire by reporting the different species isolated from the human body to date, increasing it by 28% to reach a total of 2776 species associated with human beings. They have been classified into 11 different phyla, mostly the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Finally, culturomics contributed up to 66.2% towards updating this repertoire by reporting 400 species, of which 288 were novel. This demonstrates the need to continue the culturing work, which seems essential in order to decipher the hidden human microbial content.}, }
@article {pmid29790949, year = {2018}, author = {Salas-Mani, A and Jeusette, I and Castillo, I and Manuelian, CL and Lionnet, C and Iraculis, N and Sanchez, N and Fernández, S and Vilaseca, L and Torre, C}, title = {Fecal microbiota composition changes after a BW loss diet in Beagle dogs.}, journal = {Journal of animal science}, volume = {96}, number = {8}, pages = {3102-3111}, pmid = {29790949}, issn = {1525-3163}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Body Composition ; Body Weight ; Caloric Restriction/*veterinary ; Diet, Fat-Restricted/*veterinary ; Dietary Fiber ; Dogs/*physiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; *Metagenomics ; Obesity/prevention &amp; control/veterinary ; }, abstract = {In developed countries, dogs and cats frequently suffer from obesity. Recently, gut microbiota composition in humans has been related to obesity and metabolic diseases. This study aimed to evaluate changes in body composition, and gut microbiota composition in obese Beagle dogs after a 17-wk BW loss program. A total of six neutered adult Beagle dogs with an average initial BW of 16.34 ± 1.52 kg and BCS of 7.8 ± 0.1 points (9-point scale) were restrictedly fed with a hypocaloric, low-fat and high-fiber dry-type diet. Body composition was assessed with dual-energy X-ray absorptiometry scan, before (T0) and after (T1) BW loss program. Individual stool samples were collected at T0 and T1 for the 16S rRNA analyses of gut microbiota. Taxonomic analysis was done with amplicon-based metagenomic results, and functional analysis of the metabolic potential of the microbial community was done with shotgun metagenomic results. All dogs reached their ideal BW at T1, with an average weekly proportion of BW loss of -1.07 ± 0.03% of starting BW. Body fat (T0, 7.02 ± 0.76 kg) was reduced by half (P < 0.001), while bone (T0, 0.56 ± 0.06 kg) and muscle mass (T0, 8.89 ± 0.80 kg) remained stable (P > 0.05). The most abundant identified phylum was Firmicutes (T0, 74.27 ± 0.08%; T1, 69.38 ± 0.07%), followed by Bacteroidetes (T0, 12.68 ± 0.08%; T1, 16.68 ± 0.05%), Fusobacteria (T0, 7.45 ± 0.02%; T1, 10.18 ± 0.03%), Actinobacteria (T0, 4.53 ± 0.02%; T1, 3.34 ± 0.01%), and Proteobacteria (T0, 1.06 ± 0.01%; T1, 1.40 ± 0.00%). At genus level, the presence of Clostridium, Lactobacillus, and Dorea, at T1 decreased (P = 0.028), while Allobaculum increased (P = 0.046). Although the microbiota communities at T0 and T1 showed a low separation level when compared (Anosim's R value = 0.39), they were significantly biodiverse (P = 0.01). Those differences on microbiota composition could be explained by 13 genus (α = 0.05, linear discriminant analysis (LDA) score > 2.0). Additionally, differences between both communities could also be explained by the expression of 18 enzymes and 27 pathways (α = 0.05, LDA score > 2.0). In conclusion, restricted feeding of a low-fat and high-fiber dry-type diet successfully modifies gut microbiota in obese dogs, increasing biodiversity with a different representation of microbial genus and metabolic pathways.}, }
@article {pmid29790941, year = {2018}, author = {Batut, B and Gravouil, K and Defois, C and Hiltemann, S and Brugère, JF and Peyretaillade, E and Peyret, P}, title = {ASaiM: a Galaxy-based framework to analyze microbiota data.}, journal = {GigaScience}, volume = {7}, number = {6}, pages = {}, pmid = {29790941}, issn = {2047-217X}, mesh = {Base Sequence ; Metagenomics ; *Microbiota ; *Software ; *Statistics as Topic ; }, abstract = {Background: New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies.<br><br>Findings: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore, and visualize microbiota information from raw metataxonomic, metagenomic, or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io).<br><br>Conclusions: Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation, and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible, and shareable.}, }
@article {pmid29789015, year = {2018}, author = {Panebianco, C and Andriulli, A and Pazienza, V}, title = {Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {92}, pmid = {29789015}, issn = {2049-2618}, support = {RC1703GA31//Ministero della Salute/International ; RC1503GA40//Ministero della Salute/International ; }, mesh = {Antineoplastic Agents/*metabolism/*therapeutic use ; Bacteria/*metabolism ; Dysbiosis/*chemically induced ; Gastrointestinal Microbiome/*physiology ; Humans ; Intestines/microbiology ; Neoplasms/*drug therapy/microbiology ; Prebiotics ; Probiotics/*therapeutic use ; Synbiotics ; }, abstract = {Cancer is a major health burden worldwide, and despite continuous advances in medical therapies, resistance to standard drugs and adverse effects still represent an important cause of therapeutic failure. There is a growing evidence that gut bacteria can affect the response to chemo- and immunotherapeutic drugs by modulating either efficacy or toxicity. Moreover, intratumor bacteria have been shown to modulate chemotherapy response. At the same time, anticancer treatments themselves significantly affect the microbiota composition, thus disrupting homeostasis and exacerbating discomfort to the patient. Here, we review the existing knowledge concerning the role of the microbiota in mediating chemo- and immunotherapy efficacy and toxicity and the ability of these therapeutic options to trigger dysbiotic condition contributing to the severity of side effects. In addition, we discuss the use of probiotics, prebiotics, synbiotics, postbiotics, and antibiotics as emerging strategies for manipulating the microbiota in order to improve therapeutic outcome or at least ensure patients a better quality of life all along of anticancer treatments.}, }
@article {pmid29788417, year = {2018}, author = {Patil, RD and Ellison, MJ and Wolff, SM and Shearer, C and Wright, AM and Cockrum, RR and Austin, KJ and Lamberson, WR and Cammack, KM and Conant, GC}, title = {Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes.}, journal = {Journal of animal science}, volume = {96}, number = {6}, pages = {2113-2124}, pmid = {29788417}, issn = {1525-3163}, mesh = {Animal Feed/*analysis ; Animals ; Female ; *Gastrointestinal Microbiome ; *Metabolic Networks and Pathways ; *Metagenomics ; Rumen/metabolism/microbiology ; Sheep/microbiology/*physiology ; }, abstract = {Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not. We conducted shotgun sequencing of microbial DNA from the rumen contents of 16 sheep that differed in their residual feed intake (RFI), a measure of feed efficiency. Metagenomic reads from each sheep were mapped onto a database-derived microbial metabolic network, which was linked to the sheep metabolic network by interface metabolites (metabolites transferred from microbes to host). No single enzyme was identified as being significantly different in abundance between the low and high RFI animals (P > 0.05, Wilcoxon test). However, when we analyzed the metabolic network as a whole, we found several differences between efficient and inefficient animals. Microbes from low RFI (efficient) animals use a suite of enzymes closer in network space to the host's reactions than those of the high RFI (inefficient) animals. Similarly, low RFI animals have microbial metabolic networks that, on average, contain reactions using shorter carbon chains than do those of high RFI animals, potentially allowing the host animals to extract metabolites more efficiently. Finally, the efficient animals possess community networks with greater Shannon diversity among their enzymes than do inefficient ones. Thus, our system approach to the ruminal microbiome identified differences attributable to feed efficiency in the structure of the microbes' community metabolic network that were undetected at the level of individual microbial taxa or reactions.}, }
@article {pmid29783653, year = {2018}, author = {Li, H and Liu, X and Chen, F and Zuo, K and Wu, C and Yan, Y and Chen, W and Lin, W and Xie, Q}, title = {Avian Influenza Virus Subtype H9N2 Affects Intestinal Microbiota, Barrier Structure Injury, and Inflammatory Intestinal Disease in the Chicken Ileum.}, journal = {Viruses}, volume = {10}, number = {5}, pages = {}, pmid = {29783653}, issn = {1999-4915}, mesh = {Animals ; Chickens/*virology ; Cytokines/genetics/metabolism ; DNA, Bacterial/genetics ; Enteritis/metabolism ; Escherichia coli/metabolism ; *Gastrointestinal Microbiome ; Influenza A Virus, H9N2 Subtype/*physiology ; Influenza in Birds/immunology/metabolism/*microbiology ; Intestinal Mucosa/*injuries ; Metagenomics ; RNA, Messenger/metabolism ; RNA, Ribosomal, 16S/genetics ; Specific Pathogen-Free Organisms ; }, abstract = {Avian influenza virus subtype H9N2 (H9N2 AIV) has caused significant losses to the poultry industry due to the high mortality associated with secondary infections attributable to E. coli. This study tries to address the underlying secondary mechanisms after H9N2 AIV infection. Initially, nine day-old specific pathogen-free chickens were assigned to control (uninfected) and H9N2-infected groups, respectively. Using Illumina sequencing, histological examination, and quantitative real-time PCR, it was found that H9N2 AIV caused intestinal microbiota disorder, injury, and inflammatory damage to the intestinal mucosa. Notably, the genera Escherichia, especially E. coli, significantly increased (p < 0.01) at five days post-infection (dpi), while Lactobacillus, Enterococcus, and other probiotic organisms were significantly reduced (p < 0.01). Simultaneously, the mRNA expression of tight junction proteins (ZO-1, claudin 3, and occludin), TFF2, and Muc2 were significantly reduced (p < 0.01), indicating the destruction of the intestinal epithelial cell tight junctions and the damage of mucin layer construction. Moreover, the mRNA expression of proinflammatory cytokines IFN-γ, IL-22, IFN-α, and IL-17A in intestinal epithelial cells were significantly upregulated, resulting in the inflammatory response and intestinal injury. Our findings may provide a theoretical basis for observed gastroenteritis-like symptoms such as diarrhea and secondary E. coli infection following H9N2 AIV infection.}, }
@article {pmid29773467, year = {2018}, author = {Daliri, EB and Tango, CN and Lee, BH and Oh, DH}, title = {Human microbiome restoration and safety.}, journal = {International journal of medical microbiology : IJMM}, volume = {308}, number = {5}, pages = {487-497}, doi = {10.1016/j.ijmm.2018.05.002}, pmid = {29773467}, issn = {1618-0607}, mesh = {Anti-Bacterial Agents ; Bacteria/classification/isolation &amp; purification ; Diet ; Dysbiosis/*therapy ; Fecal Microbiota Transplantation/*adverse effects/methods ; Gastrointestinal Microbiome/*physiology ; Humans ; Probiotics/*administration &amp; dosage ; }, abstract = {The human gut microbiome consists of many bacteria which are in symbiotic relationship with human beings. The gut microbial metabolism, as well as the microbial-host co-metabolism, has been found to greatly influence health and disease. Factors such as diet, antibiotic use and lifestyle have been associated with alterations in the gut microbial community and may result in several pathological conditions. For this reason, several strategies including fecal microbiota transplant and probiotic administration have been applied and proven to be feasible and effective in restoring the gut microbiota in humans. Yet, safety concerns such as potential health risks that may arise from such interventions and how these strategies are regulated need to be addressed. Also, it will be important to know if these microbiome restoration strategies can have a profound impact on health. This review provides an overview of our current knowledge of the microbiome restoration strategies and safety issues on how these strategies are regulated.}, }
@article {pmid29768437, year = {2018}, author = {Willmann, C and Mata, X and Hanghoej, K and Tonasso, L and Tisseyre, L and Jeziorski, C and Cabot, E and Chevet, P and Crubézy, E and Orlando, L and Esclassan, R and Thèves, C}, title = {Oral health status in historic population: Macroscopic and metagenomic evidence.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0196482}, pmid = {29768437}, issn = {1932-6203}, mesh = {DNA, Ancient/isolation &amp; purification ; DNA, Bacterial/genetics/history/isolation &amp; purification ; Dental Caries/history/microbiology/pathology ; Female ; France ; Health Status ; History, 18th Century ; Humans ; Male ; Metagenomics ; Microbiota/genetics ; Oral Health/*history ; Paleodontology ; Periodontitis/history/microbiology/pathology ; Rural Population/history ; }, abstract = {Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macroscopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces viscosus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olsenella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or periodontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual.}, }
@article {pmid29762899, year = {2018}, author = {Zhang, X and Chen, Y and Zhu, J and Zhang, M and Ho, CT and Huang, Q and Cao, J}, title = {Metagenomics Analysis of Gut Microbiota in a High Fat Diet-Induced Obesity Mouse Model Fed with (-)-Epigallocatechin 3-O-(3-O-Methyl) Gallate (EGCG3″Me).}, journal = {Molecular nutrition &amp; food research}, volume = {62}, number = {13}, pages = {e1800274}, doi = {10.1002/mnfr.201800274}, pmid = {29762899}, issn = {1613-4133}, mesh = {Animals ; Diet, High-Fat ; Disease Models, Animal ; Gallic Acid/*analogs &amp; derivatives/pharmacology ; *Gastrointestinal Microbiome ; Male ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*microbiology ; }, abstract = {SCOPE: (-)-Epigallocatechin 3-O-(3-O-methyl) gallate (EGCG3″Me) has been shown to have a modulatory effect on human intestinal microbiota, and the relationship between intestinal flora and obesity has attracted more and more attention recently. Here, the potential link between EGCG3″Me and gut microbiota composition, as well as the underlying mechanisms of the anti-obesity activity of EGCG3″Me are investigated.<br><br>METHODS AND RESULTS: EGCG3″Me was prepared from oolong tea by column chromatography, and the influence of EGCG3″Me on intestinal microbiota was analyzed using a human-flora-associated high fat diet (HFD)-induced obesity mouse model by metagenomics. EGCG3″Me showed a weight reducing effect, ameliorated the HFD-induced gut dysbiosis, and significantly decreased the ratio of Firmicutes/Bacteroidetes. Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database provided significant differences in differentially expressed genes in response to EGCG3″Me treatment. The results showed enrichment of genes involved in the biosynthesis of amino acids, the two-component system, ATP-binding cassette (ABC) transporters, purine metabolism, and carbon metabolism.<br><br>CONCLUSION: An EGCG3″Me supplemented diet produces promising effects on gut microecology by enhancing beneficial microbial populations and by affecting metabolic pathways including amino acids biosynthesis, the two-component system, and ABC transporters, contributing to the improvement of host health.}, }
@article {pmid29760079, year = {2018}, author = {Wang, GD and Zhang, BL and Zhou, WW and Li, YX and Jin, JQ and Shao, Y and Yang, HC and Liu, YH and Yan, F and Chen, HM and Jin, L and Gao, F and Zhang, Y and Li, H and Mao, B and Murphy, RW and Wake, DB and Zhang, YP and Che, J}, title = {Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {22}, pages = {E5056-E5065}, pmid = {29760079}, issn = {1091-6490}, mesh = {Animals ; Anura/*genetics/*physiology ; Gene Flow/*genetics ; *Genetic Speciation ; Hybridization, Genetic ; Metagenomics ; Phylogeny ; Selection, Genetic ; Tibet ; }, abstract = {Tibetan frogs, Nanorana parkeri, are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome. Selection accounts for 579 broadly scattered, highly divergent regions (HDRs) of the genome, which involve 365 genes. These genes fall into 51 gene ontology (GO) functional classes, 14 of which are likely to be important in driving reproductive isolation. GO enrichment analyses of E reveal many overrepresented functional categories associated with adaptation to high elevations, including blood circulation, response to hypoxia, and UV radiation. Four genes, including DNAJC8 in the brain, TNNC1 and ADORA1 in the heart, and LAMB3 in the lung, differ in levels of expression between low- and high-elevation populations. High-altitude adaptation plays an important role in maintaining and driving continuing divergence and reproductive isolation. Use of total genomes enabled recognition of selection and adaptation in and between populations, as well as documentation of evolution along a stepped cline toward speciation.}, }
@article {pmid29759899, year = {2018}, author = {Belgini, DRB and Siqueira, VM and Oliveira, DM and Fonseca, SG and Piccin-Santos, V and Dias, RS and Quartaroli, L and Souza, RS and Torres, APR and Sousa, MP and Silva, CM and Silva, CC and De Paula, SO and Oliveira, VM}, title = {Integrated diversity analysis of the microbial community in a reverse osmosis system from a Brazilian oil refinery.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {5}, pages = {473-486}, doi = {10.1016/j.syapm.2018.03.007}, pmid = {29759899}, issn = {1618-0984}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biodiversity ; Biofilms/growth &amp; development ; Brazil ; Fungi/*classification/genetics/isolation &amp; purification/physiology ; Metagenomics ; *Microbial Consortia ; *Oil and Gas Industry ; Osmosis ; Waste Water/*microbiology ; Water Purification/*methods ; }, abstract = {Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality. In this study, the microbial diversity of feedwater and reverse osmosis membranes was investigated using a combination of culture-dependent and culture-independent methods in order to characterize the microorganisms colonizing and deteriorating the membranes. In total, 37 bacterial isolates, 17 filamentous fungi and approximately 400 clones were obtained and analyzed. Among the bacterial genera identified, the most represented were Sphingobium, Acidovorax, Microbacterium, Rhizobium and Shinella. The results revealed genera that acted as candidate key players in initial biofilm formation in membrane systems, and provided important information concerning the microbial ecology of oligotrophic aquatic systems.}, }
@article {pmid29758429, year = {2018}, author = {Najar, IN and Sherpa, MT and Das, S and Das, S and Thakur, N}, title = {Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry.}, journal = {The Science of the total environment}, volume = {637-638}, number = {}, pages = {730-745}, doi = {10.1016/j.scitotenv.2018.05.037}, pmid = {29758429}, issn = {1879-1026}, mesh = {Archaea ; Biodiversity ; *Ecology ; Hot Springs/*microbiology ; India ; Phylogeny ; RNA, Ribosomal, 16S ; Sikkim ; }, abstract = {Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, pH, alkalinity, Ca2+, Mg2+, Cl2+, and sulfur were main environmental variables influencing the microbial community composition and diversity. Also the piper diagram suggested that the water of both the hot springs are Ca-HCO3- type and can be predicted as shallow fresh ground waters. This study has provided an insight into the ecological interaction of the diverse microbial communities and associated physicochemical parameters, which will help in determining the future studies on different biogeochemical pathways in these hot springs.}, }
@article {pmid29750384, year = {2018}, author = {Kosnicki, KL and Penprase, JC and Cintora, P and Torres, PJ and Harris, GL and Brasser, SM and Kelley, ST}, title = {Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome.}, journal = {Addiction biology}, volume = {}, number = {}, pages = {}, pmid = {29750384}, issn = {1369-1600}, support = {R21 AA023291/AA/NIAAA NIH HHS/United States ; }, abstract = {Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans. The gut microbiota of rats voluntarily consuming a 20 percent ethanol solution, on alternate days, were compared with a non-exposed control group to identify differential taxonomic and functional profiles. Gut microbial diversity profiles were determined using culture-independent amplification, next-generation sequencing and bioinformatic analysis of bacterial 16S ribosomal RNA gene sequence libraries. Our results showed that, compared with controls, ethanol-consuming rats experienced a significant decline in the biodiversity of their gut microbiomes, a state generally associated with dysbiosis. We also observed significant shifts in the overall diversity of the gut microbial communities and a dramatic change in the relative abundance of particular microbes, such as the Lactobacilli. We also compared our results to human fecal microbiome data collected as part of the citizen science American Gut Project. In contrast to the rat data, human drinkers had significantly higher gut microbial biodiversity than non-drinkers. However, we also observed that microbes that differed among the human subjects displayed similar trends in the rat model, including bacteria implicated in metabolic disease.}, }
@article {pmid29748902, year = {2018}, author = {Escudero, L and Oetiker, N and Gallardo, K and Tebes-Cayo, C and Guajardo, M and Nuñez, C and Davis-Belmar, C and Pueyo, JJ and Chong Díaz, G and Demergasso, C}, title = {A thiotrophic microbial community in an acidic brine lake in Northern Chile.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {8}, pages = {1403-1419}, doi = {10.1007/s10482-018-1087-8}, pmid = {29748902}, issn = {1572-9699}, support = {1100795//Fondecyt/ ; 32002137//BHP Minerals Americas/ ; }, mesh = {Bacteria/*classification/metabolism ; Biodiversity ; Carbon Cycle ; Chile ; DNA, Bacterial/genetics ; Energy Metabolism ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salts ; Sulfur/*metabolism ; }, abstract = {The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.}, }
@article {pmid29743119, year = {2018}, author = {Zolfo, M and Asnicar, F and Manghi, P and Pasolli, E and Tett, A and Segata, N}, title = {Profiling microbial strains in urban environments using metagenomic sequencing data.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {9}, pmid = {29743119}, issn = {1745-6150}, mesh = {Acinetobacter/genetics ; Genome, Bacterial/genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; }, abstract = {BACKGROUND: The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context. It is thus currently unclear whether such methods, that have proven successful at distinguishing even closely related strains in human microbiomes, are also effective in urban settings for tasks such as cultivation-free pathogen detection and microbial surveillance. Here, we aimed at a) testing the currently available metagenomic profiling tools on urban metagenomics; b) characterizing the organisms in urban environment at the resolution of single strain and c) discussing the biological insights that can be inferred from such methods.<br><br>RESULTS: We applied three complementary methods on the 1614 metagenomes of the CAMDA 2017 challenge. With MetaMLST we identified 121 known sequence-types from 15 species of clinical relevance. For instance, we identified several Acinetobacter strains that were close to the nosocomial opportunistic pathogen A. nosocomialis. With StrainPhlAn, a generalized version of the MetaMLST approach, we inferred the phylogenetic structure of Pseudomonas stutzeri strains and suggested that the strain-level heterogeneity in environmental samples is higher than in the human microbiome. Finally, we also probed the functional potential of the different strains with PanPhlAn. We further showed that SNV-based and pangenome-based profiling provide complementary information that can be combined to investigate the evolutionary trajectories of microbes and to identify specific genetic determinants of virulence and antibiotic resistances within closely related strains.<br><br>CONCLUSION: We show that strain-level methods developed primarily for the analysis of human microbiomes can be effective for city-associated microbiomes. In fact, (opportunistic) pathogens can be tracked and monitored across many hundreds of urban metagenomes. However, while more effort is needed to profile strains of currently uncharacterized species, this work poses the basis for high-resolution analyses of microbiomes sampled in city and mass transportation environments.<br><br>REVIEWERS: This article was reviewed by Alexandra Bettina Graf, Daniel Huson and Trevor Cickovski.}, }
@article {pmid29740407, year = {2018}, author = {Nooij, S and Schmitz, D and Vennema, H and Kroneman, A and Koopmans, MPG}, title = {Overview of Virus Metagenomic Classification Methods and Their Biological Applications.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {749}, pmid = {29740407}, issn = {1664-302X}, abstract = {Metagenomics poses opportunities for clinical and public health virology applications by offering a way to assess complete taxonomic composition of a clinical sample in an unbiased way. However, the techniques required are complicated and analysis standards have yet to develop. This, together with the wealth of different tools and workflows that have been proposed, poses a barrier for new users. We evaluated 49 published computational classification workflows for virus metagenomics in a literature review. To this end, we described the methods of existing workflows by breaking them up into five general steps and assessed their ease-of-use and validation experiments. Performance scores of previous benchmarks were summarized and correlations between methods and performance were investigated. We indicate the potential suitability of the different workflows for (1) time-constrained diagnostics, (2) surveillance and outbreak source tracing, (3) detection of remote homologies (discovery), and (4) biodiversity studies. We provide two decision trees for virologists to help select a workflow for medical or biodiversity studies, as well as directions for future developments in clinical viral metagenomics.}, }
@article {pmid29739908, year = {2018}, author = {Gladieux, P}, title = {Updates in the Language of Histoplasma Biodiversity.}, journal = {mBio}, volume = {9}, number = {3}, pages = {}, pmid = {29739908}, issn = {2150-7511}, mesh = {*Biodiversity ; Biological Evolution ; Genetic Speciation ; *Histoplasma ; Humans ; Metagenomics ; Phylogeny ; }, abstract = {In a recent article, Sepúlveda et al. (mBio 8:e01339-17, 2017, https://doi.org/10.1128/mBio.01339-17) investigated the genetic structure and evolutionary history of the human pathogen Histoplasma Using whole-genome resequencing data, Sepúlveda et al. found that the Histoplasma genus is composed of at least four strongly differentiated lineages. Their tour de force is to use a smart combination of population genomic approaches to show that the advanced stage of intraspecific divergence observed within Histoplasma does not simply reflect population structure, but instead results from previously unidentified speciation events. The four independently evolving Histoplasma lineages are elevated to the species status and assigned names. The newly described species exhibit medically important differences in phenotype, and these findings, therefore, have important epidemiological implications. This work provides a blueprint for phylogenomic species recognition in fungi, opening the way for a new age of enlightenment in which fungal species are diagnosed using highly discriminatory tools within a hypothesis-testing framework.}, }
@article {pmid29738477, year = {2018}, author = {Klimenko, NS and Tyakht, AV and Popenko, AS and Vasiliev, AS and Altukhov, IA and Ischenko, DS and Shashkova, TI and Efimova, DA and Nikogosov, DA and Osipenko, DA and Musienko, SV and Selezneva, KS and Baranova, A and Kurilshikov, AM and Toshchakov, SM and Korzhenkov, AA and Samarov, NI and Shevchenko, MA and Tepliuk, AV and Alexeev, DG}, title = {Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project.}, journal = {Nutrients}, volume = {10}, number = {5}, pages = {}, pmid = {29738477}, issn = {2072-6643}, mesh = {Bacteroidetes/genetics/isolation &amp; purification ; Bifidobacterium/genetics/isolation &amp; purification ; Clostridium/genetics/isolation &amp; purification ; Cluster Analysis ; *Diet ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Methanobrevibacter/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sample Size ; Sequence Analysis, DNA ; }, abstract = {Personalized nutrition is of increasing interest to individuals actively monitoring their health. The relations between the duration of diet intervention and the effects on gut microbiota have yet to be elucidated. Here we examined the associations of short-term dietary changes, long-term dietary habits and lifestyle with gut microbiota. Stool samples from 248 citizen-science volunteers were collected before and after a self-reported 2-week personalized diet intervention, then analyzed using 16S rRNA sequencing. Considerable correlations between long-term dietary habits and gut community structure were detected. A higher intake of vegetables and fruits was associated with increased levels of butyrate-producing Clostridiales and higher community richness. A paired comparison of the metagenomes before and after the 2-week intervention showed that even a brief, uncontrolled intervention produced profound changes in community structure: resulting in decreased levels of Bacteroidaceae, Porphyromonadaceae and Rikenellaceae families and decreased alpha-diversity coupled with an increase of Methanobrevibacter, Bifidobacterium, Clostridium and butyrate-producing Lachnospiraceae- as well as the prevalence of a permatype (a bootstrapping-based variation of enterotype) associated with a higher diversity of diet. The response of microbiota to the intervention was dependent on the initial microbiota state. These findings pave the way for the development of an individualized diet.}, }
@article {pmid29729565, year = {2018}, author = {Chen, L and Hu, C and Lok-Shun Lai, N and Zhang, W and Hua, J and Lam, PKS and Lam, JCW and Zhou, B}, title = {Acute exposure to PBDEs at an environmentally realistic concentration causes abrupt changes in the gut microbiota and host health of zebrafish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {240}, number = {}, pages = {17-26}, doi = {10.1016/j.envpol.2018.04.062}, pmid = {29729565}, issn = {1873-6424}, mesh = {Animals ; Bacteria ; Female ; Gastrointestinal Microbiome/*drug effects ; Halogenated Diphenyl Ethers/metabolism/*toxicity ; Intestinal Mucosa/metabolism ; Liver/metabolism ; Male ; Metagenomics ; Water Pollutants, Chemical/*toxicity ; Zebrafish/microbiology/*physiology ; }, abstract = {Contamination from lower brominated PBDEs is ubiquitous in the environments. However, their effects on gut microbiota and intestinal health have not yet been investigated. This study exposed adult zebrafish to an environmentally realistic concentration of pentaBDE mixture (DE-71) at 5.0 ng/L for 7 days, after which metagenomic sequencing of the intestinal microbiome was conducted and host physiological activities in the intestine and liver were also examined. The results showed that acute exposure to DE-71 significantly shifted the gut microbial community in a sex-specific manner. Certain genera (e.g., Mycoplasma, Ruminiclostridium, unclassified Firmicutes sensu stricto, and Fusobacterium) disappeared from the DE-71-exposed intestines, resulting in decreased bacterial diversity. Bacterial metabolic functions in guts were also affected by DE-71, namely those covering energy metabolism, virulence, respiration, cell division, cell signaling, and stress response. In addition, measurement of diverse sensitive biomarkers showed that the health of male intestines was remarkably compromised by the DE-71 exposure, as indicated by the disruption to its neural signaling (serotonin), epithelial barrier integrity (tight junction protein 2), inflammatory response (interleukin 1β), oxidative stress and antioxidant capacity, as well as detoxifying potential (ethoxyresorufin-O-deethylase activity). However, female intestines maintained intact physiological activities. Compared to the direct impact on intestines, a latent effect of DE-71 was observed in livers. Co-occurrence network analysis demonstrated that the gut bacteria vigorously interacted to establish the fittest community under DE-71 stress by promoting the reproduction of favorable genera, while diminishing the survival of unfavorable ones. Significant correlations between the zebrafish gut microbiota and physiological activities (e.g., oxidative stress, detoxification, neurotransmission, and epithelial integrity) were also observed. Overall, this study has demonstrated, for the first time, the high susceptibility of gut microbiota and intestinal health of zebrafish to DE-71, thus warranting more work to reveal its mode of toxicity.}, }
@article {pmid29721711, year = {2018}, author = {Goodfellow, M and Nouioui, I and Sanderson, R and Xie, F and Bull, AT}, title = {Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {8}, pages = {1315-1332}, doi = {10.1007/s10482-018-1088-7}, pmid = {29721711}, issn = {1572-9699}, mesh = {Actinobacteria/*classification/genetics/isolation &amp; purification/metabolism ; Altitude ; Anti-Bacterial Agents/isolation &amp; purification ; *Biodiversity ; Chile ; *Desert Climate ; Ecosystem ; Metagenomics ; *Phylogeny ; *Soil Microbiology ; Species Specificity ; }, abstract = {An &quot;in house&quot; taxonomic approach to drug discovery led to the isolation of diverse actinobacteria from hyper-arid, extreme hyper-arid and very high altitude Atacama Desert soils. A high proportion of the isolates were assigned to novel taxa, with many showing activity in standard antimicrobial plug assays. The application of more advanced taxonomic and screening strategies showed that strains classified as novel species of Lentzea and Streptomyces synthesised new specialised metabolites thereby underpinning the premise that the extreme abiotic conditions in the Atacama Desert favour the development of a unique actinobacterial diversity which is the basis of novel chemistry. Complementary metagenomic analyses showed that the soils encompassed an astonishing degree of actinobacterial 'dark matter', while rank-abundance analyses showed them to be highly diverse habitats mainly composed of rare taxa that have not been recovered using culture-dependent methods. The implications of these pioneering studies on future bioprospecting campaigns are discussed.}, }
@article {pmid29718202, year = {2018}, author = {Wu, L and McCluskey, K and Desmeth, P and Liu, S and Hideaki, S and Yin, Y and Moriya, O and Itoh, T and Kim, CY and Lee, JS and Zhou, Y and Kawasaki, H and Hazbón, MH and Robert, V and Boekhout, T and Lima, N and Evtushenko, L and Boundy-Mills, K and Bunk, B and Moore, ERB and Eurwilaichitr, L and Ingsriswang, S and Shah, H and Yao, S and Jin, T and Huang, J and Shi, W and Sun, Q and Fan, G and Li, W and Li, X and Kurtböke, I and Ma, J}, title = {The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species.}, journal = {GigaScience}, volume = {7}, number = {5}, pages = {}, pmid = {29718202}, issn = {2047-217X}, mesh = {Bacteria/*genetics ; Fungi/*genetics ; Genomics/*methods ; Prokaryotic Cells/*metabolism ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; }, abstract = {Genomic information is essential for taxonomic, phylogenetic, and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microorganisms. Hence, the GCM aims to promote research by deep-mining genomic data.}, }
@article {pmid29705928, year = {2018}, author = {Bonilla, JO and Kurth, DG and Cid, FD and Ulacco, JH and Gil, RA and Villegas, LB}, title = {Prokaryotic and eukaryotic community structure affected by the presence of an acid mine drainage from an abandoned gold mine.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {5}, pages = {699-711}, pmid = {29705928}, issn = {1433-4909}, support = {PICT 2013 No. 3170//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, mesh = {Acids/analysis ; Actinobacteria/isolation &amp; purification ; Diatoms/isolation &amp; purification ; *Extreme Environments ; Fungi/isolation &amp; purification ; Gammaproteobacteria/isolation &amp; purification ; Geologic Sediments/chemistry/*microbiology ; Gold/analysis ; Metagenome ; Metals, Heavy/analysis ; *Microbiota ; Mining ; }, abstract = {The acid mine drainage that originates in the abandoned gold mine in San Luis, Argentina, is released into La Carolina stream. The aim of this study was to determine the influence of this mine drainage on the physicochemical parameters of the area studied and on both prokaryotic and eukaryotic community structure. In addition, specific relationships between microbial taxonomic groups and physicochemical parameters were established. The drainage that flows into La Carolina stream acidifies the stream and increases its sulfate, Zn, Cd and Te concentrations. Microbial analysis showed that prokaryotic community structure is mainly affected by pH values. Actinobacteria and Gammaproteobacteria were abundant in samples characterized by low pH values, while Nitrospirae, Chloroflexi, Deltaproteobacteria, Thaumarchaeota and Euryarchaeota were associated with high concentrations of heavy metals. Otherwise, Alphaproteobacteria was present in samples taken in sunlit areas. Regarding eukaryotic community structure, the sunlight had the greatest impact. Inside the mine, in the absence of light, fungi and protists members were the most abundant microorganisms, while those samples taken in the presence of light displayed algae (green algae and diatoms) as the most abundant ones. After receiving the mine drainage, the stream showed a decrease in the diatom abundance and green algae predominated.}, }
@article {pmid29705728, year = {2018}, author = {Ticinesi, A and Milani, C and Guerra, A and Allegri, F and Lauretani, F and Nouvenne, A and Mancabelli, L and Lugli, GA and Turroni, F and Duranti, S and Mangifesta, M and Viappiani, A and Ferrario, C and Dodi, R and Dall'Asta, M and Del Rio, D and Ventura, M and Meschi, T}, title = {Understanding the gut-kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers.}, journal = {Gut}, volume = {67}, number = {12}, pages = {2097-2106}, doi = {10.1136/gutjnl-2017-315734}, pmid = {29705728}, issn = {1468-3288}, mesh = {Adult ; Aged ; Bacteria/classification/isolation &amp; purification ; Bacterial Typing Techniques ; Biodiversity ; Calcium Oxalate/analysis ; Case-Control Studies ; DNA, Bacterial/analysis ; Energy Intake/physiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; Nephrolithiasis/metabolism/*microbiology ; Oxalates/metabolism ; RNA, Ribosomal, 16S/analysis ; Recurrence ; Young Adult ; }, abstract = {OBJECTIVES: The involvement of the gut microbiota in the pathogenesis of calcium nephrolithiasis has been hypothesised since the discovery of the oxalate-degrading activity of Oxalobacter formigenes, but never comprehensively studied with metagenomics. The aim of this case-control study was to compare the faecal microbiota composition and functionality between recurrent idiopathic calcium stone formers (SFs) and controls.<br><br>DESIGN: Faecal samples were collected from 52 SFs and 48 controls (mean age 48±11). The microbiota composition was analysed through 16S rRNA microbial profiling approach. Ten samples (five SFs, five controls) were also analysed with deep shotgun metagenomics sequencing, with focus on oxalate-degrading microbial metabolic pathways. Dietary habits, assessed through a food-frequency questionnaire, and 24-hour urinary excretion of prolithogenic and antilithogenic factors, including calcium and oxalate, were compared between SFs and controls, and considered as covariates in the comparison of microbiota profiles.<br><br>RESULTS: SFs exhibited lower faecal microbial diversity than controls (Chao1 index 1460±363vs 1658±297, fully adjusted p=0.02 with stepwise backward regression analysis). At multivariate analyses, three taxa (Faecalibacterium, Enterobacter, Dorea) were significantly less represented in faecal samples of SFs. The Oxalobacter abundance was not different between groups. Faecal samples from SFs exhibited a significantly lower bacterial representation of genes involved in oxalate degradation, with inverse correlation with 24-hour oxalate excretion (r=-0.87, p=0.002). The oxalate-degrading genes were represented in several bacterial species, whose cumulative abundance was inversely correlated with oxaluria (r=-0.85, p=0.02).<br><br>CONCLUSIONS: Idiopathic calcium SFs exhibited altered gut microbiota composition and functionality that could contribute to nephrolithiasis physiopathology.}, }
@article {pmid29705130, year = {2018}, author = {Kudo, T and Kobiyama, A and Rashid, J and Reza, MS and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Segawa, S and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis.}, journal = {Gene}, volume = {665}, number = {}, pages = {174-184}, doi = {10.1016/j.gene.2018.04.072}, pmid = {29705130}, issn = {1879-0038}, mesh = {Animals ; *Bacteria/genetics/metabolism ; Bays/*microbiology ; *Genes, Bacterial ; Metagenomics/methods ; *Seasons ; Seawater/*microbiology ; Sulfonium Compounds/*metabolism ; *Water Microbiology ; }, abstract = {Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio Currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.}, }
@article {pmid29705129, year = {2018}, author = {Reza, MS and Kobiyama, A and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kudo, T and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay.}, journal = {Gene}, volume = {665}, number = {}, pages = {185-191}, doi = {10.1016/j.gene.2018.04.074}, pmid = {29705129}, issn = {1879-0038}, mesh = {*Archaea/genetics/growth &amp; development ; *Bacteria/genetics/growth &amp; development ; Bays/*microbiology ; Microbial Consortia/*physiology ; *Plankton/genetics/growth &amp; development ; *Seasons ; *Water Microbiology ; }, abstract = {The Ofunato Bay in the northeastern Pacific Ocean area of Japan possesses the highest biodiversity of marine organisms in the world and has attracted much attention due to its economic and environmental importance. We report here a shotgun metagenomic analysis of the year-round variation in free-living bacterioplankton collected across the entire length of the bay. Phylogenetic differences among spring, summer, autumn and winter bacterioplankton suggested that members of Proteobacteria tended to decrease at high water temperatures and increase at low temperatures. It was revealed that Candidatus Pelagibacter varied seasonally, reaching as much as 60% of all sequences at the genus level in the surface waters during winter. This increase was more evident in the deeper waters, where they reached up to 75%. The relative abundance of Planktomarina also rose during winter and fell during summer. A significant component of the winter bacterioplankton community was Archaea (mainly represented by Nitrosopumilus), as their relative abundance was very low during spring and summer but high during winter. In contrast, Actinobacteria and Cyanobacteria appeared to be higher in abundance during high-temperature periods. It was also revealed that Bacteroidetes constituted a significant component of the summer bacterioplankton community, being the second largest bacterial phylum detected in the Ofunato Bay. Its members, notably Polaribacter and Flavobacterium, were found to be high in abundance during spring and summer, particularly in the surface waters. Principal component analysis and hierarchal clustering analyses showed that the bacterial communities in the Ofunato Bay changed seasonally, likely caused by the levels of organic matter, which would be deeply mixed with surface runoff in the winter.}, }
@article {pmid29705124, year = {2018}, author = {Reza, MS and Kobiyama, A and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kudo, T and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay.}, journal = {Gene}, volume = {665}, number = {}, pages = {192-200}, doi = {10.1016/j.gene.2018.04.075}, pmid = {29705124}, issn = {1879-0038}, mesh = {*Archaea/classification/genetics/growth &amp; development ; *Bacteria/classification/genetics/growth &amp; development ; Bays/*microbiology ; Metagenomics ; Microbial Consortia/*physiology ; *Seasons ; *Water Microbiology ; }, abstract = {The Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias Coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 μm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 μm filters, targeting the free-living fraction only. From the 0.27-0.34 Gb WGS library, 0.9 × 106-1.2 × 106 reads from three sampling stations revealed 29 bacterial phyla (~80% of assigned reads), 3 archaeal phyla (~4%) and 59 eukaryotic phyla (~15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0-19.6% Planktomarina (Family Rhodobacteraceae) and 13.7-17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5-6.1%), Flavobacterium (1.8-2.6%), Sphingobacterium (1.4-1.6%) and Cellulophaga (1.4-2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8-15.2%, 3.6-4.9% and 2.1-3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.}, }
@article {pmid29704757, year = {2018}, author = {Campanaro, S and Treu, L and Kougias, PG and Luo, G and Angelidaki, I}, title = {Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants.}, journal = {Water research}, volume = {140}, number = {}, pages = {123-134}, doi = {10.1016/j.watres.2018.04.043}, pmid = {29704757}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Biofuels ; Bioreactors/*microbiology ; Manure ; *Metagenome ; Metagenomics/methods ; Microbiota/*physiology ; Sewage/microbiology ; Waste Disposal, Fluid ; Waste Water ; }, abstract = {The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome. Canonical correspondence analysis was used to determine the influence of biotic and environmental factors on MAGs abundance and to investigate the methanogenic performance of the biogas plants. Prediction of the functional properties of MAGs was obtained analyzing their KEGG pathways and their carbohydrate active domains. Network analysis allowed investigation of species-species associations and shed light on syntrophic interactions between members belonging to the anaerobic digestion dark matter (phylum Fermentibacteria). By stratifying and comparing different levels of information, it was predicted that some MAGs have a crucial role in the manure-supplemented thermophilic biogas plants and it was highlighted the importance of the glycine cleavage system in complementing the &quot;truncated&quot; Wood-Ljungdahl pathway.}, }
@article {pmid29694379, year = {2018}, author = {Garris, HW and Baldwin, SA and Taylor, J and Gurr, DB and Denesiuk, DR and Van Hamme, JD and Fraser, LH}, title = {Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0196032}, pmid = {29694379}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics/metabolism ; Biodiversity ; Hydrogen-Ion Concentration ; Metagenomics/*methods ; Mining ; Nitrates/metabolism ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Soil/chemistry ; Water/chemistry ; Wetlands ; }, abstract = {We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6 km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.}, }
@article {pmid29694348, year = {2018}, author = {Hoffman, KL and Hutchinson, DS and Fowler, J and Smith, DP and Ajami, NJ and Zhao, H and Scheet, P and Chow, WH and Petrosino, JF and Daniel, CR}, title = {Oral microbiota reveals signs of acculturation in Mexican American women.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0194100}, pmid = {29694348}, issn = {1932-6203}, support = {CA016672/NH/NIH HHS/United States ; R25CA057730/NH/NIH HHS/United States ; }, mesh = {*Acculturation ; Adult ; Aged ; Emigrants and Immigrants ; Female ; Fusobacterium/*isolation &amp; purification ; Humans ; *Mexican Americans ; Microbiota/*physiology ; Middle Aged ; Mouth/*microbiology ; Prevotella/*isolation &amp; purification ; Streptococcus/*isolation &amp; purification ; Young Adult ; }, abstract = {The oral microbiome has been linked to a number of chronic inflammatory conditions, including obesity, diabetes, periodontitis, and cancers of the stomach and liver. These conditions disproportionately affect Mexican American women, yet few studies have examined the oral microbiota in this at-risk group. We characterized the 16S rDNA oral microbiome in 369 non-smoking women enrolled in the MD Anderson Mano a Mano Mexican American Cohort Study. Lower bacterial diversity, a potential indicator of oral health, was associated with increased age and length of US residency among recent immigrants. Grouping women by overarching bacterial community type (e.g., &quot;Streptococcus,&quot; &quot;Fusobacterium,&quot; and &quot;Prevotella&quot; clusters), we observed differences across a number of acculturation-related variables, including nativity, age at immigration, time in the US, country of longest residence, and a multi-dimensional acculturation scale. Participants in the cluster typified by higher abundance of Streptococcus spp. exhibited the lowest bacterial diversity and appeared the most acculturated as compared to women in the &quot;Prevotella&quot; group. Computationally-predicted functional analysis suggested the Streptococcus-dominated bacterial community had greater potential for carbohydrate metabolism while biosynthesis of essential amino acids and nitrogen metabolism prevailed among the Prevotella-high group. Findings suggest immigration and adaption to life in the US, a well-established mediator of disease risk, is associated with differences in oral microbial profiles in Mexican American women. These results warrant further investigation into the joint and modifying effects of acculturation and oral bacteria on the health of Mexican American women and other immigrant populations. The oral microbiome presents an easily accessible biomarker of disease risk, spanning biological, behavioral, and environmental factors.}, }
@article {pmid29690922, year = {2018}, author = {Jaenicke, S and Albaum, SP and Blumenkamp, P and Linke, B and Stoye, J and Goesmann, A}, title = {Flexible metagenome analysis using the MGX framework.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {76}, pmid = {29690922}, issn = {2049-2618}, mesh = {*Database Management Systems ; *Metagenome ; Metagenomics/*methods ; Microbiota ; Reproducibility of Results ; User-Computer Interface ; Workflow ; }, abstract = {BACKGROUND: The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as metagenomics; in particular, the recent advances in sequencing technologies have enabled researchers to study even the most complex communities. Metagenome analysis, the assignment of sequences to taxonomic and functional entities, however, remains a tedious task: large amounts of data need to be processed. There are a number of approaches addressing particular aspects, but scientific questions are often too specific to be answered by a general-purpose method.<br><br>RESULTS: We present MGX, a flexible and extensible client/server-framework for the management and analysis of metagenomic datasets; MGX features a comprehensive set of adaptable workflows required for taxonomic and functional metagenome analysis, combined with an intuitive and easy-to-use graphical user interface offering customizable result visualizations. At the same time, MGX allows to include own data sources and devise custom analysis pipelines, thus enabling researchers to perform basic as well as highly specific analyses within a single application.<br><br>CONCLUSIONS: With MGX, we provide a novel metagenome analysis platform giving researchers access to the most recent analysis tools. MGX covers taxonomic and functional metagenome analysis, statistical evaluation, and a wide range of visualizations easing data interpretation. Its default taxonomic classification pipeline provides equivalent or superior results in comparison to existing tools.}, }
@article {pmid29689266, year = {2018}, author = {Nakatsu, G and Zhou, H and Wu, WKK and Wong, SH and Coker, OO and Dai, Z and Li, X and Szeto, CH and Sugimura, N and Lam, TY and Yu, AC and Wang, X and Chen, Z and Wong, MC and Ng, SC and Chan, MTV and Chan, PKS and Chan, FKL and Sung, JJ and Yu, J}, title = {Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes.}, journal = {Gastroenterology}, volume = {155}, number = {2}, pages = {529-541.e5}, doi = {10.1053/j.gastro.2018.04.018}, pmid = {29689266}, issn = {1528-0012}, mesh = {Austria/epidemiology ; Biomarkers, Tumor/*analysis ; Case-Control Studies ; Cohort Studies ; Colonoscopy ; Colorectal Neoplasms/diagnostic imaging/mortality/pathology/*virology ; Cross-Sectional Studies ; Dysbiosis/diagnostic imaging/*virology ; Feces/virology ; Female ; France/epidemiology ; Gastrointestinal Microbiome/*genetics ; Germany/epidemiology ; Hong Kong/epidemiology ; Humans ; Male ; Metagenomics ; Middle Aged ; Sensitivity and Specificity ; Survival Analysis ; Viruses/*genetics ; }, abstract = {BACKGROUND &amp; AIMS: Patients with colorectal cancer (CRC) have a different gut microbiome signature than individuals without CRC. Little is known about the viral component of CRC-associated microbiome. We aimed to identify and validate viral taxonomic markers of CRC that might be used in detection of the disease or predicting outcome.<br><br>METHODS: We performed shotgun metagenomic analyses of viromes of fecal samples from 74 patients with CRC (cases) and 92 individuals without CRC (controls) in Hong Kong (discovery cohort). Viral sequences were classified by taxonomic alignment against an integrated microbial reference genome database. Viral markers associated with CRC were validated using fecal samples from 3 separate cohorts: 111 patients with CRC and 112 controls in Hong Kong, 46 patients with CRC and 63 controls in Austria, and 91 patients with CRC and 66 controls in France and Germany. Using abundance profiles of CRC-associated virome genera, we constructed random survival forest models to identify those associated with patient survival times.<br><br>RESULTS: The diversity of the gut bacteriophage community was significantly increased in patients with CRC compared with controls. Twenty-two viral taxa discriminated cases from controls with an area under the receiver operating characteristic curve of 0.802 in the discovery cohort. The viral markers were validated in 3 cohorts, with area under the receiver operating characteristic curves of 0.763, 0.736, and 0.715, respectively. Clinical subgroup analysis showed that dysbiosis of the gut virome was associated with early- and late-stage CRC. A combination of 4 taxonomic markers associated with reduced survival of patients with CRC (log-rank test, P = 8.1 × 10-6) independently of tumor stage, lymph node metastases, or clinical parameters. We found altered interactions between bacteriophages and oral bacterial commensals in fecal samples from patients with CRC compared with controls.<br><br>CONCLUSIONS: In a metagenomic analysis of fecal samples from patients and controls, we identified virome signatures associated with CRC. These data might be used to develop tools to identify individuals with CRC or predict outcomes.}, }
@article {pmid29687353, year = {2018}, author = {Allali, I and Boukhatem, N and Bouguenouch, L and Hardi, H and Boudouaya, HA and Cadenas, MB and Ouldim, K and Amzazi, S and Azcarate-Peril, MA and Ghazal, H}, title = {Gut microbiome of Moroccan colorectal cancer patients.}, journal = {Medical microbiology and immunology}, volume = {207}, number = {3-4}, pages = {211-225}, pmid = {29687353}, issn = {1432-1831}, mesh = {Adult ; Aged ; Cluster Analysis ; Colorectal Neoplasms/*complications/*microbiology ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Fatty Acids/analysis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Morocco ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Surveys and Questionnaires ; Young Adult ; }, abstract = {Although colorectal cancer is the third leading cause of death in Morocco, there are no studies of the microbiome changes associated with the disease in the Moroccan population. The aim of our study was to compare the stool microbiome of Moroccan cancer patients with healthy individuals. We analyzed the microbiome composition of samples from 11 CRC patients and 12 healthy individuals by 16S rRNA amplicon sequencing. Principal coordinate analysis of samples revealed defined cancer versus healthy clusters. Our findings showed that cancer samples had higher proportions of Firmicutes (T = 50.5%; N = 28.4%; p = 0.04), specifically of Clostridia (T = 48.3%; N = 19.0%; p = 0.002), and Fusobacteria (T = 0.1%; N = 0.0%; p = 0.02), especially of Fusobacteriia (T = 0.1%; N = 0.0%; p = 0.02), while Bacteroidetes were enriched in healthy samples (T = 35.1%; N = 62.8%; p = 0.06), particularly the class Bacteroidia (T = 35.1%; N = 62.6%; p = 0.06). Porphyromonas, Clostridium, Ruminococcus, Selenomonas, and Fusobacterium were significantly overrepresented in diseased patients, similarly to other studies. Predicted functional information showed that bacterial motility proteins, flagellar assembly, and fatty acid biosynthesis metabolism were significantly overrepresented in cancer patients, while amino acid metabolism and glycan biosynthesis were overrepresented in controls. This suggests that involvement of these functional metagenomes is similar and relevant in the carcinogenesis process, independent of the origin of the samples. Results from this study allowed identification of bacterial taxa relevant to the Moroccan population and encourages larger studies to facilitate population-directed therapeutic approaches.}, }
@article {pmid29685174, year = {2018}, author = {Fan, X and Peters, BA and Jacobs, EJ and Gapstur, SM and Purdue, MP and Freedman, ND and Alekseyenko, AV and Wu, J and Yang, L and Pei, Z and Hayes, RB and Ahn, J}, title = {Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {59}, pmid = {29685174}, issn = {2049-2618}, support = {R01 CA159036/CA/NCI NIH HHS/United States ; U01CA182370/CA/NCI NIH HHS/United States ; R21CA183887/CA/NCI NIH HHS/United States ; Pancreas Cancer Action Network Career Development Award//American Association for Cancer Research/International ; P30CA016087/CA/NCI NIH HHS/United States ; R03CA159414/CA/NCI NIH HHS/United States ; R01CA159036/CA/NCI NIH HHS/United States ; R01CA164964/CA/NCI NIH HHS/United States ; R01 CA164964/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; *Alcohol Drinking ; Female ; Humans ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Public Health Surveillance ; RNA, Ribosomal, 16S/genetics ; United States ; }, abstract = {BACKGROUND: Dysbiosis of the oral microbiome can lead to local oral disease and potentially to cancers of the head, neck, and digestive tract. However, little is known regarding exogenous factors contributing to such microbial imbalance.<br><br>RESULTS: We examined the impact of alcohol consumption on the oral microbiome in a cross-sectional study of 1044 US adults. Bacterial 16S rRNA genes from oral wash samples were amplified, sequenced, and assigned to bacterial taxa. We tested the association of alcohol drinking level (non-drinker, moderate drinker, or heavy drinker) and type (liquor, beer, or wine) with overall microbial composition and individual taxon abundance. The diversity of oral microbiota and overall bacterial profiles differed between heavy drinkers and non-drinkers (α-diversity richness p = 0.0059 and β-diversity unweighted UniFrac p = 0.0036), and abundance of commensal order Lactobacillales tends to be decreased with higher alcohol consumption (fold changes = 0.89 and 0.94 for heavy and moderate drinkers, p trend = 0.005 [q = 0.064]). Additionally, certain genera were enriched in subjects with higher alcohol consumption, including Actinomyces, Leptotrichia, Cardiobacterium, and Neisseria; some of these genera contain oral pathogens, while Neisseria can synthesize the human carcinogen acetaldehyde from ethanol. Wine drinkers may differ from non-drinkers in microbial diversity and profiles (α-diversity richness p = 0.048 and β-diversity unweighted UniFrac p = 0.059) after controlling for drinking amount, while liquor and beer drinkers did not. All significant differences between drinkers and non-drinkers remained after exclusion of current smokers.<br><br>CONCLUSIONS: Our results, from a large human study of alcohol consumption and the oral microbiome, indicate that alcohol consumption, and heavy drinking in particular, may influence the oral microbiome composition. These findings may have implications for better understanding the potential role that oral bacteria play in alcohol-related diseases.}, }
@article {pmid29684865, year = {2018}, author = {Kurokawa, S and Kishimoto, T and Mizuno, S and Masaoka, T and Naganuma, M and Liang, KC and Kitazawa, M and Nakashima, M and Shindo, C and Suda, W and Hattori, M and Kanai, T and Mimura, M}, title = {The effect of fecal microbiota transplantation on psychiatric symptoms among patients with irritable bowel syndrome, functional diarrhea and functional constipation: An open-label observational study.}, journal = {Journal of affective disorders}, volume = {235}, number = {}, pages = {506-512}, doi = {10.1016/j.jad.2018.04.038}, pmid = {29684865}, issn = {1573-2517}, mesh = {Adult ; Anxiety Disorders/*psychology ; Constipation/psychology/*therapy ; Depressive Disorder/*psychology ; Diarrhea/psychology/*therapy ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; Gastrointestinal Diseases ; Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/psychology/*therapy ; Male ; Middle Aged ; }, abstract = {BACKGROUNDS: The intestinal microbiota is considered as a potential common underpinning pathophysiology of Functional Gastrointestinal Disorders (FGIDs) and psychiatric disorders such as depression and anxiety. Fecal Microbiota Transplantation (FMT) has been reported to have therapeutic effects on diseases related to dysbiosis, but few studies have evaluated its effect on psychiatric symptoms.<br><br>METHODS: We followed 17 patients with either Irritable Bowel Syndrome (IBS), Functional Diarrhea (FDr) or Functional Constipation (FC) who underwent FMT for the treatment of gastrointestinal symptoms and observation of psychiatric symptoms. Changes in Hamilton Rating Scale for Depression (HAM-D) and subscale of sleep-related items, Hamilton Rating Scale for Anxiety (HAM-A) and Quick Inventory for Depressive Symptoms (QIDS) between baseline and 4 weeks after FMT, and relationship with the intestinal microbiota were measured.<br><br>RESULTS: At baseline, 12 out of 17 patients were rated with HAM-D ≥ 8. Significant improvement in HAM-D total and sleep subscale score, HAM-A and QIDS were observed (p = 0.007, p = 0.007, p = 0.01, p = 0.007, respectively). Baseline Shannon index indicated that microbiota showed lower diversity in patients with HAM-D ≥ 8 compared to those of healthy donors and patients with HAM-D < 8. There was a significant correlation between baseline Shannon index and HAM-D score, and a correlation between Shannon index change and HAM-D improvement after FMT.<br><br>LIMITATIONS: The small sample size with no control group.<br><br>CONCLUSIONS: Our results suggest that depression and anxiety symptoms may be improved by FMT regardless of gastrointestinal symptom change in patients with IBS, FDr and FC, and the increase of microbiota diversity may help to improve patient's mood.}, }
@article {pmid29681561, year = {2018}, author = {Tandon, K and Yang, SH and Wan, MT and Yang, CC and Baatar, B and Chiu, CY and Tsai, JW and Liu, WC and Tang, SL}, title = {Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan.}, journal = {Microbes and environments}, volume = {33}, number = {2}, pages = {120-126}, pmid = {29681561}, issn = {1347-4405}, mesh = {*Air Microbiology ; Bacteria/*classification/genetics ; *Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spatio-Temporal Analysis ; Taiwan ; *Water Microbiology ; }, abstract = {Very few studies have attempted to profile the microbial communities in the air above freshwater bodies, such as lakes, even though freshwater sources are an important part of aquatic ecosystems and airborne bacteria are the most dispersible microorganisms on earth. In the present study, we investigated microbial communities in the waters of two high mountain sub-alpine montane lakes-located 21 km apart and with disparate trophic characteristics-and the air above them. Although bacteria in the lakes had locational differences, their community compositions remained constant over time. However, airborne bacterial communities were diverse and displayed spatial and temporal variance. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria were dominant in both lakes, with different relative abundances between lakes, and Parcubacteria (OD1) was dominant in air samples for all sampling times, except two. We also identified certain shared taxa between lake water and the air above it. The results obtained on these communities in the present study provide putative candidates to study how airborne communities shape lake water bacterial compositions and vice versa.}, }
@article {pmid29680562, year = {2018}, author = {Ribicic, D and Netzer, R and Hazen, TC and Techtmann, SM and Drabløs, F and Brakstad, OG}, title = {Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater.}, journal = {Marine pollution bulletin}, volume = {129}, number = {1}, pages = {370-378}, doi = {10.1016/j.marpolbul.2018.02.034}, pmid = {29680562}, issn = {1879-3363}, mesh = {Biodegradation, Environmental ; Environmental Monitoring/*methods ; *Metagenome ; Microbial Consortia/*genetics ; Norway ; Petroleum/*analysis ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {Oil biodegradation as a weathering process has been extensively investigated over the years, especially after the Deepwater Horizon blowout. In this study, we performed microcosm experiments at 5 °C with chemically dispersed oil in non-amended seawater. We link biodegradation processes with microbial community and metagenome dynamics and explain the succession based on substrate specialization. Reconstructed genomes and 16S rRNA gene analysis revealed that Bermanella and Zhongshania were the main contributors to initial n-alkane breakdown, while subsequent abundances of Colwellia and microorganisms closely related to Porticoccaceae were involved in secondary n‑alkane breakdown and beta‑oxidation. Cycloclasticus, Porticoccaceae and Spongiiabcteraceae were associated with degradation of mono- and poly-cyclic aromatics. Successional pattern of genes coding for hydrocarbon degrading enzymes at metagenome level, and reconstructed genomic content, revealed a high differentiation of bacteria involved in hydrocarbon biodegradation. A cooperation among oil degrading microorganisms is thus needed for the complete substrate transformation.}, }
@article {pmid29678199, year = {2018}, author = {Huson, DH and Albrecht, B and Bağcı, C and Bessarab, I and Górska, A and Jolic, D and Williams, RBH}, title = {MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {6}, pmid = {29678199}, issn = {1745-6150}, support = {NSF PHY-1748958//National Science Foundation/International ; }, mesh = {*Algorithms ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets.<br><br>METHODS: We describe a new LCA-based algorithm for taxonomic binning, and an interval-tree based algorithm for functional binning, that are explicitly designed for long reads and assembled contigs. We provide a new interactive tool for investigating the alignment of long reads against reference sequences. For taxonomic and functional binning, we propose to use LAST to compare long reads against the NCBI-nr protein reference database so as to obtain frame-shift aware alignments, and then to process the results using our new methods.<br><br>RESULTS: All presented methods are implemented in the open source edition of MEGAN, and we refer to this new extension as MEGAN-LR (MEGAN long read). We evaluate the LAST+MEGAN-LR approach in a simulation study, and on a number of mock community datasets consisting of Nanopore reads, PacBio reads and assembled PacBio reads. We also illustrate the practical application on a Nanopore dataset that we sequenced from an anammox bio-rector community.<br><br>REVIEWERS: This article was reviewed by Nicola Segata together with Moreno Zolfo, Pete James Lockhart and Serghei Mangul.<br><br>CONCLUSION: This work extends the applicability of the widely-used metagenomic analysis software MEGAN to long reads. Our study suggests that the presented LAST+MEGAN-LR pipeline is sufficiently fast and accurate.}, }
@article {pmid29676472, year = {2018}, author = {Hao, DC and Zhang, CR and Xiao, PG}, title = {The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing.}, journal = {Journal of basic microbiology}, volume = {58}, number = {6}, pages = {501-512}, doi = {10.1002/jobm.201700663}, pmid = {29676472}, issn = {1521-4028}, mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Biodegradation, Environmental ; Environmental Pollutants/adverse effects ; Fungi/classification/genetics/isolation &amp; purification ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Genes, Viral/genetics ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Plant Roots/*microbiology ; *Rhizosphere ; *Soil Microbiology ; Taxus/*microbiology ; Viruses/classification/genetics/isolation &amp; purification ; }, abstract = {In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539). KEGG analysis predicted numerous functional genes; 7101 Unigenes belong to &quot;Xenobiotics biodegradation and metabolism.&quot; A total of 12,040 Unigenes involved in defense mechanisms (e.g., xenobiotic metabolism) were annotated by eggNOG. Talaromyces addition could influence not only the diversity and structure of microbial communities of Taxus rhizosphere, but also the relative abundance of functional genes, including metabolic genes, antibiotic resistant genes, and genes involved in pathogen-host interaction, bacterial virulence, and bacterial secretion system. The structure and function of rhizosphere microbiome could be sensitive to non-native microbe addition, which could impact on the pollutant degradation. This study, complementary to the amplicon sequencing, more objectively reflects the native microbiome of Taxus rhizosphere and its response to environmental pressure, and lays a foundation for potential combination of phytoremediation and bioaugmentation.}, }
@article {pmid29669589, year = {2018}, author = {Coelho, LP and Kultima, JR and Costea, PI and Fournier, C and Pan, Y and Czarnecki-Maulden, G and Hayward, MR and Forslund, SK and Schmidt, TSB and Descombes, P and Jackson, JR and Li, Q and Bork, P}, title = {Similarity of the dog and human gut microbiomes in gene content and response to diet.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {72}, pmid = {29669589}, issn = {2049-2618}, support = {686070//Horizon 2020 Framework Programme (BE)/International ; }, mesh = {Animals ; *Diet ; Dogs ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; Mice ; *Microbiota ; Obesity ; Swine ; }, abstract = {BACKGROUND: Gut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metagenomics to investigate the relationship between the gut metagenomes of dogs, humans, mice, and pigs.<br><br>RESULTS: We present a dog gut microbiome gene catalog containing 1,247,405 genes (based on 129 metagenomes and a total of 1.9 terabasepairs of sequencing data). Based on this catalog and taxonomic abundance profiling, we show that the dog microbiome is closer to the human microbiome than the microbiome of either pigs or mice. To investigate this similarity in terms of response to dietary changes, we report on a randomized intervention with two diets (high-protein/low-carbohydrate vs. lower protein/higher carbohydrate). We show that diet has a large and reproducible effect on the dog microbiome, independent of breed or sex. Moreover, the responses were in agreement with those observed in previous human studies.<br><br>CONCLUSIONS: We conclude that findings in dogs may be predictive of human microbiome results. In particular, a novel finding is that overweight or obese dogs experience larger compositional shifts than lean dogs in response to a high-protein diet.}, }
@article {pmid29668682, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Koutra, D and Schloss, PD}, title = {Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.}, journal = {PLoS computational biology}, volume = {14}, number = {4}, pages = {e1006099}, pmid = {29668682}, issn = {1553-7358}, support = {T32AI007528/NH/NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; P30DK034933/NH/NIH HHS/United States ; U01AI124255/NH/NIH HHS/United States ; U19AI09087/NH/NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Bacteriophages/*genetics/*physiology ; Computational Biology ; Diet ; Humans ; Metagenomics ; Microbial Consortia/genetics/physiology ; Microbiota/*genetics/*physiology ; Models, Biological ; Phylogeography ; Skin/microbiology/virology ; }, abstract = {Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.}, }
@article {pmid29668334, year = {2018}, author = {Amrane, S and Raoult, D and Lagier, JC}, title = {Metagenomics, culturomics, and the human gut microbiota.}, journal = {Expert review of anti-infective therapy}, volume = {16}, number = {5}, pages = {373-375}, doi = {10.1080/14787210.2018.1467268}, pmid = {29668334}, issn = {1744-8336}, mesh = {Culture Techniques/*methods ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; }, }
@article {pmid29667329, year = {2018}, author = {Bista, I and Carvalho, GR and Tang, M and Walsh, K and Zhou, X and Hajibabaei, M and Shokralla, S and Seymour, M and Bradley, D and Liu, S and Christmas, M and Creer, S}, title = {Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.12888}, pmid = {29667329}, issn = {1755-0998}, abstract = {New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here, we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (three different amplicons) and shotgun mitogenome sequencing. Additionally, we used individual COI barcoding and de novo mitochondrial genome sequencing, to provide reference sequences for OTU assignment and metagenome mapping (mitogenome skimming), respectively. We found that, even though both methods occasionally failed to recover very low abundance species, metabarcoding was less consistent, by failing to recover some species with higher abundances, probably due to primer bias. Shotgun sequencing results provided highly significant correlations between read number and biomass in all but one species. Conversely, the read-biomass relationships obtained from metabarcoding varied across amplicons. Specifically, we found significant relationships for eight of 13 (amplicons B1FR-450 bp, FF130R-130 bp) or four of 13 (amplicon FFFR, 658 bp) species. Combining the results of all three COI amplicons (multiamplicon approach) improved the read-biomass correlations for some of the species. Overall, mitogenomic sequencing yielded more informative predictions of biomass content from bulk macroinvertebrate communities than metabarcoding. However, for large-scale ecological studies, metabarcoding currently remains the most commonly used approach for diversity assessment.}, }
@article {pmid29667264, year = {2018}, author = {Xu, Y and Jia, YH and Chen, L and Huang, WM and Yang, DQ}, title = {Metagenomic analysis of oral microbiome in young children aged 6-8 years living in a rural isolated Chinese province.}, journal = {Oral diseases}, volume = {24}, number = {6}, pages = {1115-1125}, doi = {10.1111/odi.12871}, pmid = {29667264}, issn = {1601-0825}, mesh = {Child ; China ; Dentition, Mixed ; Female ; Humans ; Male ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; *Rural Population ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The mixed dentition is an important transition period from primary teeth to permanent teeth. However, the caries prevalence of first permanent molar in mixed dentitions was about 30%, which almost represent the caries rate of permanent teeth in this period of time. Therefore, we assessed the oral bacterial profiles in young children (age 6-8) with mixed dentition with or without first molar caries for providing the research basis of caries etiology.<br><br>METHODS: We collected samples of supragingival plaque and saliva from the children living in Guizhou, a rural isolated province in China. Then, we performed DNA extraction and purification followed by 454 pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA and compared our results with those of previous research.<br><br>RESULTS: (i) We analyzed 48,320 unique sequences that represented 18 phyla, 29 classes, 44 orders, 74 families, 129 genera, 15,003 species-level OUT in plaque and saliva samples; (ii) longitudinally, there was the &quot;healthy core microbiome&quot; between healthy deciduous dentition and early mixed dentition, for example, Neisseria, Porphyromonas, Selenomonas etc.; (iii) horizontally, there also existed the &quot;healthy core microbiome&quot; in early mixed dentition, for example, Neisseria, Streptococcus, Prevotella etc.; (iv) the dominant bacteria detected by Lefse in caries group including Actinomycetaceae, Streptobacillus (p < 0.05) and those in caries-free group including Gammaproteobacteria, Pasteurellaceae, Aggregatibacter, Chloroflexi, (p < 0.05).<br><br>CONCLUSIONS: The oral cavity is a highly heterogeneous ecosystem with the &quot;healthy core microbiome&quot; in children, although microbial composition shifts along with aging. In addition, the abundance and diversity of microbiota vary between caries and caries-free groups verify the ecological plaque hypothesis.}, }
@article {pmid29666288, year = {2018}, author = {Nowicki, EM and Shroff, R and Singleton, JA and Renaud, DE and Wallace, D and Drury, J and Zirnheld, J and Colleti, B and Ellington, AD and Lamont, RJ and Scott, DA and Whiteley, M}, title = {Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis.}, journal = {mBio}, volume = {9}, number = {2}, pages = {}, pmid = {29666288}, issn = {2150-7511}, support = {R01 DE026963/DE/NIDCR NIH HHS/United States ; }, mesh = {Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; *Gene Expression Profiling ; Gingivitis/*microbiology/*pathology ; Humans ; *Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, abstract = {Over half of adults experience gingivitis, a mild yet treatable form of periodontal disease caused by the overgrowth of oral microbes. Left untreated, gingivitis can progress to a more severe and irreversible disease, most commonly chronic periodontitis. While periodontal diseases are associated with a shift in the oral microbiota composition, it remains unclear how this shift impacts microbiota function early in disease progression. Here, we analyzed the transition from health to gingivitis through both 16S v4-v5 rRNA amplicon and metatranscriptome sequencing of subgingival plaque samples from individuals undergoing an experimental gingivitis treatment. Beta-diversity analysis of 16S rRNA reveals that samples cluster based on disease severity and patient but not by oral hygiene status. Significant shifts in the abundance of several genera occurred during disease transition, suggesting a dysbiosis due to development of gingivitis. Comparing taxonomic abundance with transcriptomic activity revealed concordance of bacterial diversity composition between the two quantification assays in samples originating from both healthy and diseased teeth. Metatranscriptome sequencing analysis indicates that during the early stages of transition to gingivitis, a number of virulence-related transcripts were significantly differentially expressed in individual and across pooled patient samples. Upregulated genes include those involved in proteolytic and nucleolytic processes, while expression levels of those involved in surface structure assembly and other general virulence functions leading to colonization or adaptation within the host are more dynamic. These findings help characterize the transition from health to periodontal disease and identify genes associated with early disease.IMPORTANCE Although more than 50% of adults have some form of periodontal disease, there remains a significant gap in our understanding of its underlying cause. We initiated this study in order to better characterize the progression from oral health to disease. We first analyzed changes in the abundances of specific microorganisms in dental plaque collected from teeth during health and gingivitis, the mildest form of periodontal disease. We found that the clinical score of disease and patient from whom the sample originated but not tooth brushing are significantly correlated with microbial community composition. While a number of virulence-related gene transcripts are differentially expressed in gingivitis samples relative to health, not all are increased, suggesting that the overall activity of the microbiota is dynamic during disease transition. Better understanding of which microbes are present and their function during early periodontal disease can potentially lead to more targeted prophylactic approaches to prevent disease progression.}, }
@article {pmid29665523, year = {2018}, author = {Osimani, A and Milanović, V and Garofalo, C and Cardinali, F and Roncolini, A and Sabbatini, R and De Filippis, F and Ercolini, D and Gabucci, C and Petruzzelli, A and Tonucci, F and Clementi, F and Aquilanti, L}, title = {Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR.}, journal = {International journal of food microbiology}, volume = {276}, number = {}, pages = {54-62}, doi = {10.1016/j.ijfoodmicro.2018.04.013}, pmid = {29665523}, issn = {1879-3460}, mesh = {Animals ; *Biodiversity ; Denaturing Gradient Gel Electrophoresis ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Insecta/*microbiology ; *Metagenomics ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; *Real-Time Polymerase Chain Reaction ; Thailand ; }, abstract = {The present study aimed to identify the microbiota present in six species of processed edible insects produced in Thailand and marketed worldwide via the internet, namely, giant water bugs (Belostoma lutarium), black ants (Polyrhachis), winged termites (alates, Termitoidae), rhino beetles (Hyboschema contractum), mole crickets (Gryllotalpidae), and silkworm pupae (Bombyx mori). For each species, two samples of boiled, dried and salted insects were purchased. The microbial DNA was extracted from the insect samples and subjected to polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), high-throughput sequencing and qualitative real-time PCR assays. The microbiota of the analyzed samples were widely characterized by the presence of spore-forming bacteria mainly represented by the genera Bacillus and Clostridium. Moreover, the genera Anaerobacillus, Paenibacillus, Geobacillus, Pseudomonas, Stenotrophomonas, Massilia, Delftia, Lactobacillus, Staphylococcus, Streptococcus, Vagococcus, and Vibrio were also detected. Real-time PCR allowed for ascertainment of the absence of Coxiella burnetii, Shiga toxin-producing E. coli (STEC), and Pseudomonas aeruginosa in all samples. The results of this study confirm the importance of combining different molecular techniques to characterize the biodiversity of complex ecosystems such as edible insects. The presence of potential human pathogens suggests the need for a careful application of good manufacturing practices during insect processing. This study provides further data that will be useful in risk analyses of edible insects as a novel food source.}, }
@article {pmid29664968, year = {2018}, author = {Betiku, OC and Yeoman, CJ and Gaylord, TG and Americus, B and Olivo, S and Duff, GC and Sealey, WM}, title = {Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195967}, pmid = {29664968}, issn = {1932-6203}, mesh = {Animal Feed ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Oncorhynchus mykiss/*microbiology ; Plant Proteins, Dietary ; *Water Microbiology ; }, abstract = {A two-phase feeding study evaluating performance of rainbow trout and comparing luminal and mucosal gastrointestinal tract (GIT) bacterial community compositions when fed two alternative protein diets in two rearing systems was conducted. Alternative protein diets (animal protein and plant protein diets) balanced with crystalline amino acids: lysine, methionine and threonine or unbalanced, were fed to rainbow trout in two separate water systems (recirculating (RR) and flow-through (FF)) for a period of 16 weeks. The four diets, each contained 38% digestible protein and 20% fats, were fed to rainbow trout with an average weight of 12.02 ± 0.61 g, and sorted at 30 fish/tank and 12 tanks per dietary treatment. Phase 1 lasted for 8 weeks after which fish from each tank were randomly divided, with one-half moved to new tanks of the opposing system (i.e. from RR to FF and vice versa). The remaining halves were retained in their initial tank and system, and fed their original diets for another 8 weeks (phase 2). After the 16th week, 3 fish/tank were sampled for each of proximate analysis, body indexes and 16S rRNA analysis of GIT microbiota. Fish weight (P = 0.0008, P = 0.0030, P<0.0010) and body fat (P = 0.0008, P = 0.0041, P = 0.0177) were significantly affected by diet, diet quality (balanced or unbalanced) and system, respectively. Feed intake (P = 0.0008) and body energy (P<0.0010) were altered by system. Body indexes were not affected by dietary treatment and water systems. Compositional dissimilarities existed between samples from the rearing water and GIT locations (ANOSIM: (R = 0.29, P = 0.0010), PERMANOVA: R = 0.39, P = 0.0010), but not in dietary samples (ANOSIM: R = 0.004, P = 0.3140, PERMANOVA: R = 0.008, P = 0.4540). Bacteria were predominantly from the phyla Proteobacteria, Firmicutes and Bacteroidetes. Their abundance differed with more dissimilarity in the luminal samples (ANOSIM: R = 0.40, P = 0.0010, PERMANOVA: R = 0.56, P = 0.0010) than those from the mucosal intestine (ANOSIM: R = 0.37, P = 0.0010, PERMANOVA: R = 0.41, P = 0.0010). Bacteria generally associated with carbohydrate and certain amino acids metabolism were observed in the mucosal intestine while rearing water appeared to serve as the main route of colonization of Aeromonas and Acinetobacter in the rainbow trout.}, }
@article {pmid29661230, year = {2018}, author = {Gomez-Silvan, C and Leung, MHY and Grue, KA and Kaur, R and Tong, X and Lee, PKH and Andersen, GL}, title = {A comparison of methods used to unveil the genetic and metabolic pool in the built environment.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {71}, pmid = {29661230}, issn = {2049-2618}, support = {G-2015-13977//Alfred P. Sloan Foundation/International ; 11276116//Research Grants Council, University Grants Committee/International ; }, mesh = {*Built Environment ; *Environmental Microbiology ; Humans ; *Metabolomics/methods ; *Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting.<br><br>RESULTS: We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community.<br><br>CONCLUSIONS: Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.}, }
@article {pmid29660711, year = {2018}, author = {Kotoky, R and Rajkumari, J and Pandey, P}, title = {The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil.}, journal = {Journal of environmental management}, volume = {217}, number = {}, pages = {858-870}, doi = {10.1016/j.jenvman.2018.04.022}, pmid = {29660711}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; Hydrocarbons/*metabolism ; Microbiota ; Plant Roots ; *Rhizosphere ; Soil ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.}, }
@article {pmid29659617, year = {2018}, author = {Mohamed Ramli, N and Giatsis, C and Md Yusoff, F and Verreth, J and Verdegem, M}, title = {Resistance and resilience of small-scale recirculating aquaculture systems (RAS) with or without algae to pH perturbation.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195862}, pmid = {29659617}, issn = {1932-6203}, mesh = {Ammonia/chemistry ; *Aquaculture ; Bacteria/classification/genetics ; Biodiversity ; *Chlorophyta ; *Fresh Water ; *Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; Nitrogen/chemistry ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Water Quality ; }, abstract = {The experimental set-up of this study mimicked recirculating aquaculture systems (RAS) where water quality parameters such as dissolved oxygen, pH, temperature, and turbidity were controlled and wastes produced by fish and feeding were converted to inorganic forms. A key process in the RAS was the conversion of ammonia to nitrite and nitrite to nitrate through nitrification. It was hypothesized that algae inclusion in RAS would improve the ammonia removal from the water; thereby improving RAS water quality and stability. To test this hypothesis, the stability of the microbiota community composition in a freshwater RAS with (RAS+A) or without algae (RAS-A) was challenged by introducing an acute pH drop (from pH 7 to 4 during three hours) to the system. Stigeoclonium nanum, a periphytic freshwater microalga was used in this study. No significant effect of the algae presence was found on the resistance to the acute pH drop on ammonia conversion to nitrite and nitrite conversion to nitrate. Also the resilience of the ammonia conversion to the pH drop disruption was not affected by the addition of algae. This could be due to the low biomass of algae achieved in the RAS. However, with regard to the conversion step of nitrite to nitrate, RAS+A was significantly more resilient than RAS-A. In terms of overall bacterial communities, the composition and predictive function of the bacterial communities was significantly different between RAS+A and RAS-A.}, }
@article {pmid29654556, year = {2018}, author = {Jung, DH and Seo, DH and Kim, GY and Nam, YD and Song, EJ and Yoon, S and Park, CS}, title = {The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {11}, pages = {4927-4936}, doi = {10.1007/s00253-018-8971-z}, pmid = {29654556}, issn = {1432-0614}, support = {no. 2017R1A2B4004218//National Research Foundation of Korea/ ; }, mesh = {Animals ; Bacteria/isolation &amp; purification/metabolism ; Cattle ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Humans ; Rumen/*microbiology ; Starch/*metabolism/*pharmacology ; }, abstract = {Resistant starch (RS) in the diet reaches the large intestine without degradation, where it is decomposed by the commensal microbiota. The fermentation of RS produces secondary metabolites including short-chain fatty acids (SCFAs), which have been linked to a variety of physiological and health effects. Therefore, the availability of RS as a prebiotic is a current issue. The objectives of this study were (1) to use metagenomics to observe microbial flora changes in Bos taurus coreanae rumen fluid in the presence of RS and (2) to isolate RS-degrading microorganisms. The major microbial genus in a general rumen fluid was Succiniclasticum sp., whereas Streptococcus sp. immediately predominated after the addition of RS into the culture medium and was then drastically replaced by Lactobacillus sp. The presence of Bifidobacterium sp. was also observed continuously. Several microorganisms with high RS granule-degrading activity were identified and isolated, including B. choerinum FMB-1 and B. pseudolongum FMB-2. B. choerinum FMB-1 showed the highest RS-hydrolyzing activity and degraded almost 60% of all substrates tested. Coculture experiments demonstrated that Lactobacillus brevis ATCC 14869, which was isolated from human feces, could grow using reducing sugars generated from RS by B. choerinum FMB-1. These results suggest that Bifidobacterium spp., especially B. choerinum FMB-1, are the putative primary degrader of RS in rumen microbial flora and could be further studied as probiotic candidates.}, }
@article {pmid29642940, year = {2018}, author = {Dai, Z and Coker, OO and Nakatsu, G and Wu, WKK and Zhao, L and Chen, Z and Chan, FKL and Kristiansen, K and Sung, JJY and Wong, SH and Yu, J}, title = {Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {70}, pmid = {29642940}, issn = {2049-2618}, support = {766613, 14106145, 14111216//RGC-GRF/International ; 2016YFC1303200//135 Program Project China/International ; 2013CB531401//973 Program China/International ; 2014BAI09B05//National Key Technology R&amp;D Program/International ; }, mesh = {Aged ; Bacteria/*classification/*genetics ; Cell Transformation, Neoplastic ; Colorectal Neoplasms/diagnosis/*etiology ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Gene Ontology ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; }, abstract = {BACKGROUND: Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort the structure of microbial dysbiosis in CRC and lead to inconsistent results among studies. In this regard, our study targeted at exploring changes in gut microbiota that are universal across populations at species level.<br><br>RESULTS: Based on the combined analysis of 526 metagenomic samples from Chinese, Austrian, American, and German and French cohorts, seven CRC-enriched bacteria (Bacteroides fragilis, Fusobacterium nucleatum, Porphyromonas asaccharolytica, Parvimonas micra, Prevotella intermedia, Alistipes finegoldii, and Thermanaerovibrio acidaminovorans) have been identified across populations. The seven enriched bacterial markers classified cases from controls with an area under the receiver-operating characteristics curve (AUC) of 0.80 across the different populations. Abundance correlation analysis demonstrated that CRC-enriched and CRC-depleted bacteria respectively formed their own mutualistic networks, in which the latter was disjointed in CRC. The CRC-enriched bacteria have been found to be correlated with lipopolysaccharide and energy biosynthetic pathways.<br><br>CONCLUSIONS: Our study identified potential diagnostic bacterial markers that are robust across populations, indicating their potential universal use for non-invasive CRC diagnosis. We also elucidated the ecological networks and functional capacities of CRC-associated microbiota.}, }
@article {pmid29636446, year = {2018}, author = {Zhou, X and Guang, X and Sun, D and Xu, S and Li, M and Seim, I and Jie, W and Yang, L and Zhu, Q and Xu, J and Gao, Q and Kaya, A and Dou, Q and Chen, B and Ren, W and Li, S and Zhou, K and Gladyshev, VN and Nielsen, R and Fang, X and Yang, G}, title = {Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1276}, pmid = {29636446}, issn = {2041-1723}, mesh = {Adaptation, Biological ; Animals ; Biological Evolution ; China ; Chromosome Mapping ; *Genome ; *Metagenomics ; *Phylogeny ; Porpoises/classification/*genetics ; Reproductive Isolation ; Rivers ; Seawater ; Water-Electrolyte Balance ; }, abstract = {Cetaceans (whales, dolphins, and porpoises) are a group of mammals adapted to various aquatic habitats, from oceans to freshwater rivers. We report the sequencing, de novo assembly and analysis of a finless porpoise genome, and the re-sequencing of an additional 48 finless porpoise individuals. We use these data to reconstruct the demographic history of finless porpoises from their origin to the occupation into the Yangtze River. Analyses of selection between marine and freshwater porpoises identify genes associated with renal water homeostasis and urea cycle, such as urea transporter 2 and angiotensin I-converting enzyme 2, which are likely adaptations associated with the difference in osmotic stress between ocean and rivers. Our results strongly suggest that the critically endangered Yangtze finless porpoises are reproductively isolated from other porpoise populations and harbor unique genetic adaptations, supporting that they should be considered a unique incipient species.}, }
@article {pmid29636439, year = {2018}, author = {Brown, CT and Xiong, W and Olm, MR and Thomas, BC and Baker, R and Firek, B and Morowitz, MJ and Hettich, RL and Banfield, JF}, title = {Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.}, journal = {mBio}, volume = {9}, number = {2}, pages = {}, pmid = {29636439}, issn = {2150-7511}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R01 GM103600/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*chemistry/classification/genetics ; Biota ; Enterocolitis, Necrotizing/microbiology/pathology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; *Hospitalization ; Humans ; Infant, Newborn ; *Infant, Premature ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Proteome/*analysis ; Proteomics ; }, abstract = {During the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC), a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants. In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context.IMPORTANCE Humans are colonized by microbes at birth, a process that is important to health and development. However, much remains to be known about the fine-scale microbial dynamics that occur during the colonization period. We conducted a genome-resolved study of microbial community composition, replication rates, and proteomes during the first 3 months of life of both healthy and sick premature infants. Infants were found to be colonized by similar microbes, but each underwent a distinct colonization trajectory. Interestingly, related microbes colonizing different infants were found to have distinct proteomes, indicating that microbiome function is not only driven by which organisms are present, but also largely depends on microbial responses to the unique set of physiological conditions in the infant gut.}, }
@article {pmid29631628, year = {2018}, author = {Mason, MR and Chambers, S and Dabdoub, SM and Thikkurissy, S and Kumar, PS}, title = {Characterizing oral microbial communities across dentition states and colonization niches.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {67}, pmid = {29631628}, issn = {2049-2618}, support = {T32-DE014320/DE/NIDCR NIH HHS/United States ; R01 DE022579/DE/NIDCR NIH HHS/United States ; F30- DE024940/DE/NIDCR NIH HHS/United States ; F30 DE024940/DE/NIDCR NIH HHS/United States ; T32 DE014320/DE/NIDCR NIH HHS/United States ; R01-DE022579/DE/NIDCR NIH HHS/United States ; }, mesh = {Biodiversity ; Cross-Sectional Studies ; *Dentition ; Gingiva/microbiology ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; }, abstract = {METHODS: The present study aimed to identify patterns and processes in acquisition of oral bacteria and to characterize the microbiota of different dentition states and habitats. Mucosal, salivary, supragingival, and subgingival biofilm samples were collected from orally and systemically healthy children and mother-child dyads in predentate, primary, mixed, and permanent dentitions. 16S rRNA gene sequences were compared to the Human Oral Microbiome Database (HOMD). Functional potential was inferred using PICRUSt.<br><br>RESULTS: Unweighted and weighted UniFrac distances were significantly smaller between each mother-predentate dyad than infant-unrelated female dyads. Predentate children shared a median of 85% of species-level operational taxonomic units (s-OTUs) and 100% of core s-OTUs with their mothers. Maternal smoking, but not gender, mode of delivery, feeding habits, or type of food discriminated between predentate microbial profiles. The primary dentition demonstrated expanded community membership, structure, and function when compared to the predentate stage, as well as significantly lower similarity between mother-child dyads. The primary dentition also included 85% of predentate core s-OTUs. Subsequent dentitions exhibited over 90% similarity to the primary dentition in phylogenetic and functional structure. Species from the predentate mucosa as well as new microbial assemblages were identified in the primary supragingival and subgingival microbiomes. All individuals shared 65% of species between supragingival and subgingival habitats; however, the salivary microbiome exhibited less than 35% similarity to either habitat.<br><br>CONCLUSIONS: Within the limitations of a cross-sectional study design, we identified two definitive stages in oral bacterial colonization: an early predentate imprinting and a second wave with the eruption of primary teeth. Bacterial acquisition in the oral microbiome is influenced by the maternal microbiome. Personalization begins with the eruption of primary teeth; however, this is limited to phylogeny; functionally, individuals exhibit few differences, suggesting that microbial assembly may follow a defined schematic that is driven by the functional requirements of the ecosystem. This early microbiome forms the foundation upon which newer communities develop as more colonization niches emerge, and expansion of biodiversity is attributable to both introduction of new species and increase in abundance of predentate organisms.}, }
@article {pmid29631623, year = {2018}, author = {Shkoporov, AN and Ryan, FJ and Draper, LA and Forde, A and Stockdale, SR and Daly, KM and McDonnell, SA and Nolan, JA and Sutton, TDS and Dalmasso, M and McCann, A and Ross, RP and Hill, C}, title = {Reproducible protocols for metagenomic analysis of human faecal phageomes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {68}, pmid = {29631623}, issn = {2049-2618}, support = {SFI/14/SP APC/B3032//Science Foundation Ireland/Ireland ; SFI/12/RC/2273//Science Foundation Ireland/Ireland ; N/A//Janssen Biotech, Inc/International ; }, mesh = {Bacteria/classification/genetics ; Bacteriophages/*genetics ; Feces/*virology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {BACKGROUND: Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing. The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing.<br><br>RESULTS: Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at + 4 °C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples.<br><br>CONCLUSIONS: The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results.}, }
@article {pmid29625974, year = {2018}, author = {Taboada, B and Isa, P and Gutiérrez-Escolano, AL and Del Ángel, RM and Ludert, JE and Vázquez, N and Tapia-Palacios, MA and Chávez, P and Garrido, E and Espinosa, AC and Eguiarte, LE and López, S and Souza, V and Arias, CF}, title = {The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, pmid = {29625974}, issn = {1098-5336}, abstract = {The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare.IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its &quot;lost world&quot; status.}, }
@article {pmid29624889, year = {2018}, author = {Michał, B and Gagat, P and Jabłoński, S and Chilimoniuk, J and Gaworski, M and Mackiewicz, P and Marcin, Ł}, title = {PhyMet2 : a database and toolkit for phylogenetic and metabolic analyses of methanogens.}, journal = {Environmental microbiology reports}, volume = {10}, number = {3}, pages = {378-382}, doi = {10.1111/1758-2229.12648}, pmid = {29624889}, issn = {1758-2229}, abstract = {The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge of microbes stems from difficulties concerning their isolation and culture in laboratory conditions, which is necessary for describing their phenotype, among other things, for biotechnological purposes. An important component of the understudied ecosystems is methanogens, archaea producing a potent greenhouse-effect gas methane. Therefore, we created PhyMet2 , the first database that combines descriptions of methanogens and their culturing conditions with genetic information. The database contains a set of utilities that facilitate interactive data browsing, data comparison, phylogeny exploration and searching for sequence homologues. The most unique feature of the database is the web server MethanoGram, which can be used to significantly reduce the time and cost of searching for the optimal culturing conditions of methanogens by predicting them based on 16S RNA sequences. The database will aid many researchers in exploring the world of methanogens and their applications in biotechnological processes. PhyMet2 with the MethanoGram predictor is available at http://metanogen.biotech.uni.wroc.pl.}, }
@article {pmid29621268, year = {2018}, author = {Peoples, LM and Donaldson, S and Osuntokun, O and Xia, Q and Nelson, A and Blanton, J and Allen, EE and Church, MJ and Bartlett, DH}, title = {Vertically distinct microbial communities in the Mariana and Kermadec trenches.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195102}, pmid = {29621268}, issn = {1932-6203}, mesh = {Adaptation, Biological ; Biodiversity ; Geologic Sediments/*microbiology ; Hydrostatic Pressure ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Oceans and Seas ; *Water Microbiology ; }, abstract = {Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct microbial communities compared to those at shallower depths due to high hydrostatic pressures, topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of the communities present in the bottom waters of the Kermadec and Mariana trenches. Estimates of microbial protein production indicate active populations under in situ hydrostatic pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and size fraction are important drivers of microbial community structure. Many putative hadal bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter, are similar to members identified in other trenches. Most of the differences between the two trench microbiomes consists of taxa belonging to the Gammaproteobacteria whose distributions extend throughout the water column. Growth and survival estimates of representative isolates of these taxa under deep-sea conditions suggest that some members may descend from shallower depths and exist as a potentially inactive fraction of the hadal zone. We conclude that the distinct pelagic communities residing in these two trenches, and perhaps by extension other trenches, reflect both cosmopolitan hadal bathytypes and ubiquitous genera found throughout the water column.}, }
@article {pmid29615108, year = {2018}, author = {Cornuault, JK and Petit, MA and Mariadassou, M and Benevides, L and Moncaut, E and Langella, P and Sokol, H and De Paepe, M}, title = {Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {65}, pmid = {29615108}, issn = {2049-2618}, mesh = {Animals ; Bacteriophages/*physiology/ultrastructure ; Biodiversity ; Colitis/etiology ; DNA Damage ; Dysbiosis ; Faecalibacterium prausnitzii/*virology ; *Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Inflammatory Bowel Diseases/etiology ; Metagenome ; Metagenomics/methods ; Mice ; Retroelements ; Symbiosis ; }, abstract = {BACKGROUND: Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases.<br><br>METHODS: We identified 18 prophages in 15 genomes of F. prausnitzii, used comparative genomics to define eight phage clades, and annotated the genome of the type phage of each clade. For two of the phages, we studied prophage induction in vitro and in vivo in mice. Finally, we aligned reads from already published viral metagenomic data onto the newly identified phages.<br><br>RESULTS: We show that each phage clade represents a novel viral genus and that a surprisingly large fraction of them (10 of the 18 phages) codes for a diversity-generating retroelement, which could contribute to their adaptation to the digestive tract environment. We obtained either experimental or in silico evidence of activity for at least one member of each genus. In addition, four of these phages are either significantly more prevalent or more abundant in stools of IBD patients than in those of healthy controls.<br><br>CONCLUSION: Since IBD patients generally have less F. prausnitzii in their microbiota than healthy controls, the higher prevalence or abundance of some of its phages may indicate that they are activated during disease. This in turn suggests that phages could trigger or aggravate F. prausnitzii depletion in patients. Our results show that prophage detection in sequenced strains of the microbiota can usefully complement viral metagenomic studies.}, }
@article {pmid29609653, year = {2018}, author = {De Vrieze, J and Pinto, AJ and Sloan, WT and Ijaz, UZ}, title = {The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {63}, pmid = {29609653}, issn = {2049-2618}, support = {NE/L011956/1//Natural Environment Research Council/International ; EP/M016811/1//Engineering and Physical Sciences Research Council/International ; }, mesh = {*Anaerobiosis ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing.<br><br>RESULTS: A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles.<br><br>CONCLUSIONS: In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion.}, }
@article {pmid29609258, year = {2018}, author = {Shao, DT and Wei, WW}, title = {[Progress in research of human microbiota for upper gastrointestinal tumors and precancerous lesions].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {39}, number = {3}, pages = {382-386}, doi = {10.3760/cma.j.issn.0254-6450.2018.03.025}, pmid = {29609258}, issn = {0254-6450}, mesh = {Esophageal Neoplasms/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Neoplasms/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Lactobacillus ; Metagenomics/methods/trends ; *Microbiota ; Precancerous Conditions/*microbiology ; Prognosis ; Research/*trends ; Risk Factors ; Stomach Neoplasms/microbiology ; }, abstract = {With the widely application of the metagenomics, the relationship between microbiota and disease has become a hot research topic. Understanding the potential association between upper gastrointestinal cancer or precancerous lesions and microbiota may play an important role in the early detection, clinical diagnosis and treatment, and prognostic evaluation of upper gastrointestinal cancer. Therefore, a literature retrieval was conducted by using PubMed, Embase and wanfang databases to summarize the latest research progress in the microbiota of upper gastrointestinal cancer, including oral, esophageal, gastric cancer and precancerous lesions. Lower microbial diversity or richness in esophageal cancer and precancerous lesions and specific prognostic biomarkers for esophageal cancer were found. Lactobacillus richness showed an increase trend during the process from gastritis to gastric cancer. This paper summarizes the progress in the research of potential biological etiology of upper gastrointestinal cancer from the perspective of metagenomics in order to provide evidence on the, prevention and control of upper gastrointestinal cancer.}, }
@article {pmid29596453, year = {2018}, author = {Konstantinou, D and Gerovasileiou, V and Voultsiadou, E and Gkelis, S}, title = {Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0195001}, pmid = {29596453}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Cyanobacteria/classification/genetics/*physiology ; Mediterranean Region ; Phylogeny ; Porifera/classification/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Sponge-cyanobacteria associations have attracted research interest from an ecological, evolutionary and biotechnological perspective. Current knowledge is, in its majority, &quot;hidden&quot; in metagenomics research studying the entire microbial communities of sponges, while knowledge on these associations is totally missing for certain geographic areas. In this study, we (a) investigated the occurrence of cyanobacteria in 18 sponge species, several of which are studied for the first time for their cyanobionts, from a previously unexplored eastern Mediterranean ecoregion, the Aegean Sea, (b) isolated sponge-associated cyanobacteria, and characterized them based on a polyphasic (morphological-morphometric and molecular phylogenetic analysis) approach, and (c) conducted a meta-analysis on the global diversity of sponge species hosting cyanobacteria, as well as the diversity of cyanobacterial symbionts. Our research provided new records for nine sponge species, previously unknown for this association, while the isolated cyanobacteria were found to form novel clades within Synechococcus, Leptolyngbyaceae, Pseudanabaenaceae, and Schizotrichaceae, whose taxonomic status requires further investigation; this is the first report of a Schizotrichaceae cyanobacterium associated with sponges. The extensive evaluation of the literature along with the new data from the Aegean Sea raised the number of sponge species known for hosting cyanobacteria to 320 and showed that the cyanobacterial diversity reported from sponges is yet underestimated.}, }
@article {pmid29591722, year = {2019}, author = {Wilson, JJ and Brandon-Mong, GJ and Gan, HM and Sing, KW}, title = {High-throughput terrestrial biodiversity assessments: mitochondrial metabarcoding, metagenomics or metatranscriptomics?.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {30}, number = {1}, pages = {60-67}, doi = {10.1080/24701394.2018.1455189}, pmid = {29591722}, issn = {2470-1408}, mesh = {Animals ; Arthropods/genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods/standards ; Electron Transport Complex IV/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods/standards ; Insect Proteins/genetics ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Reference Standards ; *Transcriptome ; }, abstract = {Consensus on the optimal high-throughput sequencing (HTS) approach to examine biodiversity in mixed terrestrial arthropod samples has not been reached. Metatranscriptomics could increase the proportion of taxonomically informative mitochondrial reads in HTS outputs but has not been investigated for terrestrial arthropod samples. We compared the efficiency of 16S rRNA metabarcoding, metagenomics and metatranscriptomics for detecting species in a mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa). 16S rRNA metabarcoding and nuclear rRNA-depleted metatranscriptomics had the highest detection rate with 97% of input species detected. Based on cytochrome c oxidase I, metagenomics had the highest detection rate with 82% of input species detected, but metatranscriptomics produced a larger proportion of reads matching (Sanger) reference sequences. Metatranscriptomics with nuclear rRNA depletion may offer advantages over metabarcoding through reducing the number of spurious operational taxonomic units while retaining high detection rates, and offers natural enrichment of mitochondrial sequences which may enable increased species detection rates compared with metagenomics.}, }
@article {pmid29590046, year = {2018}, author = {Zhao, L and Zhang, F and Ding, X and Wu, G and Lam, YY and Wang, X and Fu, H and Xue, X and Lu, C and Ma, J and Yu, L and Xu, C and Ren, Z and Xu, Y and Xu, S and Shen, H and Zhu, X and Shi, Y and Shen, Q and Dong, W and Liu, R and Ling, Y and Zeng, Y and Wang, X and Zhang, Q and Wang, J and Wang, L and Wu, Y and Zeng, B and Wei, H and Zhang, M and Peng, Y and Zhang, C}, title = {Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6380}, pages = {1151-1156}, doi = {10.1126/science.aao5774}, pmid = {29590046}, issn = {1095-9203}, mesh = {Adult ; Aged ; Bacteria/classification/genetics/metabolism ; China ; Diabetes Mellitus, Type 2/*therapy ; Diet ; Dietary Fiber/*metabolism ; Fatty Acids, Volatile/*metabolism ; Feces ; Female ; Fermentation ; *Gastrointestinal Microbiome ; Glucagon-Like Peptide 1/metabolism ; Glycated Hemoglobin A/analysis ; Humans ; Hydrogen Sulfide/metabolism ; Indoles/metabolism ; Male ; Metagenomics ; Middle Aged ; }, abstract = {The gut microbiota benefits humans via short-chain fatty acid (SCFA) production from carbohydrate fermentation, and deficiency in SCFA production is associated with type 2 diabetes mellitus (T2DM). We conducted a randomized clinical study of specifically designed isoenergetic diets, together with fecal shotgun metagenomics, to show that a select group of SCFA-producing strains was promoted by dietary fibers and that most other potential producers were either diminished or unchanged in patients with T2DM. When the fiber-promoted SCFA producers were present in greater diversity and abundance, participants had better improvement in hemoglobin A1c levels, partly via increased glucagon-like peptide-1 production. Promotion of these positive responders diminished producers of metabolically detrimental compounds such as indole and hydrogen sulfide. Targeted restoration of these SCFA producers may present a novel ecological approach for managing T2DM.}, }
@article {pmid29588360, year = {2018}, author = {Corvelo, A and Clarke, WE and Robine, N and Zody, MC}, title = {taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time.}, journal = {Genome research}, volume = {28}, number = {5}, pages = {751-758}, pmid = {29588360}, issn = {1549-5469}, mesh = {Bacteria/classification/genetics ; Computational Biology/*methods ; Databases, Nucleic Acid ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Reproducibility of Results ; Rivers/microbiology ; *Software ; Species Specificity ; Water Microbiology ; }, abstract = {High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classification tool. Using a combination of simulated and real metagenomics data sets, we demonstrate that taxMaps is more sensitive and more precise than widely used taxonomic classifiers and is capable of delivering classification accuracy comparable to that of BLASTN, but at up to three orders of magnitude less computational cost.}, }
@article {pmid29587880, year = {2018}, author = {Gasc, C and Peyret, P}, title = {Hybridization capture reveals microbial diversity missed using current profiling methods.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {61}, pmid = {29587880}, issn = {2049-2618}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; *Metagenome ; *Metagenomics/methods ; *Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Soil Microbiology ; }, abstract = {BACKGROUND: Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method has resulted in the discovery of many unexpected evolutionary lineages. However, amplicon sequencing is subject to numerous biases, with some taxa being missed, and is limited by the read length of second-generation sequencing platforms, which drastically reduces the phylogenetic resolution.<br><br>RESULTS: Here, we describe a hybridization capture strategy that allows the enrichment of 16S rRNA genes from metagenomic samples and enables an exhaustive identification and a complete reconstruction of the biomarker. Applying this approach to a microbial mock community and a soil sample, we demonstrated that hybridization capture is able to reveal greater microbial diversity than 16S rDNA amplicon sequencing and shotgun sequencing. The reconstruction of full-length 16S rRNA genes facilitated the improvement of phylogenetic resolution and the discovery of novel prokaryotic taxa.<br><br>CONCLUSIONS: Our results demonstrate that hybridization capture can lead to major breakthroughs in our understanding of microbial diversity, overcoming the limitations of conventional 16S rRNA gene studies. If applied to a broad range of environmental samples, this innovative approach could reveal the undescribed diversity of the still underexplored microbial communities and could provide a better understanding of ecosystem function.}, }
@article {pmid29587819, year = {2018}, author = {Dickson, LB and Ghozlane, A and Volant, S and Bouchier, C and Ma, L and Vega-Rúa, A and Dusfour, I and Jiolle, D and Paupy, C and Mayanja, MN and Kohl, A and Lutwama, JJ and Duong, V and Lambrechts, L}, title = {Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {207}, pmid = {29587819}, issn = {1756-3305}, support = {ANR-16-CE35-0004-01//Agence Nationale de la Recherche/International ; ANR-17-ERC2-0016-01//Agence Nationale de la Recherche/International ; ANR-10-LABX-62-IBEID//Investissement d'Avenir program Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases/International ; 734584//European Union's Horizon 2020 research and innovation programme under ZikaPLAN/International ; 2015-FED-192//Programme Opérationnel FEDER-Guadeloupe-Conseil Régional/International ; MC_UU_12014//Medical Research Council/United Kingdom ; ANR10-INBS-09-08//France Génomique consortium/International ; }, mesh = {Aedes/*microbiology ; Animals ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Host-associated microbes, collectively known as the microbiota, play an important role in the biology of multicellular organisms. In mosquito vectors of human pathogens, the gut bacterial microbiota influences vectorial capacity and has become the subject of intense study. In laboratory studies of vector biology, genetic effects are often inferred from differences between geographically and genetically diverse colonies of mosquitoes that are reared in the same insectary. It is unclear, however, to what extent genetic effects can be confounded by uncontrolled differences in the microbiota composition among mosquito colonies. To address this question, we used 16S metagenomics to compare the midgut bacterial microbiome of six laboratory colonies of Aedes aegypti recently derived from wild populations representing the geographical range and genetic diversity of the species.<br><br>RESULTS: We found that the diversity, abundance, and community structure of the midgut bacterial microbiome was remarkably similar among the six different colonies of Ae. aegypti, regardless of their geographical origin. We also confirmed the relatively low complexity of bacterial communities inhabiting the mosquito midgut.<br><br>CONCLUSIONS: Our finding that geographically diverse colonies of Ae. aegypti reared in the same insectary harbor a similar gut bacterial microbiome supports the conclusion that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype. Thus, uncontrolled differences in microbiota composition are unlikely to represent a significant confounding factor in genetic studies of vector biology.}, }
@article {pmid29576590, year = {2018}, author = {Okamoto, H and Koizumi, S and Shimizu, H and Cho, O and Sugita, T}, title = {Characterization of the Axillary Microbiota of Japanese Male Subjects with Spicy and Milky Odor Types by Pyrosequencing.}, journal = {Biocontrol science}, volume = {23}, number = {1}, pages = {1-5}, doi = {10.4265/bio.23.1}, pmid = {29576590}, issn = {1884-0205}, mesh = {Adult ; Axilla/*microbiology ; Bacteria/classification/genetics ; Biodiversity ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Japan ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; *Odorants ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Malodorants in the human axilla are produced from human biogenic precursors by axillary bacterial enzymes. In the present study, we used pyrosequencing analysis to identify the axillary bacterial microbiota of 13 Japanese male subjects with cumin-like, spicy body odor (C type), and 9 with milky, skin-based body odor (M type). Anaerococcus, Corynebacterium, and Staphylococcus predominated in both C- and M-type subjects, followed by Moraxella and Peptoniphilus. These genera accounted for 96.2-99.9% of the total bacterial population, except in the microbiota of one C-type subject. However, the axillary bacteria in C-type subjects were more abundant than that in M-type subjects. These results suggest that the level of colonization by axillary bacteria is important for the production of malodorants.}, }
@article {pmid29572583, year = {2018}, author = {Verma, D and Garg, PK and Dubey, AK}, title = {Insights into the human oral microbiome.}, journal = {Archives of microbiology}, volume = {200}, number = {4}, pages = {525-540}, doi = {10.1007/s00203-018-1505-3}, pmid = {29572583}, issn = {1432-072X}, support = {SERB/LS-824/2013//Science and Engineering recruitment Board, New Delhi, India/ ; }, mesh = {Bacteria/genetics ; Health ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host's metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.}, }
@article {pmid29568746, year = {2018}, author = {Wu, H and Cai, L and Li, D and Wang, X and Zhao, S and Zou, F and Zhou, K}, title = {Metagenomics Biomarkers Selected for Prediction of Three Different Diseases in Chinese Population.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {2936257}, pmid = {29568746}, issn = {2314-6141}, mesh = {Algorithms ; Arthritis, Rheumatoid/*microbiology ; Asian Continental Ancestry Group/*genetics ; Biomarkers/*metabolism ; Diabetes Mellitus, Type 2/*microbiology ; Dysbiosis/genetics ; Female ; Humans ; Liver Cirrhosis/*microbiology ; Male ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; ROC Curve ; }, abstract = {The dysbiosis of human microbiome has been proven to be associated with the development of many human diseases. Metagenome sequencing emerges as a powerful tool to investigate the effects of microbiome on diseases. Identification of human gut microbiome markers associated with abnormal phenotypes may facilitate feature selection for multiclass classification. Compared with binary classifiers, multiclass classification models deploy more complex discriminative patterns. Here, we developed a pipeline to address the challenging characterization of multilabel samples. In this study, a total of 300 biomarkers were selected from the microbiome of 806 Chinese individuals (383 controls, 170 with type 2 diabetes, 130 with rheumatoid arthritis, and 123 with liver cirrhosis), and then logistic regression prediction algorithm was applied to those markers as the model intrinsic features. The estimated model produced an F1 score of 0.9142, which was better than other popular classification methods, and an average receiver operating characteristic (ROC) of 0.9475 showed a significant correlation between these selected biomarkers from microbiome and corresponding phenotypes. The results from this study indicate that machine learning is a vital tool in data mining from microbiome in order to identify disease-related biomarkers, which may contribute to the application of microbiome-based precision medicine in the future.}, }
@article {pmid29567298, year = {2018}, author = {Stensvold, CR and van der Giezen, M}, title = {Associations between Gut Microbiota and Common Luminal Intestinal Parasites.}, journal = {Trends in parasitology}, volume = {34}, number = {5}, pages = {369-377}, doi = {10.1016/j.pt.2018.02.004}, pmid = {29567298}, issn = {1471-5007}, mesh = {Blastocystis/*physiology ; Dientamoeba/*physiology ; *Environmental Biomarkers ; Gastrointestinal Microbiome/*physiology ; Host-Parasite Interactions/*physiology ; Humans ; Intestinal Diseases, Parasitic/*microbiology ; Intestines/microbiology/parasitology ; }, abstract = {The development and integration of DNA-based methods in research and clinical microbiology laboratories have enabled standardised and comprehensive detection and differentiation of the microbes colonising our guts. For instance, the single-celled parasites Blastocystis and Dientamoeba appear to be much more common than previously thought, especially so in healthy individuals. While increasing evidence appears to suggest limited pathogenicity of these parasites, next-generation-sequencing-based studies have helped us to appreciate links between parasite colonisation and certain host phenotypical characteristics and gut microbial profiles. The fundamental question remains as to whether such parasites are merely indicators or active manipulators of gut microbiota structure and function. In this article, we collate existing evidence that these parasites are, at minimum, indicators of intestinal microbiota structure.}, }
@article {pmid29567068, year = {2018}, author = {Górska, A and Peter, S and Willmann, M and Autenrieth, I and Schlaberg, R and Huson, DH}, title = {Dynamics of the human gut phageome during antibiotic treatment.}, journal = {Computational biology and chemistry}, volume = {74}, number = {}, pages = {420-427}, doi = {10.1016/j.compbiolchem.2018.03.011}, pmid = {29567068}, issn = {1476-928X}, mesh = {Anti-Bacterial Agents/administration &amp; dosage/*pharmacology ; Ciprofloxacin/administration &amp; dosage/*pharmacology ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/*drug effects/microbiology ; Healthy Volunteers ; Humans ; Metagenomics ; }, abstract = {Bacterial viruses contribute to the dynamics of the microbiome communities, as they are involved in the horizontal gene transfer. Previously we studied changes in the gut microbiome of the two healthy individuals over the course of a 6-days antibiotics treatment and subsequent 28 days recovery time (Willmann et al., 2015). Now, from the same samples, the virus-like particles were isolated and sequenced. As the phage sequences are currently poorly represented in reference databases, the reads had to be assembled, annotated and their abundance had to be evaluated via reads mapping. We analyzed and compared patterns of changes in abundance of the phage scaffolds and scaffolds with antibiotics resistant genes, in both phage and whole-genome metagenomic sets. We observed an increase in abundance of scaffolds carrying antibiotic-resistant genes in response to the treatment.}, }
@article {pmid29566905, year = {2017}, author = {Jazayeri, O and Daghighi, SM and Rezaee, F}, title = {Lifestyle alters GUT-bacteria function: Linking immune response and host.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {31}, number = {6}, pages = {625-635}, doi = {10.1016/j.bpg.2017.09.009}, pmid = {29566905}, issn = {1532-1916}, mesh = {Bacteria/*pathogenicity ; Bacterial Physiological Phenomena/*immunology ; Gastrointestinal Microbiome/*immunology ; Humans ; *Life Style ; Microbiota/*immunology ; }, abstract = {Microbiota in human is a &quot;mixture society&quot; of different species (i.e. bacteria, viruses, funguses) populations with a different way of relationship classification to Human. Human GUT serves as the host of the majority of different bacterial populations (GUT flora, more than 500 species), which are with us (&quot;from the beginning&quot;) in an innate manner known as the commensal (no harm to each other) and symbiotic (mutual benefit) relationship. A homeostatic balance of host-bacteria relationship is very important and vital for a normal health process. However, this beneficial relationship and delicate homeostatic state can be disrupted by the imbalance of microbiome-composition of gut microbiota, expressing a pathogenic state. A strict homeostatic balance of microbiome-composition strongly depends on several factors; 1- lifestyle, 2- geography, 3- ethnicities, 4- &quot;mom&quot; as prime of the type of bacterial colonization in infant and 5- the disease. With such diversity in individuals combined with huge number of different bacterial species and their interactions, it is wise to perform an in-depth systems biology (e.g. genomics, proteomics, glycomics, and etcetera) analysis of personalized microbiome. Only in this way, we are able to generate a map of complete GUT microbiota and, in turn, to determine its interaction with host and intra-interaction with pathogenic bacteria. A specific microbiome analysis provides us the knowledge to decipher the nature of interactions between the GUT microbiota and the host and its response to the invading bacteria in a pathogenic state. The GUT-bacteria composition is independent of geography and ethnicity but lifestyle well affects GUT-bacteria composition and function. Microbiome knowledge obtained by systems biology also helps us to change the behavior of GUT microbiota in response to the pathogenic microbes as protection. Functional microbiome changes in response to environmental factors will be discussed in this review.}, }
@article {pmid29564487, year = {2018}, author = {Pulikkan, J and Maji, A and Dhakan, DB and Saxena, R and Mohan, B and Anto, MM and Agarwal, N and Grace, T and Sharma, VK}, title = {Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1102-1114}, pmid = {29564487}, issn = {1432-184X}, mesh = {Adolescent ; Autism Spectrum Disorder/*microbiology ; Bacteria/classification/isolation &amp; purification ; Biomarkers/analysis ; Child ; Child, Preschool ; DNA, Bacterial/analysis ; Dysbiosis/*epidemiology/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; India/epidemiology ; Male ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; }, abstract = {Autism spectrum disorder (ASD) is a term associated with a group of neurodevelopmental disorders. The etiology of ASD is not yet completely understood; however, a disorder in the gut-brain axis is emerging as a prominent factor leading to autism. To identify the taxonomic composition and markers associated with ASD, we compared the fecal microbiota of 30 ASD children diagnosed using Childhood Autism Rating Scale (CARS) score, DSM-5 approved AIIMS-modified INCLEN Diagnostic Tool for Autism Spectrum Disorder (INDT-ASD), and Indian Scale for Assessment of Autism (ISAA) tool, with family-matched 24 healthy children from Indian population using next-generation sequencing (NGS) of 16S rRNA gene amplicon. Our study showed prominent dysbiosis in the gut microbiome of ASD children, with higher relative abundances of families Lactobacillaceae, Bifidobacteraceae, and Veillonellaceae, whereas the gut microbiome of healthy children was dominated by the family Prevotellaceae. Comparative meta-analysis with a publicly available dataset from the US population consisting of 20 ASD and 20 healthy control samples from children of similar age, revealed a significantly high abundance of genus Lactobacillus in ASD children from both the populations. The results reveal the microbial dysbiosis and an association of selected Lactobacillus species with the gut microbiome of ASD children.}, }
@article {pmid29555111, year = {2018}, author = {Pandit, RJ and Hinsu, AT and Patel, SH and Jakhesara, SJ and Koringa, PG and Bruno, F and Psifidi, A and Shah, SV and Joshi, CG}, title = {Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {4}, pages = {374-385}, doi = {10.1016/j.syapm.2018.02.002}, pmid = {29555111}, issn = {1618-0984}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/*classification/genetics ; Cattle ; *Diet ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/genetics ; Rumen/*microbiology ; }, abstract = {Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.}, }
@article {pmid29554948, year = {2018}, author = {Walsh, AM and Crispie, F and O'Sullivan, O and Finnegan, L and Claesson, MJ and Cotter, PD}, title = {Species classifier choice is a key consideration when analysing low-complexity food microbiome data.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {50}, pmid = {29554948}, issn = {2049-2618}, support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; 11/PI/1137//Science Foundation Ireland/Ireland ; 13/SIRG/2160//Science Foundation Ireland/Ireland ; }, mesh = {Bacteria/classification/*genetics ; Base Sequence/genetics ; Computational Biology/methods ; DNA, Bacterial/*genetics ; Food Microbiology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with respect to choice of species classification tool, platform, or sequencing depth. Here, we benchmarked the performances of three high-throughput short-read sequencing platforms, the Illumina MiSeq, NextSeq 500, and Ion Proton, for shotgun metagenomics of food microbiota. Briefly, we sequenced six kefir DNA samples and a mock community DNA sample, the latter constructed by evenly mixing genomic DNA from 13 food-related bacterial species. A variety of bioinformatic tools were used to analyse the data generated, and the effects of sequencing depth on these analyses were tested by randomly subsampling reads.<br><br>RESULTS: Compositional analysis results were consistent between the platforms at divergent sequencing depths. However, we observed pronounced differences in the predictions from species classification tools. Indeed, PERMANOVA indicated that there was no significant differences between the compositional results generated by the different sequencers (p = 0.693, R2 = 0.011), but there was a significant difference between the results predicted by the species classifiers (p = 0.01, R2 = 0.127). The relative abundances predicted by the classifiers, apart from MetaPhlAn2, were apparently biased by reference genome sizes. Additionally, we observed varying false-positive rates among the classifiers. MetaPhlAn2 had the lowest false-positive rate, whereas SLIMM had the greatest false-positive rate. Strain-level analysis results were also similar across platforms. Each platform correctly identified the strains present in the mock community, but accuracy was improved slightly with greater sequencing depth. Notably, PanPhlAn detected the dominant strains in each kefir sample above 500,000 reads per sample. Again, the outputs from functional profiling analysis using SUPER-FOCUS were generally accordant between the platforms at different sequencing depths. Finally, and expectedly, metagenome assembly completeness was significantly lower on the MiSeq than either on the NextSeq (p = 0.03) or the Proton (p = 0.011), and it improved with increased sequencing depth.<br><br>CONCLUSIONS: Our results demonstrate a remarkable similarity in the results generated by the three sequencing platforms at different sequencing depths, and, in fact, the choice of bioinformatics methodology had a more evident impact on results than the choice of sequencer did.}, }
@article {pmid29551526, year = {2018}, author = {Santos, JC and Tarvin, RD and O'Connell, LA and Blackburn, DC and Coloma, LA}, title = {Diversity within diversity: Parasite species richness in poison frogs assessed by transcriptomics.}, journal = {Molecular phylogenetics and evolution}, volume = {125}, number = {}, pages = {40-50}, doi = {10.1016/j.ympev.2018.03.015}, pmid = {29551526}, issn = {1095-9513}, mesh = {Animals ; Anura/*genetics/*parasitology ; Biodiversity ; *Gene Expression Profiling ; Genetic Speciation ; Host-Parasite Interactions/genetics ; Parasites/*physiology ; Phylogeny ; Poisons ; Species Specificity ; Transcriptome/genetics ; }, abstract = {Symbionts (e.g., endoparasites and commensals) play an integral role in their host's ecology, yet in many cases their diversity is likely underestimated. Although endoparasites are traditionally characterized using morphology, sequences of conserved genes, and shotgun metagenomics, host transcriptomes constitute an underused resource to identify these organisms' diversity. By isolating non-host transcripts from host transcriptomes, individual host tissues can now simultaneously reveal their endoparasite species richness (i.e., number of different taxa) and provide insights into parasite gene expression. These approaches can be used in host taxa whose endoparasites are mostly unknown, such as those of tropical amphibians. Here, we focus on the poison frogs (Dendrobatidae) as hosts, which are a Neotropical clade known for their bright coloration and defensive alkaloids. These toxins are an effective protection against vertebrate predators (e.g., snakes and birds), bacteria, and skin-biting ectoparasites (e.g., mosquitoes); however, little is known about their deterrence against eukaryotic endoparasites. With de novo transcriptomes of dendrobatids, we developed a bioinformatics pipeline for endoparasite identification that uses host annotated RNA-seq data and set of a priori parasite taxonomic terms, which are used to mine for specific endoparasites. We found a large community of helminths and protozoans that were mostly restricted to the digestive tract and a few systemic parasites (e.g., Trypanosoma). Contrary to our expectations, all dendrobatid frogs regardless of the presence of alkaloid defenses have endoparasites, with their highest species richness located in the frog digestive tract. Some of these organisms (e.g., roundworms) might prove to be generalists, as they were not found to be co-diversifying with their frog hosts. We propose that endoparasites may escape poison frogs' chemical defenses by colonizing tissues with fewer alkaloids than the frog's skin, where most toxins are stored.}, }
@article {pmid29546438, year = {2018}, author = {Rua, CPJ and de Oliveira, LS and Froes, A and Tschoeke, DA and Soares, AC and Leomil, L and Gregoracci, GB and Coutinho, R and Hajdu, E and Thompson, CC and Berlinck, RGS and Thompson, FL}, title = {Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {825-838}, pmid = {29546438}, issn = {1432-184X}, support = {CNE E-26/110.735/2013//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; CIMAR 1986/2014//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; BIOTA/BIOprospecTA grant 2013/50228-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/17616- 7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, mesh = {Alkaloids/*metabolism ; Animals ; Bacteria/*enzymology/genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Biodiversity ; Bromine/metabolism ; Gene Transfer, Horizontal ; Hydrolases/*genetics/metabolism ; Phylogeny ; Porifera/chemistry/*microbiology ; Secondary Metabolism ; }, abstract = {Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.}, }
@article {pmid29544175, year = {2018}, author = {Wang, C and Jiang, K and Zhou, J and Wu, B}, title = {Solidago canadensis invasion affects soil N-fixing bacterial communities in heterogeneous landscapes in urban ecosystems in East China.}, journal = {The Science of the total environment}, volume = {631-632}, number = {}, pages = {702-713}, doi = {10.1016/j.scitotenv.2018.03.061}, pmid = {29544175}, issn = {1879-1026}, mesh = {Biodiversity ; China ; *Ecosystem ; Environmental Monitoring ; *Introduced Species ; Soil/chemistry ; *Soil Microbiology ; Solidago/*growth &amp; development ; }, abstract = {Soil nitrogen-fixing bacterial communities (SNB) can increase the level of available soil N via biological N-fixation to facilitate successful invasion of several invasive plant species (IPS). Meanwhile, landscape heterogeneity can greatly enhance regional invasibility and increase the chances of successful invasion of IPS. Thus, it is important to understand the soil micro-ecological mechanisms driving the successful invasion of IPS in heterogeneous landscapes. This study performed cross-site comparisons, via metagenomics, to comprehensively analyze the effects of Solidago canadensis invasion on SNB in heterogeneous landscapes in urban ecosystems. Rhizospheric soil samples of S. canadensis were obtained from nine urban ecosystems [Three replicate quadrats (including uninvaded sites and invaded sites) for each type of urban ecosystem]. S. canadensis invasion did not significantly affect soil physicochemical properties, the taxonomic diversity of plant communities, or the diversity and richness of SNB. However, some SNB taxa (i.e., f_Micromonosporaceae, f_Oscillatoriaceae, and f_Bacillaceae) changed significantly with S. canadensis invasion. Thus, S. canadensis invasion may alter the community structure, rather than the diversity and richness of SNB, to facilitate its invasion process. Of the nine urban ecosystems, the diversity and richness of SNB was highest in farmland wasteland. Accordingly, the community invasibility of farmland wasteland may be higher than that of the other types of urban ecosystem. In brief, landscape heterogeneity, rather than S. canadensis invasion, was the strongest controlling factor for the diversity and richness of SNB. One possible reason may be the differences in soil electrical conductivity and the taxonomic diversity of plant communities in the nine urban ecosystems, which can cause notable shifts in the diversity and richness of SNB.}, }
@article {pmid29543361, year = {2018}, author = {Malone, EW and Perkin, JS and Leckie, BM and Kulp, MA and Hurt, CR and Walker, DM}, title = {Which species, how many, and from where: Integrating habitat suitability, population genomics, and abundance estimates into species reintroduction planning.}, journal = {Global change biology}, volume = {24}, number = {8}, pages = {3729-3748}, doi = {10.1111/gcb.14126}, pmid = {29543361}, issn = {1365-2486}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources ; Fishes/*genetics ; Genetic Variation ; Metagenomics ; Population Density ; Rivers ; }, abstract = {Extirpated organisms are reintroduced into their former ranges worldwide to combat species declines and biodiversity losses. The growing field of reintroduction biology provides guiding principles for reestablishing populations, though criticisms remain regarding limited integration of initial planning, modeling frameworks, interdisciplinary collaborations, and multispecies approaches. We used an interdisciplinary, multispecies, quantitative framework to plan reintroductions of three fish species into Abrams Creek, Great Smoky Mountains National Park, USA. We first assessed the appropriateness of habitat at reintroduction sites for banded sculpin (Cottus carolinae), greenside darter (Etheostoma blennioides), and mottled sculpin (Cottus bairdii) using species distribution modeling. Next, we evaluated the relative suitability of nine potential source stock sites using population genomics, abundance estimates, and multiple-criteria decision analysis (MCDA) based on known correlates of reintroduction success. Species distribution modeling identified mottled sculpin as a poor candidate, but banded sculpin and greenside darter as suitable candidates for reintroduction based on species-habitat relationships and habitats available in Abrams Creek. Genotyping by sequencing revealed acceptable levels of genetic diversity at all candidate source stock sites, identified population clusters, and allowed for estimating the number of fish that should be included in translocations. Finally, MCDA highlighted priorities among candidate source stock sites that were most likely to yield successful reintroductions based on differential weightings of habitat assessment, population genomics, and the number of fish available for translocation. Our integrative approach represents a unification of multiple recent advancements in the field of reintroduction biology and highlights the benefit of shifting away from simply choosing nearby populations for translocation to an information-based science with strong a priori planning coupled with several suggested posteriori monitoring objectives. Our framework can be applied to optimize reintroduction successes for a multitude of organisms and advances in the science of reintroduction biology by simultaneously addressing a variety of past criticisms of the field.}, }
@article {pmid29540507, year = {2018}, author = {Succurro, A and Ebenhöh, O}, title = {Review and perspective on mathematical modeling of microbial ecosystems.}, journal = {Biochemical Society transactions}, volume = {46}, number = {2}, pages = {403-412}, pmid = {29540507}, issn = {1470-8752}, mesh = {*Ecosystem ; Metagenomics ; *Microbiota ; *Models, Biological ; }, abstract = {Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial 'who is there?'<br><br>QUESTION: An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment. Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act. Differential equation models and constraint-based stoichiometric models are deterministic approaches that can successfully provide a macroscopic description of the outcome from microscopic behaviors. In this mini-review, we present classical and recent applications of these modeling methods and illustrate the potential of their integration. Indeed, approaches that can capture multiple scales are needed in order to understand emergent patterns in ecosystems and their dynamics regulated by different spatio-temporal phenomena. We finally discuss promising examples of methods proposing the integration of differential equations with constraint-based stoichiometric models and argue that more work is needed in this direction.}, }
@article {pmid29540269, year = {2018}, author = {Villamil, SI and Huerlimann, R and Morianos, C and Sarnyai, Z and Maes, GE}, title = {Adverse effect of early-life high-fat/high-carbohydrate (&quot;Western&quot;) diet on bacterial community in the distal bowel of mice.}, journal = {Nutrition research (New York, N.Y.)}, volume = {50}, number = {}, pages = {25-36}, doi = {10.1016/j.nutres.2017.11.008}, pmid = {29540269}, issn = {1879-0739}, abstract = {Obesity and other lifestyle diseases in modern society can be related to historical dietary changes from diets balanced in omega-6 and omega-3 to the unbalanced &quot;Western-type&quot; diet. It is recognized that diet influences the murine and human gut microbiome, and most research indicates that microbial diversity and composition are altered by high-fat diets (HFDs). However, good knowledge about the effects of early exposure to HFD on the maturation and structure of the bacterial community is limited. Using mice as model, we hypothesized that an HFD alters the early dynamic of the gut bacterial community toward an unstable/unhealthy state. By sequencing the V3 and V4 regions of the 16S ribosomal ribonucleic acid gene, we investigated the bacterial community in fecal samples of mice fed a control diet and an HFD at weaning (sampling time 1) and after 8 weeks of dietary intervention (11weeks of age; sampling time 2). Natural temporal microbiome maturation was evidenced by a general increase in microbial diversity and shifts in microbial community between sampling times 1 and 2 toward a mature community. However, the HFD led to significant structural segregation of the microbiome compared with controls; the HFD diet repressed health-enhancing bacteria (eg, Bifidobacterium and Akkermansia) and promoted health-detracting bacteria (ie, those associated with gut disorders, eg, Dorea). We suggest that early-life consumption of HFD negatively impacts the natural gut bacterial community maturation leading toward a potentially persistent unhealthy stage.}, }
@article {pmid29526926, year = {2018}, author = {Do, TH and Le, NG and Dao, TK and Nguyen, TMP and Le, TL and Luu, HL and Nguyen, KHV and Nguyen, VL and Le, LA and Phung, TN and van Straalen, NM and Roelofs, D and Truong, NH}, title = {Metagenomic insights into lignocellulose-degrading genes through Illumina-based de novo sequencing of the microbiome in Vietnamese native goats' rumen.}, journal = {The Journal of general and applied microbiology}, volume = {64}, number = {3}, pages = {108-116}, doi = {10.2323/jgam.2017.08.004}, pmid = {29526926}, issn = {1349-8037}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/classification/*enzymology/*genetics ; Base Sequence ; DNA, Bacterial/genetics ; Databases, Genetic ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/genetics ; Glycoside Hydrolases/*genetics/metabolism ; Goats/*microbiology ; Lignin/metabolism ; Metagenome/*genetics ; Metagenomics ; Open Reading Frames ; Rumen/*microbiology ; Vietnam ; }, abstract = {The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats' rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes' modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.}, }
@article {pmid29526222, year = {2018}, author = {Andeta, AF and Vandeweyer, D and Woldesenbet, F and Eshetu, F and Hailemicael, A and Woldeyes, F and Crauwels, S and Lievens, B and Ceusters, J and Vancampenhout, K and Van Campenhout, L}, title = {Fermentation of enset (Ensete ventricosum) in the Gamo highlands of Ethiopia: Physicochemical and microbial community dynamics.}, journal = {Food microbiology}, volume = {73}, number = {}, pages = {342-350}, doi = {10.1016/j.fm.2018.02.011}, pmid = {29526222}, issn = {1095-9998}, mesh = {Biodiversity ; Clostridium/classification/genetics/isolation &amp; purification/metabolism ; Ethiopia ; Fermentation ; Hydrogen-Ion Concentration ; Lactobacillales/classification/*isolation &amp; purification/metabolism ; Musaceae/chemistry/metabolism/*microbiology ; Temperature ; }, abstract = {Enset (Ensete ventricosum) provides staple food for 15 million people in Ethiopia after fermentation into kocho. The fermentation process has hardly been investigated and is prone to optimization. The aim of this study was to investigate the physicochemical and microbial dynamics of fermentation practices in the Gamo highlands. These practices show local variation, but two steps were omnipresent: scraping of the pseudostem and fermenting it in a pit or a bamboo basket. Enset plants were fragmented and fermented for two months in order to investigate the physicochemical (temperature, moisture content, pH and titratable acidity) and microbial dynamics (total viable aerobic counts, counts of Enterobacteriaceae, lactic acid bacteria, yeasts and moulds and Clostridium spores counts, and Illumina Miseq sequencing). Samples were taken on days 1, 7, 15, 17, 31 and 60. The pH decreased, whereas the titratable acidity increased during fermentation. Of all counts those of lactic acid bacteria and Clostridium spores increased during fermentation. Leuconostoc mesenteroides initiated the fermentation. Later on, Prevotella paludivivens, Lactobacillus sp. and Bifidobacterium minimum dominated. These three species are potential candidates for the development of a starter culture.}, }
@article {pmid29524068, year = {2018}, author = {Wang, C and Li, Q and Li, J}, title = {Gut microbiota and its implications in small bowel transplantation.}, journal = {Frontiers of medicine}, volume = {12}, number = {3}, pages = {239-248}, pmid = {29524068}, issn = {2095-0225}, mesh = {Biomarkers ; *Gastrointestinal Microbiome ; Graft Rejection/*immunology ; Humans ; Immunity, Mucosal ; Intestine, Small/*microbiology/*transplantation ; Metagenomics ; Transplantation Tolerance/*immunology ; }, abstract = {The gut microbiota is mainly composed of a diverse population of commensal bacterial species and plays a pivotal role in the maintenance of intestinal homeostasis, immune modulation and metabolism. The influence of the gut microbiota on solid organ transplantation has recently been recognized. In fact, several studies indicated that acute and chronic allograft rejection in small bowel transplantation (SBT) is closely associated with the alterations in microbial patterns in the gut. In this review, we focused on the recent findings regarding alterations in the microbiota following SBTand the potential roles of these alterations in the development of acute and chronic allograft rejection. We also reviewed important advances with respect to the interplays between the microbiota and host immune systems in SBT. Furthermore, we explored the potential of the gut microbiota as a microbial marker and/or therapeutic target for the predication and intervention of allograft rejection and chronic dysfunction. Given that current research on the gut microbiota has become increasingly sophisticated and comprehensive, large cohort studies employing metagenomic analysis and multivariate linkage should be designed for the characterization of host-microbe interaction and causality between microbiota alterations and clinical outcomes in SBT. The findings are expected to provide valuable insights into the role of gut microbiota in the development of allograft rejection and other transplant-related complications and introduce novel therapeutic targets and treatment approaches in clinical practice.}, }
@article {pmid29523545, year = {2018}, author = {Patin, NV and Pratte, ZA and Regensburger, M and Hall, E and Gilde, K and Dove, ADM and Stewart, FJ}, title = {Microbiome Dynamics in a Large Artificial Seawater Aquarium.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {10}, pages = {}, pmid = {29523545}, issn = {1098-5336}, abstract = {Artificial habitats for animals have high commercial and societal value. Microbial communities (microbiomes) in such habitats may play ecological roles similar to those in nature. However, this hypothesis remains largely untested. Georgia Aquarium's Ocean Voyager (OV) exhibit is a closed-system aquatic habitat that mimics the oligotrophic open ocean and houses thousands of large marine animals, including fish, sea turtles, and whale sharks. We present a 14-month time series characterizing the OV water column microbiome. The composition and stability of the microbiome differed from those of natural marine environments with similar chemical features. The composition shifted dramatically over the span of 2 weeks and was characterized by bloom events featuring members of two heterotrophic bacterial lineages with cosmopolitan distributions in the oceans. The relative abundances of these lineages were inversely correlated, suggesting an overlap in ecological niches. Transcript mapping to metagenome-assembled genomes (MAGs) of these taxa identified unique characteristics, including the presence and activity of genes for the synthesis and degradation of cyanophycin, an amino acid polymer linked to environmental stress and found frequently in cyanobacteria but rarely in heterotrophic bacteria. The dominant MAGs also contained and transcribed plasmid-associated sequences, suggesting a role for conjugation in adaptation to the OV environment. These findings indicate a highly dynamic microbiome despite the stability of the physical and chemical parameters of the water column. Characterizing how such fluctuations affect microbial function may inform our understanding of animal health in closed aquaculture systems.IMPORTANCE Public aquariums play important societal roles, for example, by promoting science education and helping conserve biodiversity. The health of aquarium animals depends on interactions with the surrounding microbiome. However, the extent to which aquariums recreate a stable and natural microbial ecosystem is uncertain. This study describes the taxonomic composition of the water column microbiome over 14 months in a large indoor aquatic habitat, the Ocean Voyager exhibit at the Georgia Aquarium. Despite stable water column conditions, the exhibit experienced blooms in which the abundance of a single bacterial strain increased to over 65% of the community. Genome analysis indicated that the OV's dominant strains share unique adaptations, notably genes for storage polymers associated with environmental stress. These results, interpreted alongside data from natural ocean systems and another artificial seawater aquarium, suggest a highly dynamic aquarium microbiome and raise questions of how microbiome stability may affect the ecological health of the habitat.}, }
@article {pmid29522953, year = {2018}, author = {Cai, L and Chen, TB and Zheng, SW and Liu, HT and Zheng, GD}, title = {Decomposition of lignocellulose and readily degradable carbohydrates during sewage sludge biodrying, insights of the potential role of microorganisms from a metagenomic analysis.}, journal = {Chemosphere}, volume = {201}, number = {}, pages = {127-136}, doi = {10.1016/j.chemosphere.2018.02.177}, pmid = {29522953}, issn = {1879-1298}, mesh = {Carbohydrate Metabolism ; Carbohydrates/*analysis ; Hot Temperature ; Lignin/*analysis ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Sewage/*chemistry/microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Sewage sludge biodrying is a waste treatment method that uses bio-heat generated from organic degradation to remove moisture from sewage sludge. Lignocellulose and carbohydrate decomposition is important when assessing biodrying performance. This study investigated lignocellulose and carbohydrate decomposition, and the potential microbial functions during biodrying. We determined the lignocellulose and carbohydrate contents, assayed related enzyme activity, performed a complete metagenomic study on sewage sludge biodrying material during the thermophilic phase, annotated potential genetic function involved in the decomposition, and summarized the key metabolic pathways. The results indicated that lignocellulose, readily degradable carbohydrates, and starch, significantly decomposed after biodrying. During the thermophilic phase, the majority of lignocellulose and carbohydrate-related enzymes showed significantly higher activity, and glycoside hydrolases and glycosyl transferases showed higher gene counts and reads. Moreover, the top five microorganisms enriched with carbohydrate-active enzyme genes, i.e., Bacillus, Intrasporangium, Tetrasphaera, Rhodobacter, and Streptomyces, were also among the top ten ecologically dominant genera. These findings highlight the crucial phases for biodrying process, reveal the ecologically functional diversity of biodrying-originated microbial consortia, and suggest potential candidates for optimizing biodrying decomposition.}, }
@article {pmid29521257, year = {2018}, author = {Cano, RJ and Toranzos, GA}, title = {Future Technologies.}, journal = {Microbiology spectrum}, volume = {6}, number = {2}, pages = {}, doi = {10.1128/microbiolspec.EMF-0015-2018}, pmid = {29521257}, issn = {2165-0497}, mesh = {Computational Biology/methods/standards ; Data Analysis ; *Environmental Microbiology ; Environmental Monitoring/*methods/*standards ; Forensic Genetics/*methods/*standards ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods/standards ; Microbiota/*genetics/physiology ; Quality Control ; Reproducibility of Results ; Research ; Research Design ; }, abstract = {Microbiome analysis of environmental samples may represent the next frontier in environmental microbial forensics. Next-generation sequencing technologies significantly increased the available genetic data that could be used as evidentiary material. It is not clear, however, whether the microbiome can scale across institutions using forensic-based evidence due to the data resource requirements and the associated costs of maintaining these databases. A successful microbiome study is impacted by the quality of the information gathered and the steps in sample processing and data analysis. To ascertain the validity of methods and the results obtained, there needs to be a stringent procedure to validate the methods and ensure that the results are comparable and reproducible, not only within the laboratory but also between laboratories conducting similar research. Of primary importance for meaningful microbiome studies is an experimental design that leads to carefully executed, controlled, and reproducible studies. The microbiome literature contains a fair share of anecdotal descriptions of microbial community composition and &quot;diagnostic&quot; relative abundance of the taxa therein. These studies are now being supplemented by experimental designs that feature repeated measurements, error estimates, correlations of microbiota with covariates, and increasingly sophisticated statistical tests that enhance the robustness of data analysis and study conclusions. It is imperative to be careful, especially when carrying out attribution studies, to be fully aware of the possible biases included in a specific sample being analyzed.}, }
@article {pmid29515540, year = {2018}, author = {Cuadrat, RRC and Ionescu, D and Dávila, AMR and Grossart, HP}, title = {Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {251}, pmid = {29515540}, issn = {1664-302X}, abstract = {Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.}, }
@article {pmid29511180, year = {2018}, author = {Hu, Y and Sanders, JG and Łukasik, P and D'Amelio, CL and Millar, JS and Vann, DR and Lan, Y and Newton, JA and Schotanus, M and Kronauer, DJC and Pierce, NE and Moreau, CS and Wertz, JT and Engel, P and Russell, JA}, title = {Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {964}, pmid = {29511180}, issn = {2041-1723}, mesh = {Amino Acids/metabolism ; Ammonia/metabolism ; Animals ; Ants/*microbiology/*physiology ; Diet ; *Gastrointestinal Microbiome/genetics ; Geography ; Herbivory/*physiology ; Metagenome ; Metagenomics ; Nitrogen/*metabolism ; Nitrogen Fixation/genetics ; Nitrogen Isotopes ; Symbiosis ; Urea/metabolism ; Urease/metabolism ; Uric Acid/metabolism ; }, abstract = {Nitrogen acquisition is a major challenge for herbivorous animals, and the repeated origins of herbivory across the ants have raised expectations that nutritional symbionts have shaped their diversification. Direct evidence for N provisioning by internally housed symbionts is rare in animals; among the ants, it has been documented for just one lineage. In this study we dissect functional contributions by bacteria from a conserved, multi-partite gut symbiosis in herbivorous Cephalotes ants through in vivo experiments, metagenomics, and in vitro assays. Gut bacteria recycle urea, and likely uric acid, using recycled N to synthesize essential amino acids that are acquired by hosts in substantial quantities. Specialized core symbionts of 17 studied Cephalotes species encode the pathways directing these activities, and several recycle N in vitro. These findings point to a highly efficient N economy, and a nutritional mutualism preserved for millions of years through the derived behaviors and gut anatomy of Cephalotes ants.}, }
@article {pmid29500976, year = {2018}, author = {Tang, X and Guo, Y and Jiang, B and Liu, S}, title = {Metagenomic approaches to understanding bacterial communication during the anammox reactor start-up.}, journal = {Water research}, volume = {136}, number = {}, pages = {95-103}, doi = {10.1016/j.watres.2018.02.054}, pmid = {29500976}, issn = {1879-2448}, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Bioreactors/*microbiology ; Metagenomics ; Nitrogen/chemistry ; Waste Water/chemistry/*microbiology ; }, abstract = {Increasing attention has been paid to the anammox community for its significant function in high-efficiency wastewater treatment. However, bacterial interaction in terms of bacterial communication is still elusive. This study firstly explored the intra- and interspecific communication of bacteria in the anammox community using metagenomic sequence data obtained during bioreactor operation. We verified the existence of multiple bacterial communication gene (BCG) subtypes by alignment with the constructed BCG database containing 11 identified gene subtypes. Bacterial communication was more active at the initial start-up than in the high loading-rate phase, and was correlated with the gradually decreasing bacterial diversity. Hdts, one of the key genes that produced the intraspecific signaling molecule AHL, and RpfF, the key gene that produced the intra- and interspecific signaling molecule DSF, were the primary communication engines in the anammox community because of their high abundance. Anammox bacteria mainly used Hdts genes to communicate with others, while RpfF gene played a core role characterized by their multiple correlations with other BCG subtypes. Interestingly, bacteria with abundant BCGs were more inclined to interact with the bacteria with the same functional traits, indicating the potential communication-related interaction among these bacteria in addition to the frequently reported substrate co-utilization. This highlights the primary importance of AHL and DSF for the anammox community, and thereby hints at a potential strategy for the target regulation of the signals to improve anammox viability and competitive capacity in wastewater treatment.}, }
@article {pmid29500689, year = {2018}, author = {Xia, H and Wang, Y and Shi, C and Atoni, E and Zhao, L and Yuan, Z}, title = {Comparative Metagenomic Profiling of Viromes Associated with Four Common Mosquito Species in China.}, journal = {Virologica Sinica}, volume = {33}, number = {1}, pages = {59-66}, pmid = {29500689}, issn = {1995-820X}, mesh = {Animals ; *Biodiversity ; China ; Culicidae/*virology ; Host Specificity ; *Metagenomics ; Mosquito Vectors/*virology ; Viral Tropism ; Viruses/*classification/genetics/*isolation &amp; purification ; }, abstract = {Vast viruses are thought to be associated with mosquitoes. Anopheles sinensis, Armigeres subalbatus, Culex quinquefasciatus, and Culex tritaeniorhynchus are very common mosquito species in China, and whether the virome structure in each species is species-specific has not been evaluated. In this study, a total of 2222 mosquitoes were collected from the same geographic location, and RNAs were sequenced using the Illumina Miseq platform. After querying to the Refseq database, a total of 3,435,781, 2,223,509, 5,727,523, and 6,387,867 paired-end reads were classified under viral sequences from An. sinensis, Ar. subalbatus, Cx. quinquefasciatus, and Cx. tritaeniorhynchus, respectively, with the highest prevalence of virus-associated reads being observed in Cx. quinquefasciatus. The metagenomic comparison analysis showed that the virus-related reads were distributed across 26 virus families, together with an unclassified group of viruses. Anelloviridae, Circoviridae, Genomoviridae, Iridoviridae, Mesoniviridae, Microviridae, Myoviridae, Parvoviridae, Phenuiviridae, and Podoviridae were the top ten significantly different viral families among the four species. Further analysis reveals that the virome is species-specific in four mosquito samples, and several viral sequences which maybe belong to novel viruses are discovered for the first time in those mosquitoes. This investigation provides a basis for a comprehensive knowledge on the mosquito virome status in China.}, }
@article {pmid29499759, year = {2018}, author = {Eng, A and Borenstein, E}, title = {Taxa-function robustness in microbial communities.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {45}, pmid = {29499759}, issn = {2049-2618}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; DP2 AT007802-01//National Institutes of Health (US)/International ; }, mesh = {Bacteria/*classification/*genetics ; Biodiversity ; Cellular Microenvironment/*physiology ; Computer Simulation ; Environment ; Female ; Gastrointestinal Tract/microbiology ; Humans ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Vagina/microbiology ; }, abstract = {BACKGROUND: The species composition of a microbial community is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies. These perturbations to a community's taxonomic profile naturally also alter the community's functional profile-the aggregate set of genes encoded by community members-ultimately altering the community's overall functional capacities. The magnitude of such functional changes and the specific shift that will occur in each function, however, are strongly dependent on how genes are distributed across community members' genomes. This gene distribution, in turn, is determined by the taxonomic composition of the community and would markedly differ, for example, between communities composed of species with similar genomic content vs. communities composed of species whose genomes encode relatively distinct gene sets. Combined, these observations suggest that community functional robustness to taxonomic perturbations could vary widely across communities with different compositions, yet, to date, a systematic study of the inherent link between community composition and robustness is lacking.<br><br>RESULTS: In this study, we examined how a community's taxonomic composition influences the robustness of that community's functional profile to taxonomic perturbation (here termed taxa-function robustness) across a wide array of environments. Using a novel simulation-based computational model to quantify this taxa-function robustness in host-associated and non-host-associated communities, we find notable differences in robustness between communities inhabiting different body sites, including significantly higher robustness in gut communities compared to vaginal communities that cannot be attributed solely to differences in species richness. We additionally find between-site differences in the robustness of specific functions, some of which are potentially related to site-specific environmental conditions. These taxa-function robustness differences are most strongly associated with differences in overall functional redundancy, though other aspects of gene distribution also influence taxa-function robustness in certain body environments, and are sufficient to cluster communities by environment. Further analysis revealed a correspondence between our robustness estimates and taxonomic and functional shifts observed across human-associated communities.<br><br>CONCLUSIONS: Our analysis approach revealed intriguing taxa-function robustness variation across environments and identified features of community and gene distribution that impact robustness. This approach could be further applied for estimating taxa-function robustness in novel communities and for informing the design of synthetic communities with specific robustness requirements.}, }
@article {pmid29498741, year = {2018}, author = {Valeriani, F and Crognale, S and Protano, C and Gianfranceschi, G and Orsini, M and Vitali, M and Spica, VR}, title = {Metagenomic analysis of bacterial community in a travertine depositing hot spring.}, journal = {The new microbiologica}, volume = {41}, number = {2}, pages = {126-135}, pmid = {29498741}, issn = {1121-7138}, mesh = {Bacteria/*genetics/isolation &amp; purification ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Hot Springs/*microbiology ; Metagenomics/*methods ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Several factors influence bacteria biodiversity in hot springs. The impact of biotic and abiotic pathways on travertine deposition plays a key role in microbial ecology and in the final composition of the waterborne microbiota. The metabolism of some bacterial groups such as photoautotrophs or lithoautotrophs influences water chemistry, favoring carbonate precipitation processes. The role of microbial mats in mineral precipitation processes is not fully clarified. For the first time, a comprehensive metagenomic analysis has been undertaken in the historical Bullicame hot spring. Bacterial biodiversity was characterized and biomineralization activities were assigned to different genera. A higher biodiversity in mat samples compared to water samples was observed: Shannon index of 3.34 and 0.86, respectively. Based on the functional assignment of each Operational Taxonomic Unit, the bacteria involved in biologically- induced mineralization are prevalent in mat and released in the water. According to the principle that each geothermal water specimen has distinctive physic-chemical characteristics, our results suggest new interacting bio-actions within these ecosystems. The saturation index and the chemical composition, as the high concentration of sulfur species and HCO3, can be linked to create a selective environment where pioneer communities are able to live and shape the ecosystem.}, }
@article {pmid29497869, year = {2018}, author = {Tan, Z and Wang, Y and Yang, T and Ao, H and Chen, S and Xing, K and Zhang, F and Zhao, X and Liu, J and Wang, C}, title = {Differences in gut microbiota composition in finishing Landrace pigs with low and high feed conversion ratios.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {9}, pages = {1673-1685}, pmid = {29497869}, issn = {1572-9699}, support = {BAIC02-2016//Beijing Innovation Consortium of Agriculture Research System/ ; }, mesh = {Amino Acids/metabolism ; Animal Feed/*analysis ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Carbohydrate Metabolism ; Cecum/microbiology ; Colon/microbiology ; DNA, Bacterial/genetics ; Discriminant Analysis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Intestine, Small/microbiology ; Metabolic Networks and Pathways ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Swine ; }, abstract = {The goal of this study was to evaluate the microbial communities in the gut and feces from female finishing Landrace pigs with high and low feed conversion ratio (FCR) by 16S rRNA gene amplicon sequencing. Many potential biomarkers can distinguish between high and low FCR groups in the duodenum, ileum, cecum, colon, and rectum, according to linear discriminant analysis effect sizes. The relative abundance of microbes were tested by Mann-Whitney test between the high and low FCR groups in different organs: Campylobacter, Prevotella and Sphaerochaeta were different in the duodenum (P < 0.05); Sanguibacter, Kingella and Anaeroplasma in jejunum; Anaeroplasma, Arthrobacter, Kingella, Megasphaera and SMB53 in the ileum; Butyricicoccus, Campylobacter, Mitsuokella, and Coprobacillus in the cecum; Lactococcus and Peptococcus in the colon; Staphylococcus in the rectum; and Rothia in feces. The prevalence of microbial genera in certain locations could potentially be used as biomarkers to distinguish between high and low FCR. Functional prediction clustering analysis suggested that bacteria in the hindgut mainly participated in carbohydrate metabolism and amino acid metabolism, and different in the relative abundance of metabolic pathways, as predicted from the microbial taxa present, were identified by comparing the high and low groups of each location. The results may provide insights for the alteration of the intestinal microbial communities to improve the growth rate of pigs.}, }
@article {pmid29497601, year = {2018}, author = {Lin, W and Jiang, W and Hu, X and Gao, L and Ai, D and Pan, H and Niu, C and Yuan, K and Zhou, X and Xu, C and Huang, Z}, title = {Ecological Shifts of Supragingival Microbiota in Association with Pregnancy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {24}, pmid = {29497601}, issn = {2235-2988}, mesh = {Adult ; *Biodiversity ; Female ; Gingiva/*microbiology ; Hormones ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; Pregnancy ; RNA, Ribosomal, 16S ; Saliva/microbiology ; }, abstract = {Pregnancy is a physiological process with pronounced hormonal fluctuations in females, and relatively little is known regarding how pregnancy influences the ecological shifts of supragingival microbiota. In this study, supragingival plaques and salivary hormones were collected from 11 pregnant women during pregnancy (P1, ≤14 weeks; P2, 20-25 weeks; P3, 33-37 weeks) and the postpartum period (P4, 6 weeks after childbirth). Seven non-pregnant volunteers were sampled at the same time intervals. The microbial genetic repertoire was obtained by 16S rDNA sequencing. Our results indicated that the Shannon diversity in P3 was significantly higher than in the non-pregnant group. The principal coordinates analysis showed distinct clustering according to gestational status, and the partial least squares discriminant analysis identified 33 genera that may contribute to this difference. There were differentially distributed genera, among which Neisseria, Porphyromonas, and Treponema were over-represented in the pregnant group, while Streptococcus and Veillonella were more abundant in the non-pregnant group. In addition, 53 operational taxonomic units were observed to have positive correlations with sex hormones in a redundancy analysis, with Prevotella spp. and Treponema spp. being most abundant. The ecological events suggest that pregnancy has a role in shaping an at-risk-for-harm microbiota and provide a basis for etiological studies of pregnancy-associated oral dysbiosis.}, }
@article {pmid29497412, year = {2018}, author = {Garrido-Sanz, D and Manzano, J and Martín, M and Redondo-Nieto, M and Rivilla, R}, title = {Metagenomic Analysis of a Biphenyl-Degrading Soil Bacterial Consortium Reveals the Metabolic Roles of Specific Populations.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {232}, pmid = {29497412}, issn = {1664-302X}, abstract = {Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source. This consortium is able to grow on biphenyl, benzoate, and protocatechuate. Whole-community DNA extracted from the consortium was used to analyze biodiversity by Illumina sequencing of a 16S rRNA gene amplicon library and to determine the metagenome by whole-genome shotgun Illumina sequencing. Biodiversity analysis shows that the consortium consists of 24 operational taxonomic units (≥97% identity). The consortium is dominated by strains belonging to the genus Pseudomonas, but also contains betaproteobacteria and Rhodococcus strains. whole-genome shotgun (WGS) analysis resulted in contigs containing 78.3 Mbp of sequenced DNA, representing around 65% of the expected DNA in the consortium. Bioinformatic analysis of this metagenome has identified the genes encoding the enzymes implicated in three pathways for the conversion of biphenyl to benzoate and five pathways from benzoate to tricarboxylic acid (TCA) cycle intermediates, allowing us to model the whole biodegradation network. By genus assignment of coding sequences, we have also been able to determine that the three biphenyl to benzoate pathways are carried out by Rhodococcus strains. In turn, strains belonging to Pseudomonas and Bordetella are the main responsible of three of the benzoate to TCA pathways while the benzoate conversion into TCA cycle intermediates via benzoyl-CoA and the catechol meta-cleavage pathways are carried out by beta proteobacteria belonging to genera such as Achromobacter and Variovorax. We have isolated a Rhodococcus strain WAY2 from the consortium which contains the genes encoding the three biphenyl to benzoate pathways indicating that this strain is responsible for all the biphenyl to benzoate transformations. The presented results show that metagenomic analysis of consortia allows the identification of bacteria active in biodegradation processes and the assignment of specific reactions and pathways to specific bacterial groups.}, }
@article {pmid29495531, year = {2018}, author = {Chen, H and Wu, H and Yan, B and Zhao, H and Liu, F and Zhang, H and Sheng, Q and Miao, F and Liang, Z}, title = {Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism?.}, journal = {International journal of molecular sciences}, volume = {19}, number = {3}, pages = {}, pmid = {29495531}, issn = {1422-0067}, mesh = {Biodiversity ; Genetic Variation ; Metagenome ; Metagenomics/methods ; *Microbiota ; Plants, Medicinal/classification/genetics/metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics ; Salvia miltiorrhiza/classification/genetics/metabolism/*microbiology ; Seeds/metabolism/*microbiology ; }, abstract = {Seed microbiome includes special endophytic or epiphytic microbial taxa associated with seeds, which affects seed germination, plant growth, and health. Here, we analyzed the core microbiome of 21 Salvia miltiorrhiza seeds from seven different geographic origins using 16S rDNA and ITS amplicon sequencing, followed by bioinformatics analysis. The whole bacterial microbiome was classified into 17 microbial phyla and 39 classes. Gammaproteobacteria (67.6%), Alphaproteobacteria (15.6%), Betaproteobacteria (2.6%), Sphingobacteria (5.0%), Bacilli (4.6%), and Actinobacteria (2.9%) belonged to the core bacterial microbiome. Dothideomycetes comprised 94% of core fungal microbiome in S. miltiorrhiza seeds, and another two dominant classes were Leotiomycetes (3.0%) and Tremellomycetes (2.0%). We found that terpenoid backbone biosynthesis, degradation of limonene, pinene, and geraniol, and prenyltransferases, were overrepresented in the core bacterial microbiome using phylogenetic examination of communities by reconstruction of unobserved states (PICRUSt) software. We also found that the bacterial genera Pantoea, Pseudomonas, and Sphingomonas were enriched core taxa and overlapped among S. miltiorrhiza, maize, bean, and rice, while a fungal genus, Alternaria, was shared within S. miltiorrhiza, bean, and Brassicaceae families. These findings highlight that seed-associated microbiomeis an important component of plant microbiomes, which may be a gene reservoir for secondary metabolism in medicinal plants.}, }
@article {pmid29494648, year = {2018}, author = {Bhogoju, S and Nahashon, S and Wang, X and Darris, C and Kilonzo-Nthenge, A}, title = {A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0191029}, pmid = {29494648}, issn = {1932-6203}, mesh = {Animal Feed ; Animals ; Galliformes/genetics/*microbiology ; Gastrointestinal Microbiome/*genetics ; *Metagenome ; Metagenomics ; Phylogeny ; Poultry/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Probiotics are live microbial feed supplements that promote growth and health to the host by minimizing non-essential and pathogenic microorganisms in the host's gastrointestinal tract (GIT). The campaign to minimize excessive use of antibiotics in poultry production has necessitated development of probiotics with broad application in multiple poultry species. Design of such probiotics requires understanding of the diversity or similarity in microbial profiles among avian species of economic importance. Therefore, the objective of this research was to establish and compare the microbial profiles of the GIT of Guinea fowl and chicken and to establish the microbial diversity or similarity between the two avian species. A metagenomic approach consisting of the amplification and sequence analysis of the hypervariable regions V1-V9 of the 16S rRNA gene was used to identify the GIT microbes. Collectively, we detected more than 150 microbial families. The total number of microbial species detected in the chicken GIT was higher than that found in the Guinea Fowl GIT. Our studies also revealed phylogenetic diversity among the microbial species found in chicken and guinea fowl. The phylum Firmicutes was most abundant in both avian species whereas Phylum Actinobacteria was most abundant in chickens than Guinea fowls. The diversity of the microbial profiles found in broiler chickens and Guinea fowls suggest that the design of effective avian probiotics would require species specificity.}, }
@article {pmid29491015, year = {2018}, author = {Amrane, S and Bachar, D and Lagier, JC and Raoult, D}, title = {Clostridium scindens Is Present in the Gut Microbiota during Clostridium difficile Infection: a Metagenomic and Culturomic Analysis.}, journal = {Journal of clinical microbiology}, volume = {56}, number = {5}, pages = {}, pmid = {29491015}, issn = {1098-660X}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteriological Techniques ; Child ; Clostridium/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Clostridium Infections/*microbiology ; Diarrhea/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; Middle Aged ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, }
@article {pmid29490093, year = {2018}, author = {Mulukutla, SN and Hsu, JW and Gaba, R and Bohren, KM and Guthikonda, A and Iyer, D and Ajami, NJ and Petrosino, JF and Hampe, CS and Ram, N and Jahoor, F and Balasubramanyam, A}, title = {Arginine Metabolism Is Altered in Adults with A-β + Ketosis-Prone Diabetes.}, journal = {The Journal of nutrition}, volume = {148}, number = {2}, pages = {185-193}, pmid = {29490093}, issn = {1541-6100}, support = {R01 DK026190/DK/NIDDK NIH HHS/United States ; R01 DK101411/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Arginine/administration &amp; dosage/blood/*metabolism ; Blood Glucose/analysis ; Body Mass Index ; Diabetes Mellitus, Type 1/*metabolism/physiopathology ; Diabetes Mellitus, Type 2/physiopathology ; Female ; Gastrointestinal Microbiome/physiology ; Glucose/administration &amp; dosage ; Glucose Clamp Technique ; Humans ; Hyperglycemia ; Insulin/blood/metabolism ; Insulin Secretion ; Insulin-Secreting Cells/*physiology ; Kinetics ; Male ; Metabolomics/methods ; Middle Aged ; Nitric Oxide/metabolism ; Ornithine/blood ; }, abstract = {Background: A-β + ketosis-prone diabetes (KPD) is a subset of type 2 diabetes in which patients have severe but reversible β cell dysfunction of unknown etiology. Plasma metabolomic analysis indicates that abnormal arginine metabolism may be involved.<br><br>Objective: The objective of this study was to determine the relation between gut microbiome and arginine metabolism and the relation between arginine availability and β cell function in KPD patients compared with control participants.<br><br>Methods: Kinetics of arginine and related metabolites were measured with stable isotope tracers, and insulin secretory responses to arginine and glucose were determined under euglycemic and hyperglycemic conditions in 6 KPD patients and 6 age-, gender-, and body mass index-matched control participants. Glucose potentiation of arginine-induced insulin secretion was performed in a different set of 6 KPD and 3 control participants.<br><br>Results: Arginine availability was higher in KPD patients during euglycemia [53.5 ± 4.3 (mean ± SEM) compared with 40.3 ± 2.4 μmol · kg lean body mass (LBM)-1 · h-1, P = 0.03] but declined more in response to hyperglycemia (Δ 10.15 ± 2.6 compared with Δ 3.20 ± 1.3 μmol · kg LBM-1 · h-1, P = 0.041). During hyperglycemia, ornithine flux was not different between groups but after an arginine bolus, plasma ornithine AUC trended higher in KPD patients (3360 ± 294 compared with 2584 ± 259 min · μmol · L-1, P = 0.08). In both euglycemia and hyperglycemia, the first-phase insulin responses to glucose stimulation were lower in KPD patients (euglycemic insulin AUC 282 ± 108 compared with 926 ± 257 min · μU · mL-1, P = 0.02; hyperglycemic insulin AUC 358 ± 79 compared with 866 ± 292 min · μU · mL-1, P = 0.05), but exogenous arginine restored first-phase insulin secretion in KPD patients to the level of control participants.<br><br>Conclusion: Compared with control participants, KPD patients have increased arginine availability in the euglycemic state, indicating a higher requirement. This is compromised during hyperglycemia, with an inadequate supply of arginine to sustain metabolic functions such as insulin secretion. Exogenous arginine administration restores a normal insulin secretory response.}, }
@article {pmid29486880, year = {2018}, author = {Bodewes, R}, title = {Novel viruses in birds: Flying through the roof or is a cage needed?.}, journal = {Veterinary journal (London, England : 1997)}, volume = {233}, number = {}, pages = {55-62}, doi = {10.1016/j.tvjl.2017.12.023}, pmid = {29486880}, issn = {1532-2971}, mesh = {Animals ; Animals, Domestic/virology ; Animals, Wild/virology ; Bird Diseases/virology ; Birds/*virology ; Chickens/virology ; Columbidae/virology ; Ducks/virology ; Endangered Species ; Virus Diseases/veterinary ; Viruses/isolation &amp; purification/pathogenicity ; }, abstract = {Emerging viral diseases continue to have a major global impact on human beings and animals. To be able to take adequate measures in case of an outbreak of an emerging disease, rapid detection of the causative agent is a crucial first step. In this review, various aspects of virus discovery are discussed, with a special focus on recently discovered viruses in birds. Novel viruses with a potential major impact have been discovered in domestic and wild bird species in recent years using various virus discovery methods. Only a few studies report the detection of novel viruses in endangered bird species, although increased knowledge about viruses circulating in these species is important. Additional studies focusing on the exact role of a novel virus in disease and on the impact of a novel virus on bird populations are often lacking. Intensive collaboration between different disciplines is needed to obtain useful information about the role of these novel viruses.}, }
@article {pmid29482646, year = {2018}, author = {Louca, S and Doebeli, M and Parfrey, LW}, title = {Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {41}, pmid = {29482646}, issn = {2049-2618}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Base Sequence/genetics ; Gene Dosage/*genetics ; Genome, Bacterial/genetics ; Humans ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology. Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions of bacterial and archaeal taxa in microbial communities. Because different organisms contain different 16S gene copy numbers (GCNs), sequence variant counts are biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods and based on sequenced genomes, in order to correct for these biases. However, the accuracy of those predictions has not been independently assessed. Here, we systematically evaluate the predictability of 16S GCNs across bacterial and archaeal clades, based on ∼ 6,800 public sequenced genomes and using several phylogenetic methods. Further, we assess the accuracy of GCNs predicted by three recently published tools (PICRUSt, CopyRighter, and PAPRICA) over a wide range of taxa and for 635 microbial communities from varied environments. We find that regardless of the phylogenetic method tested, 16S GCNs could only be accurately predicted for a limited fraction of taxa, namely taxa with closely to moderately related representatives (≲15% divergence in the 16S rRNA gene). Consistent with this observation, we find that all considered tools exhibit low predictive accuracy when evaluated against completely sequenced genomes, in some cases explaining less than 10% of the variance. Substantial disagreement was also observed between tools (R2<0.5) for the majority of tested microbial communities. The nearest sequenced taxon index (NSTI) of microbial communities, i.e., the average distance to a sequenced genome, was a strong predictor for the agreement between GCN prediction tools on non-animal-associated samples, but only a moderate predictor for animal-associated samples. We recommend against correcting for 16S GCNs in microbiome surveys by default, unless OTUs are sufficiently closely related to sequenced genomes or unless a need for true OTU proportions warrants the additional noise introduced, so that community profiles remain interpretable and comparable between studies.}, }
@article {pmid29482639, year = {2018}, author = {Marotz, CA and Sanders, JG and Zuniga, C and Zaramela, LS and Knight, R and Zengler, K}, title = {Improving saliva shotgun metagenomics by chemical host DNA depletion.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {42}, pmid = {29482639}, issn = {2049-2618}, support = {R21 AR071731/AR/NIAMS NIH HHS/United States ; AR071731/AR/NIAMS NIH HHS/United States ; n/a//Center for Microbiome Innovation/International ; }, mesh = {Azides/*chemistry ; Bacteria/genetics ; DNA/*chemistry ; Fungi/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Propidium/*analogs &amp; derivatives/chemistry ; Saliva/*microbiology ; Sequence Analysis, DNA ; Viruses/genetics ; }, abstract = {BACKGROUND: Shotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencing approaches that assess taxonomy but not function and are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in microbial populations because few DNA sequence reads are from the microbial component. We developed and optimized a novel method for enriching microbial DNA from human oral samples and compared its efficiency and potential taxonomic bias with commercially available kits.<br><br>RESULTS: Three commercially available host depletion kits were directly compared with size filtration and a novel method involving osmotic lysis and treatment with propidium monoazide (lyPMA) in human saliva samples. We evaluated the percentage of shotgun metagenomic sequencing reads aligning to the human genome, and taxonomic biases of those not aligning, compared to untreated samples. lyPMA was the most efficient method of removing host-derived sequencing reads compared to untreated sample (8.53 ± 0.10% versus 89.29 ± 0.03%). Furthermore, lyPMA-treated samples exhibit the lowest taxonomic bias compared to untreated samples.<br><br>CONCLUSION: Osmotic lysis followed by PMA treatment is a cost-effective, rapid, and robust method for enriching microbial sequence data in shotgun metagenomics from fresh and frozen saliva samples and may be extensible to other host-derived sample types.}, }
@article {pmid29476620, year = {2018}, author = {Chappell, CR and Fukami, T}, title = {Nectar yeasts: a natural microcosm for ecology.}, journal = {Yeast (Chichester, England)}, volume = {35}, number = {6}, pages = {417-423}, doi = {10.1002/yea.3311}, pmid = {29476620}, issn = {1097-0061}, mesh = {Animals ; Bacteria ; Biota ; Flowers ; Models, Biological ; *Plant Nectar ; Pollination ; *Social Behavior ; *Social Environment ; *Yeasts ; }, abstract = {The species of yeasts that colonize floral nectar can modify the mutualistic relationships between plants and pollinators by changing the chemical properties of nectar. Recent evidence supporting this possibility has led to increased interest among ecologists in studying these fungi as well as the bacteria that interact with them in nectar. Although not fully explored, nectar yeasts also constitute a promising natural microcosm that can be used to facilitate development of general ecological theory. We discuss the methodological and conceptual advantages of using nectar yeasts from this perspective, including simplicity of communities, tractability of dispersal, replicability of community assembly, and the ease with which the mechanisms of species interactions can be studied in complementary experiments conducted in the field and the laboratory. To illustrate the power of nectar yeasts as a study system, we discuss several topics in community ecology, including environmental filtering, priority effects, and metacommunity dynamics. An exciting new direction is to integrate metagenomics and comparative genomics into nectar yeast research to address these fundamental ecological topics.}, }
@article {pmid29474068, year = {2018}, author = {Lu, T and Ke, M and Peijnenburg, WJGM and Zhu, Y and Zhang, M and Sun, L and Fu, Z and Qian, H}, title = {Investigation of Rhizospheric Microbial Communities in Wheat, Barley, and Two Rice Varieties at the Seedling Stage.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {11}, pages = {2645-2653}, doi = {10.1021/acs.jafc.7b06155}, pmid = {29474068}, issn = {1520-5118}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Hordeum/*growth &amp; development/microbiology ; Oryza/*growth &amp; development/microbiology ; Rhizosphere ; Seedlings/growth &amp; development/microbiology ; *Soil Microbiology ; Triticum/*growth &amp; development/microbiology ; }, abstract = {The plant rhizosphere microbiota plays multiple roles in plant growth. We investigated the taxonomic and functional variations in the rhizosphere microbial community, examining both prokaryotes and eukaryotes, of four crops at the seedling stage: wheat, barley, and two rice varieties (indica and japonica) seeded in paddy soil. The diversity of rhizosphere communities in these four species was determined. Results showed that wheat and barley had much stronger selection effects than rice for the rhizosphere microbial community. Functional metagenomic profiling indicated that a series of sequences related to glycan, limonene, and pinene degradation pathways as well as some relatively rare functions related to N or S metabolism were enriched in the rhizosphere soil. We conclude that the four tested crops induced the formation of the microbial community with specific features that may influence the plant growth but stochastic processes also appreciably influenced the functional selection.}, }
@article {pmid29472560, year = {2018}, author = {Taş, N and Prestat, E and Wang, S and Wu, Y and Ulrich, C and Kneafsey, T and Tringe, SG and Torn, MS and Hubbard, SS and Jansson, JK}, title = {Landscape topography structures the soil microbiome in arctic polygonal tundra.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {777}, pmid = {29472560}, issn = {2041-1723}, mesh = {Arctic Regions ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Carbon/metabolism ; Climate Change ; Methane/metabolism ; *Microbiota ; Permafrost/*microbiology ; Soil/chemistry ; Soil Microbiology ; Tundra ; }, abstract = {In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH4 oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N2O, reflecting low N2O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions.}, }
@article {pmid29471863, year = {2018}, author = {Petrosino, JF}, title = {The microbiome in precision medicine: the way forward.}, journal = {Genome medicine}, volume = {10}, number = {1}, pages = {12}, pmid = {29471863}, issn = {1756-994X}, support = {R01 AI108588/AI/NIAID NIH HHS/United States ; HHSN267200700014C/DK/NIDDK NIH HHS/United States ; R01 MH112356/MH/NIMH NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Disease ; Humans ; *Microbiota ; Phenotype ; *Precision Medicine ; }, abstract = {Novel associations between the human microbiome and health and disease are routinely emerging, and important host-microbiome interactions are targets for new diagnostics and therapeutics. Understanding how broadly host-microbe associations are maintained across populations is revealing individualized host-microbiome phenotypes that can be integrated with other 'omics' data sets to enhance precision medicine.}, }
@article {pmid29469169, year = {2018}, author = {Fountain, MT and Bennett, J and Cobo-Medina, M and Conde Ruiz, R and Deakin, G and Delgado, A and Harrison, R and Harrison, N}, title = {Alimentary microbes of winter-form Drosophila suzukii.}, journal = {Insect molecular biology}, volume = {27}, number = {3}, pages = {383-392}, doi = {10.1111/imb.12377}, pmid = {29469169}, issn = {1365-2583}, mesh = {Animals ; DNA, Ribosomal Spacer/analysis ; Drosophila/*microbiology ; England ; *Gastrointestinal Microbiome ; *Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seasons ; }, abstract = {Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a damaging pest of fruit. Reproductively diapausing adults overwinter in woodlands and remain active on warmer winter days. It is unknown if this adult phase of the lifecycle feeds during the winter period, and what the food source may be. This study characterized the flora in the digestive tract of D. suzukii using a metagenomics approach. Live D. suzukii were trapped in four woodlands in the south of England and their guts dissected for DNA extraction and amplicon-based metagenomics sequencing (internal transcribed spacer and 16S rRNA). Analysis at genus and family taxonomic levels showed high levels of diversity with no differences in digestive tract bacterial or fungal biota between woodland sites of winter-form D. suzukii. Female D. suzukii at one site appeared to have higher bacterial diversity in the alimentary canal than males, but there was a site, sex interaction. Many of the biota were associated with cold, wet climatic conditions and decomposition. This study provides the first evidence that winter-form D. suzukii may be opportunistic feeders during the winter period and are probably exploiting food sources associated with moisture on decomposing vegetation during this time. A core gut microbiome has been identified for winter-form D. suzukii.}, }
@article {pmid29468143, year = {2018}, author = {Gigliucci, F and von Meijenfeldt, FAB and Knijn, A and Michelacci, V and Scavia, G and Minelli, F and Dutilh, BE and Ahmad, HM and Raangs, GC and Friedrich, AW and Rossen, JWA and Morabito, S}, title = {Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {25}, pmid = {29468143}, issn = {2235-2988}, mesh = {Biodiversity ; Child, Preschool ; Computational Biology/methods ; Escherichia coli Infections/*microbiology ; Feces/*microbiology ; *Gastrointestinal Microbiome ; *Host-Pathogen Interactions ; Humans ; Infant ; Infant, Newborn ; *Metagenome ; *Metagenomics/methods ; *Shiga-Toxigenic Escherichia coli/genetics/pathogenicity ; Virulence/genetics ; }, abstract = {The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.}, }
@article {pmid29463661, year = {2018}, author = {He, Z and Zhang, P and Wu, L and Rocha, AM and Tu, Q and Shi, Z and Wu, B and Qin, Y and Wang, J and Yan, Q and Curtis, D and Ning, D and Van Nostrand, JD and Wu, L and Yang, Y and Elias, DA and Watson, DB and Adams, MWW and Fields, MW and Alm, EJ and Hazen, TC and Adams, PD and Arkin, AP and Zhou, J}, title = {Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29463661}, issn = {2150-7511}, mesh = {Biota/*drug effects ; *Ecosystem ; *Environmental Pollution ; Groundwater/*chemistry/*microbiology ; Hydrogen-Ion Concentration ; Metagenome/drug effects ; Nitrates/analysis ; Tennessee ; Uranium/analysis ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology.}, }
@article {pmid29454999, year = {2018}, author = {Wang, J and Tang, L and Zhou, H and Zhou, J and Glenn, TC and Shen, CL and Wang, JS}, title = {Long-term treatment with green tea polyphenols modifies the gut microbiome of female sprague-dawley rats.}, journal = {The Journal of nutritional biochemistry}, volume = {56}, number = {}, pages = {55-64}, pmid = {29454999}, issn = {1873-4847}, support = {R24 TW009489/TW/FIC NIH HHS/United States ; U01 AT006691/AT/NCCIH NIH HHS/United States ; }, abstract = {Green tea polyphenols (GTP) have been shown to exert a spectrum of health benefits to animals and humans. It is plausible that the beneficial effects of GTP are a result of its interaction with the gut microbiota. This study evaluated the effect of long-term treatment with GTP on the gut microbiota of experimental rats and the potential linkage between changes of the gut microbiota with the beneficial effects of GTP. Six-month-old Sprague-Dawley rats were randomly allocated into three dosing regimens (0, 0.5%, and 1.5% of GTP) and followed for 6 months. At the end of month 3 or month 6, half of the animals from each group were sacrificed and their colon contents were collected for microbiome analysis using 16S ribosomal RNA and shotgun metagenomic community sequencing. GTP treatment significantly decreased the biodiversity and modified the microbial community in a dose-dependent manner; similar patterns were observed at both sampling times. Multiple operational taxonomic units and phylotypes were modified: the phylotypes Bacteroidetes and Oscillospira, previously linked to the lean phenotype in human and animal studies, were enriched; and Peptostreptococcaceae previously linked to colorectal cancer phenotype was depleted in GTP treated groups in a dose-dependent manner. Several microbial gene orthologs were modified, among which genes related to energy production and conversion were consistently enriched in samples from month 6 in a dose-dependent manner. This study showed that long-term treatment with GTP induced a dose-dependent modification of the gut microbiome in experimental rats, which might be linked to beneficial effects of GTP.}, }
@article {pmid29454931, year = {2018}, author = {Jansson, JK and Hofmockel, KS}, title = {The soil microbiome-from metagenomics to metaphenomics.}, journal = {Current opinion in microbiology}, volume = {43}, number = {}, pages = {162-168}, doi = {10.1016/j.mib.2018.01.013}, pmid = {29454931}, issn = {1879-0364}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Physiological Phenomena/genetics ; Biodiversity ; Carbon/metabolism ; Metabolic Networks and Pathways ; Metagenomics ; Microbiota/*genetics/physiology ; *Phenotype ; Phylogeny ; *Soil Microbiology ; }, abstract = {Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiome and available resources. Here we describe examples of opportunities towards gaining understanding of the soil metaphenome.}, }
@article {pmid29453765, year = {2018}, author = {Mahajan, R and Attri, S and Sharma, K and Singh, N and Sharma, D and Goel, G}, title = {Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples.}, journal = {Molecular biology reports}, volume = {45}, number = {3}, pages = {297-308}, pmid = {29453765}, issn = {1573-4978}, support = {INT/RUS/RFBR/P-175//Department of Science and Technology, Ministry of Science and Technology/ ; }, mesh = {Animals ; DNA/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Feces/chemistry ; Humans ; Metagenomics/methods ; Microbiota/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Soil/chemistry ; }, abstract = {Cost-effectiveness, quality, time-effectiveness and ease of the methodology are the most crucial factors in isolating quality DNA from wide variety of samples. Thus, research efforts focusing on the development of an efficient DNA extraction protocol is the need of the hour. The present study therefore, focuses on development of an efficient, rapid and free of inhibitory substances based methodology for extracting metagenomic DNA from diverse environmental samples viz. anaerobic biogas digesta, ruminant stomach, human feces, soil, and microbial starter cultures used for preparation of fermented food. PCR-DGGE based analysis and quality metagenomic library preparation, using DNA extraction methodology, validates the developed protocol. The developed protocol is cost effective, capable of isolating DNA from small sample size (100-1000 µl), time efficient (1.5-2.0 h protocol) and results in significantly higher DNA yield (4-8 times increased yield) when compared to previously available DNA extraction method and a commercial DNA extraction kit. The DNA extracted from the samples using different protocols was evaluated based on its ability to identify diverse microbial species using PCR-DGGE profiles targeting variable region within the 16S rRNA gene. The results of microbial community analysis revealed comparability of the developed protocol to commercial kits, in effectively identifying dominant representatives of the microbial community in different samples. Using the DNA extracted from the presented methodology, metagenomic libraries were prepared, which were found suitable for sequencing on Illumina platform.}, }
@article {pmid29446650, year = {2018}, author = {Guilhot, E and Khelaifia, S and La Scola, B and Raoult, D and Dubourg, G}, title = {Methods for culturing anaerobes from human specimen.}, journal = {Future microbiology}, volume = {13}, number = {}, pages = {369-381}, doi = {10.2217/fmb-2017-0170}, pmid = {29446650}, issn = {1746-0921}, mesh = {Antioxidants ; Bacteria, Anaerobic/*growth &amp; development/*isolation &amp; purification ; Bacteriological Techniques ; Coculture Techniques ; Culture Media/chemistry ; Humans ; Metagenomics ; *Microbiota ; Single-Cell Analysis ; Specimen Handling ; }, abstract = {Anaerobes represent the dominating population in the human gut microbiota and play a key role in gut homeostasis. In addition, several anaerobes are now considered as probiotics and they remain essential to several processes in the field of biotechnology. With the implementation of MALDI-TOF MS in routine laboratories, anaerobes are no longer neglected in clinical microbiology, as their identification is made easy. However, the isolation and identification of anaerobic bacteria, remains time consuming, fastidious and costly. Various strategies have been developed, from sampling to culturing human specimens, which will be discussed in this paper. Also, particular attention is paid to isolating species with special medical importance, as for contribution to the field of culturomics.}, }
@article {pmid29444186, year = {2018}, author = {Donovan, PD and Gonzalez, G and Higgins, DG and Butler, G and Ito, K}, title = {Identification of fungi in shotgun metagenomics datasets.}, journal = {PloS one}, volume = {13}, number = {2}, pages = {e0192898}, pmid = {29444186}, issn = {1932-6203}, mesh = {Animals ; Antarctic Regions ; Ascomycota/classification/genetics/isolation &amp; purification ; Candida tropicalis/genetics/pathogenicity ; Databases, Genetic ; Fungi/classification/*genetics/pathogenicity ; Humans ; Metagenome ; *Metagenomics ; Mice ; Microbiota/genetics ; Phylogeny ; Soil Microbiology ; Swine ; Zoonoses/microbiology ; }, abstract = {Metagenomics uses nucleic acid sequencing to characterize species diversity in different niches such as environmental biomes or the human microbiome. Most studies have used 16S rRNA amplicon sequencing to identify bacteria. However, the decreasing cost of sequencing has resulted in a gradual shift away from amplicon analyses and towards shotgun metagenomic sequencing. Shotgun metagenomic data can be used to identify a wide range of species, but have rarely been applied to fungal identification. Here, we develop a sequence classification pipeline, FindFungi, and use it to identify fungal sequences in public metagenome datasets. We focus primarily on animal metagenomes, especially those from pig and mouse microbiomes. We identified fungi in 39 of 70 datasets comprising 71 fungal species. At least 11 pathogenic species with zoonotic potential were identified, including Candida tropicalis. We identified Pseudogymnoascus species from 13 Antarctic soil samples initially analyzed for the presence of bacteria capable of degrading diesel oil. We also show that Candida tropicalis and Candida loboi are likely the same species. In addition, we identify several examples where contaminating DNA was erroneously included in fungal genome assemblies.}, }
@article {pmid29440402, year = {2018}, author = {Grébert, T and Doré, H and Partensky, F and Farrant, GK and Boss, ES and Picheral, M and Guidi, L and Pesant, S and Scanlan, DJ and Wincker, P and Acinas, SG and Kehoe, DM and Garczarek, L}, title = {Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {9}, pages = {E2010-E2019}, pmid = {29440402}, issn = {1091-6490}, mesh = {*Acclimatization ; Chlorophyll/chemistry ; Color ; Computer Simulation ; Cyanobacteria/*genetics ; Ecosystem ; Ecotype ; Light ; Likelihood Functions ; Metagenome ; *Oceans and Seas ; Photosynthesis/physiology ; Phycobilisomes/*physiology ; Phylogeny ; Pigmentation ; Seawater/*microbiology ; Synechococcus/*genetics ; }, abstract = {Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined due to the lack of a single-genetic marker resolving all pigment types (PTs). Here, we developed and employed a robust method based on three distinct marker genes (cpcBA, mpeBA, and mpeW) to estimate the relative abundance of all known Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to reveal the global distribution of Synechococcus PTs and to define their environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified populations in which CA4 might be nonfunctional due to the lack of specific CA4 genes, notably in warm high-nutrient low-chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study provides important insights into the ecology of Synechococcus and highlights the complex interactions between vertical phylogeny, pigmentation, and environmental parameters that shape Synechococcus community structure and evolution.}, }
@article {pmid29439741, year = {2018}, author = {Xiong, W and Wang, Y and Sun, Y and Ma, L and Zeng, Q and Jiang, X and Li, A and Zeng, Z and Zhang, T}, title = {Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {34}, pmid = {29439741}, issn = {2049-2618}, support = {31702290//the National Natural Science Foundation of China/International ; 31672608//the National Natural Science Foundation of China/International ; GRF7201/11E//Hong Kong/International ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*classification/drug effects/genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; Bifidobacterium/classification/drug effects/genetics/isolation &amp; purification ; Chickens ; Chlortetracycline/pharmacology ; *Drug Resistance, Bacterial ; Escherichia/classification/drug effects/genetics/isolation &amp; purification ; Feces/*microbiology ; Gene Regulatory Networks ; Klebsiella/classification/drug effects/genetics/isolation &amp; purification ; Metagenomics ; Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels.<br><br>RESULTS: The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline.<br><br>CONCLUSIONS: We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.}, }
@article {pmid29439665, year = {2018}, author = {Feng, G and Xie, T and Wang, X and Bai, J and Tang, L and Zhao, H and Wei, W and Wang, M and Zhao, Y}, title = {Metagenomic analysis of microbial community and function involved in cd-contaminated soil.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {11}, pmid = {29439665}, issn = {1471-2180}, mesh = {Amino Acids/metabolism ; Bacteria/classification/*drug effects/genetics/metabolism ; Biodiversity ; Cadmium/metabolism/*toxicity ; China ; DNA, Bacterial ; Environmental Pollution ; Fatty Acids/metabolism ; Metabolic Networks and Pathways ; *Metagenomics ; Metals, Heavy/metabolism ; Microbial Consortia/*drug effects ; Nucleotides/metabolism ; Open Reading Frames ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/metabolism/*toxicity ; }, abstract = {BACKGROUND: Soil contaminated with the heavy metal Cadmium (Cd) is a widespread problem in many parts of the world. Based on metagenomic analysis, we investigated the functional potential and structural diversity of the microbial community in Cd-contaminated and non-contaminated soil samples and we explored the associated metabolic pathway network in cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG).<br><br>RESULTS: The results showed that microorganisms in these soils were quite abundant, and many of them possessed numerous physiological functions. However, Cd-contamination has the potential to reduce the microbial diversity and further alter the community structure in the soil. Notably, function analysis of the crucial microorganisms (e. g. Proteobacteria, Sulfuricella and Thiobacillus) indicated that these bacteria and their corresponding physiological functions were important for the community to cope with Cd pollution. The COG annotation demonstrated that the predominant category was the microbial metabolism cluster in both soil samples, while the relative abundance of metabolic genes was increased in the Cd-contaminated soil. The KEGG annotation results exhibited that the non-contaminated soil had more genes, pathways, modules, orthologies and enzymes involved in metabolic pathways of microbial communities than the Cd-contaminated soil. The relative abundance of some dominant KEGG pathways increased in the Cd contaminated soil, and they were mostly enriched to the metabolism, biosynthesis and degradation of amino acids, fatty acids and nucleotides, which was related to Cd tolerance of the microorganisms.<br><br>CONCLUSIONS: Cd-contamination can decrease the taxonomic species of microbes in soil and change the soil microbial composition. The functional pathways involved in the soil change with microbial structure variation, many of which are related to the heavy metal tolerance of soil microbes. The Cd-contaminated soil microbes is a potential resource for exploring cadmium resistant or tolerant bacteria.}, }
@article {pmid29438346, year = {2018}, author = {Wang, C and Zaheer, M and Bian, F and Quach, D and Swennes, AG and Britton, RA and Pflugfelder, SC and de Paiva, CS}, title = {Sjögren-Like Lacrimal Keratoconjunctivitis in Germ-Free Mice.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, pmid = {29438346}, issn = {1422-0067}, support = {P30 CA125123/CA/NCI NIH HHS/United States ; T32 AI053831/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 AI036211/AI/NIAID NIH HHS/United States ; P30 EY002520/EY/NEI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 EY026893/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; CD4-Positive T-Lymphocytes/immunology ; Fecal Microbiota Transplantation ; Female ; Germ-Free Life/*immunology ; Homeodomain Proteins/genetics/metabolism ; Immunity, Innate ; Interferon-gamma/metabolism ; Keratoconjunctivitis/immunology/*microbiology/therapy ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota ; }, abstract = {Commensal bacteria play an important role in the formation of the immune system but their role in the maintenance of immune homeostasis at the ocular surface and lacrimal gland remains poorly understood. This study investigated the eye and lacrimal gland phenotype in germ-free and conventional C57BL/6J mice. Our results showed that germ-free mice had significantly greater corneal barrier disruption, greater goblet cell loss, and greater total inflammatory cell and CD4⁺ T cell infiltration within the lacrimal gland compared to the conventionally housed group. A greater frequency of CD4⁺IFN-γ⁺ cells was observed in germ-free lacrimal glands. Females exhibited a more severe phenotype compared to males. Adoptive transfer of CD4⁺ T cells isolated from female germ-free mice into RAG1KO mice transferred Sjögren-like lacrimal keratoconjunctivitis. Fecal microbiota transplant from conventional mice reverted dry eye phenotype in germ-free mice and decreased CD4⁺IFN-γ⁺ cells to levels similar to conventional C57BL/6J mice. These findings indicate that germ-free mice have a spontaneous lacrimal keratoconjunctivitis similar to that observed in Sjögren syndrome patients and demonstrate that commensal bacteria function in maintaining immune homeostasis on the ocular surface. Thus, manipulation of intestinal commensal bacteria has the potential to become a novel therapeutic approach to treat Sjögren Syndrome.}, }
@article {pmid29433401, year = {2018}, author = {Alex, CE and Kubiski, SV and Li, L and Sadeghi, M and Wack, RF and McCarthy, MA and Pesavento, JB and Delwart, E and Pesavento, PA}, title = {Amdoparvovirus Infection in Red Pandas (Ailurus fulgens).}, journal = {Veterinary pathology}, volume = {55}, number = {4}, pages = {552-561}, doi = {10.1177/0300985818758470}, pmid = {29433401}, issn = {1544-2217}, mesh = {Ailuridae/*virology ; Animals ; Endangered Species ; Feces/virology ; Female ; *Genetic Variation ; Genome, Viral/*genetics ; In Situ Hybridization/veterinary ; Male ; Metagenomics ; Microscopy, Electron/veterinary ; Parvoviridae Infections/diagnostic imaging/pathology/*veterinary/virology ; Parvovirinae/genetics/*isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Virus Shedding ; }, abstract = {Aleutian mink disease virus is the type species in the genus Amdoparvovirus, and in mink and other Mustelidae can cause either subclinical disease or fatal chronic immune stimulation and immune complex disease. The authors describe a novel amdoparvovirus in the endangered red panda (Ailurus fulgens), discovered using viral metagenomics. The authors analyzed the prevalence, tissue distribution, and disease association by PCR, in situ hybridization, electron microscopy, and histology in a group of 6 red pandas from a single zoological collection. The study incorporates a fecal shedding survey and analysis of tissues from 4 necropsied animals over a 12-year span. The tentatively named red panda amdoparvovirus (RpAPV) was detected in the feces and/or tissues of all animals tested. At necropsy of 1 geriatric animal, infection was associated with pyogranulomatous peritonitis, pancreatitis, and myocarditis. Other animals had detectable low-level viral nucleic acid in lymph nodes and both oral and intestinal epithelium at the time of necropsy. Full-length genome sequences of RpAPV strains from 2 animals had 12% sequence divergence, demonstrating genetic diversity even among in-contact animals. RpAPV is a persistent infection in this cohort of red pandas, and has variable clinical expression.}, }
@article {pmid29432849, year = {2018}, author = {Joshi, A and Lanjekar, V and Dhakephalkar, PK and Dagar, SS}, title = {Cultivation of multiple genera of hydrogenotrophic methanogens from different environmental niches.}, journal = {Anaerobe}, volume = {50}, number = {}, pages = {64-68}, doi = {10.1016/j.anaerobe.2018.02.001}, pmid = {29432849}, issn = {1095-8274}, mesh = {Animals ; *Environmental Microbiology ; Feces/microbiology ; Geologic Sediments/microbiology ; Hydrogen/*metabolism ; Metagenome ; Metagenomics/methods ; Methane/*metabolism ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Rumen/microbiology ; }, abstract = {Six genera of hydrogenotrophic methanogens, namely Methanobrevibacter, Methanobacterium, Methanocorpusculum, Methanothermobacter, Methanoculleus, and Methanospirillum were cultivated from diverse environmental niches like rumen, feces, gut, and sediments using BY medium. We also report a putative novel genus and two novel species of methanogens isolated from termite, Indian star tortoise, and green iguana.}, }
@article {pmid29428461, year = {2018}, author = {Perfumo, A and Banat, IM and Marchant, R}, title = {Going Green and Cold: Biosurfactants from Low-Temperature Environments to Biotechnology Applications.}, journal = {Trends in biotechnology}, volume = {36}, number = {3}, pages = {277-289}, doi = {10.1016/j.tibtech.2017.10.016}, pmid = {29428461}, issn = {1879-3096}, mesh = {Antarctic Regions ; Bacteria/metabolism ; Biodegradation, Environmental ; *Biotechnology ; *Cold Temperature ; Enzymes/biosynthesis ; Glycolipids/*biosynthesis/*chemical synthesis ; Lakes/microbiology ; Metagenomics ; Soil Microbiology ; Surface-Active Agents/*chemical synthesis/metabolism ; Water Microbiology ; }, abstract = {Approximately 80% of the Earth's biosphere is cold, at an average temperature of 5°C, and is populated by a diversity of microorganisms that are a precious source of molecules with high biotechnological potential. Biosurfactants from cold-adapted organisms can interact with multiple physical phases - water, ice, hydrophobic compounds, and gases - at low and freezing temperatures and be used in sustainable (green) and low-energy-impact (cold) products and processes. We review the biodiversity of microbial biosurfactants produced in cold habitats and provide a perspective on the most promising future applications in environmental and industrial technologies. Finally, we encourage exploring the cryosphere for novel types of biosurfactants via both culture screening and functional metagenomics.}, }
@article {pmid29427960, year = {2018}, author = {Fontana, A and Campanaro, S and Treu, L and Kougias, PG and Cappa, F and Morelli, L and Angelidaki, I}, title = {Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes.}, journal = {Water research}, volume = {134}, number = {}, pages = {181-191}, doi = {10.1016/j.watres.2018.02.001}, pmid = {29427960}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Bioreactors/*microbiology ; *Cheese ; Metagenomics ; Methane/metabolism ; Waste Water ; }, abstract = {The present research is the first comprehensive study regarding the thermophilic anaerobic degradation of cheese wastewater, which combines the evaluation of different reactor configurations (i.e. single and two-stage continuous stirred tank reactors) on the process efficiency and the in-depth characterization of the microbial community structure using genome-centric metagenomics. Both reactor configurations showed acidification problems under the tested organic loading rates (OLRs) of 3.6 and 2.4 g COD/L-reactor day and the hydraulic retention time (HRT) of 15 days. However, the two-stage design reached a methane yield equal to 95% of the theoretical value, in contrast with the single stage configuration, which reached a maximum of 33% of the theoretical methane yield. The metagenomic analysis identified 22 new population genomes and revealed that the microbial compositions between the two configurations were remarkably different, demonstrating a higher methanogenic biodiversity in the two-stage configuration. In fact, the acidogenic reactor of the serial configuration was almost solely composed by the lactose degrader Bifidobacterium crudilactis UC0001. The predictive functional analyses of the main population genomes highlighted specific metabolic pathways responsible for the AD process and the mechanisms of main intermediates production. Particularly, the acetate accumulation experienced by the single stage configuration was mainly correlated to the low abundant syntrophic acetate oxidizer Tepidanaerobacter acetatoxydans UC0018 and to the absence of aceticlastic methanogens.}, }
@article {pmid29427518, year = {2018}, author = {Guirro, M and Costa, A and Gual-Grau, A and Mayneris-Perxachs, J and Torrell, H and Herrero, P and Canela, N and Arola, L}, title = {Multi-omics approach to elucidate the gut microbiota activity: Metaproteomics and metagenomics connection.}, journal = {Electrophoresis}, volume = {39}, number = {13}, pages = {1692-1701}, doi = {10.1002/elps.201700476}, pmid = {29427518}, issn = {1522-2683}, abstract = {Over the last few years, the application of high-throughput meta-omics methods has provided great progress in improving the knowledge of the gut ecosystem and linking its biodiversity to host health conditions, offering complementary support to classical microbiology. Gut microbiota plays a crucial role in relevant diseases such as obesity or cardiovascular disease (CVD), and its regulation is closely influenced by several factors, such as dietary composition. In fact, polyphenol-rich diets are the most palatable treatment to prevent hypertension associated with CVD, although the polyphenol-microbiota interactions have not been completely elucidated. For this reason, the aim of this study was to evaluate microbiota effect in obese rats supplemented by hesperidin, after being fed with cafeteria or standard diet, using a multi meta-omics approaches combining strategy of metagenomics and metaproteomics analysis. We reported that cafeteria diet induces obesity, resulting in changes in the microbiota composition, which are related to functional alterations at proteome level. In addition, hesperidin supplementation alters microbiota diversity and also proteins involved in important metabolic pathways. Overall, going deeper into strategies to integrate omics sciences is necessary to understand the complex relationships between the host, gut microbiota, and diet.}, }
@article {pmid29425888, year = {2018}, author = {Rajpoot, M and Sharma, AK and Sharma, A and Gupta, GK}, title = {Understanding the microbiome: Emerging biomarkers for exploiting the microbiota for personalized medicine against cancer.}, journal = {Seminars in cancer biology}, volume = {52}, number = {Pt 1}, pages = {1-8}, doi = {10.1016/j.semcancer.2018.02.003}, pmid = {29425888}, issn = {1096-3650}, mesh = {*Biomarkers, Tumor ; Genetic Variation ; Humans ; Metagenomics/methods/trends ; Microbiota/*genetics ; Neoplasms/*diagnosis/*microbiology ; Precision Medicine/*methods/trends ; Sequence Analysis, DNA/methods ; }, abstract = {The human body is a home to more than 1 trillion microbes with a diverse variety of commensal microbes that play a crucial role towards the health of the individual. These microbes occupy different habitats such as gut, skin, vagina, oral etc. Not only the types and abundance of microbes are different in different organs, but also these may differ in different individuals. The genome of these microbiota and their ecosystem constitute to form a microbiome. Factors such as diet, environment, host genetics etc. may be the reason behind the wide microbial diversity. A number of studies performed on human microbiome have revealed that microbiota present in healthy and diseased individuals are distinct. Altered microbiome is many a times the reason behind the overexpression of genes which may cause complex diseases including cancer. Manipulation of the human microbiome can be done by microbial supplements such as probiotics or synbiotics, diet or prebiotics and microbial suppression strategies using antibiotics. Recent advances in genome sequencing technologies and metagenomic analysis provide us the broader understanding of these commensal microbes and highlighting the distinctive features of microbiome during healthy and disease states. Molecular pathological epidemiology (MPE) studies have been very helpful in providing insights into the pathological process behind disease evolution and progression by determining the specific etiological factors. New emerging field of research targets the microbiome for therapeutic purposes by which personalized medicines can be made for treating various types of tumors. Screening programmes might be helpful in identifying patients who are at the verge of developing cancer and in delivering appropriate approaches according to individual risk modes so that disease could be prevented.}, }
@article {pmid29423379, year = {2018}, author = {Li, Q and Wang, C and Tang, C and Zhao, X and He, Q and Li, J}, title = {Identification and Characterization of Blood and Neutrophil-Associated Microbiomes in Patients with Severe Acute Pancreatitis Using Next-Generation Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {5}, pmid = {29423379}, issn = {2235-2988}, mesh = {Acute Disease ; Adult ; Aged ; Biomarkers ; Comorbidity ; Female ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/immunology ; Humans ; Male ; Metabolome ; *Metagenome ; *Metagenomics ; *Microbiota ; Middle Aged ; Neutrophils/metabolism/*microbiology ; Pancreatitis/*complications/diagnosis/metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; Sepsis/diagnosis/*etiology/metabolism ; Young Adult ; }, abstract = {Infectious complications are a leading cause of death for patients with severe acute pancreatitis (SAP). Yet, our knowledge about details of the blood microbial landscape in SAP patients remains limited. Recently, some studies have reported that the peripheral circulation harbors a diverse bacterial community in healthy and septic subjects. The objective of this study was to examine the presence of the blood bacterial microbiome in SAP patients and its potential role in the development of infectious complications. Here we conducted a prospective observational study on a cohort of 50 SAP patients and 12 healthy subjects to profile the bacterial composition in the blood. The patients were subgrouped into uninfected (n = 17), infected (n = 16), and septic (n = 17) cases. Applying 16S rDNA-based next-generation sequencing technique, we investigated blood and neutrophil-associated microbiomes in SAP patients, and assessed their connections with immunological alterations. Based on the sequencing data, a diverse bacterial microbiota was found in peripheral blood and neutrophils from the healthy and SAP subjects. As compared to healthy controls, the blood and neutrophil-associated microbiomes in the patients were significantly altered, with an expansion in Bacteroidetes and Firmicutes as well as a decrease in Actinobacteria. Variations in the microbiome composition in patients were associated with immunological disorders, including altered lymphocyte subgroups, elevated levels of serum cytokines and altered proteomic profiles of neutrophils. However, no significant compositional difference was observed between the patient subgroups, implying that the microbiota alterations might not be linked to presence/absence of infectious complications in SAP. Together, we present an initial description of the blood and neutrophil-associated bacterial profiles in SAP patients, offering novel evidence for the existence of the blood microbiome. Identification of the blood microbiome provides novel insights into characteristics and diagnostics of bacteremia in the patients. Further study is required to assess the possible implications of the blood microbiome in health and diseases.}, }
@article {pmid29415902, year = {2018}, author = {Kishida, S and Kato-Mori, Y and Hagiwara, K}, title = {Influence of changes in the intestinal microflora on the immune function in mice.}, journal = {The Journal of veterinary medical science}, volume = {80}, number = {3}, pages = {440-446}, pmid = {29415902}, issn = {1347-7439}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Concanavalin A/metabolism ; Cytokines/metabolism ; Flow Cytometry ; Gastrointestinal Microbiome/drug effects/*immunology ; Immunity/immunology/*physiology ; Mice/immunology/microbiology ; Mice, Inbred BALB C/immunology/microbiology ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; Spleen/cytology ; T-Lymphocyte Subsets/immunology/physiology ; }, abstract = {The composition of the intestinal microbiota is related to the health and immune function of the host. Administration of antibiotics affects the composition of the intestinal microbiota. However, the effects of immune function on the composition of the intestinal microbiota are still unclear. In this study, we investigated the lymphocyte composition and determined the relationships between lymphocyte function and the intestinal microbiota following antibiotic treatment in mice. To change the composition of the intestinal microbiota, mice were treated with or without antibiotics. Analysis of intestinal microbiota was performed by metagenomic analysis targeting 16S rRNA. Lymphocyte subsets of splenocytes were measured by flow cytometry. For functional analysis of T cells, splenocytes were stimulated with concanavalin (Con A), and cytokine gene expression was measured by real-time polymerase chain reaction. Firmicutes were predominant in the control group, whereas Bacteroidetes predominated in the antibiotic-treated group, as determined by metagenomic analysis. The diversity of the microbiota decreased in the antibiotic-treated group. Analysis of lymphocyte subsets showed that CD3+ cells decreased, whereas CD19+ cells increased in the antibiotic-treated group. All cytokine genes in splenocytes treated with Con A were downregulated in the antibiotic-treated group; in particular, genes encoding interferon-γ, interleukin (IL)-6, and IL-13 significantly decreased. Taken together, these results revealed that changes in the composition of the intestinal microbiota by antibiotic treatment influenced the population of lymphocytes in splenocytes and affected the immune response.}, }
@article {pmid29414445, year = {2018}, author = {Quatrini, R and Johnson, DB}, title = {Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH.}, journal = {Current opinion in microbiology}, volume = {43}, number = {}, pages = {139-147}, doi = {10.1016/j.mib.2018.01.011}, pmid = {29414445}, issn = {1879-0364}, mesh = {Acids/*pharmacology ; Archaea/genetics/*growth &amp; development/physiology ; Hydrogen-Ion Concentration ; Metagenomics ; Microbial Consortia/drug effects/physiology ; Microbial Viability ; Microbiota/*drug effects/genetics/*physiology ; Phylogeny ; Proteobacteria/genetics/*growth &amp; development/physiology ; }, abstract = {Extremely acidic environments have global distribution and can have natural or, increasingly, anthropogenic origins. Extreme acidophiles grow optimally at pH 3 or less, have multiple strategies for tolerating stresses that accompany high levels of acidity and are scattered in all three domains of the tree of life. Metagenomic studies have expanded knowledge of the diversity of extreme acidophile communities, their ecological networks and their metabolic potentials, both confirmed and inferred. High resolution compositional and functional profiling of these microbiomes have begun to reveal spatial diversity patterns at global, regional, local, zonal and micro-scales. Future integration of genomic and other meta-omic data will offer new opportunities to utilize acidic microbiomes and to engineer beneficial interactions within them in biotechnologies.}, }
@article {pmid29405134, year = {2017}, author = {Desikan, P}, title = {Our microbial signatures.}, journal = {Indian journal of medical microbiology}, volume = {35}, number = {4}, pages = {443-444}, doi = {10.4103/ijmm.IJMM_17_250}, pmid = {29405134}, issn = {1998-3646}, mesh = {Biological Variation, Individual ; *Dysbiosis ; Healthy Volunteers ; Humans ; Metagenomics ; *Microbiota ; }, }
@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 &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {37}, number = {5}, pages = {851-857}, 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.}, }
@article {pmid29404427, year = {2018}, author = {Hester, ER and Harpenslager, SF and van Diggelen, JMH and Lamers, LL and Jetten, MSM and Lüke, C and Lücker, S and Welte, CU}, title = {Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities.}, journal = {mSystems}, volume = {3}, number = {1}, pages = {}, pmid = {29404427}, issn = {2379-5077}, support = {339880//European Research Council/International ; }, abstract = {Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O, and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acidobacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities. IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.}, }
@article {pmid29404279, year = {2018}, author = {Ziklo, N and Vidgen, ME and Taing, K and Huston, WM and Timms, P}, title = {Dysbiosis of the Vaginal Microbiota and Higher Vaginal Kynurenine/Tryptophan Ratio Reveals an Association with Chlamydia trachomatis Genital Infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {1}, pmid = {29404279}, issn = {2235-2988}, mesh = {Chlamydia Infections/*metabolism/*microbiology ; Chlamydia trachomatis/*physiology ; Cytokines/metabolism ; *Dysbiosis ; Female ; Humans ; Inflammation Mediators/metabolism ; Kynurenine/metabolism ; Metagenome ; Metagenomics/methods ; *Microbiota ; Tryptophan/metabolism ; Vagina/*metabolism/*microbiology ; }, abstract = {The natural course of Chlamydia trachomatis urogenital tract infections varies between individuals. While protective immunity can occur, some women can become reinfected, contributing to the development of severe pathology. While the reasons for these differences are unknown, an individual's response to induced interferon-γ (IFN-γ) is suggested to be critical. IFN-γ induction of the enzyme indoleamine 2,3-dioxygenase, which depletes tryptophan, may be the key. One hypothesis suggests that indole-producing bacteria in the vaginal microbiota can provide a substrate for the Chlamydia to synthesize tryptophan, rescuing the Chlamydia from host IFN-γ attack. We studied a cohort of 25 women who were either, Chlamydia negative, Chlamydia positive with a single infection, or Chlamydia positive with repeated infection, to test our hypothesis. We characterized their vaginal microbiota, cytokine response, as well as their tryptophan, kynurenine and indole concentrations directly in vaginal secretions. We found that C. trachomatis urogenital tract infections either initial or repeat infections, were associated with elevated vaginal kynurenine/tryptophan ratios, primarily as a result of elevated kynurenine levels. In addition, vaginal microbiota of community state type (CST) IV showed significantly lower vaginal tryptophan levels compared to CST I and III, which might be related to a higher abundance of indole producers found within this group. Furthermore, we found a higher abundance of indole producers in women who cleared their Chlamydia infection post antibiotic treatment. This study demonstrates for the first time in vivo, the association between high vaginal kynurenine/tryptophan ratios and C. trachomatis infections. In addition, tryptophan depletion was associated with vaginal microbiota of CST IV.}, }
@article {pmid29396619, year = {2018}, author = {Mehetre, G and Shah, M and Dastager, SG and Dharne, MS}, title = {Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India.}, journal = {Archives of microbiology}, volume = {200}, number = {5}, pages = {753-770}, doi = {10.1007/s00203-018-1484-4}, pmid = {29396619}, issn = {1432-072X}, support = {EMR/2014/000483//Science and Engineering Research Board/ ; }, mesh = {Amylases/analysis ; Bacteria/enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/analysis ; Biodiversity ; Hot Springs/*microbiology ; India ; Peptide Hydrolases/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Xylosidases/analysis ; }, abstract = {Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India. Molecular, phylogenetic and predictive functional characterization of the isolated bacterial population was done using 16S rRNA sequencing coupled with Tax4Fun tools. Furthermore, representative isolates were screened for important enzymes (cellulase, xylanase, amylase, and protease) and heavy metal tolerance (chromium, arsenic) properties. A total of 454 bacterial isolates obtained were mapped into 57 unique bacterial genera and 4 different bacterial phyla. Interestingly, 37 genera not previously isolated from Indian hot springs, were isolated for the first time in the present study. However, most of these genera (23 out of 37) were reported only in metagenomics studies from Indian and global hot springs. Furthermore, around 14 genera not previously cultivated and not detected in metagenomics studies of hot springs are documented here. The metabolic potential was ascertained by determining the abundance of specific genes using in silico based Tax4Fun tool, which identified around 315 metabolic pathways for metabolism of carbohydrates, synthesis of secondary metabolites and degradation of xenobiotic compounds. Bioprospection study revealed that 33 and 25 bacterial genera were positive for enzyme production and resistance to the heavy metals, respectively. The present study revealed the advantages of cultivation methods using a comprehensive multiple isolation approach for exploring untapped and unique bacterial diversity, and also utilities for various biotechnological and environmental applications.}, }
@article {pmid29396587, year = {2018}, author = {Mahony, J and Lugli, GA and van Sinderen, D and Ventura, M}, title = {Impact of gut-associated bifidobacteria and their phages on health: two sides of the same coin?.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {5}, pages = {2091-2099}, doi = {10.1007/s00253-018-8795-x}, pmid = {29396587}, issn = {1432-0614}, mesh = {Animals ; Bacteriophages/classification/genetics/isolation &amp; purification/*physiology ; Bifidobacterium/classification/genetics/*physiology/virology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology/*virology ; Humans ; }, abstract = {Bifidobacteria are among the first microbial colonisers of the human infant gut post-partum. Their early appearance and dominance in the human infant gut and the reported health-promoting or probiotic status of several bifidobacterial strains has culminated in intensive research efforts that focus on their activities as part of the gut microbiota and the concomitant implications for human health. In this mini-review, we evaluate current knowledge on the genomics of this diverse bacterial genus, and on the genetic and functional adaptations that have underpinned the success of bifidobacteria in colonising the infant gut. The growing interest in functional genomics of bifidobacteria has also created interest in the interactions of bifidobacteria and their (bacterio)phages. While virulent phages of bifidobacteria have yet to be isolated, the incidence of integrated (pro)phages in bifidobacterial genomes are widely reported and this mini-review considers the role of these so-called bifidoprophages in modulating bifidobacterial populations in the human gastrointestinal tract and the implications for existing and future development of probiotic therapies.}, }
@article {pmid29396546, year = {2018}, author = {Gonzalez-Martinez, A and Sihvonen, M and Muñoz-Palazon, B and Rodriguez-Sanchez, A and Mikola, A and Vahala, R}, title = {Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2208}, pmid = {29396546}, issn = {2045-2322}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Arctic Regions ; Bacteria/classification/genetics/*isolation &amp; purification ; Bioreactors/*microbiology ; *Biota ; Finland ; Fungi/classification/genetics/*isolation &amp; purification ; Metagenomics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/microbiology ; Waste Water/*microbiology ; Water Purification ; }, abstract = {Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.}, }
@article {pmid29395346, year = {2018}, author = {Limborg, MT and Alberdi, A and Kodama, M and Roggenbuck, M and Kristiansen, K and Gilbert, MTP}, title = {Applied Hologenomics: Feasibility and Potential in Aquaculture.}, journal = {Trends in biotechnology}, volume = {36}, number = {3}, pages = {252-264}, doi = {10.1016/j.tibtech.2017.12.006}, pmid = {29395346}, issn = {1879-3096}, mesh = {Animals ; *Aquaculture ; Epigenomics ; *Feasibility Studies ; Fishes/*microbiology ; Food Industry ; Gastrointestinal Microbiome/genetics/immunology ; Genome, Microbial/genetics/immunology ; Humans ; Immune System/immunology/microbiology ; *Metagenomics ; Proteomics ; Transcriptome ; }, abstract = {Aquaculture will play an essential role in feeding a growing human population, but several biological challenges impede sustainable growth of production. Emerging evidence across all areas of life has revealed the importance of the intimate biological interactions between animals and their associated gut microbiota. Based on challenges in aquaculture, we leverage current knowledge in molecular biology and host microbiota interactions to propose an applied holo-omic framework that integrates molecular data including genomes, transcriptomes, epigenomes, proteomes, and metabolomes for analyzing fish and their gut microbiota as interconnected and coregulated systems. With an eye towards aquaculture, we discuss the feasibility and potential of our holo-omic framework to improve growth, health, and sustainability in any area of food production, including livestock and agriculture.}, }
@article {pmid29382070, year = {2018}, author = {D'Argenio, V}, title = {Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, pmid = {29382070}, issn = {1422-0067}, mesh = {*Gastrointestinal Microbiome ; Genomics/*methods/standards ; Humans ; *Metagenome ; Transcriptome ; }, abstract = {The study of the human microbiome has become a very popular topic. Our microbial counterpart, in fact, appears to play an important role in human physiology and health maintenance. Accordingly, microbiome alterations have been reported in an increasing number of human diseases. Despite the huge amount of data produced to date, less is known on how a microbial dysbiosis effectively contributes to a specific pathology. To fill in this gap, other approaches for microbiome study, more comprehensive than 16S rRNA gene sequencing, i.e., shotgun metagenomics and metatranscriptomics, are becoming more widely used. Methods standardization and the development of specific pipelines for data analysis are required to contribute to and increase our understanding of the human microbiome relationship with health and disease status.}, }
@article {pmid29380873, year = {2018}, author = {Bapatla, KG and Singh, A and Yeddula, S and Patil, RH}, title = {Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua.}, journal = {Journal of basic microbiology}, volume = {58}, number = {3}, pages = {217-226}, doi = {10.1002/jobm.201700462}, pmid = {29380873}, issn = {1521-4028}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Tract/microbiology ; Helianthus/parasitology ; High-Throughput Nucleotide Sequencing ; Lepidoptera/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soybeans/parasitology ; }, abstract = {The insect gut has been the house of many taxonomically and physiologically diverse groups of microbial colonizers as symbionts and commensals, which are evolving to support the physiological requirement of insects. Lepidoptera is one of the important family of class hexapoda, comprising agriculture insect pest Spodoptera litura and Spilosoma obliqua. Information on gut microbiota and their functional role in these insects was meager to elucidate the wide-ranging survivalist mechanisms. In this context, we analyzed the composition, diversity and functional role of gut bacteria in S. litura and S. obliqua collected from soybean and sunflower crops, respectively, using Next Generation Sequencing of 16S rRNA. A total of 3427 and 206 Operation Taxonomic Units (OTUs) were identified in S. litura and S. obliqua gut metagenome, respectively. Highest number of sequences were annotated to unclassified bacteria (34%), followed by Proteobacteria (27%), and Chlorobi (14%) in S. litura, while S. obliqua has significant representation of Firmicutes (48%), followed by Bacteroidetes (20%), and unclassified bacteria (11%). Functionality of both metagenomes revealed, high abundance of ammonia oxidizers (20.1 58.0%) followed by relative abundance of detoxifying processes - dehalogenation (17.4-41.2%) and aromatic hydrocarbons degradation (1.1-3.1%). This study highlights the significance of the inherent microbiome of two defoliators in shaping the metagenome for nutrition and detoxifying the chemical molecules, and opens an avenue for exploring role of insect gut bacteria in host selection, metabolic endurance of insecticides and synergistic or agonistic mechanisms inside gut of insects feeding on insect-resistant biotech crops.}, }
@article {pmid29379124, year = {2018}, author = {Xu, S and Lin, Y and Zeng, D and Zhou, M and Zeng, Y and Wang, H and Zhou, Y and Zhu, H and Pan, K and Jing, B and Ni, X}, title = {Bacillus licheniformis normalize the ileum microbiota of chickens infected with necrotic enteritis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1744}, pmid = {29379124}, issn = {2045-2322}, mesh = {Animals ; Bacillus licheniformis/*growth &amp; development ; Biological Therapy/methods ; Chickens ; Clostridium Infections/complications/microbiology/therapy/*veterinary ; Clostridium perfringens/growth &amp; development ; Diet/methods ; *Dysbiosis ; Enteritis/complications/microbiology/therapy/*veterinary ; *Gastrointestinal Microbiome ; Ileum/*microbiology ; Metagenomics ; Necrosis/complications/microbiology/therapy/veterinary ; Poultry Diseases/*microbiology ; Sequence Analysis, DNA ; Treatment Outcome ; }, abstract = {Necrotic enteritis (NE) is a severe intestinal disease, which can change gut microbiota and result in a high cost for the poultry industry worldwide. However, little is known regarding how the gut microbiota of NE chicken ileum are changed by Bacillus licheniformis. This study was conducted to investigate how ileum microbiota structure was changed by B. licheniformis in broiler chickens challenged with Clostridium perfringens-induced NE through Illumina MiSeq sequencing. The broilers were randomly separated into four groups: the negative control group (NC), the positive control group (PC), the fishmeal and coccidia group (FC), and the PC group supplied with feed containing B. licheniformis (BL). Compared to the PC and FC, alpha diversity, beta diversity, and the bacterial taxa of the ileum microbiota were more similar in BL and NC. Some genera, which were related to the NE control, became insignificant in BL with NC, such as Lactobacillus, Lactococcus, Bacteroides, Ruminococcus and Helicobacter. The PICRUSt analysis revealed that a tumour suppressor gene, p53, which was negatively correlated with Helicobacter, was enriched in the BL group. Our findings showed that the ileum microbiota disorder caused by NE in chickens was normalized by dietary B. licheniformis supplementation.}, }
@article {pmid29371626, year = {2018}, author = {Carradec, Q and Pelletier, E and Da Silva, C and Alberti, A and Seeleuthner, Y and Blanc-Mathieu, R and Lima-Mendez, G and Rocha, F and Tirichine, L and Labadie, K and Kirilovsky, A and Bertrand, A and Engelen, S and Madoui, MA and Méheust, R and Poulain, J and Romac, S and Richter, DJ and Yoshikawa, G and Dimier, C and Kandels-Lewis, S and Picheral, M and Searson, S and ,  and Jaillon, O and Aury, JM and Karsenti, E and Sullivan, MB and Sunagawa, S and Bork, P and Not, F and Hingamp, P and Raes, J and Guidi, L and Ogata, H and de Vargas, C and Iudicone, D and Bowler, C and Wincker, P}, title = {A global ocean atlas of eukaryotic genes.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {373}, pmid = {29371626}, issn = {2041-1723}, support = {294823//European Research Council/International ; }, mesh = {Amino Acid Sequence ; Animals ; *Aquatic Organisms ; Atlases as Topic ; Bacteria/classification/genetics ; Biodiversity ; Ecosystem ; Eukaryota/classification/*genetics ; Eukaryotic Cells/cytology/*metabolism ; *Metagenome ; Metagenomics/methods ; Oceans and Seas ; *Phylogeny ; Phytoplankton/classification/genetics ; Seawater ; Viruses/classification/genetics ; Zooplankton/classification/*genetics ; }, abstract = {While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.}, }
@article {pmid29367606, year = {2018}, author = {Shangpliang, HNJ and Rai, R and Keisam, S and Jeyaram, K and Tamang, JP}, title = {Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1532}, pmid = {29367606}, issn = {2045-2322}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cultured Milk Products/*microbiology ; High-Throughput Nucleotide Sequencing ; India ; Metagenomics ; }, abstract = {Naturally fermented milk (NFM) products are popular ethnic fermented foods in Arunachal Pradesh and Sikkim states of India. The present study is the first to have documented the bacterial community in 54 samples of NFM products viz. chhurpi, churkam, dahi and gheu/mar by high-throughput Illumina amplicon sequencing. Metagenomic investigation showed that Firmicutes (Streptococcaceae, Lactobacillaceae) and Proteobacteria (Acetobacteraceae) were the two predominant members of the bacterial communities in these products. Lactococcus lactis and Lactobacillus helveticus were the predominant lactic acid bacteria while Acetobacter spp. and Gluconobacter spp. were the predominant acetic acid bacteria present in these products.}, }
@article {pmid29362424, year = {2018}, author = {Verma, MK and Ahmed, V and Gupta, S and Kumar, J and Pandey, R and Mandhan, V and Chauhan, NS}, title = {Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1397}, pmid = {29362424}, issn = {2045-2322}, mesh = {Bacterial Proteins/*genetics ; Bacteroidetes/genetics/*isolation &amp; purification ; Cloning, Molecular ; Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Humans ; Metagenomics/*methods ; Phylogeny ; *Salt Tolerance ; }, abstract = {Every niche in the biosphere is touched by the seemingly endless capacity of microbes to transform the world around them by adapting swiftly and flexibly to the environmental changes, likewise the gastrointestinal tract is no exception. The ability to cope with rapid changes in external osmolarity is an important aspect of gut microbes for their survival and colonization. Identification of these survival mechanisms is a pivotal step towards understanding genomic suitability of a symbiont for successful human gut colonization. Here we highlight our recent work applying functional metagenomics to study human gut microbiome to identify candidate genes responsible for the salt stress tolerance. A plasmid borne metagenomic library of Bacteroidetes enriched human fecal metagenomic DNA led to identification of unique salt osmotolerance clones SR6 and SR7. Subsequent gene analysis combined with functional studies revealed that TLSRP1 within pSR7 and TMSRP1 and ABCTPP of pSR6 are the active loci responsible for osmotolerance through an energy dependent mechanism. Our study elucidates the novel genetic machinery involved in bestowing osmotolerance in Prevotella and Bacteroidetes, the predominant microbial groups in a North Indian population. This study unravels an alternative method for imparting ionic stress tolerance, which may be prevalent in the human gut microbiome.}, }
@article {pmid29361802, year = {2018}, author = {D'Auria, G and Artacho, A and Rojas, RA and Bautista, JS and Méndez, R and Gamboa, MT and Gamboa, JR and Gómez-Cruz, R}, title = {Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs.}, journal = {Genes}, volume = {9}, number = {1}, pages = {}, pmid = {29361802}, issn = {2073-4425}, abstract = {New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300-500 mg L-1 H2S and <0.1 mg L-1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample.}, }
@article {pmid29355422, year = {2018}, author = {Mira, A}, title = {Oral Microbiome Studies: Potential Diagnostic and Therapeutic Implications.}, journal = {Advances in dental research}, volume = {29}, number = {1}, pages = {71-77}, doi = {10.1177/0022034517737024}, pmid = {29355422}, issn = {1544-0737}, mesh = {Bacteria/classification ; Biofilms/classification ; Biomarkers/analysis ; Dental Caries/immunology/*microbiology/*prevention &amp; control ; Humans ; In Situ Hybridization, Fluorescence/methods ; Metagenomics ; Microbiota/*physiology ; Microfluidics ; Mouth/*microbiology ; Prebiotics ; Probiotics/pharmacology ; Saliva/microbiology ; }, abstract = {Understanding the microbiology of dental caries is not a mere academic exercise; it provides the basis for preventive, diagnostic, and treatment strategies and gives the dentist a theoretical framework to become a better professional. The last years have seen the development of new research methodologies, ranging from high-throughput sequencing or &quot;omics&quot; techniques to new fluorescence microscopy applications and microfluidics, which have allowed the study of the oral microbiome to an unprecedented level of detail. Those studies have provided new insights about oral biofilm formation, biomarkers of caries risk, microbial etiology, appropriate sampling, identification of health-associated bacteria, and new anticaries strategies, among others. Several pitfalls are associated with the new technologies, including a small number of samples per study group, elevated cost, and genus- or species-based analyses that do not take into consideration intraspecies variability. However, the new data strongly suggest that saliva may not be an appropriate sample for etiological studies or for bacterial caries-risk tests, that microbial composition alone may be insufficient to predict caries risk, and that antimicrobial or immunization strategies targeting single species are unlikely to be effective. Strategies directed toward modulation of the oral biofilm, such as pre- and probiotics, emerge as promising new approaches to prevent tooth decay.}, }
@article {pmid29355278, year = {2018}, author = {Cheng, M and Zhang, X and Zhu, J and Cheng, L and Cao, J and Wu, Z and Weng, P and Zheng, X}, title = {A metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity mice fed with oolong tea polyphenols.}, journal = {Food &amp; function}, volume = {9}, number = {2}, pages = {1079-1087}, doi = {10.1039/c7fo01570d}, pmid = {29355278}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Camellia sinensis/*chemistry ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/metabolism/microbiology ; Plant Extracts/*administration &amp; dosage ; Polyphenols/*administration &amp; dosage ; Tea/chemistry/metabolism ; }, abstract = {To investigate the modulatory effect of oolong tea polyphenols (OTP) on intestinal microbiota, OTP was prepared by column chromatography and its influence on the gut flora structure was analyzed by high-throughput sequencing with a human flora-associated high fat diet (HFD) induced obesity mouse model. We observed a robust increase in bacterial biodiversity and the abundance of genera known to be butyrate- and acetate-producing bacteria. A large increase in Bacteroidetes with a decrease in Firmicutes was observed after the administration of OTP for 4 weeks, and the corresponding decrease in the Firmicutes/Bacteroidetes ratio reflected the positive modulatory effect of OTP on the intestinal microbiota. In addition, KEGG pathways for the biosynthesis of amino acids, carbon metabolism, and the ribosome were among the most differentially expressed genes after OTP intervention. The current study revealed that OTP rich in tea catechins, especially O-methylated derivatives, may have prebiotic-like activity and can be used as a functional food component with potential therapeutic utility to prevent obesity-related metabolic disorders by manipulating the intestinal microbiota.}, }
@article {pmid29354879, year = {2018}, author = {Cerqueira, T and Barroso, C and Froufe, H and Egas, C and Bettencourt, R}, title = {Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {387-403}, pmid = {29354879}, issn = {1432-184X}, support = {M3.1.2/F/052/2011//Direção Regional da Ciência e Tecnologia/ ; UID/MAR/04292/2013 granted to MARE//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Archaea/classification/genetics/metabolism ; Autotrophic Processes ; Azores ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Carbon/metabolism ; Carbon Cycle ; Chemoautotrophic Growth/physiology ; Citric Acid Cycle ; Epsilonproteobacteria/metabolism ; Geologic Sediments/*microbiology ; Hydrothermal Vents/*microbiology ; Metagenome/physiology ; *Metagenomics ; Methane/metabolism ; Microbiota/*physiology ; Nitrogen/metabolism ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfur/metabolism ; }, abstract = {The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.}, }
@article {pmid29351302, year = {2018}, author = {Bzhalava, Z and Hultin, E and Dillner, J}, title = {Extension of the viral ecology in humans using viral profile hidden Markov models.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190938}, pmid = {29351302}, issn = {1932-6203}, mesh = {Algorithms ; Computational Biology ; Contig Mapping/statistics &amp; numerical data ; Databases, Protein/statistics &amp; numerical data ; Humans ; Markov Chains ; Metagenomics/statistics &amp; numerical data ; *Microbiota ; Phylogeny ; Viral Proteins/genetics ; Viruses/classification/*genetics/*isolation &amp; purification ; }, abstract = {When human samples are sequenced, many assembled contigs are &quot;unknown&quot;, as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, &quot;vFam&quot;. We used HMMER3 analysis of &quot;unknown&quot; human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family). In summary, we find that analysis using the HMMER3 algorithm and the &quot;vFam&quot; database greatly extended the detection of viruses in biospecimens from humans.}, }
@article {pmid29347966, year = {2018}, author = {Zhou, W and Gay, N and Oh, J}, title = {ReprDB and panDB: minimalist databases with maximal microbial representation.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {15}, pmid = {29347966}, issn = {2049-2618}, support = {K22 AI119231/AI/NIAID NIH HHS/United States ; }, mesh = {Access to Information ; Algorithms ; Computational Biology/methods ; *Databases, Genetic ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*methods ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {BACKGROUND: Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes.<br><br>RESULTS: We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets.<br><br>CONCLUSIONS: reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.}, }
@article {pmid29346588, year = {2018}, author = {Cridland, JM and Ramirez, SR and Dean, CA and Sciligo, A and Tsutsui, ND}, title = {Genome Sequencing of Museum Specimens Reveals Rapid Changes in the Genetic Composition of Honey Bees in California.}, journal = {Genome biology and evolution}, volume = {10}, number = {2}, pages = {458-472}, pmid = {29346588}, issn = {1759-6653}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bees/*genetics ; California ; Chromosome Mapping ; *Evolution, Molecular ; Genetics, Population ; *Genome, Insect ; Introduced Species ; Metagenomics ; Pollination ; Polymorphism, Single Nucleotide ; Population Dynamics ; }, abstract = {The western honey bee, Apis mellifera, is an enormously influential pollinator in both natural and managed ecosystems. In North America, this species has been introduced numerous times from a variety of different source populations in Europe and Africa. Since then, feral populations have expanded into many different environments across their broad introduced range. Here, we used whole genome sequencing of historical museum specimens and newly collected modern populations from California (USA) to analyze the impact of demography and selection on introduced populations during the past 105 years. We find that populations from both northern and southern California exhibit pronounced genetic changes, but have changed in different ways. In northern populations, honey bees underwent a substantial shift from western European to eastern European ancestry since the 1960s, whereas southern populations are dominated by the introgression of Africanized genomes during the past two decades. Additionally, we identify an isolated island population that has experienced comparatively little change over a large time span. Fine-scale comparison of different populations and time points also revealed SNPs that differ in frequency, highlighting a number of genes that may be important for recent adaptations in these introduced populations.}, }
@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 &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {37}, number = {5}, pages = {823-831}, pmid = {29340898}, issn = {1435-4373}, mesh = {Bacteria/classification/genetics ; Bacterial Typing Techniques/methods ; Cross Infection/*epidemiology/*microbiology/prevention &amp; 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.}, }
@article {pmid29334978, year = {2018}, author = {Wang, H and Li, S and Mahmood, A and Yang, S and Wang, X and Shen, Q and Shan, T and Deng, X and Li, J and Hua, X and Cui, L and Delwart, E and Zhang, W}, title = {Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes.}, journal = {Virology journal}, volume = {15}, number = {1}, pages = {11}, pmid = {29334978}, issn = {1743-422X}, mesh = {Animals ; Biodiversity ; Cattle ; Cattle Diseases/*virology ; DNA Viruses/*genetics ; *DNA, Circular ; *DNA, Viral ; Forests ; *Genetic Variation ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Phylogeny ; Sequence Analysis, DNA ; *Viral Load ; Virus Diseases/*veterinary ; }, abstract = {BACKGROUND: Free-range cattle are common in the Northeast China area, which have close contact with farmers and may carry virus threatening to cattle and farmers.<br><br>METHODS: Using viral metagenomics we analyzed the virome in plasma samples collected from 80 cattle from the forested region of Northeast China.<br><br>RESULTS: The virome of cattle plasma is composed of the viruses belonging to the families including Parvoviridae, Papillomaviridae, Picobirnaviridae, and divergent viral genomes showing sequence similarity to circular Rep-encoding single stranded (CRESS) DNA viruses. Five such CRESS-DNA genomes were full characterized, with Rep sequences related to circovirus and gemycircularvirus. Three bovine parvoviruses belonging to two different genera were also characterized.<br><br>CONCLUSION: The virome in plasma samples of cattle from the forested region of Northeast China was revealed, which further characterized the diversity of viruses in cattle plasma.}, }
@article {pmid29334812, year = {2018}, author = {Ding, W and Ma, C and Zhang, W and Chiang, H and Tam, C and Xu, Y and Zhang, G and Qian, PY}, title = {Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses.}, journal = {Biofouling}, volume = {34}, number = {1}, pages = {111-122}, doi = {10.1080/08927014.2017.1409891}, pmid = {29334812}, issn = {1029-2454}, mesh = {4-Butyrolactone/*analogs &amp; derivatives/pharmacology ; Biofilms/*drug effects ; Biofouling/*prevention &amp; control ; Cell Adhesion ; Metagenomics ; Microbial Consortia/*genetics ; Polyesters/*pharmacology ; Polyurethanes/*pharmacology ; Seawater ; Surface Properties ; Transcriptome ; }, abstract = {Butenolide is an environmentally friendly antifouling natural product, but its efficiency and mechanism in preventing biofilm formation have not been examined. Furthermore, controlling the release of butenolide from paints into seawater is technically challenging. A coating was developed by mixing butenolide with a biodegradable polymer, poly (ε-caprolactone)-based polyurethane, and a one-month in situ anti-biofilm test was conducted in a subtidal area. The constant release of butenolide from the surface suggested that its release was well controlled. Direct observation and confocal microscope investigation indicated that the coating was effective against both biofilm formation and attachment of large fouling organisms. Metatranscriptomic analysis of biofilm samples implied that the coating selectively inhibited the adhesion of microbes from a variety of phyla and targeted particular functional pathways including energy metabolism, drug transport and toxin release. These integrated analyses demonstrated the potential application of this butenolide/polymer coating as an anti-biofilm material.}, }
@article {pmid29330574, year = {2018}, author = {Koizumi, T and Hattori, M and Nara, K}, title = {Ectomycorrhizal fungal communities in alpine relict forests of Pinus pumila on Mt. Norikura, Japan.}, journal = {Mycorrhiza}, volume = {28}, number = {2}, pages = {129-145}, pmid = {29330574}, issn = {1432-1890}, support = {25660115//Japan Society for the Promotion of Science/ ; 16J07343//Japan Society for the Promotion of Science/ ; }, mesh = {Altitude ; *Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; *Forests ; Japan ; Mycorrhizae/genetics/*physiology ; Pinus/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Ectomycorrhizal (ECM) symbioses are indispensable for the establishment of host trees, yet available information of ECM symbiosis in alpine forests is scarce. Pinus pumila is a typical ice age relict tree species in Japan and often forms monodominant dwarf vegetation above the tree line in mountains. We studied ECM fungi colonizing P. pumila on Mt. Norikura, Japan, with reference to host developmental stages, i.e., from current-year seedlings to mature trees. ECM fungal species were identified based on rDNA ITS sequences. Ninety-two ECM fungal species were confirmed from a total of 2480 root tips examined. Species in /suillus-rhizopogon and /wilcoxina were dominant in seedling roots. ECM fungal diversity increased with host development, due to the addition of species-rich fungal lineages (/cenococcum, /cortinarius, and /russula-lactarius) in late-successional stages. Such successional pattern of ECM fungi is similar to those in temperate pine systems, suggesting the predominant role of /suillus-rhizopogon in seedling establishment, even in relict alpine habitats fragmented and isolated for a geological time period. Most of the ECM fungi detected were also recorded in Europe or North America, indicating their potential Holarctic distribution and the possibility of their comigration with P. pumila through land bridges during ice ages. In addition, we found significant effects of soil properties on ECM fungal communities, which explained 34.1% of the total variation of the fungal communities. While alpine vegetation is regarded as vulnerable to the ongoing global warming, ECM fungal communities associated with P. pumila could be altered by the edaphic change induced by the warming.}, }
@article {pmid29330424, year = {2018}, author = {Cui, X and Ye, L and Li, J and Jin, L and Wang, W and Li, S and Bao, M and Wu, S and Li, L and Geng, B and Zhou, X and Zhang, J and Cai, J}, title = {Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {635}, pmid = {29330424}, issn = {2045-2322}, mesh = {Adult ; Aged ; Bacteria/*classification/genetics/isolation &amp; purification ; Butyrates/analysis ; Dysbiosis/*diagnosis ; Female ; Gastrointestinal Microbiome ; Heart Failure/*complications ; Humans ; Male ; Metabolomics/*methods ; Metagenomics/*methods ; Methylamines/analysis ; Middle Aged ; Phylogeny ; }, abstract = {Previous studies suggested a possible gut microbiota dysbiosis in chronic heart failure (CHF). However, direct evidence was lacking. In this study, we investigated the composition and metabolic patterns of gut microbiota in CHF patients to provide direct evidence and comprehensive understanding of gut microbiota dysbiosis in CHF. We enrolled 53 CHF patients and 41 controls. Metagenomic analyses of faecal samples and metabolomic analyses of faecal and plasma samples were then performed. We found that the composition of gut microbiota in CHF was significantly different from controls. Faecalibacterium prausnitzii decrease and Ruminococcus gnavus increase were the essential characteristics in CHF patients' gut microbiota. We also observed an imbalance of gut microbes involved in the metabolism of protective metabolites such as butyrate and harmful metabolites such as trimethylamine N-oxide in CHF patients. Metabolic features of both faecal and plasma samples from CHF patients also significantly changed. Moreover, alterations in faecal and plasma metabolic patterns correlated with gut microbiota dysbiosis in CHF. Taken together, we found that CHF was associated with distinct gut microbiota dysbiosis and pinpointed the specific core bacteria imbalance in CHF, along with correlations between changes in certain metabolites and gut microbes.}, }
@article {pmid29330119, year = {2018}, author = {Jin, W and Wang, Y and Li, Y and Cheng, Y and Zhu, W}, title = {Temporal changes of the bacterial community colonizing wheat straw in the cow rumen.}, journal = {Anaerobe}, volume = {50}, number = {}, pages = {1-8}, doi = {10.1016/j.anaerobe.2018.01.004}, pmid = {29330119}, issn = {1095-8274}, mesh = {Animal Feed/*microbiology ; Animals ; *Bacteria/classification/ultrastructure ; Biodiversity ; Biomass ; Cattle ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Rumen/*microbiology ; Triticum/*microbiology ; }, abstract = {This study used Miseq pyrosequencing and scanning electron microscopy to investigate the temporal changes in the bacterial community tightly attached to wheat straw in the cow rumen. The wheat straw was incubated in the rumens and samples were recovered at various times. The wheat straw degradation exhibited three phases: the first degradation phase occurred within 0.5 h, and the second degradation phase occurred after 6 h, with a stalling phase occurring between 0.5 and 6 h. Scanning electron microscopy revealed the colonization of the microorganisms on the wheat straw over time. The bacterial communities at 0.5, 6, 24, and 72 h were determined, corresponding to the degradation phases. Firmicutes and Bacteroidetes were the two most dominant phyla in the bacterial communities at the four time points. Principal coordinate analysis (PCoA) showed that the bacterial communities at the four time points were distinct from each other. The wheat straw-associated bacteria stabilized at the phylum level after 0.5 h of rumen incubation, and only modest phylum-level and family-level changes were observed for most taxa between 0.5 h and 72 h. The relative abundance of the dominant genera, Butyrivibrio, Coprococcus, Ruminococcus, Succiniclasticum, Clostridium, Prevotella, YRC22, CF231, and Treponema, changed significantly over time (P < .05). However, at the genus level, unclassified taxa accounted for 70.3% ± 6.1% of the relative abundance, indicating their probable importance in the degradation of wheat straw as well as in the temporal changes of the bacterial community. Thus, understanding the function of these unclassified taxa is of great importance for targeted improvement of forage use efficiency in ruminants. Collectively, our results revealed distinct degradation phases of wheat straw and corresponding changes in the colonized bacterial community.}, }
@article {pmid29329230, year = {2018}, author = {Atoni, E and Wang, Y and Karungu, S and Waruhiu, C and Zohaib, A and Obanda, V and Agwanda, B and Mutua, M and Xia, H and Yuan, Z}, title = {Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China.}, journal = {Viruses}, volume = {10}, number = {1}, pages = {}, pmid = {29329230}, issn = {1999-4915}, mesh = {Animals ; China/epidemiology ; Computational Biology ; Culex/*virology ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Insect Viruses/*classification ; Kenya/epidemiology ; *Metagenomics ; *Microbiota ; Phylogeny ; }, abstract = {Many blood-feeding arthropods are known vectors of viruses that are a source of unprecedented global health concern. Mosquitoes are an integral part of these arthropod vectors. Advancements in next-generation sequencing and bioinformatics has expanded our knowledge on the richness of viruses harbored by arthropods. In the present study, we applied a metagenomic approach to determine the intercontinental virome diversity of Culex quinquefasciatus and Culex tritaeniorhynchus in Kwale, Kenya and provinces of Hubei and Yunnan in China. Our results showed that viromes from the three locations were strikingly diverse and comprised 30 virus families specific to vertebrates, invertebrates, plants, and protozoa as well as unclassified group of viruses. Though sampled at different times, both Kwale and Hubei mosquito viromes were dominated by vertebrate viruses, in contrast to the Yunnan mosquito virome, which was dominated by insect-specific viruses. However, each virome was unique in terms of virus proportions partly influenced by type of ingested meals (blood, nectar, plant sap, environment substrates). The dominant vertebrate virus family in the Kwale virome was Papillomaviridae (57%) while in Hubei it was Herpesviridae (30%) and the Yunnan virome was dominated by an unclassified viruses group (27%). Given that insect-specific viruses occur naturally in their hosts, they should be the basis for defining the viromes. Hence, the dominant insect-specific viruses in Kwale, Hubei, and Yunnan were Baculoviridae, Nimaviridae and Iflaviridae, respectively. Our study is preliminary but contributes to growing and much needed knowledge, as mosquito viromes could be manipulated to prevent and control pathogenic arboviruses.}, }
@article {pmid29327481, year = {2018}, author = {Bahram, M and Vanderpool, D and Pent, M and Hiltunen, M and Ryberg, M}, title = {The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics.}, journal = {Environmental microbiology reports}, volume = {10}, number = {2}, pages = {155-166}, doi = {10.1111/1758-2229.12612}, pmid = {29327481}, issn = {1758-2229}, mesh = {Agaricales/classification/*genetics/isolation &amp; purification/physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Fruiting Bodies, Fungal/classification/genetics/isolation &amp; purification/physiology ; Genome, Fungal ; Metagenomics ; *Microbiota ; Phylogeny ; Symbiosis ; }, abstract = {Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.}, }
@article {pmid29327330, year = {2018}, author = {Miao, L and Liu, Z}, title = {Microbiome analysis and -omics studies of microbial denitrification processes in wastewater treatment: recent advances.}, journal = {Science China. Life sciences}, volume = {61}, number = {7}, pages = {753-761}, doi = {10.1007/s11427-017-9228-2}, pmid = {29327330}, issn = {1869-1889}, mesh = {Bacteria/classification/enzymology/genetics/*metabolism ; Carbon/chemistry/metabolism ; *Denitrification/genetics/physiology ; *Metagenomics ; *Microbiota ; Nitrates/chemistry/metabolism ; Nitrogen/chemistry/metabolism ; Proteomics ; Waste Disposal, Fluid ; Waste Water/chemistry/*microbiology ; }, abstract = {Nitrogen pollution is an increasingly severe worldwide problem because of drainage of nitrogen-containing wastewater and intensive application of nitrogen-containing fertilizers. Denitrification, a key process in nitrogen cycles, is commonly employed for nitrogen removal in engineered wastewater treatment systems. Biological denitrification is performed by denitrifying microbes (bacteria) that use nitrate as terminal electron acceptor. Better understanding the functions of diverse microbial populations in denitrification-based wastewater treatment systems, and the interactions of these populations with operating environments, is essential for improving both treatment performance and system stability. Recent advances in &quot;meta-omics&quot; (e. g., genomics, transcriptomics, proteomics, metabolomics), other molecular biology tools, and microbiome analysis have greatly enhanced such understanding. This minireview summarizes recent findings regarding microbial community structure and composition, key functional microbes and their physiology, functional genes involved in nitrogen cycle, and responses of microbes and their genes to changes of environmental factors or operating parameters, in denitrification processes in wastewater treatment systems. Of particular interest are heterotrophic denitrification systems (which require alternative organic carbon sources) and the autotrophic denitrification systems (which do not require an external carbon source). Integrated microbiome and -omics approaches have great future potential for determination of optimal environmental and biotechnological parameters, novel process development, and improvement of nitrogen removal efficiency and system stability.}, }
@article {pmid29321767, year = {2017}, author = {Soliman, T and Reimer, JD and Yang, SY and Villar-Briones, A and Roy, MC and Jenke-Kodama, H}, title = {Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2451}, pmid = {29321767}, issn = {1664-302X}, abstract = {Microbial community diversity and chemodiversity were investigated in marine sediments adjacent to the Okinawan &quot;Kaichu-Doro&quot; Causeway, which was constructed 46 years ago to connect a group of four islands (Henza-jima, Miyagi-jima, Ikei-jima, Hamahiga-jima) to the Okinawan main island. This causeway was not built on pilings, but by land reclamation; hence, it now acts as a long, thin peninsula. The construction of this causeway was previously shown to have influenced the surrounding marine ecosystem, causing ecosystem fragmentation and loss of water circulation. In this study, we collected sediment cores (n = 10) from five paired sites in 1 m water depths. Each pair of sites consisted of one site each on the immediate north and south sides of the causeway. Originally the members of each pair were much closer to each other (<150 m) than to other pairs, but now the members of each pair are isolated by the causeway. Each core was 60-80 cm long and was divided into 15-cm layers. We examined the vertical diversity of microbial communities and chemical compounds to determine the correlation between chemodiversity and microbial communities among marine sediment cores and layers. Principal coordinate analyses (PCoA) of detected compounds and of bacterial and archaeal operational taxonomic units (OTUs) revealed that the north and south sides of the causeway are relatively isolated, with each side having unique microbial OTUs. Additionally, some bacterial families (e.g., Acidaminobacteraceae, Rhizobiaceae, and Xanthomonadaceae) were found only on the south side of Kaichu-Doro. Interestingly, we found that the relative abundance of OTUs for some microbial families increased from top to bottom, but this was reversed in some other families. We conclude that the causeway has altered microbial community composition and metabolite profiles in marine sediments.}, }
@article {pmid29321640, year = {2018}, author = {Ehsani, E and Hernandez-Sanabria, E and Kerckhof, FM and Props, R and Vilchez-Vargas, R and Vital, M and Pieper, DH and Boon, N}, title = {Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {340}, pmid = {29321640}, issn = {2045-2322}, mesh = {*Biodiversity ; *Ecosystem ; Metagenome ; Metagenomics/methods ; *Microbiota ; Models, Theoretical ; Phenotype ; }, abstract = {The effect of initial evenness on the temporal trajectory of synthetic communities in comprehensive, low-volume microcosm studies remains unknown. We used flow cytometric fingerprinting and 16S rRNA gene amplicon sequencing to assess the impact of time on community structure in one hundred synthetic ecosystems of fixed richness but varying initial evenness. Both methodologies uncovered a similar reduction in diversity within synthetic communities of medium and high initial evenness classes. However, the results of amplicon sequencing showed that there were no significant differences between and within the communities in all evenness groups at the end of the experiment. Nevertheless, initial evenness significantly impacted the cell density of the community after five medium transfers. Highly even communities retained the highest cell densities at the end of the experiment. The relative abundances of individual species could be associated to particular evenness groups, suggesting that their presence was dependent on the initial evenness of the synthetic community. Our results reveal that using synthetic communities for testing ecological hypotheses requires prior assessment of initial evenness, as it impacts temporal dynamics.}, }
@article {pmid29312205, year = {2017}, author = {Karimi, E and Ramos, M and Gonçalves, JMS and Xavier, JR and Reis, MP and Costa, R}, title = {Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2499}, pmid = {29312205}, issn = {1664-302X}, abstract = {Current knowledge of sponge microbiome functioning derives mostly from comparative analyses with bacterioplankton communities. We employed a metagenomics-centered approach to unveil the distinct features of the Spongia officinalis endosymbiotic consortium in the context of its two primary environmental vicinities. Microbial metagenomic DNA samples (n = 10) from sponges, seawater, and sediments were subjected to Hiseq Illumina sequencing (c. 15 million 100 bp reads per sample). Totals of 10,272 InterPro (IPR) predicted protein entries and 784 rRNA gene operational taxonomic units (OTUs, 97% cut-off) were uncovered from all metagenomes. Despite the large divergence in microbial community assembly between the surveyed biotopes, the S. officinalis symbiotic community shared slightly greater similarity (p < 0.05), in terms of both taxonomy and function, to sediment than to seawater communities. The vast majority of the dominant S. officinalis symbionts (i.e., OTUs), representing several, so-far uncultivable lineages in diverse bacterial phyla, displayed higher residual abundances in sediments than in seawater. CRISPR-Cas proteins and restriction endonucleases presented much higher frequencies (accompanied by lower viral abundances) in sponges than in the environment. However, several genomic features sharply enriched in the sponge specimens, including eukaryotic-like repeat motifs (ankyrins, tetratricopeptides, WD-40, and leucine-rich repeats), and genes encoding for plasmids, sulfatases, polyketide synthases, type IV secretion proteins, and terpene/terpenoid synthases presented, to varying degrees, higher frequencies in sediments than in seawater. In contrast, much higher abundances of motility and chemotaxis genes were found in sediments and seawater than in sponges. Higher cell and surface densities, sponge cell shedding and particle uptake, and putative chemical signaling processes favoring symbiont persistence in particulate matrices all may act as mechanisms underlying the observed degrees of taxonomic connectivity and functional convergence between sponges and sediments. The reduced frequency of motility and chemotaxis genes in the sponge microbiome reinforces the notion of a prevalent mutualistic mode of living inside the host. This study highlights the S. officinalis &quot;endosymbiome&quot; as a distinct consortium of uncultured prokaryotes displaying a likely &quot;sit-and-wait&quot; strategy to nutrient foraging coupled to sophisticated anti-viral defenses, unique natural product biosynthesis, nutrient utilization and detoxification capacities, and both microbe-microbe and host-microbe gene transfer amenability.}, }
@article {pmid29311667, year = {2018}, author = {Trosvik, P and Rueness, EK and de Muinck, EJ and Moges, A and Mekonnen, A}, title = {Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {20}, pmid = {29311667}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Cercopithecinae ; Chloroplasts/genetics ; *Ecology ; *Gastrointestinal Microbiome ; Geography ; Metagenomics/methods ; Microbiota ; RNA, Ribosomal, 16S ; Seasons ; }, abstract = {Human activities can cause habitat degradation that may alter the types and quality of available food resources and thus influence the microbiomes of wild animal populations. Furthermore, seasonal shifts in food availability may cause adaptive responses in the gut microbiome to meet the need for different metabolic capabilities. Here, we demonstrate local-scale population structure in the gastrointestinal microbiotas of Chlorocebus monkeys, in southern Ethiopia, in response to varying degrees of human encroachment. We further provide evidence of adaptation to ecological conditions associated with the dry and wet seasons, and show seasonal effects to be more pronounced in areas with limited human activity. Finally, we report species-level microbiota differences between the endemic Ethiopian Bale monkey, an ecological specialist, and generalist Chlorocebus species from the same geographical region.}, }
@article {pmid29311639, year = {2018}, author = {Segobola, J and Adriaenssens, E and Tsekoa, T and Rashamuse, K and Cowan, D}, title = {Exploring Viral Diversity in a Unique South African Soil Habitat.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {111}, pmid = {29311639}, issn = {2045-2322}, mesh = {Bacteriophages/classification/genetics ; *Biodiversity ; Computational Biology/methods ; Genome, Viral ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Soil Microbiology ; South Africa ; Viruses/*classification/genetics/ultrastructure ; }, abstract = {The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.}, }
@article {pmid29311585, year = {2018}, author = {Odamaki, T and Bottacini, F and Kato, K and Mitsuyama, E and Yoshida, K and Horigome, A and Xiao, JZ and van Sinderen, D}, title = {Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {85}, pmid = {29311585}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Bifidobacterium longum/*classification/*genetics ; Child ; Child, Preschool ; Gastrointestinal Microbiome ; Gene Order ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Infant ; Infant, Newborn ; Japan ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; Multigene Family ; Phylogeny ; Young Adult ; }, abstract = {Bifidobacterium longum subsp. longum represents one of the most prevalent bifidobacterial species in the infant, adult and elderly (human) gut. In the current study, we performed a comparative genome analysis involving 145 B. longum representatives, including 113 B. longum subsp. longum strains obtained from healthy Japanese subjects aged between 0 and 98 years. Although MCL clustering did not reveal any correlation between isolated strains and subject age, certain characteristics appear to be more prevalent among strains corresponding to specific host ages, such as genes involved in carbohydrate metabolism and environmental response. Remarkably, a substantial number of strains appeared to have been transmitted across family members, a phenomenon that was shown not to be confined to mother-infant pairs. This suggests that the ubiquitous distribution of B. longum subsp. longum across the human lifespan is at least partly due to extensive transmission between relatives. Our findings form a foundation for future research aimed at unraveling the mechanisms that allow B. longum strains to successfully transfer between human hosts, where they then colonize and persist in the gut environment throughout the host's lifespan.}, }
@article {pmid29304124, year = {2018}, author = {Krehenwinkel, H and Fong, M and Kennedy, S and Huang, EG and Noriyuki, S and Cayetano, L and Gillespie, R}, title = {The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0189188}, pmid = {29304124}, issn = {1932-6203}, mesh = {Animals ; Arthropods/classification/*genetics/*microbiology ; Biodiversity ; DNA/*analysis/*genetics ; DNA Barcoding, Taxonomic/*methods/statistics &amp; numerical data ; DNA Primers ; Ecosystem ; Hawaii ; Metagenome ; Metagenomics/methods/statistics &amp; numerical data ; Microbiota/*genetics ; Polymerase Chain Reaction/methods ; Selection Bias ; }, abstract = {PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer choice, annealing temperature and cycle number. Our results show that DNA degradation does indeed bias community analyses. However, the effect of this bias is of minor importance compared to that induced by changes in PCR conditions. Analyses of the macro and microbiome from passively collected arthropod samples are thus well worth pursuing.}, }
@article {pmid29301588, year = {2018}, author = {Greay, TL and Gofton, AW and Paparini, A and Ryan, UM and Oskam, CL and Irwin, PJ}, title = {Recent insights into the tick microbiome gained through next-generation sequencing.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {12}, pmid = {29301588}, issn = {1756-3305}, support = {130100050//Australian Research Council/International ; 130100050//Bayer Australia Ltd/International ; 130100050//Bayer AG (Germany)/International ; }, mesh = {Animals ; High-Throughput Nucleotide Sequencing/*statistics &amp; numerical data ; Metagenomics/*methods ; *Microbiota ; Ticks/*microbiology ; }, abstract = {The tick microbiome comprises communities of microorganisms, including viruses, bacteria and eukaryotes, and is being elucidated through modern molecular techniques. The advent of next-generation sequencing (NGS) technologies has enabled the genes and genomes within these microbial communities to be explored in a rapid and cost-effective manner. The advantages of using NGS to investigate microbiomes surpass the traditional non-molecular methods that are limited in their sensitivity, and conventional molecular approaches that are limited in their scalability. In recent years the number of studies using NGS to investigate the microbial diversity and composition of ticks has expanded. Here, we provide a review of NGS strategies for tick microbiome studies and discuss the recent findings from tick NGS investigations, including the bacterial diversity and composition, influential factors, and implications of the tick microbiome.}, }
@article {pmid29298732, year = {2018}, author = {Luna, PN and Hasegawa, K and Ajami, NJ and Espinola, JA and Henke, DM and Petrosino, JF and Piedra, PA and Sullivan, AF and Camargo, CA and Shaw, CA and Mansbach, JM}, title = {The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {2}, pmid = {29298732}, issn = {2049-2618}, support = {R01 AI-114552/NH/NIH HHS/United States ; UG3 OD-023253/NH/NIH HHS/United States ; R01 AI-108588/NH/NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; U01 AI-087881/NH/NIH HHS/United States ; }, mesh = {Bronchiolitis/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Hospitalization ; Humans ; Infant ; Longitudinal Studies ; Male ; Microbiota ; Nasal Cavity/*microbiology ; Nasopharynx/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Staphylococcus/classification/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: The airway microbiome is a subject of great interest for the study of respiratory disease. Anterior nare samples are more accessible than samples from deeper within the nasopharynx. However, the correlation between the microbiota found in the anterior nares and the microbiota found within the nasopharynx is unknown. We assessed the anterior nares and nasopharyngeal microbiota to determine (1) the relation of the microbiota from these two upper airway sites and (2) if associations were maintained between the microbiota from these two sites and two bronchiolitis severity outcomes.<br><br>RESULTS: Among 815 infants hospitalized at 17 US centers for bronchiolitis with optimal 16S rRNA gene sequence reads from both nasal swab and nasopharyngeal aspirate samples, there were strong intra-individual correlations in the microbial communities between the two sample types, especially relating to Haemophilus and Moraxella genera. By contrast, we found a high abundance of Staphylococcus genus in the nasal swabs-a pattern not found in the nasopharyngeal samples and not informative when predicting the dominant nasopharyngeal genera. While these disparities may have been due to sample processing differences (i.e., nasal swabs were mailed at ambient temperature to emulate processing of future parent collected swabs while nasopharyngeal aspirates were mailed on dry ice), a previously reported association between Haemophilus-dominant nasopharyngeal microbiota and the increased severity of bronchiolitis was replicated utilizing the nasal swab microbiota and the same outcome measures: intensive care use (adjusted OR 6.43; 95% CI 2.25-20.51; P < 0.001) and hospital length-of-stay (adjusted OR 4.31; 95% CI, 1.73-11.11; P = 0.002). Additionally, Moraxella-dominant nasopharyngeal microbiota was previously identified as protective against intensive care use, a result that was replicated when analyzing the nasal swab microbiota (adjusted OR 0.30; 95% CI, 0.11-0.64; P = 0.01).<br><br>CONCLUSIONS: While the microbiota of the anterior nares and the nasopharynx are distinct, there is considerable overlap between the bacterial community compositions from these two anatomic sites. Despite processing differences between the samples, these results indicate that microbiota severity associations from the nasopharynx are recapitulated in the anterior nares, suggesting that nasal swab samples not only are effective sample types, but also can be used to detect microbial risk markers.}, }
@article {pmid29297295, year = {2017}, author = {Herath, D and Tang, SL and Tandon, K and Ackland, D and Halgamuge, SK}, title = {CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.}, journal = {BMC bioinformatics}, volume = {18}, number = {Suppl 16}, pages = {571}, pmid = {29297295}, issn = {1471-2105}, mesh = {*Algorithms ; Base Sequence ; Cluster Analysis ; *Contig Mapping ; Databases, Genetic ; Genome ; Humans ; Metagenome ; Metagenomics/*methods ; *Workflow ; }, abstract = {BACKGROUND: In metagenomics, the separation of nucleotide sequences belonging to an individual or closely matched populations is termed binning. Binning helps the evaluation of underlying microbial population structure as well as the recovery of individual genomes from a sample of uncultivable microbial organisms. Both supervised and unsupervised learning methods have been employed in binning; however, characterizing a metagenomic sample containing multiple strains remains a significant challenge. In this study, we designed and implemented a new workflow, Coverage and composition based binning of Metagenomes (CoMet), for binning contigs in a single metagenomic sample. CoMet utilizes coverage values and the compositional features of metagenomic contigs. The binning strategy in CoMet includes the initial grouping of contigs in guanine-cytosine (GC) content-coverage space and refinement of bins in tetranucleotide frequencies space in a purely unsupervised manner. With CoMet, the clustering algorithm DBSCAN is employed for binning contigs. The performances of CoMet were compared against four existing approaches for binning a single metagenomic sample, including MaxBin, Metawatt, MyCC (default) and MyCC (coverage) using multiple datasets including a sample comprised of multiple strains.<br><br>RESULTS: Binning methods based on both compositional features and coverages of contigs had higher performances than the method which is based only on compositional features of contigs. CoMet yielded higher or comparable precision in comparison to the existing binning methods on benchmark datasets of varying complexities. MyCC (coverage) had the highest ranking score in F1-score. However, the performances of CoMet were higher than MyCC (coverage) on the dataset containing multiple strains. Furthermore, CoMet recovered contigs of more species and was 18 - 39% higher in precision than the compared existing methods in discriminating species from the sample of multiple strains. CoMet resulted in higher precision than MyCC (default) and MyCC (coverage) on a real metagenome.<br><br>CONCLUSIONS: The approach proposed with CoMet for binning contigs, improves the precision of binning while characterizing more species in a single metagenomic sample and in a sample containing multiple strains. The F1-scores obtained from different binning strategies vary with different datasets; however, CoMet yields the highest F1-score with a sample comprised of multiple strains.}, }
@article {pmid29297282, year = {2017}, author = {Tran, Q and Pham, DT and Phan, V}, title = {Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities.}, journal = {BMC bioinformatics}, volume = {18}, number = {Suppl 14}, pages = {499}, pmid = {29297282}, issn = {1471-2105}, mesh = {Algorithms ; Bacteria/*genetics/*isolation &amp; purification ; Genetic Markers ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Quantification and identification of microbial genomes based on next-generation sequencing data is a challenging problem in metagenomics. Although current methods have mostly focused on analyzing bacteria whose genomes have been sequenced, such analyses are, however, complicated by the presence of unknown bacteria or bacteria whose genomes have not been sequence.<br><br>RESULTS: We propose a method for detecting unknown bacteria in environmental samples. Our approach is unique in its utilization of short reads only from 16S rRNA genes, not from entire genomes. We show that short reads from 16S rRNA genes retain sufficient information for detecting unknown bacteria in oral microbial communities.<br><br>CONCLUSION: In our experimentation with bacterial genomes from the Human Oral Microbiome Database, we found that this method made accurate and robust predictions at different read coverages and percentages of unknown bacteria. Advantages of this approach include not only a reduction in experimental and computational costs but also a potentially high accuracy across environmental samples due to the strong conservation of the 16S rRNA gene.}, }
@article {pmid29293960, year = {2018}, author = {Fang, C and Zhong, H and Lin, Y and Chen, B and Han, M and Ren, H and Lu, H and Luber, JM and Xia, M and Li, W and Stein, S and Xu, X and Zhang, W and Drmanac, R and Wang, J and Yang, H and Hammarström, L and Kostic, AD and Kristiansen, K and Li, J}, title = {Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.}, journal = {GigaScience}, volume = {7}, number = {3}, pages = {1-8}, pmid = {29293960}, issn = {2047-217X}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; T32 HG002295/HG/NHGRI NIH HHS/United States ; T32 GM074897/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Computational Biology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Background: More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of 2 Illumina platforms.<br><br>Findings: Using fecal samples from 20 healthy individuals, we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform vs the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the 2 Illumina platforms against each other. By a newly developed overall accuracy quality control method, an average of 82.45 million high-quality reads (96.06% of raw reads) per sample, with 90.56% of bases scoring Q30 and above, was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02%-3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias toward genes with higher GC content being enriched on the HiSeq platforms.<br><br>Conclusions: Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.}, }
@article {pmid29293631, year = {2018}, author = {Villegas, LEM and Campolina, TB and Barnabe, NR and Orfano, AS and Chaves, BA and Norris, DE and Pimenta, PFP and Secundino, NFC}, title = {Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190352}, pmid = {29293631}, issn = {1932-6203}, mesh = {Aedes/*microbiology/virology ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mosquito Vectors ; RNA, Ribosomal, 16S/genetics ; Zika Virus Infection/*microbiology ; }, abstract = {Zika is a re-emerging infection that has been considered a major threat to global public health. Currently at least 100 countries are at risk of Zika virus (ZIKV) transmission. Aedes aegypti is the main mosquito vector in the Americas. This vector is exposed to, and interacts symbiotically with a variety of microorganisms in its environment, which may result in the formation of a lifetime association. Here, the unknown effect that ZIKV exerts on the dynamic bacterial community harbored by this mosquito vector was investigated using a metagenomic analysis of its microbiota. Groups of Ae. aegypti were experimentally fed on sugar, blood and blood mixed with ZIKV, and held for 3 to 7 days after blood meal and eggs development respectively. The infected groups were processed by qPCR to confirm the presence of ZIKV. All groups were analyzed by metagenomics (Illumina Hiseq Sequencing) and 16S rRNA amplicon sequences were obtained to create bacterial taxonomic profiles. A core microbiota and exclusive bacterial taxa were identified that incorporate 50.5% of the predicted reads from the dataset, with 40 Gram-negative and 9 Gram-positive families. To address how ZIKV invasion may disturb the ecological balance of the Ae. aegypti microbiota, a CCA analysis coupled with an explanatory matrix was performed to support the biological interpretation of shifts in bacterial signatures. Two f-OTUs appeared as potential biomarkers of ZIKV infection: Rhodobacteraceae and Desulfuromonadaceae. Coincidentally, both f-OTUs were exclusively present in the ZIKV- infected blood-fed and ZIKV- infected gravid groups. In conclusion, this study shows that bacterial symbionts act as biomarkers of the insect physiological states and how they respond as a community when ZIKV invades Ae. aegypti. Basic knowledge of local haematophagous vectors and their associated microbiota is relevant when addressing transmission of vector-borne infectious diseases in their regional surroundings.}, }
@article {pmid29292539, year = {2018}, author = {Porter, TM and Hajibabaei, M}, title = {Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis.}, journal = {Molecular ecology}, volume = {27}, number = {2}, pages = {313-338}, doi = {10.1111/mec.14478}, pmid = {29292539}, issn = {1365-294X}, mesh = {*Biodiversity ; Computational Biology/methods ; DNA/*genetics ; DNA Barcoding, Taxonomic/methods ; *Environmental Monitoring ; *Genomics ; High-Throughput Nucleotide Sequencing ; }, abstract = {The purpose of this review is to present the most common and emerging DNA-based methods used to generate data for biodiversity and biomonitoring studies. As environmental assessment and monitoring programmes may require biodiversity information at multiple levels, we pay particular attention to the DNA metabarcoding method and discuss a number of bioinformatic tools and considerations for producing DNA-based indicators using operational taxonomic units (OTUs), taxa at a variety of ranks and community composition. By developing the capacity to harness the advantages provided by the newest technologies, investigators can &quot;scale up&quot; by increasing the number of samples and replicates processed, the frequency of sampling over time and space, and even the depth of sampling such as by sequencing more reads per sample or more markers per sample. The ability to scale up is made possible by the reduced hands-on time and cost per sample provided by the newest kits, platforms and software tools. Results gleaned from broad-scale monitoring will provide opportunities to address key scientific questions linked to biodiversity and its dynamics across time and space as well as being more relevant for policymakers, enabling science-based decision-making, and provide a greater socio-economic impact. As genomic approaches are continually evolving, we provide this guide to methods used in biodiversity genomics.}, }
@article {pmid29284535, year = {2017}, author = {Pires, ACAM and Villegas, LEM and Campolina, TB and Orfanó, AS and Pimenta, PFP and Secundino, NFC}, title = {Bacterial diversity of wild-caught Lutzomyia longipalpis (a vector of zoonotic visceral leishmaniasis in Brazil) under distinct physiological conditions by metagenomics analysis.}, journal = {Parasites &amp; vectors}, volume = {10}, number = {1}, pages = {627}, pmid = {29284535}, issn = {1756-3305}, support = {305512/2014-5//Brazilian Council for Scientific and Technological Development- CNPq- Research fellowship/International ; 308849/2015-9//Brazilian Council for Scientific and Technological Development- CNPq (Research fellowship)/International ; 00242-12//Fundação de Amparo à Pesquisa do Estado de Minas Gerais (BR) FAPEMIG/International ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; Brazil ; *Gastrointestinal Microbiome ; Insect Vectors/*microbiology ; Metagenomics ; Psychodidae/*microbiology ; }, abstract = {BACKGROUND: The leishmaniases are a group of diseases caused by protozoans of the genus Leishmania, which are transmitted by the bite of phlebotomine sand flies. In the New World, Lutzomyia longipalpis is the most important vector of visceral leishmaniasis and is a proven vector for Leishmania infantum chagasi in Brazil. During development within the vector, Leishmania can interact with a variety of microorganisms such as fungi and bacteria. The presence of bacteria in the midgut of sand flies can influence the development and survival of the parasite.<br><br>RESULTS: The bacteria-targeted metagenomic analysis revealed different community compositions between the distinct physiological stages of those tested. The amplicon-oriented metagenomic profiling revealed 64 bacterial genera and 46 families. By crossing the taxa indices from each experimental condition a core composed of 6 genera was identified (Enterobacter, Serratia, Stenotrophomonas, Enhydrobacter, Pseudomonas and Chryseobacterium).<br><br>CONCLUSIONS: The observed dynamic nature of the bacterial community expands the knowledge pertaining to the tripartite host-microbiota-pathogen interactions. Further studies addressing how laboratory and field collected communities differ are critical to successfully develop control strategies based on bacterial symbionts and paratransgenesis, as already tested in other arthropod vectors.}, }
@article {pmid29277868, year = {2018}, author = {Maltez Thomas, A and Prata Lima, F and Maria Silva Moura, L and Maria da Silva, A and Dias-Neto, E and Setubal, JC}, title = {Comparative Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1704}, number = {}, pages = {243-260}, doi = {10.1007/978-1-4939-7463-4_8}, pmid = {29277868}, issn = {1940-6029}, mesh = {Computational Biology ; Humans ; Metagenomics/*methods ; *Microbiota ; Mouth Mucosa/*microbiology ; Sequence Analysis, DNA/methods ; Software ; Tongue/*microbiology ; }, abstract = {Thanks in large part to newer, better, and cheaper DNA sequencing technologies, an enormous number of metagenomic sequence datasets have been and continue to be generated, covering a huge variety of environmental niches, including several different human body sites. Comparing these metagenomes and identifying their commonalities and differences is a challenging task, due not only to the large amounts of data, but also because there are several methodological considerations that need to be taken into account to ensure an appropriate and sound comparison between datasets. In this chapter, we describe current techniques aimed at comparing metagenomes generated by 16S ribosomal RNA and shotgun DNA sequencing, emphasizing methodological issues that arise in these comparative studies. We provide a detailed case study to illustrate some of these techniques using data from the Human Microbiome Project comparing the microbial communities from ten buccal mucosa samples with ten tongue dorsum samples in terms of alpha diversity, beta diversity, and their taxonomic and functional profiles.}, }
@article {pmid29273717, year = {2017}, author = {Albanese, D and Donati, C}, title = {Strain profiling and epidemiology of bacterial species from metagenomic sequencing.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {2260}, pmid = {29273717}, issn = {2041-1723}, mesh = {Bacteria/*genetics ; Bifidobacterium longum/genetics ; *Computational Biology ; Databases, Genetic ; Enterococcus faecalis/genetics ; Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Neisseria meningitidis/genetics ; Polymorphism, Single Nucleotide ; Propionibacterium acnes/genetics ; Staphylococcus aureus/genetics ; Staphylococcus epidermidis/genetics ; Streptococcus pneumoniae/genetics ; }, abstract = {Microbial communities are often composed by complex mixtures of multiple strains of the same species, characterized by a wide genomic and phenotypic variability. Computational methods able to identify, quantify and classify the different strains present in a sample are essential to fully exploit the potential of metagenomic sequencing in microbial ecology, with applications that range from the epidemiology of infectious diseases to the characterization of the dynamics of microbial colonization. Here we present a computational approach that uses the available genomic data to reconstruct complex strain profiles from metagenomic sequencing, quantifying the abundances of the different strains and cataloging them according to the population structure of the species. We validate the method on synthetic data sets and apply it to the characterization of the strain distribution of several important bacterial species in real samples, showing how its application provides novel insights on the structure and complexity of the microbiota.}, }
@article {pmid29272899, year = {2017}, author = {Shah, A and Shanahan, E and Macdonald, GA and Fletcher, L and Ghasemi, P and Morrison, M and Jones, M and Holtmann, G}, title = {Systematic Review and Meta-Analysis: Prevalence of Small Intestinal Bacterial Overgrowth in Chronic Liver Disease.}, journal = {Seminars in liver disease}, volume = {37}, number = {4}, pages = {388-400}, doi = {10.1055/s-0037-1608832}, pmid = {29272899}, issn = {1098-8971}, mesh = {Bacteria/*growth &amp; development ; Disease Progression ; *Dysbiosis ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Intestine, Small/*microbiology ; Liver Diseases/diagnosis/epidemiology/*microbiology ; Prevalence ; Prognosis ; Risk Factors ; }, abstract = {The authors conducted a meta-analysis of the prevalence of small intestinal bacterial overgrowth (SIBO) in patients with chronic liver disease (CLD) and controls. Using the search terms &quot;small intestinal bacterial overgrowth (SIBO)&quot; and &quot;chronic liver disease (CLD)&quot; or &quot;cirrhosis,&quot; 19 case-control studies were identified. Utilizing breath tests, the prevalence of SIBO in CLD was 35.80% (95% CI, 32.60-39.10) compared with 8.0% (95% CI, 5.70-11.00) in controls. Using culture techniques, the prevalence was 68.31% (95% CI, 59.62-76.00) in CLD patients as compared with 7.94% (95% CI, 3.44-12.73) in controls. No difference between cirrhotic and noncirrhotic patients was found. SIBO is significantly more frequent in CLD patients as compared with controls. The association of SIBO and CLD was not confined to patients with advanced CLD, suggesting that SIBO is not a consequence of advanced liver disease but may play a role in the progression of CLD.}, }
@article {pmid29272370, year = {2018}, author = {Laenen, L and Vergote, V and Kafetzopoulou, LE and Wawina, TB and Vassou, D and Cook, JA and Hugot, JP and Deboutte, W and Kang, HJ and Witkowski, PT and Köppen-Rung, P and Krüger, DH and Licková, M and Stang, A and Striešková, L and Szemeš, T and Markowski, J and Hejduk, J and Kafetzopoulos, D and Van Ranst, M and Yanagihara, R and Klempa, B and Maes, P}, title = {A Novel Hantavirus of the European Mole, Bruges Virus, Is Involved in Frequent Nova Virus Coinfections.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {45-55}, pmid = {29272370}, issn = {1759-6653}, support = {P20 GM103516/GM/NIGMS NIH HHS/United States ; R01 AI075057/AI/NIAID NIH HHS/United States ; U54 MD007601/MD/NIMHD NIH HHS/United States ; }, mesh = {Animals ; Coinfection ; Europe/epidemiology ; Evolution, Molecular ; Genome, Viral ; Hantavirus/*genetics/physiology ; Hantavirus Infections/epidemiology/*virology ; Host-Pathogen Interactions ; Humans ; Moles/*virology ; *Phylogeny ; }, abstract = {Hantaviruses are zoonotic viruses with a complex evolutionary history of virus-host coevolution and cross-species transmission. Although hantaviruses have a broad reservoir host range, virus-host relationships were previously thought to be strict, with a single virus species infecting a single host species. Here, we describe Bruges virus, a novel hantavirus harbored by the European mole (Talpa europaea), which is the well-known host of Nova virus. Phylogenetic analyses of all three genomic segments showed tree topology inconsistencies, suggesting that Bruges virus has emerged from cross-species transmission and ancient reassortment events. A high number of coinfections with Bruges and Nova viruses was detected, but no evidence was found for reassortment between these two hantaviruses. These findings highlight the complexity of hantavirus evolution and the importance of further investigation of hantavirus-reservoir relationships.}, }
@article {pmid29269503, year = {2018}, author = {Chu, BTT and Petrovich, ML and Chaudhary, A and Wright, D and Murphy, B and Wells, G and Poretsky, R}, title = {Metagenomics Reveals the Impact of Wastewater Treatment Plants on the Dispersal of Microorganisms and Genes in Aquatic Sediments.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {5}, pages = {}, pmid = {29269503}, issn = {1098-5336}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; *Metagenome ; *Microbiota ; Waste Water/*microbiology ; Wisconsin ; }, abstract = {Wastewater treatment plants (WWTPs) release treated effluent containing mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and microorganisms into the environment, yet little is known about their influence on nearby microbial communities and the retention of these factors in receiving water bodies. Our research aimed to characterize the genes and organisms from two different WWTPs that discharge into Lake Michigan, as well as from surrounding lake sediments to determine the dispersal and fate of these factors with respect to distance from the effluent outfall. Shotgun metagenomics coupled to distance-decay analyses showed a higher abundance of genes identical to those in WWTP effluent genes in sediments closer to outfall sites than in sediments farther away, indicating their possible WWTP origin. We also found genes attributed to organisms, such as those belonging to Helicobacteraceae, Legionellaceae, Moraxellaceae, and Neisseriaceae, in effluent from both WWTPs and decreasing in abundance in lake sediments with increased distance from WWTPs. Moreover, our results showed that the WWTPs likely influence the ARG composition in lake sediments close to the effluent discharge. Many of these ARGs were located on MGEs in both the effluent and sediment samples, indicating a relatively broad propensity for horizontal gene transfer (HGT). Our approach allowed us to specifically link genes to organisms and their genetic context, providing insight into WWTP impacts on natural microbial communities. Overall, our results suggest a substantial influence of wastewater effluent on gene content and microbial community structure in the sediments of receiving water bodies.IMPORTANCE Wastewater treatment plants (WWTPs) release their effluent into aquatic environments. Although treated, effluent retains many genes and microorganisms that have the potential to influence the receiving water in ways that are poorly understood. Here, we tracked the genetic footprint, including genes specific to antibiotic resistance and mobile genetic elements and their associated organisms, from WWTPs to lake sediments. Our work is novel in that we used metagenomic data sets to comprehensively evaluate total gene content and the genetic and taxonomic context of specific genes in environmental samples putatively impacted by WWTP inputs. Based on two different WWTPs with different treatment processes, our findings point to an influence of WWTPs on the presence, abundance, and composition of these factors in the environment.}, }
@article {pmid29268781, year = {2017}, author = {Carda-Diéguez, M and Ghai, R and Rodríguez-Valera, F and Amaro, C}, title = {Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {162}, pmid = {29268781}, issn = {2049-2618}, support = {BES-2012-052361//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; AGL2014-58933-P (cofunded with FEDER funds)//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; 17-04828S//Grantová Agentura České Republiky/International ; CGL2016-76273-P [AEI/FEDER, EU]//AEI/FEDER/EU/International ; CGL2015-71523-REDC (Acciones de dinamización &quot;REDES DE EXCELENCIA&quot; CONSOLIDER)//Dirección General de Investigación Científica y Técnica/International ; Prometeo II/2014/012 &quot;AQUAMET&quot;//Generalitat Valenciana/International ; }, mesh = {Anguilla/anatomy &amp; histology/*microbiology ; Animals ; Animals, Wild/microbiology ; Bacteria/genetics/isolation &amp; purification/*pathogenicity ; DNA, Bacterial ; Evolution, Molecular ; Genomic Islands ; Genomics ; Humans ; Metagenomics ; Microbiota/*genetics ; Mucus/*microbiology ; Skin/*microbiology ; Vibrio/genetics/isolation &amp; purification/pathogenicity ; *Water Microbiology ; }, abstract = {BACKGROUND: Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host.<br><br>RESULTS: Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibrio vulnificus and Vibrio cholerae/Vibrio metoecus being the most abundant ones in SMS from estuary and lake, respectively. Functions encoded in the SMS-microbiome differed significantly from those in the W-microbiome and allowed us to predict that successful mucus colonizers should have specific genes for (i) attachment (mainly by forming biofilms), (ii) bacterial competence and communication, and (iii) resistance to mucosal innate immunity, predators (amoeba), and heavy metals/drugs. In addition, we found several mobile genetic elements (mainly integrative conjugative elements) as well as a series of evidences suggesting that bacteria exchange DNA in SMS. Further, we isolated and sequenced a V. metoecus strain from SMS. This isolate shares pathogenicity islands with V. cholerae O1 from intestinal infections that are absent in the rest of sequenced V. metoecus strains, all of them from water and extra-intestinal infections.<br><br>CONCLUSIONS: We have obtained metagenomic and genomic evidence in favor of the hypothesis on the role of fish mucosal surfaces as a specialized habitat selecting microbes capable of colonizing and persisting on other comparable mucosal surfaces, e.g., the human intestine.}, }
@article {pmid29261736, year = {2017}, author = {Camacho-Ortiz, A and Gutiérrez-Delgado, EM and Garcia-Mazcorro, JF and Mendoza-Olazarán, S and Martínez-Meléndez, A and Palau-Davila, L and Baines, SD and Maldonado-Garza, H and Garza-González, E}, title = {Randomized clinical trial to evaluate the effect of fecal microbiota transplant for initial Clostridium difficile infection in intestinal microbiome.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0189768}, pmid = {29261736}, issn = {1932-6203}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/genetics ; Biodiversity ; Clostridium Infections/drug therapy/*therapy ; Demography ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Genotype ; Humans ; Male ; Metagenomics ; Microbial Sensitivity Tests ; Middle Aged ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Tissue Donors ; Vancomycin/therapeutic use ; Young Adult ; }, abstract = {OBJECTIVE: The aim of this study was to evaluate the impact of fecal donor-unrelated donor mix (FMT-FURM) transplantation as first-line therapy for C. difficile infection (CDI) in intestinal microbiome.<br><br>METHODS: We designed an open, two-arm pilot study with oral vancomycin (250mg every 6 h for 10-14 days) or FMT-FURM as treatments for the first CDI episode in hospitalized adult patients in Hospital Universitario &quot;Dr. Jose Eleuterio Gonzalez&quot;. Patients were randomized by a closed envelope method in a 1: 1 ratio to either oral vancomycin or FMT-FURM. CDI resolution was considered when there was a reduction on the Bristol scale of at least 2 points, a reduction of at least 50% in the number of bowel movements, absence of fever, and resolution of abdominal pain (at least two criteria). From each patient, a fecal sample was obtained at days 0, 3, and 7 after treatment. Specimens were cultured to isolate C. difficile, and isolates were characterized by PCR. Susceptibility testing of isolates was performed using the agar dilution method. Fecal samples and FMT-FURM were analyzed by 16S rRNA sequencing.<br><br>RESULTS: We included 19 patients; 10 in the vancomycin arm and 9 in the FMT-FURM arm. However, one of the patients in the vancomycin arm and two patients in the FMT-FURM arm were eliminated. Symptoms resolved in 8/9 patients (88.9%) in the vancomycin group, while symptoms resolved in 4/7 patients (57.1%) after the first FMT-FURM dose (P = 0.26) and in 5/7 patients (71.4%) after the second dose (P = 0.55). During the study, no adverse effects attributable to FMT-FURM were observed in patients. Twelve isolates were recovered, most isolates carried tcdB, tcdA, cdtA, and cdtB, with an 18-bp deletion in tcdC. All isolates were resistant to ciprofloxacin and moxifloxacin but susceptible to metronidazole, linezolid, fidaxomicin, and tetracycline. In the FMT-FURM group, the bacterial composition was dominated by Firmicutes, Bacteroidetes, and Proteobacteria at all-time points and the microbiota were remarkably stable over time. The vancomycin group showed a very different pattern of the microbial composition when comparing to the FMT-FURM group over time.<br><br>CONCLUSION: The results of this preliminary study showed that FMT-FURM for initial CDI is associated with specific bacterial communities that do not resemble the donors' sample.}, }
@article {pmid29259289, year = {2018}, author = {Ogilvie, LA and Nzakizwanayo, J and Guppy, FM and Dedi, C and Diston, D and Taylor, H and Ebdon, J and Jones, BV}, title = {Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking.}, journal = {The ISME journal}, volume = {12}, number = {4}, pages = {942-958}, pmid = {29259289}, issn = {1751-7370}, support = {G0901553//Medical Research Council/United Kingdom ; MR/N006496/1//Medical Research Council/United Kingdom ; }, mesh = {Bacteriophages/*genetics ; Ecosystem ; Environmental Monitoring ; Feces/virology ; Gastrointestinal Tract/virology ; *Genome, Viral ; Humans ; *Metagenome ; Metagenomics ; Microbiota ; }, abstract = {Just as the expansion in genome sequencing has revealed and permitted the exploitation of phylogenetic signals embedded in bacterial genomes, the application of metagenomics has begun to provide similar insights at the ecosystem level for microbial communities. However, little is known regarding this aspect of bacteriophage associated with microbial ecosystems, and if phage encode discernible habitat-associated signals diagnostic of underlying microbiomes. Here we demonstrate that individual phage can encode clear habitat-related 'ecogenomic signatures', based on relative representation of phage-encoded gene homologues in metagenomic data sets. Furthermore, we show the ecogenomic signature encoded by the gut-associated ɸB124-14 can be used to segregate metagenomes according to environmental origin, and distinguish 'contaminated' environmental metagenomes (subject to simulated in silico human faecal pollution) from uncontaminated data sets. This indicates phage-encoded ecological signals likely possess sufficient discriminatory power for use in biotechnological applications, such as development of microbial source tracking tools for monitoring water quality.}, }
@article {pmid29255284, year = {2018}, author = {Costea, PI and Hildebrand, F and Arumugam, M and Bäckhed, F and Blaser, MJ and Bushman, FD and de Vos, WM and Ehrlich, SD and Fraser, CM and Hattori, M and Huttenhower, C and Jeffery, IB and Knights, D and Lewis, JD and Ley, RE and Ochman, H and O'Toole, PW and Quince, C and Relman, DA and Shanahan, F and Sunagawa, S and Wang, J and Weinstock, GM and Wu, GD and Zeller, G and Zhao, L and Raes, J and Knight, R and Bork, P}, title = {Enterotypes in the landscape of gut microbial community composition.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {8-16}, pmid = {29255284}, issn = {2058-5276}, support = {MR/M50161X/1//Medical Research Council/United Kingdom ; P30 AI045008/AI/NIAID NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; UH2 DK083981/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Biodiversity ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.}, }
@article {pmid29255014, year = {2018}, author = {Bergauer, K and Fernandez-Guerra, A and Garcia, JAL and Sprenger, RR and Stepanauskas, R and Pachiadaki, MG and Jensen, ON and Herndl, GJ}, title = {Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {3}, pages = {E400-E408}, pmid = {29255014}, issn = {1091-6490}, support = {268595//European Research Council/International ; }, mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/*metabolism ; Atlantic Ocean ; Bacteria/genetics/*metabolism ; Bacterial Proteins/*metabolism ; Biodiversity ; Genome, Archaeal ; Genome, Bacterial ; Metagenomics ; Proteomics/*methods ; Seawater ; *Water Microbiology ; }, abstract = {The phylogenetic composition of the heterotrophic microbial community is depth stratified in the oceanic water column down to abyssopelagic layers. In the layers below the euphotic zone, it has been suggested that heterotrophic microbes rely largely on solubilized particulate organic matter as a carbon and energy source rather than on dissolved organic matter. To decipher whether changes in the phylogenetic composition with depth are reflected in changes in the bacterial and archaeal transporter proteins, we generated an extensive metaproteomic and metagenomic dataset of microbial communities collected from 100- to 5,000-m depth in the Atlantic Ocean. By identifying which compounds of the organic matter pool are absorbed, transported, and incorporated into microbial cells, intriguing insights into organic matter transformation in the deep ocean emerged. On average, solute transporters accounted for 23% of identified protein sequences in the lower euphotic and ∼39% in the bathypelagic layer, indicating the central role of heterotrophy in the dark ocean. In the bathypelagic layer, substrate affinities of expressed transporters suggest that, in addition to amino acids, peptides and carbohydrates, carboxylic acids and compatible solutes may be essential substrates for the microbial community. Key players with highest expression of solute transporters were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria, accounting for 40%, 11%, and 10%, respectively, of relative protein abundances. The in situ expression of solute transporters indicates that the heterotrophic prokaryotic community is geared toward the utilization of similar organic compounds throughout the water column, with yet higher abundances of transporters targeting aromatic compounds in the bathypelagic realm.}, }
@article {pmid29246178, year = {2017}, author = {Razavi, M and Marathe, NP and Gillings, MR and Flach, CF and Kristiansson, E and Joakim Larsson, DG}, title = {Discovery of the fourth mobile sulfonamide resistance gene.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {160}, pmid = {29246178}, issn = {2049-2618}, support = {942-2015-750//Svenska Forskningsrådet Formas/ ; 521-2013-8633//Vetenskapsrådet/ ; 2015-02492//Vetenskapsrådet (SE)/ ; }, mesh = {Aminoglycosides/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Bioprospecting ; Cross Infection/microbiology ; Dihydropteroate Synthase/genetics/isolation &amp; purification ; Drug Resistance, Microbial/*genetics ; Escherichia coli/drug effects/genetics ; Genes, Bacterial ; Humans ; India ; *Integrons/genetics ; Metagenomics ; Microbial Consortia/genetics ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Sulfonamides/*pharmacology ; beta-Lactams/pharmacology ; }, abstract = {BACKGROUND: Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long- and short-read technologies to maintain both accuracy and context.<br><br>RESULTS: Up to 89% of identified open reading frames encode known resistance genes, or variations thereof (> 1000). We identified putative novel ARGs to aminoglycosides, beta-lactams, trimethoprim, rifampicin, and chloramphenicol, including several novel OXA variants, providing reduced susceptibility to carbapenems. One dihydropteroate synthase gene, with less than 34% amino acid identity to the three known mobile sulfonamide resistance genes (sul1-3), provided complete resistance when expressed in Escherichia coli. The mobilized gene, here named sul4, is the first mobile sulfonamide resistance gene discovered since 2003. Analyses of adjacent DNA suggest that sul4 has been decontextualized from a set of chromosomal genes involved in folate synthesis in its original host, likely within the phylum Chloroflexi. The presence of an insertion sequence common region element could provide mobility to the entire integron. Screening of 6489 metagenomic datasets revealed that sul4 is already widespread in seven countries across Asia and Europe.<br><br>CONCLUSIONS: Our findings show that exploring integrons from environmental communities with a history of antibiotic exposure can provide an efficient way to find novel, mobile resistance genes. The mobilization of a fourth sulfonamide resistance gene is likely to provide expanded opportunities for sulfonamide resistance to spread, with potential impacts on both human and animal health.}, }
@article {pmid29243150, year = {2018}, author = {Naik, OA and Shashidhar, R and Rath, D and Bandekar, JR and Rath, A}, title = {Characterization of multiple antibiotic resistance of culturable microorganisms and metagenomic analysis of total microbial diversity of marine fish sold in retail shops in Mumbai, India.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {7}, pages = {6228-6239}, pmid = {29243150}, issn = {1614-7499}, support = {2012/37B/50/BRNS//Board of Research in Nuclear Sciences/ ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/genetics ; Biodiversity ; Drug Resistance, Multiple, Bacterial/*genetics ; Fishes/*microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; India ; Integrons/genetics ; *Metagenomics ; Microbial Sensitivity Tests ; Plasmids/genetics ; }, abstract = {Marine fish species were analyzed for culturable and total metagenomic microbial diversity, antibiotic resistance (AR) pattern, and horizontal gene transfer in culturable microorganisms. We observed a high AR microbial load of 3 to 4 log CFU g-1. Many fish pathogens like Providencia, Staphylococcus, Klebsiella pneumoniae, Enterobacter, Vagococcus, and Aeromonas veronii were isolated. Photobacterium and Vibrio were two major fish and human pathogens which were identified in the fish metagenome. Other pathogens that were identified were Shewanella, Acinetobacter, Psychrobacter, and Flavobacterium. Most of these pathogens were resistant to multiple antibiotics such as erythromycin, kanamycin, neomycin, streptomycin, penicillin, cefotaxime, bacitracin, rifampicin, trimethoprim, ciprofloxacin, and doxycycline with a high multiple antibiotic resistance index of 0.54-0.77. The fish microflora showed high prevalence of AR genes like bla TEM, Class I integron, tetA, aph(3')-IIIa, ermB, aadA, and sul1. Nineteen of 26 AR isolates harbored Class I integrons showing high co-resistance to trimethoprim, kanamycin, doxycycline, and cefotaxime. Mobile R-plasmids from 6 of the 12 AR pathogens were transferred to recipient E. coli after conjugation. The transconjugants harbored the same R-plasmid carrying bla CTX-M, dfr1, tetA, bla TEM, and cat genes. This study confirms that fish is a potential carrier of AR pathogens which can enter the human gut via food chain. To the best of our knowledge, this is the first study in the Indian subcontinent reporting a direct evidence of spread of AR pathogens to humans from specific marine fish consumption.}, }
@article {pmid29242367, year = {2017}, author = {Costea, PI and Coelho, LP and Sunagawa, S and Munch, R and Huerta-Cepas, J and Forslund, K and Hildebrand, F and Kushugulova, A and Zeller, G and Bork, P}, title = {Subspecies in the global human gut microbiome.}, journal = {Molecular systems biology}, volume = {13}, number = {12}, pages = {960}, pmid = {29242367}, issn = {1744-4292}, mesh = {Escherichia coli/physiology ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; *Microbiota/genetics ; Phenotype ; Phylogeography ; Species Specificity ; }, abstract = {Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies-specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro-inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.}, }
@article {pmid29232848, year = {2017}, author = {Vernocchi, P and Del Chierico, F and Quagliariello, A and Ercolini, D and Lucidi, V and Putignani, L}, title = {A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics.}, journal = {Nutrients}, volume = {9}, number = {12}, pages = {}, pmid = {29232848}, issn = {2072-6643}, mesh = {Bacteria/*genetics ; Case-Control Studies ; Child, Preschool ; Cystic Fibrosis/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics/*methods ; Phylogeny ; *Probiotics ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Cystic fibrosis (CF) is a life-limiting hereditary disorder that results in aberrant mucosa in the lungs and digestive tract, chronic respiratory infections, chronic inflammation, and the need for repeated antibiotic treatments. Probiotics have been demonstrated to improve the quality of life of CF patients. We investigated the distribution of gut microbiota (GM) bacteria to identify new potential probiotics for CF patients on the basis of GM patterns. Fecal samples of 28 CF patients and 31 healthy controls (HC) were collected and analyzed by 16S rRNA-based pyrosequencing analysis of GM, to produce CF-HC paired maps of the distribution of operational taxonomic units (OTUs), and by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) for Kyoto Encyclopedia of Genes and Genomes (KEGG) biomarker prediction. The maps were scanned to highlight the distribution of bacteria commonly claimed as probiotics, such as bifidobacteria and lactobacilli, and of butyrate-producing colon bacteria, such as Eubacterium spp. and Faecalibacterium prausnitzii. The analyses highlighted 24 OTUs eligible as putative probiotics. Eleven and nine species were prevalently associated with the GM of CF and HC subjects, respectively. Their KEGG prediction provided differential CF and HC pathways, indeed associated with health-promoting biochemical activities in the latter case. GM profiling and KEGG biomarkers concurred in the evaluation of nine bacterial species as novel putative probiotics that could be investigated for the nutritional management of CF patients.}, }
@article {pmid29228991, year = {2017}, author = {Auffret, MD and Dewhurst, RJ and Duthie, CA and Rooke, JA and John Wallace, R and Freeman, TC and Stewart, R and Watson, M and Roehe, R}, title = {The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {159}, pmid = {29228991}, issn = {2049-2618}, support = {BB/N01720X/1 and BB/N016742/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animal Feed/adverse effects/*analysis ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteriocins/pharmacology ; Bacteroidetes/drug effects/genetics/pathogenicity ; Cattle/*microbiology ; Chloramphenicol/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Firmicutes/drug effects/genetics/pathogenicity ; *Genes, Bacterial ; Humans ; Metagenomics/methods ; *Microbiota ; Proteobacteria/drug effects/genetics/pathogenicity ; Red Meat/analysis ; Rumen/*microbiology ; Virulence ; }, abstract = {BACKGROUND: The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate.<br><br>RESULTS: Two hundred and four genes associated with antimicrobial resistance (AMR), colonisation, communication or pathogenicity functions were identified from 4966 metagenomic genes using KEGG identification. Both the diversity and abundance of these genes were higher in concentrate-fed animals. Chloramphenicol and microcin resistance genes were dominant in samples from forage-fed animals (P < 0.001), while aminoglycoside and streptomycin resistances were enriched in concentrate-fed animals. The concentrate-based diet also increased the relative abundance of Proteobacteria, which includes many animal and zoonotic pathogens. A high ratio of Proteobacteria to (Firmicutes + Bacteroidetes) was confirmed as a good indicator for rumen dysbiosis, with eight cases all from concentrate-fed animals. Finally, network analysis demonstrated that the resistance/pathogenicity genes are potentially useful as biomarkers for health risk assessment of the ruminal microbiome.<br><br>CONCLUSIONS: Diet has important effects on the complement of AMR genes in the rumen microbial community, with potential implications for human and animal health.}, }
@article {pmid29228901, year = {2017}, author = {Forsell, J and Bengtsson-Palme, J and Angelin, M and Johansson, A and Evengård, B and Granlund, M}, title = {The relation between Blastocystis and the intestinal microbiota in Swedish travellers.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {231}, pmid = {29228901}, issn = {1471-2180}, mesh = {Adult ; Biodiversity ; Blastocystis/*classification/physiology ; Blastocystis Infections/epidemiology/*microbiology/*parasitology/transmission ; Feces/microbiology/parasitology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Prevalence ; Sweden/epidemiology ; *Travel ; Young Adult ; }, abstract = {BACKGROUND: Blastocystis sp. is a unicellular eukaryote that is commonly found in the human intestine. Its ability to cause disease is debated and a subject for ongoing research. In this study, faecal samples from 35 Swedish university students were examined through shotgun metagenomics before and after travel to the Indian peninsula or Central Africa. We aimed at assessing the impact of travel on Blastocystis carriage and seek associations between Blastocystis and the bacterial microbiota.<br><br>RESULTS: We found a prevalence of Blastocystis of 16/35 (46%) before travel and 15/35 (43%) after travel. The two most commonly Blastocystis subtypes (STs) found were ST3 and ST4, accounting for 20 of the 31 samples positive for Blastocystis. No mixed subtype carriage was detected. All ten individuals with a typable ST before and after travel maintained their initial ST. The composition of the gut bacterial community was not significantly different between Blastocystis-carriers and non-carriers. Interestingly, the presence of Blastocystis was accompanied with higher abundances of the bacterial genera Sporolactobacillus and Candidatus Carsonella. Blastocystis carriage was positively associated with high bacterial genus richness, and negatively correlated to the Bacteroides-driven enterotype. These associations were both largely dependent on ST4 - a subtype commonly described from Europe - while the globally prevalent ST3 did not show such significant relationships.<br><br>CONCLUSIONS: The high rate of Blastocystis subtype persistence found during travel indicates that long-term carriage of Blastocystis is common. The associations between Blastocystis and the bacterial microbiota found in this study could imply a link between Blastocystis and a healthy microbiota as well as with diets high in vegetables. Whether the associations between Blastocystis and the microbiota are resulting from the presence of Blastocystis, or are a prerequisite for colonization with Blastocystis, are interesting questions for further studies.}, }
@article {pmid29227468, year = {2018}, author = {Beaulaurier, J and Zhu, S and Deikus, G and Mogno, I and Zhang, XS and Davis-Richardson, A and Canepa, R and Triplett, EW and Faith, JJ and Sebra, R and Schadt, EE and Fang, G}, title = {Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.}, journal = {Nature biotechnology}, volume = {36}, number = {1}, pages = {61-69}, pmid = {29227468}, issn = {1546-1696}, support = {R01 GM114472/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/genetics ; Cluster Analysis ; DNA Methylation/*genetics ; Environmental Microbiology ; Genome, Bacterial/genetics ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Plasmids/genetics ; Sequence Analysis, DNA ; }, abstract = {Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing. Our method takes advantage of these endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins. We validate our method using synthetic and real microbiome sequences. In addition to genome binning, we show that our method links plasmids and other mobile genetic elements to their host species in a real microbiome sample. Incorporation of DNA methylation information into shotgun metagenomics analyses will complement existing methods to enable more accurate sequence binning.}, }
@article {pmid29223543, year = {2018}, author = {Cowart, DA and Murphy, KR and Cheng, CC}, title = {Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula.}, journal = {Marine genomics}, volume = {37}, number = {}, pages = {148-160}, doi = {10.1016/j.margen.2017.11.003}, pmid = {29223543}, issn = {1876-7478}, mesh = {Animals ; Antarctic Regions ; Aquatic Organisms ; *Biodiversity ; DNA/*analysis ; High-Throughput Nucleotide Sequencing/methods ; *Invertebrates ; *Metagenome ; Metagenomics/*methods ; *Vertebrates ; }, abstract = {The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditi