@article {pmid30649386, year = {2019}, author = {Van Gompel, L and Luiken, REC and Sarrazin, S and Munk, P and Knudsen, BE and Hansen, RB and Bossers, A and Aarestrup, FM and Dewulf, J and Wagenaar, JA and Mevius, DJ and Schmitt, H and Heederik, DJJ and Dorado-García, A and Smit, LAM and , }, title = {The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1093/jac/dky518}, pmid = {30649386}, issn = {1460-2091}, abstract = {Objectives: Previous studies in food-producing animals have shown associations between antimicrobial use (AMU) and resistance (AMR) in specifically isolated bacterial species. Multi-country data are scarce and only describe between-country differences. Here we investigate associations between the pig faecal mobile resistome and characteristics at the farm-level across Europe.<br><br>Methods: A cross-sectional study was conducted among 176 conventional pig farms from nine European countries. Twenty-five faecal samples from fattening pigs were pooled per farm and acquired resistomes were determined using shotgun metagenomics and the Resfinder reference database, i.e. the full collection of horizontally acquired AMR genes (ARGs). Normalized fragments resistance genes per kilobase reference per million bacterial fragments (FPKM) were calculated. Specific farm-level data (AMU, biosecurity) were collected. Random-effects meta-analyses were performed by country, relating farm-level data to relative ARG abundances (FPKM).<br><br>Results: Total AMU during fattening was positively associated with total ARG (total FPKM). Positive associations were particularly observed between widely used macrolides and tetracyclines, and ARGs corresponding to the respective antimicrobial classes. Significant AMU-ARG associations were not found for β-lactams and only few colistin ARGs were found, despite high use of these antimicrobial classes in younger pigs. Increased internal biosecurity was directly related to higher abundances of ARGs mainly encoding macrolide resistance. These effects of biosecurity were independent of AMU in mutually adjusted models.<br><br>Conclusions: Using resistome data in association studies is unprecedented and adds accuracy and new insights to previously observed AMU-AMR associations. Major components of the pig resistome are positively and independently associated with on-farm AMU and biosecurity conditions.}, }
@article {pmid30649204, year = {2019}, author = {Saha, S and Johnson, J and Pal, S and Weinstock, G and Rajasekaran, S}, title = {MSC: a metagenomic sequence classification algorithm.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/bty1071}, pmid = {30649204}, issn = {1367-4811}, abstract = {Motivation: Metagenomics is the study of genetic materials directly sampled from natural habitats. It has the potential to reveal previously hidden diversity of microscopic life largely due to the existence of highly parallel and low-cost next-generation sequencing (NGS) technology. Conventional approaches align metagenomic reads onto known reference genomes to identify microbes in the sample. Since such a collection of reference genomes is very large, the approach often needs high-end computing machines with large memory which is not often available to researchers. Alternative approaches follow an alignment-free methodology where the presence of a microbe is predicted using the information about the unique k-mers present in the microbe genomes. However, such approaches suffer from high false positives due to trading off the value of k with the computational resources. In this article we propose a highly efficient metagenomic sequence classification algorithm (MSC) that is a hybrid of both approaches. Instead of aligning reads to the full genomes, MSC aligns reads onto a set of carefully chosen, shorter and highly discriminating model sequences built from the unique k-mers of each of the target sequences.<br><br>Results: Microbiome researchers are generally interested in two objectives of a taxonomic classifier: 1) to detect prevalence, i.e., the taxa present in a sample, and 2) to estimate their relative abundances. MSC is primarily designed to detect prevalence and experimental results show that MSC is indeed a more effective and efficient algorithm compared to the other state-of-the-art algorithms in terms of accuracy, memory, and runtime. Moreover, MSC outputs an approximate estimate of the abundances.<br><br>Availability: The implementations are freely available for non-commercial purposes. They can be downloaded from https://drive.google.com/open?id=1XirkAamkQ3ltWvI1W1igYQFusp9DHtVl.}, }
@article {pmid30649168, year = {2019}, author = {Griffith, JC and Morgan, XC}, title = {Invited Commentary: Improving accessibility of the Human Microbiome Project data through integration with R/Bioconductor.}, journal = {American journal of epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/aje/kwz007}, pmid = {30649168}, issn = {1476-6256}, abstract = {Alterations in the composition of the microbiota have been implicated in many diseases. The Human Microbiome Project (HMP) provides a comprehensive reference dataset of the &quot;normal&quot; human microbiome of 242 healthy adults at five major body sites. The HMP used both 16S ribosomal RNA gene sequencing and whole-genome metagenomic sequencing to profile the subjects' microbial communities. However, accessing and analyzing the HMP dataset still presents technical and bioinformatic challenges, as researchers must import the microbiome data, integrate phylogenetic trees, and access and merge public and restricted metadata. In this issue, the HMP16SData R/Bioconductor package developed by Schiffer and colleagues (Am J Epidemiol. XXX; XX (XX): XX-XXX) greatly simplifies access to the HMP data by combining 16S taxonomic abundance data, public patient metadata, and phylogenetic trees as a single data object. The authors also provide an interface for users with approved dbGaP projects to easily retrieve and merge the controlled-access HMP metadata. This package has a broad range of appeal to researchers across disciplines and with various levels of expertise in using R and/or other statistical tools. This will translate to improved data accessibility for public health research, with data from healthy individuals serving as a reference for disease-associated studies.}, }
@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 {pmid30648419, year = {2019}, author = {BenIsrael, M and Wanner, P and Aravena, R and Parker, BL and Haack, EA and Tsao, DT and Dunfield, KE}, title = {Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis.}, journal = {International journal of phytoremediation}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/15226514.2018.1523873}, pmid = {30648419}, issn = {1549-7879}, abstract = {Biodegradation is an important mechanism of action of phytoremediation systems, but performance evaluation is challenging. We applied metagenomic molecular approaches and compound-specific stable carbon isotope analysis to assess biodegradation of toluene in the vadose zone at an urban pilot field system where hybrid poplars were planted to remediate legacy impacts to an underlying shallow fractured bedrock aquifer. Carbon isotope ratios were compared spatio-temporally between toluene dissolved in groundwater and in the vapor phase. Enrichment of 13C from toluene in the vapor phase compared to groundwater provided evidence for biodegradation in the vadose zone. Total bacterial abundance (16S rRNA) and abundance and expression of degradation genes were determined in rhizosphere soil (DNA and RNA) and roots (DNA) using quantitative PCR. Relative abundances of degraders in the rhizosphere were on average higher at greater depths, except for enrichment of PHE-encoding communities that more strongly followed patterns of toluene concentrations detected. Quantification of RMO and PHE gene transcripts supported observations of active aerobic toluene degradation. Finally, spatially-variable numbers of toluene degraders were detected in poplar roots. We present multiple lines of evidence for biodegradation in the vadose zone at this site, contributing to our understanding of mechanisms of action of the phytoremediation system.}, }
@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 {pmid30647460, year = {2019}, author = {Rubin-Blum, M and Antony, CP and Sayavedra, L and Martínez-Pérez, C and Birgel, D and Peckmann, J and Wu, YC and Cardenas, P and MacDonald, I and Marcon, Y and Sahling, H and Hentschel, U and Dubilier, N}, title = {Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0346-7}, pmid = {30647460}, issn = {1751-7370}, support = {N/A//Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation)/ ; 679849//EC | Horizon 2020 (Horizon 2020 - Research and Innovation Framework Programme)/ ; 679849//EC | European Research Council (ERC)/ ; GBMF3811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, abstract = {Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 clade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host-symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.}, }
@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 {pmid29405826, year = {2018}, author = {Huang, YY and Martínez-Del Campo, A and Balskus, EP}, title = {Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity.}, journal = {Gut microbes}, volume = {9}, number = {5}, pages = {437-451}, pmid = {29405826}, issn = {1949-0984}, mesh = {Anaerobiosis ; Bacteria/classification/*enzymology/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Hydro-Lyases/genetics/*metabolism ; Hydroxyproline/chemistry/*metabolism ; Metabolic Networks and Pathways ; Metagenome ; Microbiota ; Phylogeny ; }, abstract = {The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ1-pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.}, }
@article {pmid30645605, year = {2019}, author = {Kim, SH and Kang, PA and Han, K and Lee, SW and Rhee, S}, title = {Crystal structure of chloramphenicol-metabolizing enzyme EstDL136 from a metagenome.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210298}, doi = {10.1371/journal.pone.0210298}, pmid = {30645605}, issn = {1932-6203}, abstract = {Metagenomes often convey novel biological activities and therefore have gained considerable attention for use in biotechnological applications. Recently, metagenome-derived EstDL136 was found to possess chloramphenicol (Cm)-metabolizing features. Sequence analysis showed EstDL136 to be a member of the hormone-sensitive lipase (HSL) family with an Asp-His-Ser catalytic triad and a notable substrate specificity. In this study, we determined the crystal structures of EstDL136 and in a complex with Cm. Consistent with the high sequence similarity, the structure of EstDL136 is homologous to that of the HSL family. The active site of EstDL136 is a relatively shallow pocket that could accommodate Cm as a substrate as opposed to the long acyl chain substrates typical of the HSL family. Mutational analyses further suggested that several residues in the vicinity of the active site play roles in the Cm-binding of EstDL136. These results provide structural and functional insights into a metagenome-derived EstDL136.}, }
@article {pmid30644013, year = {2019}, author = {Wang, G and Ren, Y and Ng, TB and Streit, WR and Ye, X}, title = {High-throughput amplicon sequencing demonstrates extensive diversity of xylanase genes in the sediment of soda lake Dabusu.}, journal = {Biotechnology letters}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10529-019-02646-w}, pmid = {30644013}, issn = {1573-6776}, support = {31301406//National Natural Science Foundation of China/ ; 2014FJPT02//the Marine Biological Engineering Platform for Innovative Services/ ; 2017-3059//China Scholarship Council/ ; }, abstract = {OBJECTIVE: To explore the diversity of glycoside hydrolase family 10 xylanase genes in the sediment of soda lake Dabusu by using high-throughput amplicon sequencing based on the Illumina HiSeq2500 platform.<br><br>RESULTS: A total of 227,420 clean reads, representing approximately 49.5 M bp, were obtained. Operational taxonomic unit (OTU) classification, with a 95% sequence identity cut-off, resulted in 467 OTUs with 392 annotated as GH10 xylanase, exhibiting 35-99% protein sequence identity with their closest-related xylanases in GenBank. Above 75% of the total OTUs demonstrated less than 80% identity with known xylanases. In addition, xylanases derived from the sediment were found to be affiliated to 12 different phyla, with Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and Basidiomycota being the dominant phyla. Moreover, barcode sequence had a major effect on abundance with only a minor effect on diversity.<br><br>CONCLUSIONS: High-throughput amplicon sequencing offers insight into xylanase gene diversity at a substantially higher resolution and lesser cost than library cloning and Sanger sequencing, facilitating a more thorough understanding of xylanase distribution and ecology.}, }
@article {pmid30643883, year = {2019}, author = {Franco Filho, LC and Barata, RR and Cardoso, JF and Massafra, JMV and Lemos, PDS and Casseb, LMN and Cruz, ACR and Nunes, MRT}, title = {Metagenomic Analysis of Samples from Three Bat Species Collected in the Amazon Rain Forest.}, journal = {Microbiology resource announcements}, volume = {8}, number = {2}, pages = {}, doi = {10.1128/MRA.01422-18}, pmid = {30643883}, issn = {2576-098X}, abstract = {We report here the sequencing of five microbiome samples collected from different bat species in the Amazon rain forest. All contigs matching virus sequences were assigned to members of the Retroviridae family, while the bacterial contigs matched several bacterial species mostly belonging to the Proteobacteria phylum.}, }
@article {pmid30643240, year = {2019}, author = {Nakamoto, N and Sasaki, N and Aoki, R and Miyamoto, K and Suda, W and Teratani, T and Suzuki, T and Koda, Y and Chu, PS and Taniki, N and Yamaguchi, A and Kanamori, M and Kamada, N and Hattori, M and Ashida, H and Sakamoto, M and Atarashi, K and Narushima, S and Yoshimura, A and Honda, K and Sato, T and Kanai, T}, title = {Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-018-0333-1}, pmid = {30643240}, issn = {2058-5276}, abstract = {Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease and its frequent complication with ulcerative colitis highlights the pathogenic role of epithelial barrier dysfunction. Intestinal barrier dysfunction has been implicated in the pathogenesis of PSC, yet its underlying mechanism remains unknown. Here, we identify Klebsiella pneumonia in the microbiota of patients with PSC and demonstrate that K. pneumoniae disrupts the epithelial barrier to initiate bacterial translocation and liver inflammatory responses. Gnotobiotic mice inoculated with PSC-derived microbiota exhibited T helper 17 (TH17) cell responses in the liver and increased susceptibility to hepatobiliary injuries. Bacterial culture of mesenteric lymph nodes in these mice isolated K. pneumoniae, Proteus mirabilis and Enterococcus gallinarum, which were prevalently detected in patients with PSC. A bacterial-organoid co-culture system visualized the epithelial-damaging effect of PSC-derived K. pneumoniae that was associated with bacterial translocation and susceptibility to TH17-mediated hepatobiliary injuries. We also show that antibiotic treatment ameliorated the TH17 immune response induced by PSC-derived microbiota. These results highlight the role of pathobionts in intestinal barrier dysfunction and liver inflammation, providing insights into therapeutic strategies for PSC.}, }
@article {pmid30643213, year = {2019}, author = {Ronda, C and Chen, SP and Cabral, V and Yaung, SJ and Wang, HH}, title = {Metagenomic engineering of the mammalian gut microbiome in situ.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41592-018-0301-y}, pmid = {30643213}, issn = {1548-7105}, abstract = {Engineering of microbial communities in open environments remains challenging. Here we describe a platform used to identify and modify genetically tractable mammalian microbiota by engineering community-wide horizontal gene transfer events in situ. With this approach, we demonstrate that diverse taxa in the mouse gut microbiome can be modified directly with a desired genetic payload. In situ microbiome engineering in living animals allows novel capabilities to be introduced into established communities in their native milieu.}, }
@article {pmid30643200, year = {2019}, author = {González, JM and Hernández, L and Manzano, I and Pedrós-Alió, C}, title = {Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0347-6}, pmid = {30643200}, issn = {1751-7370}, abstract = {Dimethylsulfoniopropionate (DMSP) is produced mainly by phytoplankton and bacteria. It is relatively abundant and ubiquitous in the marine environment, where bacterioplankton make use of it readily as both carbon and sulfur sources. In one transformation pathway, part of the molecule becomes dimethylsulfide (DMS), which escapes into the atmosphere and plays an important role in the sulfur exchange between oceans and atmosphere. Through its other dominant catabolic pathway, bacteria are able to use it as sulfur source. During the past few years, a number of genes involved in its transformation have been characterized. Identifying genes in taxonomic groups not amenable to conventional methods of cultivation is challenging. Indeed, functional annotation of genes in environmental studies is not straightforward, considering that particular taxa are not well represented in the available sequence databases. Furthermore, many genes belong to families of paralogs with similar sequences but perhaps different functions. In this study, we develop in silico approaches to infer protein function of an environmentally important gene (dmdA) that carries out the first step in the sulfur assimilation from DMSP. The method combines a set of tools to annotate a targeted gene in genome databases and metagenome assemblies. The method will be useful to identify genes that carry out key biochemical processes in the environment.}, }
@article {pmid30642389, year = {2019}, author = {Li, F and Hitch, TCA and Chen, Y and Creevey, CJ and Guan, LL}, title = {Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {6}, doi = {10.1186/s40168-019-0618-5}, pmid = {30642389}, issn = {2049-2618}, support = {BB/E/W/10964A01 and BBS/OS/GC/000011B//BBSRC/ ; 2013R029R//Alberta Livestock and Meat Agency/ ; 2015P008R//Alberta Livestock and Meat Agency/ ; Discovery//Natural Sciences and Engineering Research Council of Canada/ ; Doctoral Scholarship//Alberta Innovates - Technology Futures/ ; Scholarship//GPLER/ ; }, abstract = {BACKGROUND: Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome.<br><br>RESULTS: Rumen metagenomes were more closely clustered together and thus more conserved among individuals than metatranscriptomes, suggesting that inter-individual functional variations at the RNA level were higher than those at the DNA level. However, while mRNA enrichment significantly increased the sequencing depth of mRNA and generated similar functional profiles to total RNA-based metatranscriptomics, it led to biased abundance estimation of several transcripts. We observed divergent rumen microbial composition (metatranscriptomic level) and functional potentials (metagenomic level) among three breeds, but differences in functional activity (metatranscriptomic level) were less apparent. Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes) were detected between cattle with high and low feed efficiency, and most of them were breed-specific.<br><br>CONCLUSIONS: Metatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts.}, }
@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/ ; }, 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 {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 {pmid30294753, year = {2018}, author = {Reis, AC and Čvančarová, M and Liu, Y and Lenz, M and Hettich, T and Kolvenbach, BA and Corvini, PF and Nunes, OC}, title = {Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {23}, pages = {10299-10314}, doi = {10.1007/s00253-018-9411-9}, pmid = {30294753}, issn = {1432-0614}, support = {160332//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CH)/ ; SFRH/BD/95814/2013//Fundação para a Ciência e a Tecnologia/ ; UID/EQU/00511/2013 - POCI-01-0145-FEDER-006939//Fundação para a Ciência e a Tecnologia/ ; NORTE-01-0145-FEDER-000005//Comissão de Coordenação e Desenvolvimento Regional do Norte/ ; }, mesh = {Achromobacter denitrificans/*metabolism ; Actinobacteria/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Biodegradation, Environmental ; Cloning, Molecular ; Gene Expression Regulation, Bacterial ; Gene Library ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/microbiology ; Sulfamethoxazole/*metabolism ; }, abstract = {In the last decade, biological degradation and mineralization of antibiotics have been increasingly reported feats of environmental bacteria. The most extensively described example is that of sulfonamides that can be degraded by several members of Actinobacteria and Proteobacteria. Previously, we reported sulfamethoxazole (SMX) degradation and partial mineralization by Achromobacter denitrificans strain PR1, isolated from activated sludge. However, further studies revealed an apparent instability of this metabolic trait in this strain. Here, we investigated this instability and describe the finding of a low-abundance and slow-growing actinobacterium, thriving only in co-culture with strain PR1. This organism, named GP, shared highest 16S rRNA gene sequence similarity (94.6-96.9%) with the type strains of validly described species of the genus Leucobacter. This microbial consortium was found to harbor a homolog to the sulfonamide monooxygenase gene (sadA) also found in other sulfonamide-degrading bacteria. This gene is overexpressed in the presence of the antibiotic, and evidence suggests that it codes for a group D flavin monooxygenase responsible for the ipso-hydroxylation of SMX. Additional side reactions were also detected comprising an NIH shift and a Baeyer-Villiger rearrangement, which indicate an inefficient biological transformation of these antibiotics in the environment. This work contributes to further our knowledge in the degradation of this ubiquitous micropollutant by environmental bacteria.}, }
@article {pmid30640944, year = {2019}, author = {Hjelmsø, MH and Mollerup, S and Jensen, RH and Pietroni, C and Lukjancenko, O and Schultz, AC and Aarestrup, FM and Hansen, AJ}, title = {Metagenomic analysis of viruses in toilet waste from long distance flights-A new procedure for global infectious disease surveillance.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210368}, doi = {10.1371/journal.pone.0210368}, pmid = {30640944}, issn = {1932-6203}, abstract = {Human viral pathogens are a major public health threat. Reliable information that accurately describes and characterizes the global occurrence and transmission of human viruses is essential to support national and global priority setting, public health actions, and treatment decisions. However, large areas of the globe are currently without surveillance due to limited health care infrastructure and lack of international cooperation. We propose a novel surveillance strategy, using metagenomic analysis of toilet material from international air flights as a method for worldwide viral disease surveillance. The aim of this study was to design, implement, and evaluate a method for viral analysis of airplane toilet waste enabling simultaneous detection and quantification of a wide range of human viral pathogens. Toilet waste from 19 international airplanes was analyzed for viral content, using viral capture probes followed by high-throughput sequencing. Numerous human pathogens were detected including enteric and respiratory viruses. Several geographic trends were observed with samples originating from South Asia having significantly higher viral species richness as well as higher abundances of salivirus A, aichivirus A and enterovirus B, compared to samples originating from North Asia and North America. In addition, certain city specific trends were observed, including high numbers of rotaviruses in airplanes departing from Islamabad. Based on this study we believe that central sampling and analysis at international airports could be a useful supplement for global viral surveillance, valuable for outbreak detection and for guiding public health resources.}, }
@article {pmid30640905, year = {2019}, author = {Ravi, A and Ereqat, S and Al-Jawabreh, A and Abdeen, Z and Abu Shamma, O and Hall, H and Pallen, MJ and Nasereddin, A}, title = {Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus.}, journal = {PLoS neglected tropical diseases}, volume = {13}, number = {1}, pages = {e0006805}, doi = {10.1371/journal.pntd.0006805}, pmid = {30640905}, issn = {1935-2735}, abstract = {BACKGROUND: Across the world, ticks act as vectors of human and animal pathogens. Ticks rely on bacterial endosymbionts, which often share close and complex evolutionary links with tick-borne pathogens. As the prevalence, diversity and virulence potential of tick-borne agents remain poorly understood, there is a pressing need for microbial surveillance of ticks as potential disease vectors.<br><br>We developed a two-stage protocol that includes 16S-amplicon screening of pooled samples of hard ticks collected from dogs, sheep and camels in Palestine, followed by shotgun metagenomics on individual ticks to detect and characterise tick-borne pathogens and endosymbionts. Two ticks isolated from sheep yielded an abundance of reads from the genus Rickettsia, which were assembled into draft genomes. One of the resulting genomes was highly similar to Rickettsia massiliae strain MTU5. Analysis of signature genes showed that the other represents the first genome sequence of the potential pathogen Candidatus Rickettsia barbariae. Ticks from a dog and a sheep yielded draft genome sequences of Coxiella strains. A sheep tick yielded sequences from the sheep pathogen Anaplasma ovis, while Hyalomma ticks from camels yielded sequences belonging to Francisella-like endosymbionts. From the metagenome of a dog tick from Jericho, we generated a genome sequence of a canine parvovirus.<br><br>SIGNIFICANCE: Here, we have shown how a cost-effective two-stage protocol can be used to detect and characterise tick-borne pathogens and endosymbionts. In recovering genome sequences from an unexpected pathogen (canine parvovirus) and a previously unsequenced pathogen (Candidatus Rickettsia barbariae), we demonstrate the open-ended nature of metagenomics. We also provide evidence that ticks can carry canine parvovirus, raising the possibility that ticks might contribute to the spread of this troublesome virus.}, }
@article {pmid30640566, year = {2019}, author = {Dubourg, G and Raoult, D and Fenollar, F}, title = {Emerging methodologies for pathogen identification in bloodstream infections: an update.}, journal = {Expert review of molecular diagnostics}, volume = {}, number = {}, pages = {}, doi = {10.1080/14737159.2019.1568241}, pmid = {30640566}, issn = {1744-8352}, abstract = {INTRODUCTION: Bloodstream infections (BSIs) remain a major public health burden worldwide, particularly in high-income countries as they are associated with a significant mortality rate. As early administration of appropriate antimicrobial therapy is a major prognostic factor, there remain unmet needs for shortening BSI diagnosis. Current blood cultures (BC) processing to identify pathogens involved in BSI is not compatible with such delays, although it remains the gold standard. Areas covered: Herein, we review and discuss emerging or ongoing assessed methodologies dedicated to shorten the identification of microorganisms involved in BSI and published since 2015. A particular focus on the economical and clinical impact of these approaches is provided when hindsight is sufficient. Methods to shorten antibiotic susceptibility testing are also reviewed. Expert commentary: Post-culture approaches have encountered a huge success as they are reliable, fast and easy to implement in the laboratory. In particular, the MALDI-TOF MS was shown to be a cost-effective method when combined with antimicrobial stewardship policies. However, further research is needed to optimize methods performed on whole blood in particular next generation sequencing methods, as they represent an opportunity to substantially improve management of high-risk patients.}, }
@article {pmid30639767, year = {2019}, author = {Davis, WJ and Amses, KR and Benny, GL and Carter-House, D and Chang, Y and Grigoriev, I and Smith, ME and Spatafora, JW and Stajich, JE and James, TY}, title = {Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ympev.2019.01.006}, pmid = {30639767}, issn = {1095-9513}, abstract = {Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.}, }
@article {pmid30637962, year = {2019}, author = {Asante, J and Osei Sekyere, J}, title = {Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: Advances and applications.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12735}, pmid = {30637962}, issn = {1758-2229}, abstract = {Our inability to cultivate most micro-organisms, specifically bacteria, in the laboratory has for many years restricted our view and understanding of the bacterial meta-resistome in all living and non-living environments. As a result, reservoirs, sources, and distribution of antibiotic resistance genes (ARGS) and antibiotic-producers, as well as the effects of human activity and antibiotics on the selection and dissemination of ARGs were not well comprehended. With the advances made in the fields of metagenomics and metatranscriptomics, many of the hitherto little-understood concepts are becoming clearer. Further, the discovery of antibiotics such as lugdinin and lactocillin from the human microbiota, buttressed the importance of these new fields. Metagenomics and metatranscriptomics are becoming important clinical diagnostic tools for screening and detecting pathogens and ARGs, assessing the effects of antibiotics, other xenobiotics, and human activity on the environment, characterizing the microbiome and the environmental resistome with lesser turnaround time and decreasing cost, as well as discovering antibiotic-producers. However, challenges with accurate binning, skewed ARGs databases, detection of less abundant and allelic variants of ARGs, and efficient mobilome characterization remain. Ongoing efforts in long-read, phased- and single-cell sequencing, strain-resolved binning, chromosomal-conformation capture, DNA-methylation binning, and deep-learning bioinformatic approaches offer promising prospects in reconstructing complete strain-level genomes and mobilomes from metagenomes. This article is protected by copyright. All rights reserved.}, }
@article {pmid30637337, year = {2018}, author = {Bayer, K and Jahn, MT and Slaby, BM and Moitinho-Silva, L and Hentschel, U}, title = {Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00150-18}, pmid = {30637337}, issn = {2379-5077}, abstract = {Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae, and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features of Chloroflexi sponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism, and respiration. Clade-specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, but only amino acid utilization by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding components involved in cofactor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by the fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM) method. Carbohydrate degradation potential was reported previously for &quot;Candidatus Poribacteria&quot; and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus, sponge microbes may not only provide nutrients to the sponge host, but they may also contribute to dissolved organic matter (DOM) recycling and primary productivity in reef ecosystems via a pathway termed the sponge loop. IMPORTANCEChloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought.}, }
@article {pmid30636420, year = {2019}, author = {Gunasekera, SP and Meyer, JL and Ding, Y and Abboud, KA and Luo, D and Campbell, JE and Angerhofer, A and Goodsell, JL and Raymundo, LJ and Liu, J and Ye, T and Luesch, H and Teplitski, M and Paul, VJ}, title = {Chemical and Metagenomic Studies of the Lethal Black Band Disease of Corals Reveal Two Broadly Distributed, Redox-Sensitive Mixed Polyketide/Peptide Macrocycles.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.8b00804}, pmid = {30636420}, issn = {1520-6025}, abstract = {Black band disease (BBD), a lethal, polymicrobial disease consortium dominated by the cyanobacterium Roseofilum reptotaenium, kills many species of corals worldwide. To uncover chemical signals or cytotoxins that could be important in proliferation of Roseofilum and the BBD layer, we examined the secondary metabolites present in geographically diverse collections of BBD from Caribbean and Pacific coral reefs. Looekeyolide A (1), a 20-membered macrocyclic compound formed by a 16-carbon polyketide chain, 2-deamino-2-hydroxymethionine, and d-leucine, and its autoxidation product looekeyolide B (2) were extracted as major compounds (∼1 mg g-1 dry wt) from more than a dozen field-collected BBD samples. Looekeyolides A and B were also produced by a nonaxenic R. reptotaenium culture under laboratory conditions at similar concentrations. R. reptotaenium genomes that were constructed from four different metagenomic data sets contained a unique nonribosomal peptide/polyketide biosynthetic cluster that is likely responsible for the biosynthesis of the looekeyolides. Looekeyolide A, which readily oxidizes to looekeyolide B, may play a biological role in reducing H2O2 and other reactive oxygen species that could occur in the BBD layer as it overgrows and destroys coral tissue.}, }
@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 {pmid30024981, year = {2018}, author = {Douglass, AP and Offei, B and Braun-Galleani, S and Coughlan, AY and Martos, AAR and Ortiz-Merino, RA and Byrne, KP and Wolfe, KH}, title = {Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names.}, journal = {PLoS pathogens}, volume = {14}, number = {7}, pages = {e1007138}, pmid = {30024981}, issn = {1553-7374}, support = {105341/Z/14/Z//Wellcome Trust/United Kingdom ; }, mesh = {Candida/*classification/*genetics ; *Metagenomics ; Phylogeny ; Pichia/*classification/*genetics ; }, abstract = {We investigated genomic diversity of a yeast species that is both an opportunistic pathogen and an important industrial yeast. Under the name Candida krusei, it is responsible for about 2% of yeast infections caused by Candida species in humans. Bloodstream infections with C. krusei are problematic because most isolates are fluconazole-resistant. Under the names Pichia kudriavzevii, Issatchenkia orientalis and Candida glycerinogenes, the same yeast, including genetically modified strains, is used for industrial-scale production of glycerol and succinate. It is also used to make some fermented foods. Here, we sequenced the type strains of C. krusei (CBS573T) and P. kudriavzevii (CBS5147T), as well as 30 other clinical and environmental isolates. Our results show conclusively that they are the same species, with collinear genomes 99.6% identical in DNA sequence. Phylogenetic analysis of SNPs does not segregate clinical and environmental isolates into separate clades, suggesting that C. krusei infections are frequently acquired from the environment. Reduced resistance of strains to fluconazole correlates with the presence of one gene instead of two at the ABC11-ABC1 tandem locus. Most isolates are diploid, but one-quarter are triploid. Loss of heterozygosity is common, including at the mating-type locus. Our PacBio/Illumina assembly of the 10.8 Mb CBS573T genome is resolved into 5 complete chromosomes, and was annotated using RNAseq support. Each of the 5 centromeres is a 35 kb gene desert containing a large inverted repeat. This species is a member of the genus Pichia and family Pichiaceae (the methylotrophic yeasts clade), and so is only distantly related to other pathogenic Candida species.}, }
@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 {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 {pmid30635385, year = {2019}, author = {Fredriksen, L and Stokke, R and Jensen, MS and Westereng, B and Jameson, JK and Steen, IH and Eijsink, VGH}, title = {Discovery of a thermostable GH10 xylanase with broad substrate specificity from the Arctic Mid-Ocean Ridge vent system.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02970-18}, pmid = {30635385}, issn = {1098-5336}, abstract = {A two-domain GH10 xylanase encoding gene (amor_gh10a) was discovered from a metagenomic dataset, generated after in situ incubation of a lignocellulosic substrate in hot sediments on the sea floor of the Arctic Mid-Ocean Ridge (AMOR). AMOR_GH10A comprises a signal peptide, a carbohydrate-binding module belonging to a previously uncharacterized family, and a catalytic glycosyl hydrolase (GH10) domain. The enzyme shares the highest sequence identity (42%) with a hypothetical protein from Verrucomicrobia bacterium, and its GH10 domain shares low identity (24-28%) with functionally characterized xylanases. Purified AMOR_GH10A showed thermophilic and halophilic properties and was active towards various xylans. Uniquely, the enzyme showed high activity towards amorphous cellulose, glucomannan, and xyloglucan and was more active towards cellopentaose than towards xylopentaose. Binding assays showed that the N-terminal domain of this broad-specificity GH10 binds strongly to amorphous cellulose, as well as to microcrystalline cellulose, birchwood glucuronoxylan, barley β-glucan and konjac glucomannan, confirming its classification as a novel CBM (CBM85).ImportanceHot springs at the sea bottom harbor unique biodiversity and are a promising source of enzymes with interesting properties. We describe the functional characterization of a thermophilic and halophilic multi-domain xylanase originating from the Arctic Mid-Ocean Ridge vent system, belonging to the well-studied family 10 of glycosyl hydrolases (GH10). This xylanase, AMOR_GH10A, has a surprisingly wide substrate range and is more active towards cellopentaose compared to xylopentaose. This substrate promiscuity is unique for the GH10 family and could prove useful in industrial applications. Emphasizing the versatility of AMOR_GH10A, its N-terminal domain binds to both xylans and glycans, while not showing significant sequence similarities to any known carbohydrate-binding module (CBM) in the CAZy database. Thus, this N-terminal domain lays the foundation for the new CBM85 family.}, }
@article {pmid30635078, year = {2019}, author = {Zhao, L and Rosario, K and Breitbart, M and Duffy, S}, title = {Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range.}, journal = {Advances in virus research}, volume = {103}, number = {}, pages = {71-133}, doi = {10.1016/bs.aivir.2018.10.001}, pmid = {30635078}, issn = {1557-8399}, abstract = {While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.}, }
@article {pmid30635058, year = {2019}, author = {Simon, JC and Marchesi, JR and Mougel, C and Selosse, MA}, title = {Host-microbiota interactions: from holobiont theory to analysis.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {5}, doi = {10.1186/s40168-019-0619-4}, pmid = {30635058}, issn = {2049-2618}, abstract = {In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series &quot;Host-microbiota interactions: from holobiont theory to analysis,&quot; we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.}, }
@article {pmid30635018, year = {2019}, author = {Akorli, J and Namaali, PA and Ametsi, GW and Egyirifa, RK and Pels, NAP}, title = {Generational conservation of composition and diversity of field-acquired midgut microbiota in Anopheles gambiae (sensu lato) during colonization in the laboratory.}, journal = {Parasites &amp; vectors}, volume = {12}, number = {1}, pages = {27}, doi = {10.1186/s13071-019-3287-0}, pmid = {30635018}, issn = {1756-3305}, support = {DEL-15-007: Awandare//DELTAS Africa/ ; }, abstract = {BACKGROUND: The gut microbiota is known to play a role in a mosquito vector's life history, a subject of increasing research. Laboratory experiments are essential for such studies and require laboratory colonies. In this study, the conservation of field-obtained midgut microbiota was evaluated in laboratory-reared Anopheles gambiae (s.l.) mosquitoes continuously hatched in water from field breeding habitats.<br><br>METHODS: Pupae and late instars were obtained from the field and reared, and the emerged adults were blood-fed. The eggs obtained from them were hatched in either water from the field or in dechlorinated tap water. The mosquito colonies were maintained for 10 generations. Midguts of female adults from unfed F0 (emerging from field-caught pupae and larvae), F5 and F10 were dissected out and genomic DNA was extracted for 16S metagenomic sequencing. The sequences were compared to investigate the diversity and bacterial compositional differences using ANCOM and correlation clustering methods.<br><br>RESULTS: Less than 10% of the bacterial families identified had differential relative abundances between generational groups and accounted for 46% of the variation observed. Although diversity reduced in F10 mosquitoes during laboratory colonization (Shannon-Weaver; P-value < 0.05), 50% of bacterial genera were conserved in those bred continuously in field-water compared to 38% in those bred in dechlorinated tap water.<br><br>CONCLUSIONS: To our knowledge, this study is the first report on the assessment of gut bacterial community of mosquitoes during laboratory colonization and recommends the use of water from the natural breeding habitats if they are intended for microbiota research.}, }
@article {pmid30635006, year = {2019}, author = {Brinkmann, A and Hekimoğlu, O and Dinçer, E and Hagedorn, P and Nitsche, A and Ergünay, K}, title = {A cross-sectional screening by next-generation sequencing reveals Rickettsia, Coxiella, Francisella, Borrelia, Babesia, Theileria and Hemolivia species in ticks from Anatolia.}, journal = {Parasites &amp; vectors}, volume = {12}, number = {1}, pages = {26}, doi = {10.1186/s13071-018-3277-7}, pmid = {30635006}, issn = {1756-3305}, support = {not applicable//Alexander von Humboldt-Stiftung (DE)/ ; }, abstract = {BACKGROUND: Ticks participate as arthropod vectors in the transmission of pathogenic microorganisms to humans. Several tick-borne infections have reemerged, along with newly described agents of unexplored pathogenicity. In an attempt to expand current information on tick-associated bacteria and protozoans, we performed a cross-sectional screening of ticks, using next-generation sequencing. Ticks seeking hosts and infesting domestic animals were collected in four provinces across the Aegean, Mediterranean and Central Anatolia regions of Turkey and analyzed by commonly used procedures and platforms.<br><br>RESULTS: Two hundred and eighty ticks comprising 10 species were evaluated in 40 pools. Contigs from tick-associated microorganisms were detected in 22 (55%) questing and 4 feeding (10%) tick pools, with multiple microorganisms identified in 12 pools. Rickettsia 16S ribosomal RNA gene, gltA, sca1 and ompA sequences were present in 7 pools (17.5%), comprising feeding Haemaphysalis parva and questing/hunting Rhipicephalus bursa, Rhipicephalus sanguineus (sensu lato) and Hyalomma marginatum specimens. A near-complete genome and conjugative plasmid of a Rickettsia hoogstraalii strain could be characterized in questing Ha. parva. Coxiella-like endosymbionts were identified in pools of questing (12/40) as well as feeding (4/40) ticks of the genera Rhipicephalus, Haemaphysalis and Hyalomma. Francisella-like endosymbionts were also detected in 22.5% (9/40) of the pools that comprise hunting Hyalomma ticks in 8 pools. Coxiella-like and Francisella-like endosymbionts formed phylogenetically distinct clusters associated with their tick hosts. Borrelia turcica was characterized in 5% (2/40) of the pools, comprising hunting Hyalomma aegyptium ticks. Co-infection of Coxiella-like endosymbiont and Babesia was noted in a questing R. sanguineus (s.l.) specimen. Furthermore, protozoan 18S rRNA gene sequences were detected in 4 pools of questing/hunting ticks (10%) and identified as Babesia ovis, Hemolivia mauritanica, Babesia and Theileria spp.<br><br>CONCLUSIONS: Our metagenomic approach enabled identification of diverse pathogenic and non-pathogenic microorganisms in questing and feeding ticks in Anatolia.}, }
@article {pmid30632609, year = {2019}, author = {Hamada, T and Nowak, JA and Milner, DA and Song, M and Ogino, S}, title = {Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms.}, journal = {The Journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1002/path.5236}, pmid = {30632609}, issn = {1096-9896}, abstract = {Molecular pathological epidemiology (MPE) is an integrative transdisciplinary field that addresses heterogeneous effects of exogenous and endogenous factors (collectively termed &quot;exposures&quot;), including microorganisms, on disease occurrence and consequence utilising molecular pathological signatures of the disease. In parallel with the paradigm of precision medicine, findings from MPE research can provide aetiological insights into tailored strategies of disease prevention and treatment. Due to the availability of molecular pathological tests on tumours, the MPE approach has been utilised predominantly in research on cancers including breast, lung, prostate, and colorectal carcinomas. Mounting evidence indicates that the microbiome (inclusive of viruses, bacteria, fungi, and parasites) plays an important role in a variety of human diseases including neoplasms. An alteration of the microbiome may be not only a cause of neoplasia but also an informative biomarker that indicates or mediates the association of an epidemiological exposure with health conditions and outcomes. To adequately educate and train investigators in this emerging area, we herein propose the integration of microbiology into the MPE model (termed &quot;microbiology-MPE&quot;), which can improve our understanding of the complex interactions of environment, tumour cells, the immune system, and microbes in the tumour microenvironment during the carcinogenic process. Using this approach, we can examine how lifestyle factors, dietary patterns, medications, environmental exposures, and germline genetics influence cancer development and progression through impacting the microbial communities in the human body. Further integration of other disciplines (e.g. pharmacology, immunology, nutrition) into microbiology-MPE would expand this developing research frontier. With the advent of high-throughput next-generation sequencing technologies, researchers now have increasing access to large-scale metagenomics as well as other omics data (e.g. genomics, epigenomics, proteomics, and metabolomics) in population-based research. The integrative field of microbiology-MPE will open new opportunities for personalised medicine and public health.}, }
@article {pmid30632017, year = {2019}, author = {Altan, E and Seguin, MA and Leutenegger, CM and Phan, TG and Deng, X and Delwart, E}, title = {Nasal virome of dogs with respiratory infection signs include novel taupapillomaviruses.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11262-019-01634-6}, pmid = {30632017}, issn = {1572-994X}, support = {5149.14//Blood Systems Research Institute/ ; }, abstract = {Using viral metagenomics, we characterized the mammalian virome of nasal swabs from 57 dogs with unexplained signs of respiratory infection showing mostly negative results using the IDEXX Canine Respiratory Disease RealPCR™ Panel. We identified canine parainfluenza virus 5, canine respiratory coronavirus, carnivore bocaparvovirus 3, canine circovirus and canine papillomavirus 9. Novel canine taupapillomaviruses (CPV21-23) were also identified in 3 dogs and their complete genome sequenced showing L1 nucleotide identity ranging from 68.4 to 70.3% to their closest taupapillomavirus relative. Taupapillomavirus were the only mammalian viral nucleic acids detected in two affected dogs, while a third dog was coinfected with low levels of canine parainfluenza 5. A role for these taupapillomavirues in canine respiratory disease remains to be determined.}, }
@article {pmid30631958, year = {2019}, author = {Haddad-Boubaker, S and Joffret, ML and Pérot, P and Bessaud, M and Meddeb, Z and Touzi, H and Delpeyroux, F and Triki, H and Eloit, M}, title = {Metagenomic analysis identifies human adenovirus 31 in children with acute flaccid paralysis in Tunisia.}, journal = {Archives of virology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00705-018-04141-5}, pmid = {30631958}, issn = {1432-8798}, support = {ANR-10-LABX-62-IBEID//Instituto Nacional de Biotecnologia Estrutural e Química Medicinal em Doenças Infecciosas (BR)/ ; S-CM15010-05B//Fondation Total/ ; }, abstract = {A variety of viruses can cause acute flaccid paralysis (AFP). However, the causative agent, sometimes, remains undetermined. Metagenomics helps in identifying viruses not diagnosed by conventional methods. Stool samples from AFP (n = 104) and non-AFP (n = 114) cases that tested enterovirus-negative by WHO standard methods were investigated. A metagenomics approach, first used on five pools of four samples each, revealed the presence of adenovirus sequences. Amplification in A549 cells and full-genome sequencing were used for complete virus identification and for designing a PCR assay to screen individual related samples. Metagenomic analysis showed that adenovirus sequences that were closely to the A31 and A61 genotypes were the most abundant. Two out of the corresponding 20 individual samples were found positive by PCR, and isolates were obtained in cell culture. Phylogenetic analysis based on complete genome sequences showed that the viruses belong to HAdV-A31 genotype (98-100% nucleotide sequence identity). PCR analysis of stool samples from all AFP and non-AFP cases revealed that a larger proportion of the positive samples were from AFP cases (17.3%) than from non-AFP cases (2.4%). These results open the way to studies aiming to test a possible role of HAdV-A31 in the pathogenesis of AFP.}, }
@article {pmid30631769, year = {2018}, author = {Klaumann, F and Correa-Fiz, F and Franzo, G and Sibila, M and Núñez, JI and Segalés, J}, title = {Current Knowledge on Porcine circovirus 3 (PCV-3): A Novel Virus With a Yet Unknown Impact on the Swine Industry.}, journal = {Frontiers in veterinary science}, volume = {5}, number = {}, pages = {315}, doi = {10.3389/fvets.2018.00315}, pmid = {30631769}, issn = {2297-1769}, abstract = {Porcine circovirus 3 (PCV-3) is a recently described virus belonging to the family Circoviridae. It represents the third member of genus Circovirus able to infect swine, together with PCV-1, considered non-pathogenic, and PCV-2, one of the most economically relevant viruses for the swine worldwide industry. PCV-3 was originally found by metagenomics analyses in 2015 in tissues of pigs suffering from porcine dermatitis and nephropathy syndrome, reproductive failure, myocarditis and multisystemic inflammation. The lack of other common pathogens as potential infectious agents of these conditions prompted the suspicion that PCV-3 might etiologically be involved in disease occurrence. Subsequently, viral genome was detected in apparently healthy pigs, and retrospective studies indicated that PCV-3 was already present in pigs by early 1990s. In fact, current evidence suggests that PCV-3 is a rather widespread virus worldwide. Recently, the virus DNA has also been found in wild boar, expanding the scope of infection susceptibility among the Suidae family; also, the potential reservoir role of this species for the domestic pig has been proposed. Phylogenetic studies with available PCV-3 partial and complete sequences from around the world have revealed high nucleotide identity (>96%), although two main groups and several subclusters have been described as well. Moreover, it has been proposed the existence of a most common ancestor dated around 50 years ago. Taking into account the economic importance and the well-known effects of PCV-2 on the swine industry, a new member of the same family like PCV-3 should not be neglected. Studies on epidemiology, pathogenesis, immunity and diagnosis are guaranteed in the next few years. Therefore, the present review will update the current knowledge and future trends of research on PCV-3.}, }
@article {pmid30631651, year = {2019}, author = {Gardner, PP and Watson, RJ and Morgan, XC and Draper, JL and Finn, RD and Morales, SE and Stott, MB}, title = {Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6160}, doi = {10.7717/peerj.6160}, pmid = {30631651}, issn = {2167-8359}, abstract = {Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.}, }
@article {pmid30631318, year = {2018}, author = {Shao, L and Ling, Z and Chen, D and Liu, Y and Yang, F and Li, L}, title = {Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3166}, doi = {10.3389/fmicb.2018.03166}, pmid = {30631318}, issn = {1664-302X}, abstract = {Early detection and effective interventions for liver cirrhosis (LC) remain an urgent unmet clinical need. Inspired from intestinal disorders in LC patients, we investigated the associations between gut microbiome and disease progression based on a raw metagenomic dataset of 47 healthy controls, 49 compensated, and 46 decompensated LC patients from our previous study, and a metabolomic dataset of urine samples from the same controls/patients using ultra-performance liquid chromatography/mass spectrophotometry system. It was found that the combination and relative abundance of gut microbiome, the inter-microbiome regulatory networks, and the microbiome-host correlation patterns varied during disease progression. The significant reduction of bacteria involved in fermentation of plant cell wall polysaccharides and resistant starch (such as Alistipes sp. HG5, Clostridium thermocellum) contributed to the reduced supply of energy sources, the disorganized self-feeding and cross-feeding networks and the thriving of some opportunistic pathogens in genus Veillonella. The marked decrease of butyrate-producing bacteria and increase of Ruminococcus gnavus implicated in degradation of elements from the mucus layer provided an explanation for the impaired intestinal barrier function and systematic inflammation in LC patients. Our results pave the way for further developments in early detection and intervention of LC targeting on gut microbiome.}, }
@article {pmid30631102, year = {2019}, author = {Weiland-Bräuer, N and Fischer, MA and Pinnow, N and Schmitz, RA}, title = {Potential role of host-derived quorum quenching in modulating bacterial colonization in the moon jellyfish Aurelia aurita.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {34}, doi = {10.1038/s41598-018-37321-z}, pmid = {30631102}, issn = {2045-2322}, abstract = {Multicellular organisms can be regarded as metaorganisms, comprising of a macroscopic host interacting with associated microorganisms. Within this alliance, the host has to ensure attracting beneficial bacteria and defending against pathogens to establish and maintain a healthy homeostasis. Here, we obtained several lines of evidence arguing that Aurelia aurita uses interference with bacterial quorum sensing (QS) - quorum quenching (QQ) - as one host defense mechanism. Three A. aurita-derived proteins interfering with bacterial QS were identified by functionally screening a metagenomic library constructed from medusa-derived mucus. Native expression patterns of these host open reading frames (ORFs) differed in the diverse life stages (associated with different microbiota) pointing to a specific role in establishing the developmental stage-specific microbiota. Highly increased expression of all QQ-ORFs in germ-free animals further indicates their impact on the microbiota. Moreover, incubation of native animals with pathogenic bacteria induced expression of the identified QQ-ORFs arguing for a host defense strategy against confronting bacteria by interference with bacterial QS. In agreement, immobilized recombinant QQ proteins induced restructuring of polyp-associated microbiota through changing abundance and operational taxonomic unit composition. Thus, we hypothesize that additional to the immune system host-derived QQ-activities potentially control bacterial colonization.}, }
@article {pmid30630933, year = {2019}, author = {Jiang, X and Hall, AB and Arthur, TD and Plichta, DR and Covington, CT and Poyet, M and Crothers, J and Moses, PL and Tolonen, AC and Vlamakis, H and Alm, EJ and Xavier, RJ}, title = {Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut.}, journal = {Science (New York, N.Y.)}, volume = {363}, number = {6423}, pages = {181-187}, doi = {10.1126/science.aau5238}, pmid = {30630933}, issn = {1095-9203}, abstract = {Phase variation, the reversible alternation between genetic states, enables infection by pathogens and colonization by commensals. However, the diversity of phase variation remains underexplored. We developed the PhaseFinder algorithm to quantify DNA inversion-mediated phase variation. A systematic search of 54,875 bacterial genomes identified 4686 intergenic invertible DNA regions (invertons), revealing an enrichment in host-associated bacteria. Invertons containing promoters often regulate extracellular products, underscoring the importance of surface diversity for gut colonization. We found invertons containing promoters regulating antibiotic resistance genes that shift to the ON orientation after antibiotic treatment in human metagenomic data and in vitro, thereby mitigating the cost of antibiotic resistance. We observed that the orientations of some invertons diverge after fecal microbiota transplant, potentially as a result of individual-specific selective forces.}, }
@article {pmid30629718, year = {2019}, author = {Gruenstaeudl, M and Hartmaring, Y}, title = {EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210347}, doi = {10.1371/journal.pone.0210347}, pmid = {30629718}, issn = {1932-6203}, abstract = {BACKGROUND: The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant and fungal DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant and fungal DNA barcoding.<br><br>METHODS: A Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called 'checklists') for a subsequent upload to the annotated sequence section of the European Nucleotide Archive (ENA). The software tool, titled 'EMBL2checklists', automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates files that can be uploaded via the interactive Webin submission system of ENA.<br><br>RESULTS: EMBL2checklists provides a simple, platform-independent tool that automates the conversion of common DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in four recent investigations, including plant phylogenetic and fungal metagenomic studies.<br><br>DISCUSSION: EMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant and fungal biologists without bioinformatics expertise to generate submission-ready checklists from common DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.}, }
@article {pmid30629604, year = {2019}, author = {Mayday, MY and Khan, LM and Chow, ED and Zinter, MS and DeRisi, JL}, title = {Miniaturization and optimization of 384-well compatible RNA sequencing library preparation.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0206194}, doi = {10.1371/journal.pone.0206194}, pmid = {30629604}, issn = {1932-6203}, abstract = {Preparation of high-quality sequencing libraries is a costly and time-consuming component of metagenomic next generation sequencing (mNGS). While the overall cost of sequencing has dropped significantly over recent years, the reagents needed to prepare sequencing samples are likely to become the dominant expense in the process. Furthermore, libraries prepared by hand are subject to human variability and needless waste due to limitations of manual pipetting volumes. Reduction of reaction volumes, combined with sub-microliter automated dispensing of reagents without consumable pipette tips, has the potential to provide significant advantages. Here, we describe the integration of several instruments, including the Labcyte Echo 525 acoustic liquid handler and the iSeq and NovaSeq Illumina sequencing platforms, to miniaturize and automate mNGS library preparation, significantly reducing the cost and the time required to prepare samples. Through the use of External RNA Controls Consortium (ERCC) spike-in RNAs, we demonstrated the fidelity of the miniaturized preparation to be equivalent to full volume reactions. Furthermore, detection of viral and microbial species from cell culture and patient samples was also maintained in the miniaturized libraries. For 384-well mNGS library preparations, we achieved cost savings of over 80% in materials and reagents alone, and reduced preparation time by 90% compared to manual approaches, without compromising quality or representation within the library.}, }
@article {pmid30629185, year = {2019}, author = {Stewart, CJ and Mansbach, JM and Ajami, NJ and Petrosino, JF and Zhu, Z and Liang, L and Camargo, CA and Hasegawa, K}, title = {Serum metabolome is associated with nasopharyngeal microbiota and disease severity among infants with bronchiolitis.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiz021}, pmid = {30629185}, issn = {1537-6613}, abstract = {Background: Emerging evidence suggests relations of nasopharyngeal metabolome and microbiota with bronchiolitis severity. However, the influence of host systemic metabolism on disease pathobiology remains unclear. We aimed to examine metabolome profiles and their association with higher severity, defined by use of positive pressure ventilation (PPV), in infants hospitalized for bronchiolitis.<br><br>Methods: In 140 infants with bronchiolitis, metabolomic profiling was performed on serum: n=70 in the training dataset and n=70 independent samples in the test dataset. We also profiled the nasopharyngeal airway microbiota and examined its association with the serum metabolites.<br><br>Results: Serum metabolome profiles differed by bronchiolitis severity (P<0.001). In total, 20 metabolites in the training dataset were significantly associated with the risk of PPV and 18 metabolites remained significant following adjustment for confounders (FDR<0.10). Phosphatidylcholine metabolites were associated with higher risks of PPV use, while metabolites from the plasmalogen sub-pathway were associated with lower risks. The test dataset validated these findings (FDR<0.05). Streptococcus abundance was positively associated with metabolites that are associated with higher risks of PPV.<br><br>Conclusions: Serum metabolomic signatures were associated with both the nasopharyngeal microbiota and bronchiolitis severity. Our findings advance research into the complex interrelations between airway microbiome, host systemic response, and pathobiology of bronchiolitis.}, }
@article {pmid30627872, year = {2019}, author = {Wang, Q and Wang, K and Wu, W and Giannoulatou, E and Ho, JWK and Li, L}, title = {Host and microbiome multi-omics integration: applications and methodologies.}, journal = {Biophysical reviews}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12551-018-0491-7}, pmid = {30627872}, issn = {1867-2450}, support = {81330011, 81330014, 81790631, 81790633, 81570512, and 81121002//National Natural Science Foundation of China/ ; 81721091//Science Fund for Creative Research Groups/ ; 100848//National Heart Foundation of Australia/ ; 101204//National Heart Foundation of Australia/ ; }, abstract = {The study of the microbial community-the microbiome-associated with a human host is a maturing research field. It is increasingly clear that the composition of the human's microbiome is associated with various diseases such as gastrointestinal diseases, liver diseases and metabolic diseases. Using high-throughput technologies such as next-generation sequencing and mass spectrometry-based metabolomics, we are able to comprehensively sequence the microbiome-the metagenome-and associate these data with the genomic, epigenomics, transcriptomic and metabolic profile of the host. Our review summarises the application of integrating host omics with microbiome as well as the analytical methods and related tools applied in these studies. In addition, potential future directions are discussed.}, }
@article {pmid30626904, year = {2019}, author = {Delgado, B and Bach, A and Guasch, I and González, C and Elcoso, G and Pryce, JE and Gonzalez-Recio, O}, title = {Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11}, doi = {10.1038/s41598-018-36673-w}, pmid = {30626904}, issn = {2045-2322}, abstract = {The current research was carried out to determine the associations between the rumen microbiota and traits related with feed efficiency in a Holstein cattle population (n = 30) using whole metagenome sequencing. Improving feed efficiency (FE) is important for a more sustainable livestock production. The variability for the efficiency of feed utilization in ruminants is partially controlled by the gastrointestinal microbiota. Modulating the microbiota composition can promote a more sustainable and efficient livestock. This study revealed that most efficient cows had larger relative abundance of Bacteroidetes (P = 0.041) and Prevotella (P = 0.003), while lower, but non-significant (P = 0.119), relative abundance of Firmicutes. Methanobacteria (P = 0.004) and Methanobrevibacter (P = 0.003) were also less abundant in the high-efficiency cows. A de novo metagenome assembly was carried out using de Bruijn graphs in MEGAHIT resulting in 496,375 contigs. An agnostic pre-selection of microbial contigs allowed high classification accuracy for FE and intake levels using hierarchical classification. These microbial contigs were also able to predict FE and intake levels with accuracy of 0.19 and 0.39, respectively, in an independent population (n = 31). Nonetheless, a larger potential accuracy up to 0.69 was foreseen in this study for datasets that allowed a larger statistical power. Enrichment analyses showed that genes within these contigs were mainly involved in fatty acids and cellulose degradation pathways. The findings indicated that there are differences between the microbiota compositions of high and low-efficiency animals both at the taxonomical and gene levels. These differences are even more evident in terms of intake levels. Some of these differences remain even between populations under different diets and environments, and can provide information on the feed utilization performance without information on the individual intake level.}, }
@article {pmid30626868, year = {2019}, author = {Singh, R and Chandrashekharappa, S and Bodduluri, SR and Baby, BV and Hegde, B and Kotla, NG and Hiwale, AA and Saiyed, T and Patel, P and Vijay-Kumar, M and Langille, MGI and Douglas, GM and Cheng, X and Rouchka, EC and Waigel, SJ and Dryden, GW and Alatassi, H and Zhang, HG and Haribabu, B and Vemula, PK and Jala, VR}, title = {Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {89}, doi = {10.1038/s41467-018-07859-7}, pmid = {30626868}, issn = {2041-1723}, abstract = {The importance of gut microbiota in human health and pathophysiology is undisputable. Despite the abundance of metagenomics data, the functional dynamics of gut microbiota in human health and disease remain elusive. Urolithin A (UroA), a major microbial metabolite derived from polyphenolics of berries and pomegranate fruits displays anti-inflammatory, anti-oxidative, and anti-ageing activities. Here, we show that UroA and its potent synthetic analogue (UAS03) significantly enhance gut barrier function and inhibit unwarranted inflammation. We demonstrate that UroA and UAS03 exert their barrier functions through activation of aryl hydrocarbon receptor (AhR)- nuclear factor erythroid 2-related factor 2 (Nrf2)-dependent pathways to upregulate epithelial tight junction proteins. Importantly, treatment with these compounds attenuated colitis in pre-clinical models by remedying barrier dysfunction in addition to anti-inflammatory activities. Cumulatively, the results highlight how microbial metabolites provide two-pronged beneficial activities at gut epithelium by enhancing barrier functions and reducing inflammation to protect from colonic diseases.}, }
@article {pmid30626052, year = {2019}, author = {Cheong, DE and Park, SY and Lim, HD and Kim, GJ}, title = {An Alternative Platform for Protein Expression Using an Innate Whole Expression Module from Metagenomic DNA.}, journal = {Microorganisms}, volume = {7}, number = {1}, pages = {}, doi = {10.3390/microorganisms7010009}, pmid = {30626052}, issn = {2076-2607}, support = {NRF-2017030616//The Intelligent Synthetic Biology Center program of the National Research Foundation (NRF) funded by the Ministry of Science/ ; 20170305//ICT &amp; Future Planning and by a grant from the Marine Biotechnology Program funded by the Ministry of Oceans and Fisheries, Korea/ ; 2017R1D1A1B03035338//Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Education/ ; }, abstract = {Many integrated gene clusters beyond a single genetic element are commonly trapped as the result of promoter traps in (meta)genomic DNA libraries. Generally, a single element, which is mainly the promoter, is deduced from the resulting gene clusters and employed to construct a new expression vector. However, expression patterns of target proteins under the incorporated promoter are often inconsistent with those shown in clones harboring plasmids with gene clusters. These results suggest that the integrated set of gene clusters with diverse cis- and trans-acting elements is evolutionarily tuned as a complete set for gene expression, and is an expression module with all the components for the expression of a nested open reading frame (ORF). This possibility is further supported by truncation and/or serial deletion analysis of this module in which the expression of the nested ORF is highly fluctuated or reduced frequently, despite being supported by plentiful cis-acting elements in the spanning regions around the ORF such as the promoter, ribosome binding site (RBS), terminator, and 3'-/5'-UTRs for gene expression. Here, we examined whether an innate module with a naturally overexpressed gene could be considered as a scaffold for an expression system. For a proof-of-principle study, we mined a complete expression module with an innately overexpressed ORF in E. coli from a metagenomics DNA library, and incorporated it into a vector that had no regulatory element for expressing the insert. We obtained successful expression of several inserts such as MBP, GFPuv, β-glucosidase, and esterase using this simple construct without tuning and codon optimization of the target insert.}, }
@article {pmid30626002, year = {2019}, author = {Rechenberger, J and Samaras, P and Jarzab, A and Behr, J and Frejno, M and Djukovic, A and Sanz, J and González-Barberá, EM and Salavert, M and López-Hontangas, JL and Xavier, KB and Debrauwer, L and Rolain, JM and Sanz, M and Garcia-Garcera, M and Wilhelm, M and Ubeda, C and Kuster, B}, title = {Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae.}, journal = {Proteomes}, volume = {7}, number = {1}, pages = {}, doi = {10.3390/proteomes7010002}, pmid = {30626002}, issn = {2227-7382}, support = {031L0089//Bundesministerium für Bildung und Forschung/ ; }, abstract = {The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date, and the first metaproteomic study addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable future addition to the analysis of patient cohorts.}, }
@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}, 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 {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 {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 {pmid30625356, year = {2019}, author = {Jia, ML and Zhong, XL and Lin, ZW and Dong, BX and Li, G}, title = {Expression and characterization of an esterase belonging to a new family via isolation from a metagenomic library of paper mill sludge.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijbiomac.2019.01.025}, pmid = {30625356}, issn = {1879-0003}, abstract = {A new bacterial lipolytic enzyme Est903 was obtained from paper mill sludge via metagenomic approach. Est903 displayed moderate similarities to two lipolytic enzymes from Rhodopirellula islandica and contained a distinctive pentapeptide motif (GFSAG) that differed from those of all known fourteen families of bacterial lipolytic enzymes. Est903 was regarded as from a new bacterial lipolytic enzyme family through multiple sequence alignment and phylogenetic analysis. The recombinant Est903 showed the highest activity for ρ-nitrophenol butyrate. The pH optimum and temperature optimum of the recombinant enzyme was 9.0 and 51 °C, respectively. Also, this enzyme displayed moderate thermostability, high activity under alkaline conditions, and good tolerance against several organic solvents. In addition, the compatibility test and washing performance analysis revealed that Est903 had good compatibility with commercial laundry detergent and high cleaning ability of oil stains. These good properties make Est903 a potential candidate in organic synthesis or detergent industry.}, }
@article {pmid30624643, year = {2019}, author = {Baldrian, P}, title = {The known and the unknown in soil microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz005}, pmid = {30624643}, issn = {1574-6941}, abstract = {The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions. Also the analysis of processes exemplified by enzyme activity measurements is still imperfect. In the future, it is important to look at soil at a finer detail to obtain a better picture on the properties of individual microbes, their in situ interactions, metabolic rates and activity at a scale relevant to individual microbes. Scaling up is needed as well to get answers at ecosystem or biome levels and to enable global modelling. The recent development of novel tools including metabolomics, identification of genomes in metagenomics sequencing datasets or collection of trait data have the potential to bring soil ecology further. It will, however, always remain a highly demanding scientific discipline.}, }
@article {pmid30623484, year = {2019}, author = {Zhai, J and Knox, K and Twigg, HL and Zhou, H and Zhou, JJ}, title = {Exact variance component tests for longitudinal microbiome studies.}, journal = {Genetic epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/gepi.22185}, pmid = {30623484}, issn = {1098-2272}, support = {DMS-1645093//National Science Foundation/ ; GM105785//National Institute of General Medical Sciences/ ; GM053275//National Institute of General Medical Sciences/ ; HG006139//National Human Genome Research Institute/ ; K01DK106116//National Institute of Diabetes and Digestive and Kidney Diseases/ ; New Investigator Award//Arizona Biomedical Research Commission/ ; }, abstract = {In metagenomic studies, testing the association between microbiome composition and clinical outcomes translates to testing the nullity of variance components. Motivated by a lung human immunodeficiency virus (HIV) microbiome project, we study longitudinal microbiome data by using variance component models with more than two variance components. Current testing strategies only apply to models with exactly two variance components and when sample sizes are large. Therefore, they are not applicable to longitudinal microbiome studies. In this paper, we propose exact tests (score test, likelihood ratio test, and restricted likelihood ratio test) to (a) test the association of the overall microbiome composition in a longitudinal design and (b) detect the association of one specific microbiome cluster while adjusting for the effects from related clusters. Our approach combines the exact tests for null hypothesis with a single variance component with a strategy of reducing multiple variance components to a single one. Simulation studies demonstrate that our method has a correct type I error rate and superior power compared to existing methods at small sample sizes and weak signals. Finally, we apply our method to a longitudinal pulmonary microbiome study of HIV-infected patients and reveal two interesting genera Prevotella and Veillonella associated with forced vital capacity. Our findings shed light on the impact of the lung microbiome on HIV complexities. The method is implemented in the open-source, high-performance computing language Julia and is freely available at https://github.com/JingZhai63/VCmicrobiome.}, }
@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 = {}, number = {}, pages = {}, 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/ ; }, 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 {pmid30623212, year = {2019}, author = {de Sousa, AGG and Tomasino, MP and Duarte, P and Fernández-Méndez, M and Assmy, P and Ribeiro, H and Surkont, J and Leite, RB and Pereira-Leal, JB and Torgo, L and Magalhães, C}, title = {Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-01314-2}, pmid = {30623212}, issn = {1432-184X}, support = {244646//Research Council of Norway/ ; NORTE-01-0145-FEDER-000031//Structured Program of R&amp;D&amp;I MarInfo/ ; Arktis 2030//Norwegian Ministries of Foreign Affairs and Climate and Environment/ ; NITROLIMIT - PTDC 2017 - PTDC/CTA-AMB/30997/2017//Funda??o para a Ci?ncia e a Tecnologia/ ; }, abstract = {One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.}, }
@article {pmid30622518, year = {2018}, author = {Fujiwara, K and Iwanami, T and Fujikawa, T}, title = {Alterations of Candidatus Liberibacter asiaticus-Associated Microbiota Decrease Survival of Ca. L. asiaticus in in vitro Assays.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3089}, doi = {10.3389/fmicb.2018.03089}, pmid = {30622518}, issn = {1664-302X}, abstract = {Phloem-inhabiting bacterial phytopathogens often have smaller genomes than other bacterial phytopathogens. It is thought that they depend on both other phloem microbiota and phloem nutrients for colonization of the host. However, the mechanism underlying associations between phloem-inhabiting phytopathogens and other phloem microbiota are poorly understood. Here, we demonstrate that the survival of Candidatus Liberibacter asiaticus (CLas), a cause of huanglongbing (citrus greening disease), depends on interplay with a specific subset of CLas-associated microbiota. CLas was not susceptible to oxytetracycline in vitro. However, oxytetracycline treatment eliminated a particular sub-community dominated by the Comamonadaceae, Flavobacteriaceae, Microbacteriaceae, and Pseudomonadaceae, decreasing CLas survival. We speculate that CLas uses ecological services derived from CLas-associated microbiota to colonize the host and to construct a pathogen-associated community that stimulates disease development.}, }
@article {pmid30622259, year = {2019}, author = {Karkman, A and Pärnänen, K and Larsson, DGJ}, title = {Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {80}, doi = {10.1038/s41467-018-07992-3}, pmid = {30622259}, issn = {2041-1723}, abstract = {Discharge of treated sewage leads to release of antibiotic resistant bacteria, resistance genes and antibiotic residues to the environment. However, it is unclear whether increased abundance of antibiotic resistance genes in sewage and sewage-impacted environments is due to on-site selection pressure by residual antibiotics, or is simply a result of fecal contamination with resistant bacteria. Here we analyze relative resistance gene abundance and accompanying extent of fecal pollution in publicly available metagenomic data, using crAssphage sequences as a marker of human fecal contamination (crAssphage is a bacteriophage that is exceptionally abundant in, and specific to, human feces). We find that the presence of resistance genes can largely be explained by fecal pollution, with no clear signs of selection in the environment, with the exception of environments polluted by very high levels of antibiotics from manufacturing, where selection is evident. Our results demonstrate the necessity to take into account fecal pollution levels to avoid making erroneous assumptions regarding environmental selection of antibiotic resistance.}, }
@article {pmid30622080, year = {2019}, author = {Cota-Ruiz, K and López de Los Santos, Y and Hernández-Viezcas, JA and Delgado-Rios, M and Peralta-Videa, JR and Gardea-Torresdey, JL}, title = {A comparative metagenomic and spectroscopic analysis of soils from an international point of entry between the US and Mexico.}, journal = {Environment international}, volume = {123}, number = {}, pages = {558-566}, doi = {10.1016/j.envint.2018.12.055}, pmid = {30622080}, issn = {1873-6750}, abstract = {The Paso del Norte region is characterized by its dynamic industries and active agriculture. Throughout the years, urban and agricultural soils from this region have been exposed to xenobiotics, heavy metals, and excess of hydrocarbons. In this study, samples of urban [domestic workshops (DW)] and agricultural-intended (AI) soils from different sites of Ciudad Juárez, Mexico were evaluated for their fertility, element content, and microbial diversity. Chemical analyses showed that nitrites, nitrates, P, K, Mg, and Mn were predominantly higher in AI soils, compared to DW soils (p ≤ 0.05). The composition of soil microbial communities showed that Proteobacteria phylum was the most abundant in both soils (67%, p ≤ 0.05). In AI soils, Paracoccus denitrificans was reduced (p ≤ 0.05), concurring with an increment in nitrates, while the content of nitrogen was negatively correlated with the rhizobium group (r2 = -0.65, p ≤ 0.05). In DW soils, the Firmicutes phylum represented up to ~25%, and the relative abundance of Proteobacteria strongly correlated with a higher Cu content (r2 = 0.99, p ≤ 0.0001). The monotypic genus Sulfuricurvum was found only in oil-contaminated soil samples. Finally, all samples showed the presence of the recently created phylum Candidatus saccharibacteria. These results describe the productivity parameters of AI soils and its correlation to the microbial diversity, which are very important to understand and potentiate the productivity of soils. The data also suggest that soils impacted with hydrocarbons and metal(oid)s allow the reproduction of microorganisms with the potential to alleviate contaminated sites.}, }
@article {pmid30621881, year = {2019}, author = {Jagadeesan, B and Gerner-Smidt, P and Allard, MW and Leuillet, S and Winkler, A and Xiao, Y and Chaffron, S and Van Der Vossen, J and Tang, S and Katase, M and McClure, P and Kimura, B and Ching Chai, L and Chapman, J and Grant, K}, title = {The use of next generation sequencing for improving food safety: Translation into practice.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {96-115}, doi = {10.1016/j.fm.2018.11.005}, pmid = {30621881}, issn = {1095-9998}, abstract = {Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.}, }
@article {pmid30621868, year = {2019}, author = {Ottesen, A and Ramachandran, P and Reed, E and Gu, G and Gorham, S and Ducharme, D and Newell, M and Rideout, S and Turini, T and Hill, T and Strain, E and Brown, E}, title = {Metagenome tracking biogeographic agroecology: Phytobiota of tomatoes from Virginia, Maryland, North Carolina and California.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {132-136}, doi = {10.1016/j.fm.2018.12.001}, pmid = {30621868}, issn = {1095-9998}, abstract = {Describing baseline microbiota associated with agricultural commodities in the field is an important step towards improving our understanding of a wide range of important objectives from plant pathology and horticultural sustainability, to food safety. Environmental pressures on plants (wind, dust, drought, water, temperature) vary by geography and characterizing the impact of these variable pressures on phyllosphere microbiota will contribute to improved stewardship of fresh produce for both plant and human health. A higher resolution understanding of the incidence of human pathogens on food plants and co-occurring phytobiota using metagenomic approaches (metagenome tracking) may contribute to improved source attribution and risk assessment in cases where human pathogens become introduced to agro-ecologies. Between 1990 and 2007, as many as 1990 culture-confirmed Salmonella illnesses were linked to tomatoes from as many as 12 multistate outbreaks (Bell et al., 2012; Bell et al., 2015; Bennett et al., 2014; CDC, 2004; CDC, 2007; Greene et al., 2005a; Gruszynski et al., 2014). When possible, source attribution for these incidents revealed a biogeographic trend, most events were associated with eastern growing regions. To improve our understanding of potential biogeographically linked trends in contamination of tomatoes by Salmonella, we profiled microbiota from the surfaces of tomatoes from Virginia, Maryland, North Carolina and California. Bacterial profiles from California tomatoes were completely different than those of Maryland, Virginia and North Carolina (which were highly similar to each other). A statistically significant enrichment of Firmicutes taxa was observed in California phytobiota compared to the three eastern states. Rhizobiaceae, Sphingobacteriaceae and Xanthobacteraceae were the most abundant bacterial families associated with tomatoes grown in eastern states. These baseline metagenomic profiles of phyllosphere microbiota may contribute to improved understanding of how certain ecologies provide supportive resources for human pathogens on plants and how components of certain agro-ecologies may play a role in the introduction of human pathogens to plants.}, }
@article {pmid30621867, year = {2019}, author = {Marino, M and Dubsky de Wittenau, G and Saccà, E and Cattonaro, F and Spadotto, A and Innocente, N and Radovic, S and Piasentier, E and Marroni, F}, title = {Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {123-131}, doi = {10.1016/j.fm.2018.12.007}, pmid = {30621867}, issn = {1095-9998}, abstract = {The microbiota of different types of Italian high-moisture Mozzarella cheese produced using cow or buffalo milk, acidified with natural or selected cultures, and sampled at the dairy or at the mass market, was evaluated using a Next Generation Sequencing approach, in order to identify possible drivers of the bacterial diversity. Cow Mozzarella and buffalo Mozzarella acidified with commercial cultures were dominated by Streptococcus thermophilus, while buffalo samples acidified with natural whey cultures showed similar prevalence of L. delbrueckii subsp. bulgaricus, L. helveticus and S. thermophilus. Moreover, several species of non-starter lactic acid bacteria were frequently detected. The diversity in cow Mozzarella microbiota was much higher than that of water buffalo samples. Cluster analysis clearly separated cow's cheeses from buffalo's ones, the former having a higher prevalence of psychrophilic taxa, and the latter of Lactobacillus and Streptococcus. A higher prevalence of psychrophilic species and potential spoilers was observed in samples collected at the mass retail, suggesting that longer exposures to cooling temperatures and longer production-to-consumption times could significantly affect microbiota diversity. Our results could help in detecting some kind of thermal abuse during the production or storage of mozzarella cheese.}, }
@article {pmid30621760, year = {2018}, author = {Gerner, SM and Rattei, T and Graf, AB}, title = {Assessment of urban microbiome assemblies with the help of targeted in silico gold standards.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {22}, doi = {10.1186/s13062-018-0225-6}, pmid = {30621760}, issn = {1745-6150}, support = {Call 19-19 Project UrbanMetagenApp//MA23/ ; }, abstract = {BACKGROUND: Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metagenome samples. The only in silico approach that allows us to find unknown species, is the assembly and classification of draft genomes from a metagenomic dataset. In this study we (1) investigate the applicability of an assembly and binning approach for urban metagenome datasets, and (2) develop a new method for the generation of in silico gold standards to better understand the specific challenges of such datasets and provide a guide in the selection of available software.<br><br>RESULTS: We applied combinations of three assembly (Megahit, SPAdes and MetaSPAdes) and three binning tools (MaxBin, MetaBAT and CONCOCT) to whole genome shotgun datasets from the CAMDA 2017 Challenge. Complex in silico gold standards with a simulated bacterial fraction were generated for representative samples of each surface type and city. Using these gold standards, we found the combination of SPAdes and MetaBAT to be optimal for urban metagenome datasets by providing the best trade-off between the number of high-quality genome draft bins (MIMAG standards) retrieved, the least amount of misassemblies and contamination. The assembled draft genomes included known species like Propionibacterium acnes but also novel species according to respective ANI values.<br><br>CONCLUSIONS: In our work, we showed that, even for datasets with high diversity and low sequencing depth from urban environments, assembly and binning-based methods can provide high-quality genome drafts. Of vital importance to retrieve high-quality genome drafts is sequence depth but even more so a high proportion of the bacterial sequence fraction too achieve high coverage for bacterial genomes. In contrast to read-based methods relying on database knowledge, genome-centric methods as applied in this study can provide valuable information about unknown species and strains as well as functional contributions of single community members within a sample. Furthermore, we present a method for the generation of sample-specific highly complex in silico gold standards.<br><br>REVIEWERS: This article was reviewed by Craig Herbold, Serghei Mangul and Yana Bromberg.}, }
@article {pmid30621600, year = {2019}, author = {Imhann, F and Van der Velde, KJ and Barbieri, R and Alberts, R and Voskuil, MD and Vich Vila, A and Collij, V and Spekhorst, LM and der Sloot Kwj, V and Peters, V and Van Dullemen, HM and Visschedijk, MC and Eam, F and Swertz, MA and Dijkstra, G and Weersma, RK}, title = {The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1.}, journal = {BMC gastroenterology}, volume = {19}, number = {1}, pages = {5}, doi = {10.1186/s12876-018-0917-5}, pmid = {30621600}, issn = {1471-230X}, support = {016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 92.003.577//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; MLDS D16-14//Maag Lever Darm Stichting/ ; CD14-04//Maag Lever Darm Stichting (NL)/ ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal tract. Patients with IBD can experience a wide range of symptoms, but the pathophysiological mechanisms that cause these individual differences in clinical presentation remain largely unknown. In consequence, IBD is currently classified into subtypes using clinical characteristics. If we are to develop a more targeted treatment approach, molecular subtypes of IBD need to be discovered that can be used as new drug targets. To achieve this, we need multiple layers of molecular data generated from the same IBD patients.<br><br>CONSTRUCTION AND CONTENT: We initiated the 1000IBD project (https://1000ibd.org) to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, we have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1215 participants have been enrolled in the project and enrolment is on-going. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing.<br><br>UTILITY AND DISCUSSION: All molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive (https://ega-archive.org , accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. Future releases will comprise many more additional phenotypes and -omics data layers. 1000IBD data can be used by other researchers as a replication cohort, a dataset to test new software tools, or a dataset for applying new statistical models.<br><br>CONCLUSIONS: We report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets.}, }
@article {pmid30620035, year = {2019}, author = {Huo, L and Hug, JJ and Fu, C and Bian, X and Zhang, Y and Müller, R}, title = {Heterologous expression of bacterial natural product biosynthetic pathways.}, journal = {Natural product reports}, volume = {}, number = {}, pages = {}, doi = {10.1039/c8np00091c}, pmid = {30620035}, issn = {1460-4752}, abstract = {Covering: 2013 to June 2018Heterologous expression of natural product biosynthetic pathways is of increasing interest in microbial biotechnology, drug discovery and optimization. It empowers not only the robust production of valuable biomolecules in more amenable heterologous hosts but also permits the generation of novel analogs through biosynthetic engineering. This strategy also facilitates the discovery of novel bioactive compounds following the functional expression of cryptic biosynthetic gene clusters (BGCs) from fastidious original producers or metagenomic DNA in surrogate hosts, thus facilitating genome mining in the post-genomic era. This review discusses recent advances and trends pertaining to the heterologous production of bacterial natural products, with an emphasis on new techniques, heterologous hosts, and novel chemistry since 2013.}, }
@article {pmid30619927, year = {2019}, author = {Kadnikov, VV and Mardanov, AV and Frank, YA and Beletsky, AV and Karnachuk, OV and Ravin, NV}, title = {Genomes of three bacteriophages from the deep subsurface aquifer.}, journal = {Data in brief}, volume = {22}, number = {}, pages = {488-491}, doi = {10.1016/j.dib.2018.12.045}, pmid = {30619927}, issn = {2352-3409}, abstract = {Viral particles have been detected in the underground biosphere where they could be one of the main factors impacting microbial diversity, biogeochemistry and evolution. To characterize the viral component in the deep subsurface biosphere, we sequenced the metagenome of subsurface aquifer located in the Tomsk region of Russia, sampled via 2.8-km-deep borehole 5P. The de novo assembly of metagenomics sequences yielded three circular genomes assigned to bacteriophages of the order Caudovirales. The annotated genome sequences of these bacteriophages have been deposited in the GenBank database under the accession numbers MK113949, MK113950 and MK113951.}, }
@article {pmid30619848, year = {2018}, author = {Nishiyama, E and Higashi, K and Mori, H and Suda, K and Nakamura, H and Omori, S and Maruyama, S and Hongoh, Y and Kurokawa, K}, title = {The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {6}, number = {}, pages = {202}, doi = {10.3389/fbioe.2018.00202}, pmid = {30619848}, issn = {2296-4185}, abstract = {Diverse microorganisms specifically inhabit extreme environments, such as hot springs and deep-sea hydrothermal vents. To test the hypothesis that the microbial community structure is predictable based on environmental factors characteristic of such extreme environments, we conducted correlation analyses of microbial taxa/functions and environmental factors using metagenomic and 61 types of physicochemical data of water samples from nine hot springs in the Kirishima area (Kyusyu, Japan), where hot springs with diverse chemical properties are distributed in a relatively narrow area. Our metagenomic analysis revealed that the samples can be classified into two major types dominated by either phylum Crenarchaeota or phylum Aquificae. The correlation analysis showed that Crenarchaeota dominated in nutrient-rich environments with high concentrations of ions and total carbons, whereas Aquificae dominated in nutrient-poor environments with low ion concentrations. These environmental factors were also important explanatory variables in the generalized linear models constructed to predict the abundances of Crenarchaeota or Aquificae. Functional enrichment analysis of genes also revealed that the separation of the two major types is primarily attributable to genes involved in autotrophic carbon fixation, sulfate metabolism and nitrate reduction. Our results suggested that Aquificae and Crenarchaeota play a vital role in the Kirishima hot spring water ecosystem through their metabolic pathways adapted to each environment. Our findings provide a basis to predict microbial community structures in hot springs from environmental parameters, and also provide clues for the exploration of biological resources in extreme environments.}, }
@article {pmid30619804, year = {2018}, author = {Bachmann, NL and Rockett, RJ and Timms, VJ and Sintchenko, V}, title = {Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics.}, journal = {Frontiers in public health}, volume = {6}, number = {}, pages = {363}, doi = {10.3389/fpubh.2018.00363}, pmid = {30619804}, issn = {2296-2565}, abstract = {Whole genome sequencing (WGS) plays an increasing role in communicable disease control through high-resolution outbreak tracing, laboratory surveillance and diagnostics. However, WGS has traditionally relied on microbial culture in order to obtain pathogen specific DNA for sequencing. This has severely limited the application of whole genome sequencing on pathogens with fastidious culturing requirements. In addition, the widespread adoption of culture-independent diagnostic tests has reduced availability of cultured isolates for confirmatory testing and surveillance. These recent developments have created demand for the implementation of techniques enabling direct sequencing of microbial genomes in clinical samples without having to culture an isolate. However, sequencing of specific organisms from clinical samples can be affected by high levels of contaminating DNA from the host and other commensal microorganisms. Several methods have been introduced for selective lysis of host cells and/or separate specific organisms from a clinical sample. This review examines the different approaches for sample preparation that have been used in diagnostic and public health laboratories for metagenomic sequencing.}, }
@article {pmid30619779, year = {2018}, author = {Hu, YL and Pang, W and Huang, Y and Zhang, Y and Zhang, CJ}, title = {The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {433}, doi = {10.3389/fcimb.2018.00433}, pmid = {30619779}, issn = {2235-2988}, abstract = {Objective: Dysbiosis of gastric microbiota such as Helicobacter pylori plays a significant role in pathogenesis and progression of gastric cancer. Our aim was to evaluate the composition and functional effects of gastric microbiota in superficial gastritis (SG) and advanced gastric adenocarcinoma (GC). Methods: We carried out shotgun metagenomic sequencing on gastric wash samples from 6 patients with GC and 5 patients with SG. The taxonomic composition was profiled using MetaPhlAn2 and functional gene pathway was profiled using HUMAnN2. Differences in microbial composition and pathways between the two patient groups were assessed via LEfSe. Results: The gastric microbiota in GC patients was characterized by reduced species richness, enrichment of 13 bacterial taxa and depletion of 31 taxa (q < 0.05). The most representative taxa which were abundant in GC corresponded to the commensals or opportunistic pathogens that usually colonize the oral cavity, including genera Neisseria, Alloprevotella, and Aggregatibacter, species Streptococcus_mitis_oralis_pneumoniae and strain Porphyromonas_endodontalis.t_GCF_000174815. Each of the three GC-associated genera could separate GC from SG completely. In particular, Sphingobium yanoikuyae, a bacterium capable of degrading carcinogenic compounds, was depleted in GC. Functionally, pathways associated with the biosynthesis of lipopolysaccharide (LPS) and L-arginine were enriched in GC, whereas pathways involved in the fermentation of short chain fatty acids (SCFAs) and branched amino acid metabolism were more abundant in SG. Conclusions: Our results present new alterations in the gastric microbiome in patients with GC from a whole-genome perspective, suggesting that microbiome composition and function can be used for prognosis and diagnosis of GC.}, }
@article {pmid30619503, year = {2018}, author = {Cai, FF and Zhou, WJ and Wu, R and Su, SB}, title = {Systems biology approaches in the study of Chinese herbal formulae.}, journal = {Chinese medicine}, volume = {13}, number = {}, pages = {65}, doi = {10.1186/s13020-018-0221-x}, pmid = {30619503}, issn = {1749-8546}, abstract = {Systems biology is an academic field that attempts to integrate different levels of information to understand how biological systems function. It is the study of the composition of all components of a biological system and their interactions under specific conditions. The core of systems biology is holistic and systematic research, which is different from the manner of thinking and research of all other branches of biology to date. Chinese herbal formulae (CHF) are the main form of Chinese medicine and are composed of single Chinese herbal medicines (CHMs) with pharmacological and pharmacodynamic compatibility. When single CHMs are combined into CHF, the result is different from the original effect of a single drug and can be better adapted to more diseases with complex symptoms. CHF represent a complex system with multiple components, targets and effects. Therefore, the use of systems biology is conducive to revealing the complex characteristics of CHF. With the rapid development of omics technologies, systems biology has been widely and increasingly applied to the study of the basis of the pharmacological substances, action targets and mechanisms of CHF. To meet the challenges of multiomics synthesis-intensive studies and system dynamics research in CHF, this paper reviews the common techniques of genomics, transcriptomics, proteomics, metabolomics, and metagenomics and their applications in research on CHF.}, }
@article {pmid30619215, year = {2018}, author = {Han, M and Yang, P and Zhong, C and Ning, K}, title = {The Human Gut Virome in Hypertension.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3150}, doi = {10.3389/fmicb.2018.03150}, pmid = {30619215}, issn = {1664-302X}, abstract = {Objectives: Previous studies have reported that the gut microbiome has an important link with the development of hypertension. Though previous researches have focused on the links of gut bacteria with hypertension, little has been known about the linkage of gut viruses to hypertension and the development of hypertension, largely due to the lack of data mining tools for such investigation. In this work, we have analyzed 196 fecal metagenomic data related to hypertension aiming to profile the gut virome and link the gut virome to pre-hypertension and hypertension. Design: Here, we have applied a statistically sound method for mining of gut virome data and linking gut virome to hypertension. We characterized the viral composition and bacterial composition of 196 samples, identified the viral-type of each sample and linked gut virome to hypertension. Results: We stratified these 196 fecal samples into two viral-types and selected 32 viruses as the biomarkers for these groups. We found that viruses could have a superior resolution and discrimination power than bacteria for differentiation of healthy samples and pre-hypertension samples, as well as hypertension samples. Moreover, as to the co-occurrence networks linking viruses and bacteria, we found increasingly pervasive virus-bacteria linkages from healthy people to pre-hypertension people to hypertension patients. Conclusion: Overall, our results have shown ample indications of the link between human gut virome and hypertension, and could help provide microbial solutions toward early diagnoses of hypertension.}, }
@article {pmid30619209, year = {2018}, author = {Suzuki, S and Nealson, KH and Ishii, S}, title = {Genomic and in-situ Transcriptomic Characterization of the Candidate Phylum NPL-UPL2 From Highly Alkaline Highly Reducing Serpentinized Groundwater.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3141}, doi = {10.3389/fmicb.2018.03141}, pmid = {30619209}, issn = {1664-302X}, abstract = {Serpentinization is a process whereby water interacts with reduced mantle rock called peridotite to produce a new suite of minerals (e.g., serpentine), a highly alkaline fluid, and hydrogen. In previous reports, we identified abundance of microbes of the candidate phylum NPL-UPA2 in a serpentinization site called The Cedars. Here, we report the first metagenome assembled genome (MAG) of the candidate phylum as well as the in-situ gene expression. The MAG of the phylum NPL-UPA2, named Unc8, is only about 1 Mbp and its biosynthetic properties suggest it should be capable of independent growth. In keeping with the highly reducing niche of Unc8, its genome encodes none of the known oxidative stress response genes including superoxide dismutases. With regard to energy metabolism, the MAG of Unc8 encodes all enzymes for Wood-Ljungdahl acetogenesis pathway, a ferredoxin:NAD+ oxidoreductase (Rnf) and electron carriers for flavin-based electron bifurcation (Etf, Hdr). Furthermore, the transcriptome of Unc8 in the waters of The Cedars showed enhanced levels of gene expression in the key enzymes of the Wood-Ljungdahl pathway [e.g., Carbon monoxide dehydrogenase /Acetyl-CoA synthase complex (CODH/ACS), Rnf, Acetyl-CoA synthetase (Acd)], which indicated that the Unc8 is an acetogen. However, the MAG of Unc8 encoded no well-known hydrogenase genes, suggesting that the energy metabolism of Unc8 might be focused on CO as the carbon and energy sources for the acetate formation. Given that CO could be supplied via abiotic reaction associated with deep subsurface serpentinization, while available CO2 would be at extremely low concentrations in this high pH environment, CO-associated metabolism could provide advantageous approach. The CODH/ACS in Unc8 is a Bacteria/Archaea hybrid type of six-subunit complex and the electron carriers, Etf and Hdr, showed the highest similarity to those in Archaea, suggesting that archaeal methanogenic energy metabolism was incorporated into the bacterial acetogenesis in NPL-UPA2. Given that serpentinization systems are viewed as potential habitats for early life, and that acetogenesis via the Wood-Ljungdahl pathway is proposed as an energy metabolism of Last Universal Common Ancestor, a phylogenetically distinct acetogen from an early earth analog site may provide important insights in primordial lithotrophs and their habitat.}, }
@article {pmid30619206, year = {2018}, author = {Guo, M and Chen, J and Li, Q and Fu, Y and Fan, G and Ma, J and Peng, L and Zeng, L and Chen, J and Wang, Y and Lee, SM}, title = {Dynamics of Gut Microbiome in Giant Panda Cubs Reveal Transitional Microbes and Pathways in Early Life.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3138}, doi = {10.3389/fmicb.2018.03138}, pmid = {30619206}, issn = {1664-302X}, abstract = {Adult giant pandas (Ailuropoda melanoleuca) express transitional characteristics in that they consume bamboos, despite their carnivore-like digestive tracts. Their genome contains no cellulolytic enzymes; therefore, understanding the development of the giant panda gut microbiome, especially in early life, is important for decoding the rules underlying gut microbial formation, inheritance and dietary transitions. With deep metagenomic sequencing, we investigated the gut microbiomes of two newborn giant panda brothers and their parents living in Macao, China, from 2016 to 2017. Both giant panda cubs exhibited progressive increases in gut microbial richness during growth, particularly from the 6th month after birth. Enterobacteriaceae dominated the gut microbial compositions in both adult giant pandas and cubs. A total of 583 co-abundance genes (CAGs) and about 79 metagenomic species (MGS) from bacteria or viruses displayed significant changes with age. Seven genera (Shewanella, Oblitimonas, Helicobacter, Haemophilus, Aeromonas, Listeria, and Fusobacterium) showed great importance with respect to gut microbial structural determination in the nursing stage of giant panda cubs. Furthermore, 10 orthologous gene functions and 44 pathways showed significant changes with age. Of the significant pathways, 16 from Escherichia, Klebsiella, Propionibacterium, Lactobacillus, and Lactococcus displayed marked differences between parents and their cubs at birth, while 29 pathways from Escherichia, Campylobacter and Lactobacillus exhibited significant increase in cubs from 6 to 9 months of age. In addition, oxidoreductases, transferases, and hydrolases dominated the significantly changed gut microbial enzymes during the growth of giant panda cubs, while few of them were involved in cellulose degradation. The findings indicated diet-stimulated gut microbiome transitions and the important role of Enterobacteriaceae in the guts of giant panda in early life.}, }
@article {pmid30619174, year = {2018}, author = {Sharma, A and Schmidt, M and Kiesel, B and Mahato, NK and Cralle, L and Singh, Y and Richnow, HH and Gilbert, JA and Arnold, W and Lal, R}, title = {Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3095}, doi = {10.3389/fmicb.2018.03095}, pmid = {30619174}, issn = {1664-302X}, abstract = {Hot spring-associated viruses, particularly the archaeal viruses, remain under-examined compared to bacteriophages. Previous metagenomic studies of the Manikaran hot springs in India suggested an abundance of viral DNA, which prompted us to examine the virus-host (bacterial and archaeal) interactions in sediment and microbial mat samples collected from the thermal discharges. Here, we characterize the viruses (both bacterial and archaeal) from this Himalayan hot spring using both metagenomics assembly and electron microscopy. We utilized four shotgun samples from sediment (78-98°C) and two from microbial mats (50°C) to reconstruct 65 bacteriophage genomes (24-200 kb). We also identified 59 archaeal viruses that were notably abundant across the sediment samples. Whole-genome analyses of the reconstructed bacteriophage genomes revealed greater genomic conservation in sediments (65%) compared to microbial mats (49%). However, a minimal phage genome was still maintained across both sediment and microbial mats suggesting a common origin. To complement the metagenomic data, scanning-electron and helium-ion microscopy were used to reveal diverse morphotypes of Caudovirales and archaeal viruses. The genome level annotations provide further evidence for gene-level exchange between virus and host in these hot springs, and augments our knowledgebase for bacteriophages, archaeal viruses and Clustered Regularly Interspaced Short Palindromic Repeat cassettes, which provide a critical resource for studying viromes in extreme natural environments.}, }
@article {pmid30619142, year = {2018}, author = {Nasko, DJ and Chopyk, J and Sakowski, EG and Ferrell, BD and Polson, SW and Wommack, KE}, title = {Family A DNA Polymerase Phylogeny Uncovers Diversity and Replication Gene Organization in the Virioplankton.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3053}, doi = {10.3389/fmicb.2018.03053}, pmid = {30619142}, issn = {1664-302X}, abstract = {Shotgun metagenomics, which allows for broad sampling of viral diversity, has uncovered genes that are widely distributed among virioplankton populations and show linkages to important biological features of unknown viruses. Over 25% of known dsDNA phage carry the DNA polymerase I (polA) gene, making it one of the most widely distributed phage genes. Because of its pivotal role in DNA replication, this enzyme is linked to phage lifecycle characteristics. Previous research has suggested that a single amino acid substitution might be predictive of viral lifestyle. In this study Chesapeake Bay virioplankton were sampled by shotgun metagenomic sequencing (using long and short read technologies). More polA sequences were predicted from this single viral metagenome (virome) than from 86 globally distributed virome libraries (ca. 2,100, and 1,200, respectively). The PolA peptides predicted from the Chesapeake Bay virome clustered with 69% of PolA peptides from global viromes; thus, remarkably the Chesapeake Bay virome captured the majority of known PolA peptide diversity in viruses. This deeply sequenced virome also expanded the diversity of PolA sequences, increasing the number of PolA clusters by 44%. Contigs containing polA sequences were also used to examine relationships between phylogenetic clades of PolA and other genes within unknown viral populations. Phylogenic analysis revealed five distinct groups of phages distinguished by the amino acids at their 762 (Escherichia coli IAI39 numbering) positions and replication genes. DNA polymerase I sequences from Tyr762 and Phe762 groups were most often neighbored by ring-shaped superfamily IV helicases and ribonucleotide reductases (RNRs). The Leu762 groups had non-ring shaped helicases from superfamily II and were further distinguished by an additional helicase gene from superfamily I and the lack of any identifiable RNR genes. Moreover, we found that the inclusion of ribonucleotide reductase associated with PolA helped to further differentiate phage diversity, chiefly within lytic podovirus populations. Altogether, these data show that DNA Polymerase I is a useful marker for observing the diversity and composition of the virioplankton and may be a driving factor in the divergence of phage replication components.}, }
@article {pmid30619134, year = {2018}, author = {Porcar, M and Louie, KB and Kosina, SM and Van Goethem, MW and Bowen, BP and Tanner, K and Northen, TR}, title = {Microbial Ecology on Solar Panels in Berkeley, CA, United States.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3043}, doi = {10.3389/fmicb.2018.03043}, pmid = {30619134}, issn = {1664-302X}, abstract = {Solar panels can be found practically all over the world and represent a standard surface that can be colonized by microbial communities that are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations and desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also standard devices to study the microbial communities and their colonization process from different areas of Earth. We report here a comprehensive description of the microbial communities associated with solar panels in Berkeley, CA, United States. Cultivable bacteria were isolated to characterize their adhesive capabilities, and UV- and desiccation-resistance properties. Furthermore, a parallel culture-independent metagenomic and metabolomic approach has allowed us to gain insight on the taxonomic and functional nature of these communities. Metagenomic analysis was performed using the Illumina HiSeq2500 sequencing platform, revealing that the bacterial population of the Berkeley solar panels is composed mainly of Actinobacteria, Bacteroidetes and Proteobacteria, as well as lower amounts of Deinococcus-Thermus and Firmicutes. Furthermore, a clear predominance of Hymenobacter sp. was also observed. A functional analysis revealed that pathways involved in the persistence of microbes on solar panels (i.e., stress response, capsule development, and metabolite repair) and genes assigned to carotenoid biosynthesis were common to all metagenomes. On the other hand, genes involved in photosynthetic pathways and general autotrophic subsystems were rare, suggesting that these pathways are not critical for persistence on solar panels. Metabolomics was performed using a liquid chromatography tandem mass spectrometry (LC-MS/MS) approach. When comparing the metabolome of the solar panels from Berkeley and from Valencia (Spain), a very similar composition in polar metabolites could be observed, although some metabolites appeared to be differentially represented (for example, trigonelline, pantolactone and 5-valerolactone were more abundant in the samples from Valencia than in the ones from Berkeley). Furthermore, triglyceride metabolites were highly abundant in all the solar panel samples, and both locations displayed similar profiles. The comparison of the taxonomic profile of the Californian solar panels with those previously described in Spain revealed striking similarities, highlighting the central role of both selective pressures and the ubiquity of microbial populations in the colonization and establishment of microbial communities.}, }
@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}, 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 {pmid30619117, year = {2018}, author = {López-García, A and Pineda-Quiroga, C and Atxaerandio, R and Pérez, A and Hernández, I and García-Rodríguez, A and González-Recio, O}, title = {Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3010}, doi = {10.3389/fmicb.2018.03010}, pmid = {30619117}, issn = {1664-302X}, abstract = {Background: Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several tools are available, although the literature is scarce on studies that compare the performance of different bioinformatics pipelines on rumen microbiota when 16S rRNA amplicons are analyzed. The impact of the pipeline on the outcome of the results is also unknown, mainly in terms of the output from studies using these tools as an intermediate phenotype (pseudophenotypes). This study compares two commonly used software (Quantitative Insights Into Microbial Ecology) (QIIME) and mothur, and two microbial gene data bases (GreenGenes and SILVA) for 16S rRNA gene analysis, using metagenome read data collected from rumen content of a cohort of dairy cows. Results: We compared the relative abundance (RA) of the identified OTUs at the genus level. Both tools presented a high degree of agreement at identifying the most abundant genera: Bifidobacterium, Butyrivibrio, Methanobrevibacter, Prevotella, and Succiniclasticum (RA > 1%), regardless the database. There were no statistical differences between mothur and QIIME (P > 0.05) at estimating the overall RA of the most abundant (RA > 10%) genera, either using SILVA or GreenGenes. However, differences were found at RA < 10% (P < 0.05) when using GreenGenes as database, with mothur assigning OTUs to a larger number of genera and in larger RA for these less frequent microorganisms. With this database mothur resulted in larger richness (P < 0.05), more favorable rarefaction curves and a larger analytic sensitivity. These differences caused significant and relevant differences between tools at identifying the dissimilarity of microbiotas between pairs of animals. However, these differences were attenuated, but not erased, when SILVA was used as the reference database. Conclusion: The findings showed that the SILVA database seemed a preferred reference dataset for classifying OTUs from rumen microbiota. If this database was used, both QIIME and mothur produced comparable richness and diversity, and also in the RA of most common rumen microbes. However, important differences were found for less common microorganisms which impacted on the beta diversity calculated between pipelines. This may have relevant implications at studying global rumen microbiota.}, }
@article {pmid30619102, year = {2018}, author = {Gupta, A and Dutta, A and Sarkar, J and Panigrahi, MK and Sar, P}, title = {Low-Abundance Members of the Firmicutes Facilitate Bioremediation of Soil Impacted by Highly Acidic Mine Drainage From the Malanjkhand Copper Project, India.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2882}, doi = {10.3389/fmicb.2018.02882}, pmid = {30619102}, issn = {1664-302X}, abstract = {Sulfate- and iron-reducing heterotrophic bacteria represented minor proportion of the indigenous microbial community of highly acidic, oligotrophic acid mine drainage (AMD), but they can be successfully stimulated for in situ bioremediation of an AMD impacted soil (AIS). These anaerobic microorganisms although played central role in sulfate- and metal-removal, they remained inactive in the AIS due to the paucity of organic carbon and extreme acidity of the local environment. The present study investigated the scope for increasing the abundance and activity of inhabitant sulfate- and iron-reducing bacterial populations of an AIS from Malanjkhand Copper Project. An AIS of pH 3.5, high soluble SO42- (7838 mg/l) and Fe (179 mg/l) content was amended with nutrients (cysteine and lactate). Thorough geochemical analysis, 16S rRNA gene amplicon sequencing and qPCR highlighted the intrinsic metabolic abilities of native bacteria in AMD bioremediation. Following 180 days incubation, the nutrient amended AIS showed marked increase in pH (to 6.6) and reduction in soluble -SO42- (95%), -Fe (50%) and other heavy metals. Concomitant to physicochemical changes a vivid shift in microbial community composition was observed. Members of the Firmicutes present as a minor group (1.5% of total community) in AIS emerged as the single most abundant taxon (∼56%) following nutrient amendments. Organisms affiliated to Clostridiaceae, Peptococcaceae, Veillonellaceae, Christensenellaceae, Lachnospiraceae, Bacillaceae, etc. known for their fermentative, iron and sulfate reducing abilities were prevailed in the amended samples. qPCR data corroborated with this change and further revealed an increase in abundance of dissimilatory sulfite reductase gene (dsrB) and specific bacterial taxa. Involvement of these enhanced populations in reductive processes was validated by further enrichments and growth in sulfate- and iron-reducing media. Amplicon sequencing of these enrichments confirmed growth of Firmicutes members and proved their sulfate- and iron-reduction abilities. This study provided a better insight on ecological perspective of Firmicutes members within the AMD impacted sites, particularly their involvement in sulfate- and iron-reduction processes, in situ pH management and bioremediation.}, }
@article {pmid30618066, year = {2019}, author = {Flores-Uribe, J and Hevroni, G and Ghai, R and Pushkarev, A and Inoue, K and Kandori, H and Béjà, O}, title = {Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12730}, pmid = {30618066}, issn = {1758-2229}, abstract = {Microbial heliorhodopsins are a new type of rhodopsins, currently believed to engage in light sensing, with an opposite membrane topology compared to type-1 and type-2 rhodopsins. We determined heliorhodopsins presence/absence is monoderms and diderms representatives from the Tara Oceans and freshwater metagenomes as well as metagenome assembled genome collections. Heliorhodopsins are absent in diderms, confirming our previous observations in cultured Proteobacteria. We do not rule out the possibility that heliorhodopsins serve as light sensors. However, this does not easily explain their absence from diderms. Based on these observations, we speculate on the putative role of heliorhodopsins in light-driven transport of amphiphilic molecules. This article is protected by copyright. All rights reserved.}, }
@article {pmid30616913, year = {2018}, author = {Martinez, MA and Woodcroft, BJ and Ignacio Espinoza, JC and Zayed, AA and Singleton, CM and Boyd, JA and Li, YF and Purvine, S and Maughan, H and Hodgkins, SB and Anderson, D and Sederholm, M and Temperton, B and Bolduc, B and Saleska, SR and Tyson, GW and Rich, VI and ,  and Saleska, SR and Tyson, GW and Rich, VI}, title = {Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.syapm.2018.12.003}, pmid = {30616913}, issn = {1618-0984}, abstract = {The phylum Caldiserica was identified from the hot spring 16S rRNA gene lineage 'OP5' and named for the sole isolate Caldisericum exile, a hot spring sulfur-reducing chemoheterotroph. Here we characterize 7 Caldiserica metagenome-assembled genomes (MAGs) from a thawing permafrost site in Stordalen Mire, Arctic Sweden. By 16S rRNA and marker gene phylogenies, and average nucleotide and amino acid identities, these Stordalen Mire Caldiserica (SMC) MAGs form part of a divergent clade from C. exile. Genome and meta-transcriptome and proteome analyses suggest that unlike Caldisericum, the SMCs (i) are carbohydrate- and possibly amino acid fermenters that can use labile plant compounds and peptides, and (ii) encode adaptations to low temperature. The SMC clade rose to community dominance within permafrost, with a peak metagenome-based relative abundance of ∼60%. It was also physiologically active in the upper seasonally-thawed soil. Beyond Stordalen Mire, analysis of 16S rRNA gene surveys indicated a global distribution of this clade, predominantly in anaerobic, carbon-rich and cold environments. These findings establish the SMCs as four novel phenotypically and ecologically distinct species within a single novel genus, distinct from C. exile clade at the phylum level. The SMCs are thus part of a novel cold-habitat phylum for an understudied, globally-distributed superphylum encompassing the Caldiserica. We propose the names Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., Ca. Cryosericum gen. nov., Ca. Cryosericum septentrionale sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., and Ca. C. terrychapinii sp. nov.}, }
@article {pmid30453071, year = {2019}, author = {Aguilar, C and Miller, MJ and Loaiza, JR and Krahe, R and De León, LF}, title = {Mitogenomics of Central American weakly-electric fishes.}, journal = {Gene}, volume = {686}, number = {}, pages = {164-170}, doi = {10.1016/j.gene.2018.11.045}, pmid = {30453071}, issn = {1879-0038}, mesh = {Animals ; Cytochromes b/*genetics ; Electric Fish/*classification/*genetics ; Fish Proteins/*genetics ; *Metagenome ; *Phylogeny ; }, abstract = {Electric fishes are a diverse group of freshwater organisms with the ability to generate electric organ discharges (EODs) that are used for communication and electrolocation. This group (ca. 200 species) has originated in South America, and six species colonized the Central American Isthmus. Here, we assembled the complete mitochondrial genomes (mitogenomes) for three Central American electric fishes (i.e. Sternopygus dariensis, Brachyhypopomus occidentalis, and Apteronotus rostratus), and, based on these data, explored their phylogenetic position among Gymnotiformes. The three mitogenomes show the same gene order, as reported for other fishes, with a size ranging from 16,631 to 17,093 bp. We uncovered a novel 60 bp intergenic spacer (IGS) located between the COII and tRNALys genes, which appears to be unique to the Apteronotidae. Furthermore, phylogenetic relationships supported the traditional monophyly of Gymnotiformes, with the three species positioned within their respective family. In addition, the genus Apteronotus belongs to the early diverging lineage of the order. Finally, we found high sequence divergence (13%) between our B. occidentalis specimen and a sequence previously reported in GenBank, suggesting that the prior mitogenome of B. occidentalis represents a different South American species. Indeed, phylogenetic analyses using Cytochrome b gene across the genus placed the previously reported individual within B. bennetti. Our study provides novel mitogenome resources that will advance our understanding of the diversity and phylogenetic history of Neotropical fishes.}, }
@article {pmid30616051, year = {2018}, author = {Zhao, R and Feng, J and Liu, J and Fu, W and Li, X and Li, B}, title = {Deciphering of microbial community and antibiotic resistance genes in activated sludge reactors under high selective pressure of different antibiotics.}, journal = {Water research}, volume = {151}, number = {}, pages = {388-402}, doi = {10.1016/j.watres.2018.12.034}, pmid = {30616051}, issn = {1879-2448}, abstract = {Currently, the effects of high antibiotic concentrations on the performance of microbiota and antibiotic resistance genes (ARGs) in activated sludge (AS) process are not well characterized. Lab-scale batch reactors were performed to evaluate the dynamics of microbial community and ARGs in response to six antibiotics at different concentrations using high-throughput sequencing-based 16S rRNA gene and metagenomic analyses. The presence of antibiotics remarkably decreased the microbial diversity, caused a great change of the microbiota structure, and exerted a selective pressure on the enrichment of potential antibiotic resistant bacteria (ARB), such as Arthrobacter, Thauera, Geothrix, Rudaea, Aridibacter, Conexibacter, Terrimonas, etc. High antibiotic selective pressures increased ARG abundance but simultaneously reduced ARG number. In total, 491 ARG subtypes belonging to 20 ARG types were detected and kanamycin treatment showed the highest ARG abundances. A core set of 54 ARG subtypes that accounted for 66.7%-99.6% of the total ARG abundances were shared by all samples. The increase of the abundances of both corresponding and non-corresponding ARGs under a specific antibiotic treatment revealed the collateral effects of antibiotic selective pressure. Microbial community may play an important role in the composition of ARGs. Network analysis indicated that both internal-type and external-type of ARGs exhibited higher non-random co-occurrence incidences and 18 genera were speculated as the possible hosts for multiple ARGs. This study deciphered the profiles and relationships between microbial community and ARGs in AS process treating wastewater with high antibiotic concentrations and could provide helpful guidance for controlling the development and dissemination of ARB and ARGs.}, }
@article {pmid30612540, year = {2019}, author = {Singh, I and Kuscuoglu, M and Harkins, DM and Sutton, G and Fouts, DE and Nelson, KE}, title = {OMeta: an ontology-based, data-driven metadata tracking system.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {8}, doi = {10.1186/s12859-018-2580-9}, pmid = {30612540}, issn = {1471-2105}, support = {HHSN272200900007C,U19AI110819//National Institute of Allergy and Infectious Diseases/ ; }, abstract = {BACKGROUND: The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association studies which identify genetic determinants of pathogen virulence and drug resistance, as well as phylogenetic studies designed to track the origin and spread of disease outbreaks. These omics studies are complex and often employ multiple assay technologies including genomics, metagenomics, transcriptomics, proteomics, and metabolomics. To maximize the impact of omics studies, it is essential that data be accompanied by detailed contextual metadata (e.g., specimen, spatial-temporal, phenotypic characteristics) in clear, organized, and consistent formats. Over the years, many metadata standards developed by various metadata standards initiatives have arisen; the Genomic Standards Consortium's minimal information standards (MIxS), the GSCID/BRC Project and Sample Application Standard. Some tools exist for tracking metadata, but they do not provide event based capabilities to configure, collect, validate, and distribute metadata. To address this gap in the scientific community, an event based data-driven application, OMeta, was created that allows users to quickly configure, collect, validate, distribute, and integrate metadata.<br><br>RESULTS: A data-driven web application, OMeta, has been developed for use by researchers consisting of a browser-based interface, a command-line interface (CLI), and server-side components that provide an intuitive platform for configuring, capturing, viewing, and sharing metadata. Project and sample metadata can be set based on existing standards or based on projects goals. Recorded information includes details on the biological samples, procedures, protocols, and experimental technologies, etc. This information can be organized based on events, including sample collection, sample quantification, sequencing assay, and analysis results. OMeta enables configuration in various presentation types: checkbox, file, drop-box, ontology, and fields can be configured to use the National Center for Biomedical Ontology (NCBO), a biomedical ontology server. Furthermore, OMeta maintains a complete audit trail of all changes made by users and allows metadata export in comma separated value (CSV) format for convenient deposition of data into public databases.<br><br>CONCLUSIONS: We present, OMeta, a web-based software application that is built on data-driven principles for configuring and customizing data standards, capturing, curating, and sharing metadata.}, }
@article {pmid30462522, year = {2019}, author = {Shi, Z and Fultz, RS and Engevik, MA and Gao, C and Hall, A and Major, A and Mori-Akiyama, Y and Versalovic, J}, title = {Distinct roles of histamine H1- and H2-receptor signaling pathways in inflammation-associated colonic tumorigenesis.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {316}, number = {1}, pages = {G205-G216}, doi = {10.1152/ajpgi.00212.2018}, pmid = {30462522}, issn = {1522-1547}, abstract = {Inflammatory bowel disease (IBD) is a well-known risk factor for the development of colorectal cancer. Prior studies have demonstrated that microbial histamine can ameliorate intestinal inflammation in mice. We tested the hypothesis whether microbe-derived luminal histamine suppresses inflammation-associated colon cancer in Apcmin/+ mice. Mice were colonized with the human-derived Lactobacillus reuteri. Chronic inflammation was induced by repeated cycles of low-dose dextran sulfate sodium (DSS). Mice that were given histamine-producing L. reuteri via oral gavage developed fewer colonic tumors, despite the presence of a complex mouse gut microbiome. We further demonstrated that administration of a histamine H1-receptor (H1R) antagonist suppressed tumorigenesis, while administration of histamine H2-receptor (H2R) antagonist significantly increased both tumor number and size. The bimodal functions of histamine include protumorigenic effects through H1R and antitumorigenic effects via H2R, and these results were supported by gene expression profiling studies on tumor specimens of patients with colorectal cancer. Greater ratios of gene expression of H2R (HRH2) vs. H1R (HRH1) were correlated with improved overall survival outcomes in patients with colorectal cancer. Additionally, activation of H2R suppressed phosphorylation of mitogen-activated protein kinases (MAPKs) and inhibited chemokine gene expression induced by H1R activation in colorectal cancer cells. Moreover, the combination of a H1R antagonist and a H2R agonist yielded potent suppression of lipopolysaccharide-induced MAPK signaling in macrophages. Given the impact on intestinal epithelial and immune cells, simultaneous modulation of H1R and H2R signaling pathways may be a promising therapeutic target for the prevention and treatment of inflammation-associated colorectal cancer. NEW &amp; NOTEWORTHY Histamine-producing Lactobacillus reuteri can suppress development of inflammation-associated colon cancer in an established mouse model. The net effects of histamine may depend on the relative activity of H1R and H2R signaling pathways in the intestinal mucosa. Our findings suggest that treatment with H1R or H2R antagonists could yield opposite effects. However, by harnessing the ability to block H1R signaling while stimulating H2R signaling, novel strategies for suppression of intestinal inflammation and colorectal neoplasia could be developed.}, }
@article {pmid30297823, year = {2018}, author = {Peek, J and Lilic, M and Montiel, D and Milshteyn, A and Woodworth, I and Biggins, JB and Ternei, MA and Calle, PY and Danziger, M and Warrier, T and Saito, K and Braffman, N and Fay, A and Glickman, MS and Darst, SA and Campbell, EA and Brady, SF}, title = {Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4147}, pmid = {30297823}, issn = {2041-1723}, support = {P41 GM103403/GM/NIGMS NIH HHS/United States ; R35 GM118130//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; R01 GM114450/GM/NIGMS NIH HHS/United States ; R35 GM118130/GM/NIGMS NIH HHS/United States ; 5U01 GM110714//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; P30 CA008748/CA/NCI NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; OPP1117928//Bill and Melinda Gates Foundation/International ; S10 RR027037/RR/NCRR NIH HHS/United States ; 1R35 GM122559//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; R35 GM122559/GM/NIGMS NIH HHS/United States ; R01 GM114450//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; }, mesh = {Aminobenzoates/chemistry ; Antibiotics, Antitubercular/biosynthesis/chemistry/pharmacology ; Bacteria/genetics/metabolism ; Bacterial Proteins/antagonists &amp; inhibitors/genetics/metabolism ; DNA-Directed RNA Polymerases/antagonists &amp; inhibitors/genetics/metabolism ; Drug Resistance, Bacterial/*drug effects/genetics ; Humans ; Hydroxybenzoates/chemistry ; Metagenomics/methods ; Molecular Structure ; Mutation ; Mycobacterium tuberculosis/*drug effects/genetics/metabolism ; Rifampin/chemistry/metabolism/*pharmacology ; Rifamycins/chemistry/pharmacology ; Soil Microbiology ; Tuberculosis/microbiology/*prevention &amp; control ; }, abstract = {Rifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (RifR). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant RifR mutations. Our structural and mechanistic analyses reveal the basis for Kang inhibition of RifR RNAP. Unlike Rifs, Kangs function through a mechanism that includes interfering with 5'-initiating substrate binding. Our results suggest that examining soil microbiomes for new analogues of clinically used antibiotics may uncover metabolites capable of circumventing clinically important resistance mechanisms.}, }
@article {pmid30082726, year = {2018}, author = {Luijk, R and Dekkers, KF and van Iterson, M and Arindrarto, W and Claringbould, A and Hop, P and Boomsma, DI and van Duijn, CM and van Greevenbroek, MMJ and Veldink, JH and Wijmenga, C and Franke, L and 't Hoen, PAC and Jansen, R and van Meurs, J and Mei, H and Slagboom, PE and Heijmans, BT and van Zwet, EW and , }, title = {Genome-wide identification of directed gene networks using large-scale population genomics data.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3097}, pmid = {30082726}, issn = {2041-1723}, mesh = {Cohort Studies ; Endopeptidases/genetics ; Epistasis, Genetic ; Gene Expression ; Gene Expression Profiling ; Gene Expression Regulation ; *Gene Regulatory Networks ; *Genetics, Population ; Genotype ; Humans ; Linkage Disequilibrium ; *Metagenomics ; Minor Histocompatibility Antigens/genetics ; Phenotype ; Proto-Oncogene Proteins c-bcl-2/genetics ; Sequence Analysis, RNA ; Transcription Factors/genetics ; Transcription, Genetic ; Transcriptome ; Zinc Fingers ; }, abstract = {Identification of causal drivers behind regulatory gene networks is crucial in understanding gene function. Here, we develop a method for the large-scale inference of gene-gene interactions in observational population genomics data that are both directed (using local genetic instruments as causal anchors, akin to Mendelian Randomization) and specific (by controlling for linkage disequilibrium and pleiotropy). Analysis of genotype and whole-blood RNA-sequencing data from 3072 individuals identified 49 genes as drivers of downstream transcriptional changes (Wald P < 7 × 10-10), among which transcription factors were overrepresented (Fisher's P = 3.3 × 10-7). Our analysis suggests new gene functions and targets, including for SENP7 (zinc-finger genes involved in retroviral repression) and BCL2A1 (target genes possibly involved in auditory dysfunction). Our work highlights the utility of population genomics data in deriving directed gene expression networks. A resource of trans-effects for all 6600 genes with a genetic instrument can be explored individually using a web-based browser.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-01313-3}, pmid = {30612183}, issn = {1432-184X}, 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 {pmid30612083, year = {2018}, author = {Zhu, X and Campanaro, S and Treu, L and Kougias, PG and Angelidaki, I}, title = {Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics.}, journal = {Water research}, volume = {151}, number = {}, pages = {271-279}, doi = {10.1016/j.watres.2018.12.041}, pmid = {30612083}, issn = {1879-2448}, abstract = {In typical anaerobic digestion (AD) systems, the microbial functional assertion is hampered by synchronised versatile metabolism required for heterogeneous substrates degradation. Thus, the intricate methanogenic process from organic compounds remains an enigma after decades of empirical operation. In this study, simplified AD microbial communities were obtained with substrate specifications and continuous reactor operation. Genome-centric metagenomic approach was followed to holistically investigate the metabolic pathways of the AD and the microbial synergistic networks. In total, 63 metagenome assembled genomes (MAGs) were assembled from 8 metagenomes acquired in specific methanogenic niches. The metabolic pathways were reconstructed from the annotated genes and their dynamicity under experimental conditions. The results show that the methanogenic niches nourish unique metabolism beyond current knowledge acquired from cultivation-based methods. A novel glucose mineralization model without acetate formation was proposed and asserted in a pair of syntrophs: Clostridiaceae sp. and Methanoculleus thermophilus. Moreover, the catabolic pathway was elucidated in uncharacterized syntrophic acetate oxidizers, Synergistaceae spp. A remarkable evolutionary insight is the discovery that electron transport and energy conservation mechanisms impose selective pressure on syntrophic partners. Overall, the functional roles of the individual microbes tightly rely on the catabolic pathways and cannot always be physiologically defined in accordance with conventional four-step AD concept. The substrate-specific systems provided a traceable microbial community to dissecting the AD process. The genome-centric metagenomics successfully constructed genomes of microbes that have not been previously isolated and illustrated metabolic pathways that beyond the current knowledge of AD process. This study provides new perspectives to unravel the AD microbial ecology and suggests more attention should be paid on uncharacterized metabolism specifically harboured by AD microbial communities.}, }
@article {pmid30612042, year = {2018}, author = {Gahan, ME and Bowman, S and Chevalier, R and Rossi, R and Nelson, M and Roffey, P and Xu, B and Power, D and McNevin, D}, title = {Bacillus species at the Canberra Airport: A comparison of real-time polymerase chain reaction and massively parallel sequencing for identification.}, journal = {Forensic science international}, volume = {295}, number = {}, pages = {169-178}, doi = {10.1016/j.forsciint.2018.12.011}, pmid = {30612042}, issn = {1872-6283}, abstract = {Anthrax, caused by the Gram-positive, spore forming bacterium Bacillus anthracis, is a disease with naturally occurring outbreaks in many parts of the world, primarily in domestic and wild herbivores. Due to the movement of people and stock, B. anthracis could, however, be at transportation hubs including airports. The continuous threat to national and international security from a biological agent release, or hoax attack, is a very real concern. Sensitive, robust and rapid (hours-day) methods to identify biological agents, including B. anthracis, and distinguish pathogenic from non-pathogenic species, is an essential cornerstone to national security. The aim of this project was to determine the presence of Bacillus species at the Canberra Airport using two massively parallel sequencing (MPS) approaches and compare with previous results using real-time polymerase chain reaction (qPCR). Samples were collected daily for seven days each month from August 2011-July 2012 targeting movement of people, luggage and freight into and out of the Canberra Airport. Extracted DNA was analysed using qPCR specific for B. anthracis. A subset of samples was analysed using two MPS approaches. Approach one, using the Ion PGM™ (Thermo Fisher Scientific; TFS) and an in-house assay, targeted the two B. anthracis virulence plasmids (cya and capB genes) and a single conserved region of the 16S rRNA gene. Approach two, using the Ion S5™ (TFS) and the commercial Ion 16S™ Metagenomics Kit (TFS), targeted multiple regions within the bacterial 16S rRNA gene. Overall there was consistency between the two MPS approaches and between MPS and qPCR, however, MPS was more sensitive, particularly for plasmid detection. Whilst the broad-range 16S genomic target(s) used in both MPS approaches in this study was able to generate a metagenomic fingerprint of the bacterial community at the Canberra Airport, it could not resolve Bacillus species beyond the level of the Bacillus cereus group. The inclusion of B. anthracis virulence plasmid targets in the in-house assay did allow for the potential presumptive identifications of pathogenic species. No plasmid targets were in the Ion 16S™ Metagenomics Kit. This study shows the choice of target(s) is key in MPS assay development and should be carefully considered to ensure the assay is fit for purpose, whether as an initial screening (presumptive) or a more specific (but not entirely confirmatory) test. Identification approaches may also benefit from a combination of MPS and qPCR as each has benefits and limitations.}, }
@article {pmid30610394, year = {2019}, author = {Feng, R and Xu, M and Li, J and Huang, S and Zhao, G and Tu, X and Sun, G and Guo, J}, title = {Structure and predictive functional profiling of microbial communities in two biotrickling filters treated with continuous/discontinuous waste gases.}, journal = {AMB Express}, volume = {9}, number = {1}, pages = {2}, doi = {10.1186/s13568-018-0726-9}, pmid = {30610394}, issn = {2191-0855}, support = {U1701243//National Natural Science Foundation of China/ ; 2014A020216022//Science and Technology Project of Guangdong Province, China/ ; 2016B070701017//Science and Technology Project of Guangdong Province, China/ ; 2016A030310314//Science and Technology Project of Guangdong Province, China/ ; 201504010014//Science and Technology Project of Guangzhou/ ; 201704020204//Science and Technology Project of Guangzhou/ ; 201707010377//Science and Technology Project of Guangzhou/ ; }, abstract = {Two biotrickling filters were operated in continuous (BTF1) and discontinuous (BTF2) modes at a constant empty bed residence time of 60 s for 60 days. From day 60, the operation mode of each BTF was oppositely switched. Higher removal efficiencies of five aromatic pollutants were recorded with BTF1 (> 77.2%). The switch in the operation mode did not alter the removal performance of BTF1. Comparatively, BTF2 was not successfully acclimated in the discontinuous operation mode. Once the mode had been switched to continuous mode, the removal efficiencies of BTF2 on all pollutants increased drastically and finally exceeded the values observed in BTF1, with the single exception of p-xylene. Principle coordinate analysis and analysis of similarities (ANOSIM) showed that the structure of the microbial communities differed considerably between both BTFs (R = 1.000, p < 0.01) as well as before and after the switch in BTF2 (R = 0.996, p < 0.01). The random forest model demonstrated that Mycobacterium, Burkholderia, and Comamonas were the three most important bacterial genera contributing to the differences in microbial communities between the two BTFs. Metagenomics inferred by PICUSt (phylogenetic investigation of communities by reconstruction of unobserved states) indicated that BTF2 had high degradation potential for aromatic pollutants, although those genes involved in biofilm formation were less active in BTF2 than those in BTF1.}, }
@article {pmid30610284, year = {2019}, author = {Xia, Y and Tan, D and Akbary, R and Kong, J and Seviour, R and Kong, Y}, title = {Aqueous raw and ripe Pu-erh tea extracts alleviate obesity and alter cecal microbiota composition and function in diet-induced obese rats.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-018-09581-2}, pmid = {30610284}, issn = {1432-0614}, support = {ZD2015015//Yunnan Provincial Department of Education/ ; 2016FA052//Yunnan Provincial Science and Technology Department/ ; 31860029//National Natural Science Foundation of China/ ; }, abstract = {Pu-erh tea is attracting increased attention worldwide because of its unique flavor and health effects, but its impact on the composition and function of the gut microbiota remains unclear. The aim of this study was to investigate the effects of aqueous extracts of fermented (ripe) and non-fermented (raw) Pu-erh teas on the composition and function of the intestinal microbiota of rats with diet-induced obesity. We conducted a comparative metagenomic and meta-proteomic investigation of the microbial communities in cecal samples taken from obese rats treated with or without extracts of raw or ripe Pu-erh teas. By analyzing the composition and diversity of 16S rRNA amplicons and expression profiles of 814 distinct proteins, we found that despite differences in the chemical compositions of raw and ripe Pu-erh teas, administration of either tea at two doses (0.15- and 0.40-g/kg body weight) significantly (P < 0.05) increased microbial diversity and changed the composition of cecal microbiota by increasing the relative abundances of Firmicutes and decreasing those of Bacteroidetes. Community metabolic processes, including sucrose metabolism, glycolysis, and syntheses of proteins, rRNAs, and antibiotics were significantly (P < 0.05) promoted or had a tendency (0.10 < P < 0.05) to be promoted due to the enrichment of relevant enzymes. Furthermore, evidence at population, molecular, and metabolic levels indicated that polyphenols of raw Pu-erh tea and their metabolites potentially promote Akkermansia muciniphila growth by stimulating a type II and III secretion system protein, the elongation factor Tu, and a glyceraldehyde-3-phosphate dehydrogenase. This study provides new evidence for the prebiotic effects of Pu-erh tea.}, }
@article {pmid30609942, year = {2019}, author = {Yang, SH and Tandon, K and Lu, CY and Wada, N and Shih, CJ and Hsiao, SS and Jane, WN and Lee, TC and Yang, CM and Liu, CT and Denis, V and Wu, YT and Wang, LT and Huang, L and Lee, DC and Wu, YW and Yamashiro, H and Tang, SL}, title = {Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {3}, doi = {10.1186/s40168-018-0616-z}, pmid = {30609942}, issn = {2049-2618}, support = {MOST 105-2621-B-001-004-MY3//Ministry of Science and Technology, Taiwan/ ; }, abstract = {BACKGROUND: Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a green layer beneath coral tissues, the anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris is dominant in the skeleton of Isopora palifera. However, due to inherent challenges in studying anaerobic microbes in coral skeleton, the reason for its niche preference and function are largely unknown.<br><br>RESULTS: This study characterized a diverse and dynamic community of endolithic microbes shaped by the availability of light and oxygen. In addition, anaerobic bacteria isolated from the coral skeleton were cultured for the first time to experimentally clarify the role of these GSB. This characterization includes GSB's abundance, genetic and genomic profiles, organelle structure, and specific metabolic functions and activity. Our results explain the advantages endolithic GSB receive from living in coral skeletons, the potential metabolic role of a clade of coral-associated Prosthecochloris (CAP) in the skeleton, and the nitrogen fixation ability of CAP.<br><br>CONCLUSION: We suggest that the endolithic microbial community in coral skeletons is diverse and dynamic and that light and oxygen are two crucial factors for shaping it. This study is the first to demonstrate the ability of nitrogen uptake by specific coral-associated endolithic bacteria and shed light on the role of endolithic bacteria in coral skeletons.}, }
@article {pmid30609941, year = {2019}, author = {Zhong, H and Penders, J and Shi, Z and Ren, H and Cai, K and Fang, C and Ding, Q and Thijs, C and Blaak, EE and Stehouwer, CDA and Xu, X and Yang, H and Wang, J and Wang, J and Jonkers, DMAE and Masclee, AAM and Brix, S and Li, J and Arts, ICW and Kristiansen, K}, title = {Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {2}, doi = {10.1186/s40168-018-0608-z}, pmid = {30609941}, issn = {2049-2618}, support = {ID0E5LAG8456//European Foundation for the Study of Diabetes (DE)/ ; ID0EGNAG8457//Netherlands Asthma Foundation/ ; ID0EQOAG8458//Shenzhen Municipal Government of China/ ; ID0E1PAG8459//ZonMW/JPI HDHL Intestinal Microbiomics/ ; ID0EERAG8460//Stichting Astma Bestrijding/ ; ID0E1PAG8461//Dutch Biobanking and Biomolecular Resources Infrastructure (BBMRI-NL)/ ; ID0E1PAG8462//Netherlands Asthma Foundation/ ; }, abstract = {BACKGROUND: The gut microbiota evolves from birth and is in early life influenced by events such as birth mode, type of infant feeding, and maternal and infant antibiotics use. However, we still have a gap in our understanding of gut microbiota development in older children, and to what extent early events and pre-school lifestyle modulate the composition of the gut microbiota, and how this impinges on whole body metabolic regulation in school-age children.<br><br>RESULTS: Taking advantage of the KOALA Birth Cohort Study, a long-term prospective birth cohort in the Netherlands with extensive collection of high-quality host metadata, we applied shotgun metagenomics sequencing and systematically investigated the gut microbiota of children at 6-9 years of age. We demonstrated an overall adult-like gut microbiota in the 281 Dutch school-age children and identified 3 enterotypes dominated by the genera Bacteroides, Prevotella, and Bifidobacterium, respectively. Importantly, we found that breastfeeding duration in early life and pre-school dietary lifestyle correlated with the composition and functional competences of the gut microbiota in the children at school age. The correlations between pre-school dietary lifestyle and metabolic phenotypes exhibited a striking enterotype dependency. Thus, an inverse correlation between high dietary fiber consumption and low plasma insulin levels was only observed in individuals with the Bacteroides and Prevotella enterotypes, but not in Bifidobacterium enterotype individuals in whom the gut microbiota displayed overall lower microbial gene richness, alpha-diversity, functional potential for complex carbohydrate fermentation, and butyrate and succinate production. High total fat consumption and elevated plasma free fatty acid levels in the Bifidobacterium enterotype are associated with the co-occurrence of Streptococcus.<br><br>CONCLUSIONS: Our work highlights the persistent effects of breastfeeding duration and pre-school dietary lifestyle in affecting the gut microbiota in school-age children and reveals distinct compositional and functional potential in children according to enterotypes. The findings underscore enterotype-specific links between the host metabolic phenotypes and dietary patterns, emphasizing the importance of microbiome-based stratification when investigating metabolic responses to diets. Future diet intervention studies are clearly warranted to examine gut microbe-diet-host relationships to promote knowledge-based recommendations in relation to improving metabolic health in children.}, }
@article {pmid30609847, year = {2019}, author = {Bustamante-Brito, R and Vera-Ponce de León, A and Rosenblueth, M and Martínez-Romero, JC and Martínez-Romero, E}, title = {Metatranscriptomic Analysis of the Bacterial Symbiont Dactylopiibacterium carminicum from the Carmine Cochineal Dactylopius coccus (Hemiptera: Coccoidea: Dactylopiidae).}, journal = {Life (Basel, Switzerland)}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/life9010004}, pmid = {30609847}, issn = {2075-1729}, support = {IN207718//Universidad Nacional Autónoma de México/ ; 253116//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {The scale insect Dactylopius coccus produces high amounts of carminic acid, which has historically been used as a pigment by pre-Hispanic American cultures. Nowadays carmine is found in food, cosmetics, and textiles. Metagenomic approaches revealed that Dactylopius spp. cochineals contain two Wolbachia strains, a betaproteobacterium named Candidatus Dactylopiibacterium carminicum and Spiroplasma, in addition to different fungi. We describe here a transcriptomic analysis indicating that Dactylopiibacterium is metabolically active inside the insect host, and estimate that there are over twice as many Dactylopiibacterium cells in the hemolymph than in the gut, with even fewer in the ovary. Albeit scarce, the transcripts in the ovaries support the presence of Dactylopiibacterium in this tissue and a vertical mode of transmission. In the cochineal, Dactylopiibacterium may catabolize plant polysaccharides, and be active in carbon and nitrogen provisioning through its degradative activity and by fixing nitrogen. In most insects, nitrogen-fixing bacteria are found in the gut, but in this study they are shown to occur in the hemolymph, probably delivering essential amino acids and riboflavin to the host from nitrogen substrates derived from nitrogen fixation.}, }
@article {pmid30608881, year = {2019}, author = {Kayser, BD and Lhomme, M and Prifti, E and Da Cunha, C and Marquet, F and Chain, F and Naas, I and Pelloux, V and Dao, MC and Kontush, A and Rizkalla, SW and Aron-Wisnewsky, J and Bermúdez-Humarán, LG and Oakley, F and Langella, P and Clément, K and Dugail, I}, title = {Phosphatidylglycerols are induced by gut dysbiosis and inflammation, and favorably modulate adipose tissue remodeling in obesity.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {}, number = {}, pages = {fj201801897R}, doi = {10.1096/fj.201801897R}, pmid = {30608881}, issn = {1530-6860}, abstract = {Lipidomic techniques can improve our understanding of complex lipid interactions that regulate metabolic diseases. Here, a serum phospholipidomics analysis identified associations between phosphatidylglycerols (PGs) and gut microbiota dysbiosis. Compared with the other phospholipids, serum PGs were the most elevated in patients with low microbiota gene richness, which were normalized after a dietary intervention that restored gut microbial diversity. Serum PG levels were positively correlated with metagenomic functional capacities for bacterial LPS synthesis and host markers of low-grade inflammation; transcriptome databases identified PG synthase, the first committed enzyme in PG synthesis, as a potential mediator. Experiments in mice and cultured human-derived macrophages demonstrated that LPS induces PG release. Acute PG treatment in mice altered adipose tissue gene expression toward remodeling and inhibited ex vivo lipolysis in adipose tissue, suggesting that PGs favor lipid storage. Indeed, several PG species were associated with the severity of obesity in mice and humans. Finally, despite enrichment in PGs in bacterial membranes, experiments employing gnotobiotic mice colonized with recombinant PG overproducing Lactococcus lactis showed limited direct contribution of microbial PGs to the host. In summary, PGs are inflammation-responsive lipids indirectly regulated by the gut microbiota via endotoxins and regulate adipose tissue homeostasis in obesity.-Kayser, B. D., Lhomme, M., Prifti, E., Da Cunha, C., Marquet, F., Chain, F., Naas, I., Pelloux, V., Dao, M.-C., Kontush, A., Rizkalla, S. W., Aron-Wisnewsky, J., Bermúdez-Humarán, L. G., Oakley, F., Langella, P., Clément, K., Dugail, I. Phosphatidylglycerols are induced by gut dysbiosis and inflammation, and favorably modulate adipose tissue remodeling in obesity.}, }
@article {pmid30606844, year = {2019}, author = {Kafetzopoulou, LE and Pullan, ST and Lemey, P and Suchard, MA and Ehichioya, DU and Pahlmann, M and Thielebein, A and Hinzmann, J and Oestereich, L and Wozniak, DM and Efthymiadis, K and Schachten, D and Koenig, F and Matjeschk, J and Lorenzen, S and Lumley, S and Ighodalo, Y and Adomeh, DI and Olokor, T and Omomoh, E and Omiunu, R and Agbukor, J and Ebo, B and Aiyepada, J and Ebhodaghe, P and Osiemi, B and Ehikhametalor, S and Akhilomen, P and Airende, M and Esumeh, R and Muoebonam, E and Giwa, R and Ekanem, A and Igenegbale, G and Odigie, G and Okonofua, G and Enigbe, R and Oyakhilome, J and Yerumoh, EO and Odia, I and Aire, C and Okonofua, M and Atafo, R and Tobin, E and Asogun, D and Akpede, N and Okokhere, PO and Rafiu, MO and Iraoyah, KO and Iruolagbe, CO and Akhideno, P and Erameh, C and Akpede, G and Isibor, E and Naidoo, D and Hewson, R and Hiscox, JA and Vipond, R and Carroll, MW and Ihekweazu, C and Formenty, P and Okogbenin, S and Ogbaini-Emovon, E and Günther, S and Duraffour, S}, title = {Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.}, journal = {Science (New York, N.Y.)}, volume = {363}, number = {6422}, pages = {74-77}, doi = {10.1126/science.aau9343}, pmid = {30606844}, issn = {1095-9203}, abstract = {The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.}, }
@article {pmid30606403, year = {2019}, author = {Gong, J and Noel, S and Pluznick, JL and Hamad, ARA and Rabb, H}, title = {Gut Microbiota-Kidney Cross-Talk in Acute Kidney Injury.}, journal = {Seminars in nephrology}, volume = {39}, number = {1}, pages = {107-116}, doi = {10.1016/j.semnephrol.2018.10.009}, pmid = {30606403}, issn = {1558-4488}, abstract = {The recent surge in research on the intestinal microbiota has greatly changed our understanding of human biology. Significant technical advances in DNA sequencing analysis and its application to metagenomics and metatranscriptomics has profoundly enhanced our ability to quantify and track complex microbial communities and to begin understanding their impact on human health and disease. This has led to a better understanding of the relationships between the intestinal microbiome and renal physiology/pathophysiology. In this review, we discuss the interactions between intestinal microbiota and kidney. We focus on select aspects including the intestinal barrier, immunologic and soluble mediators of microbiome effects, and effects of dysbiosis on acute kidney injury. Relevant studies on microbiome changes in other renal diseases are highlighted. We also introduce potential mechanisms of intervention with regard to gut microbiota in renal diseases.}, }
@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/ ; }, 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 {pmid30605507, year = {2017}, author = {Vera-Ponce de León, A and Ormeño-Orrillo, E and Ramírez-Puebla, ST and Rosenblueth, M and Degli Esposti, M and Martínez-Romero, J and Martínez-Romero, E}, title = {Candidatus Dactylopiibacterium carminicum, a Nitrogen-Fixing Symbiont of Dactylopius Cochineal Insects (Hemiptera: Coccoidea: Dactylopiidae).}, journal = {Genome biology and evolution}, volume = {9}, number = {9}, pages = {2237-2250}, doi = {10.1093/gbe/evx156}, pmid = {30605507}, issn = {1759-6653}, abstract = {The domesticated carmine cochineal Dactylopius coccus (scale insect) has commercial value and has been used for more than 500 years for natural red pigment production. Besides the domesticated cochineal, other wild Dactylopius species such as Dactylopius opuntiae are found in the Americas, all feeding on nutrient poor sap from native cacti. To compensate nutritional deficiencies, many insects harbor symbiotic bacteria which provide essential amino acids or vitamins to their hosts. Here, we characterized a symbiont from the carmine cochineal insects, Candidatus Dactylopiibacterium carminicum (betaproteobacterium, Rhodocyclaceae family) and found it in D. coccus and in D. opuntiae ovaries by fluorescent in situ hybridization, suggesting maternal inheritance. Bacterial genomes recovered from metagenomic data derived from whole insects or tissues both from D. coccus and from D. opuntiae were around 3.6 Mb in size. Phylogenomics showed that dactylopiibacteria constituted a closely related clade neighbor to nitrogen fixing bacteria from soil or from various plants including rice and other grass endophytes. Metabolic capabilities were inferred from genomic analyses, showing a complete operon for nitrogen fixation, biosynthesis of amino acids and vitamins and putative traits of anaerobic or microoxic metabolism as well as genes for plant interaction. Dactylopiibacterium nif gene expression and acetylene reduction activity detecting nitrogen fixation were evidenced in D. coccus hemolymph and ovaries, in congruence with the endosymbiont fluorescent in situ hybridization location. Dactylopiibacterium symbionts may compensate for the nitrogen deficiency in the cochineal diet. In addition, this symbiont may provide essential amino acids, recycle uric acid, and increase the cochineal life span.}, }
@article {pmid30212260, year = {2019}, author = {Santoro, AE and Richter, RA and Dupont, CL}, title = {Planktonic Marine Archaea.}, journal = {Annual review of marine science}, volume = {11}, number = {}, pages = {131-158}, doi = {10.1146/annurev-marine-121916-063141}, pmid = {30212260}, issn = {1941-0611}, abstract = {Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.}, }
@article {pmid30605809, year = {2018}, author = {Bai, Y and Ruan, X and Wang, F and Antoine, G and van der Hoek, JP}, title = {Sulfonamides removal under different redox conditions and microbial response to sulfonamides stress during riverbank filtration: A laboratory column study.}, journal = {Chemosphere}, volume = {220}, number = {}, pages = {668-677}, doi = {10.1016/j.chemosphere.2018.12.167}, pmid = {30605809}, issn = {1879-1298}, abstract = {Riverbank filtration (RBF) as a barrier of pathogenic microorganisms and organic micropollutants recently has been proven capable of removing sulfonamides. However, the study about the effect of redox conditions on biodegradation of common and persistent sulfonamides in RBF is limited and the response of microbial communities to sulfonamides stress during RBF is unknown. In this study, two column set-ups (with residence time 5 days and 11 days respectively), simulating different redox conditions of riverbank filtration systems, were operated for seven months to investigate 1) the long-term effect of redox conditions on ng∙L-1 level sulfonamides (sulfapyridine, sulfadiazine, sulfamethoxazole, sulfamethazine, sulfaquinoxaline) removal, and 2) the microbial community evolution represented by the phylogenetic and metabolic function shift under non-lethal selective pressures of sulfonamides. The results showed that sulfonamides were more degradable under anoxic conditions than oxic and suboxic conditions. In the sulfonamides stressed community, the phylogenetic diversity increased slightly. Relative abundance of an intrinsic sulfonamides resistant bacteria Bacillus spp. increased, suggesting that sulfonamide resistance developed in specific bacteria under sulfonamides contamination pressure in RBF systems. At the same time, an activated transport function in the stressed microbial community was noticed. The predicted relative abundance of gene folP, which encodes dihydropteroate synthase, also increased significantly, indicating a detoxification mechanism and sulfonamides resistance potential under non-lethal selective pressures of sulfonamides in RBF systems.}, }
@article {pmid30605153, year = {2019}, author = {Xiao, L and Feng, Q and Liang, S and Sonne, SB and Xia, Z and Qiu, X and Li, X and Long, H and Zhang, J and Zhang, D and Liu, C and Fang, Z and Chou, J and Glanville, J and Hao, Q and Kotowska, D and Colding, C and Licht, TR and Wu, D and Yu, J and Sung, JJY and Liang, Q and Li, J and Jia, H and Lan, Z and Tremaroli, V and Dworzynski, P and Nielsen, HB and Bäckhed, F and Doré, J and Le Chatelier, E and Ehrlich, SD and Lin, JC and Arumugam, M and Wang, J and Madsen, L and Kristiansen, K}, title = {Amendments: Author Correction: A catalog of the mouse gut metagenome.}, journal = {Nature biotechnology}, volume = {37}, number = {1}, pages = {102}, doi = {10.1038/nbt0119-102a}, pmid = {30605153}, issn = {1546-1696}, }
@article {pmid30604012, year = {2019}, author = {Tyagi, A and Singh, B and Billekallu Thammegowda, NK and Singh, NK}, title = {Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-018-1615-y}, pmid = {30604012}, issn = {1432-072X}, support = {YSS/2014/000269//Science and Engineering Research Board/ ; }, abstract = {Gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. With the presence of 36 phyla, 326 families and 985 genera, the fish gut microbiota was found to be quite diverse in nature. However, at the phylum level, more than three-fourths of gut microbes belonged to Proteobacteria. Very low prevalence of commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) in fish gut suggested the need to search for alternative probiotics for aquaculture use. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy metabolism (4%) and fermentation (2%). In conformity with herbivorous feeding habit of L. rohita, gut microbiome also had pathways for the degradation of cellulose, hemicellulose, chitin, pectin, starch, and other complex carbohydrates. High prevalence of Actinobacteria and antibiotic biosynthesis pathways in the fish gut microbiome indicated its potential for bioprospecting of potentially novel natural antibiotics. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment. The role of ARGs in fish gut microbiome needs further investigations.}, }
@article {pmid30602367, year = {2019}, author = {Chen, YY and Chen, DQ and Chen, L and Liu, JR and Vaziri, ND and Guo, Y and Zhao, YY}, title = {Microbiome-metabolome reveals the contribution of gut-kidney axis on kidney disease.}, journal = {Journal of translational medicine}, volume = {17}, number = {1}, pages = {5}, doi = {10.1186/s12967-018-1756-4}, pmid = {30602367}, issn = {1479-5876}, support = {81673578//National Natural Science Foundation of China/ ; 81603271//National Natural Science Foundation of China/ ; 81872985//National Natural Science Foundation of China/ ; }, abstract = {Dysbiosis represents changes in composition and structure of the gut microbiome community (microbiome), which may dictate the physiological phenotype (health or disease). Recent technological advances and efforts in metagenomic and metabolomic analyses have led to a dramatical growth in our understanding of microbiome, but still, the mechanisms underlying gut microbiome-host interactions in healthy or diseased state remain elusive and their elucidation is in infancy. Disruption of the normal gut microbiota may lead to intestinal dysbiosis, intestinal barrier dysfunction, and bacterial translocation. Excessive uremic toxins are produced as a result of gut microbiota alteration, including indoxyl sulphate, p-cresyl sulphate, and trimethylamine-N-oxide, all implicated in the variant processes of kidney diseases development. This review focuses on the pathogenic association between gut microbiota and kidney diseases (the gut-kidney axis), covering CKD, IgA nephropathy, nephrolithiasis, hypertension, acute kidney injury, hemodialysis and peritoneal dialysis in clinic. Targeted interventions including probiotic, prebiotic and symbiotic measures are discussed for their potential of re-establishing symbiosis, and more effective strategies for the treatment of kidney diseases patients are suggested. The novel insights into the dysbiosis of the gut microbiota in kidney diseases are helpful to develop novel therapeutic strategies for preventing or attenuating kidney diseases and complications.}, }
@article {pmid30602085, year = {2018}, author = {Park, SC and Won, S}, title = {Evaluation of 16S rRNA Databases for Taxonomic Assignments Using Mock Community.}, journal = {Genomics &amp; informatics}, volume = {16}, number = {4}, pages = {e24}, doi = {10.5808/GI.2018.16.4.e24}, pmid = {30602085}, issn = {1598-866X}, abstract = {Taxonomy identification is fundamental to all microbiology studies. Particularly in metagenomics, which identify the composition of microorganisms using thousands of sequences, its importance is even greater. Identification is inevitably affected by the choice of database. This study was conducted to evaluate the accuracy of three widely used 16S databases, Greengenes, Silva, and EzBioCloud, and to suggest basic guidelines for selecting reference databases. Using public mock community data, each database was used to assign taxonomy and to test its accuracy. We showed that EzBioCloud performs well compared to other existing databases.}, }
@article {pmid30602083, year = {2018}, author = {Kang, S and Kim, YC}, title = {The Genome-Based Virus Taxonomy with ICTV Database Extension.}, journal = {Genomics &amp; informatics}, volume = {16}, number = {4}, pages = {e22}, doi = {10.5808/GI.2018.16.4.e22}, pmid = {30602083}, issn = {1598-866X}, abstract = {In 1966, the International Classification of Viruses (ICNV) was established to standardize the naming of viruses. In 1975, the organization was renamed 'ICTV', by which it is still known today. The primary virus classification provided by ICTV in 1971 was for viruses infecting vertebrates, which includes 19 genera, 2 families, and a further 24 unclassified groups. Presently, the 10th virus taxonomy has been published. However, early classification of viruses was based on the clinical results of &quot;in vivo&quot; and &quot;in vitro&quot;, as well as on the shape of PhynoType virus. However, due to the development of next-generation sequencing (NGS) and the accompanying bioinformatics analysis pipelines, a reconstruction of the classification system has been proposed. At a meeting held in Boston, USA between June 9-11, 2016, even there was an in-depth discussion regarding the classification of viruses using Metagenomic data. One suggested activity that arose from the meeting was that viral taxonomy should be reconstructed, based on genotype and bioinformatics analysis &quot;in silico&quot;. This article describes our efforts to achieve this goal by construction of a web-based system and extension of an associated database, based on ICTV taxonomy. This virus taxonomy web system was specifically designed to extend the virus taxonomy up to strain and isolation, which was then connected with the NCBI database to facilitate searching for specific viral genes; there are also links to journals provided by the EMBL RESTful API that improve accessibility for academic groups.}, }
@article {pmid30602082, year = {2018}, author = {Jeon, SJ and Galvão, KN}, title = {An Advanced Understanding of Uterine Microbial Ecology Associated with Metritis in Dairy Cows.}, journal = {Genomics &amp; informatics}, volume = {16}, number = {4}, pages = {e21}, doi = {10.5808/GI.2018.16.4.e21}, pmid = {30602082}, issn = {1598-866X}, abstract = {Metritis, the inflammation of the uterus caused by polymicrobial infections, is a prevalent and costly disease to the dairy industry as it decreases milk yield, survival, and the welfare of dairy cows. Although the antibiotic ceftiofur is widely used for the treatment of metritis, endometrium and ovary function is compromised, resulting in subfertility and infertility. According to culture-dependent studies, uterine pathogens include Escherichia coli, Trueperella pyogenes, Fusobacterium necrophorum, and Prevotella melaninogenica. Recent studies using high-throughput sequencing claimed that metritis is a microbiota-associated disease. Herein, we propose that metritis is associated with uterine microbiota with high abundance of Bacteroides, Porphyromonas, and Fusobacterium, but rare bacteria such as Escherichia coli and Helcococcus ovis cannot be ignored.}, }
@article {pmid30601862, year = {2019}, author = {Thornbury, M and Sicheri, J and Slaine, P and Getz, LJ and Finlayson-Trick, E and Cook, J and Guinard, C and Boudreau, N and Jakeman, D and Rohde, J and McCormick, C}, title = {Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0209221}, doi = {10.1371/journal.pone.0209221}, pmid = {30601862}, issn = {1932-6203}, abstract = {Plant cell walls are composed of cellulose, hemicellulose, and lignin, collectively known as lignocellulose. Microorganisms degrade lignocellulose to liberate sugars to meet metabolic demands. Using a metagenomic sequencing approach, we previously demonstrated that the microbiome of the North American porcupine (Erethizon dorsatum) is replete with genes that could encode lignocellulose-degrading enzymes. Here, we report the identification, synthesis and partial characterization of four novel genes from the porcupine microbiome encoding putative lignocellulose-degrading enzymes: β-glucosidase, α-L-arabinofuranosidase, β-xylosidase, and endo-1,4-β-xylanase. These genes were identified via conserved catalytic domains associated with cellulose- and hemicellulose-degradation. Phylogenetic trees were created for each of these putative enzymes to depict genetic relatedness to known enzymes. Candidate genes were synthesized and cloned into plasmid expression vectors for inducible protein expression and secretion. The putative β-glucosidase fusion protein was efficiently secreted but did not permit Escherichia coli (E. coli) to use cellobiose as a sole carbon source, nor did the affinity purified enzyme cleave p-Nitrophenyl β-D-glucopyranoside (p-NPG) substrate in vitro over a range of physiological pH levels (pH 5-7). The putative hemicellulose-degrading β-xylosidase and α-L-arabinofuranosidase enzymes also lacked in vitro enzyme activity, but the affinity purified endo-1,4-β-xylanase protein cleaved a 6-chloro-4-methylumbelliferyl xylobioside substrate in acidic and neutral conditions, with maximal activity at pH 7. At this optimal pH, KM, Vmax, and kcat were determined to be 32.005 ± 4.72 μM, 1.16x10-5 ± 3.55x10-7 M/s, and 94.72 s-1, respectively. Thus, our pipeline enabled successful identification and characterization of a novel hemicellulose-degrading enzyme from the porcupine microbiome. Progress towards the goal of introducing a complete lignocellulose-degradation pathway into E. coli will be accelerated by combining synthetic metagenomic approaches with functional metagenomic library screening, which can identify novel enzymes unrelated to those found in available databases.}, }
@article {pmid30600356, year = {2019}, author = {Kadnikov, VV and Mardanov, AV and Beletsky, AV and Karnachuk, OV and Ravin, NV}, title = {Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle.}, journal = {Extremophiles : life under extreme conditions}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00792-018-01073-5}, pmid = {30600356}, issn = {1433-4909}, support = {14-14-01016//Russian Science Foundation/ ; }, abstract = {Bacteria of candidate phylum OP8 (Aminicenantes) have been identified in various terrestrial and marine ecosystems as a result of molecular analysis of microbial communities. So far, none of the representatives of Aminicenantes have been isolated in a pure culture. We assembled the near-complete genome of a member of Aminicenantes from the metagenome of the 2-km-deep subsurface thermal aquifer in Western Siberia and used genomic data to analyze the metabolic pathways of this bacterium and its ecological role. This bacterium, designated BY38, was predicted to be rod shaped, it lacks flagellar machinery but twitching motility is encoded. Analysis of the BY38 genome revealed a variety of glycosyl hydrolases that can enable utilization of carbohydrates, including chitin, cellulose, starch, mannose, galactose, fructose, fucose, rhamnose, maltose and arabinose. The reconstructed central metabolic pathways suggested that Aminicenantes bacterium BY38 is an anaerobic organotroph capable of fermenting carbohydrates and proteinaceous substrates and performing anaerobic respiration with nitrite. In the deep subsurface aquifer Aminicenantes probably act as destructors of buried organic matter and produce hydrogen and acetate. Based on phylogenetic and genomic analyses, the novel bacterium is proposed to be classified as Candidatus Saccharicenans subterraneum.}, }
@article {pmid30599960, year = {2019}, author = {Xie, M and Wu, J and An, F and Yue, X and Tao, D and Wu, R and Lee, Y}, title = {An integrated metagenomic/metaproteomic investigation of microbiota in dajiang-meju, a traditional fermented soybean product in Northeast China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {115}, number = {}, pages = {414-424}, doi = {10.1016/j.foodres.2018.10.076}, pmid = {30599960}, issn = {1873-7145}, abstract = {Dajiang-meju have been used as major ingredients for the preparation of traditional spontaneously fermented soybean paste in Northeast China. In this work, we sequenced and analyzed the metagenome of 12 dajiang-meju samples. To complement the metagenome analysis, we analyzed the taxonomic and functional diversity of the microbiota by metaproteomics (LC-MS/MS). The analysis of metagenomic data revealed that the communities were primarily dominated by Enterobacter, Enterococcus, Leuconostoc, Lactobacillus, Citrobacter and Leclercia. Moreover, changes in the functional levels were monitored, and metaproteomic analysis revealed that most of the proteins were mainly expressed by members of Rhizopus, Penicillium and Geotrichum. The number of sequences allocated to fungi in the fermentation process decreased, whereas the number of sequences assigned to bacteria increased with time of fermentation. In addition, functional metagenomic profiling indicated that a series of sequences related to carbohydrates and amino acids metabolism were enriched. Additionally, enzymes associated with glycolysis metabolic pathways were presumed to contribute to the generation of flavor in dajiang-meju. Proteins from different dajiang-meju samples involved in global and overview maps, carbohydrate metabolism, nucleic acid metabolism and energy metabolism were differentially expressed. This information improves the understanding of microbial metabolic patterns with respect to the metaproteomes of dajiang-meju and provides a powerful tool for studying the fermentation process of soybean products.}, }
@article {pmid30599936, year = {2019}, author = {Danneskiold-Samsøe, NB and Dias de Freitas Queiroz Barros, H and Santos, R and Bicas, JL and Cazarin, CBB and Madsen, L and Kristiansen, K and Pastore, GM and Brix, S and Maróstica Júnior, MR}, title = {Interplay between food and gut microbiota in health and disease.}, journal = {Food research international (Ottawa, Ont.)}, volume = {115}, number = {}, pages = {23-31}, doi = {10.1016/j.foodres.2018.07.043}, pmid = {30599936}, issn = {1873-7145}, abstract = {Numerous microorganisms colonize the human gastrointestinal tract playing pivotal roles in relation to digestion and absorption of dietary components. They biotransform food components and produce metabolites, which in combination with food components shape and modulate the host immune system and metabolic responses. Reciprocally, the diet modulates the composition and functional capacity of the gut microbiota, which subsequently influence host biochemical processes establishing a system of mutual interaction and inter-dependency. Macronutrients, fibers, as well as polyphenols and prebiotics are strong drivers shaping the composition of the gut microbiota. Especially, short-chain fatty acids produced from ingested fibers and tryptophan metabolites are key in modulating host immune responses. Since reciprocal interactions between diet, host, and microbiota are personal, understanding this complex network of interactions calls for novel use of large datasets and the implementation of machine learning algorithms and artificial intelligence. In this review, we aim to provide a base for future investigations of how interactions between food components and gut microbiota may influence or even determine human health and disease.}, }
@article {pmid30599328, year = {2018}, author = {Yun, YM and Kim, M and Kim, H and Kim, DH and Kwon, EE and Kang, S}, title = {Increased biodegradability of low-grade coal wastewater in anaerobic membrane bioreactor by adding yeast wastes.}, journal = {Journal of environmental management}, volume = {234}, number = {}, pages = {36-43}, doi = {10.1016/j.jenvman.2018.12.083}, pmid = {30599328}, issn = {1095-8630}, abstract = {Demineralization is required in upgrading low-grade coal to serve as an alternative energy resource for the production of fuel and valuable chemicals but generates a large amount of low-grade coal wastewater (LCWW). The objective of this study was to investigate the effects of a co-substrate on an anaerobic membrane bioreactor (AnMBR) treating LCWW. CH4 was not produced during the operation fed by LCWW alone. When yeast wastes (YW) were supplemented, there was a gradual increase in the biodegradability of LCWW, achieving 182 CH4 mL/g COD with 58% COD removal efficiency. The analysis of physicochemical characteristics in the effluent of AnMBR, done by excitation-emission matrix (EEM) and size exclusion chromatography (SEC), showed that the proportion of soluble microbial products (SMPs) and aromatic group with high-molecular weight (>1 kDa) increased. Microbial analysis revealed that the increased dominance of bacteria Comamonas, Methanococcus, and Methanosarcina facilitated biodegradation of LCWW in the presence of YW.}, }
@article {pmid30598099, year = {2018}, author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T}, title = {A latent allocation model for the analysis of microbial composition and disease.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 19}, pages = {519}, doi = {10.1186/s12859-018-2530-6}, pmid = {30598099}, issn = {1471-2105}, abstract = {BACKGROUND: Establishing the relationship between microbiota and specific diseases is important but requires appropriate statistical methodology. A specialized feature of microbiome count data is the presence of a large number of zeros, which makes it difficult to analyze in case-control studies. Most existing approaches either add a small number called a pseudo-count or use probability models such as the multinomial and Dirichlet-multinomial distributions to explain the excess zero counts, which may produce unnecessary biases and impose a correlation structure taht is unsuitable for microbiome data.<br><br>RESULTS: The purpose of this article is to develop a new probabilistic model, called BERnoulli and MUltinomial Distribution-based latent Allocation (BERMUDA), to address these problems. BERMUDA enables us to describe the differences in bacteria composition and a certain disease among samples. We also provide a simple and efficient learning procedure for the proposed model using an annealing EM algorithm.<br><br>CONCLUSION: We illustrate the performance of the proposed method both through both the simulation and real data analysis. BERMUDA is implemented with R and is available from GitHub (https://github.com/abikoushi/Bermuda).}, }
@article {pmid30598080, year = {2018}, author = {Chen, HM and Chang, TH and Lin, FM and Liang, C and Chiu, CM and Yang, TL and Yang, T and Huang, CY and Cheng, YN and Chang, YA and Chang, PY and Weng, SL}, title = {Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 10}, pages = {876}, doi = {10.1186/s12864-018-5284-7}, pmid = {30598080}, issn = {1471-2164}, abstract = {BACKGROUND: One of the most common and recurrent vaginal infections is bacterial vaginosis (BV). The diagnosis is based on changes to the &quot;normal&quot; vaginal microbiome; however, the normal microbiome appears to differ according to reproductive status and ethnicity, and even among individuals within these groups. The Amsel criteria and Nugent score test are widely used for diagnosing BV; however, these tests are based on different criteria, and so may indicate distinct changes in the vaginal microbial community. Nevertheless, few studies have compared the results of these test against metagenomics analysis.<br><br>METHODS: Vaginal flora samples from 77 participants were classified according to the Amsel criteria and Nugent score test. The microbiota composition was analyzed using 16S ribosome RNA gene amplicon sequencing. Bioinformatics analysis and multivariate statistical analysis were used to evaluate the microbial diversity and function.<br><br>RESULTS: Only 3 % of the participants diagnosed BV negative using the Amsel criteria (A-) were BV-positive according to the Nugent score test (N+), while over half of the BV-positive patients using the Amsel criteria (A+) were BV-negative according to the Nugent score test (N-). Thirteen genera showed significant differences in distribution among BV status defined by BV tests (e.g., A - N-, A + N- and A + N+). Variations in the four most abundant taxa, Lactobacillus, Gardnerella, Prevotella, and Escherichia, were responsible for most of this dissimilarity. Furthermore, vaginal microbial diversity differed significantly among the three groups classified by the Nugent score test (N-, N+, and intermediate flora), but not between the Amsel criteria groups. Numerous predictive microbial functions, such as bacterial chemotaxis and bacterial invasion of epithelial cells, differed significantly among multiple BV test, but not between the A- and A+ groups.<br><br>CONCLUSIONS: Metagenomics analysis can greatly expand our current understanding of vaginal microbial diversity in health and disease. Metagenomics profiling may also provide more reliable diagnostic criteria for BV testing.}, }
@article {pmid30597257, year = {2018}, author = {Ngara, TR and Zhang, H}, title = {Recent Advances in Function-based Metagenomic Screening.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.gpb.2018.01.002}, pmid = {30597257}, issn = {2210-3244}, abstract = {Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identification of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening, and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.}, }
@article {pmid30597002, year = {2018}, 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 = {}, number = {}, 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 {pmid30596893, year = {2018}, author = {Gonnella, G and Niehus, N and Kurtz, S}, title = {GfaViz: Flexible and interactive visualization of GFA sequence graphs.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/bty1046}, pmid = {30596893}, issn = {1367-4811}, abstract = {Summary: The Graphical Fragment Assembly (GFA) formats are emerging standard formats for the representation of sequence graphs. While GFA 1 was primarely targeting assembly graphs, the newer GFA 2 format introduces several features, which makes it suitable for representing other kinds of information, such as scaffolding graphs, variation graphs, alignment graphs, and colored metagenomic graphs. Here, we present GfaViz, an interactive graphical tool for the visualization of sequence graphs in GFA format. The software supports all new features of GFA 2 and introduces conventions for their visualization. The user can choose between two different layouts and multiple styles for representing single elements or groups. All customizations can be stored in custom tags of the GFA format itself, without requiring external configuration files. Stylesheets are supported for storing standard configuration options for groups of files. The visualizations can be exported to raster and vector graphics formats. A command line interface allows for batch generation of images.<br><br>GfaViz is available at https://github.com/ggonnella/gfaviz.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@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 {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 {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 {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 {pmid28642609, year = {2017}, author = {Banerjee, S and Tian, T and Wei, Z and Peck, KN and Shih, N and Chalian, AA and O'Malley, BW and Weinstein, GS and Feldman, MD and Alwine, J and Robertson, ES}, title = {Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4036}, pmid = {28642609}, issn = {2045-2322}, support = {P30 CA016520/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; Carcinoma, Squamous Cell/epidemiology/*etiology ; Computational Biology/methods ; Host-Parasite Interactions ; Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth Neoplasms/epidemiology/*etiology ; Mutagenesis, Insertional ; Oropharyngeal Neoplasms/epidemiology/*etiology ; Parasites/classification/genetics ; Reproducibility of Results ; }, abstract = {The microbiome is fundamentally one of the most unique organs in the human body. Dysbiosis can result in critical inflammatory responses and result in pathogenesis contributing to neoplastic events. We used a pan-pathogen array technology (PathoChip) coupled with next-generation sequencing to establish microbial signatures unique to human oral and oropharyngeal squamous cell carcinomas (OCSCC/OPSCC). Signatures for DNA and RNA viruses including oncogenic viruses, gram positive and negative bacteria, fungi and parasites were detected. Cluster and topological analyses identified 2 distinct groups of microbial signatures related to OCSCCs/OPSCCs. Results were validated by probe capture next generation sequencing; the data from which also provided a comprehensive map of integration sites and chromosomal hotspots for micro-organism genomic insertions. Identification of these microbial signatures and their integration sites may provide biomarkers for OCSCC/OPSCC diagnosis and prognosis as well as novel avenues for study of their potential role in OCSCCs/OPSCCs.}, }
@article {pmid30592753, year = {2018}, author = {Thissen, JB and Isshiki, M and Jaing, C and Nagao, Y and Lebron Aldea, D and Allen, JE and Izui, M and Slezak, TR and Ishida, T and Sano, T}, title = {A novel variant of torque teno virus 7 identified in patients with Kawasaki disease.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209683}, doi = {10.1371/journal.pone.0209683}, pmid = {30592753}, issn = {1932-6203}, abstract = {Kawasaki disease (KD), first identified in 1967, is a pediatric vasculitis of unknown etiology that has an increasing incidence in Japan and many other countries. KD can cause coronary artery aneurysms. Its epidemiological characteristics, such as seasonality and clinical picture of acute systemic inflammation with prodromal intestinal/respiratory symptoms, suggest an infectious etiology for KD. Interestingly, multiple host genotypes have been identified as predisposing factors for KD. To explore experimental methodology for identifying etiological agent(s) for KD and to optimize epidemiological study design (particularly the sample size) for future studies, we conducted a pilot study. For a 1-year period, we prospectively enrolled 11 patients with KD. To each KD patient, we assigned two control individuals (one with diarrhea and the other with respiratory infections), matched for age, sex, and season of diagnosis. During the acute phase of disease, we collected peripheral blood, nasopharyngeal aspirate, and feces. We also determined genotypes, to identify those that confer susceptibility to KD. There was no statistically significant difference in the frequency of the risk genotypes between KD patients and control subjects. We also used unbiased metagenomic sequencing to analyze these samples. Metagenomic sequencing and PCR detected torque teno virus 7 (TTV7) in two patients with KD (18%), but not in control subjects (P = 0.111). Sanger sequencing revealed that the TTV7 found in the two KD patients contained almost identical variants in nucleotide and identical changes in resulting amino acid, relative to the reference sequence. Additionally, we estimated the sample size that would be required to demonstrate a statistical correlation between TTV7 and KD. Future larger scale studies with carefully optimized metagenomic sequencing experiments and adequate sample size are warranted to further examine the association between KD and potential pathogens, including TTV7.}, }
@article {pmid30592383, year = {2018}, author = {van Dijkhuizen, EHP and Del Chierico, F and Malattia, C and Russo, A and Pires Marafon, D and Ter Haar, NM and Magni-Manzoni, S and Vastert, SJ and Dallapiccola, B and Prakken, B and Martini, A and De Benedetti, F and Putignani, L and , }, title = {Microbiome analytics of the gut microbiota in juvenile idiopathic arthritis patients: an observational, longitudinal cohort study.}, journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)}, volume = {}, number = {}, pages = {}, doi = {10.1002/art.40827}, pmid = {30592383}, issn = {2326-5205}, abstract = {OBJECTIVES: To assess the composition of gut microbiota in Italian and Dutch juvenile idiopathic arthritis (JIA) patients at baseline, in inactive disease and persistent activity, compared to healthy controls.<br><br>METHODS: In a prospective, multicenter, observational cohort study, fecal samples were collected of 78 Italian and 21 Dutch treatment-naïve JIA patients at baseline with less than 6 months disease duration and compared to 107 geography-matched samples of healthy children. Furthermore, 44 follow up samples in inactive disease and 25 in persistent activity were analyzed. Gut microbiota composition was determined by 16S rRNA-based-metagenomics. The α- and β-diversity were computed, and log-ratios of relative abundance were compared between patients and healthy controls using random forest models and logistic regression.<br><br>RESULTS: Italian baseline samples showed reduced richness compared to healthy controls (p <0.001). Random forest distinguished Italian baseline samples from controls and suggested differences between Dutch samples and controls (area under the curve >0.99 and 0.71, respectively). Mainly the Operational Taxonomic Units (OTUs) Erysipelotrichaceae (increased in patients), Allobaculum (decreased) and Faecalibacterium prausnitzii (increased) showed different relative abundance in Italian baseline samples compared to controls after controlling for multiple comparisons. Some OTUs differed between Dutch samples and healthy controls, but no evidence remained after controlling for multiple comparisons. No differences were found in paired analysis between Italian baseline and inactive disease samples.<br><br>CONCLUSIONS: We found evidence for dysbiosis in JIA patients. Only patient/control status, age and geographical origin appeared to be drivers of the microbiota profiles, regardless of disease activity stage, inflammation and autoimmunity markers. This article is protected by copyright. All rights reserved.}, }
@article {pmid30590681, year = {2018}, author = {Mandal, RK and Crane, RJ and Berkley, JA and Gumbi, W and Wambua, J and Ngoi, JM and Ndungu, FM and Schmidt, NW}, title = {Longitudinal analysis of infant stool bacteria communities before and after acute febrile malaria and artemether/lumefantrine treatment.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiy740}, pmid = {30590681}, issn = {1537-6613}, abstract = {Background: Gut microbiota were recently shown to impact malaria disease progression and outcome, and prior studies have shown that Plasmodium infections increase the likelihood of enteric bacteria causing systemic infections. Currently, it is not known if Plasmodium infection impacts human gut microbiota as a prelude to bacteremia, or whether antimalarials effect gut microbiota. Our goal was to determine to what degree Plasmodium infections and antimalarial treatment affect human gut microbiota.<br><br>Methods: 100 Kenyan infants underwent active surveillance for malaria from birth to ten months of age. Each malaria episode was treated with artemether/lumefantrine (AL). Any other treatments, including antibiotics, were recorded. Stool samples were collected on an approximate bi-weekly basis. Ten children were selected on the basis of stool samples having been collected before (n=27) or after (n=17) a malaria episode, and without antibiotics having been administered between collections. These samples were subjected to 16S rRNA gene (V3-V4 region) sequencing.<br><br>Results: Bacterial community network analysis revealed no obvious differences in the before and after malaria/AL samples, which was consistent with no difference in alpha and beta diversity and taxonomic analysis at the family and genus level with one exception. At the sequence variant (SV) level, akin to bacterial species, only one of the top 100 SVs was significantly different. Additionally, predicted metagenome analysis revealed no significant difference in metagenomic capacity between before and after malaria/AL samples. Intriguingly, number of malaria episodes, one versus two, explained significant variation in gut microbiota composition of the infants.<br><br>Conclusions: In-depth bioinformatics analysis of stool bacteria has revealed for the first time that human malaria episode/AL treatment have minimal effects on gut microbiota in Kenyan infants.}, }
@article {pmid30590603, year = {2018}, author = {Mansbach, JM and Hasegawa, K and Piedra, PA and Avadhanula, V and Petrosino, JF and Sullivan, AF and Espinola, JA and Camargo, CA}, title = {Haemophilus-dominant nasopharyngeal microbiota is associated with delayed clearance of respiratory syncytial virus in infants hospitalized for bronchiolitis.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiy741}, pmid = {30590603}, issn = {1537-6613}, abstract = {The relation of nasopharyngeal microbiota to the clearance of respiratory syncytial virus (RSV) in infants hospitalized for bronchiolitis is not known. In a multicenter cohort, we found 106 of 557 (19%) infants hospitalized with RSV bronchiolitis had the same RSV subtype 3 weeks later (i.e., delayed clearance of RSV). Using 16S rRNA gene sequencing and a clustering approach, infants with a Haemophilus-dominant microbiota profile at hospitalization were more likely than those with a mixed-profile to have delayed clearance after adjusting for 11 factors, including viral load. Nasopharyngeal microbiota composition is associated with delayed RSV clearance.}, }
@article {pmid30589932, year = {2018}, author = {Gonzales, JA and Hinterwirth, A and Shantha, J and Wang, K and Zhong, L and Cummings, SL and Qian, Y and Wilson, MR and Acharya, NR and Doan, T}, title = {Association of Ocular Inflammation and Rubella Virus Persistence.}, journal = {JAMA ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1001/jamaophthalmol.2018.6185}, pmid = {30589932}, issn = {2168-6173}, abstract = {Importance: Metagenomic deep sequencing (MDS) demonstrates that persistent and active rubella virus (RV) infection is associated with Fuchs heterochromic iridocyclitis (FHI).<br><br>Objective: To assess the utility of MDS in identifying RV infection in patients with uveitis.<br><br>This case series assessed 6 patients diagnosed by MDS with RV-associated uveitis at a tertiary uveitis referral center in the United States.<br><br>Exposures: Prior RV infection.<br><br>Main Outcomes and Measures: Clinical examination findings, slitlamp photography, corneal confocal imaging, and infectious pathogen genome obtained from RNA sequencing.<br><br>Results: Six white men (age range, 36-61 years) were diagnosed with RV-associated uveitis by MDS. Three patients exhibited iris heterochromia associated with their uveitis in classic FHI fashion. The other 3 patients had less classic FHI features and exhibited anterior vitritis. Three patients had in vivo corneal confocal microscopy, with 2 demonstrating stellate keratic precipitates in addition to endothelial infiltration, spotlike holes, and enlarged intercellular boundaries. Of these 3 patients, 1 patient exhibited polymorphism and polymegathism of the endothelial cells.<br><br>Conclusions and Relevance: These findings suggest that persistent RV infection is associated with recurrent or chronic anterior or anterior-intermediate uveitis as well as corneal endothelial cell damage. Ophthalmologists should consider RV infection as a potential cause of hypertensive anterior and intermediate uveitis.}, }
@article {pmid30589606, year = {2018}, 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 = {}, number = {}, pages = {}, doi = {10.1089/omi.2018.0176}, pmid = {30589606}, issn = {1557-8100}, 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 {pmid30588856, year = {2018}, author = {Fajardo, C and García-Cantalejo, J and Botías, P and Costa, G and Nande, M and Martin, M}, title = {New insights into the impact of nZVI on soil microbial biodiversity and functionality.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/10934529.2018.1535159}, pmid = {30588856}, issn = {1532-4117}, abstract = {Nanoscale zero-valent iron (nZVI) is a strong reducing agent used for in situ remediation of soil. The impacts of nZVI (5-10% w/w) on the soil microbial biodiversity and functionality of two soils (Lufa 2.2 and 2.4) were assessed. Illumina MiSeq technology was used to evaluate the structure of soil microbiomes after 21 days of exposure. Proteobacteria, Verrucomicrobia, Firmicutes and Actinobacteria were the most abundant phyla in both soils. However, the dynamics of bacterial community composition following nZVI addition differed. nZVI exposure induced pronounced shifts in the microbial composition of soil 2.4, but not in soil 2.2; an increase in Verrucomicrobia abundance was the unique common taxonomic pattern observed in both soils. The PICRUSt approach was applied to predict the functional composition of each metagenome. Environmental information processing function (membrane transport) was decreased in both nZVI-spiked soils, although soil 2.4 samples were enriched in functions involved in cellular processes and metabolism. The effects of nZVI on autochthonous bacterial communities clearly varied with the soil type assessed; changes at the phylogenetic level appeared to be more abundant than those observed at the functional level, and thus, the overall effort of the soil ecosystem might involve the maintenance of functionality following nZVI exposure.}, }
@article {pmid30588567, year = {2018}, author = {Wei, F and Wu, Q and Hu, Y and Huang, G and Nie, Y and Yan, L}, title = {Conservation metagenomics: a new branch of conservation biology.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11427-018-9423-3}, pmid = {30588567}, issn = {1869-1889}, abstract = {Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade, increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology, nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.}, }
@article {pmid30588558, year = {2018}, author = {Al-Ajlan, A and El Allali, A}, title = {CNN-MGP: Convolutional Neural Networks for Metagenomics Gene Prediction.}, journal = {Interdisciplinary sciences, computational life sciences}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12539-018-0313-4}, pmid = {30588558}, issn = {1867-1462}, support = {1-17-02-001-0025//http://dx.doi.org/10.13039/501100004919/ ; }, abstract = {Accurate gene prediction in metagenomics fragments is a computationally challenging task due to the short-read length, incomplete, and fragmented nature of the data. Most gene-prediction programs are based on extracting a large number of features and then applying statistical approaches or supervised classification approaches to predict genes. In our study, we introduce a convolutional neural network for metagenomics gene prediction (CNN-MGP) program that predicts genes in metagenomics fragments directly from raw DNA sequences, without the need for manual feature extraction and feature selection stages. CNN-MGP is able to learn the characteristics of coding and non-coding regions and distinguish coding and non-coding open reading frames (ORFs). We train 10 CNN models on 10 mutually exclusive datasets based on pre-defined GC content ranges. We extract ORFs from each fragment; then, the ORFs are encoded numerically and inputted into an appropriate CNN model based on the fragment-GC content. The output from the CNN is the probability that an ORF will encode a gene. Finally, a greedy algorithm is used to select the final gene list. Overall, CNN-MGP is effective and achieves a 91% accuracy on testing dataset. CNN-MGP shows the ability of deep learning to predict genes in metagenomics fragments, and it achieves an accuracy higher than or comparable to state-of-the-art gene-prediction programs that use pre-defined features.}, }
@article {pmid30587202, year = {2018}, author = {Hu, Z and Weng, X and Xu, C and Lin, Y and Cheng, C and Wei, H and Chen, W}, title = {Metagenomic next-generation sequencing as a diagnostic tool for toxoplasmic encephalitis.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {17}, number = {1}, pages = {45}, doi = {10.1186/s12941-018-0298-1}, pmid = {30587202}, issn = {1476-0711}, support = {NSFC 81701973//National Natural Science Foundation of China/ ; QNRC2016059//project of Jiangsu province medical youth talent/ ; ZKX17040//Nanjing medical science and technique development foundation/ ; }, abstract = {BACKGROUND: More than 100 different pathogens can cause encephalitis. Testing of all the neurological pathogens by conventional methods can be difficult. Metagenomic next-generation sequencing (NGS) could identify the infectious agents in a target-independent manner. The role of this novel method in clinical diagnostic microbiology still needs to be evaluated. In present study, we used metagenomic NGS to search for an infectious etiology in a human immunodeficiency virus (HIV)-infected patient with lethally diffuse brain lesions. Sequences mapping to Toxoplasma gondii were unexpectedly detected.<br><br>CASE PRESENTATION: A 31-year-old HIV-infected patient presented to hospital in a critical ill condition with a Glasgow coma scale score of 3. Brain magnetic resonance imaging showed diffuse brain abnormalities with contrast enhancement. Metagenomic NGS was performed on DNA extract from 300 μL patient's cerebrospinal fluid (CSF) with the BGISEQ-50 platform. The sequencing detection identified 65,357 sequence reads uniquely aligned to the Toxoplasma gondii genome. Presence of Toxoplasma gondii genome in CSF was further verified by Toxoplasma gondii-specific polymerase chain reaction and Sanger sequencing. Altogether, those results confirmed the diagnosis of toxoplasmic encephalitis.<br><br>CONCLUSIONS: This study suggests that metagenomic NGS may be a useful diagnostic tool for toxoplasmic encephalitis. As metagenomic NGS is able to identify all pathogens in a single run, it may be a promising strategy to explore the clinical causative pathogens in central nervous system infections with atypical features.}, }
@article {pmid30587114, year = {2018}, author = {Tyakht, AV and Manolov, AI and Kanygina, AV and Ischenko, DS and Kovarsky, BA and Popenko, AS and Pavlenko, AV and Elizarova, AV and Rakitina, DV and Baikova, JP and Ladygina, VG and Kostryukova, ES and Karpova, IY and Semashko, TA and Larin, AK and Grigoryeva, TV and Sinyagina, MN and Malanin, SY and Shcherbakov, PL and Kharitonova, AY and Khalif, IL and Shapina, MV and Maev, IV and Andreev, DN and Belousova, EA and Buzunova, YM and Alexeev, DG and Govorun, VM}, title = {Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {968}, doi = {10.1186/s12864-018-5306-5}, pmid = {30587114}, issn = {1471-2164}, support = {16-15-00258//Russian Science Foundation/ ; }, abstract = {BACKGROUND: Crohn's disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated.<br><br>METHODS: We performed a metagenomic study investigating the gut microbiota of patients with Crohn's disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability.<br><br>RESULTS: The abnormal shifts in the microbial community structures in Crohn's disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes.<br><br>CONCLUSIONS: The genomic diversity of Crohn's disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn's disease and the development of new strategies for the prevention and treatment of this disease.}, }
@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 {pmid30586509, year = {2018}, author = {Johnson, RC and Deming, C and Conlan, S and Zellmer, CJ and Michelin, AV and Lee-Lin, S and Thomas, PJ and Park, M and Weingarten, RA and Less, J and Dekker, JP and Frank, KM and Musser, KA and McQuiston, JR and Henderson, DK and Lau, AF and Palmore, TN and Segre, JA}, title = {Investigation of a Cluster of Sphingomonas koreensis Infections.}, journal = {The New England journal of medicine}, volume = {379}, number = {26}, pages = {2529-2539}, doi = {10.1056/NEJMoa1803238}, pmid = {30586509}, issn = {1533-4406}, abstract = {BACKGROUND: Plumbing systems are an infrequent but known reservoir for opportunistic microbial pathogens that can infect hospitalized patients. In 2016, a cluster of clinical sphingomonas infections prompted an investigation.<br><br>METHODS: We performed whole-genome DNA sequencing on clinical isolates of multidrug-resistant Sphingomonas koreensis identified from 2006 through 2016 at the National Institutes of Health (NIH) Clinical Center. We cultured S. koreensis from the sinks in patient rooms and performed both whole-genome and shotgun metagenomic sequencing to identify a reservoir within the infrastructure of the hospital. These isolates were compared with clinical and environmental S. koreensis isolates obtained from other institutions.<br><br>RESULTS: The investigation showed that two isolates of S. koreensis obtained from the six patients identified in the 2016 cluster were unrelated, but four isolates shared more than 99.92% genetic similarity and were resistant to multiple antibiotic agents. Retrospective analysis of banked clinical isolates of sphingomonas from the NIH Clinical Center revealed the intermittent recovery of a clonal strain over the past decade. Unique single-nucleotide variants identified in strains of S. koreensis elucidated the existence of a reservoir in the hospital plumbing. Clinical S. koreensis isolates from other facilities were genetically distinct from the NIH isolates. Hospital remediation strategies were guided by results of microbiologic culturing and fine-scale genomic analyses.<br><br>CONCLUSIONS: This genomic and epidemiologic investigation suggests that S. koreensis is an opportunistic human pathogen that both persisted in the NIH Clinical Center infrastructure across time and space and caused health care-associated infections. (Funded by the NIH Intramural Research Programs.).}, }
@article {pmid30585382, year = {2018}, author = {Meier, DV and Pjevac, P and Bach, W and Markert, S and Schweder, T and Jamieson, J and Petersen, S and Amann, R and Meyerdierks, A}, title = {Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14514}, pmid = {30585382}, issn = {1462-2920}, abstract = {Metal-sulfides are wide-spread in marine benthic habitats. At deep-sea hydrothermal vents they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. While microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we performed 16S rRNA gene based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n=4) and metaproteome (n=1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate-reducing Nitrospirae and sulfide-oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr-clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide-oxidizers potentially facilitating metal-sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitats. This article is protected by copyright. All rights reserved.}, }
@article {pmid30584534, year = {2018}, author = {Ranjan, R and Rani, A and Finn, PW and Perkins, DL}, title = {Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {6074918}, doi = {10.1155/2018/6074918}, pmid = {30584534}, issn = {2314-6141}, abstract = {It is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of this study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced, and to determine if the data are comparable on different platforms. In this study, we perform ultradeep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We performed sequencing analysis using different Illumina platforms, with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others, and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.}, }
@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 {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 {pmid30583205, year = {2018}, author = {Awasthi, MK and Chen, H and Awasthi, SK and Duan, Y and Liu, T and Pandey, A and Varjani, S and Zhang, Z}, title = {Application of metagenomic analysis for detection of the reduction in the antibiotic resistance genes (ARGs) by the addition of clay during poultry manure composting.}, journal = {Chemosphere}, volume = {220}, number = {}, pages = {137-145}, doi = {10.1016/j.chemosphere.2018.12.103}, pmid = {30583205}, issn = {1879-1298}, abstract = {The aim of the study was to reduce relative abundance of antibiotic resistant genes (ARGs) in the poultry manure (PM) compost by adding clay and to determine the mechanism of this effect. Five doses of clay additive [at 0% (T1), 2% (T2), 4% (T3), 6% (T4), 8% (T5) and 10% (T6) based on PM dry weight] were compared to explore the mechanism of reduction in ARGs in the PM compost by the addition of clay. The results confirmed that in the initial raw PM from the breeding farm, the ARG concentrations were 1.7-3.01 times higher than that in the domestic PM. High doses of the clay additive play an important role in reduction in the ARGs and are the main factor responsible for significant variations in ARG abundance between the treatment groups. Therefore, we recommend adding high doses of clay (HDC) as an effective means to reduce the maximum percentage of ARGs in PM compost. A heat map correlation study confirmed that HDC addition during the composting process reduced the bioavailable fractions of toxic metals originating from the chicken feed and significantly impacted ARG dispersion.}, }
@article {pmid30583171, year = {2018}, author = {Sofo, A and Mininni, AN and Fausto, C and Scagliola, M and Crecchio, C and Xiloyannis, C and Dichio, B}, title = {Evaluation of the possible persistence of potential human pathogenic bacteria in olive orchards irrigated with treated urban wastewater.}, journal = {The Science of the total environment}, volume = {658}, number = {}, pages = {763-767}, doi = {10.1016/j.scitotenv.2018.12.264}, pmid = {30583171}, issn = {1879-1026}, abstract = {Under suitable conditions, low-quality, treated urban wastewater (TWW) is an additional water resource for irrigation in water-scarce environments but its use in agriculture requires a careful monitoring of a range of hygiene parameters, including human pathogenic bacteria (HPB). DNA-based microbiological analyses on soil, xylem sap, and leaves surface (phyllosphere) were carried out in an olive (Olea europaea L.) grove located in Southern Italy (Basilicata region). The experimental grove has been managed in two plots for 18 years. The experimental plot (WWtr) was drip irrigated daily with TWW (2800 m3 ha-1 year-1), while the control plot (RFtr) was rainfed. The results of the 16S-rRNA-based metagenomic analysis demonstrated that the phyllosphere had the lowest number of potential HPB (6), compared to soil (22) and xylem (26) compartments. Gammaproteobacteria, including potential HPB, like Pseudomonas and Acinetobacter spp., were significantly higher in WWtr soil and xylem sap, compared to RFtr. A similar trend was observed for Burkholderia spp. (Betaproteobacteria) and Mycobacterium spp. (Actinobacteria). The Firmicutes Enterococcus, Staphylococcus and Streptococcus spp. were more abundant in WWtr xylem sap. The pathogenic Clostridium perfringens was found higher on WWtr leaves (relative abundance 7.17 in WWtr and 1.33 in RFtr) and Enterococcus faecalis in WWtr xylem sap (93.22 in WWtr and 7.08 in RFtr). On the basis of the results obtained, the irrigation with TWW can be considered a realistic and safe agronomic practice in Mediterranean orchards, and an opportunity for farmers and consumers.}, }
@article {pmid30582346, year = {2018}, author = {Rizo, J and Guillén, D and Farrés, A and Díaz-Ruiz, G and Sánchez, S and Wacher, C and Rodríguez-Sanoja, R}, title = {Omics in traditional vegetable fermented foods and beverages.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/10408398.2018.1551189}, pmid = {30582346}, issn = {1549-7852}, abstract = {For a long time, food microbiota has been studied using traditional microbiological techniques. With the arrival of molecular or culture-independent techniques, a strong understanding of microbiota dynamics has been achieved. However, analyzing the functional role of microbial communities is not an easy task. The application of omics sciences to the study of fermented foods would provide the metabolic and functional understanding of the microbial communities and their impact on the fermented product, including the molecules that define its aroma and flavor, as well as its nutritional properties. Until now, most omics studies have focused on commercial fermented products, such as cheese, wine, bread and beer, but traditional fermented foods have been neglected. Therefore, the information that allows to relate the present microbiota in the food and its properties remains limited. In this review, reports on the applications of omics in the study of traditional fermented foods and beverages are reviewed to propose new ways to analyze the fermentation phenomena.}, }
@article {pmid30582061, year = {2018}, author = {Pérez-Wohlfeil, E and Torreno, O and Bellis, LJ and Fernandes, PL and Leskosek, B and Trelles, O}, title = {Training bioinformaticians in High Performance Computing.}, journal = {Heliyon}, volume = {4}, number = {12}, pages = {e01057}, doi = {10.1016/j.heliyon.2018.e01057}, pmid = {30582061}, issn = {2405-8440}, abstract = {In the last decade, bioinformatics has become an indispensable branch of modern science research, experiencing an explosion in financial support, developed applications and data collection. The growth of the datasets that are emerging from research laboratories, industry, the health sector, etc., are increasingly raising the levels of demand in computing power and storage. Processing biological data, in the large scales of these datasets, often requires the use of High Performance Computing (HPC) resources, especially when dealing with certain types of omics data, such as genomic and metagenomic data. Such computational resources not only require substantial investments, but they also involve high maintenance costs. More importantly, in order to keep good returns from the investments, specific training needs to be put in place to ensure that wasting is minimized. Furthermore, given that bioinformatics is a highly interdisciplinary field where several other domains intersect (such as biology, chemistry, physics and computer science), researchers from these areas also require bioinformatics-specific training in HPC, in order to fully take advantage of supercomputing centers. In this document, we describe our experience in training researchers from several different disciplines in HPC, as applied to bioinformatics under the framework of the leading European bioinformatics platform ELIXIR, and analyze both the content and outcomes of the course.}, }
@article {pmid30581925, year = {2019}, author = {Kabeer, FA and Jabir, T and Krishnan, KP and Abdulla, MH}, title = {Metagenomic data of fungal community in Kongsfjorden, Arctic using Illumina next generation sequencing.}, journal = {Data in brief}, volume = {22}, number = {}, pages = {195-198}, doi = {10.1016/j.dib.2018.12.026}, pmid = {30581925}, issn = {2352-3409}, abstract = {The data represents the diversity and distribution of fungal communities in Kongsfjorden, Arctic. The metagenomic DNA analysis was performed using next generation sequencing technology (Illumina MiSeq). Sequence data from amplified internal transcribed spacers (ITS) 2 region with fungal-specific primers exposed 83,417 sequences belonging to 7 operational taxonomic units (OTUs). Five of these OTUs belonged to Ascomycota, and one each to Basidiomycota and unclassified group. Aspergillus, Candida, Emericella and Nakaseomyces were the different genera identified and they belonged to the fungal orders Helotiales, Eurotiales and Saccharomycetales. The data explored the presence of important fungal communities in the Arctic marine ecosystem. Metagenome data is now available at NCBI under the Sequence Read Archive (SRA) database with accession no. SRP152688.}, }
@article {pmid30581850, year = {2018}, author = {Chen, WP and Chang, SH and Tang, CY and Liou, ML and Tsai, SJ and Lin, YL}, title = {Composition Analysis and Feature Selection of the Oral Microbiota Associated with Periodontal Disease.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {3130607}, doi = {10.1155/2018/3130607}, pmid = {30581850}, issn = {2314-6141}, abstract = {Periodontitis is an inflammatory disease involving complex interactions between oral microorganisms and the host immune response. Understanding the structure of the microbiota community associated with periodontitis is essential for improving classifications and diagnoses of various types of periodontal diseases and will facilitate clinical decision-making. In this study, we used a 16S rRNA metagenomics approach to investigate and compare the compositions of the microbiota communities from 76 subgingival plagues samples, including 26 from healthy individuals and 50 from patients with periodontitis. Furthermore, we propose a novel feature selection algorithm for selecting features with more information from many variables with a combination of these features and machine learning methods were used to construct prediction models for predicting the health status of patients with periodontal disease. We identified a total of 12 phyla, 124 genera, and 355 species and observed differences between health- and periodontitis-associated bacterial communities at all phylogenetic levels. We discovered that the genera Porphyromonas, Treponema, Tannerella, Filifactor, and Aggregatibacter were more abundant in patients with periodontal disease, whereas Streptococcus, Haemophilus, Capnocytophaga, Gemella, Campylobacter, and Granulicatella were found at higher levels in healthy controls. Using our feature selection algorithm, random forests performed better in terms of predictive power than other methods and consumed the least amount of computational time.}, }
@article {pmid30581671, year = {2018}, author = {Linz, AM and He, S and Stevens, SLR and Anantharaman, K and Rohwer, RR and Malmstrom, RR and Bertilsson, S and McMahon, KD}, title = {Freshwater carbon and nutrient cycles revealed through reconstructed population genomes.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e6075}, doi = {10.7717/peerj.6075}, pmid = {30581671}, issn = {2167-8359}, abstract = {Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.}, }
@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 {pmid30581419, year = {2018}, author = {Mutuku, JM and Wamonje, FO and Mukeshimana, G and Njuguna, J and Wamalwa, M and Choi, SK and Tungadi, T and Djikeng, A and Kelly, K and Domelevo Entfellner, JB and Ghimire, SR and Mignouna, HD and Carr, JP and Harvey, JJW}, title = {Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2939}, doi = {10.3389/fmicb.2018.02939}, pmid = {30581419}, issn = {1664-302X}, abstract = {Two closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean (Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well as other nutritional, agronomic, and economic benefits. Previous studies using antibody-based assays and indicator plants indicated that BCMV and BCMNV are both prevalent in bean fields in the region but these approaches cannot distinguish between these potyviruses or detect other viruses that may threaten the crop. In this study, we utilized next generation shotgun sequencing for a metagenomic examination of viruses present in bean plants growing at two locations in Kenya: the University of Nairobi Research Farm in Nairobi's Kabete district and at sites in Kirinyaga County. RNA was extracted from leaves of bean plants exhibiting apparent viral symptoms and sequenced on the Illumina MiSeq platform. We detected BCMNV, cucumber mosaic virus (CMV), and Phaseolus vulgaris alphaendornaviruses 1 and 2 (PvEV1 and 2), with CMV present in the Kirinyaga samples. The CMV strain detected in this study was most closely related to Asian strains, which suggests that it may be a recent introduction to the region. Surprisingly, and in contrast to previous surveys, BCMV was not detected in plants at either location. Some plants were infected with PvEV1 and 2. The detection of PvEV1 and 2 suggests these seed transmitted viruses may be more prevalent in Eastern African bean germplasm than previously thought.}, }
@article {pmid30581271, year = {2018}, author = {Rojas-Feria, M and Romero-García, T and Fernández Caballero-Rico, JÁ and Pastor Ramírez, H and Avilés-Recio, M and Castro-Fernandez, M and Chueca Porcuna, N and Romero-Gόmez, M and García, F and Grande, L and Del Campo, JA}, title = {Modulation of faecal metagenome in Crohn's disease: Role of microRNAs as biomarkers.}, journal = {World journal of gastroenterology}, volume = {24}, number = {46}, pages = {5223-5233}, doi = {10.3748/wjg.v24.i46.5223}, pmid = {30581271}, issn = {2219-2840}, abstract = {BACKGROUND: The gut microbiota plays a key role in the maintenance of intestinal homeostasis and the development and activation of the host immune system. It has been shown that commensal bacterial species can regulate the expression of host genes. 16S rRNA gene sequencing has shown that the microbiota in inflammatory bowel disease (IBD) is abnormal and characterized by reduced diversity. MicroRNAs (miRNAs) have been explored as biomarkers and therapeutic targets, since they are able to regulate specific genes associated with Crohn's disease (CD). In this work, we aim to investigate the composition of gut microbiota of active treatment-naïve adult CD patients, with miRNA profile from gut microbiota.<br><br>AIM: To investigate the composition of gut microbiota of active treatment-naïve adult CD patients, with miRNA profile from gut microbiota.<br><br>METHODS: Patients attending the outpatient clinics at Valme University Hospital without relevant co-morbidities were matched according to age and gender. Faecal samples of new-onset CD patients, free of treatment, and healthy controls were collected. Faecal samples were homogenized, and DNA was amplified by PCR using primers directed to the 16S bacterial rRNA gene. Pyrosequencing was performed using GS-Junior platform. For sequence analysis, MG-RAST server with the database Ribosomal Project was used. MiRNA profile and their relative abundance were analyzed by quantitative PCR.<br><br>RESULTS: Microbial community was characterized using 16S rRNA gene sequencing in 29 samples (n = 13 CD patients, and n = 16 healthy controls). The mean Shannon diversity was higher in the healthy control population compared to CD group (5.5 vs 3.7). A reduction in Firmicutes and an increase in Bacteroidetes were found. Clostridia class was also significantly reduced in CD. Principal components analysis showed a grouping pattern, identified in most of the subjects in both groups, showing a marked difference between control and CD groups. A functional metabolic study showed that a lower metabolism of carbohydrates (P = 0.000) was found in CD group, while the metabolism of lipids was increased. In CD patients, three miRNAs were induced in affected mucosa: mir-144 (6.2 ± 1.3 fold), mir-519 (21.8 ± 3.1) and mir-211 (2.3 ± 0.4).<br><br>CONCLUSION: Changes in microbial function in active non-treated CD subjects and three miRNAs in affected vs non-affected mucosa have been found. miRNAs profile may serve as a biomarker.}, }
@article {pmid30580413, year = {2019}, author = {Bridier, A}, title = {Exploring Foodborne Pathogen Ecology and Antimicrobial Resistance in the Light of Shotgun Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1918}, number = {}, pages = {229-245}, doi = {10.1007/978-1-4939-9000-9_19}, pmid = {30580413}, issn = {1940-6029}, abstract = {In this chapter, applications of shotgun metagenomics for taxonomic profiling and functional investigation of food microbial communities with a focus on antimicrobial resistance (AMR) were overviewed in the light of last data in the field. Potentialities of metagenomic approach, along with the challenges encountered for a wider and routinely use in food safety was discussed.}, }
@article {pmid30580031, year = {2018}, author = {Dyrhovden, R and Nygaard, RM and Patel, R and Ulvestad, E and Kommedal, Ø}, title = {The bacterial etiology of pleural empyema. A descriptive and comparative metagenomic study.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2018.11.030}, pmid = {30580031}, issn = {1469-0691}, abstract = {OBJECTIVES: The view of pleural empyema as a complication of bacterial pneumonia is changing since many patients lack evidence of underlying pneumonia. To further our understanding of pathophysiological mechanisms, we conducted in-depth microbiological characterization of empyemas in clinically well-characterized patients and investigated observed microbial parallels between pleural empyemas and brain abscesses.<br><br>METHODS: Culture- and/or 16S rRNA gene PCR positive pleural fluids were analyzed using massive parallel sequencing of the 16S rRNA and rpoB genes. Clinical details were evaluated by medical record review. Comparative analysis with brain abscesses was performed using metagenomic data from a national Norwegian study.<br><br>RESULTS: Sixty-four subjects with empyema were included. Thirty-seven had a well-defined microbial etiology, while 27, all of whom had community-acquired infections, did not. In the latter subset, Fusobacterium nucleatum and/or Streptococcus intermedius was detected in 26 patients, of which 18 had additional facultative and/or anaerobic species in various combinations. For this group, there was 65.5% species overlap with brain abscesses; predisposing factors included dental infection, minor chest trauma, chronic obstructive pulmonary disease, drug abuse, alcoholism and diabetes mellitus. Altogether, massive parallel sequencing yielded 385 bacterial detections, whereas culture detected 38 (10%) and 16S rRNA gene PCR/Sanger-based sequencing detected 87 (23%).<br><br>CONCLUSIONS: A subgroup of pleural empyema appears to be caused by a set of bacteria not normally considered to be involved in pneumonia. The empyemas have a similar microbial profile to oral/sinus-derived brain abscesses, supporting spread from the oral cavity, possibly hematogenously. We suggest reserving the term &quot;primary empyema&quot; for these infections.}, }
@article {pmid30579332, year = {2018}, author = {Getachew, B and Aubee, JI and Schottenfeld, RS and Csoka, AB and Thompson, KM and Tizabi, Y}, title = {Ketamine interactions with gut-microbiota in rats: relevance to its antidepressant and anti-inflammatory properties.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {222}, doi = {10.1186/s12866-018-1373-7}, pmid = {30579332}, issn = {1471-2180}, support = {R03AA022479//National Institute on Alcohol Abuse and Alcoholism/ ; R21AG047474//National Institute on Aging/ ; }, abstract = {BACKGROUND: Appreciable evidence suggest that dysbiosis in microbiota, reflected in gut microbial imbalance plays a key role in the pathogenesis of neuropsychiatric disorders including depression and inflammatory diseases. Recently, the antidepressant properties of ketamine have gained prominence due to its fast and long lasting effects. Additional uses for ketamine in inflammatory disorders such as irritable bowel syndrome have been suggested. However, ketamine's exact mechanism of action and potential effects on microbiome is not known. Here, we examined the effects of low dose ketamine, known to induce antidepressant effects, on stool microbiome profile in adult male Wistar rats. Animals (5/group) were injected intraperitoneally with ketamine (2.5 mg/kg) or saline, daily for 7 days and sacrificed on day 8 when intestinal stools were collected and stored at - 80 °C. DNA was extracted from the samples and the 16 S rRNA gene-based microbiota analysis was performed using 16S Metagenomics application.<br><br>RESULTS: At genus-level, ketamine strikingly amplified Lactobacillus, Turicibacter and Sarcina by 3.3, 26 and 42 fold, respectively. Conversely, opportunistic pathogens Mucispirillum and Ruminococcus were reduced by approximately 2.6 and 26 fold, respectively, in ketamine group. Low levels of Lactobacillus and Turicibacter are associated with various disorders including depression and administration of certain species of Lactobacillus ameliorates depressive-like behavior in animal models. Hence, some of the antidepressant effects of ketamine might be mediated through its interaction with these gut bacteria. Additionally, high level of Ruminococcus is positively associated with the severity of irritable bowel syndrome (IBS), and some species of Mucispirillum have been associated with intestinal inflammation. Indirect evidence of anti-inflammatory role of Sarcina has been documented. Hence, some of the anti-inflammatory effects of ketamine and its usefulness in specific inflammatory diseases including IBS may be mediated through its interaction with these latter bacteria.<br><br>CONCLUSION: Our data suggest that at least some of the antidepressant and anti-inflammatory effects of daily ketamine treatment for 7 days may be mediated via its interaction with specific gut bacteria. These findings further validate the usefulness of microbiome as a target for therapeutic intervention and call for more detailed investigation of microbiome interaction with central mediators of mood and/or inflammatory disorders.}, }
@article {pmid30579213, year = {2018}, author = {Reddy, B and Dubey, SK}, title = {River Ganges water as reservoir of microbes with antibiotic and metal ion resistance genes: High throughput metagenomic approach.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {246}, number = {}, pages = {443-451}, doi = {10.1016/j.envpol.2018.12.022}, pmid = {30579213}, issn = {1873-6424}, abstract = {The large scale usage of antibiotics and trace elements leads to their progressive release in the environment, and ultimately the spread of antibiotic resistance genes (ARGs) and metal ion resistance genes (MRGs) in bacteria. A high-throughput metagenomic sequencing of the microbial community in water and sediments in the river Ganges harboring resistance genes was performed. The results revealed that the river harbors a broad spectrum of resistance genes with high abundance in sediments. The highly dominant ARGs type was beta-lactam, multidrug/efflux and elfamycin. The ARGs such as (tuf, parY, ileS, mfd) were highly abundant in water and sediments. The MRGs subtype acn was the most abundant metal resistance gene in water and sediments. Majority of ARGs types showed significant (p ≤ 0.05) positive correlation with the MRGs types in the river environment suggesting their distribution and transfer to be possibly linked. Taxonomic classification revealed that Proteobacteria and Actinobacteria were the two most abundant phyla in water and sediments. Arcobacter, Terrimicrobium, Acidibacter and Pseudomonas were the most abundant genera. This study suggests that antibiotics and metals are the driving force for the emergence of resistance genes, and their subsequent propagation and accumulation in the environmental bacteria. The present metagenomic investigation highlights significance of such study, and attracts attention for the mitigation of pollutants associated with the propagation of ARGs and MRGs in the river environment.}, }
@article {pmid30579193, year = {2018}, 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}, 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 {pmid30578963, year = {2018}, author = {Piewngam, P and Quiñones, M and Thirakittiwatthana, W and Yungyuen, T and Otto, M and Kiratisin, P}, title = {Composition of the intestinal microbiota in extended-spectrum β-lactamase-producing Enterobacteriaceae carriers and non-carriers in Thailand.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijantimicag.2018.12.006}, pmid = {30578963}, issn = {1872-7913}, abstract = {There is increasing recognition that the intestinal microbiota govern human well-being and prevent diseases. Intestinal colonization by antibiotic-resistant pathogens, however, can lead to the spread of resistance as well as serious infections. Extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E) represent particularly dangerous pathogens, which are known to asymptomatically colonize the intestinal tract in the community. Here, we performed a 16S rRNA metagenomics sequence analysis to analyze differences in the microbiota composition between ESBL-E carriers and non-carriers in Thailand, where ESBL-E carriage rates are notoriously high. The most notable difference we detected was that the phylum Bacteroidetes, and in particular, the species Bacteroides uniformis, were significantly more abundant in ESBL-E non-carriers than carriers. The Shannon diversity index in non-carriers (5.10 ± 0.69) was also lower than that in ESBL-E carriers (5.39 ± 0.48) without statistical significance (P = 0.13). The overall beta diversity difference of the intestinal microbiota of ESBL-E carriers as compared to non-carriers was statistically significant (Adonis on weighted unifrac: R2=0.14, P = 0.005). Furthermore, ESBL-E carriage was significantly lower in farmers than other occupations. Our findings suggest that a dynamic interaction exists between microbiota diversity and ESBL-E carriage, which is possibly driven by dietary composition and may be exploited using probiotic approaches to control the spread of ESBL-E.}, }
@article {pmid30578804, year = {2018}, author = {Kinsella, CM and Deijs, M and van der Hoek, L}, title = {Enhanced bioinformatic profiling of VIDISCA libraries for virus detection and discovery.}, journal = {Virus research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.virusres.2018.12.010}, pmid = {30578804}, issn = {1872-7492}, abstract = {VIDISCA is a next-generation sequencing (NGS) library preparation method designed to enrich viral nucleic acids from samples before highly-multiplexed low depth sequencing. Reliable detection of known viruses and discovery of novel divergent viruses from NGS data require dedicated analysis tools that are both sensitive and accurate. Existing software was utilised to design a new bioinformatic workflow for high-throughput detection and discovery of viruses from VIDISCA data. The workflow leverages the VIDISCA library preparation molecular biology, specifically the use of Mse1 restriction enzyme which produces biological replicate library inserts from identical genomes. The workflow performs total metagenomic analysis for classification of non-viral sequence including parasites and host, and separately carries out virus specific analyses. Ribosomal RNA sequence is removed to increase downstream analysis speed and remaining reads are clustered at 100% identity. Known and novel viruses are sensitively detected via alignment to a virus-only protein database, and false positives are removed. A new cluster-profiling analysis takes advantage of the viral biological replicates produced by Mse1 digestion, using read clustering to flag the presence of short genomes at very high copy number. Importantly, this analysis ensures that highly repeated sequences are identified even if no homology is detected, as is shown here with the detection of a novel gokushovirus genome from human faecal matter. The workflow was validated using read data derived from serum and faeces samples taken from HIV-1 positive adults, and serum samples from pigs that were infected with atypical porcine pestivirus.}, }
@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}, 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 {pmid30576749, year = {2018}, author = {Langlais, M and Thibodeau, A and Fravalo, P}, title = {A metagenomic analysis of the pre-enrichment step for the isolation of Salmonella spp. from pig feces.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mimet.2018.12.014}, pmid = {30576749}, issn = {1872-8359}, abstract = {The bacterial short pre-enrichment culture step is important for the proper detection and isolation of Salmonella spp. from pig feces. Using metagenomics, we showed that pre-enrichment of Salmonella was favored not only by inhibiting the growth of competing bacteria but also by increasing its fitness.}, }
@article {pmid30576430, year = {2018}, author = {Casto, AM and Adler, AL and Makhsous, N and Crawford, K and Qin, X and Kuypers, JM and Huang, ML and Zerr, DM and Greninger, AL}, title = {Prospective real-time metagenomic sequencing during norovirus outbreak reveals discrete transmission clusters.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciy1020}, pmid = {30576430}, issn = {1537-6591}, abstract = {Background: Norovirus outbreaks in hospital settings are a common challenge for infection prevention teams. Given the high burden of norovirus in most communities, it can be difficult to distinguish between on-going in-hospital transmission of virus and new introductions from the community and challenging to understand the long-term impacts of outbreak-associated viruses within medical systems using traditional epidemiological approaches alone.<br><br>Methods: Real-time metagenomic sequencing during an on-going norovirus outbreak associated with a retrospective cohort study.<br><br>Results: We describe a hospital-associated norovirus outbreak that affected 13 patients over a 27-day period in a large tertiary pediatric hospital and was chronologically associated with a spike in self-reported gastrointestinal symptoms among staff. Real-time metagenomic next-generation sequencing (mNGS) of norovirus genomes demonstrated that 10 chronologically overlapping hospital-acquired norovirus cases were partitioned into three discrete transmission clusters. Sequencing data also revealed close genetic relationships between some hospital-acquired and some community-acquired cases. Finally, this data was used to demonstrate chronic viral shedding by an immunocompromised hospital-acquired case patient. Analysis of serial samples from this patient provided novel insights into the evolution of norovirus within an immunocompromised host.<br><br>Conclusions: This study documents one of the first applications of real-time mNGS during a hospital-associated viral outbreak. Given its demonstrated ability to detect transmission patterns within outbreaks and elucidate the long-term impacts of outbreak-associated viral strains on patients and medical systems, mNGS constitutes a powerful resource to help infection control teams understand, prevent, and respond to viral outbreaks.}, }
@article {pmid30575381, year = {2018}, author = {Kim, SH and Lu, W and Ahmadi, MK and Montiel, D and Ternei, MA and Brady, SF}, title = {Atolypenes, Tricyclic Bacterial Sesterterpenes Discovered Using a Multiplexed In Vitro Cas9-TAR Gene Cluster Refactoring Approach.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.8b00361}, pmid = {30575381}, issn = {2161-5063}, abstract = {Most natural product biosynthetic gene clusters identified in bacterial genomic and metagenomic sequencing efforts are silent under laboratory growth conditions. Here, we describe a scalable biosynthetic gene cluster activation method wherein the gene clusters are disassembled at interoperonic regions in vitro using CRISPR/Cas9 and then reassembled with PCR-amplified, short DNAs, carrying synthetic promoters, using transformation assisted recombination (TAR) in yeast. This simple, cost-effective, and scalable method allows for the simultaneous generation of combinatorial libraries of refactored gene clusters, eliminating the need to understand the transcriptional hierarchy of the silent genes. In two test cases, this in vitro disassembly-TAR reassembly method was used to create collections of promoter-replaced gene clusters that were tested in parallel to identify versions that enabled secondary metabolite production. Activation of the atolypene (ato) gene cluster led to the characterization of two unprecedented bacterial cyclic sesterterpenes, atolypene A (1) and B (2), which are moderately cytotoxic to human cancer cell lines. This streamlined in vitro disassembly- in vivo reassembly method offers a simplified approach for silent gene cluster refactoring that should facilitate the discovery of natural products from silent gene clusters cloned from either metagenomes or cultured bacteria.}, }
@article {pmid30575285, year = {2018}, author = {Arif, M and Gauthier, J and Sugier, K and Iudicone, D and Jaillon, O and Wincker, P and Peterlongo, P and Madoui, MA}, title = {Discovering Millions of Plankton Genomic Markers from the Atlantic Ocean and the Mediterranean Sea.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.12985}, pmid = {30575285}, issn = {1755-0998}, abstract = {Comparison of the molecular diversity in all plankton populations present in geographically distant water columns may allow for a holistic view of the connectivity, isolation and adaptation of organisms in the marine environment. In this context, a large-scale detection and analysis of genomic variants directly in metagenomic data appeared as a powerful strategy for the identification of genetic structures and genes under natural selection in plankton. Here, we used DiscoSnp++, a reference-free variant caller, to produce genetic variants from large-scale metagenomic data and assessed its accuracy on the copepod Oithona nana in terms of variant calling, allele frequency estimation and population genomic statistics by comparing it to the state-of-the-art method. DiscoSnp++ produces variants leading to similar conclusions regarding the genetic structure and identification of loci under natural selection. DiscoSnp++ was then applied to 120 metagenomic samples from four size fractions, including prokaryotes, protists and zooplankton sampled from 39 Tara Oceans sampling stations located in the Atlantic Ocean and the Mediterranean Sea to produce a new set of marine genomic markers containing more than 19 million of variants. This new genomic resource can be used by the community to relocate these markers on their plankton genomes or transcriptomes of interest. This resource will be updated with new marine expeditions and the increase of metagenomic data (availability: http://bioinformatique.rennes.inria.fr/taravariants/). This article is protected by copyright. All rights reserved.}, }
@article {pmid30574802, year = {2018}, author = {Murphy, R and Morgan, XC and Wang, XY and Wickens, K and Purdie, G and Fitzharris, P and Otal, A and Lawley, B and Stanley, T and Barthow, C and Crane, J and Mitchell, EA and Tannock, GW}, title = {Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-13}, doi = {10.3920/BM2017.0191}, pmid = {30574802}, issn = {1876-2891}, abstract = {Probiotic Lactobacillus rhamnosus HN001 given in early life has been shown to reduce infant eczema risk, but its effect on gut microbiota development has not been quantitatively and functionally examined. The aim of this study was to investigate the impact of early life probiotic exposure on the composition and functional capacity of infant gut microbiota from birth to 2 years considering the effects of age, delivery mode, antibiotics, pets and eczema. We performed shotgun metagenomic sequencing analysis of 650 infant faecal samples, collected at birth, 3, 12, and 24 months, as part of a randomised, controlled, 3-arm trial assessing the effect of L. rhamnosus HN001, Bifidobacterium animalis subsp. lactis HN019 supplementation on eczema development in 474 infants. There was a 50% reduced eczema risk in the HN001 probiotic group compared to placebo. Both mothers (from 35 weeks gestation until 6 months post-partum if breastfeeding) and infants (from birth to 2 years) received either a placebo or one of two probiotics, L. rhamnosus HN001 (6×109 cfu), or B. animalis subsp. lactis HN019 (9×109 cfu). L. rhamnosus HN001 probiotic supplementation was associated with increased overall glycerol-3 phosphate transport capacity and enrichment of L. rhamnosus. There were no other significant changes in infant gut microbiota composition or diversity. Increased capacity to transport glycerol-3-phosphate was positively correlated with relative abundance of L. rhamnosus. Children who developed eczema had gut microbiota with increased capacity for glycosaminoglycan degradation and flagellum assembly but had no significant differences in microbiota composition or diversity. Early life HN001 probiotic use is associated with both increased L. rhamnosus and increased infant gut microbiota functional capacity to transport glycerol-3 phosphate. The mechanistic relationship of such functional alteration in gut microbiota with reduced eczema risk and long-term health merits further investigation.}, }
@article {pmid30574559, year = {2018}, author = {Leigh, BA and Bordenstein, SR and Brooks, AW and Mikaelyan, A and Bordenstein, SR}, title = {Finer-Scale Phylosymbiosis: Insights from Insect Viromes.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00131-18}, pmid = {30574559}, issn = {2379-5077}, abstract = {Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern whereby the ecological relatedness (e.g., beta diversity relationships) of host-associated microbial communities parallels the phylogeny of the host species. Representing the most abundant biological entities on the planet and common members of the animal-associated microbiome, viruses can be influential members of host-associated microbial communities that may recapitulate, reinforce, or ablate phylosymbiosis. Here we sequence the metagenomes of purified viral communities from three different parasitic wasp Nasonia species, one cytonuclear introgression line of Nasonia, and the flour moth outgroup Ephestia kuehniella. Results demonstrate complete phylosymbiosis between the viral metagenome and insect phylogeny. Across all Nasonia contigs, 69% of the genes in the viral metagenomes are either new to the databases or uncharacterized, yet over 99% of the contigs have at least one gene with similarity to a known sequence. The core Nasonia virome spans 21% of the total contigs, and the majority of that core is likely derived from induced prophages residing in the genomes of common Nasonia-associated bacterial genera: Proteus, Providencia, and Morganella. We also assemble the first complete viral particle genomes from Nasonia-associated gut bacteria. Taken together, results reveal the first complete evidence for phylosymbiosis in viral metagenomes, new genome sequences of viral particles from Nasonia-associated gut bacteria, and a large set of novel or uncharacterized genes in the Nasonia virome. This work suggests that phylosymbiosis at the host-microbiome level will likely extend to the host-virome level in other systems as well. IMPORTANCE Viruses are the most abundant biological entity on the planet and interact with microbial communities with which they associate. The virome of animals is often dominated by bacterial viruses, known as bacteriophages or phages, which can (re)structure bacterial communities potentially vital to the animal host. Beta diversity relationships of animal-associated bacterial communities in laboratory and wild populations frequently parallel animal phylogenetic relationships, a pattern termed phylosymbiosis. However, little is known about whether viral communities also exhibit this eco-evolutionary pattern. Metagenomics of purified viruses from recently diverged species of Nasonia parasitoid wasps reared in the lab indicates for the first time that the community relationships of the virome can also exhibit complete phylosymbiosis. Therefore, viruses, particularly bacteriophages here, may also be influenced by animal evolutionary changes either directly or indirectly through the tripartite interactions among hosts, bacteria, and phage communities. Moreover, we report several new bacteriophage genomes from the common gut bacteria in Nasonia.}, }
@article {pmid30574558, year = {2018}, author = {Fahimipour, AK and Ben Mamaar, S and McFarland, AG and Blaustein, RA and Chen, J and Glawe, AJ and Kline, J and Green, JL and Halden, RU and Van Den Wymelenberg, K and Huttenhower, C and Hartmann, EM}, title = {Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00200-18}, pmid = {30574558}, issn = {2379-5077}, abstract = {Humans purposefully and inadvertently introduce antimicrobial chemicals into buildings, resulting in widespread compounds, including triclosan, triclocarban, and parabens, in indoor dust. Meanwhile, drug-resistant infections continue to increase, raising concerns that buildings function as reservoirs of, or even select for, resistant microorganisms. Support for these hypotheses is limited largely since data describing relationships between antimicrobials and indoor microbial communities are scant. We combined liquid chromatography-isotope dilution tandem mass spectrometry with metagenomic shotgun sequencing of dust collected from athletic facilities to characterize relationships between indoor antimicrobial chemicals and microbial communities. Elevated levels of triclosan and triclocarban, but not parabens, were associated with distinct indoor microbiomes. Dust of high triclosan content contained increased Gram-positive species with diverse drug resistance capabilities, whose pangenomes were enriched for genes encoding osmotic stress responses, efflux pump regulation, lipid metabolism, and material transport across cell membranes; such triclosan-associated functional shifts have been documented in laboratory cultures but not yet from buildings. Antibiotic-resistant bacterial isolates were cultured from all but one facility, and resistance often increased in buildings with very high triclosan levels, suggesting links between human encounters with viable drug-resistant bacteria and local biocide conditions. This characterization uncovers complex relationships between antimicrobials and indoor microbiomes: some chemicals elicit effects, whereas others may not, and no single functional or resistance factor explained chemical-microbe associations. These results suggest that anthropogenic chemicals impact microbial systems in or around buildings and their occupants, highlighting an emergent need to identify the most important indoor, outdoor, and host-associated sources of antimicrobial chemical-resistome interactions. IMPORTANCE The ubiquitous use of antimicrobial chemicals may have undesired consequences, particularly on microbes in buildings. This study shows that the taxonomy and function of microbes in indoor dust are strongly associated with antimicrobial chemicals-more so than any other feature of the buildings. Moreover, we identified links between antimicrobial chemical concentrations in dust and culturable bacteria that are cross-resistant to three clinically relevant antibiotics. These findings suggest that humans may be influencing the microbial species and genes that are found indoors through the addition and removal of particular antimicrobial chemicals.}, }
@article {pmid30574136, year = {2018}, author = {Brotto, AC and Annavajhala, MK and Chandran, K}, title = {Metatranscriptomic Investigation of Adaptation in NO and N2O Production From a Lab-Scale Nitrification Process Upon Repeated Exposure to Anoxic-Aerobic Cycling.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3012}, doi = {10.3389/fmicb.2018.03012}, pmid = {30574136}, issn = {1664-302X}, abstract = {The molecular mechanisms of microbial adaptation to repeated anoxic-aerobic cycling were investigated by integrating whole community gene expression (metatranscriptomics) and physiological responses, including the production of nitric (NO) and nitrous (N2O) oxides. Anoxic-aerobic cycling was imposed for 17 days in a lab-scale full-nitrification mixed culture system. Prior to cycling, NO and N2O levels were sustained at 0.097 ± 0.006 and 0.054 ± 0.019 ppmv, respectively. Once the anoxic-aerobic cycling was initiated, peak emissions were highest on the first day (9.8 and 1.3 ppmv, respectively). By the end of day 17, NO production returned to pre-cycling levels (a peak of 0.12 ± 0.007 ppmv), while N2O production reached a new baseline (a peak of 0.32 ± 0.05 ppmv), one order of magnitude higher than steady-state conditions. Concurrently, post-cycling transcription of norBQ and nosZ returned to pre-cycling levels after an initial 5.7- and 9.5-fold increase, while nirK remained significantly expressed (1.6-fold) for the duration of and after cycling conditions. The imbalance in nirK and nosZ mRNA abundance coupled with continuous conversion of NO to N2O might explain the elevated post-cycling baseline for N2O. Metatranscriptomic investigation notably indicated possible NO production by NOB under anoxic-aerobic cycling through a significant increase in nirK expression. Opposing effects on AOB (down-regulation) and NOB (up-regulation) CO2 fixation were observed, suggesting that nitrifying bacteria are differently impacted by anoxic-aerobic cycling. Genes encoding the terminal oxidase of the electron transport chain (ccoNP, coxBC) were the most significantly transcribed, highlighting a hitherto unexplored pathway to manage high electron fluxes resulting from increased ammonia oxidation rates, and leading to overall, increased NO and N2O production. In sum, this study identified underlying metabolic processes and mechanisms contributing to NO and N2O production through a systems-level interrogation, which revealed the differential ability of specific microbial groups to adapt to sustained operational conditions in engineered biological nitrogen removal processes.}, }
@article {pmid30572955, year = {2018}, author = {Pyzik, A and Ciezkowska, M and Krawczyk, PS and Sobczak, A and Drewniak, L and Dziembowski, A and Lipinski, L}, title = {Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production.}, journal = {Microbial cell factories}, volume = {17}, number = {1}, pages = {197}, doi = {10.1186/s12934-018-1043-3}, pmid = {30572955}, issn = {1475-2859}, support = {PBS1/A8/3/2012//Narodowe Centrum Badań i Rozwoju/ ; POIG.01.01.02-14-054/09-00//Narodowe Centrum Badań i Rozwoju/ ; POIG.02.02.00-14-024/08-00//Narodowe Centrum Badań i Rozwoju/ ; }, abstract = {BACKGROUND: Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways.<br><br>RESULTS: A comprehensive metagenomic approach was used to compare seven environmental communities, originating from an agricultural biogas plant, cattle-associated samples, a lowland bog, sewage sludge from a wastewater treatment plant and sediments from an ancient gold mine. In addition to the native consortia, two laboratory communities cultivated on maize silage as the sole substrate were also analyzed. Results showed that all anaerobic communities harbored genes of all known methanogenesis pathways, but their abundance varied greatly between environments and that genes were encoded by different methanogens. Identification of microorganisms directly involved in different stages of methane production revealed that hydrogenotrophic methanogens, such as Methanoculleus, Methanobacterium, Methanobrevibacter, Methanocorpusculum or Methanoregula, predominated in most native communities, whereas acetoclastic Methanosaeta seemed to be the key methanogen in the wastewater treatment plant. Furthermore, in many environments, the methylotrophic pathway carried out by representatives of Methanomassiliicoccales, such as Candidatus Methanomethylophilus and Candidatus Methanoplasma, seemed to play an important role in methane production. In contrast, in stable laboratory reactors substrate versatile Methanosarcina predominated.<br><br>CONCLUSIONS: The metagenomic approach presented in this study allowed for deep exploration and comparison of nine environments in which methane production occurs. Different abundance of methanogenesis-related functions was observed and the functions were analyzed in the phylogenetic context in order to identify microbes directly involved in methane production. In addition, a comparison of two metagenomic analytical tools, MG-RAST and MetAnnotate, revealed that combination of both allows for a precise characterization of methanogenic communities.}, }
@article {pmid28592823, year = {2017}, author = {Cardoso, DC and Sandionigi, A and Cretoiu, MS and Casiraghi, M and Stal, L and Bolhuis, H}, title = {Comparison of the active and resident community of a coastal microbial mat.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2969}, pmid = {28592823}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Seawater ; *Water Microbiology ; }, abstract = {Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potential stable pool of extracellular DNA. Here we focused on the active microbial community by comparing 16S rRNA sequences obtained from the ribosomal RNA pool with gene sequences obtained from the DNA fraction. In addition, we aimed to establish an optimal and feasible sampling protocol that takes potential spatial and temporal heterogeneity into account. The coastal microbial mat investigated here was sampled randomly and at regular time points during one 24-h period. DNA and RNA was extracted and after conversion of the RNA fraction to cDNA, the V1-V3 and the V3-V4 regions of the 16S rRNA gene were targeted for high-throughput amplicon sequencing. We show that the community composition varies little in time and space whereas two amplified 16S regions gave significant different results. The largest differences were found when comparing the &quot;resident community&quot; (DNA) with the &quot;active community&quot; (cDNA/RNA); in the latter, Cyanobacteria dominated for almost 95% while they represented 60% of the resident fraction.}, }
@article {pmid30572101, year = {2018}, author = {Wang, S and Li, N and Zou, H and Wu, M}, title = {Gut microbiome-based secondary metabolite biosynthetic gene clusters detection in Parkinson's disease.}, journal = {Neuroscience letters}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.neulet.2018.12.021}, pmid = {30572101}, issn = {1872-7972}, abstract = {The microbiota of individuals with Parkinson's disease (PD) has been the focus of research in recent years. However, the mechanisms underlying the interactions between the gut microbiome and the brain, as well as its role in PD pathogenesis, remain to be elucidated. In this study, we used a systematic approach to predict putative biosynthetic gene clusters (BGCs) from the raw metagenomic data of the gut microbiome, and identified 43 BGCs that were significantly enriched in the PD patients. Fourteen of these clusters originated from microbes that were not increased in the patients, and the most significantly enriched one encoded a putative efflux protein and a radical SAM protein, indicating a potential role in PD. Based on a random forest classifier, these BGCs can be used to correctly discriminate between PD patients and healthy controls, with a cross-validated AUC of 0.91 from the 31 early stage PD patients and 28 healthy controls. Our study provides an alternative method to analyze the microbiota of PD patients, and further increase our understanding of this disease.}, }
@article {pmid30569277, year = {2018}, author = {Wang, H and Zhang, W and Yang, S and Kong, N and Yu, H and Zheng, H and Gao, F and Tong, W and Li, L and Wang, X and Deng, X and Delwart, E and Shan, T}, title = {Asian black bear (Ursus thibetanus) picornavirus related to seal aquamavirus A.}, journal = {Archives of virology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00705-018-4101-6}, pmid = {30569277}, issn = {1432-8798}, support = {2017YFC1200201//National Key Research and Development Programs of China/ ; 2016YFD0500103//National Key Research and Development Programs of China/ ; 31872478//National Natural Science Foundation of China (CN)/ ; 81741062//National Natural Science Foundation of China (CN)/ ; }, abstract = {The complete genome of a bear picornavirus 1 (BePV-1) in the viscera of an Asian black bear (Ursus thibetanus) from China was characterized using viral metagenomics and RT-PCR/Sanger sequencing. The genome of BePV1 is 6703 nt long, contains a type-IV IRES 5'UTR with the '8-like' motif, encodes a 2053-aa-long polyprotein showing a 3-4-4 organization pattern and two 2A genes. BePV-1 showed the highest overall genome nucleotide sequence identity of 71.7% to a picornavirus genome from an Arctic ringed seal (Phoca hispida) from Canada, classified as a member of the species Aquamavirus A, currently the only one in the genus Aquamavirus. Phylogenetic and genetic distance analyses of P1 and 3D indicated that Asian bear picornavirus (aquamavirus B) represents the second sequenced member of the genus Aquamavirus.}, }
@article {pmid30568647, year = {2018}, author = {Yang, Q and Zhang, M and Zhang, M and Wang, C and Liu, Y and Fan, X and Li, H}, title = {Characterization of a Novel, Cold-Adapted, and Thermostable Laccase-Like Enzyme With High Tolerance for Organic Solvents and Salt and Potent Dye Decolorization Ability, Derived From a Marine Metagenomic Library.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2998}, doi = {10.3389/fmicb.2018.02998}, pmid = {30568647}, issn = {1664-302X}, abstract = {Synthetic dyes are widely used in many industries, but they cause serious environmental problems due to their carcinogenic and mutagenic properties. In contrast to traditional physical and chemical treatments, biodegradation is generally considered an environmental-friendly, efficient, and inexpensive way to eliminate dye contaminants. Here, a novel laccase-like enzyme Lac1326 was cloned from a marine metagenomic library. It showed a maximum activity at 60°C, and it retained more than 40% of its maximal activity at 10°C and more than 50% at 20-70°C. Interestingly, the laccase behaved stably below 50°C, even in commonly used water-miscible organic solvents. The enzyme decolorized all tested dyes with high decolorization efficiency. This thermostable enzyme with high decolorization activity and excellent tolerance of organic solvents and salt has remarkable potential for bioremediation of dye wastewater. It is thus proposed as an industrial enzyme.}, }
@article {pmid30568637, year = {2018}, author = {Ni, G and Simone, D and Palma, D and Broman, E and Wu, X and Turner, S and Dopson, M}, title = {A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2945}, doi = {10.3389/fmicb.2018.02945}, pmid = {30568637}, issn = {1664-302X}, abstract = {Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed 'acid mine drainage (AMD)'] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of 'microbial fuel cells' that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbe-mineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-like population had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylyl-sulfate released electrons and the extracellular electron transfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganic sulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.}, }
@article {pmid30567928, year = {2018}, author = {Vich Vila, A and Imhann, F and Collij, V and Jankipersadsing, SA and Gurry, T and Mujagic, Z and Kurilshikov, A and Bonder, MJ and Jiang, X and Tigchelaar, EF and Dekens, J and Peters, V and Voskuil, MD and Visschedijk, MC and van Dullemen, HM and Keszthelyi, D and Swertz, MA and Franke, L and Alberts, R and Festen, EAM and Dijkstra, G and Masclee, AAM and Hofker, MH and Xavier, RJ and Alm, EJ and Fu, J and Wijmenga, C and Jonkers, DMAE and Zhernakova, A and Weersma, RK}, title = {Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.}, journal = {Science translational medicine}, volume = {10}, number = {472}, pages = {}, doi = {10.1126/scitranslmed.aap8914}, pmid = {30567928}, issn = {1946-6242}, abstract = {Changes in the gut microbiota have been associated with two of the most common gastrointestinal diseases, inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). Here, we performed a case-control analysis using shotgun metagenomic sequencing of stool samples from 1792 individuals with IBD and IBS compared with control individuals in the general population. Despite substantial overlap between the gut microbiome of patients with IBD and IBS compared with control individuals, we were able to use gut microbiota composition differences to distinguish patients with IBD from those with IBS. By combining species-level profiles and strain-level profiles with bacterial growth rates, metabolic functions, antibiotic resistance, and virulence factor analyses, we identified key bacterial species that may be involved in two common gastrointestinal diseases.}, }
@article {pmid30567558, year = {2018}, author = {Cheng, J and Hu, H and Kang, Y and Chen, W and Fang, W and Wang, K and Zhang, Q and Fu, A and Zhou, S and Cheng, C and Cao, Q and Wang, F and Lee, S and Zhou, Z}, title = {Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {17}, number = {1}, pages = {43}, doi = {10.1186/s12941-018-0294-5}, pmid = {30567558}, issn = {1476-0711}, support = {2016-I2M-1-016//Chinese Academy of Medical Sciences/ ; }, abstract = {BACKGROUND: Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathogens detection, many cases are culture-negative, especially in patients who had received long-term antibiotic treatment, and precise diagnosis has therefore become a major challenge in the clinic. Metagenomic sequencing can provide both information on the pathogenic strain and the antibiotic susceptibility profile of patient samples without culturing, offering a powerful method to deal with culture-negative cases.<br><br>METHODS: To assess the feasibility of a metagenomic approach to detect the causative pathogens in resected valves from IE patients, we employed both next-generation sequencing and Oxford Nanopore Technologies MinION nanopore sequencing for pathogens and antimicrobial resistance detection in seven culture-negative IE patients. Using our in-house developed bioinformatics pipeline, we analyzed the sequencing results generated from both platforms for the direct identification of pathogens from the resected valves of seven clinically culture-negative IE patients according to the modified Duke criteria.<br><br>RESULTS: Our results showed both metagenomics methods can be applied for the causative pathogen detection in all IE samples. Moreover, we were able to simultaneously characterize respective antimicrobial resistance features.<br><br>CONCLUSION: Metagenomic methods for IE detection can provide clinicians with valuable information to diagnose and treat IE patients after valve replacement surgery. However, more efforts should be made to optimize protocols for sample processing, sequencing and bioinformatics analysis.}, }
@article {pmid30565684, year = {2018}, author = {Wang, JC and Bergeron, M and Andersen, H and Tikhtman, R and Haslam, D and Hunter, T and Herr, AB and de Alarcon, A}, title = {Feasibility of shotgun metagenomics to assess microbial ecology of pediatric tracheostomy tubes.}, journal = {The Laryngoscope}, volume = {}, number = {}, pages = {}, doi = {10.1002/lary.27356}, pmid = {30565684}, issn = {1531-4995}, abstract = {OBJECTIVE: Biofilm formation on medical devices such as tracheostomy tubes (TTs) is a serious problem. The clinical impact of biofilms on the airway is still unclear. Biofilms may play a role in granulation tissue development, recurrent airway infections, and failure of laryngotracheal reconstructions. The microbial ecology on TTs has yet to be elucidated. The purpose of this study was to determine the feasibility of shotgun metagenomics to assess the biodistribution of microorganisms on TTs.<br><br>METHODS: Four TTs were collected from pediatric patients (1.4-10.2 years) with (n = 2) and without (n = 2) granulation tissue formation. Duration of TT placement prior to retrieval from patients ranged from 5 to 365 days. DNA extraction was performed using the MO BIO UltraClean Microbial Isolation (Mo Bio Laboratories, Carlsbad, CA). Library generation using Nextera XT adapters (Illumina Inc., San Diego, CA) and metagenomic shotgun sequencing was performed using the Illumina NextSeq500 (Illumina Inc, San Diego, CA). Salinibacter ruber, a species not found in mammalian microbiome communities, was used as a DNA standard and represented 0.7% to 5.7% of the microbiome, ensuring good quality and abundance of sample DNA.<br><br>RESULTS: Metagenomic shotgun sequencing was successful for all patients. In TTs associated with granuloma, Fusobacterium nucleatum, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae were predominant, most of which are considered pathogens. From TTs without granulomas, Neisseria mucosa, Neisseria sicca, Acinetobacter baumannii, and Haemophilus parainfluenzae were identified, primarily consistent with respiratory microbiome.<br><br>CONCLUSION: This study reveals that metagenomic shotgun sequencing of biofilms formed on pediatric TTs is feasible with an apparent difference in microbiome for patients with granulation tissue. Further studies are necessary to elucidate the pathogenesis of microbial ecology and its role in airway disease in patients with TTs.<br><br>LEVEL OF EVIDENCE: 2c. Laryngoscope, 2018.}, }
@article {pmid30565288, year = {2018}, author = {Beck, ES and Ramachandran, PS and Khan, LM and Sample, HA and Zorn, KC and O'Connell, EM and Nash, T and Reich, DS and Venkatesan, A and DeRisi, JL and Nath, A and Wilson, MR}, title = {Clinicopathology Conference: 41 year old woman with chronic relapsing meningitis.}, journal = {Annals of neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ana.25400}, pmid = {30565288}, issn = {1531-8249}, }
@article {pmid30565165, year = {2018}, author = {Serena, G and Fasano, A}, title = {Use of Probiotics to Prevent Celiac Disease and IBD in Pediatrics.}, journal = {Advances in experimental medicine and biology}, volume = {}, number = {}, pages = {}, doi = {10.1007/5584_2018_317}, pmid = {30565165}, issn = {0065-2598}, abstract = {The incidence of chronic inflammatory diseases (CIDs) is increasing worldwide. Their dramatic rise associated with limited effective strategies to slow down these epidemics calls for a better understanding of their pathophysiology in order to decrease the burdens on childhood. Several cross-sectional studies have demonstrated the association between intestinal dysbiosis and active diseases. Although informative, these studies do not mechanistically link alterations of the microflora with disease pathogenesis and, therefore, with potential therapeutic targets. More prospective studies are needed to determine whether intestinal dysbiosis plays a causative role in the onset and development of CIDs. Furthermore, given the complexity of the microflora interaction with the host, it is necessary to design a systems-level model of interactions between the host and the development of disease by integrating microbiome, metagenomics, metatranscriptomics, and metabolomics with either clinical either environmental data.In this chapter we will discuss the current knowledge regarding the microbiome's contribution to celiac disease and inflammatory bowel disease with a particular focus on how probiotics may be used as potential preventive therapy for CIDs.}, }
@article {pmid30564225, year = {2018}, author = {Liu, J and Chang, R and Zhang, X and Wang, Z and Wen, J and Zhou, T}, title = {Non-isoflavones Diet Incurred Metabolic Modifications Induced by Constipation in Rats via Targeting Gut Microbiota.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3002}, doi = {10.3389/fmicb.2018.03002}, pmid = {30564225}, issn = {1664-302X}, abstract = {Isoflavones, presenting in leguminous plants and the normal chow diet, are known to alter intestinal microbiota, yet their deficiency has not been widely studied for its effect on constipation in biochemical state of rats. Our previous study discovered the differences in pharmacokinetic traits of isoflavones from Semen sojae praeparatum fed with normal chow diet (ISO) and non-isoflavones diet (NISO). To gain insight into the key role of intestinal microbiota in constipation and metabolic differences caused by isoflavones deficiency, we observed a significant decrease in fecal pellet numbers, fecal water content, intestinal transit rate together with the serum concentrations of substance P (SP) and vasoactive intestinal peptide (VIP) in NISO group, compared with those in the ISO group. Following 16S rRNA compositional sequencing, results excluded the changes in intestinal microbiota over time and highlighted that a total of 5 phyla and 21 genera changed significantly, among which Firmicutes, Bacteroidetes, Blautia, Prevotella, Lactobacillus and Bifidobacterium were closely related to constipation. In addition, Lactobacillus, produceing β-glucosidase which contribute to biotransform glycosides into aglycons and exert the bioactivities consequently, was decreased after non-isoflavones diet intake. Meanwhile, predicted metagenomics indicated that the pathway of glycan biosynthesis and metabolism was markedly down-regulated after non-isoflavones diet intake. Taken together, the findings suggested that the changes in the dietary components could alter the biochemical state of rats, which may be triggered by the abnormal modifications facilitated by β-glucosidase-producing bacteria. Our study shed a new strategy to explore the relationship among disease phenotypes (D), intestinal microbiota (I), enzymes (E) and traits of metabolism (T) named as &quot;DIET,&quot; which can provide a reference for further study of the mechanism in regulation of intestinal bacteria-mediated diet on diseases.}, }
@article {pmid30564204, year = {2018}, author = {Vigneron, A and Cruaud, P and Mohit, V and Martineau, MJ and Culley, AI and Lovejoy, C and Vincent, WF}, title = {Multiple Strategies for Light-Harvesting, Photoprotection, and Carbon Flow in High Latitude Microbial Mats.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2881}, doi = {10.3389/fmicb.2018.02881}, pmid = {30564204}, issn = {1664-302X}, abstract = {Microbial mats are ubiquitous in polar freshwater ecosystems and sustain high concentrations of biomass despite the extreme seasonal variations in light and temperature. Here we aimed to resolve genomic adaptations for light-harvesting, bright-light protection, and carbon flow in mats that undergo seasonal freeze-up. To bracket a range of communities in shallow water habitats, we sampled cyanobacterial mats in the thawed littoral zone of two lakes situated at the northern and southern limits of the Canadian Arctic permafrost zone. We applied a multiphasic approach using pigment profiles from high performance liquid chromatography, Illumina MiSeq sequencing of the 16S and 18S rRNA genes, and metagenomic analysis. The mats shared a taxonomic and functional core microbiome, dominated by oxygenic cyanobacteria with light-harvesting and photoprotective pigments, bacteria with bacteriochlorophyll, and bacteria with light-driven Type I rhodopsins. Organisms able to use light for energy related processes represented up to 85% of the total microbial community, with 15-30% attributable to cyanobacteria and 55-70% attributable to other bacteria. The proportion of genes involved in anaplerotic CO2 fixation was greater than for genes associated with oxygenic photosynthesis. Diverse heterotrophic bacteria, eukaryotes (including metazoans and fungi) and viruses co-occurred in both communities. The results indicate a broad range of strategies for capturing sunlight and CO2, and for the subsequent flow of energy and carbon in these complex, light-driven microbial ecosystems.}, }
@article {pmid30563894, year = {2018}, author = {Sutherland, MC and Tran, NL and Tillman, DE and Jarodsky, JM and Yuan, J and Kranz, RG}, title = {Structure-Function Analysis of the Bifunctional CcsBA Heme Exporter and Cytochrome c Synthetase.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, doi = {10.1128/mBio.02134-18}, pmid = {30563894}, issn = {2150-7511}, abstract = {Although intracellular heme trafficking must occur for heme protein assembly, only a few heme transporters have been unequivocally discovered and nothing is known about their structure or mechanisms. Cytochrome c biogenesis in prokaryotes requires the transport of heme from inside to outside for stereospecific attachment to cytochrome c via two thioether bonds (at CXXCH). The CcsBA integral membrane protein was shown to transport and attach heme (and thus is a cytochrome c synthetase), but the structure and mechanisms underlying these two activities are poorly understood. We employed a new cysteine/heme crosslinking tool that traps endogenous heme in heme binding sites. We combined these data with a comprehensive imidazole correction approach (for heme ligand interrogation) to map heme binding sites. Results illuminate the process of heme transfer through the membrane to an external binding site (called the WWD domain). Using meta-genomic data (GREMLIN) and Rosetta modeling programs, a structural model of the transmembrane (TM) regions in CcsBA were determined. The heme mapping data were then incorporated to model the TM heme binding site (with TM-His1 and TM-His2 as ligands) and the external heme binding WWD domain (with P-His1 and P-His2 as ligands). Other periplasmic structure/function studies facilitated modeling of the full CcsBA protein as a framework for understanding the mechanisms. Mechanisms are proposed for heme transport from TM-His to WWD/P-His and subsequent stereospecific attachment of heme. A ligand exchange of the P-His1 for histidine of CXXCH at the synthetase active site is suggested.IMPORTANCE The movement or trafficking of heme is critical for cellular functions (e.g., oxygen transport and energy production); however, intracellular heme is tightly regulated due to its inherent cytotoxicity. These factors, combined with the transient nature of transport, have resulted in a lack of direct knowledge on the mechanisms of heme binding and trafficking. Here, we used the cytochrome c biogenesis system II pathway as a model to study heme trafficking. System II is composed of two integral membrane proteins (CcsBA) which function to transport heme across the membrane and stereospecifically position it for covalent attachment to apocytochrome c We mapped two heme binding domains in CcsBA and suggest a path for heme trafficking. These data, in combination with metagenomic coevolution data, are used to determine a structural model of CcsBA, leading to increased understanding of the mechanisms for heme transport and the cytochrome c synthetase function of CcsBA.}, }
@article {pmid30563591, year = {2018}, author = {Kafetzopoulou, LE and Efthymiadis, K and Lewandowski, K and Crook, A and Carter, D and Osborne, J and Aarons, E and Hewson, R and Hiscox, JA and Carroll, MW and Vipond, R and Pullan, ST}, title = {Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {23}, number = {50}, pages = {}, doi = {10.2807/1560-7917.ES.2018.23.50.1800228}, pmid = {30563591}, issn = {1560-7917}, abstract = {BackgroundThe recent global emergence and re-emergence of arboviruses has caused significant human disease. Common vectors, symptoms and geographical distribution make differential diagnosis both important and challenging. AimTo investigate the feasibility of metagenomic sequencing for recovering whole genome sequences of chikungunya and dengue viruses from clinical samples.MethodsWe performed metagenomic sequencing using both the Illumina MiSeq and the portable Oxford Nanopore MinION on clinical samples which were real-time reverse transcription-PCR (qRT-PCR) positive for chikungunya (CHIKV) or dengue virus (DENV), two of the most important arboviruses. A total of 26 samples with a range of representative clinical Ct values were included in the study.ResultsDirect metagenomic sequencing of nucleic acid extracts from serum or plasma without viral enrichment allowed for virus identification, subtype determination and elucidated complete or near-complete genomes adequate for phylogenetic analysis. One PCR-positive CHIKV sample was also found to be coinfected with DENV. ConclusionsThis work demonstrates that metagenomic whole genome sequencing is feasible for the majority of CHIKV and DENV PCR-positive patient serum or plasma samples. Additionally, it explores the use of Nanopore metagenomic sequencing for DENV and CHIKV, which can likely be applied to other RNA viruses, highlighting the applicability of this approach to front-line public health and potential portable applications using the MinION.}, }
@article {pmid30562947, year = {2018}, author = {Ishii, C and Nakanishi, Y and Murakami, S and Nozu, R and Ueno, M and Hioki, K and Aw, W and Hirayama, A and Soga, T and Ito, M and Tomita, M and Fukuda, S}, title = {A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19124079}, pmid = {30562947}, issn = {1422-0067}, support = {15H01522//Japan Society for the Promotion of Science/ ; 16H04901//Japan Society for the Promotion of Science/ ; 17H05654//Japan Society for the Promotion of Science/ ; 18H04805//Japan Society for the Promotion of Science/ ; JPMJPR1537//Japan Science and Technology Agency/ ; }, abstract = {Intestinal microbiota and their metabolites are strongly associated with host physiology. Developments in DNA sequencing and mass spectrometry technologies have allowed us to obtain additional data that enhance our understanding of the interactions among microbiota, metabolites, and the host. However, the strategies used to analyze these datasets are not yet well developed. Here, we describe an original analytical strategy, metabologenomics, consisting of an integrated analysis of mass spectrometry-based metabolome data and high-throughput-sequencing-based microbiome data. Using this approach, we compared data obtained from C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber, to those from mice fed control rodent diet. The feces of the AD mice contained higher amounts of butyrate and propionate, and higher relative abundances of Oscillospira and Ruminococcus. The amount of butyrate positively correlated with the abundance of these bacterial genera. Furthermore, integrated analysis of the metabolome data and the predicted metagenomic data from Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) indicated that the abundance of genes associated with butyrate metabolism positively correlated with butyrate amounts. Thus, our metabologenomic approach is expected to provide new insights and understanding of intestinal metabolic dynamics in complex microbial ecosystems.}, }
@article {pmid29291348, year = {2018}, author = {Karst, SM and Dueholm, MS and McIlroy, SJ and Kirkegaard, RH and Nielsen, PH and Albertsen, M}, title = {Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias.}, journal = {Nature biotechnology}, volume = {36}, number = {2}, pages = {190-195}, pmid = {29291348}, issn = {1546-1696}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; Eukaryota/classification/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/classification/*genetics ; RNA, Ribosomal, 18S/*genetics ; }, abstract = {Small subunit ribosomal RNA (SSU rRNA) genes, 16S in bacteria and 18S in eukaryotes, have been the standard phylogenetic markers used to characterize microbial diversity and evolution for decades. However, the reference databases of full-length SSU rRNA gene sequences are skewed to well-studied ecosystems and subject to primer bias and chimerism, which results in an incomplete view of the diversity present in a sample. We combine poly(A)-tailing and reverse transcription of SSU rRNA molecules with synthetic long-read sequencing to generate high-quality, full-length SSU rRNA sequences, without primer bias, at high throughput. We apply our approach to samples from seven different ecosystems and obtain more than a million SSU rRNA sequences from all domains of life, with an estimated raw error rate of 0.17%. We observe a large proportion of novel diversity, including several deeply branching phylum-level lineages putatively related to the Asgard Archaea. Our approach will enable expansion of the SSU rRNA reference databases by orders of magnitude, and contribute to a comprehensive census of the tree of life.}, }
@article {pmid29222444, year = {2018}, author = {Lesser, MP and Morrow, KM and Pankey, SM and Noonan, SHC}, title = {Diazotroph diversity and nitrogen fixation in the coral Stylophora pistillata from the Great Barrier Reef.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {813-824}, pmid = {29222444}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/genetics ; *Coral Reefs ; Dinoflagellida/*metabolism ; Heterotrophic Processes ; Metagenome ; Nitrogen/*metabolism ; Nitrogen Fixation/*physiology/radiation effects ; Photosynthesis/*physiology/radiation effects ; Photosystem II Protein Complex/metabolism ; Sequence Analysis, DNA ; }, abstract = {Diazotrophs, both Bacteria and Archaea, capable of fixing nitrogen (N2), are present in the tissues and mucous, of corals and can supplement the coral holobiont nitrogen budget with fixed nitrogen (N) in the form of ammonia (NH3). Stylophora pistillata from Heron Island on the Great Barrier Reef collected at 5 and 15 m, and experimentally manipulated in the laboratory, showed that the rates of net photosynthesis, steady state quantum yields of photosystem II (PSII) fluorescence (∆Fv/Fm') and calcification varied based on irradiance as expected. Rates of N2 fixation were, however, invariant across treatments while the amount of fixed N contributing to Symbiodinium spp. N demand is irradiance dependent. Additionally, both the Symbiodinium and diazotrophic communities are significantly different based on depth, and novel Cluster V nifH gene phylotypes, which are not known to fix nitrogen, were recovered. A functional analysis using PICRUSt also showed that shallow corals were enriched in genes involved in nitrogen metabolism, and N2 fixation specifically. Corals have evolved a number of strategies to derive nitrogen from organic (e.g., heterotrophic feeding) and inorganic sources (e.g., N2 fixation) to maintain critical pathways such as protein synthesis to succeed ecologically in nitrogen-limited habitats.}, }
@article {pmid30562162, year = {2018}, author = {Peng, W and Yi, P and Yang, J and Xu, P and Wang, Y and Zhang, Z and Huang, S and Wang, Z and Zhang, C}, title = {Association of gut microbiota composition and function with a senescence-accelerated mouse model of Alzheimer's Disease using 16S rRNA gene and metagenomic sequencing analysis.}, journal = {Aging}, volume = {}, number = {}, pages = {}, doi = {10.18632/aging.101693}, pmid = {30562162}, issn = {1945-4589}, abstract = {Although an intriguing potential association of the gut microbiome with Alzheimer's disease (AD) has attracted recent interest, few studies have directly assessed this relationship or underlying mechanism. Here, we compared the gut microbiota composition and functional differentiation of senescence-accelerated mouse prone 8 (SAMP8) mice with control senescence-accelerated mouse resistant 1 (SAMR1) mice using 16S rRNA gene and metagenomic sequencing analysis, respectively. Specifically, 16S sequencing results showed that the SAMP8 mice displayed a characteristic composition of the gut microbiome that clearly differed from that of the SAMR1 mice. Moreover, network analysis revealed that the gut microbiota of SAMP8 mice had decreased correlation density and clustering of operational taxonomic units. Metagenomic results revealed that the predominant Cluster of Orthologous Groups functional category related to these changes was the metabolism cluster in SAMP8 mice. The Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation further demonstrated enrichment of the relative abundance of some dominant metabolism-related KEGG pathways in the SAMP8 mice, consistent with the suggested pathogenic mechanisms of AD. In conclusion, this study suggests that perturbations of the gut microbiota composition and the functional metagenome may be associated with AD. Further studies are warranted to elucidate the potential new mechanism contributing to AD progression.}, }
@article {pmid30561396, year = {2018}, author = {Ticinesi, A and Nouvenne, A and Tana, C and Prati, B and Cerundolo, N and Miraglia, C and De' Angelis, GL and Di Mario, F and Meschi, T}, title = {The impact of intestinal microbiota on bio-medical research: definitions, techniques and physiology of a &quot;new frontier&quot;.}, journal = {Acta bio-medica : Atenei Parmensis}, volume = {89}, number = {9-S}, pages = {52-59}, pmid = {30561396}, issn = {0392-4203}, abstract = {In recent years the metagenomics techniques have allowed to study composition and function of the intestinal microbiota. The microbiota is a new frontier of biomedical research to be explored and there is growing evidence of its fundamental health-promoting activity. The present review gives a synthetic overview on the characteristics and the role of the microbiota in the adult with particular reference to physiology, pathophysiology and relationships with the host and the environment.}, }
@article {pmid30561093, year = {2018}, author = {Cherkasov, SV and Popova, LY and Vivtanenko, TV and Demina, RR and Khlopko, YA and Balkin, AS and Plotnikov, AO}, title = {Oral microbiomes in children with asthma and dental caries.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.13020}, pmid = {30561093}, issn = {1601-0825}, abstract = {OBJECTIVE: Recently, a significant association between dental caries and the severity of bronchial asthma in children has been revealed. This finding indicates a possible relationship between the oral microbiome and the pathogenesis of asthma. The purpose of our study was to estimate differences in the dental plaque microbiota of asthmatic children with and without dental caries by 16S rDNA sequencing.<br><br>MATERIAL AND METHODS: Dental plaque samples were obtained with a spoon excavator from the occlusal surface of one deciduous tooth (the second mandibular left molar in caries-free children and the most affected tooth in caries-affected children). Total DNA was extracted from dental plaque. DNA libraries were analysed by 16S rRNA gene sequencing on the MiSeq (Illumina) platform.<br><br>RESULTS: There were no significant differences in the composition of bacterial communities from both caries-affected and caries-free children with asthma. The 'caries-enriched' genus was Veillonella (Veillonellaceae, Selenomonadales, Negativicutes). Relative abundance of Neisseria was significantly higher in caries-free children with asthma (p<0.05).<br><br>CONCLUSIONS: The most significant difference in compared bacterial communities was a higher relative abundance of Veillonella in caries-affected plaques that suggests its involvement in pathogenesis of caries. Potential respiratory pathogens are present in oral cavity of both caries-affected and caries-free asthmatic children. This article is protected by copyright. All rights reserved.}, }
@article {pmid30560161, year = {2018}, author = {Soriano, BM and Del Valle-Perez, LM and Morales-Vale, L and Rios-Velazquez, C}, title = {Datasets generated by shotgun sequencing of metagenomic libraries of the guajataca water reservoir.}, journal = {Data in brief}, volume = {21}, number = {}, pages = {2531-2535}, doi = {10.1016/j.dib.2018.11.114}, pmid = {30560161}, issn = {2352-3409}, abstract = {The Guajataca Water Reservoir (GWR) was constructed for irrigation and to bring potable water to the northwestern region of Puerto Rico. The generation of DNA sequencing data from aquatic bodies (AB) using culture-independent approaches allows the investigation of the total microbial diversity as well as the potential anthropogenic impact. Metagenomic libraries were constructed for two GWR sampling sites and genomic information access through shotgun sequencing. After removing the bacterial host cell genome and the library fosmid sequences, the environmental genome was processed through Rapid Annotation using Subsystems Technology for Metagenomes (MG-RAST). The sequences consisted primarily of bacteria (95.70%), followed by viruses (2.94%), other sequences (0.28%) and eukaryote (0.09%). The most abundant species were Enterobacter cloacae (31%), Enterobacter sp. 638 (20%), Enterobacter cancerogenus (10%) and Escherichia coli (11%). Furthermore, the subsystem data showed that 13% of the genes belong to carbohydrates functionality, 12% to clustering-based-subsystems and another 9% related to virulence-disease-and-defense (out of which 8% pertain to genes of antibiotic resistance and toxic compounds). This unique data input will serve as a baseline to a better understanding not only the microbial communities present in the AB, but also the microbial activities with potential application in biotechnological and biomedical fields.}, }
@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 {pmid30559407, year = {2018}, author = {Vatanen, T and Plichta, DR and Somani, J and Münch, PC and Arthur, TD and Hall, AB and Rudolf, S and Oakeley, EJ and Ke, X and Young, RA and Haiser, HJ and Kolde, R and Yassour, M and Luopajärvi, K and Siljander, H and Virtanen, SM and Ilonen, J and Uibo, R and Tillmann, V and Mokurov, S and Dorshakova, N and Porter, JA and McHardy, AC and Lähdesmäki, H and Vlamakis, H and Huttenhower, C and Knip, M and Xavier, RJ}, title = {Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-018-0321-5}, pmid = {30559407}, issn = {2058-5276}, abstract = {The human gut microbiome matures towards the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood data sets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides, in which we identified evidence of variability deriving from Bacteroides-targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harboured Bifidobacterium longum subsp. infantis, a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.}, }
@article {pmid30559406, year = {2018}, author = {Kintses, B and Méhi, O and Ari, E and Számel, M and Györkei, Á and Jangir, PK and Nagy, I and Pál, F and Fekete, G and Tengölics, R and Nyerges, Á and Likó, I and Bálint, A and Molnár, T and Bálint, B and Vásárhelyi, BM and Bustamante, M and Papp, B and Pál, C}, title = {Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-018-0313-5}, pmid = {30559406}, issn = {2058-5276}, abstract = {The human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs), which are ancient components of immune defence. Despite its medical importance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here, we show that AMP resistance and antibiotic resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics have revealed that AMP resistance genes originating from phylogenetically distant bacteria have only a limited potential to confer resistance in Escherichia coli, an intrinsically susceptible species. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota, with implications for disease risks.}, }
@article {pmid30559311, year = {2018}, author = {Sanford, E and Farnaes, L and Batalov, S and Bainbridge, M and Laubach, S and Worthen, HM and Tokita, M and Kingsmore, SF and Bradley, J}, title = {Concomitant diagnosis of immune deficiency and Pseudomonas sepsis in a 19 month old with ecthyma gangrenosum by host whole-genome sequencing.}, journal = {Cold Spring Harbor molecular case studies}, volume = {4}, number = {6}, pages = {}, doi = {10.1101/mcs.a003244}, pmid = {30559311}, issn = {2373-2873}, abstract = {X-linked agammaglobulinemia (XLA, OMIM#300300) is a rare monogenic primary immunodeficiency caused by mutations in the Bruton tyrosine kinase (BTK) gene. XLA is characterized by insufficient immunoglobulin levels and susceptibility to life-threatening bacterial infections. We report on a patient that presented with ecthyma gangrenosum and septicemia. Rapid trio whole-genome sequencing (rWGS) revealed an apparently de novo hemizygous pathogenic variant (c.726dupT; p.Ile243TyrfsTer15) in the BTK gene. Metagenomic analysis of rWGS sequences that did not align to the human genome revealed 770 aligned to the Pseudomonas aeruginosa PAO1 genome. The patient was diagnosed with XLA and pseudomonal sepsis.}, }
@article {pmid30559036, year = {2018}, author = {Freitas, RC and Marques, HIF and Silva, MACD and Cavalett, A and Odisi, EJ and Silva, BLD and Montemor, JE and Toyofuku, T and Kato, C and Fujikura, K and Kitazato, H and Lima, AOS}, title = {Evidence of selective pressure in whale fall microbiome proteins and its potential application to industry.}, journal = {Marine genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.margen.2018.11.004}, pmid = {30559036}, issn = {1876-7478}, abstract = {The present study addresses the microbiome of the first whale fall (YOKO 16) that has been described in the deep sea in the southern Atlantic Ocean (São Paulo Plateau; 4204 m depth), in terms of its metabolic uniqueness. Sets of ten thousand protein sequences from YOKO 16 and 29 public domain metagenomes (SRA and GenBank databases) that represent various marine, terrestrial and gut-associated microbial communities were analyzed. The determination of protein functionality, based on the KAAS server, indicated that the YOKO 16 microbiome has industrially-relevant proteins, such as proteases and lipases, that have low similarity (~50%) with previously-described enzymes. The amino acid usage in the YOKO 16 protein sequences (based on blastp and Clustal analysis) revealed a pattern of preference similar to that of extremophiles, with an increased usage of polar, charged and acidic amino acids and a decreased usage of nonpolar residues. We concluded that the targeted microbiome is of potential biotechnological use, which justifies the allocation of resources for the discovery of enzymes in deep-sea whale fall communities.}, }
@article {pmid30558669, year = {2018}, author = {Deshpande, NP and Riordan, SM and Castaño-Rodríguez, N and Wilkins, MR and Kaakoush, NO}, title = {Signatures within the esophageal microbiome are associated with host genetics, age, and disease.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {227}, doi = {10.1186/s40168-018-0611-4}, pmid = {30558669}, issn = {2049-2618}, support = {15/CDF/1-11//Cancer Institute NSW/ ; APP1111461//National Health and Medical Research Council/ ; }, abstract = {BACKGROUND: The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the host. Here, the esophageal microbiomes of 106 prospectively recruited patients were assessed using 16S rRNA and 18S rRNA amplicon sequencing as well as shotgun sequencing, and associations with age, gender, proton pump inhibitor use, host genetics, and disease were tested.<br><br>RESULTS: The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. While age was found to be a significant factor driving microbiome composition, bacterial signatures and functions such as enrichment with Gram-negative oral-associated bacteria and microbial lactic acid production were associated with the early stages of the esophageal adenocarcinoma cascade. Non-bacterial microbes such as archaea, Candida spp., and bacteriophages were also identified in low abundance in the esophageal microbiome. Specific host SNPs in NOTCH2, STEAP2-AS1, and NREP were associated with the composition of the esophageal microbiome in our cohort.<br><br>CONCLUSIONS: This study provides the most comprehensive assessment of the esophageal microbiome to date and identifies novel signatures and host markers that can be investigated further in the context of esophageal adenocarcinoma development.}, }
@article {pmid30558668, year = {2018}, author = {Davis, NM and Proctor, DM and Holmes, SP and Relman, DA and Callahan, BJ}, title = {Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {226}, doi = {10.1186/s40168-018-0605-2}, pmid = {30558668}, issn = {2049-2618}, support = {R01 DE023113//National Institute of Dental and Craniofacial Research/ ; R01 AI112401//National Institute of Allergy and Infectious Diseases/ ; }, abstract = {BACKGROUND: The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants-DNA sequences not truly present in the sample. Contaminants come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam (https://github.com/benjjneb/decontam), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples and are often found in negative controls.<br><br>RESULTS: Decontam classified amplicon sequence variants (ASVs) in a human oral dataset consistently with prior microscopic observations of the microbial taxa inhabiting that environment and previous reports of contaminant taxa. In metagenomics and marker-gene measurements of a dilution series, decontam substantially reduced technical variation arising from different sequencing protocols. The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants.<br><br>CONCLUSIONS: Decontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. Decontam integrates easily with existing MGS workflows and allows researchers to generate more accurate profiles of microbial communities at little to no additional cost.}, }
@article {pmid30217037, year = {2018}, author = {Liu, H and Liu, M and Fu, X and Zhang, Z and Zhu, L and Zheng, X and Liu, J}, title = {Astaxanthin Prevents Alcoholic Fatty Liver Disease by Modulating Mouse Gut Microbiota.}, journal = {Nutrients}, volume = {10}, number = {9}, pages = {}, pmid = {30217037}, issn = {2072-6643}, support = {31672511//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Anti-Inflammatory Agents/*pharmacology ; Biomarkers/blood ; Disease Models, Animal ; Dysbiosis ; Fatty Liver, Alcoholic/metabolism/microbiology/pathology/*prevention &amp; control ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/*drug effects/microbiology ; Inflammation Mediators/metabolism ; Lipid Metabolism/drug effects ; Liver/*drug effects/metabolism/pathology ; Male ; Metagenome/drug effects ; Mice, Inbred C57BL ; Xanthophylls/pharmacology ; }, abstract = {The development and progression of alcoholic fatty liver disease (AFLD) is influenced by the intestinal microbiota. Astaxanthin, a type of oxygenated carotenoid with strong antioxidant and anti-inflammatory properties, has been proven to relieve liver injury. However, the relationship between the gut microbiota regulation effect of astaxanthin and AFLD improvement remains unclear. The effects of astaxanthin on the AFLD phenotype, overall structure, and composition of gut microbiota were assessed in ethanol-fed C57BL/6J mice. The results showed that astaxanthin treatment significantly relieves inflammation and decreases excessive lipid accumulation and serum markers of liver injury. Furthermore, astaxanthin was shown to significantly decrease species from the phyla Bacteroidetes and Proteobacteria and the genera Butyricimonas, Bilophila, and Parabacteroides, as well as increase species from Verrucomicrobia and Akkermansia compared with the Et (ethanol)group. Thirteen phylotypes related to inflammation as well as correlated with metabolic parameters were significantly altered by ethanol, and then notably reversed by astaxanthin. Additionally, astaxanthin altered 18 and 128 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways involved in lipid metabolism and xenobiotic biodegradation and metabolism at levels 2 and 3, respectively. These findings suggest that Aakkermansia may be a potential target for the astaxanthin-induced alleviation of AFLD and may be a potential treatment for bacterial disorders induced by AFLD.}, }
@article {pmid30040978, year = {2018}, author = {Guo, Z and He, Q and Tang, C and Zhang, B and Yue, H}, title = {Identification and genomic characterization of a novel CRESS DNA virus from a calf with severe hemorrhagic enteritis in China.}, journal = {Virus research}, volume = {255}, number = {}, pages = {141-146}, doi = {10.1016/j.virusres.2018.07.015}, pmid = {30040978}, issn = {1872-7492}, mesh = {Animals ; Base Composition ; Cattle ; Cattle Diseases/pathology/*virology ; China ; DNA Virus Infections/pathology/*veterinary/virology ; DNA Viruses/*classification/*genetics/isolation &amp; purification ; DNA, Circular ; DNA, Single-Stranded ; Enteritis/pathology/*veterinary/virology ; Feces/virology ; Genome Size ; Genome, Viral/genetics ; Metagenomics ; Open Reading Frames/genetics ; *Phylogeny ; Viral Proteins ; }, abstract = {In this study, a novel circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA virus was discovered in diarrheic sample of a calf with severe hemorrhagic enteritis. The virus, named Bo-Circo-like virus CH, has a circular genome with 3909 nucleotides (nt). Six putative open reading frames (ORFs) were identified, including Rep, capsid (Cap) and four proteins of unknown function. Both the genome size and the number as well as the organization of encoded ORFs, Bo-Circo-like virus CH is most closely related to Po-Circo-like virus 21 detected in pig faeces. A preliminary survey using specific primers for the Rep region showed that 5.3% (4/75) of diarrheic samples were positive for Bo-Circo-like virus, and all 42 healthy samples were negative. In conclusion, our results indicate that Bo-Circo-like virus CH may represent a new virus in bovine. Further investigation is needed to determine the relationship between the virus infection and diarrhea.}, }
@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 {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 {pmid29085077, year = {2018}, author = {Baran, N and Goldin, S and Maidanik, I and Lindell, D}, title = {Quantification of diverse virus populations in the environment using the polony method.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {62-72}, pmid = {29085077}, issn = {2058-5276}, mesh = {Bacteriophages/*classification/genetics ; DNA Viruses/genetics ; Ecosystem ; Genes, Viral ; Genome, Viral/genetics ; Indian Ocean ; Metagenomics/*methods ; *Phylogeny ; Prochlorococcus/*virology ; Seawater/*virology ; Sequence Analysis, DNA ; Synechococcus/*virology ; }, abstract = {Viruses are globally abundant and extremely diverse in their genetic make-up and in the hosts they infect. Although they influence the abundance, diversity and evolution of their hosts, current methods are inadequate for gaining a quantitative understanding of their impact on these processes. Here we report the adaptation of the solid-phase single-molecule PCR polony method for the quantification of taxonomically relevant groups of diverse viruses. Using T7-like cyanophages as our model, we found the polony method to be far superior to regular quantitative PCR methods and droplet digital PCR when degenerate primers were used to encompass the group's diversity. This method revealed that T7-like cyanophages were highly abundant in the Red Sea in spring 2013, reaching 770,000 phages ml-1, and displaying a similar depth distribution pattern to cyanobacteria. Furthermore, the abundances of two major clades within the T7-like cyanophages differed dramatically throughout the water column: clade B phages that carry the psbA photosynthesis gene and infect either Synechococcus or Prochlorococcus were at least 20-fold more abundant than clade A phages that lack psbA and infect Synechococcus hosts. Such measurements are of paramount importance for understanding virus population dynamics and the impact of viruses on different microbial taxa and for modelling viral influence on ecosystem functioning on a global scale.}, }
@article {pmid29062087, year = {2018}, author = {Orsi, WD and Richards, TA and Francis, WR}, title = {Predicted microbial secretomes and their target substrates in marine sediment.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {32-37}, doi = {10.1038/s41564-017-0047-9}, pmid = {29062087}, issn = {2058-5276}, mesh = {Archaea/classification/enzymology/*genetics ; Bacteria/classification/enzymology/*genetics ; Carbon Cycle/*genetics ; Fungi/classification/enzymology/*genetics ; Gene Expression Profiling ; Genome, Microbial/genetics ; Geologic Sediments/*microbiology ; Metagenomics ; Open Reading Frames/genetics ; Proteogenomics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Scientific drilling has identified a biosphere in marine sediments 1 , which contain many uncultivated microbial groups known only by their DNA sequences 2-4 . Recycling of organic matter in sediments is an important component of biogeochemical cycles because marine sediments are critical for long-term carbon storage 5 . Turnover of carbon is hypothesized to be driven by the secretion of enzymes by microbial organisms 5-7 , which act to break down macromolecules into constitutive monomers that can be transported into cells. As such, the nature of the microbial secretome often influences the function of a community 6 . However, the microbial groups involved in this process and the biochemistry they encode is poorly understood. Here, we show that expressed genes from 5 to 159 meters below the seafloor 8 (mbsf) encode numerous candidate peptidases and carbohydrate-active enzymes ('CAZymes') 9 targeted for secretion. The majority (90-99%) were assigned to Bacteria, of which 12% shared the highest sequence similarity with candidate phyla 10,11 . The remaining putatively secreted proteins shared highest sequence similarity with archaeal and fungal enzymes, which peak in two redox transition zones 12 . In the shallower redox zone at 30 mbsf, 20% of the transcripts encoding putative secreted peptidases were assigned to lineages 7,13,14 of uncultivated Archaea. The target compounds of the predicted secreted proteome show a preference for necromass in the form of microbial cell envelopes as well as plankton and algal detritus. The predicted fungal secreted proteome encodes CAZymes not present in the predicted bacterial or archaeal secreted proteomes, indicating that fungi putatively play a minimal but specialized role in subseafloor carbohydrate recycling.}, }
@article {pmid28588309, year = {2017}, author = {Jiang, S and Xie, S and Lv, D and Wang, P and He, H and Zhang, T and Zhou, Y and Lin, Q and Zhou, H and Jiang, J and Nie, J and Hou, F and Chen, Y}, title = {Alteration of the gut microbiota in Chinese population with chronic kidney disease.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2870}, pmid = {28588309}, issn = {2045-2322}, mesh = {Adult ; Aged ; Bacteria/classification/genetics ; Biomarkers ; Butyrates/metabolism ; Case-Control Studies ; China/epidemiology ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Humans ; Kidney Failure, Chronic/epidemiology ; Kidney Function Tests ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Population Surveillance ; Renal Insufficiency, Chronic/diagnosis/*epidemiology/metabolism ; }, abstract = {We evaluated differences in the compositions of faecal microbiota between 52 end stage renal disease (ESRD) patients and 60 healthy controls in southern China using quantitative real-time polymerase chain reaction (qPCR) and high-throughput sequencing (16S ribosomal RNA V4-6 region) methods. The absolute quantification of total bacteria was significantly reduced in ESRD patients (p < 0.01). In three enterotypes, Prevotella was enriched in the healthy group whereas Bacteroides were prevalent in the ESRD group (LDA score > 4.5). 11 bacterial taxa were significantly overrepresented in samples from ESRD and 22 bacterial taxa were overrepresented in samples from healthy controls. The butyrate producing bacteria, Roseburia, Faecalibacterium, Clostridium, Coprococcus and Prevotella were reduced in the ESRD group (LDA values > 2.0). Canonical correspondence analysis (CCA) indicated that Cystatin C (CysC), creatinine and eGFR appeared to be the most important environmental parameters to influence the overall microbial communities. In qPCR analysis, The butyrate producing species Roseburia spp., Faecalibacterium prausnitzii, Prevotella and Universal bacteria, were negatively related to CRP and CysC. Total bacteria in faeces were reduced in patients with ESRD compared to that in healthy individuals. The enterotypes change from Prevotella to Bacteroides in ESRD patients. The gut microbiota was associated with the inflammatory state and renal function of chronic kidney disease.}, }
@article {pmid30556814, year = {2018}, author = {Roux, S and Adriaenssens, EM and Dutilh, BE and Koonin, EV and Kropinski, AM and Krupovic, M and Kuhn, JH and Lavigne, R and Brister, JR and Varsani, A and Amid, C and Aziz, RK and Bordenstein, SR and Bork, P and Breitbart, M and Cochrane, GR and Daly, RA and Desnues, C and Duhaime, MB and Emerson, JB and Enault, F and Fuhrman, JA and Hingamp, P and Hugenholtz, P and Hurwitz, BL and Ivanova, NN and Labonté, JM and Lee, KB and Malmstrom, RR and Martinez-Garcia, M and Mizrachi, IK and Ogata, H and Páez-Espino, D and Petit, MA and Putonti, C and Rattei, T and Reyes, A and Rodriguez-Valera, F and Rosario, K and Schriml, L and Schulz, F and Steward, GF and Sullivan, MB and Sunagawa, S and Suttle, CA and Temperton, B and Tringe, SG and Thurber, RV and Webster, NS and Whiteson, KL and Wilhelm, SW and Wommack, KE and Woyke, T and Wrighton, KC and Yilmaz, P and Yoshida, T and Young, MJ and Yutin, N and Allen, LZ and Kyrpides, NC and Eloe-Fadrosh, EA}, title = {Minimum Information about an Uncultivated Virus Genome (MIUViG).}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1038/nbt.4306}, pmid = {30556814}, issn = {1546-1696}, abstract = {We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.}, }
@article {pmid30555706, year = {2019}, author = {Angelakis, E and Bachar, D and Yasir, M and Musso, D and Djossou, F and Gaborit, B and Brah, S and Diallo, A and Ndombe, GM and Mediannikov, O and Robert, C and Azhar, EI and Bibi, F and Nsana, NS and Parra, HJ and Akiana, J and Sokhna, C and Davoust, B and Dutour, A and Raoult, D}, title = {Treponema species enrich the gut microbiota of traditional rural populations but are absent from urban individuals.}, journal = {New microbes and new infections}, volume = {27}, number = {}, pages = {14-21}, doi = {10.1016/j.nmni.2018.10.009}, pmid = {30555706}, issn = {2052-2975}, abstract = {There is a significant gap in our knowledge of the microbe-host relationship between urban and traditional rural populations. We conducted a large-scale study to examine the gut microbiota of different traditional rural and urban lifestyles in human populations. Using high-throughput 16S ribosomal RNA gene amplicon sequencing, we tested urban French, Saudi, Senegalese, Nigerian and Polynesian individuals as well as individuals living in traditional rural societies, including Amazonians from French Guiana, Congolese Pygmies, Saudi Bedouins and Algerian Tuaregs. The gut microbiota from individuals living in traditional rural settings clustered differently and presented significantly higher diversity than those of urban populations (p 0.01). The bacterial taxa identified by class analysis as contributing most significantly to each cluster were Phascolarctobacterium for traditional rural individuals and Bifidobacterium for urban individuals. Spirochaetae were only present in the gut microbiota of individuals from traditional rural societies, and the gut microbiota of all traditional rural populations was enriched with Treponema succinifaciens. Cross-transmission of Treponema from termites or swine to humans or the increased use of antibiotics in nontraditional populations may explain why Treponema is present only in the gut microbiota of traditional rural populations.}, }
@article {pmid30555453, year = {2018}, author = {Cernava, T and Vasfiu, Q and Erlacher, A and Aschenbrenner, IA and Francesconi, K and Grube, M and Berg, G}, title = {Adaptions of Lichen Microbiota Functioning Under Persistent Exposure to Arsenic Contamination.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2959}, doi = {10.3389/fmicb.2018.02959}, pmid = {30555453}, issn = {1664-302X}, abstract = {Host-associated microbiota play an important role in the health and persistence of more complex organisms. In this study, metagenomic analyses were used to reveal microbial community adaptations in three lichen samples as a response to different arsenic concentrations at the sampling sites. Elevated arsenic concentrations at a former mining site expanded the spectrum and number of relevant functions in the lichen-associated microorganisms. Apparent changes affected the abundance of numerous detoxification-related genes, they were substantially enhanced in arsenic-polluted samples. Complementary quantifications of the arsenite S-adenosylmethionine methyltransferase (arsM) gene showed that its abundance is not strictly responding to the environmental arsenic concentrations. The analyzed samples contained rather low numbers of the arsM gene with a maximum of 202 gene copies μl-1 in total community DNA extracts. In addition, bacterial isolates were screened for the presence of arsM. Positive isolates were exposed to different As(III) and As(V) concentrations and tolerated up to 30 mM inorganic arsenic in fluid media, while no substantial biotransformations were observed. Obtained data deepens our understanding related to adaptions of whole microbial communities to adverse environmental conditions. Moreover, this study provides the first evidence that the integrity of bacteria in the lichen holobiont is maintained by acquisition of specific resistances.}, }
@article {pmid30555447, year = {2018}, author = {Rodríguez, J and Gallampois, CMJ and Timonen, S and Andersson, A and Sinkko, H and Haglund, P and Berglund, ÅMM and Ripszam, M and Figueroa, D and Tysklind, M and Rowe, O}, title = {Effects of Organic Pollutants on Bacterial Communities Under Future Climate Change Scenarios.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2926}, doi = {10.3389/fmicb.2018.02926}, pmid = {30555447}, issn = {1664-302X}, abstract = {Coastal ecosystems are highly dynamic and can be strongly influenced by climate change, anthropogenic activities (e.g., pollution), and a combination of the two pressures. As a result of climate change, the northern hemisphere is predicted to undergo an increased precipitation regime, leading in turn to higher terrestrial runoff and increased river inflow. This increased runoff will transfer terrestrial dissolved organic matter (tDOM) and anthropogenic contaminants to coastal waters. Such changes can directly influence the resident biology, particularly at the base of the food web, and can influence the partitioning of contaminants and thus their potential impact on the food web. Bacteria have been shown to respond to high tDOM concentration and organic pollutants loads, and could represent the entry of some pollutants into coastal food webs. We carried out a mesocosm experiment to determine the effects of: (1) increased tDOM concentration, (2) organic pollutant exposure, and (3) the combined effect of these two factors, on pelagic bacterial communities. This study showed significant responses in bacterial community composition under the three environmental perturbations tested. The addition of tDOM increased bacterial activity and diversity, while the addition of organic pollutants led to an overall reduction of these parameters, particularly under concurrent elevated tDOM concentration. Furthermore, we identified 33 bacterial taxa contributing to the significant differences observed in community composition, as well as 35 bacterial taxa which responded differently to extended exposure to organic pollutants. These findings point to the potential impact of organic pollutants under future climate change conditions on the basal coastal ecosystem, as well as to the potential utility of natural bacterial communities as efficient indicators of environmental disturbance.}, }
@article {pmid30555434, year = {2018}, author = {Yamamoto, K and Shiwa, Y and Ishige, T and Sakamoto, H and Tanaka, K and Uchino, M and Tanaka, N and Oguri, S and Saitoh, H and Tsushima, S}, title = {Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2878}, doi = {10.3389/fmicb.2018.02878}, pmid = {30555434}, issn = {1664-302X}, abstract = {Root-associated microbial communities are very important in the adaptation of halophytes to coastal environments. However, little has been reported on microbial community structures related to halophytes, or on comparisons of their compositions among halophytic plant species. Here, we studied the diversity and community structure of both rhizosphere and root endosphere bacteria in two halophytic plants: Glaux maritima and Salicornia europaea. We sampled the rhizosphere, the root endosphere, and bulk control soil samples, and performed bacterial 16S rRNA sequencing using the Illumina MiSeq platform to characterize the bacterial community diversities in the rhizosphere and root endosphere of both halophytes. Among the G. maritima samples, the richness and diversity of bacteria in the rhizosphere were higher than those in the root endosphere but were lower than those of the bulk soil. In contrast for S. europaea, the bulk soil, the rhizosphere, and the root endosphere all had similar bacterial richness and diversity. The number of unique operational taxonomic units within the root endosphere, the rhizosphere, and the bulk soil were 181, 366, and 924 in G. maritima and 126, 416, and 596 in S. europaea, respectively, implying habitat-specific patterns for each halophyte. In total, 35 phyla and 566 genera were identified. The dominant phyla across all samples were Proteobacteria and Bacteroidetes. Actinobacteria was extremely abundant in the root endosphere from G. maritima. Beneficial bacterial genera were enriched in the root endosphere and rhizosphere in both halophytes. Rhizobium, Actinoplanes, and Marinomonas were highly abundant in G. maritima, whereas Sulfurimonas and Coleofasciculus were highly abundant in S. europaea. A principal coordinate analysis demonstrated significant differences in the microbiota composition associated with the plant species and type of sample. These results strongly indicate that there are clear differences in bacterial community structure and diversity between G. maritima and S. europaea. This is the first report to characterize the root microbiome of G. maritima, and to compare the diversity and community structure of rhizosphere and root endosphere bacteria between G. maritima and S. europaea.}, }
@article {pmid30555424, year = {2018}, author = {De Anda, V and Zapata-Peñasco, I and Blaz, J and Poot-Hernández, AC and Contreras-Moreira, B and González-Laffitte, M and Gámez-Tamariz, N and Hernández-Rosales, M and Eguiarte, LE and Souza, V}, title = {Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2606}, doi = {10.3389/fmicb.2018.02606}, pmid = {30555424}, issn = {1664-302X}, abstract = {To date, it remains unclear how anthropogenic perturbations influence the dynamics of microbial communities, what general patterns arise in response to disturbance, and whether it is possible to predict them. Here, we suggest the use of microbial mats as a model of study to reveal patterns that can illuminate the ecological processes underlying microbial dynamics in response to stress. We traced the responses to anthropogenic perturbation caused by water depletion in microbial mats from Cuatro Cienegas Basin (CCB), Mexico, by using a time-series spatially resolved analysis in a novel combination of three computational approaches. First, we implemented MEBS (Multi-genomic Entropy-Based Score) to evaluate the dynamics of major biogeochemical cycles across spatio-temporal scales with a single informative value. Second, we used robust Time Series-Ecological Networks (TS-ENs) to evaluate the total percentage of interactions at different taxonomic levels. Lastly, we utilized network motifs to characterize specific interaction patterns. Our results indicate that microbial mats from CCB contain an enormous taxonomic diversity with at least 100 phyla, mainly represented by members of the rare biosphere (RB). Statistical ecological analyses point out a clear involvement of anaerobic guilds related to sulfur and methane cycles during wet versus dry conditions, where we find an increase in fungi, photosynthetic, and halotolerant taxa. TS-ENs indicate that in wet conditions, there was an equilibrium between cooperation and competition (positive and negative relationships, respectively), while under dry conditions there is an over-representation of negative relationships. Furthermore, most of the keystone taxa of the TS-ENs at family level are members of the RB and the microbial mat core highlighting their crucial role within the community. Our results indicate that microbial mats are more robust to perturbation due to redundant functions that are likely shared among community members in the highly connected TS-ENs with density values close to one (≈0.9). Finally, we provide evidence that suggests that a large taxonomic diversity where all community members interact with each other (low modularity), the presence of permanent of low-abundant taxa, and an increase in competition can be potential buffers against environmental disturbance in microbial mats.}, }
@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 {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 {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 {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 {pmid30009542, year = {2018}, author = {Wilcox, TM and Zarn, KE and Piggott, MP and Young, MK and McKelvey, KS and Schwartz, MK}, title = {Capture enrichment of aquatic environmental DNA: A first proof of concept.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1392-1401}, doi = {10.1111/1755-0998.12928}, pmid = {30009542}, issn = {1755-0998}, support = {DE130100777//Australian Research Council/ ; DGE-1313190//Directorate for Biological Sciences/ ; //University of Montana/ ; 58 2014//ANU-ActewAGL Endowment Fund/ ; }, mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; DNA/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Nucleic Acid Hybridization/*methods ; Sensitivity and Specificity ; }, abstract = {Environmental DNA (eDNA) sampling-the detection of genetic material in the environment to infer species presence-has rapidly grown as a tool for sampling aquatic animal communities. A potentially powerful feature of environmental sampling is that all taxa within the habitat shed DNA and so may be detectable, creating opportunity for whole-community assessments. However, animal DNA in the environment tends to be comparatively rare, making it necessary to enrich for genetic targets from focal taxa prior to sequencing. Current metabarcoding approaches for enrichment rely on bulk amplification using conserved primer annealing sites, which can result in skewed relative sequence abundance and failure to detect some taxa because of PCR bias. Here, we test capture enrichment via hybridization as an alternative strategy for target enrichment using a series of experiments on environmental samples and laboratory-generated, known-composition DNA mixtures. Capture enrichment resulted in detecting multiple species in both kinds of samples, and postcapture relative sequence abundance accurately reflected initial relative template abundance. However, further optimization is needed to permit reliable species detection at the very low-DNA quantities typical of environmental samples (<0.1 ng DNA). We estimate that our capture protocols are comparable to, but less sensitive than, current PCR-based eDNA 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 {pmid29923321, year = {2018}, author = {Keck, F and Vasselon, V and Rimet, F and Bouchez, A and Kahlert, M}, title = {Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1299-1309}, doi = {10.1111/1755-0998.12919}, pmid = {29923321}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Diatoms/classification/genetics ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Microscopy ; Phylogeny ; Rivers/microbiology ; Sensitivity and Specificity ; }, abstract = {DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices, which are based on the estimated abundances of species in a community and their ecological profiles, can be inaccurate. We propose to compute biotic indices using phylogenetic imputation of operational taxonomic units (OTUs') ecological profiles (OTU-PITI approach). First, OTUs sequences are inserted within a reference phylogeny. Second, OTUs' ecological profiles are estimated on the basis of their phylogenetic relationships with reference species whose ecology is known. Based on these ecological profiles, biotic indices can be computed using all available OTUs. Using freshwater diatoms as a case study, we show that short DNA barcodes can be placed accurately within a phylogeny and their ecological preferences estimated with a satisfactory level of precision. In the light of these results, we tested the approach with a data set of 139 environmental samples of benthic river diatoms for which the same biotic index (specific sensitivity index) was calculated using (a) traditional microscopy, (b) OTUs with taxonomic assignment approach, (c) OTUs with phylogenetic estimation of ecological profiles (OTU-PITI) and (d) OTU with taxonomic assignment completed by the phylogenetic approach (OTU-PITI) for unclassified OTUs. Using traditional microscopy as a reference, we found that the combination of the OTUs' taxonomic assignment completed by the phylogenetic method performed satisfactorily and substantially better than the other methods tested.}, }
@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 {pmid29847023, year = {2018}, author = {Dellicour, S and Flot, JF}, title = {The hitchhiker's guide to single-locus species delimitation.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1234-1246}, doi = {10.1111/1755-0998.12908}, pmid = {29847023}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Metagenomics/*methods ; *Phylogeny ; }, abstract = {Molecular approaches to species delimitation are increasingly used to ascertain the number of species in a sample prior to taxonomic, ecological or physiological studies. Although multilocus approaches are gaining fast in popularity, single-gene methods still predominate in the literature. However, available simulation benchmarks of these methods focus exclusively on species-poor samples and/or tree-based approaches: as a result, travellers in the land of single-locus species delimitation lack a comprehensive &quot;hitchhiker's guide&quot; highlighting the sweet spots and dangers on their road. To fill this gap, we compared the performances of distance-based (ABGD, &quot;automatic barcode gap discovery&quot;), allele sharing-based (haplowebs) and tree-based approaches (GMYC, &quot;generalized mixed Yule-coalescent&quot; and PTP, &quot;Poisson tree processes&quot;) to detect interspecific boundaries in samples of 6, 60 and 120 simulated species with various speciation rates, effective population sizes, mutation rates and sampling patterns. We found that all approaches performed poorly when population sizes and speciation rates were large, with haplowebs yielding best results followed by ABGD then tree-based approaches. The latter's error type was mostly oversplitting, whereas ABGD chiefly overlumped and haplowebs leaned either way depending on simulation parameters: such widely divergent error patterns suggest that, if all three types of methods agree, then the resulting delimitation is probably correct. Perfect congruence being quite rare, travellers in search of a one-size-fit-all approach to single-locus species delimitation should forget it; however, our hitchhiker's guide raises hope that such species delimitation's Holy Grail may be found in the relatively uncharted nearby land of multilocus species delimitation.}, }
@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 {pmid29194469, year = {2018}, author = {McIver, LJ and Abu-Ali, G and Franzosa, EA and Schwager, R and Morgan, XC and Waldron, L and Segata, N and Huttenhower, C}, title = {bioBakery: a meta'omic analysis environment.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {7}, pages = {1235-1237}, pmid = {29194469}, issn = {1367-4811}, support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Metagenomics/*methods ; Microbiota/*genetics ; Reproducibility of Results ; *Software ; Workflow ; }, abstract = {Summary: bioBakery is a meta'omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured analysis modules also joined into workflows for reproducibility.<br><br>bioBakery (http://huttenhower.sph.harvard.edu/biobakery) is publicly available for local installation as individual modules and as a virtual machine image. Each individual module has been developed to perform a particular task (e.g. quantitative taxonomic profiling or statistical analysis), and they are provided with source code, tutorials, demonstration data, and validation results; the bioBakery virtual image includes the entire suite of modules and their dependencies pre-installed. Images are available for both Amazon EC2 and Google Compute Engine. All software is open source under the MIT license. bioBakery is actively maintained with a support group at biobakery-users@googlegroups.com and new tools being added upon their release.<br><br>Contact: chuttenh@hsph.harvard.edu.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid28588195, year = {2017}, author = {Kang, J and Ma, X and He, S}, title = {Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2813}, pmid = {28588195}, issn = {2045-2322}, mesh = {Animals ; Catfishes/*genetics ; Genome/genetics ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; }, abstract = {Advances in genome scanning using high-throughput sequencing technologies has led to a revolution in studies of non-model organisms. The glyptosternoid fish Creteuchiloglanis macropterus, is widely distributed in the main stem and tributaries of the Nujiang River basin. Here, we analyzed IIB restriction-site-associated DNA (2b-RAD) sequences and mitochondrial DNA sequences, to assess the genomic signature of adaptation by detecting and estimating the degree of genetic differentiation among ten Creteuchiloglanis macropterus populations from the Nujiang River. The analyses revealed significant population differentiation among the up-tributaries, main stem, mid-tributary and low-tributary. Annotation of contigs containing outlier SNPs revealed that the candidate genes showed significant enrichment in several important biological process terms between up-tributaries and low-tributary, and exhibited prominent enrichment in the term macromolecular metabolic process between all tributaries and the main stem. Population dynamics analyses indicated that the Late Pleistocene glaciations strongly influenced the demographic history of C. macropterus. Our results provide strong evidence for the utility of RAD-seq in population genetics studies, and our generated SNP resource should provide a valuable tool for population genomics studies of C. macropterus in the future.}, }
@article {pmid28539641, year = {2017}, author = {Alessi, AM and Bird, SM and Bennett, JP and Oates, NC and Li, Y and Dowle, AA and Polikarpov, I and Young, JPW and McQueen-Mason, SJ and Bruce, NC}, title = {Revealing the insoluble metasecretome of lignocellulose-degrading microbial communities.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2356}, pmid = {28539641}, issn = {2045-2322}, support = {BB/1018492/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K020358/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J014443/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biomass ; Lignin/*metabolism ; Mass Spectrometry ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota ; Oryza/growth &amp; development/microbiology ; Proteome/genetics/*metabolism ; Proteomics/*methods ; Transcriptome/genetics ; Triticum/growth &amp; development/microbiology ; }, abstract = {Microbial communities metabolize plant biomass using secreted enzymes; however, identifying extracellular proteins tightly bound to insoluble lignocellulose in these microbiomes presents a challenge, as the rigorous extraction required to elute these proteins also lyses the microbes associated with the plant biomass releasing intracellular proteins that contaminate the metasecretome. Here we describe a technique for targeting the extracellular proteome, which was used to compare the metasecretome and meta-surface-proteome of two lignocellulose-degrading communities grown on wheat straw and rice straw. A combination of mass spectrometry-based proteomics coupled with metatranscriptomics enabled the identification of a unique secretome pool from these lignocellulose-degrading communities. This method enabled us to efficiently discriminate the extracellular proteins from the intracellular proteins by improving detection of actively secreted and transmembrane proteins. In addition to the expected carbohydrate active enzymes, our new method reveals a large number of unknown proteins, supporting the notion that there are major gaps in our understanding of how microbial communities degrade lignocellulosic substrates.}, }
@article {pmid30554441, year = {2018}, author = {Curtis, K and Stewart, CJ and Robinson, M and Molfese, DL and Gosnell, SN and Kosten, TR and Petrosino, JF and De La Garza, R and Salas, R}, title = {Insular Resting State Functional Connectivity is Associated with Gut Microbiota Diversity.}, journal = {The European journal of neuroscience}, volume = {}, number = {}, pages = {}, doi = {10.1111/ejn.14305}, pmid = {30554441}, issn = {1460-9568}, abstract = {The gut microbiota has recently gained attention as a possible modulator of brain activity. A number of reports suggest that the microbiota may be associated with neuropsychiatric conditions such as major depressive disorder, autism, and anxiety. The gut microbiota is thought to influence the brain via vagus nerve signaling, among other possible mechanisms. The insula processes and integrates these vagal signals. To determine if microbiota diversity and structure modulate brain activity, we collected fecal samples and examined insular function using resting state functional connectivity (RSFC). Thirty healthy participants (non-smokers, tobacco smokers, and electronic cigarette users, n=10 each) were studied. We found that the RSFC between the insula and several regions (frontal pole left, lateral occipital cortex right, lingual gyrus right, and cerebellum 4, 5 and vermis 9) were associated with bacterial microbiota diversity and structure. In addition, two specific bacteria genera, Prevotella and Bacteroides, were specifically different in tobacco smokers and also associated with insular connectivity. In conclusion, we show that insular connectivity is associated with microbiome diversity, structure, and at least two specific bateria genera. Furthemore, this association is potentially modulated by tobacco smoking, although the sample sizes for the different smoking groups were small and this result needs validation in a larger cohort. While replication is necessary, the microbiota is a readily accesible therapeutic target for modulating insular connectivity, which has previously been shown to be abnormal in anxiety and tobacco use disorders. This article is protected by copyright. All rights reserved.}, }
@article {pmid30552986, year = {2018}, author = {Kozik, AJ and Huang, YJ}, title = {The Microbiome in Asthma: Role in pathogenesis, phenotype, and response to treatment.}, journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.anai.2018.12.005}, pmid = {30552986}, issn = {1534-4436}, }
@article {pmid30552976, year = {2018}, author = {Tikariha, H and Purohit, HJ}, title = {Assembling a genome for novel nitrogen-fixing bacteria with capabilities for utilization of aromatic hydrocarbons.}, journal = {Genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ygeno.2018.12.005}, pmid = {30552976}, issn = {1089-8646}, abstract = {Metagenome from refinery wastewater treatment plant running under nitrogen stress was analyzed for mining of novel aromatic hydrocarbon-degrading bacteria. The sequence data were assembled using metaspade followed by binning using the Metabat tool to assemble genome; where coverage and depth were calculated using bowtie and samtools. The analysis picked a novel genome belonging to family Bradyrhizobiaceae, identified based on 16S rDNA gene which was supported by CheckM and Kraken analysis. Using RAST, the assembled genome showed the capabilities for nitrogen fixation with the utilization of multiple hydrocarbon substrates with 14 different types of oxygenases as mapped by Minpath. An additional genetic feature like genes for stress and resistance towards heavy metals and antibiotic suggested that the genome has gone through the rigorous process of adaptation. If such bacteria could be cultivated then it will open the broad window of bioremediation strategies under nitrogen stress environment.}, }
@article {pmid30552020, year = {2018}, author = {Castellanos, JG and Woo, V and Viladomiu, M and Putzel, G and Lima, S and Diehl, GE and Marderstein, AR and Gandara, J and Perez, AR and Withers, DR and Targan, SR and Shih, DQ and Scherl, EJ and Longman, RS}, title = {Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis.}, journal = {Immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.immuni.2018.10.014}, pmid = {30552020}, issn = {1097-4180}, abstract = {Inflammatory bowel disease (IBD) results from a dysregulated interaction between the microbiota and a genetically susceptible host. Genetic studies have linked TNFSF15 polymorphisms and its protein TNF-like ligand 1A (TL1A) with IBD, but the functional role of TL1A is not known. Here, we found that adherent IBD-associated microbiota induced TL1A release from CX3CR1+ mononuclear phagocytes (MNPs). Using cell-specific genetic deletion models, we identified an essential role for CX3CR1+MNP-derived TL1A in driving group 3 innate lymphoid cell (ILC3) production of interleukin-22 and mucosal healing during acute colitis. In contrast to this protective role in acute colitis, TL1A-dependent expression of co-stimulatory molecule OX40L in MHCII+ ILC3s during colitis led to co-stimulation of antigen-specific T cells that was required for chronic T cell colitis. These results identify a role for ILC3s in activating intestinal T cells and reveal a central role for TL1A in promoting ILC3 barrier immunity during colitis.}, }
@article {pmid30551580, year = {2018}, author = {Ibarra-Juarez, LA and Desgarennes, D and Vázquez-Rosas-Landa, M and Villafan, E and Alonso-Sánchez, A and Ferrera-Rodríguez, O and Moya, A and Carrillo, D and Cruz, L and Carrión, G and López-Buenfil, A and García-Avila, C and Ibarra-Laclette, E and Lamelas, A}, title = {Impact of Rearing Conditions on the Ambrosia Beetle's Microbiome.}, journal = {Life (Basel, Switzerland)}, volume = {8}, number = {4}, pages = {}, doi = {10.3390/life8040063}, pmid = {30551580}, issn = {2075-1729}, abstract = {Ambrosia beetles, along with termites and leafcutter ants, are the only fungus-farming lineages within the tree of life. Bacteria harbored by ambrosia beetles may play an essential role in the nutritional symbiotic interactions with their associated fungi; however, little is known about the impact of rearing conditions on the microbiota of ambrosia beetles. We have used culture-independent methods to explore the effect of rearing conditions on the microbiome associated with Xyleborus affinis, Xyleborus bispinatus, and Xyleborus volvulus, evaluating different media in laboratory-controlled conditions and comparing wild and laboratory conditions. Our results revealed that rearing conditions affected the fungal and bacterial microbiome structure and had a strong influence on bacterial metabolic capacities. We propose that the rearing conditions influence the ambrosia-associated fungal and bacterial communities. Furthermore, bacterial microbiome flexibility may help beetles adapt to different substrates.}, }
@article {pmid30551574, year = {2018}, author = {Dias, DM and Kolba, N and Binyamin, D and Ziv, O and Regini Nutti, M and Martino, HSD and Glahn, RP and Koren, O and Tako, E}, title = {Iron Biofortified Carioca Bean (Phaseolus vulgaris L.)-Based Brazilian Diet Delivers More Absorbable Iron and Affects the Gut Microbiota In Vivo (Gallus gallus).}, journal = {Nutrients}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/nu10121970}, pmid = {30551574}, issn = {2072-6643}, abstract = {Biofortification aims to improve the micronutrient concentration and bioavailability in staple food crops. Unlike other strategies utilized to alleviate Fe deficiency, studies of the gut microbiota in the context of Fe biofortification are scarce. In this study, we performed a 6-week feeding trial in Gallus gallus (n = 15), aimed to investigate the Fe status and the alterations in the gut microbiome following the administration of Fe-biofortified carioca bean based diet (BC) versus a Fe-standard carioca bean based diet (SC). The tested diets were designed based on the Brazilian food consumption survey. Two primary outcomes were observed: (1) a significant increase in total body Hb-Fe values in the group receiving the Fe-biofortified carioca bean based diet; and (2) changes in the gut microbiome composition and function were observed, specifically, significant changes in phylogenetic diversity between treatment groups, as there was increased abundance of bacteria linked to phenolic catabolism, and increased abundance of beneficial SCFA-producing bacteria in the BC group. The BC group also presented a higher intestinal villi height compared to the SC group. Our results demonstrate that the Fe-biofortified carioca bean variety was able to moderately improve Fe status and to positively affect the intestinal functionality and bacterial populations.}, }
@article {pmid30551044, year = {2018}, author = {Duan, Y and Awasthi, SK and Liu, T and Chen, H and Zhang, Z and Wang, Q and Ren, X and Tu, Z and Awasthi, MK and Taherzadeh, MJ}, title = {Dynamics of fungal diversity and interactions with environmental elements in response to wheat straw biochar amended poultry manure composting.}, journal = {Bioresource technology}, volume = {274}, number = {}, pages = {410-417}, doi = {10.1016/j.biortech.2018.12.020}, pmid = {30551044}, issn = {1873-2976}, abstract = {The fungal dynamics and its correlation with physicochemical and gaseous emission were investigated using metagenomics and Heat map illustrator (HEMI). Five different concentrations of wheat straw biochar (WSB) were applied to poultry manure (PM) and composted for 50 days; those without the WSB treatment were used as a control. The results revealed the dominant phyla to be Chytridiomycota, Mucoromycota, Ascomycota and Basidiomycota, while Batrachochytrium, Rhizophagus, Mucor, and Puccinia were the superior genera. In particular, the diversity of Chytridiomycota and Ascomycota was more abundant among all of the treatments. Overall, the diversity of the fungal species was correspondent, but relative abundance varied significantly among all of the composts. Principle Coordinate Analysis (PCoA) and Non-Metric Multi- Dimensional Scaling (NMDS) indicated that different concentrations of WSB applied treatments have significantly distinct fungal communities. In addition, correlation analyses of fungal interactions with environmental elements via HEMI also indicate a clear difference among the treatments. Ultimately, the relative abundance of fungal composition significantly influenced the PM compost treated by the WSB.}, }
@article {pmid30547761, year = {2018}, author = {Morales-Cruz, A and Figueroa-Balderas, R and García, JF and Tran, E and Rolshausen, PE and Baumgartner, K and Cantu, D}, title = {Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {214}, doi = {10.1186/s12866-018-1343-0}, pmid = {30547761}, issn = {1471-2180}, support = {2016-1798//American Vineyard Foundation/ ; 2017-1798//American Vineyard Foundation/ ; 2018-1798//American Vineyard Foundation/ ; 2012-51181-19954//National Institute of Food and Agriculture/ ; }, abstract = {BACKGROUND: DNA metabarcoding, commonly used in exploratory microbial ecology studies, is a promising method for the simultaneous in planta-detection of multiple pathogens associated with disease complexes, such as the grapevine trunk diseases. Profiling of pathogen communities associated with grapevine trunk diseases is particularly challenging, due to the presence within an individual wood lesion of multiple co-infecting trunk pathogens and other wood-colonizing fungi, which span a broad range of taxa in the fungal kingdom. As such, we designed metabarcoding primers, using as template the ribosomal internal transcribed spacer of grapevine trunk-associated ascomycete fungi (GTAA) and compared them to two universal primer widely used in microbial ecology.<br><br>RESULTS: We first performed in silico simulations and then tested the primers by high-throughput amplicon sequencing of (i) multiple combinations of mock communities, (ii) time-course experiments with controlled inoculations, and (iii) diseased field samples from vineyards under natural levels of infection. All analyses showed that GTAA had greater affinity and sensitivity, compared to those of the universal primers. Importantly, with GTAA, profiling of mock communities and comparisons with shotgun-sequencing metagenomics of field samples gave an accurate representation of genera of important trunk pathogens, namely Phaeomoniella, Phaeoacremonium, and Eutypa, the abundances of which were over- or under-estimated with universal primers.<br><br>CONCLUSIONS: Overall, our findings not only demonstrate that DNA metabarcoding gives qualitatively and quantitatively accurate results when applied to grapevine trunk diseases, but also that primer customization and testing are crucial to ensure the validity of DNA metabarcoding results.}, }
@article {pmid30547216, year = {2018}, author = {Suleiman, M and Schröder, C and Klippel, B and Schäfers, C and Krüger, A and Antranikian, G}, title = {Extremely thermoactive archaeal endoglucanase from a shallow marine hydrothermal vent from Vulcano Island.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-018-9542-z}, pmid = {30547216}, issn = {1432-0614}, abstract = {Already-characterized microbial cellulases have proven to be highly useful for industrial processes, since they can withstand harsh industrial conditions with characteristics such as high thermo- and acid stability. These properties provide promising features for the process of plant biomass degradation and biofuel generation. Nevertheless, the number of known extremely thermoactive archaeal cellulases is low. Hence, the discovery of archaeal cellulases with different characteristics is crucial for the development of efficient and sustainable biorefinery. In this work, the metagenome of a high-temperature enrichment culture from marine environment of Vulcano Island was screened for the presence of novel endoglucanase-encoding genes of archaeal origin. The ORF vul_cel5A was detected, and the deduced protein was characterized as the most thermoactive endoglucanase described to date. Vul_Cel5A was identified as a thermoactive glycoside hydrolase family 5 endoglucanase, with the highest sequence identity (72-75%) to putative endoglucanases from archaeal genera. Vul_Cel5A showed the highest activity at notable 115 °C towards barley β-glucan (210.7 U/mg), and lichenan (209.9 U/mg), and further towards carboxymethyl cellulose (38.6 U/mg) and locust bean gum (83.0 U/mg). The endoglucanase exhibited a half-life time of 46 min at 100 °C and did not show any loss of activity after incubation for 48 h at 75 °C. Furthermore, Vul_Cel5A showed high affinity to barley β-glucan with a Km of 0.52 mg/mL and showed tolerance against various chemical reagents. Due to the outstanding high thermoactivity and thermostability and tolerance to acidic conditions, Vul_Cel5A represents a promising novel archaeal endo-β-glucanase for application in biorefineries for an efficient biomass pre-treatment.}, }
@article {pmid30547029, year = {2018}, author = {Mino, S and Yoneyama, N and Nakagawa, S and Takai, K and Sawabe, T}, title = {Enrichment and Genomic Characterization of a N2O-Reducing Chemolithoautotroph From a Deep-Sea Hydrothermal Vent.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {6}, number = {}, pages = {184}, doi = {10.3389/fbioe.2018.00184}, pmid = {30547029}, issn = {2296-4185}, abstract = {Nitrous oxide (N2O) is a greenhouse gas and also leads to stratospheric ozone depletion. In natural environments, only a single N2O sink process is the microbial reduction of N2O to N2, which is mediated by nitrous oxide reductase (NosZ) encoded by nosZ gene. The nosZ phylogeny has two distinct clades, clade I and formerly overlooked clade II. In deep-sea hydrothermal environments, several members of the class Campylobacteria are shown to harbor clade II nosZ gene and perform the complete denitrification of nitrate to N2; however, little is known about their ability to grow on exogenous N2O as the sole electron acceptor. Here, we obtained an enrichment culture from a deep-sea hydrothermal vent in the Southern Mariana Trough, which showed a respiratory N2O reduction with H2 as an electron donor. The single amplicon sequence variant (ASV) presenting 90% similarity to Hydrogenimonas species within the class Campylobacteria was predominant throughout the cultivation period. Metagenomic analyses using a combination of short-read and long-read sequence data succeeded in reconstructing a complete genome of the dominant ASV, which encoded clade II nosZ gene. This study represents the first cultivation analysis that shows the occurrence of N2O-respiring microorganisms in a deep-sea hydrothermal vent and provides the opportunity to assess their capability to reduce N2O emission from the environments.}, }
@article {pmid30545218, year = {2018}, author = {Liu, CW and Chi, L and Tu, P and Xue, J and Ru, H and Lu, K}, title = {Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic.}, journal = {Journal of proteome research}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jproteome.8b00666}, pmid = {30545218}, issn = {1535-3907}, abstract = {Quantitative metaproteomics is a relatively new research field by applying proteomics technique to study microbial proteins of microbiome, and holds the great potential to truly quantify the functional proteins actually expressed by microbes in the biological environment such as gastrointestinal tract. The significant association between arsenic exposure and gut microbiome perturbations has been reported; however, metaproteomics has not yet been applied to study arsenic induced proteome changes of microbiome. Most importantly, to our knowledge, isobaric-labeling based large-scale metaproteomics has not been reported using the advanced database search approaches such as MetaPro-IQ and matched metagenome database search strategies to provide high quantification accuracy and less missing quantification values. In the present study, a new experimental workflow coupled with isobaric labeling and MetaPro-IQ was demonstrated for metaproteomics study of arsenic induced gut microbiome perturbations. The advantages of this workflow were also discussed. For all 18 fecal samples analyzed, 7,611 protein groups were quantified without any missing values. The consistent results of expression profiles were observed between 16S rRNA gene sequencing and metaproteomics. This isobaric labeling based workflow demonstrated the significant improvement of quantitative metaproteomics for gut microbiome study.}, }
@article {pmid30544936, year = {2018}, author = {D'Argenio, V}, title = {The Prenatal Microbiome: A New Player for Human Health.}, journal = {High-throughput}, volume = {7}, number = {4}, pages = {}, doi = {10.3390/ht7040038}, pmid = {30544936}, issn = {2571-5135}, abstract = {The last few years have featured an increasing interest in the study of the human microbiome and its correlations with health status. Indeed, technological advances have allowed the study of microbial communities to reach a previously unthinkable sensitivity, showing the presence of microbes also in environments usually considered as sterile. In this scenario, microbial communities have been described in the amniotic fluid, the umbilical blood cord, and the placenta, denying a dogma of reproductive medicine that considers the uterus like a sterile womb. This prenatal microbiome may play a role not only in fetal development but also in the predisposition to diseases that may develop later in life, and also in adulthood. Thus, the aim of this review is to report the current knowledge regarding the prenatal microbiome composition, its association with pathological processes, and the future perspectives regarding its manipulation for healthy status promotion and maintenance.}, }
@article {pmid30544159, year = {2018}, author = {Pedrinho, A and Mendes, LW and Merloti, LF and da Fonseca, MC and Cannavan, FS and Tsai, SM}, title = {Forest-to-pasture conversion and recovery based on assessment of microbial communities in Eastern Amazon Rainforest.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiy236}, pmid = {30544159}, issn = {1574-6941}, abstract = {Amazon rainforest has been subjected to particularly high rates of deforestation caused mainly by the expansion of cattle pasture and agriculture. A commonly observed response to land-use change is a negative impact on biodiversity of plant and animal species. However, its effect on the soil microbial community and ecosystem functioning is still poorly understood. Here, we used DNA metagenomic sequencing approach to investigate the impact of land-use change on soil microbial community composition and its potential functions in three land-use systems (primary forest, pasture, and secondary forest) in the Amazon region. In general, the microbial community structure was influenced by changes in soil physicochemical properties. Aluminum and water holding capacity significantly correlated to overall community structure and most of microbial phyla. Taxonomic changes were followed by potential functional changes in the soil microbial community, with pasture presenting the most distinct profile in comparison with other sites. Although taxonomic structure was very distinct between sites, we observed a recovery of the potential functions in secondary forest after pasture abandonment. Our findings elucidate a significant shift in belowground microbial taxonomic and potential functional diversity following natural forest re-establishment and have implications for ecological restoration programs in tropical and sub-tropical ecosystems.}, }
@article {pmid30543873, year = {2018}, 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 = {}, number = {}, pages = {}, doi = {10.1016/j.virusres.2018.12.005}, pmid = {30543873}, issn = {1872-7492}, 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 > 1,000 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 {pmid30542336, year = {2018}, author = {Okazaki, Y and Salcher, MM and Callieri, C and Nakano, SI}, title = {The Broad Habitat Spectrum of the CL500-11 Lineage (Phylum Chloroflexi), a Dominant Bacterioplankton in Oxygenated Hypolimnia of Deep Freshwater Lakes.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2891}, doi = {10.3389/fmicb.2018.02891}, pmid = {30542336}, issn = {1664-302X}, abstract = {CL500-11 (phylum Chloroflexi) is one of the most ubiquitous and abundant bacterioplankton lineages in deep freshwater lakes inhabiting the oxygenated hypolimnion. While metagenomics predicted possible eco-physiological characteristics of this uncultured lineage, no consensus on their ecology has so far been reached, partly because their niche is not clearly understood due to a limited number of quantitative field observations. This study investigated the abundance and distribution of CL500-11 in seven deep perialpine lakes using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Samples were taken vertically (5-12 depths in each lake) and temporally (in two lakes) at the deepest point of the lakes located in Switzerland, Italy, and Austria with varying depth, trophic state, mixing regime, and water retention time. The results showed a dominance of CL500-11 in all the lakes; their proportion to total prokaryotes ranged from 4.3% (Mondsee) to 24.3% (Lake Garda) and their abundance ranged from 0.65 × 105 (Mondsee) to 1.77 × 105 (Lake Garda) cells mL-1. By summarizing available information on CL500-11 occurrence to date, we demonstrated their broad habitat spectrum, ranging from ultra-oligotrophic to meso-eutrophic lakes, while low abundances or complete absence was observed in lakes with shallow depth, low pH, and/or short water retention time (<1 year). Together with available metagenomic and geochemical evidences from literatures, here we reviewed potential substrates supporting growth of CL500-11. Overall, the present study further endorsed ubiquity and quantitative significance of CL500-11 in deep freshwater systems and narrowed the focus on their physiological characteristics and ecological importance.}, }
@article {pmid30542327, year = {2018}, author = {Dai, D and Rhoads, WJ and Edwards, MA and Pruden, A}, title = {Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2695}, doi = {10.3389/fmicb.2018.02695}, pmid = {30542327}, issn = {1664-302X}, abstract = {Hot water premise plumbing has emerged as a critical nexus of energy, water, and public health. The composition of hot water microbiomes is of special interest given daily human exposure to resident flora, especially opportunistic pathogens (OPs), which rely on complex microbial ecological interactions for their proliferation. Here, we applied shotgun metagenomic sequencing to characterize taxonomic and functional shifts in microbiomes as a function of water heater temperature setting, stagnation in distal pipes, and associated shifts in water chemistry. A cross-section of samples from controlled, replicated, pilot-scale hot water plumbing rigs representing different temperature settings (39, 42, and 51°C), stagnation periods (8 h vs. 7 days), and time-points, were analyzed. Temperature setting exhibited an overarching impact on taxonomic and functional gene composition. Further, distinct taxa were selectively enriched by specific temperature settings (e.g., Legionella at 39°C vs. Deinococcus at 51°C), while relative abundances of genes encoding corresponding cellular functions were highly consistent with expectations based on the taxa driving these shifts. Stagnation in distal taps diminished taxonomic and functional differences induced by heating the cold influent water to hot water in recirculating line. In distal taps relative to recirculating hot water, reads annotated as being involved in metabolism and growth decreased, while annotations corresponding to stress response (e.g., virulence disease and defense, and specifically antibiotic resistance) increased. Reads corresponding to OPs were readily identified by metagenomic analysis, with L. pneumophila reads in particular correlating remarkably well with gene copy numbers measured by quantitative polymerase chain reaction. Positive correlations between L. pneumophila reads and those of known protozoan hosts were also identified. Elevated proportions of genes encoding metal resistance and hydrogen metabolism were noted, which was consistent with elevated corrosion-induced metal concentrations and hydrogen generation. This study provided new insights into real-world factors influencing taxonomic and functional compositions of hot water microbiomes. Here metagenomics is demonstrated as an effective tool for screening for potential presence, and even quantities, of pathogens, while also providing diagnostic capabilities for assessing functional responses of microbiomes to various operational conditions. These findings can aid in informing future monitoring and intentional control of hot water microbiomes.}, }
@article {pmid30541977, year = {2018}, author = {}, title = {.}, journal = {Arerugi = [Allergy]}, volume = {67}, number = {10}, pages = {1412-1413}, doi = {10.15036/arerugi.67.1412}, pmid = {30541977}, issn = {0021-4884}, }
@article {pmid30541782, year = {2018}, author = {Pastrana, DV and Peretti, A and Welch, NL and Borgogna, C and Olivero, C and Badolato, R and Notarangelo, LD and Gariglio, M and FitzGerald, PC and McIntosh, CE and Reeves, J and Starrett, GJ and Bliskovsky, V and Velez, D and Brownell, I and Yarchoan, R and Wyvill, KM and Uldrick, TS and Maldarelli, F and Lisco, A and Sereti, I and Gonzalez, CM and Androphy, EJ and McBride, AA and Van Doorslaer, K and Garcia, F and Dvoretzky, I and Liu, JS and Han, J and Murphy, PM and McDermott, DH and Buck, CB}, title = {Metagenomic Discovery of 83 New Human Papillomavirus Types in Patients with Immunodeficiency.}, journal = {mSphere}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSphereDirect.00645-18}, pmid = {30541782}, issn = {2379-5042}, abstract = {Several immunodeficiencies are associated with high susceptibility to persistent and progressive human papillomavirus (HPV) infection leading to a wide range of cutaneous and mucosal lesions. However, the HPV types most commonly associated with such clinical manifestations in these patients have not been systematically defined. Here, we used virion enrichment, rolling circle amplification, and deep sequencing to identify circular DNA viruses present in skin swabs and/or wart biopsy samples from 48 patients with rare genetic immunodeficiencies, including patients with warts, hypogammaglobulinemia, infections, myelokathexis (WHIM) syndrome, or epidermodysplasia verruciformis (EV). Their profiles were compared with the profiles of swabs from 14 healthy adults and warts from 6 immunologically normal children. Individual patients were typically infected with multiple HPV types; up to 26 different types were isolated from a single patient (multiple anatomical sites, one time point). Among these, we identified the complete genomes of 83 previously unknown HPV types and 35 incomplete genomes representing possible additional new types. HPV types in the genus Gammapapillomavirus were common in WHIM patients, whereas EV patients mainly shed HPVs from the genus Betapapillomavirus. Preliminary evidence based on three WHIM patients treated with plerixafor, a leukocyte mobilizing agent, suggest that longer-term therapy may correlate with decreased HPV diversity and increased predominance of HPV types associated with childhood skin warts.IMPORTANCE Although some members of the viral family Papillomaviridae cause benign skin warts (papillomas), many human papillomavirus (HPV) infections are not associated with visible symptoms. For example, most healthy adults chronically shed Gammapapillomavirus (Gamma) virions from apparently healthy skin surfaces. To further explore the diversity of papillomaviruses, we performed viromic surveys on immunodeficient individuals suffering from florid skin warts. Our results nearly double the number of known Gamma HPV types and suggest that WHIM syndrome patients are uniquely susceptible to Gamma HPV-associated skin warts. Preliminary results suggest that treatment with the drug plerixafor may promote resolution of the unusual Gamma HPV skin warts observed in WHIM patients.}, }
@article {pmid30524416, year = {2018}, author = {Nho, SW and Abdelhamed, H and Paul, D and Park, S and Mauel, MJ and Karsi, A and Lawrence, ML}, title = {Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2855}, doi = {10.3389/fmicb.2018.02855}, pmid = {30524416}, issn = {1664-302X}, abstract = {Metagenomic analyses of microbial communities from aquatic sediments are relatively few, and there are no reported metagenomic studies on sediment from inland ponds used for aquaculture. Catfish ponds in the southeastern U.S. are eutrophic systems. They are fertilized to enhance algae growth and encourage natural food production, and catfish are fed with commercial feed from spring to fall. As result, catfish pond sediment (CPS) contains a very dense, diverse microbial community that has significant effects on the physiochemical parameters of pond dynamics. Here we conducted an in-depth metagenomic analysis of the taxonomic and metabolic capabilities of a catfish pond sediment microbiome from a southeastern U.S. aquaculture farm in Mississippi using Illumina next-generation sequencing. A total of 3.3 Gbp of sequence was obtained, 25,491,518 of which encoded predicted protein features. The pond sediment was dominated by Proteobacteria sequences, followed by Bacteroidetes, Firmicutes, Chloroflexi, and Actinobacteria. Enzyme pathways for methane metabolism/methanogenesis, denitrification, and sulfate reduction appeared nearly complete in the pond sediment metagenome profile. In particular, a large number of Deltaproteobacteria sequences and genes encoding anaerobic functional enzymes were found. This is the first study to characterize a catfish pond sediment microbiome, and it is expected to be useful for characterizing specific changes in microbial flora in response to production practices. It will also provide insight into the taxonomic diversity and metabolic capabilities of microbial communities in aquaculture. Furthermore, comparison with other environments (i.e., river and marine sediments) will reveal habitat-specific characteristics and adaptations caused by differences in nutrients, vegetation, and environmental stresses.}, }
@article {pmid30523166, year = {2018}, author = {Geoghegan, JL and Holmes, EC}, title = {Evolutionary Virology at 40.}, journal = {Genetics}, volume = {210}, number = {4}, pages = {1151-1162}, doi = {10.1534/genetics.118.301556}, pmid = {30523166}, issn = {1943-2631}, abstract = {RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.}, }
@article {pmid30523039, year = {2018}, author = {Ulrich, CM and Gigic, B and Böhm, J and Ose, J and Viskochil, R and Schneider, M and Colditz, GA and Figueiredo, JC and Grady, WM and Li, CI and Shibata, D and Siegel, EM and Toriola, AT and Ulrich, A}, title = {The ColoCare Study - A paradigm of transdisciplinary science in colorectal cancer outcomes.}, journal = {Cancer epidemiology, biomarkers &amp; prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {}, number = {}, pages = {}, doi = {10.1158/1055-9965.EPI-18-0773}, pmid = {30523039}, issn = {1538-7755}, abstract = {BACKGROUND: Colorectal cancer (CRC) is a leading cause of cancer death. Biomarkers to predict treatment outcomes are needed, as is evidence whether post-diagnosis diet and lifestyle can affect well-being and clinical outcomes. The international ColoCare Consortium aims to identify new biologic markers (e.g., metabolomic, transcriptomic, metagenomic, genetic, epigenetic, proteomic) that predict clinical outcomes, and to characterize associations between modifiable risk factors (e.g., diet, supplement use, physical activity) with short-term and long-term patient-reported and clinical outcomes among CRC patients.<br><br>METHODS/RESULTS: ColoCare is recruiting newly diagnosed CRC patients across six sites in the U.S. and one in Germany. As of April 2018 we have recruited >2,000 patients across all sites. Our projected enrollment is >4,000 multiethnic CRC patients. The study includes uniformly collected, comprehensive sets of data and biospecimens at multiple time points up to 5 years after diagnosis. Treatment and clinical data are abstracted from medical records and centrally harmonized. Biospecimens are archived according to standardized procedures. Our initial studies demonstrated metabolic differences in adipose tissue types. We further reported on associations of biological factors (e.g., inflammation, DNA methylation, metabolomics) with lifestyle factors (e.g., adiposity, smoking, physical activity, dietary supplement use) or joint associations with clinical outcomes.<br><br>CONCLUSION: ColoCare is a consortium for the investigation of multi-level factors relevant to CRC survivorship.<br><br>IMPACT: The combination of a comprehensive set of biospecimens collected at multiple time points, jointly with detailed assessments of health behaviors and other prognostic factors, results in a unique resource that facilitates wide-ranging, innovative, and impactful research on CRC.}, }
@article {pmid30523036, year = {2018}, author = {Danko, D and Meleshko, D and Bezdan, D and Mason, C and Hajirasouliha, I}, title = {Minerva: an alignment and reference free approach to deconvolve linked-reads for metagenomics.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.235499.118}, pmid = {30523036}, issn = {1549-5469}, abstract = {Emerging Linked-Read technologies (aka Read-Cloud or barcoded short-reads) have revived interest in short-read technology as a viable way to understand large-scale structure in genomes and metagenomes. Linked-Read technologies, such as the 10x Chromium system, use a microfluidic system and a specialized set of 3' barcodes (aka UIDs) to tag short DNA reads sourced from the same long fragment of DNA; subsequently, the tagged reads are sequenced on standard short read platforms. This approach results in interesting compromises. Each long fragment of DNA is only sparsely covered by reads, no information about the ordering of reads from the same fragment is preserved, and 3' barcodes match reads from roughly 2-20 long fragments of DNA. However, compared to long read technologies the cost per base to sequence is far lower, far less input DNA is required, and their base error rate is that of Illumina short-reads.In this paper, we formally describe a particular algorithmic issue common to across Linked-Read technology: the deconvolution of reads with a single 3' barcode into clusters that represent single long fragments of DNA. We introduce Minerva, A graph-based algorithm that approximately solves the barcode deconvolution problem for metagenomic data (where reference genomes may be incomplete or unavailable). Additionally, we develop two demonstrations where the deconvolution of barcoded reads improves downstream results: improving the specificity of taxonomic assignments and improving the specificity of k-mer based clustering. To the best of our knowledge, we are the first to address the problem of barcode deconvolution in metagenomics.}, }
@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}, doi = {10.1186/s40168-018-0591-4}, 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 {pmid30522523, year = {2018}, author = {Willis, JR and González-Torres, P and Pittis, AA and Bejarano, LA and Cozzuto, L and Andreu-Somavilla, N and Alloza-Trabado, M and Valentín, A and Ksiezopolska, E and Company, C and Onywera, H and Montfort, M and Hermoso, A and Iraola-Guzmán, S and Saus, E and Labeeuw, A and Carolis, C and Hecht, J and Ponomarenko, J and Gabaldón, T}, title = {Citizen science charts two major &quot;stomatotypes&quot; in the oral microbiome of adolescents and reveals links with habits and drinking water composition.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {218}, doi = {10.1186/s40168-018-0592-3}, pmid = {30522523}, issn = {2049-2618}, support = {BFU2015-67107//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; SEV-2012-02-08//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; Saca la Lengua//&quot;la Caixa&quot; Foundation/ ; }, abstract = {BACKGROUND: The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral microbiome of 1500 adolescents around Spain and its relationships with lifestyle, diet, hygiene, and socioeconomic and environmental parameters.<br><br>RESULTS: Our results provide a detailed snapshot of the adolescent oral microbiome and how it varies with lifestyle and other factors. In addition to hygiene and dietary habits, we found that the composition of tap water was related to important changes in the abundance of several bacterial genera. This points to an important role of drinking water in shaping the oral microbiota, which has been so far poorly explored. Overall, the microbiome samples of our study can be clustered into two broad compositional patterns (stomatotypes), driven mostly by Neisseria and Prevotella, respectively. These patterns show striking similarities with those found in unrelated populations.<br><br>CONCLUSIONS: We hypothesize that these stomatotypes represent two possible global optimal equilibria in the oral microbiome that reflect underlying constraints of the human oral niche. As such, they should be found across a variety of geographical regions, lifestyles, and ages.}, }
@article {pmid30522439, year = {2018}, author = {Zahariev, M and Chen, W and Visagie, CM and Lévesque, CA}, title = {Cluster oligonucleotide signatures for rapid identification by sequencing.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {395}, doi = {10.1186/s12859-018-2363-3}, pmid = {30522439}, issn = {1471-2105}, support = {97//Agriculture and Agri-Food Canada (CA)/ ; CRTI 09-462RD/CSSP 30vv01//Canadian safety and security program (CSSP), CA/ ; }, abstract = {BACKGROUND: Oligonucleotide signatures (signatures) have been widely used for studying microbial diversity and function in wet-lab settings, but using them for accurate in silico identification of organisms from high-throughput sequencing (HTS) data is only a proof of concept. Existing signature design programs for sequence signatures (signatures matching exactly one sequence) or clade signatures (signatures matching every sequence in a phylogenetic clade) are not able to identify all possible polymorphic sites for sequences with high similarity and perform poorly when handling large genome sequencing datasets.<br><br>RESULTS: We introduce cluster signatures: subsequences that match perfectly and exclusively any group of sequences in a data set. Cluster signatures provide complete recall for primer/probe design and increased discrimination between sequences beyond that of clade signatures. Using cluster signatures for in silico identification of HTS targets achieves good precision/recall and running time performance. This method has been implemented into an open source tool, the Automated Oligonucleotide Design Pipeline (adop), included in supplementary material and available at: https://bitbucket.org/wenchen_aafc/aodp_v2.0_release .<br><br>CONCLUSIONS: Cluster signatures provide a rapid and universal analysis tool to identify all possible short diagnostic DNA markers and variants from any DNA sequencing dataset. They are particularly useful in discriminating genetic material from closely related organisms and in detecting deleterious mutations in highly or perfectly conserved genomic sites.}, }
@article {pmid30473288, year = {2019}, author = {Meng, D and Li, J and Liu, T and Liu, Y and Yan, M and Hu, J and Li, X and Liu, X and Liang, Y and Liu, H and Yin, H}, title = {Effects of redox potential on soil cadmium solubility: Insight into microbial community.}, journal = {Journal of environmental sciences (China)}, volume = {75}, number = {}, pages = {224-232}, doi = {10.1016/j.jes.2018.03.032}, pmid = {30473288}, issn = {1001-0742}, mesh = {Cadmium/*chemistry/toxicity ; Metagenome ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*chemistry/toxicity ; Solubility ; }, abstract = {Understanding the role of microbes in the solubility of cadmium (Cd) is of fundamental importance for remediation of Cd toxicity. The present study aimed to identify the microbes that involved in regulating Cd solubility and to reveal possible mechanisms. Therefore, microbial communities were investigated through high-throughput sequencing approach, the molecular ecological network was constructed and metagenomes were predicted. Our results indicated that redox conditions affected both the solubility of soil Cd and the microbial communities. Anaerobic microbes, such as Anaerolineaceae, did not only play important roles in shaping the microbial community in soils, but might also be involved in regulating the Cd solubility. Two possible mechanisms that how Anaerolineaceae involved in Cd solubility are (1) Anaerolineaceae are important organic matter degraders under anoxic conditions and (2) Anaerolineaceae can co-exist with methane metabolism microbes, while methane metabolism promotes the precipitation of soluble Cd. Thus, application of Anaerolineaceae in bioremediation of soil Cadmium contamination is a potential approach. The study provided a novel insight into the role of microbial community in the regulation of Cd solubility under different redox conditions, and suggested a potential approach for the remediation of soil Cd contamination.}, }
@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 {pmid28368489, year = {2017}, author = {Storch, G}, title = {Powerful Diagnostic Methods Applied to a Unique Specimen Collection.}, journal = {The Journal of infectious diseases}, volume = {215}, number = {9}, pages = {1349-1351}, doi = {10.1093/infdis/jix151}, pmid = {28368489}, issn = {1537-6613}, mesh = {Child ; Humans ; *Metagenomics ; Pneumonia ; Polymerase Chain Reaction ; *Specimen Handling ; }, }
@article {pmid30540709, year = {2018}, author = {Chen, LA and Hourigan, SK and Grigoryan, Z and Gao, Z and Clemente, JC and Rideout, JR and Chirumamilla, S and Rabidazeh, S and Saeed, S and Elson, CO and Oliva-Hemker, M and Blaser, MJ and Sears, CL}, title = {Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1097/MPG.0000000000002210}, pmid = {30540709}, issn = {1536-4801}, abstract = {OBJECTIVES: The gut microbiome is believed to play a role in the susceptibility to and treatment of Clostridium difficile infections (CDIs). It is, however, unknown whether the gut microbiome is also affected by asymptomatic C difficile colonization. Our study aimed to evaluate the fecal microbiome of children based on C difficile colonization, and CDI risk factors, including antibiotic use and comorbid inflammatory bowel disease (IBD).<br><br>METHODS: Subjects with IBD and non-IBD controls were prospectively enrolled from pediatric clinics for a biobanking project (n = 113). A fecal sample was collected from each subject for research purposes only and was evaluated for asymptomatic toxigenic C difficile colonization. Fecal microbiome composition was determined by 16S rRNA sequencing.<br><br>RESULTS: We found reduced bacterial diversity and altered microbiome composition in subjects with C difficile colonization, concurrent antibiotic use, and/or concomitant IBD (all P < 0.05). Accounting for antibiotic use and IBD status, children colonized with C difficile had significant enrichment in taxa from the genera Ruminococcus, Eggerthella, and Clostridium. Children without C difficile had increased relative abundances of Faecalibacterium and Rikenellaceae. Imputed metagenomic functions of those colonized were enriched for genes in oxidative phosphorylation and beta-lactam resistance, whereas in the subjects without C difficile, several functions in translation and metabolism were over-represented.<br><br>CONCLUSIONS: In children, C difficile colonization, or factors that predispose to colonization such as antibiotic use and IBD status were associated with decreased gut bacterial diversity and altered microbiome composition. Averting such microbiome alterations may be a method to prevent or treat CDI.}, }
@article {pmid30538693, year = {2018}, author = {George, F and Daniel, C and Thomas, M and Singer, E and Guilbaud, A and Tessier, FJ and Revol-Junelles, AM and Borges, F and Foligné, B}, title = {Occurrence and Dynamism of Lactic Acid Bacteria in Distinct Ecological Niches: A Multifaceted Functional Health Perspective.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2899}, doi = {10.3389/fmicb.2018.02899}, pmid = {30538693}, issn = {1664-302X}, abstract = {Lactic acid bacteria (LAB) are representative members of multiple ecosystems on earth, displaying dynamic interactions within animal and plant kingdoms in respect with other microbes. This highly heterogeneous phylogenetic group has coevolved with plants, invertebrates, and vertebrates, establishing either mutualism, symbiosis, commensalism, or even parasitism-like behavior with their hosts. Depending on their location and environment conditions, LAB can be dominant or sometimes in minority within ecosystems. Whatever their origins and relative abundance in specific anatomic sites, LAB exhibit multifaceted ecological and functional properties. While some resident LAB permanently inhabit distinct animal mucosal cavities, others are provided by food and may transiently occupy the gastrointestinal tract. It is admitted that the overall gut microbiome has a deep impact on health and diseases. Here, we examined the presence and the physiological role of LAB in the healthy human and several animal microbiome. Moreover, we also highlighted some dysbiotic states and related consequences for health, considering both the resident and the so-called &quot;transionts&quot; microorganisms. Whether LAB-related health effects act collectively or follow a strain-specificity dogma is also addressed. Besides the highly suggested contribution of LAB to interplay with immune, metabolic, and even brain-axis regulation, the possible involvement of LAB in xenobiotic detoxification processes and metal equilibrium is also tackled. Recent technological developments such as functional metagenomics, metabolomics, high-content screening and design in vitro and in vivo experimental models now open new horizons for LAB as markers applied for disease diagnosis, susceptibility, and follow-up. Moreover, identification of general and more specific molecular mechanisms based on antioxidant, antimicrobial, anti-inflammatory, and detoxifying properties of LAB currently extends their selection and promising use, either as probiotics, in traditional and functional foods, for dedicated treatments and mostly for maintenance of normobiosis and homeostasis.}, }
@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}, doi = {10.1186/s12864-018-5191-y}, pmid = {30537931}, issn = {1471-2164}, 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 {pmid30536648, year = {2018}, author = {Taniguchi, H and Tanisawa, K and Sun, X and Kubo, T and Hoshino, Y and Hosokawa, M and Takeyama, H and Higuchi, M}, title = {Effects of short-term endurance exercise on gut microbiota in elderly men.}, journal = {Physiological reports}, volume = {6}, number = {23}, pages = {e13935}, doi = {10.14814/phy2.13935}, pmid = {30536648}, issn = {2051-817X}, support = {14J03810//Ministry of Education, Culture, Sports, Science, and Technology/ ; 2015-2019//Ministry of Education, Culture, Sports, Science, and Technology/ ; S1511017//Ministry of Education, Culture, Sports, Science, and Technology/ ; //Waseda University/ ; //&quot;Technologies for creating next-generation agriculture, forestry and fisheries&quot;/ ; //Strategic Research Foundation at Private Universities/ ; }, abstract = {Regular exercise reduces the risks for cardiovascular diseases. Although the gut microbiota has been associated with fitness level and cardiometabolic risk factors, the effects of exercise-induced gut microbiota changes in elderly individuals are unclear. This study evaluated whether endurance exercise modulates the gut microbiota in elderly subjects, and whether these changes are associated with host cardiometabolic phenotypes. In a randomized crossover trial, 33 elderly Japanese men participated in a 5-week endurance exercise program. 16S rRNA gene-based metagenomic analyses revealed that the effect of endurance exercise on gut microbiota diversity was not greater than interindividual differences, whereas changes in α-diversity indices during intervention were negatively correlated with changes in systolic and diastolic blood pressure, especially during exercise. Microbial composition analyses showed that the relative abundance of Clostridium difficile significantly decreased, whereas that of Oscillospira significantly increased during exercise as compared to the control period. The changes in these taxa were correlated with the changes in several cardiometabolic risk factors. The findings indicate that short-term endurance exercise has little effect on gut microbiota in elderly individuals, and that the changes in gut microbiota were associated with cardiometabolic risk factors, such as systolic and diastolic blood pressure, providing preliminary insight into the associations between the gut microbiota and cardiometabolic phenotypes.}, }
@article {pmid30535266, year = {2018}, author = {Ramachandran, PS and Cresswell, FV and Meya, DB and Crawford, ED and DeRisi, JL and Boulware, DR and Wilson, MR}, title = {Detection of Cryptococcus DNA by metagenomic next-generation sequencing in symptomatic cryptococcal antigenemia.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciy1024}, pmid = {30535266}, issn = {1537-6591}, }
@article {pmid30534962, year = {2018}, author = {Gutiérrez-García, K and Bustos-Díaz, ED and Corona-Gómez, JA and Ramos-Aboites, HE and Sélem-Mojica, N and Cruz-Morales, P and Pérez-Farrera, MA and Barona-Gómez, F and Cibrián-Jaramillo, A}, title = {Cycad coralloid roots contain bacterial communities including cyanobacteria and Caulobacter spp that encode niche-specific biosynthetic gene clusters.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evy266}, pmid = {30534962}, issn = {1759-6653}, abstract = {Cycads are the only early seed plants that have evolved a specialized root to host endophytic bacteria that fix nitrogen. To provide evolutionary and functional insights into this million-year old symbiosis, we investigate endophytic bacterial sub-communities isolated from coralloid roots of species from Dioon (Zamiaceae) sampled from their natural habitats. We employed a sub-community co-culture experimental strategy to reveal both predominant and rare bacteria, which were characterized using phylogenomics and detailed metabolic annotation. Diazotrophic plant endophytes, including Bradyrhizobium, Burkholderia, Mesorhizobium, Rhizobium and Nostoc species, dominated the epiphyte-free sub-communities. Draft genomes of six cyanobacteria species were obtained after shotgun metagenomics of selected sub-communities. This data was used for whole-genome inferences that suggest two Dioon-specific monophyletic groups, and a level of specialization characteristic of co-evolved symbiotic relationships. Furthermore, the genomes of these cyanobacteria were found to encode unique biosynthetic gene clusters, predicted to direct the synthesis of specialized metabolites, mainly involving peptides. After combining genome mining with detection of pigment emissions using multiphoton excitation fluorescence microscopy, we also show that Caulobacter species co-exist with cyanobacteria, and may interact with them by means of a novel indigoidine-like specialized metabolite. We provide an unprecedented view of the composition of the cycad coralloid root, including phylogenetic and functional patterns mediated by specialized metabolites that may be important for the evolution of ancient symbiotic adaptations.}, }
@article {pmid30534599, year = {2018}, author = {Escapa, IF and Chen, T and Huang, Y and Gajare, P and Dewhirst, FE and Lemon, KP}, title = {New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00187-18}, pmid = {30534599}, issn = {2379-5077}, abstract = {The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most next-generation sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus, and mouth. Using minimum entropy decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level, revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, 1 of these 19 species belonged to a currently uncultivated genus. Fourth, for 94% of the participants, 2 to 10 species constituted 90% of their sequences, indicating that the nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies. IMPORTANCE The eHOMD (http://www.ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes and the individual microbes in body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus, and mouth, and the lower respiratory tract, in health and disease. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (i) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (ii) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (iii) reference genomes to facilitate metagenomic, metatranscriptomic, and proteomic studies and (iv) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.}, }
@article {pmid30533941, year = {2018}, author = {Thrash, JC and Baker, BJ and Seitz, KW and Temperton, B and Campbell, LG and Rabalais, NN and Henrissat, B and Mason, OU}, title = {Metagenomic Assembly and Prokaryotic Metagenome-Assembled Genome Sequences from the Northern Gulf of Mexico &quot;Dead Zone&quot;.}, journal = {Microbiology resource announcements}, volume = {7}, number = {9}, pages = {}, doi = {10.1128/MRA.01033-18}, pmid = {30533941}, issn = {2576-098X}, abstract = {Coastal regions experiencing declining dissolved oxygen are increasing in number and severity around the world. However, despite the importance of microbial metabolism in coastal hypoxia, few metagenomic surveys exist. Our data set from within the second largest human-caused hypoxic region provides opportunities to more deeply explore the microbiology of these systems.}, }
@article {pmid30533904, year = {2018}, author = {Somayaji, V and DeNardo, D and Wilson Sayres, MA and Blake, M and Waits, K and Fontenele, RS and Kraberger, S and Varsani, A}, title = {Genome Sequence of a Single-Stranded DNA Virus Identified in Gila Monster Feces.}, journal = {Microbiology resource announcements}, volume = {7}, number = {7}, pages = {}, doi = {10.1128/MRA.00925-18}, pmid = {30533904}, issn = {2576-098X}, abstract = {The Gila monster (Heloderma suspectum) is native to the Sonoran Desert. Metagenomic analyses of a Gila monster fecal sample revealed the presence of a small, circular, single-stranded DNA virus that is most closely related to a gemykrogvirus (family Genomoviridae) genome from caribou feces sharing 88% genome-wide pairwise identity.}, }
@article {pmid30533855, year = {2018}, author = {Bresciani, L and Lemos, LN and Wale, N and Lin, JY and Strauss, AT and Duffy, MA and Rodrigues, JLM}, title = {Draft Genome Sequence of &quot;Candidatus Spirobacillus cienkowskii,&quot; a Pathogen of Freshwater Daphnia Species, Reconstructed from Hemolymph Metagenomic Reads.}, journal = {Microbiology resource announcements}, volume = {7}, number = {22}, pages = {}, doi = {10.1128/MRA.01175-18}, pmid = {30533855}, issn = {2576-098X}, abstract = {We report here the near-complete genome sequence of &quot;Candidatus Spirobacillus cienkowskii,&quot; a spiral-shaped, red-pigmented uncultivated bacterial pathogen of Daphnia spp. The genome is 2.74 Mbp in size, has a GC content of 32.1%, and contains genes associated with bacterial motility and the production of carotenoids, which could explain the distinctive red color of hosts infected with this pathogen.}, }
@article {pmid30533830, year = {2018}, author = {Harris, RL and Lau, MCY and Cadar, A and Bartlett, DH and Cason, E and van Heerden, E and Onstott, TC}, title = {Draft Genome Sequence of &quot;Candidatus Bathyarchaeota&quot; Archaeon BE326-BA-RLH, an Uncultured Denitrifier and Putative Anaerobic Methanotroph from South Africa's Deep Continental Biosphere.}, journal = {Microbiology resource announcements}, volume = {7}, number = {20}, pages = {}, doi = {10.1128/MRA.01295-18}, pmid = {30533830}, issn = {2576-098X}, abstract = {Metagenomic sequencing of fracture fluid from South Africa recovered a nearly complete &quot;Candidatus Bathyarchaeota&quot; archaeon genome. The metagenome-assembled genome of BE326-BA-RLH contains genes involved in methane metabolism and dissimilatory nitrate reduction. This study presents the first genomic evidence for potential anaerobic methane oxidation in the phylum &quot;Ca. Bathyarchaeota.&quot;}, }
@article {pmid30533778, year = {2018}, author = {Salaheen, S and Kim, SW and Karns, JS and Haley, BJ and Van Kessel, JAS}, title = {Fecal Metagenome Sequences from Lactating Dairy Cows Shedding Escherichia coli O157:H7.}, journal = {Microbiology resource announcements}, volume = {7}, number = {18}, pages = {}, doi = {10.1128/MRA.01279-18}, pmid = {30533778}, issn = {2576-098X}, abstract = {Cattle are primary reservoirs of Escherichia coli O157:H7, a causative agent of severe human infections. To facilitate analyses of the communities in which this pathogen is found, we sequenced the fecal metagenomes of 10 dairy cows shedding E. coli O157:H7 and added them to the public domain.}, }
@article {pmid30533746, year = {2018}, author = {Antelo, V and Salazar, C and Martínez, A and D'Alessandro, B and Castro, M and Betancor, L and Barcala, MV and Míguez, D and Gonnet, GH and Iraola, G}, title = {First Release of the Bacterial Biobank of the Urban Environment (BBUE).}, journal = {Microbiology resource announcements}, volume = {7}, number = {16}, pages = {}, doi = {10.1128/MRA.01201-18}, pmid = {30533746}, issn = {2576-098X}, abstract = {Metagenomics is providing a broad overview of bacterial functional diversity; however, culturing and biobanking are still essential for microbiology. Here, we present the Bacterial Biobank of the Urban Environment (BBUE), a sizable culture collection for long-term storage and characterization of the microbiota associated with urban environments relevant for public health.}, }
@article {pmid30533733, year = {2018}, author = {Lobb, B and Adegoke, AA and Ma, K and Doxey, AC and Aiyegoro, OA}, title = {Metagenomic Sequencing of Wastewater from a South African Research Farm.}, journal = {Microbiology resource announcements}, volume = {7}, number = {16}, pages = {}, doi = {10.1128/MRA.01323-18}, pmid = {30533733}, issn = {2576-098X}, abstract = {We sequenced wastewater effluent from the Agricultural Research Council-Animal Production in South Africa that conducts studies on livestock health and farm ecology. Thauera, Oscillibacter, and Pseudomonas were the most abundant genera within the community. Thirty-one different antibiotic resistance genes were identified, 10 of which are associated with tetracycline resistance.}, }
@article {pmid30533707, year = {2018}, author = {Rastrojo, A and Núñez, A and Moreno, DA and Alcamí, A}, title = {A New Putative Caulimoviridae Genus Discovered through Air Metagenomics.}, journal = {Microbiology resource announcements}, volume = {7}, number = {14}, pages = {}, doi = {10.1128/MRA.00955-18}, pmid = {30533707}, issn = {2576-098X}, abstract = {Members of the Caulimoviridae family are important plant pathogens. These circular double-stranded DNA viruses may integrate into the host genome, although this integration is not required for the viral replication cycle. Here, we describe three complete genomes belonging to a new putative Caulimoviridae genus discovered through air metagenomics.}, }
@article {pmid30533635, year = {2018}, author = {Milani, A and Zamperin, G and Fusaro, A and Salviato, A and Bano, L and Zandonà, L and Brunetta, R and Monne, I}, title = {Complete Genome Sequence of Psittacine Adenovirus 1, Identified from Poicephalus senegalus in Italy.}, journal = {Microbiology resource announcements}, volume = {7}, number = {11}, pages = {}, doi = {10.1128/MRA.01037-18}, pmid = {30533635}, issn = {2576-098X}, abstract = {Using a metagenomics approach, we were able to determine for the first time the full-genome sequence of a psittacine adenovirus 1 isolate that was recovered from the liver of a dead Senegal parrot (Poicephalus senegalus) in Italy. The results of the phylogenetic investigations revealed the existence of high genetic diversity among adenoviruses circulating in psittacine birds.}, }
@article {pmid30532742, year = {2018}, author = {Ma, JE and Jiang, HY and Li, LM and Zhang, XJ and Li, GY and Li, HM and Jin, XJ and Chen, JP}, title = {The Fecal Metagenomics of Malayan Pangolins Identifies an Extensive Adaptation to Myrmecophagy.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2793}, doi = {10.3389/fmicb.2018.02793}, pmid = {30532742}, issn = {1664-302X}, abstract = {The characteristics of flora in the intestine of an animal, including the number and abundance of different microbial species and their functions, are closely related to the diets of the animal and affect the physical condition of the host. The Malayan pangolin (Manis javanica) is an endangered species that specializes in myrmecophagy. Analyzing the microbiome in the intestine of the pangolin is imperative to protect this species. By sequencing the metagenomes of the feces of four pangolins, we constructed a non-redundant catalog of 211,868 genes representing 1,811 metagenomic species. Taxonomic annotation revealed that Bacteroidetes (49.9%), Proteobacteria (32.2%), and Firmicutes (12.6%) are the three main phyla. The annotation of gene functions identified 5,044 genes from 88 different glycoside hydrolase (GH) families in the Carbohydrate-Active enZYmes database and 114 gene modules related to chitin-degrading enzymes, corresponding to the catalytic domains of GH18 family enzymes, containing chitinase genes of classes III and V in the dataset. Fourteen gene modules corresponded to the catalytic domains of GH19 family enzymes, containing chitinase genes of classes I, II, and IV. These genes were found in 37 species belonging to four phyla: Bacteroidetes, Cyanobacteria, Firmicutes, and Proteobacteria. Moreover, when the metabolic pathways of these genes were summarized, 41,711 genes were associated with 147 unique KEGG metabolic pathways, and these genes were assigned to two Gene Ontology terms: metabolic process and catalytic activity. We also found several species that likely play roles in the digestion of cellulose and may be able to degrade chitin, including Enterobacter cloacae, Lactococcus lactis, Chitinimonas koreensis, and Chitinophaga pinensis. In addition, we identified some intestinal microflora and genes related to diseases in pangolins. Twenty-seven species were identified by STAMP analysis as differentially abundant in healthy and diseased animals: 20 species, including Cellulosilyticum lentocellum and Lactobacillus reuteri, were more abundant in healthy pangolins, while seven species, including Odoribacter splanchnicus, Marinilabilia salmonicolor, Xanthomonas citri, Xanthomonas vasicola, Oxalobacter formigenes, Prolixibacter bellariivorans, and Clostridium bolteae, were more abundant in diseased pangolins. These results will support the efforts to conserve pangolins.}, }
@article {pmid30532649, year = {2018}, author = {Lim, MY and Cho, Y and Rho, M}, title = {Diverse Distribution of Resistomes in the Human and Environmental Microbiomes.}, journal = {Current genomics}, volume = {19}, number = {8}, pages = {701-711}, doi = {10.2174/1389202919666180911130845}, pmid = {30532649}, issn = {1389-2029}, abstract = {The routine therapeutic use of antibiotics has caused resistance genes to be disseminated across microbial populations. In particular, bacterial strains having antibiotic resistance genes are frequently observed in the human microbiome. Moreover, multidrug-resistant pathogens are now widely spread, threatening public health. Such genes are transferred and spread among bacteria even in different environments. Advances in high throughput sequencing technology and computational algorithms have accelerated investigation into antibiotic resistance genes of bacteria. Such studies have revealed that the antibiotic resistance genes are located close to the mobility-associated genes, which promotes their dissemination. An increasing level of information on genomic sequences of resistome should expedite research on drug-resistance in our body and environment, thereby contributing to the development of public health policy. In this review, the high prevalence of antibiotic resistance genes and their exchange in the human and environmental microbiome is discussed with respect to the genomic contents. The relationships among diverse resistomes, related bacterial species, and the antibiotics are reviewed. In addition, recent advances in bioinformatics approaches to investigate such relationships are discussed.}, }
@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}, doi = {10.1038/sdata.2018.285}, 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 {pmid30531976, year = {2018}, author = {Franzosa, EA and Sirota-Madi, A and Avila-Pacheco, J and Fornelos, N and Haiser, HJ and Reinker, S and Vatanen, T and Hall, AB and Mallick, H and McIver, LJ and Sauk, JS and Wilson, RG and Stevens, BW and Scott, JM and Pierce, K and Deik, AA and Bullock, K and Imhann, F and Porter, JA and Zhernakova, A and Fu, J and Weersma, RK and Wijmenga, C and Clish, CB and Vlamakis, H and Huttenhower, C and Xavier, RJ}, title = {Gut microbiome structure and metabolic activity in inflammatory bowel disease.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-018-0306-4}, pmid = {30531976}, issn = {2058-5276}, abstract = {The inflammatory bowel diseases (IBDs), which include Crohn's disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome-the molecular interface between host and microbiota-are less well understood. To address this gap, we performed untargeted metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n = 155) and validation (n = 65) cohorts of CD, UC and non-IBD control patients. Metabolomic and metagenomic profiles were broadly correlated with faecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While > 50% of differentially abundant metabolite features were uncharacterized, many could be assigned putative roles through metabolomic 'guilt by association' (covariation with known metabolites). Differentially abundant species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between differentially abundant species and well-characterized differentially abundant metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome-metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.}, }
@article {pmid30530851, year = {2018}, author = {Gharaibeh, RZ and Jobin, C}, title = {Microbiota and cancer immunotherapy: in search of microbial signals.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2018-317220}, pmid = {30530851}, issn = {1468-3288}, }
@article {pmid30530602, year = {2018}, author = {Sugawara, Y and Akeda, Y and Hagiya, H and Sakamoto, N and Takeuchi, D and Shanmugakani, RK and Motooka, D and Nishi, I and Zin, KN and Aye, MM and Myint, T and Tomono, K and Hamada, S}, title = {Spreading patterns of NDM-producing Enterobacteriaceae in clinical and environmental settings in Yangon, Myanmar.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1128/AAC.01924-18}, pmid = {30530602}, issn = {1098-6596}, abstract = {The spread of carbapenemase-producing Enterobacteriaceae (CPE) has become a global concern, contributing to widespread carbapenem resistance. However, the specific dissemination patterns of carbapenemase genes have not been intensively investigated in developing countries, including Myanmar, where NDM-type carbapenemases are spreading in clinical settings. In the present study, we phenotypically and genetically characterized 91 CPE isolates obtained from clinical (n = 77) and environmental (n = 14) samples in Yangon, Myanmar. We determined the dissemination of plasmids harboring genes encoding NDM-1 and its variants using whole-genome sequencing and plasmid analysis. IncFII plasmids harboring blaNDM-5 and IncX3 plasmids harboring blaNDM-4 or blaNDM-7 were the most prevalent plasmid types identified among the isolates. The IncFII plasmids were predominantly carried by clinical isolates of Escherichia coli, and their clonal expansion was observed within the same ward of a hospital. By contrast, the IncX3 plasmids were found in phylogenetically divergent isolates from clinical and environmental samples classified into nine species, suggesting the widespread dissemination of plasmids via horizontal transfer. Half of the environmental isolates were found to possess IncX3 plasmids, and this type of plasmid was confirmed to transfer more effectively to recipient organisms at a relatively low temperature (25°C) compared to the IncFII plasmid. Moreover, various other plasmid types were identified harboring blaNDM-1, including IncFIB, IncFII, IncL/M, and IncA/C2, among clinical isolates of Klebsiella pneumoniae or Enterobacter cloacae complex. Overall, our results highlight three distinct patterns of the dissemination of blaNDM-harboring plasmids among CPE isolates in Myanmar, contributing to gaining a better understanding of their molecular epidemiology and dissemination in an endemic setting.}, }
@article {pmid30529942, year = {2018}, author = {D'Alessio, M and Durso, LM and Miller, DN and Woodbury, B and Ray, C and Snow, DD}, title = {Environmental fate and microbial effects of monensin, lincomycin, and sulfamethazine residues in soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {246}, number = {}, pages = {60-68}, doi = {10.1016/j.envpol.2018.11.093}, pmid = {30529942}, issn = {1873-6424}, abstract = {The impact of commonly-used livestock antibiotics on soil nitrogen transformations under varying redox conditions is largely unknown. Soil column incubations were conducted using three livestock antibiotics (monensin, lincomycin and sulfamethazine) to better understand the fate of the antibiotics, their effect on nitrogen transformation, and their impact on soil microbial communities under aerobic, anoxic, and denitrifying conditions. While monensin was not recovered in the effluent, lincomycin and sulfamethazine concentrations decreased slightly during transport through the columns. Sorption, and to a limited extent degradation, are likely to be the primary processes leading to antibiotic attenuation during leaching. Antibiotics also affected microbial respiration and clearly impacted nitrogen transformation. The occurrence of the three antibiotics as a mixture, as well as the occurrence of lincomycin alone affected, by inhibiting any nitrite reduction, the denitrification process. Discontinuing antibiotics additions restored microbial denitrification. Metagenomic analysis indicated that Proteobacteria, Bacteroidetes, Actinobacteria, and Chloroflexi were the predominant phyla observed throughout the study. Results suggested that episodic occurrence of antibiotics led to a temporal change in microbial community composition in the upper portion of the columns while only transient changes occurred in the lower portion. Thus, the occurrence of high concentrations of veterinary antibiotic residues could impact nitrogen cycling in soils receiving wastewater runoff or manure applications with potential longer-term microbial community changes possible at higher antibiotic concentrations.}, }
@article {pmid30529583, year = {2018}, author = {Paramsothy, S and Nielsen, S and Kamm, MA and Deshpande, NP and Faith, JJ and Clemente, JC and Paramsothy, R and Walsh, AJ and van den Bogaerde, J and Samuel, D and Leong, RWL and Connor, S and Ng, W and Lin, E and Borody, TJ and Wilkins, MR and Colombel, JF and Mitchell, HM and Kaakoush, NO}, title = {Specific Bacteria and Metabolites Associated with Response to Fecal Microbiota Transplantation in Patients with Ulcerative Colitis.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2018.12.001}, pmid = {30529583}, issn = {1528-0012}, abstract = {BACKGROUND &amp; AIMS: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized, controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy.<br><br>METHODS: We performed a double-blind trial of 81 patients with active UC randomly assigned to groups that received an initial colonoscopic infusion and then intensive multi-donor FMT or placebo enemas, 5 days/week for 8 weeks. Patients in the FMT group received blended homogenized stool from 3-7 unrelated donors. Patients in the placebo group were eligible to receive open-label FMT, after the double-blind study period. We collected 314 fecal samples from the patients at screening, every 4 weeks during treatment, and 8 weeks after the blinded or open-label FMT therapy. We also collected 160 colonoscopic large bowel biopsies from the patients at study entry, at completion of 8 weeks of blinded therapy, and at the end of open-label FMT if applicable. We analyzed the 105 fecal samples from the 14 individual donors (n=55), which were combined into 21 multi-donor batches (n=50). Bacteria in colonic and fecal samples were analyzed by both 16S rRNA gene and transcript amplicon sequencing; 285 fecal samples were analyzed by shotgun metagenomics and 60 fecal samples were analyzed for metabolome features.<br><br>RESULTS: FMT increased microbial diversity and altered composition, based on analyses of colon and fecal samples collected before vs after FMT. Diversity was greater in fecal and colon samples collected before and after FMT treatment from patients who achieved remission compared to patients who did not. Patients in remission after FMT had enrichment of Eubacterium hallii and Roseburia inulivorans, compared to patients who did not achieve remission after FMT, and had increased levels of short-chain fatty acid biosynthesis and secondary bile acids. Patients who did not achieve remission had enrichment of Fusobacterium gonidiaformans, Sutterella wadsworthensis, and Escherichia and increased levels of heme and lipopolysaccharide biosynthesis. Bacteroides in donor stool were associated with remission in patients receiving FMT, and Streptococcus in donor stool associated with no response to FMT.<br><br>CONCLUSIONS: In an analysis of fecal and colonic mucosa samples from patients receiving FMT for active UC and stool samples from donors, we associated specific bacteria and metabolic pathways with induction of remission. These findings may be of value in the design of microbe-based therapies for UC. ClinicalTrials.gov no: NCT01896635.}, }
@article {pmid30529535, year = {2018}, author = {Liu, P and Wang, W and Zhao, J and Wei, D}, title = {Screening novel β-galactosidases from a sequence-based metagenome and characterization of an alkaline β-galactosidase for the enzymatic synthesis of galactooligosaccharides.}, journal = {Protein expression and purification}, volume = {155}, number = {}, pages = {104-111}, doi = {10.1016/j.pep.2018.12.001}, pmid = {30529535}, issn = {1096-0279}, abstract = {βgalactosidases have wide industrial applications in lactose hydrolysis and transglycosylation reactions. Therefore, there is a need to mine novel and high-quality β-galactosidases with good tolerance and novel features from harsh environments and genomic databases. In this study, an Escherichia coli β-galactosidase-deficient host, ΔlacZ(DE3)pRARE, was constructed by the CRISPR-Cas9 system for screening active β-galactosidases. Of thirty selected β-galactosidases, twelve novel enzymes showed β-galactosidase activity, four of which were purified for further study. BGal_375 exhibited maximal activity at pH 8 and 50 °C. The concentrations of two types of galactooligosaccharides, tri- and tetra-saccharides, produced by BGal_375, reached 64.53 g/l and 8.32 g/l, respectively. BGal_375 displayed a Km value of 1.65 mM and kcat value of 53 s-1 for p-nitrophenyl-β-d-galactopyranoside (pNPG). BGal_137, BGal_144-3, and BGal_145-2 showed promising hydrolytic activity for pNPG. BGal_137 is a homodimer while BGal_144-3, BGal_145-2, and BGal_375 were all monomeric. This study provided an efficient solution for the identification of new β-galactosidases from metagenomic data, and an alkaline β-galactosidase efficient for the synthesis of galactooligosaccharides was obtained, which is important for potential industrial applications.}, }
@article {pmid30529208, year = {2018}, author = {Ariaeenejad, S and Hosseini, E and Maleki, M and Kavousi, K and Moosavi-Movahedi, AA and Salekdeh, GH}, title = {Identification and characterization of a novel thermostable xylanase from camel rumen metagenome.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijbiomac.2018.12.041}, pmid = {30529208}, issn = {1879-0003}, abstract = {Metagenomics has emerged to isolate novel enzymes from the uncultured microbiota in the environment. In this study, the metagenomic data obtained from camel rumen was considered as the potential source of microbial xylanase enzymes with proper activity in extreme conditions. The metagenomic data were assembled and contigs were used for in-silico identification of candidate thermostable enzyme. A novel thermostable xylanase enzyme, named PersiXyn1, with 1146 bp full-length gene which encodes a 381 amino acid protein was identified. Using the DNA template extracted from camel rumen metagenomic samples, the candidate enzyme genes were cloned and expressed in proper E. coli strains. The phylogenetic analysis showed the evolutionary position of PersiXyn1 among the known thermostable xylanases. The results of the CD analysis and determining the secondary structure of the enzyme, confirmed the presence of a high percentage of β-sheets as an important characteristic of thermophilic xylanases. The PersiXyn1 was active at a broad range of pH (6-11) and temperature (25-90 °C). The optimum pH and temperature were 8 and 40 °C respectively, and the enzyme maintained 80% of its maximum activity in the pH 8 and temperature 40 °C for 1 h. The Scanning electron microscope (SEM) micrograph of enzyme treated pulp clearly showed that the effective use of enzymes in fiber separation may reduce the cost of carton paper production. The novelty of this enzyme lies in the fact that it is highly active and stable in a broad range of pH and temperature. This study highlights the potential importance of camel microbiome for discovering novel thermostable enzymes with applications in agriculture and industries.}, }
@article {pmid30528431, year = {2018}, author = {Rascovan, N and Sjögren, KG and Kristiansen, K and Nielsen, R and Willerslev, E and Desnues, C and Rasmussen, S}, title = {Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2018.11.005}, pmid = {30528431}, issn = {1097-4172}, abstract = {Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersiniapestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.}, }
@article {pmid30528276, year = {2018}, 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 = {}, number = {}, pages = {}, doi = {10.1016/j.syapm.2018.11.001}, pmid = {30528276}, issn = {1618-0984}, 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 {pmid30526624, year = {2018}, author = {Wu, G and Niu, M and Tang, W and Hu, J and Wei, G and He, Z and Chen, Y and Jiang, Y and Chen, P}, title = {L-Fucose ameliorates high-fat diet-induced obesity and hepatic steatosis in mice.}, journal = {Journal of translational medicine}, volume = {16}, number = {1}, pages = {344}, doi = {10.1186/s12967-018-1718-x}, pmid = {30526624}, issn = {1479-5876}, support = {2016A030306043//Natural Science Foundation of Guangdong Province/ ; 2017B030314034//Natural Science Foundation of Guangdong Province/ ; 2016A020216015//China Association for Science and Technology/ ; }, abstract = {BACKGROUND: L-Fucose (Fuc), a six-deoxy hexose monosaccharide, is present endogenously in humans and animals and has a wide range of biological functions. In the present study, we aimed to examine the effect of Fuc on obesity and hepatic steatosis in mice fed a high-fat diet (HFD).<br><br>METHODS: C57BL/6 mice were fed a normal chow (NC) or HFD for 18 weeks to induce obesity and fatty liver. Fuc was administered intragastrically from the 8th week to the end of the experiment (18 weeks).<br><br>RESULTS: Metagenomic analysis showed that HFD altered the genomic profile of gut microbiota in the mice; specifically, expression of alpha-L-fucosidase, the gene responsible for Fuc generation, was markedly reduced in the HFD group compared with that in the NC group. Fuc treatment decreased body weight gain, fat accumulation, and hepatic triglyceride elevation in HFD-fed mice. In addition, Fuc decreased the levels of endotoxin-producing bacteria of the Desulfovibrionaceae family and restored HFD-induced enteric dysbiosis at both compositional and functional levels.<br><br>CONCLUSION: Our findings suggest that Fuc might be a novel strategy to treat HFD-induced obesity and fatty liver.}, }
@article {pmid30525951, year = {2018}, author = {Ma, ZF and Yusof, N and Hamid, N and Lawenko, RM and Mohammad, WMZW and Liong, MT and Sugahara, H and Odamaki, T and Xiao, J and Lee, YY}, title = {Bifidobacterium infantis M-63 improves mental health in victims with irritable bowel syndrome developed after a major flood disaster.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-10}, doi = {10.3920/BM2018.0008}, pmid = {30525951}, issn = {1876-2891}, abstract = {Individuals in a community who developed irritable bowel syndrome (IBS) after major floods have significant mental health impairment. We aimed to determine if Bifidobacterium infantis M-63 was effective in improving symptoms, psychology and quality of life measures in flood-affected individuals with IBS and if the improvement was mediated by gut microbiota changes. Design was non-randomised, open-label, controlled before-and-after. Of 53 participants, 20 with IBS were given B. infantis M-63 (1×109 cfu/sachet/day) for three months and 33 were controls. IBS symptom severity scale, hospital anxiety and depression scale, SF-36 Questionnaire, hydrogen breath testing for small intestinal bacterial overgrowth and stools for 16S rRNA metagenomic analysis were performed before and after intervention. 11 of 20 who were given probiotics (M-63) and 20 of 33 controls completed study as per-protocol. Mental well-being was improved with M-63 vs controls for full analysis (P=0.03) and per-protocol (P=0.01) populations. Within-group differences were observed for anxiety and bodily pain (both P=0.04) in the M-63 per-protocol population. Lower ratio of Firmicutes/Bacteroidetes was observed with M-63 vs controls (P=0.01) and the lower ratio was correlated with higher post-intervention mental score (P=0.04). B. infantis M-63 is probably effective in improving mental health of victims who developed IBS after floods and this is maybe due to restoration of microbial balance and the gut-brain axis. However, our conclusion must be interpreted within the context of limited sample size. The study was retrospectively registered on 12 October 2017 and the Trial Registration Number (TRN) was NCT03318614.}, }
@article {pmid30525950, year = {2018}, author = {Hibberd, AA and Yde, CC and Ziegler, ML and Honoré, AH and Saarinen, MT and Lahtinen, S and Stahl, B and Jensen, HM and Stenman, LK}, title = {Probiotic or synbiotic alters the gut microbiota and metabolism in a randomised controlled trial of weight management in overweight adults.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-16}, doi = {10.3920/BM2018.0028}, pmid = {30525950}, issn = {1876-2891}, abstract = {The gut microbiota contributes to host energy metabolism, and altered gut microbiota has been associated with obesity-related metabolic disorders. We previously reported that a probiotic alone or together with a prebiotic controls body fat mass in healthy overweight or obese individuals in a randomised, double-blind, placebo controlled clinical study (ClinicalTrials.gov NCT01978691). We now aimed to investigate whether changes in the gut microbiota may be associated with the observed clinical benefits. Faecal and plasma samples were obtained from a protocol compliant subset (n=134) of participants from a larger clinical study where participants were randomised (1:1:1:1) into four groups: (1) placebo, 12 g/d microcrystalline cellulose; (2) Litesse® Ultra™ polydextrose (LU), 12 g/day; (3) Bifidobacterium animalis subsp. lactis 420™ (B420), 1010 cfu/d in 12 g microcrystalline cellulose; (4) LU+B420, 1010 cfu/d of B420 in 12 g/d LU for 6 months of intervention. The faecal microbiota composition and metabolites were assessed as exploratory outcomes at baseline, 2, 4, 6 months, and +1 month post-intervention and correlated to obesity-related clinical outcomes. Lactobacillus and Akkermansia were more abundant with B420 at the end of the intervention. LU+B420 increased Akkermansia, Christensenellaceae and Methanobrevibacter, while Paraprevotella was reduced. Christensenellaceae was consistently increased in the LU and LU+B420 groups across the intervention time points, and correlated negatively to waist-hip ratio and energy intake at baseline, and waist-area body fat mass after 6 months treatment with LU+B420. Functional metagenome predictions indicated alterations in pathways related to cellular processes and metabolism. Plasma bile acids glycocholic acid, glycoursodeoxycholic acid, and taurohyodeoxycholic acid and tauroursodeoxycholic acid were reduced in LU+B420 compared to Placebo. Consumption of B420 and its combination with LU resulted in alterations of the gut microbiota and its metabolism, and may support improved gut barrier function and obesity-related markers.}, }
@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 {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 {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 {pmid29437920, year = {2018}, author = {Weingarten, RA and Johnson, RC and Conlan, S and Ramsburg, AM and Dekker, JP and Lau, AF and Khil, P and Odom, RT and Deming, C and Park, M and Thomas, PJ and ,  and Henderson, DK and Palmore, TN and Segre, JA and Frank, KM}, title = {Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29437920}, issn = {2150-7511}, mesh = {Bacterial Proteins/*genetics ; Carbapenem-Resistant Enterobacteriaceae/genetics/*isolation &amp; purification ; Hospitals ; Humans ; Metagenomics ; Plasmids/*analysis ; Prevalence ; *Sanitary Engineering ; *Water Microbiology ; Whole Genome Sequencing ; beta-Lactamases/*genetics ; }, abstract = {The hospital environment is a potential reservoir of bacteria with plasmids conferring carbapenem resistance. Our Hospital Epidemiology Service routinely performs extensive sampling of high-touch surfaces, sinks, and other locations in the hospital. Over a 2-year period, additional sampling was conducted at a broader range of locations, including housekeeping closets, wastewater from hospital internal pipes, and external manholes. We compared these data with previously collected information from 5 years of patient clinical and surveillance isolates. Whole-genome sequencing and analysis of 108 isolates provided comprehensive characterization of blaKPC/blaNDM-positive isolates, enabling an in-depth genetic comparison. Strikingly, despite a very low prevalence of patient infections with blaKPC-positive organisms, all samples from the intensive care unit pipe wastewater and external manholes contained carbapenemase-producing organisms (CPOs), suggesting a vast, resilient reservoir. We observed a diverse set of species and plasmids, and we noted species and susceptibility profile differences between environmental and patient populations of CPOs. However, there were plasmid backbones common to both populations, highlighting a potential environmental reservoir of mobile elements that may contribute to the spread of resistance genes. Clear associations between patient and environmental isolates were uncommon based on sequence analysis and epidemiology, suggesting reasonable infection control compliance at our institution. Nonetheless, a probable nosocomial transmission of Leclercia sp. from the housekeeping environment to a patient was detected by this extensive surveillance. These data and analyses further our understanding of CPOs in the hospital environment and are broadly relevant to the design of infection control strategies in many infrastructure settings.IMPORTANCE Carbapenemase-producing organisms (CPOs) are a global concern because of the morbidity and mortality associated with these resistant Gram-negative bacteria. Horizontal plasmid transfer spreads the resistance mechanism to new bacteria, and understanding the plasmid ecology of the hospital environment can assist in the design of control strategies to prevent nosocomial infections. A 5-year genomic and epidemiological survey was undertaken to study the CPOs in the patient-accessible environment, as well as in the plumbing system removed from the patient. This comprehensive survey revealed a vast, unappreciated reservoir of CPOs in wastewater, which was in contrast to the low positivity rate in both the patient population and the patient-accessible environment. While there were few patient-environmental isolate associations, there were plasmid backbones common to both populations. These results are relevant to all hospitals for which CPO colonization may not yet be defined through extensive surveillance.}, }
@article {pmid29402898, year = {2018}, author = {Cai, L and Tian, RM and Zhou, G and Tong, H and Wong, YH and Zhang, W and Chui, APY and Xie, JY and Qiu, JW and Ang, PO and Liu, S and Huang, H and Qian, PY}, title = {Exploring coral microbiome assemblages in the South China Sea.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2428}, pmid = {29402898}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Archaea/classification/*genetics/isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; Carbon Cycle/physiology ; China ; Coral Reefs ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbiota/*genetics ; Nitrogen Cycle/physiology ; Pacific Ocean ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfur/physiology ; Symbiosis/*physiology ; }, abstract = {Coral reefs are significant ecosystems. The ecological success of coral reefs relies on not only coral-algal symbiosis but also coral-microbial partnership. However, microbiome assemblages in the South China Sea corals remain largely unexplored. Here, we compared the microbiome assemblages of reef-building corals Galaxea (G. fascicularis) and Montipora (M. venosa, M. peltiformis, M. monasteriata) collected from five different locations in the South China Sea using massively-parallel sequencing of 16S rRNA gene and multivariate analysis. The results indicated that microbiome assemblages for each coral species were unique regardless of location and were different from the corresponding seawater. Host type appeared to drive the coral microbiome assemblages rather than location and seawater. Network analysis was employed to explore coral microbiome co-occurrence patterns, which revealed 61 and 80 co-occurring microbial species assembling the Galaxea and Montipora microbiomes, respectively. Most of these co-occurring microbial species were commonly found in corals and were inferred to play potential roles in host nutrient metabolism; carbon, nitrogen, sulfur cycles; host detoxification; and climate change. These findings suggest that the co-occurring microbial species explored might be essential to maintain the critical coral-microbial partnership. The present study provides new insights into coral microbiome assemblages in the South China Sea.}, }
@article {pmid29396559, year = {2018}, author = {Massé, A and Domart-Coulon, I and Golubic, S and Duché, D and Tribollet, A}, title = {Early skeletal colonization of the coral holobiont by the microboring Ulvophyceae Ostreobium sp.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2293}, pmid = {29396559}, issn = {2045-2322}, mesh = {Animal Shells/*microbiology ; Animals ; Anthozoa/*microbiology ; Chlorophyta/classification/genetics/*growth &amp; development ; Genetic Variation ; Metagenome ; Ribulose-Bisphosphate Carboxylase/genetics ; *Symbiosis ; }, abstract = {Ostreobium sp. (Bryopsidales, Ulvophyceae) is a major microboring alga involved in tropical reef dissolution, with a proposed symbiotic lifestyle in living corals. However, its diversity and colonization dynamics in host's early life stages remained unknown. Here, we mapped microborer distribution and abundance in skeletons of the branching coral Pocillopora damicornis from the onset of calcification in primary polyps (7 days) to budding juvenile colonies (1 and 3 months) growing on carbonate and non-carbonate substrates pre-colonized by natural biofilms, and compared them to adult colonies (in aquarium settings). Primary polyps were surprisingly already colonized by microboring filaments and their level of invasion depended on the nature of settlement substrate and the extent of its pre-colonization by microborers. Growth of early coral recruits was unaffected even when microborers were in close vicinity to the polyp tissue. In addition to morphotype observations, chloroplast-encoded rbcL gene sequence analyses revealed nine new Ostreobium clades (OTU99%) in Pocillopora coral. Recruits and adults shared one dominant rbcL clade, undetected in larvae, but also present in aquarium seawater, carbonate and non-carbonate settlement substrates, and in corals from reef settings. Our results show a substratum-dependent colonization by Ostreobium clades, and indicate horizontal transmission of Ostreobium-coral associations.}, }
@article {pmid29386563, year = {2018}, author = {Treonis, AM and Unangst, SK and Kepler, RM and Buyer, JS and Cavigelli, MA and Mirsky, SB and Maul, JE}, title = {Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2004}, pmid = {29386563}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; *Metagenome ; Soil/*parasitology ; Tylenchida/classification/*genetics ; }, abstract = {We used complementary morphological and DNA metabarcoding approaches to characterize soil nematode communities in three cropping systems, conventional till (CT), no-till (NT) and organic (ORG), from a long-term field experiment. We hypothesized that organic inputs to the ORG system would promote a more abundant nematode community, and that the NT system would show a more structured trophic system (higher Bongers MI) than CT due to decreased soil disturbance. The abundance of Tylenchidae and Cephalobidae both showed positive correlations to soil organic carbon and nitrogen, which were highest in the ORG system. The density of omnivore-predator and bacterial-feeding nematodes was reduced in NT soils compared to CT, while some plant-parasitic taxa increased. NT soils had similar Bongers MI values to CT, suggesting they contained nematode communities associated with soils experiencing comparable levels of disturbance. Metabarcoding revealed within-family differences in nematode diversity. Shannon and Simpson's index values for the Tylenchidae and Rhabditidae were higher in the ORG system than CT. Compared to morphological analysis, metabarcoding over- or underestimated the prevalence of several nematode families and detected some families not observed based on morphology. Discrepancies between the techniques require further investigation to establish the accuracy of metabarcoding for characterization of soil nematode communities.}, }
@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 {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 {pmid29033338, year = {2018}, author = {Karkman, A and Do, TT and Walsh, F and Virta, MPJ}, title = {Antibiotic-Resistance Genes in Waste Water.}, journal = {Trends in microbiology}, volume = {26}, number = {3}, pages = {220-228}, doi = {10.1016/j.tim.2017.09.005}, pmid = {29033338}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/pharmacology ; Disinfectants/pharmacology ; Drug Resistance, Microbial/*genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Metals ; Polymerase Chain Reaction/methods ; Sewage/microbiology ; Waste Water/*microbiology ; }, abstract = {Waste water and waste water treatment plants can act as reservoirs and environmental suppliers of antibiotic resistance. They have also been proposed to be hotspots for horizontal gene transfer, enabling the spread of antibiotic resistance genes between different bacterial species. Waste water contains antibiotics, disinfectants, and metals which can form a selection pressure for antibiotic resistance, even in low concentrations. Our knowledge of antibiotic resistance in waste water has increased tremendously in the past few years with advances in the molecular methods available. However, there are still some gaps in our knowledge on the subject, such as how active is horizontal gene transfer in waste water and what is the role of the waste water treatment plant in the environmental resistome? The purpose of this review is to briefly describe some of the main methods for studying antibiotic resistance in waste waters and the latest research and main knowledge gaps on the issue. In addition, some future research directions are proposed.}, }
@article {pmid28842259, year = {2018}, author = {van Gelder, S and Röhrig, N and Schattenberg, F and Cichocki, N and Schumann, J and Schmalz, G and Haak, R and Ziebolz, D and Müller, S}, title = {A cytometric approach to follow variation and dynamics of the salivary microbiota.}, journal = {Methods (San Diego, Calif.)}, volume = {134-135}, number = {}, pages = {67-79}, doi = {10.1016/j.ymeth.2017.08.009}, pmid = {28842259}, issn = {1095-9130}, mesh = {Flow Cytometry/*methods ; Humans ; Metagenome/genetics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics/isolation &amp; purification ; Saliva/*microbiology ; }, abstract = {Microbial flow cytometry is an established fast and economic technique for complex ecosystem studies and enables visualization of rapidly changing community structures by measuring characteristics of single microbial cells. Cytometric evaluation routines are available such as flowCyBar which are useful for automatic data processing. Here, a cytometric workflow was established which allows to routinely analyze salivary microbiomes on the example of ten oral healthy subjects. First, saliva was collected within a 3-month period, cytometrically analyzed and the evolution of the microbiomes followed as well as the calculation of their intra- and inter-subject similarity. Second, the respective microbiomes were stressed by exposition to high sugar or acid concentrations and immediate changes were recorded. Third, bactericide solutions were tested on their impact on the microbiomes. In all three set ups huge intra-individual variations in cytometric community structures were found to be largely absent, even under stress, while inter-individual diversity was obvious. The bacterial cell counts of saliva samples were found to vary between 3.0×107 and 6.2×108 cells per sample and subject in undisturbed environments. The application of the two bactericides did not cause noteworthy diversity changes but the loss in cell numbers by about 50% was high after treatment. Illumina® sequencing of whole microbiomes or sorted sub-microbiomes revealed typical phyla such as Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. This approach is useful for fast monitoring of individual salivary microbiomes and automatic calculation of intra- and inter-individual dynamic changes and variability and opens insight into ecological principles leading to their sustainment in their individual environment.}, }
@article {pmid28500338, year = {2017}, author = {Al-Hebshi, NN and Nasher, AT and Maryoud, MY and Homeida, HE and Chen, T and Idris, AM and Johnson, NW}, title = {Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1834}, pmid = {28500338}, issn = {2045-2322}, support = {R37 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Aged ; Biodiversity ; Carcinoma, Squamous Cell/*etiology/pathology ; Case-Control Studies ; Female ; Fusobacterium Infections/*complications/*microbiology ; *Fusobacterium nucleatum/classification/genetics ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Mouth Neoplasms/*etiology/pathology ; Pseudomonas Infections/*complications/*microbiology ; *Pseudomonas aeruginosa/classification/genetics ; }, abstract = {Studies on the possible association between bacteria and oral squamous cell carcinoma (OSCC) remain inconclusive, largely due to methodological variations/limitations. The objective of this study was to characterize the species composition as well as functional potential of the bacteriome associated with OSCC. DNA obtained from 20 fresh OSCC biopsies (cases) and 20 deep-epithelium swabs (matched control subjects) was sequenced for the V1-V3 region using Illumina's 2 × 300 bp chemistry. High quality, non-chimeric merged reads were classified to species level using a prioritized BLASTN-algorithm. Downstream analyses were performed using QIIME, PICRUSt, and LEfSe. Fusobacterium nucleatum subsp. polymorphum was the most significantly overrepresented species in the tumors followed by Pseudomonas aeruginosa and Campylobacter sp. Oral taxon 44, while Streptococcus mitis, Rothia mucilaginosa and Haemophilus parainfluenzae were the most significantly abundant in the controls. Functional prediction showed that genes involved in bacterial mobility, flagellar assembly, bacterial chemotaxis and LPS synthesis were enriched in the tumors while those responsible for DNA repair and combination, purine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, ribosome biogenesis and glycolysis/gluconeogenesis were significantly associated with the controls. This is the first epidemiological evidence for association of F. nucleatum and P. aeruginosa with OSCC. Functionally, an &quot;inflammatory bacteriome&quot; is enriched in OSSC.}, }
@article {pmid28383519, year = {2017}, author = {Li, M and Zhou, H and Pan, X and Xu, T and Zhang, Z and Zi, X and Jiang, Y}, title = {Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45697}, pmid = {28383519}, issn = {2045-2322}, mesh = {*Animal Feed ; Animals ; Biota/*drug effects ; Cecum/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet/*methods ; Geese/*microbiology ; *Manihot ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Geese are extremely adept in utilizing plant-derived roughage within their diet. However, the intestinal microbiome of geese remains limited, especially the dietary effect on microbial diversity. Cassava foliage was widely used in animal feed, but little information is available for geese. In this study, the geese were fed with control diet (CK), experimental diet supplemented with 5% cassava foliage (CF5) or 10% (CF10) for 42 days, respectively. The cecal samples were collected after animals were killed. High-throughput sequencing technology was used to investigate the microbial diversity in the caecum of geese with different dietary supplements. Taxonomic analysis indicated that the predominant phyla were distinct with different dietary treatments. The phyla Firmicutes (51.4%), Bacteroidetes (29.55%) and Proteobacteria (7.90%) were dominant in the CK group, but Bacteroidetes (65.19% and 67.29%,) Firmicutes (18.01% and 17.39%), Proteobacteria (8.72% and 10.18%), Synergistete (2.51% and 1.76%) and Spirochaetes (2.60% and 1.46%) were dominant in CF5 and CF10 groups. The abundance of Firmicutes was negatively correlated with the supplementation of cassava foliage. However, the abundance of Bacteroidetes and Proteobacteria were positively correlated with the supplementation of cassava foliage. Our study also revealed that the microbial communities were significantly different at genus levels. Genes related to nutrient and energy metabolism, immunity and signal transduction pathways were primarily enriched by the microbiome.}, }
@article {pmid28378789, year = {2017}, author = {Boers, SA and Hays, JP and Jansen, R}, title = {Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45536}, pmid = {28378789}, issn = {2045-2322}, mesh = {Bacteria/*classification/*genetics ; DNA, Ribosomal/genetics ; Metagenomics/*methods/standards ; *Microbiota ; Polymerase Chain Reaction/*methods/standards ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In the last decade, many researchers have embraced 16S rRNA gene sequencing techniques, which has led to a wealth of publications and documented differences in the composition of microbial communities derived from many different ecosystems. However, comparison between different microbiota studies is currently very difficult due to the lack of a standardized 16S rRNA gene sequencing protocol. Here we report on a novel approach employing micelle PCR (micPCR) in combination with an internal calibrator that allows for standardization of microbiota profiles via their absolute abundances. The addition of an internal calibrator allows the researcher to express the resulting operational taxonomic units (OTUs) as a measure of 16S rRNA gene copies by correcting the number of sequences of each individual OTU in a sample for efficiency differences in the NGS process. Additionally, accurate quantification of OTUs obtained from negative extraction control samples allows for the subtraction of contaminating bacterial DNA derived from the laboratory environment or chemicals/reagents used. Using equimolar synthetic microbial community samples and low biomass clinical samples, we demonstrate that the calibrated micPCR/NGS methodology possess a much higher precision and a lower limit of detection compared with traditional PCR/NGS, resulting in more accurate microbiota profiles suitable for multi-study comparison.}, }
@article {pmid30299661, year = {2017}, author = {Galach’yants, AD and Bel’kova, NL and Sukhanova, EV and Galach’yants, YP and Morozov, AA and Parfenova, VV}, title = {[Taxonomic Composition of Lake Baikal Bacterioneuston Communities].}, journal = {Mikrobiologiia}, volume = {86}, number = {2}, pages = {229-238}, pmid = {30299661}, issn = {0026-3656}, mesh = {Alphaproteobacteria/*classification/*genetics ; Lakes/*microbiology ; *Metagenome ; *Water Microbiology ; }, }
@article {pmid30521551, year = {2018}, author = {Vernocchi, P and Del Chierico, F and Russo, A and Majo, F and Rossitto, M and Valerio, M and Casadei, L and La Storia, A and De Filippis, F and Rizzo, C and Manetti, C and Paci, P and Ercolini, D and Marini, F and Fiscarelli, EV and Dallapiccola, B and Lucidi, V and Miccheli, A and Putignani, L}, title = {Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208171}, doi = {10.1371/journal.pone.0208171}, pmid = {30521551}, issn = {1932-6203}, abstract = {BACKGROUND: Cystic fibrosis (CF) is a disorder affecting the respiratory, digestive, reproductive systems and sweat glands. This lethal hereditary disease has known or suspected links to the dysbiosis gut microbiota. High-throughput meta-omics-based approaches may assist in unveiling this complex network of symbiosis modifications.<br><br>OBJECTIVES: The aim of this study was to provide a predictive and functional model of the gut microbiota enterophenotype of pediatric patients affected by CF under clinical stability.<br><br>METHODS: Thirty-one fecal samples were collected from CF patients and healthy children (HC) (age range, 1-6 years) and analysed using targeted-metagenomics and metabolomics to characterize the ecology and metabolism of CF-linked gut microbiota. The multidimensional data were low fused and processed by chemometric classification analysis.<br><br>RESULTS: The fused metagenomics and metabolomics based gut microbiota profile was characterized by a high abundance of Propionibacterium, Staphylococcus and Clostridiaceae, including Clostridium difficile, and a low abundance of Eggerthella, Eubacterium, Ruminococcus, Dorea, Faecalibacterium prausnitzii, and Lachnospiraceae, associated with overexpression of 4-aminobutyrate (GABA), choline, ethanol, propylbutyrate, and pyridine and low levels of sarcosine, 4-methylphenol, uracil, glucose, acetate, phenol, benzaldehyde, and methylacetate. The CF gut microbiota pattern revealed an enterophenotype intrinsically linked to disease, regardless of age, and with dysbiosis uninduced by reduced pancreatic function and only partially related to oral antibiotic administration or lung colonization/infection.<br><br>CONCLUSIONS: All together, the results obtained suggest that the gut microbiota enterophenotypes of CF, together with endogenous and bacterial CF biomarkers, are direct expression of functional alterations at the intestinal level. Hence, it's possible to infer that CFTR impairment causes the gut ecosystem imbalance.This new understanding of CF host-gut microbiota interactions may be helpful to rationalize novel clinical interventions to improve the affected children's nutritional status and intestinal function.}, }
@article {pmid30520232, year = {2018}, author = {Yu, Y and Gao, F and Chen, X and Zheng, S and Zhang, J}, title = {Changes in the Distal Esophageal Microbiota in Chinese Patients with Reflux Esophagitis.}, journal = {Journal of digestive diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-2980.12692}, pmid = {30520232}, issn = {1751-2980}, abstract = {OBJECTIVE: Changes in microbiota structure in the distal esophagus may be associated with the pathogenesis of gastroesophageal reflux disease. The composition of the distal esophageal microbiota between Chinese patients and healthy volunteers was compared through metagenomic high-throughput DNA sequencing and bioinformatic analyses.<br><br>METHODS: Healthy volunteers (HV) and patients with reflux esophagitis (RE) were enrolled. Distal esophageal (2 cm above the gastroesophageal junction) biopsy specimens were obtained under the endoscopy. Microbial DNA was extracted from the specimens, followed by 16S rDNA gene amplification and Illumina sequencing. Bioinformatic tools were applied to dissect the community structure and statistical methods were used to compare the differences.<br><br>RESULTS: No dramatic differences in microbiota were found in RE patients compared to the healthy controls. At the phylum level, only Bacteroidetes differed between the groups, being less abundant in the RE group. The overall number and diversity of species tended to be lower in RE patients, but there were no significant differences between the groups. Three genera, Prevotella, Helicobacter, and Moraxella, were obviously depleted in RE patients as revealed by linear discriminant analysis (LDA) effect size (LEfSe) analyses.<br><br>CONCLUSIONS: The structure of distal esophageal microbiota in Chinese RE patients showed moderate changes compared to healthy volunteers. To what extent these changes are associated with the pathogenesis of reflux esophagitis needs further investigation.}, }
@article {pmid30519555, year = {2018}, author = {Singh, JK and Sharma, RK and Ghosh, P and Kumar, A and Khan, ML}, title = {Imidazolium Based Ionic Liquids: A Promising Green Solvent for Water Hyacinth Biomass Deconstruction.}, journal = {Frontiers in chemistry}, volume = {6}, number = {}, pages = {548}, doi = {10.3389/fchem.2018.00548}, pmid = {30519555}, issn = {2296-2646}, abstract = {Water hyacinth (WH) is a troublesome aquatic weed of natural and artificial water bodies of India and other tropical countries and causing severe ecological problems. The WH biomass is low in lignin content and contains high amount of cellulose and hemicellulose, making it suitable material for conversion into liquid fuels for energy production. This study highlighted that, how different imidazolium based ionic liquids (ILs) [1-alkyl-3-methylimidazolium bromide, [Cnmim]Br (n = 2, 4, 6, 8, and 10)] with tunable properties can be employed for the degradation of WH biomass. Different characterizations techniques, such as XRD, FT-IR, SEM, and DSC are used to unravel the interplay between ILs and the biomass. In this study, it is observed that [Emim][Br] pretreated samples have maximum crystalline value (Crl = 26.38%) as compared to other ionic liquids pretreatments. FTIR data showed the removal of lignin from WH biomass by 12.77% for [Emim][Br] and 10.74% for [Edmim][Br]. SEM images have proven that [Emim][Br] pretreatment have altered the structure of biomass the most. Our results proved that IL pretreatment is a promising approach for effective treatment of WH biomass and causes high levels disruption of cellulose structure.}, }
@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}, doi = {10.1186/s12917-018-1704-9}, pmid = {30518356}, issn = {1746-6148}, 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 {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/ ; }, 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 {pmid30508036, year = {2018}, author = {Schreiber, PW and Kufner, V and Hübel, K and Schmutz, S and Zagordi, O and Kaur, A and Bayard, C and Greiner, M and Zbinden, A and Capaul, R and Böni, J and Hirsch, HH and Mueller, TF and Mueller, NJ and Trkola, A and Huber, M}, title = {Metagenomic virome sequencing in living donor-recipient kidney transplant pairs revealed JC Polyomavirus transmission.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciy1018}, pmid = {30508036}, issn = {1537-6591}, abstract = {Background: Before kidney transplantation, donors and recipients are routinely screened for viral pathogens using specific tests. Little is known about unrecognized viruses of the urinary tract that potentially result in transmission. Using an open metagenomic approach, we aimed to comprehensively assess virus transmission in living donor kidney transplantation.<br><br>Methods: Living kidney donors and their corresponding recipients were enrolled at the time of transplantation. Follow-up study visits for recipients were scheduled 4-6 weeks and 1 year thereafter. At each visit, plasma and urine samples were collected and transplant recipients were evaluated for signs of infection or other transplant-related complications. For metagenomic analysis, samples were enriched for viruses, amplified by anchored random PCR and sequenced using high-throughput metagenomic sequencing. Viruses detected by sequencing were confirmed using real-time PCR.<br><br>Results: We analyzed a total of 30 living kidney donor-recipient pairs with a follow-up of at least one year. In addition to viruses commonly detected during routine post-transplant virus monitoring, metagenomic sequencing detected JC polyomavirus (JCPyV) in urine of seven donors and their corresponding recipients. Phylogenetic analysis confirmed infection with the donor strain in six cases, suggesting transmission from transplant donor to recipient despite recipient seropositivity for JCPyV at the time of transplantation.<br><br>Conclusions: Metagenomic sequencing identified frequent transmission of JCPyV from kidney transplant donors to recipients. Considering the high incidence rate, future studies within larger cohorts are needed to define the relevance of JCPyV infection and the donor's virome for transplant outcome.}, }
@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}, 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. This article is protected by copyright. All rights reserved.}, }
@article {pmid30506399, year = {2018}, author = {Ren, F and Dong, W and Yan, DH}, title = {Endophytic bacterial communities of Jingbai Pear trees in north China analyzed with Illumina sequencing of 16S rDNA.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-018-1597-9}, pmid = {30506399}, issn = {1432-072X}, support = {CAFYBB2017MA019//The Fundamental Research Funds for the Central Non-profit Research Institution of CAF/ ; }, abstract = {Plant endophytes play a crucial role in plant growth, health and ecological function. Jingbai pear (the best quality cultivar of Pyrus ussuriensi Maxim. ex Rupr.) has important ecological and economic value in north China. Conversation of its genetics has great meanings to pear genus (Pyrus L.). However, the bacterial community associated with the cultivar remains unknown. In this study, the structure of endophytic bacterial communities associated with different tissues and soil of Jingbai Pear trees was analyzed with Illumina Miseq sequencing of bacterial 16S rDNA. This is the first report on bacterial microbiome associated with Jingbai pear. Our results demonstrated that different tissues harbored a unique bacterial assemblage. Interestingly, Cyanobacteria was the most abundant phylum, followed by Proteobacteria and Actinobacteria. Samples from three different sites (soils) had significant differences in microbial communities structure. Redundancy analysis (RDA) showed that the bacterial community structure correlated significantly with soil properties-temperature, pH, nitrogen and carbon contents. The conclusion could facilitate to understand the interaction and ecological function of endophytic bacteria with host Jingbai pear trees, so as to benefit the pear variety genetic resource conservation and protection.}, }
@article {pmid30505946, year = {2018}, author = {Scarborough, MJ and Lawson, CE and Hamilton, JJ and Donohue, TJ and Noguera, DR}, title = {Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00221-18}, pmid = {30505946}, issn = {2379-5077}, abstract = {Biomanufacturing from renewable feedstocks can offset fossil fuel-based chemical production. One potential biomanufacturing strategy is production of medium-chain fatty acids (MCFA) from organic feedstocks using either pure cultures or microbiomes. While the set of microbes in a microbiome can often metabolize organic materials of greater diversity than a single species can and while the role of specific species may be known, knowledge of the carbon and energy flow within and between organisms in MCFA-producing microbiomes is only now starting to emerge. Here, we integrated metagenomic, metatranscriptomic, and thermodynamic analyses to predict and characterize the metabolic network of an anaerobic microbiome producing MCFA from organic matter derived from lignocellulosic ethanol fermentation conversion residue. A total of 37 high-quality (>80% complete, <10% contamination) metagenome-assembled genomes (MAGs) were recovered from the microbiome, and metabolic reconstruction of the 10 most abundant MAGs was performed. Metabolic reconstruction combined with metatranscriptomic analysis predicted that organisms affiliated with Lactobacillus and Coriobacteriaceae would degrade carbohydrates and ferment sugars to lactate and acetate. Lachnospiraceae- and Eubacteriaceae-affiliated organisms were predicted to transform these fermentation products to MCFA. Thermodynamic analyses identified conditions under which H2 is expected to be either produced or consumed, suggesting a potential role of H2 partial pressure in MCFA production. From an integrated systems analysis perspective, we propose that MCFA production could be improved if microbiomes were engineered to use homofermentative instead of heterofermentative Lactobacillus and if MCFA-producing organisms were engineered to preferentially use a thioesterase instead of a coenzyme A (CoA) transferase as the terminal enzyme in reverse β-oxidation. IMPORTANCE Mixed communities of microbes play important roles in health, the environment, agriculture, and biotechnology. While tapping the combined activities of organisms within microbiomes may allow the utilization of a wider range of substrates in preference to the use of pure cultures for biomanufacturing, harnessing the metabolism of these mixed cultures remains a major challenge. Here, we predicted metabolic functions of bacteria in a microbiome that produces medium-chain fatty acids from a renewable feedstock. Our findings lay the foundation for efforts to begin addressing how to engineer and control microbiomes for improved biomanufacturing, how to build synthetic mixtures of microbes that produce valuable chemicals from renewable resources, and how to better understand the microbial communities that contribute to health, agriculture, and the environment.}, }
@article {pmid30505899, year = {2018}, author = {Rodriguez-Ramos, LE and Rios-Velazquez, C}, title = {Microbiome dataset from Clara Cave and Empalme Sinkhole waters in Puerto Rico.}, journal = {Data in brief}, volume = {21}, number = {}, pages = {1674-1677}, doi = {10.1016/j.dib.2018.11.028}, pmid = {30505899}, issn = {2352-3409}, abstract = {Camuy River Cave Park (CRCP) is an underground cave system located at the subtropical karst carved by the Camuy River in the subtropical moist forest of northern Puerto Rico (Nieves-Rivera, 2003) [1]. This article contains a metagenomic dataset from the microbial and functional diversity of Clara Cave and Empalme Sinkhole water samples. The environmental DNA (eDNA) from the samples was extracted following direct Metagenomic DNA Isolation method, followed by Next-Generation-Sequencing technology (Illumina MiSeq). The sequences were submitted to MG-RAST online server for taxonomic profile generation and functional in silico description of the samples. The data consisted of domain Bacteria (96.69%), followed up by Viruses (2.87%), Eukaryotes (0.37%), and Archaea (0.02%). The data distribution by phyla showed Proteobacteria (92.61%), Bacteroidetes (1.66%), Actinobacteria (1.12%), and Firmicutes (0.48%). The subsystem functional data showed that 12.97% of genes were related to clustering-based subsystems, 11.40% to carbohydrates, and 11.0% to amino acids and derivatives. The metagenome dataset generated will provide an understanding and comparison framework of the microbial composition and functional diversity present in caves.}, }
@article {pmid30505830, year = {2018}, author = {Esaiassen, E and Hjerde, E and Cavanagh, JP and Pedersen, T and Andresen, JH and Rettedal, SI and Støen, R and Nakstad, B and Willassen, NP and Klingenberg, C}, title = {Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants.}, journal = {Frontiers in pediatrics}, volume = {6}, number = {}, pages = {347}, doi = {10.3389/fped.2018.00347}, pmid = {30505830}, issn = {2296-2360}, abstract = {Objectives: In 2014 probiotic supplementation (Lactobacillus acidophilus and Bifidobacterium longum subspecies infantis; InfloranⓇ) was introduced as standard of care to prevent necrotizing enterocolitis (NEC) in extremely preterm infants in Norway. We aimed to evaluate the influence of probiotics and antibiotic therapy on the developing gut microbiota and antibiotic resistome in extremely preterm infants, and to compare with very preterm infants and term infants not given probiotics. Study design: A prospective, observational multicenter study in six tertiary-care neonatal units. We enrolled 76 infants; 31 probiotic-supplemented extremely preterm infants <28 weeks gestation, 35 very preterm infants 28-31 weeks gestation not given probiotics and 10 healthy full-term control infants. Taxonomic composition and collection of antibiotic resistance genes (resistome) in fecal samples, collected at 7 and 28 days and 4 months age, were analyzed using shotgun-metagenome sequencing. Results: Median (IQR) birth weight was 835 (680-945) g and 1,290 (1,150-1,445) g in preterm infants exposed and not exposed to probiotics, respectively. Two extremely preterm infants receiving probiotic developed NEC requiring surgery. At 7 days of age we found higher median relative abundance of Bifidobacterium in probiotic supplemented infants (64.7%) compared to non-supplemented preterm infants (0.0%) and term control infants (43.9%). Lactobacillus was only detected in small amounts in all groups, but the relative abundance increased up to 4 months. Extremely preterm infants receiving probiotics had also much higher antibiotic exposure, still overall microbial diversity and resistome was not different than in more mature infants at 4 weeks and 4 months. Conclusion: Probiotic supplementation may induce colonization resistance and alleviate harmful effects of antibiotics on the gut microbiota and antibiotic resistome. Clinical Trial Registration: Clinicaltrials.gov: NCT02197468. https://clinicaltrials.gov/ct2/show/NCT02197468.}, }
@article {pmid30505061, year = {2018}, author = {Du, R and Fang, Z}, title = {Statistical correction for functional metagenomic profiling of a microbial community with short NGS reads.}, journal = {Journal of applied statistics}, volume = {45}, number = {14}, pages = {2521-2535}, doi = {10.1080/02664763.2018.1426741}, pmid = {30505061}, issn = {0266-4763}, abstract = {By sequence homology search, the list of all the functions found and the counts of reads being aligned to them present the functional profile of a metagenomic sample. However, a significant obstacle has been observed in this approach due to the short read length associated with many next generation sequencing technologies. This includes artificial families, cross-annotations, length bias and conservation bias. The widely applied cutoff methods, such as BLAST E-value, are not able to solve the problems. Following the published successful procedures on the artificial families and the cross-annotation issue, we propose in this paper to use zero-truncated Poisson and Binomial (ZTP-Bin) hierarchical modelling to correct the length bias and the conservation bias. Goodness-of-fit of the modelling and cross-validation for the prediction using a bioinformatic simulated sample show the validity of this approach. Evaluated on an in vitro-simulated data set, the proposed modelling method outperforms other traditional methods. All three steps were then sequentially applied on real-life metagenomic samples to show that the proposed framework will lead to a more accurate functional profile of a short read metagenomic sample.}, }
@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}, 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 {pmid30504850, year = {2018}, author = {Letuma, P and Arafat, Y and Waqas, M and Lin, F and Lin, W and Zhang, Y and Masita, M and Fan, K and Li, Z and Lin, W}, title = {Gene mutation associated with esl mediates shifts on fungal community composition in rhizosphere soil of rice at grain-filling stage.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17521}, doi = {10.1038/s41598-018-35578-y}, pmid = {30504850}, issn = {2045-2322}, support = {31701329//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2015M580560//China Postdoctoral Science Foundation/ ; 2016J01100//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; }, abstract = {Generally, plant roots shape the rhizosphere fungal community but how individual plant genes involved in senescence affect this shaping is less studied. We used an early senescence leaf (esl) mutant rice and compared it with its isogenic wild type variety to evaluate the effect of the vacuolar H+-ATPase (VHA-A1) gene mutation on the rhizosphere fungal community structure and composition using a metagenomic pyrosequencing approach. The most predominate fungal phyla identified for both isogenic lines belonged to Ascomycota, Basidiomycota and Glomeromycota, where Ascomycota were more prevalent in the esl mutant than the wild type variety. Real-time quantitative PCR analysis confirmed a significant rise in the richness of Cladosporium cladosporioides in esl mutant rice than the wild type variety. Correlation analysis revealed four most abundant genera identified for the esl mutant and their close association with yield and biomass decline, lipid peroxidation, lower root vitality, chlorophyll degradation and limited VHA activity. Higher K+ efflux, H+ and a lower Ca2+ influx was also observed in the esl mutant which could be the reason for abnormal functioning of mutant plants. These results illustrate that besides the well-known effect of senescence on plant physiology and yield decline, it can further shape the rhizosphere fungal community.}, }
@article {pmid30504642, year = {2018}, author = {Nakagawa, T and Tsuchiya, Y and Ueda, S and Fukui, M and Takahashi, R}, title = {Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan.}, journal = {Microbes and environments}, volume = {}, number = {}, pages = {}, doi = {10.1264/jsme2.ME18103}, pmid = {30504642}, issn = {1347-4405}, abstract = {Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1073/pnas.1810550115}, pmid = {30504145}, issn = {1091-6490}, 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 {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}, 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 {pmid30502941, year = {2018}, author = {Foutel-Rodier, T and Thierry, A and Koszul, R and Marbouty, M}, title = {Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut Microbiota.}, journal = {Methods in enzymology}, volume = {612}, number = {}, pages = {183-195}, doi = {10.1016/bs.mie.2018.08.001}, pmid = {30502941}, issn = {1557-7988}, abstract = {Microbial species thrive in very diverse environments and play fundamental roles in their equilibrium and dynamics. Metagenomics consists in extracting, sequencing, and studying the DNA present in ecosystems to better understand their regulation. Ideally, the maximal amount of information would be gathered from the full sequences of the genomes, episomes, and phages present in the microbial communities. Current high-throughput DNA sequencing produces reads ranging in size from a few dozen base pairs for the most commonly used technologies to several kb for emerging single-molecule real-time sequencing techniques. Although valuable information can be extracted from processing these DNA sequences into contigs, reconstructing full genomes remains a difficult task. Clustering contigs according to their similarities or read coverage covariations gives some insights on these genomes, but remains limited as viral sequences, or recent horizontal gene transfers, often differ from their host genomes. We recently developed meta3C, a proximity ligation approach that bins contigs in a sequence-independent way by quantifying and exploiting their tridimensional collisions frequencies in vivo. This technique has demonstrated a great potential to reconstruct genomes as well as to assign plasmids and phages to their hosts. It nevertheless requires a specific processing of the microbial samples before sequencing, which has to be carefully planned.}, }
@article {pmid30514872, year = {2018}, author = {Zhou, Z and Liu, Y and Lloyd, KG and Pan, J and Yang, Y and Gu, JD and Li, M}, title = {Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea).}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0321-8}, pmid = {30514872}, issn = {1751-7370}, support = {31622002//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41506163//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Marine Benthic Group D (MBG-D) archaea, discovered by 16S rRNA gene survey decades ago, are ecologically important, yet understudied and uncultured sedimentary archaea. In this study, a comprehensive meta-analysis based on the 16S rRNA genes of MBG-D archaea showed that MBG-D archaea are one of the most frequently found archaeal lineages in global sediment with widespread distribution and high abundance, including 16 subgroups in total. Interestingly, some subgroups show significant segregations toward salinity and methane seeps. Co-occurrence analyses indicate significant non-random association of MBG-D archaea with Lokiarchaeota (in both saline and freshwater sediments) and Hadesarchaea, suggesting potential interactions among these archaeal groups. Meanwhile, based on four nearly complete metagenome-assembled genomes (MAGs) and corresponding metatranscriptomes reconstructed from mangrove and intertidal mudflat sediments, we provide insights on metabolic potentials and ecological functions of MBG-D archaea. MBG-D archaea appear to be capable of transporting and assimilating peptides and generating acetate and ethanol through fermentation. Metatranscriptomic analysis suggests high expression of genes for acetate and amino acid utilization and for peptidases, especially the M09B-type extracellular peptidase (collagenase) showing high expression levels in all four mangrove MAGs. Beyond heterotrophic central carbon metabolism, the MBG-D genomes include genes that might encode two autotrophic pathways: Wood-Ljundahl (WL) pathways using both H4MPT and H4folate as C1 carriers, and an incomplete dicarboxylate/4-hydroxybutyrate cycle with alternative bypasses from pyruvate to malate/oxaloacetate during dicarboxylation. These findings reveal MBG-D archaea as an important ubiquitous benthic sedimentary archaeal group with specific mixotrophic metabolisms, so we proposed the name Thermoprofundales as a new Order within the Class Thermoplasmata. Globally, Thermoprofundales and other benthic archaea might synergistically transform benthic organic matter, possibly playing a vital role in sedimentary carbon cycle.}, }
@article {pmid30514364, year = {2018}, author = {Vray, M and Hedible, BG and Adam, P and Tondeur, L and Manirazika, A and Randremanana, R and Mainassara, H and Briend, A and Artaud, C and von Platen, C and Altmann, M and Jambou, R}, title = {A multicenter, randomized controlled comparison of three renutrition strategies for the management of moderate acute malnutrition among children aged from 6 to 24 months (the MALINEA project).}, journal = {Trials}, volume = {19}, number = {1}, pages = {666}, doi = {10.1186/s13063-018-3027-3}, pmid = {30514364}, issn = {1745-6215}, support = {2101375618//MEAE/ ; }, abstract = {BACKGROUND: The aim of this open-label, randomized controlled trial conducted in four African countries (Madagascar, Niger, Central African Republic, and Senegal) is to compare three strategies of renutrition for moderate acute malnutrition (MAM) in children based on modulation of the gut microbiota with enriched flours alone, enriched flours with prebiotics or enriched flours coupled with antibiotic treatment.<br><br>METHODS: To be included, children aged between 6 months and 2 years are preselected based on mid-upper-arm circumference (MUAC) and are included based on a weight-for-height Z-score (WHZ) between - 3 and - 2 standard deviations (SD). As per current protocols, children receive renutrition treatment for 12 weeks and are assessed weekly to determine improvement. The primary endpoint is recovery, defined by a WHZ ≥ - 1.5 SD after 12 weeks of treatment. Data collected include clinical and socioeconomic characteristics, side effects, compliance and tolerance to interventions. Metagenomic analysis of gut microbiota is conducted at inclusion, 3 months, and 6 months. The cognitive development of children is evaluated in Senegal using only the Developmental Milestones Checklist II (DMC II) questionnaire at inclusion and at 3, 6, and 9 months. The data will be correlated with renutrition efficacy and metagenomic data.<br><br>DISCUSSION: This study will provide new insights for the treatment of MAM, as well as original data on the modulation of gut microbiota during the renutrition process to support (or not) the microbiota hypothesis of malnutrition.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov, ID: NCT03474276 Last update 28 May 2018.}, }
@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 {pmid30513931, year = {2018}, author = {Knox, MA and Gedye, KR and Hayman, DTS}, title = {The Challenges of Analysing Highly Diverse Picobirnavirus Sequence Data.}, journal = {Viruses}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/v10120685}, pmid = {30513931}, issn = {1999-4915}, support = {MAU1503//Marsden Fund/ ; MAU1701//Rutherford Discovery Fellowship/ ; }, abstract = {The reliable identification and classification of infectious diseases is critical for understanding their biology and controlling their impact. Recent advances in sequencing technology have allowed insight into the remarkable diversity of the virosphere, of which a large component remains undiscovered. For these emerging or undescribed viruses, the process of classifying unknown sequences is heavily reliant on existing nucleotide sequence information in public databases. However, due to the enormous diversity of viruses, and past focus on the most prevalent and impactful virus types, databases are often incomplete. Picobirnaviridae is a dsRNA virus family with broad host and geographic range, but with relatively little sequence information in public databases. The family contains one genus, Picobirnavirus, which may be associated with gastric illness in humans and animals. Little further information is available due in part to difficulties in identification. Here, we investigate diversity both within the genus Picobirnavirus and among other dsRNA virus types using a combined phylogenetic and functional (protein structure homology-modelling) approach. Our results show that diversity within picobirnavirus exceeds that seen between many other dsRNA genera. Furthermore, we find that commonly used practices employed to classify picobirnavirus, such as analysis of short fragments and trimming of sequences, can influence phylogenetic conclusions. The degree of phylogenetic and functional divergence among picobirnavirus sequences in our study suggests an enormous undiscovered diversity, which contributes to the undescribed &quot;viral dark matter&quot; component of metagenomic studies.}, }
@article {pmid30510769, year = {2018}, author = {Džunková, M and Martinez-Martinez, D and Gardlík, R and Behuliak, M and Janšáková, K and Jiménez, N and Vázquez-Castellanos, JF and Martí, JM and D'Auria, G and Bandara, HMHN and Latorre, A and Celec, P and Moya, A}, title = {Oxidative stress in the oral cavity is driven by individual-specific bacterial communities.}, journal = {NPJ biofilms and microbiomes}, volume = {4}, number = {}, pages = {29}, doi = {10.1038/s41522-018-0072-3}, pmid = {30510769}, issn = {2055-5008}, abstract = {The term &quot;bacterial dysbiosis&quot; is being used quite extensively in metagenomic studies, however, the identification of harmful bacteria often fails due to large overlap between the bacterial species found in healthy volunteers and patients. We hypothesized that the pathogenic oral bacteria are individual-specific and they correlate with oxidative stress markers in saliva which reflect the inflammatory processes in the oral cavity. Temporally direct and lagged correlations between the markers and bacterial taxa were computed individually for 26 volunteers who provided saliva samples during one month (21.2 ± 2.7 samples/volunteer, 551 samples in total). The volunteers' microbiomes differed significantly by their composition and also by their degree of microbiome temporal variability and oxidative stress markers fluctuation. The results showed that each of the marker-taxa pairs can have negative correlations in some volunteers while positive in others. Streptococcus mutans, which used to be associated with caries before the metagenomics era, had the most prominent correlations with the oxidative stress markers, however, these correlations were not confirmed in all volunteers. The importance of longitudinal samples collections in correlation studies was underlined by simulation of single sample collections in 1000 different combinations which produced contradictory results. In conclusion, the distinct intra-individual correlation patterns suggest that different bacterial consortia might be involved in the oxidative stress induction in each human subject. In the future, decreasing cost of DNA sequencing will allow to analyze multiple samples from each patient, which might help to explore potential diagnostic applications and understand pathogenesis of microbiome-associated oral diseases.}, }
@article {pmid30510544, year = {2018}, author = {Osimani, A and Milanović, V and Cardinali, F and Garofalo, C and Clementi, F and Ruschioni, S and Riolo, P and Isidoro, N and Loreto, N and Galarini, R and Moretti, S and Petruzzelli, A and Micci, E and Tonucci, F and Aquilanti, L}, title = {Distribution of Transferable Antibiotic Resistance Genes in Laboratory-Reared Edible Mealworms (Tenebrio molitor L.).}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2702}, doi = {10.3389/fmicb.2018.02702}, pmid = {30510544}, issn = {1664-302X}, abstract = {In the present study, the distribution of antibiotic resistance genes in laboratory-reared fresh mealworm larvae (Tenebrio molitor L.), their feeding substrates (carrots and wheatmeal), and frass was assessed. Microbial counts on selective media added with antibiotics highlighted the presence of lactic acid bacteria resistant to ampicillin and vancomycin and, more specifically, enterococci resistant to the latter antibiotic. Moreover, staphylococci resistant to gentamicin, erythromycin, tetracycline, and vancomycin were detected. Enterobacteriaceae resistant to ampicillin and gentamicin were also found, together with Pseudomonadaceae resistant to gentamicin. Some of the genes coding for resistance to macrolide-lincosamide-streptogramin B (MLSB) [erm(A), erm(C)], vancomycin [vanA, vanB], tetracycline [tet(O)], and β-lactams [mecA and blaZ] were absent in all of the samples. For the feeding substrates, organic wheatmeal was positive for tet(S) and tet(K), whereas no AR genes were detected in organic carrots. The genes tet(M), tet(K), and tet(S) were detected in both mealworms and frass, whereas gene aac-aph, coding for resistance to amynoglicosides was exclusively detected in frass. No residues for any of the 64 antibiotics belonging to 10 different drug classes were found in either the organic wheatmeal or carrots. Based on the overall results, the contribution of feed to the occurrence of antibiotic resistance (AR) genes and/or antibiotic-resistant microorganisms in mealworm larvae was hypothesized together with vertical transmission via insect egg smearing.}, }
@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}, doi = {10.1186/s12917-018-1696-5}, pmid = {30509257}, issn = {1746-6148}, support = {31372209//National Natural Science Foundation of China/ ; 2572017AA20//The Fundamental Research Funds for the Central Universities/ ; }, 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 {pmid30504079, year = {2018}, author = {Yazdanbakhsh, AR and Rafiee, M and Daraei, H and Amoozegar, MA}, title = {Responses of flocculated activated sludge to bimetallic Ag-Fe nanoparticles toxicity: Performance, activity enzymatic, and bacterial community shift.}, journal = {Journal of hazardous materials}, volume = {366}, number = {}, pages = {114-123}, doi = {10.1016/j.jhazmat.2018.11.098}, pmid = {30504079}, issn = {1873-3336}, abstract = {Ever-increasing production and use of nanoparticles (NPs) have aroused overarching concerns for their toxic effects on the environment and human. In the present study, the toxic effects of Silver (Ag) and Iron (Fe) NPs on the performance of activated sludge were investigated under continuous aerobic/anoxic/anaerobic conditions in laboratory-scale sequencing batch reactors (SBRs).Activated sludge was exposed to various concentrations (5-100 mg/L) of Ag-Fe NPs for 60 days and its response was assessed through the enzymatic activity, COD, nitrogen (TN) and phosphorus (TP) removal, toxicity tests, as well as variations in bacterial community. Compared with the pristine control sample, the exposure to NPs suppressed TN and TP removal efficiencies. Indeed, the respiration rate and biomass concentration were significantly affected by the NPs. Although the simultaneous exposure to Ag-Fe NPs did affect the integrity of cell membrane (LDH) and key enzymes activities, the higher concentration induced an increased generation of reactive oxygen species (ROS). The metagenome analysis revealed a marked shift in the microbial community structure suggesting that both heterotrophic and autotrophic communities were affected by the presence of Ag-Fe NPs. Our results provide some evidence for compounded effects of NPs in their simultaneous presence, and generate new leads for future research efforts.}, }
@article {pmid30502597, year = {2018}, author = {Yang, Y and Liu, G and Song, W and Ye, C and Lin, H and Li, Z and Liu, W}, title = {Plastics in the marine environment are reservoirs for antibiotic and metal resistance genes.}, journal = {Environment international}, volume = {123}, number = {}, pages = {79-86}, doi = {10.1016/j.envint.2018.11.061}, pmid = {30502597}, issn = {1873-6750}, abstract = {Plastics have been accumulated offshore and in the deep oceans at an unprecedented scale. Microbial communities have colonized the plastisphere, which has become a reservoir for both antibiotic and metal resistance genes (ARGs and MRGs). This is the first analysis of the diversity, abundance, and co-occurrence of ARGs and MRGs, and their relationships within the microbial community, using metagenomic data of plastic particles observed in the North Pacific Gyre obtained from the National Centre for Biotechnology Information Sequence Read Archive database. The abundance of ARGs and MRGs in microbial communities on the plastics were in the ranges 7.07 × 10-4-1.21 × 10-2 and 5.51 × 10-3-4.82 × 10-2 copies per 16S rRNA, respectively. Both the Shannon-Wiener indices and richness of ARGs and MRGs in plastics microbiota were significantly greater than those of ARGs and MRGs in seawater microbiota in the North Pacific Gyre via one-way analysis of variance. Multidrug resistance genes and multi-metal resistance genes were the main classes of genes detected in plastic microbiota. There were no significant differences in the abundance or diversity of ARGs and MRGs between macroplastics biota and microplastics biota, indicating that particle size had no effect on resistance genes. Procrustes analysis suggested that microbial community composition was the determining factor of the ARG profile but not for MRG. Some ARGs and MRGs had a higher incidence of non-random co-occurrence, suggesting that the co-effects of selection for antibiotic or metal resistance are important factors influencing the resistome of the microbiota on the plastic particles.}, }
@article {pmid30500759, year = {2018}, author = {Huang, Z and Wei, Z and Xiao, X and Tang, M and Li, B and Zhang, X}, title = {Nitrification/denitrification shaped the mercury-oxidizing microbial community for simultaneous Hg0 and NO removal.}, journal = {Bioresource technology}, volume = {274}, number = {}, pages = {18-24}, doi = {10.1016/j.biortech.2018.11.069}, pmid = {30500759}, issn = {1873-2976}, abstract = {A denitrifying/nitrifying membrane biofilm reactor for simultaneous removal of Hg0 and NO was investigated. Hg0 and NO removal efficiency attained 94.5% and 86%, respectively. The mercury-oxidizing microbial community was significantly shaped by nitrification/denitrification after the supply of gaseous Hg0and NO continuously. Dominant genera Rhodanobacter and Nitrosomonas participated in Hg0 oxidation, nitrification and denitrification simultaneously. Hg0 oxidizing bacteria (Gallionella, Rhodanobacter, Ottowia, Nitrosomonas and etc.), nitrifying bacteria (Nitrosomonas, Rhodanobacter, Diaphorobacte and etc.) and denitrifying bacteria (Nitrosomonas, Rhodanobacter, Castellaniella and etc.) co-existed in the MBfR, as shown by metagenomic sequencing. X-ray photoelectron spectroscopy (XPS) and high performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICP-MS) confirmed the formation of a mercuric species (Hg2+) from mercury bio-oxidation. Mechanism of mercury oxidation can be described as the bacterial oxidation of Hg0 in which Hg0 serves as electron donor, NO serves as electron donor in nitrification and electron acceptor in denitrification, oxygen serves as electron acceptor.}, }
@article {pmid30500755, year = {2018}, author = {Cattò, C and Garuglieri, E and Borruso, L and Erba, D and Casiraghi, MC and Cappitelli, F and Villa, F and Zecchin, S and Zanchi, R}, title = {Impacts of dietary silver nanoparticles and probiotic administration on the microbiota of an in-vitro gut model.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {245}, number = {}, pages = {754-763}, doi = {10.1016/j.envpol.2018.11.019}, pmid = {30500755}, issn = {1873-6424}, abstract = {Ingestion of silver nanoparticles (AgNPs) is inevitable linked to their widespread use in food, medicines and other consumer products. However, their effects on human microbiota at non-lethal concentrations remain poorly understood. In this study, the interactions among 1 μg mL-1 AgNPs, the intestinal microbiota, and the probiotic Bacillus subtilis (BS) were tested using in-vitro batch fermentation models inoculated with human fecal matter. Results from metagenomic investigations revealed that the core bacterial community was not affected by the exposure of AgNPs and BS at the later stage of fermentation, while the proportions of rare species changed drastically with the treatments. Furthermore, shifts in the Firmicutes/Bacteriodetes (F/B) ratios were observed after 24 h with an increase in the relative abundance of Firmicutes species and a decrease in Bacteroidetes in all fermentation cultures. The co-exposure to AgNPs and BS led to the lowest F/B ratio. Fluorescent in-situ hybridization analyses indicated that non-lethal concentration of AgNPs negatively affected the relative percentage of Faecalibacterium prausnitzii and Clostridium coccoides/Eubacterium rectales taxa in the fermentation cultures after 24 h. However, exposure to single and combined treatments of AgNPs and BS did not change the overall diversity of the fecal microflora. Functional differences in cell motility, translation, transport, and xenobiotics degradation occurred in AgNPs-treated fermentation cultures but not in AgNPs+BS-treated samples. Compared to the control samples, treated fecal cultures showed no significant statistical differences in terms of short-chain fatty acids profiles, cytotoxic and genotoxic effects on Caco-2 cell monolayers. Overall, AgNPs did not affect the composition and diversity of the core fecal microflora and its metabolic and toxic profiles. This work indicated a chemopreventive role of probiotic on fecal microflora against AgNPs, which were shown by the decrease of F/B ratio and the unaltered state of some key metabolic pathways.}, }
@article {pmid30500682, year = {2018}, author = {Whitfield, AE and Huot, OB and Martin, KM and Kondo, H and Dietzgen, RG}, title = {Plant rhabdoviruses-their origins and vector interactions.}, journal = {Current opinion in virology}, volume = {33}, number = {}, pages = {198-207}, doi = {10.1016/j.coviro.2018.11.002}, pmid = {30500682}, issn = {1879-6265}, abstract = {Classical plant rhabdoviruses infect monocot and dicot plants, have unsegmented negative-sense RNA genomes and have been taxonomically classified in the genera Cytorhabdovirus and Nucleorhabdovirus. These viruses replicate in their hemipteran vectors and are transmitted in a circulative-propagative mode and virus infection persists for the life of the insect. Based on the discovery of numerous novel rhabdoviruses in arthropods during metagenomic studies and extensive phylogenetic analyses of the family Rhabdoviridae, it is hypothesized that plant-infecting rhabdoviruses are derived from insect viruses. Analyses of viral gene function in plants and insects is beginning to reveal conserved and unique biology for these plant viruses in the two diverse hosts. New tools for insect molecular biology and infectious clones for plant rhabdoviruses are increasing our understanding of the lifestyles of these viruses.}, }
@article {pmid30499334, year = {2018}, author = {Robino, P and Ferrocino, I and Rossi, G and Dogliero, A and Alessandria, V and Grosso, L and Galosi, L and Tramuta, C and Cocolin, L and Nebbia, P}, title = {Changes in gut bacterial communities in canaries infected by Macrorhabdus ornithogaster.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {}, number = {}, pages = {1-29}, doi = {10.1080/03079457.2018.1553294}, pmid = {30499334}, issn = {1465-3338}, abstract = {Macrorhabdus ornithogaster is an opportunistic yeast that colonizes the gastric mucosa of many avian species. Until now, no studies have been focused on about the influence of a gastric infection on the balance of the intestinal microbiota of birds. In this study, 44 fecal samples from individual canaries, with and without M. ornithogaster infection, were analyzed. The detection of the yeast was evaluated by 18S rRNA PCR. In order to evaluate the impact of the Macrorhabdus infection on the bacterial communities, the culture-independent methods by the use of amplicon based sequencing as well as 16S rRNA-DGGE were adopted. The different health status of animals affected the relative abundance of the main OTUs, with a greater diversification of the gut microbiota in healthy animals if compared to the infected. In particular, Lactococcus, Pseudomonas, Acinetobacter, Lachnospiraceae, Propionibacterium and Weissella were found to be characteristic of uninfected animals (FDR <0.05), while Lactobacillus and Candidatus Arthromitus were characteristic of infected animals (FDR <0.05). Both these taxa have been reported as immunostimulatory involved in immunological disorders. In infected animals the inferred metagenome assessed by PICRUST clearly showed a positive correlation between the presence of M. ornithogaster and KEGG genes related to ether lipids metabolism, already reported to be immunostimulatory by activation of macrophages and to play a pathophysiological role in several immunological disorders. Finally, our results show an interaction between infection of the digestive tract and intestinal microbiota of pet birds and provide insight about the changing of the complex enteric bacterial community.}, }
@article {pmid30498478, year = {2018}, author = {Evans, MV and Panescu, J and Hanson, AJ and Welch, SA and Sheets, JM and Nastasi, N and Daly, RA and Cole, DR and Darrah, TH and Wilkins, MJ and Wrighton, KC and Mouser, PJ}, title = {Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2646}, doi = {10.3389/fmicb.2018.02646}, pmid = {30498478}, issn = {1664-302X}, abstract = {Hydraulic fracturing is the prevailing method for enhancing recovery of hydrocarbon resources from unconventional shale formations, yet little is understood regarding the microbial impact on biogeochemical cycling in natural-gas wells. Although the metabolisms of certain fermentative bacteria and methanogenic archaea that dominate in later produced fluids have been well studied, few details have been reported on microorganisms prevelant during the early flowback period, when oxygen and other surface-derived oxyanions and nutrients become depleted. Here, we report the isolation, genomic and phenotypic characterization of Marinobacter and Arcobacter bacterial species from natural-gas wells in the Utica-Point Pleasant and Marcellus Formations coupled to supporting geochemical and metagenomic analyses of produced fluid samples. These unconventional hydrocarbon system-derived Marinobacter sp. are capable of utilizing a diversity of organic carbon sources including aliphatic and aromatic hydrocarbons, amino acids, and carboxylic acids. Marinobacter and Arcobacter can metabolize organic nitrogen sources and have the capacity for denitrification and dissimilatory nitrate reduction to ammonia (DNRA) respectively; with DNRA and ammonification processes partially explaining high concentrations of ammonia measured in produced fluids. Arcobacter is capable of chemosynthetic sulfur oxidation, which could fuel metabolic processes for other heterotrophic, fermentative, or sulfate-reducing community members. Our analysis revealed mechanisms for growth of these taxa across a broad range of salinities (up to 15% salt), which explains their enrichment during early natural-gas production. These results demonstrate the prevalence of Marinobacter and Arcobacter during a key maturation phase of hydraulically fractured natural-gas wells, and highlight the significant role these genera play in biogeochemical cycling for this economically important energy system.}, }
@article {pmid30498254, year = {2018}, author = {Dutta, A and Dutta Gupta, S and Gupta, A and Sarkar, J and Roy, S and Mukherjee, A and Sar, P}, title = {Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17459}, doi = {10.1038/s41598-018-35940-0}, pmid = {30498254}, issn = {2045-2322}, support = {MoES/P.O.(Seismo)/1(181)/2013//Ministry of Earth Sciences (MoES)/ ; }, abstract = {Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsrB and mcrA genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha-, Beta-, Gammaproteobacteria, Actinobacteria and Firmicutes, whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.}, }
@article {pmid30498029, year = {2018}, author = {Crombie, AT and Larke-Mejia, NL and Emery, H and Dawson, R and Pratscher, J and Murphy, GP and McGenity, TJ and Murrell, JC}, title = {Poplar phyllosphere harbors disparate isoprene-degrading bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1812668115}, pmid = {30498029}, issn = {1091-6490}, abstract = {The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source. Here, we identified isoprene-degrading bacteria in poplar tree-derived microcosms by DNA stable isotope probing. The genomes of isoprene-degrading taxa were reconstructed, putative isoprene metabolic genes were identified, and isoprene-related gene transcription was analyzed by shotgun metagenomics and metatranscriptomics. Gram-positive bacteria of the genus Rhodococcus proved to be the dominant isoprene degraders, as previously found in soil. However, a wider diversity of isoprene utilizers was also revealed, notably Variovorax, a genus not previously associated with this trait. This finding was confirmed by expression of the isoprene monooxygenase from Variovorax in a heterologous host. A Variovorax strain that could grow on isoprene as the sole carbon and energy source was isolated. Analysis of its genome confirmed that it contained isoprene metabolic genes with an identical layout and high similarity to those identified by DNA-stable isotope probing and metagenomics. This study provides evidence of a wide diversity of isoprene-degrading bacteria in the isoprene-emitting tree phyllosphere and greatly enhances our understanding of the biodegradation of this important metabolite and climate-active gas.}, }
@article {pmid30497517, year = {2018}, author = {Lam, TH and Verzotto, D and Brahma, P and Ng, AHQ and Hu, P and Schnell, D and Tiesman, J and Kong, R and Ton, TMU and Li, J and Ong, M and Lu, Y and Swaile, D and Liu, P and Liu, J and Nagarajan, N}, title = {Understanding the microbial basis of body odor in pre-pubescent children and teenagers.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {213}, doi = {10.1186/s40168-018-0588-z}, pmid = {30497517}, issn = {2049-2618}, support = {APG2013/032//Agency for Science, Technology and Research/ ; }, abstract = {BACKGROUND: Even though human sweat is odorless, bacterial growth and decomposition of specific odor precursors in it is believed to give rise to body odor in humans. While mechanisms of odor generation have been widely studied in adults, little is known for teenagers and pre-pubescent children who have distinct sweat composition from immature apocrine and sebaceous glands, but are arguably more susceptible to the social and psychological impact of malodor.<br><br>RESULTS: We integrated information from whole microbiome analysis of multiple skin sites (underarm, neck, and head) and multiple time points (1 h and 8 h after bath), analyzing 180 samples in total to perform the largest metagenome-wide association study to date on malodor. Significant positive correlations were observed between odor intensity and the relative abundance of Staphylococcus hominis, Staphylococcus epidermidis, and Cutibacterium avidum, as well as negative correlation with Acinetobacter schindleri and Cutibacterium species. Metabolic pathway analysis highlighted the association of isovaleric and acetic acid production (sour odor) from enriched S. epidermidis (teen underarm) and S. hominis (child neck) enzymes and sulfur production from Staphylococcus species (teen underarm) with odor intensity, in good agreement with observed odor characteristics in pre-pubescent children and teenagers. Experiments with cultures on human and artificial sweat confirmed the ability of S. hominis and S. epidermidis to independently produce malodor with distinct odor characteristics.<br><br>CONCLUSIONS: These results showcase the power of skin metagenomics to study host-microbial co-metabolic interactions, identifying distinct pathways for odor generation from sweat in pre-pubescent children and teenagers and highlighting key enzymatic targets for intervention.}, }
@article {pmid30497364, year = {2018}, author = {Girotto, S and Comin, M and Pizzi, C}, title = {Efficient computation of spaced seed hashing with block indexing.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 15}, pages = {441}, doi = {10.1186/s12859-018-2415-8}, pmid = {30497364}, issn = {1471-2105}, abstract = {BACKGROUND: Spaced-seeds, i.e. patterns in which some fixed positions are allowed to be wild-cards, play a crucial role in several bioinformatics applications involving substrings counting and indexing, by often providing better sensitivity with respect to k-mers based approaches. K-mers based approaches are usually fast, being based on efficient hashing and indexing that exploits the large overlap between consecutive k-mers. Spaced-seeds hashing is not as straightforward, and it is usually computed from scratch for each position in the input sequence. Recently, the FSH (Fast Spaced seed Hashing) approach was proposed to improve the time required for computation of the spaced seed hashing of DNA sequences with a speed-up of about 1.5 with respect to standard hashing computation.<br><br>RESULTS: In this work we propose a novel algorithm, Fast Indexing for Spaced seed Hashing (FISH), based on the indexing of small blocks that can be combined to obtain the hashing of spaced-seeds of any length. The method exploits the fast computation of the hashing of runs of consecutive 1 in the spaced seeds, that basically correspond to k-mer of the length of the run.<br><br>CONCLUSIONS: We run several experiments, on NGS data from simulated and synthetic metagenomic experiments, to assess the time required for the computation of the hashing for each position in each read with respect to several spaced seeds. In our experiments, FISH can compute the hashing values of spaced seeds with a speedup, with respect to the traditional approach, between 1.9x to 6.03x, depending on the structure of the spaced seeds.}, }
@article {pmid30497362, year = {2018}, author = {Tangherlini, M and Miralto, M and Colantuono, C and Sangiovanni, M and Dell' Anno, A and Corinaldesi, C and Danovaro, R and Chiusano, ML}, title = {GLOSSary: the GLobal Ocean 16S subunit web accessible resource.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 15}, pages = {443}, doi = {10.1186/s12859-018-2423-8}, pmid = {30497362}, issn = {1471-2105}, abstract = {BACKGROUND: Environmental metagenomics is a challenging approach that is exponentially spreading in the scientific community to investigate taxonomic diversity and possible functions of the biological components. The massive amount of sequence data produced, often endowed with rich environmental metadata, needs suitable computational tools to fully explore the embedded information. Bioinformatics plays a key role in providing methodologies to manage, process and mine molecular data, integrated with environmental metagenomics collections. One such relevant example is represented by the Tara Ocean Project.<br><br>RESULTS: We considered the Tara 16S miTAGs released by the consortium, representing raw sequences from a shotgun metagenomics approach with similarities to 16S rRNA genes. We generated assembled 16S rDNA sequences, which were classified according to their lengths, the possible presence of chimeric reads, the putative taxonomic affiliation. The dataset was included in GLOSSary (the GLobal Ocean 16S Subunit web accessible resource), a bioinformatics platform to organize environmental metagenomics data. The aims of this work were: i) to present alternative computational approaches to manage challenging metagenomics data; ii) to set up user friendly web-based platforms to allow the integration of environmental metagenomics sequences and of the associated metadata; iii) to implement an appropriate bioinformatics platform supporting the analysis of 16S rDNA sequences exploiting reference datasets, such as the SILVA database. We organized the data in a next-generation NoSQL &quot;schema-less&quot; database, allowing flexible organization of large amounts of data and supporting native geospatial queries. A web interface was developed to permit an interactive exploration and a visual geographical localization of the data, either raw miTAG reads or 16S contigs, from our processing pipeline. Information on unassembled sequences is also available. The taxonomic affiliations of contigs and miTAGs, and the spatial distribution of the sampling sites and their associated sequence libraries, as they are contained in the Tara metadata, can be explored by a query interface, which allows both textual and visual investigations. In addition, all the sequence data were made available for a dedicated BLAST-based web application alongside the SILVA collection.<br><br>CONCLUSIONS: GLOSSary provides an expandable bioinformatics environment, able to support the scientific community in current and forthcoming environmental metagenomics analyses.}, }
@article {pmid30497052, year = {2018}, author = {Pontremoli, C and Forni, D and Sironi, M}, title = {Arenavirus genomics: novel insights into viral diversity, origin, and evolution.}, journal = {Current opinion in virology}, volume = {34}, number = {}, pages = {18-28}, doi = {10.1016/j.coviro.2018.11.001}, pmid = {30497052}, issn = {1879-6265}, abstract = {Next-generation sequencing technologies have revolutionized our knowledge of virus diversity and evolution. In the case of arenaviruses, which are the focus of this review, metagenomic/metatranscriptomic approaches identified reptile-infecting and fish-infecting viruses, also showing that bi-segmented genomes are not a universal feature of the Arenaviridae family. Novel mammarenaviruses were described, allowing inference of their geographic origin and evolutionary dynamics. Extensive sequencing of Lassa virus (LASV) genomes revealed the zoonotic nature of most human infections and a Nigerian origin of LASV, which subsequently spread westward. Future efforts will likely identify many more arenaviruses and hopefully provide insight into the ultimate origin of the family, the pathogenic potential of its members, as well as the determinants of their geographic distribution.}, }
@article {pmid30496201, year = {2018}, author = {Biscarini, F and Palazzo, F and Castellani, F and Masetti, G and Grotta, L and Cichelli, A and Martino, G}, title = {Rumen microbiome in dairy calves fed copper and grape-pomace dietary supplementations: Composition and predicted functional profile.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0205670}, doi = {10.1371/journal.pone.0205670}, pmid = {30496201}, issn = {1932-6203}, abstract = {The rumen microbiome is fundamental for the productivity and health of dairy cattle and diet is known to influence the rumen microbiota composition. In this study, grape-pomace, a natural source of polyphenols, and copper sulfate were provided as feed supplementation in 15 Holstein-Friesian calves, including 5 controls. After 75 days of supplementation, genomic DNA was extracted from the rumen liquor and prepared for 16S rRNA-gene sequencing to characterize the composition of the rumen microbiota. From this, the rumen metagenome was predicted to obtain the associated gene functions and metabolic pathways in a cost-effective manner. Results showed that feed supplementations did alter the rumen microbiome of calves. Copper and grape-pomace increased the diversity of the rumen microbiota: the Shannon's and Fisher's alpha indices were significantly different across groups (p-values 0.045 and 0.039), and Bray-Curtis distances could separate grape-pomace calves from the other two groups. Differentially abundant taxa were identified: in particular, an uncultured Bacteroidales UCG-001 genus and OTUs from genus Sarcina were the most differentially abundant in pomace-supplemented calves compared to controls (p-values 0.003 and 0.0002, respectively). Enriched taxonomies such as Ruminiclostridium and Eubacterium sp., whose functions are related to degradation of the grape- pomace constituents (e.g. flavonoids or xyloglucan) have been described (p-values 0.027/0.028 and 0.040/0.022 in Pomace vs Copper and Controls, respectively). The most abundant predicted metagenomic genes belonged to the arginine and proline metabolism and the two- component (sensor/responder) regulatory system, which were increased in the supplemented groups. Interestingly, the lipopolysaccharide biosynthetic pathway was decreased in the two supplemented groups, possibly as a result of antimicrobial effects. Methanogenic taxa also responded to the feed supplementation, and methane metabolism in the rumen was the second most different pathway (up-regulated by feed supplementations) between experimental groups.}, }
@article {pmid30496195, year = {2018}, author = {Calderoli, PA and Espínola, FJ and Dionisi, HM and Gil, MN and Jansson, JK and Lozada, M}, title = {Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0207606}, doi = {10.1371/journal.pone.0207606}, pmid = {30496195}, issn = {1932-6203}, abstract = {The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.}, }
@article {pmid30489678, year = {2018}, author = {Vieira, FR and Pecchia, JA and Segato, F and Polikarpov, I}, title = {Exploring oyster mushroom (Pleurotus ostreatus) substrate preparation by varying phase I composting time: changes in bacterial communities and physicochemical composition of biomass impacting mushroom yields.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14168}, pmid = {30489678}, issn = {1365-2672}, abstract = {AIMS: Characterization of the bacterial community composition and functionality and their impact on substrate biodegradation as well as mushroom yield.<br><br>METHODS AND RESULTS: Bacterial diversity, composition, and functionality were accessed by DNA-derived analysis for a sugarcane straw-based substrate composted for either 5, 10 or 15 days. In addition, carbon and nitrogen losses, carbohydrates conversion as well as mushroom yields were measured for the different treatments. Changes were observed in the bacterial community diversity and composition after the process started, but not during the composting process itself. Following phase I, Acinetobacter sequences were recovered in high numbers, and selected genes associated with nitrogen metabolism and lignocellulose deconstruction were mapped. Substrate physicochemical composition showed elevated carbon and nitrogen losses after 10 and 15 days of phase I with reductions in mushroom yield.<br><br>CONCLUSIONS: Acinetobacter species appear to play an important role in substrate degradation processes and a 5-days phase I period showed a significant higher mushroom yield compared to composting for either 10 or 15 days.<br><br>This study confers a better understanding of the bacterial community manipulation during the substrate preparation and their influence in substrate selectivity for the Pleurotus ostreatus cultivation. This article is protected by copyright. All rights reserved.}, }
@article {pmid30489677, year = {2018}, author = {Sánchez-González, M and Álvarez-Uribe, H and Rivera-Solís, R and González-Burgos, A and Escalante-Réndiz, D and Rojas-Herrera, R}, title = {Analysis of a phenol adapted microbial community: degradation capacity, taxonomy, and metabolic description.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14166}, pmid = {30489677}, issn = {1365-2672}, abstract = {AIMS: In this study, the ability of the consortium MR-01 to degrade phenol was determined. The effects of this chemical on the taxonomy and the metabolic behavior was analyzed through metagenomics.<br><br>METHODS AND RESULTS: Consortium MR-01 was acclimated in a sub-lethal concentration of phenol. After this process, the capacity to degrade this molecule was analyzed. Results showed that degradation increased with the increment of the initial phenol concentration. Metagenomic analysis indicate that the consortium metabolized phenol under aerobic conditions using phenol 2-monooxygenase and the meta cleavage pathway. Sequence of the enzymes involved in the phenol degradation were ascribed to the Actinomycetales and Chloroflexales orders, with relative abundances <1%. The most abundant genera were part of the Sphingomonadales order; however, the role of these species in the consortium is not clear.<br><br>CONCLUSIONS: Consortium MR-01 degrades efficiently high concentrations of phenol. The participation of extremophiles in the degradation process and the emergence of beneficial metabolic dependencies between the community members, are some of the strategies used by the consortium to survive and develop under harsh environmental conditions.<br><br>This is one of the few studies describing the taxonomy and metabolic profile of a phenol degrading consortium. This article is protected by copyright. All rights reserved.}, }
@article {pmid30487783, year = {2018}, author = {Dai, T and Zhang, Y and Ning, D and Su, Z and Tang, Y and Huang, B and Mu, Q and Wen, D}, title = {Dynamics of Sediment Microbial Functional Capacity and Community Interaction Networks in an Urbanized Coastal Estuary.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2731}, doi = {10.3389/fmicb.2018.02731}, pmid = {30487783}, issn = {1664-302X}, abstract = {Coastal estuaries and bays are exposed to both natural and anthropogenic environmental changes, inflicting intensive stress on the microbial communities inhabiting these areas. However, it remains unclear how microbial community diversity and their eco-functions are affected by anthropogenic disturbances rather than natural environmental changes. Here, we explored sediment microbial functional genes dynamics and community interaction networks in Hangzhou Bay (HZB), one of the most severely polluted bays on China's eastern coast. The results indicated key microbial functional gene categories, including N, P, S, and aromatic compound metabolism, and stress response, displayed significant spatial dynamics along environmental gradients. Sensitive feedbacks of key functional gene categories to N and P pollutants demonstrated potential impacts of human-induced seawater pollutants to microbial functional capacity. Seawater ammonia and dissolved inorganic nitrogen (DIN) was identified as primary drivers in selecting adaptive populations and varying community composition. Network analysis revealed distinct modules that were stimulated in inner or outer bay. Importantly, the network keystone species, which played a fundamental role in community interactions, were strongly affected by N-pollutants. Our results provide a systematic understanding of the microbial compositional and functional dynamics in an urbanized coastal estuary, and highlighted the impact of human activities on these communities.}, }
@article {pmid30487780, year = {2018}, author = {Tan, KS and Yan, Y and Koh, WLH and Li, L and Choi, H and Tran, T and Sugrue, R and Wang, Y and Chow, VT}, title = {Comparative Transcriptomic and Metagenomic Analyses of Influenza Virus-Infected Nasal Epithelial Cells From Multiple Individuals Reveal Specific Nasal-Initiated Signatures.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2685}, doi = {10.3389/fmicb.2018.02685}, pmid = {30487780}, issn = {1664-302X}, abstract = {In vitro and in vivo research based on cell lines and animals are likely to be insufficient in elucidating authentic biological and physiological phenomena mimicking human systems, especially for generating pre-clinical data on targets and biomarkers. There is an obvious need for a model that can further bridge the gap in translating pre-clinical findings into clinical applications. We have previously generated a model of in vitro differentiated human nasal epithelial cells (hNECs) which elucidated the nasal-initiated repertoire of immune responses against respiratory viruses such as influenza A virus and rhinovirus. To assess their clinical utility, we performed a microarray analysis of influenza virus-infected hNECs to elucidate nasal epithelial-initiated responses. This was followed by a metagenomic analysis which revealed transcriptomic changes comparable with clinical influenza datasets. The primary target of influenza infection was observed to be the initiator of innate and adaptive immune genes, leaning toward type-1 inflammatory activation. In addition, the model also elucidated a down-regulation of metabolic processes specific to the nasal epithelium, and not present in other models. Furthermore, the hNEC model detected all 11 gene signatures unique to influenza infection identified from a previous study, thus supporting the utility of nasal-based diagnosis in clinical settings. In conclusion, this study highlights that hNECs can serve as a model for nasal-based clinical translational studies and diagnosis to unravel nasal epithelial responses to influenza in the population, and as a means to identify novel molecular diagnostic markers of severity.}, }
@article {pmid30487175, year = {2018}, author = {Kriaa, A and Bourgin, M and Potiron, A and Mkaouar, H and Jablaoui, A and Gerard, P and Maguin, E and Rhimi, M}, title = {Microbial impact on cholesterol and bile acid metabolism: current status and future prospects.}, journal = {Journal of lipid research}, volume = {}, number = {}, pages = {}, doi = {10.1194/jlr.R088989}, pmid = {30487175}, issn = {1539-7262}, abstract = {Recently, the gut microbiota has emerged as a crucial factor that influences cholesterol metabolism. Ever since, significant interest is shown on investigating these host-microbiome interactions to uncover microbiome-mediated functions on cholesterol and bile acid metabolism. Indeed, changes in gut bacterial composition and hence their derived metabolites have been previously reported to subsequently impact the metabolic processes and have been linked to several diseases. In this context, associations between a disrupted gut microbiome, impaired bile acid metabolism and cholesterol dysregulation have been highlighted. Extensive advances in metagenomic and metabolomic studies in this field have allowed us to further our understanding of the role of intestinal bacteria in metabolic health and disease. However, only few have provided mechanistic insights into their impact on cholesterol metabolism. Identifying the myriad functions and the interactions of these bacteria to maintain cholesterol homeostasis remain until now an important challenge in such a field of research. In this review, we discuss the impact of gut microbiota on cholesterol metabolism, its association with disease settings and the potential of modulating gut microbiota as a promising therapeutic target to lower hypercholesterolemia.}, }
@article {pmid30486337, year = {2018}, author = {Malacrinò, A}, title = {Meta-Omics Tools in the World of Insect-Microorganism Interactions.}, journal = {Biology}, volume = {7}, number = {4}, pages = {}, doi = {10.3390/biology7040050}, pmid = {30486337}, issn = {2079-7737}, abstract = {Microorganisms are able to influence several aspects of insects' life, and this statement is gaining increasing strength, as research demonstrates it daily. At the same time, new sequencing technologies are now available at a lower cost per base, and bioinformatic procedures are becoming more user-friendly. This is triggering a huge effort in studying the microbial diversity associated to insects, and especially to economically important insect pests. The importance of the microbiome has been widely acknowledged for a wide range of animals, and also for insects this topic is gaining considerable importance. In addition to bacterial-associates, the insect-associated fungal communities are also gaining attention, especially those including plant pathogens. The use of meta-omics tools is not restricted to the description of the microbial world, but it can be also used in bio-surveillance, food safety assessment, or even to bring novelties to the industry. This mini-review aims to give a wide overview of how meta-omics tools are fostering advances in research on insect-microorganism interactions.}, }
@article {pmid30485448, year = {2018}, author = {Chang, Y and Desirò, A and Na, H and Sandor, L and Lipzen, A and Clum, A and Barry, K and Grigoriev, IV and Martin, FM and Stajich, JE and Smith, ME and Bonito, G and Spatafora, JW}, title = {Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.15613}, pmid = {30485448}, issn = {1469-8137}, abstract = {Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non-Dikarya order with ectomycorrhizal members. They also form mycorrhizal-like association with some non-Spermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal-lifestyle signatures and whether Endogonales originated around the same time as land plants did. We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing. After binning the metagenome data, we assembled and annotated the Endogonaceae genomes. We performed comparative analysis on plant-cell-wall-degrading-enzymes (PCWDEs) and small secreted proteins (SSPs). We inferred phylogenetic placement of Endogonaceae and estimated the ages of Endogonaceae and Endogonales with expanded taxon sampling. Endogonaceae have large genomes with high repeat content, low diversity of PCWDEs, but without elevated SSP/secretome ratios. Dating analysis estimated that Endogonaceae originated in the Permian-Triassic boundary and Endogonales originated in the mid-late Silurian. Mycoplasma-related endobacterium sequences were identified in three Endogonaceae genomes. Endogonaceae genomes possess typical signatures of mycorrhizal lifestyle. The early origin of Endogonales suggests that the mycorrhizal association between Endogonales and plants might have played an important role during the colonization of land by plants. This article is protected by copyright. All rights reserved.}, }
@article {pmid30482864, year = {2018}, author = {Langelier, C and Kalantar, KL and Moazed, F and Wilson, MR and Crawford, ED and Deiss, T and Belzer, A and Bolourchi, S and Caldera, S and Fung, M and Jauregui, A and Malcolm, K and Lyden, A and Khan, L and Vessel, K and Quan, J and Zinter, M and Chiu, CY and Chow, ED and Wilson, J and Miller, S and Matthay, MA and Pollard, KS and Christenson, S and Calfee, CS and DeRisi, JL}, title = {Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1809700115}, pmid = {30482864}, issn = {1091-6490}, abstract = {Lower respiratory tract infections (LRTIs) lead to more deaths each year than any other infectious disease category. Despite this, etiologic LRTI pathogens are infrequently identified due to limitations of existing microbiologic tests. In critically ill patients, noninfectious inflammatory syndromes resembling LRTIs further complicate diagnosis. To address the need for improved LRTI diagnostics, we performed metagenomic next-generation sequencing (mNGS) on tracheal aspirates from 92 adults with acute respiratory failure and simultaneously assessed pathogens, the airway microbiome, and the host transcriptome. To differentiate pathogens from respiratory commensals, we developed a rules-based model (RBM) and logistic regression model (LRM) in a derivation cohort of 20 patients with LRTIs or noninfectious acute respiratory illnesses. When tested in an independent validation cohort of 24 patients, both models achieved accuracies of 95.5%. We next developed pathogen, microbiome diversity, and host gene expression metrics to identify LRTI-positive patients and differentiate them from critically ill controls with noninfectious acute respiratory illnesses. When tested in the validation cohort, the pathogen metric performed with an area under the receiver-operating curve (AUC) of 0.96 (95% CI, 0.86-1.00), the diversity metric with an AUC of 0.80 (95% CI, 0.63-0.98), and the host transcriptional classifier with an AUC of 0.88 (95% CI, 0.75-1.00). Combining these achieved a negative predictive value of 100%. This study suggests that a single streamlined protocol offering an integrated genomic portrait of pathogen, microbiome, and host transcriptome may hold promise as a tool for LRTI diagnosis.}, }
@article {pmid30482837, year = {2018}, author = {Wolf, YI and Kazlauskas, D and Iranzo, J and Lucía-Sanz, A and Kuhn, JH and Krupovic, M and Dolja, VV and Koonin, EV}, title = {Origins and Evolution of the Global RNA Virome.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, doi = {10.1128/mBio.02329-18}, pmid = {30482837}, issn = {2150-7511}, abstract = {Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (-) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas -RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy.IMPORTANCE The majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different Baltimore classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.}, }
@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 = {}, doi = {10.1128/mBio.01631-18}, pmid = {30482830}, issn = {2150-7511}, 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 {pmid30482513, year = {2018}, author = {Díaz-Sánchez, S and Hernández-Jarguín, A and Torina, A and de Mera, IGF and Blanda, V and Caracappa, S and Gortazar, C and de la Fuente, J}, title = {Characterization of the bacterial microbiota in wild-caught Ixodes ventalloi.}, journal = {Ticks and tick-borne diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ttbdis.2018.11.014}, pmid = {30482513}, issn = {1877-9603}, abstract = {Exploring the microbial diversity of ticks is crucial to understand geographical dispersion and pathogen transmission. Tick microbes participate in many biological processes implicated in the acquisition, maintenance, and transmission of pathogens, and actively promote host phenotypic changes, and adaptation to new environments. The microbial community of Ixodes ventalloi still remains unexplored. In this study, the bacterial microbiota of wild-caught I. ventalloi was characterized using shotgun-metagenomic sequencing in samples from unfed adults collected during December 2013-January 2014 in two locations from Sicily, Italy. The microbiota identified in I. ventalloi was mainly composed of symbiotic, commensal, and environmental bacteria. Interestingly, we identified the genera Anaplasma and Borrelia as members of the microbiota of I. ventalloi. These results advance our information on I. ventalloi microbiota composition, with potential implications in tick-host adaptation, geographic expansion, and vector competence.}, }
@article {pmid30482240, year = {2018}, author = {Huang, P and Zhang, Y and Xiao, K and Jiang, F and Wang, H and Tang, D and Liu, D and Liu, B and Liu, Y and He, X and Liu, H and Liu, X and Qing, Z and Liu, C and Huang, J and Ren, Y and Yun, L and Yin, L and Lin, Q and Zeng, C and Su, X and Yuan, J and Lin, L and Hu, N and Cao, H and Huang, S and Guo, Y and Fan, W and Zeng, J}, title = {The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {211}, doi = {10.1186/s40168-018-0590-5}, pmid = {30482240}, issn = {2049-2618}, support = {2017YFD0501500//National Key R&amp;D Program of China/ ; 2016YFD0501308//National Key R&amp;D Program of China/ ; 2016YFC1200600//National Key R&amp;D Program of China/ ; JCYJ20150630165133395//Shenzhen Science and Technology Program/ ; ZDSYS20141118170111640//Fund of Key Laboratory of Shenzhen/ ; }, abstract = {BACKGROUND: Sub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, Macleaya cordata extract (MCE), with effective ingredients of benzylisoquinoline alkaloids, is a potential alternative to antibiotic growth promoters. Altered intestinal microbiota play important roles in growth promotion, but the underlying mechanism remains unknown.<br><br>RESULTS: We generated 1.64 terabases of metagenomic data from 495 chicken intestinal digesta samples and constructed a comprehensive chicken gut microbial gene catalog (9.04 million genes), which is also the first gene catalog of an animal's gut microbiome that covers all intestinal compartments. Then, we identified the distinctive characteristics and temporal changes in the foregut and hindgut microbiota. Next, we assessed the impact of MCE on chickens and gut microbiota. Chickens fed with MCE had improved growth performance, and major microbial changes were confined to the foregut, with the predominant role of Lactobacillus being enhanced, and the amino acids, vitamins, and secondary bile acids biosynthesis pathways being upregulated, but lacked the accumulation of antibiotic-resistance genes. In comparison, treatment with chlortetracycline similarly enriched some biosynthesis pathways of nutrients in the foregut microbiota, but elicited an increase in antibiotic-producing bacteria and antibiotic-resistance genes.<br><br>CONCLUSION: The reference gene catalog of the chicken gut microbiome is an important supplement to animal gut metagenomes. Metagenomic analysis provides insights into the growth-promoting mechanism of MCE, and underscored the importance of utilizing safe and effective growth promoters.}, }
@article {pmid30481710, year = {2018}, author = {Abia, ALK and Alisoltani, A and Ubomba-Jaswa, E and Dippenaar, MA}, title = {Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments.}, journal = {The Science of the total environment}, volume = {655}, number = {}, pages = {831-841}, doi = {10.1016/j.scitotenv.2018.11.302}, pmid = {30481710}, issn = {1879-1026}, abstract = {Recent studies have identified cemeteries as potential environmental reservoirs of multi-drug resistant pathogenic bacteria that could contaminate groundwater sources posing public health threats. However, these findings were based on the identification of culturable bacteria and at times not below burial grounds. Investigation on the bacterial diversity and functional profiles of bacterial communities above and below burial grounds in human cemeteries are few. The current study used high-throughput sequencing techniques to determine the bacterial composition and their associated functional profiles in cemetery soil samples collected at the surface and below burial ground in two South African cemeteries (Maitland Cemetery in Cape Town and Fontein Street Cemetery in Middelburg) to evaluate the potential health threat to surrounding populations through contamination of groundwater. Significant differences were observed between sample depths with the clustering of the surface (0 m) and the 2 m samples into separate groups. Pseudomonas and Corynebacterium were the most abundant genera across all samples. Pseudomonas and Rhodococcus were the dominant genera in the 2 m samples while Prauserella and Staphylococcus were dominant in the surface samples. The 2 m samples showed a lower alpha diversity but recorded higher proportions of human diseases functional classes compared to the surface samples. Human disease functional profiles revealed involvement, in infectious (cholera), neurodegenerative (Alzheimer's disease) cardiovascular (hypertrophic cardiomyopathy) immune system (Systemic lupus erythematosus) metabolic (Type I &amp; II diabetes) diseases and cancer. Antibiotic resistance and antibiotics synthesis signatures were also identified. Thus, cemeteries could be potential sources of microbial and antibiotic pollution in groundwater, especially in areas with shallow water tables such as Maitland. Selection of sites for use as cemeteries should, therefore, require a proper understanding of the hydrogeological characteristics of the selected site. However, further studies are required to trace the actual movement of these pollutants into groundwater resources.}, }
@article {pmid30479613, year = {2018}, author = {Sukul, P and Lupilov, N and Leichert, LI}, title = {Corrigendum: Characterization of ML-005, a Novel Metaproteomics-Derived Esterase.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2716}, doi = {10.3389/fmicb.2018.02716}, pmid = {30479613}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2018.01925.].}, }
@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}, doi = {10.1038/s41467-018-07476-4}, pmid = {30479342}, issn = {2041-1723}, support = {R01 AI036040/AI/NIAID NIH HHS/United States ; R37 AI036040/AI/NIAID NIH HHS/United States ; }, 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 {pmid30478535, year = {2018}, author = {Cui, J and Cui, H and Yang, M and Du, S and Li, J and Li, Y and Liu, L and Zhang, X and Li, S}, title = {Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade.}, journal = {Protein &amp; cell}, volume = {}, number = {}, pages = {}, doi = {10.1007/s13238-018-0596-6}, pmid = {30478535}, issn = {1674-8018}, abstract = {The development of gastritis is associated with an increased risk of gastric cancer. Current invasive gastritis diagnostic methods are not suitable for monitoring progress. In this work based on 78 gastritis patients and 50 healthy individuals, we observed that the variation of tongue-coating microbiota was associated with the occurrence and development of gastritis. Twenty-one microbial species were identified for differentiating tongue-coating microbiomes of gastritis and healthy individuals. Pathways such as microbial metabolism in diverse environments, biosynthesis of antibiotics and bacterial chemotaxis were up-regulated in gastritis patients. The abundance of Campylobacter concisus was found associated with the gastric precancerous cascade. Furthermore, Campylobacter concisus could be detected in tongue coating and gastric fluid in a validation cohort containing 38 gastritis patients. These observations provided biological evidence of tongue diagnosis in traditional Chinese medicine, and indicated that tongue-coating microbiome could be a potential non-invasive biomarker, which might be suitable for long-term monitoring of gastritis.}, }
@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}, doi = {10.1038/s41467-018-07426-0}, pmid = {30478343}, issn = {2041-1723}, 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 {pmid30477901, year = {2018}, author = {Youssef, NH and Farag, IF and Hahn, CR and Premathilake, H and Fry, E and Hart, M and Huffaker, K and Bird, E and Hambright, J and Hoff, WD and Elshahed, MS}, title = {Candidatus Krumholzbacterium zodletonensis gen. nov., sp nov, the first representative of the candidate phylum Krumholzbacterota phyl. nov. recovered from an anoxic sulfidic spring using genome resolved metagenomics.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.syapm.2018.11.002}, pmid = {30477901}, issn = {1618-0984}, abstract = {The accumulation of genomes of uncultured organisms has highlighted the need for devising a taxonomic and nomenclature scheme to validate names and prevent redundancies. We here report on the recovery and analysis of four phylogenetically related genomes recovered from an anoxic sulfide and sulfur-rich spring (Zodletone spring) in southwestern Oklahoma. Phylogenetic analysis based on 120 single copy markers attested to their position as a novel distinct bacterial phylum. Genomic analysis suggests Gram-negative flagellated organisms that possess type IV pili. The organisms are predicted to be rod-shaped, slow-growers, with an anoxic, heterotrophic, and fermentative lifestyle. Predicted substrate utilization pattern includes multiple amino acids, dipeptides, tripeptides, and oligpopeptides; as well as few sugars. Predicted auxotrophies include proline, vitamin B6, lipoic acid, biotin, and vitamin B12. Assessment of the putative global distribution pattern of this novel lineage suggests its preference to anoxic marine, terrestrial, hydrocarbon-impacted, and freshwater habitats. We propose the candidatus name Krumholzbacterium zodletonensis gen. nov, sp. nov. for Zgenome0171T, with the genome serving as the type material for the novel family Krumholzbacteriaceae fam. nov., order Krumholzbacteriales ord. nov., class Krumholzbacteria class nov., and phylum Krumholzbacterota phyl. nov. The type material genome assembly is deposited in GenBank under accession number QTKG01000000.}, }
@article {pmid30477563, year = {2018}, author = {Sinha, R and Ahsan, H and Blaser, M and Caporaso, JG and Carmical, JR and Chan, AT and Fodor, A and Gail, MH and Harris, CC and Helzlsouer, K and Huttenhower, C and Knight, R and Kong, HH and Lai, GY and Hutchinson, DLS and Le Marchand, L and Li, H and Orlich, MJ and Shi, J and Truelove, A and Verma, M and Vogtmann, E and White, O and Willett, W and Zheng, W and Mahabir, S and Abnet, C}, title = {Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {210}, doi = {10.1186/s40168-018-0596-z}, pmid = {30477563}, issn = {2049-2618}, abstract = {The National Cancer Institute (NCI) sponsored a 2-day workshop, &quot;Next Steps in Studying the Human Microbiome and Health in Prospective Studies,&quot; in Bethesda, Maryland, May 16-17, 2017. The workshop brought together researchers in the field to discuss the challenges of conducting microbiome studies, including study design, collection and processing of samples, bioinformatics and statistical methods, publishing results, and ensuring reproducibility of published results. The presenters emphasized the great potential of microbiome research in understanding the etiology of cancer. This report summarizes the workshop and presents practical suggestions for conducting microbiome studies, from workshop presenters, moderators, and participants.}, }
@article {pmid30476443, year = {2018}, author = {Vikram, A and Miller, E and Arthur, TM and Bosilevac, JM and Wheeler, TL and Schmidt, JW}, title = {Similar Levels of Antimicrobial Resistance in U.S. Food Service Ground Beef Products with and without a &quot;Raised without Antibiotics&quot; Claim.}, journal = {Journal of food protection}, volume = {81}, number = {12}, pages = {2007-2018}, doi = {10.4315/0362-028X.JFP-18-299}, pmid = {30476443}, issn = {1944-9097}, abstract = {U.S. ground beef with &quot;raised without antibiotics&quot; (RWA) label claims are perceived as harboring fewer bacteria with antimicrobial resistance (AMR) than are found in conventional (CONV) ground beef with no such label claim. A total of 370 ground beef samples from CONV (n = 191) and RWA (n = 179) production systems were collected over 13 months from three food service suppliers. The following bacteria were cultured: Escherichia coli, tetracycline-resistant (TETr) E. coli, third-generation cephalosporin-resistant (3GCr) E. coli, Salmonella enterica, TETr S. enterica, 3GCr S. enterica, nalidixic acid-resistant S. enterica, Enterococcus spp., erythromycin-resistant Enterococcus spp., TETr Enterococcus spp., Staphylococcus aureus, and methicillin-resistant S. aureus. TETr E. coli was more frequently detected in CONV ground beef (CONV, 54.2%; RWA, 35.2%; P < 0.01), but supplier (P < 0.01) and production system × suppler interaction (P < 0.01) effects were also significant. Metagenomic DNA was isolated from each sample, and equal amounts of metagenomic DNA were pooled by supplier, month, and production system for 75 pooled samples (38 CONV, 37 RWA). The abundance of aac(6')-Ie-aph(2″)-Ia, aadA1, blaCMY-2, blaCTX-M, blaKPC-2, erm(B), mecA, tet(A), tet(B), and tet(M) genes was assessed by quantitative PCR. The tet(A) (2.9-log2-fold change, P = 0.04) and tet(B) (5.6-log2-fold change) (P = 0.03) genes were significantly more abundant in RWA ground beef. Phylogenetic analyses revealed that ground beef microbiomes differed more by supplier than by production system. These results were consistent with prior research suggesting antimicrobial use in U.S. beef cattle has minimal impact on the AMR of bacteria found in these products. These results should spur a reevaluation of assumptions regarding the impact of antimicrobial use during U.S. beef production on the AMR of bacteria in ground beef.}, }
@article {pmid30475995, year = {2018}, author = {Czajkowski, MD and Vance, DP and Frese, SA and Casaburi, G}, title = {GenCoF: A graphical user interface to rapidly remove human genome contaminants from metagenomic datasets.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/bty963}, pmid = {30475995}, issn = {1367-4811}, abstract = {Summary: The removal of human genomic reads from shotgun metagenomic sequencing is a critical step in protecting subject privacy. Freely available tools addressing this issue require advanced programming knowledge or are limited by analytical time and data load due to their server-based nature. Here, we compared the most cited tools for host-DNA removal using synthetic and real metagenomic datasets. Then, we integrated the most efficient pipeline in a graphical user interface to make these tools available without command line use. This interface, GenCoF, rapidly removes human genome contaminants from metagenomic datasets. Additionally, the tool offers quality-filtering, data reduction and interactive modification of any parameter in order to customize the analysis. GenCoF offers both quality and host-associated filtering in a non-commercial, freely available tool in a local, interactive and easy-to-use interface.<br><br>GenCoF is freely available (under a GPL license) for Mac OS and Linux at https://github.com/MattCzajkowski/GenCoF.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30474490, year = {2018}, author = {Jonsson, V and Österlund, T and Nerman, O and Kristiansson, E}, title = {Modelling of zero-inflation improves inference of metagenomic gene count data.}, journal = {Statistical methods in medical research}, volume = {}, number = {}, pages = {962280218811354}, doi = {10.1177/0962280218811354}, pmid = {30474490}, issn = {1477-0334}, abstract = {Metagenomics enables the study of gene abundances in complex mixtures of microorganisms and has become a standard methodology for the analysis of the human microbiome. However, gene abundance data is inherently noisy and contains high levels of biological and technical variability as well as an excess of zeros due to non-detected genes. This makes the statistical analysis challenging. In this study, we present a new hierarchical Bayesian model for inference of metagenomic gene abundance data. The model uses a zero-inflated overdispersed Poisson distribution which is able to simultaneously capture the high gene-specific variability as well as zero observations in the data. By analysis of three comprehensive datasets, we show that zero-inflation is common in metagenomic data from the human gut and, if not correctly modelled, it can lead to substantial reductions in statistical power. We also show, by using resampled metagenomic data, that our model has, compared to other methods, a higher and more stable performance for detecting differentially abundant genes. We conclude that proper modelling of the gene-specific variability, including the excess of zeros, is necessary to accurately describe gene abundances in metagenomic data. The proposed model will thus pave the way for new biological insights into the structure of microbial communities.}, }
@article {pmid30472727, year = {2018}, author = {Pérez, MM and Martins, LMS and Dias, MS and Pereira, CA and Leite, JA and Gonçalves, ECS and de Almeida, PZ and de Freitas, EN and Tostes, RC and Ramos, SG and de Zoete, MR and Ryffel, B and Silva, JS and Carlos, D}, title = {IL-17/IL-17R axis elicits intestinal neutrophil migration, restrains gut dysbiosis and LPS translocation in high-fat diet-induced metabolic syndrome model.}, journal = {Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imm.13028}, pmid = {30472727}, issn = {1365-2567}, abstract = {Sound evidence supports a role for interleukin-17 (IL-17)-producing delta-gamma (γδ) T cells and IL-17-producing helper T cells (Th17) in intestinal homeostasis, especially in intestinal barrier integrity. In the present study, we aimed to evaluate the role of IL-17 cytokine in the regulation of intestinal immunity and obesity-induced metabolic syndrome (MetS) in an experimental murine model. C57BL/6 wild-type (WT) mice and mice lacking the IL-17 cytokine receptor (IL-17RA-/-) were fed either a control diet (CD) or a high-fat diet (HFD) for nine weeks. Our data demonstrate that IL-17RA-/- mice are protected against obesity, but develop hyperglycemia, hyperinsulinemia and insulin resistance. In parallel, HFD-fed IL-17RA-/- mice display intense inflammation in the ileum compared to WT mice on the HFD. IL-17RA-/- mice fed the HFD exhibit impaired neutrophil migration to the intestinal mucosa and reduced gene expression of the CXCL-1 chemokine and CXCR-2 receptor in the ileum. Interestingly, the populations of neutrophils (CD11b+ Ly6G+) and anti-inflammatory macrophages (CD11b+ CX3CR1+) are increased in the mesenteric lymph nodes of these mice. IL-17RA-/- mice on the HFD also display increased commensal bacterial translocation into the bloodstream and elevated lipopolysaccharide (LPS) levels in the visceral adipose tissue (VAT). Metagenomic analysis of bacterial 16S gene revealed increased Proteobacteria and Bacteroidetes phyla, the main representatives of gram-negative bacteria, and reduced Akkemansia muciniphila in the fecal samples of IL-17RA-/- mice fed the HFD. Together, these data indicate that IL-17/IL-17R axis drives intestinal neutrophil migration, limits gut dysbiosis and attenuates LPS translocation to VAT, resulting in protection to MetS. This article is protected by copyright. All rights reserved.}, }
@article {pmid30472682, year = {2018}, author = {Coker, OO and Nakatsu, G and Dai, RZ and Wu, WKK and Wong, SH and Ng, SC and Chan, FKL and Sung, JJY and Yu, J}, title = {Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2018-317178}, pmid = {30472682}, issn = {1468-3288}, abstract = {OBJECTIVES: Bacteriome and virome alterations are associated with colorectal cancer (CRC). Nevertheless, the gut fungal microbiota in CRC remains largely unexplored. We aimed to characterise enteric mycobiome in CRC.<br><br>DESIGN: Faecal shotgun metagenomic sequences of 184 patients with CRC, 197 patients with adenoma and 204 control subjects from Hong Kong were analysed (discovery cohort: 73 patients with CRC and 92 control subjects; validation cohort: 111 patients with CRC, 197 patients with adenoma and 112 controls from Hong Kong). CRC-associated fungal markers and ecological changes were also validated in additional independent cohorts of 90 patients with CRC, 42 patients with adenoma and 66 control subjects of published repository sequences from Germany and France. Assignment of taxonomies was performed by exact k-mer alignment against an integrated microbial reference genome database.<br><br>RESULTS: Principal component analysis revealed separate clusters for CRC and control (p<0.0001), with distinct mycobiomes in early-stage and late-stage CRC (p=0.0048). Basidiomycota:Ascomycota ratio was higher in CRC (p=0.0042), with increase in Malasseziomycetes (p<0.0001) and decrease in Saccharomycetes (p<0.0001) and Pneumocystidomycetes (p=0.0017). Abundances of 14 fungal biomarkers distinguished CRC from controls with an area under the receiver-operating characteristic curve (AUC) of 0.93 and validated AUCs of 0.82 and 0.74 in independent Chinese cohort V1 and European cohort V2, respectively. Further ecological analysis revealed higher numbers of co-occurring fungal intrakingdom and co-exclusive bacterial-fungal correlations in CRC (p<0.0001). Moreover, co-occurrence interactions between fungi and bacteria, mostly contributed by fungal Ascomycota and bacterial Proteobacteria in control, were reverted to co-exclusive interplay in CRC (p=0.00045).<br><br>CONCLUSIONS: This study revealed CRC-associated mycobiome dysbiosis characterised by altered fungal composition and ecology, signifying that the gut mycobiome might play a role in CRC.}, }
@article {pmid30470770, year = {2018}, author = {Sang, S and Zhang, X and Dai, H and Hu, BX and Ou, H and Sun, L}, title = {Diversity and predictive metabolic pathways of the prokaryotic microbial community along a groundwater salinity gradient of the Pearl River Delta, China.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17317}, doi = {10.1038/s41598-018-35350-2}, pmid = {30470770}, issn = {2045-2322}, support = {2016YFC0402805//Ministry of Science and Technology of the People&amp;apos;s Republic of China (Chinese Ministry of Science and Technology)/ ; 2016YFC0402805//Ministry of Science and Technology of the People&amp;apos;s Republic of China (Chinese Ministry of Science and Technology)/ ; }, abstract = {Almost half of the groundwater in the Pearl River Delta (PRD) contains salt water originally derived from paleo-seawater due to the Holocene transgression, which then generates intense physicochemical gradients in the mixing zone between freshwater and saltwater. Although some studies have been conducted on the hydrological and geochemical characteristics of groundwater in the PRD to monitor the intrusion of seawater, little attention has been paid to the microbial community of this particular region. In this study, we implemented a high-throughput sequencing analysis to characterize the microbial communities along a salinity gradient in the PRD aquifer, China. Our results indicated that the microbial community composition varied significantly depending on the salinity of the aquifer. The presence of abundant anaerobic microorganisms of the genera Desulfovibrio and Methanococcus in certain saltwater samples may be responsible for the gas generation of H2S and CH4 in the stratum. In saline water samples (TDS > 10 g/L), the linear discriminant analysis effect size (LEfSe) analysis found two biomarkers that usually live in marine environments, and the aquifers of the PRD still contained large quantity of saltwater, indicating that the impact of the paleo-seawater has lasted to this day. The predictive metagenomic analysis revealed that the metabolic pathways present in the groundwater samples studied, included the degradation of pesticides and refractory organics (dichlorodiphenyltrichloroethane (DDT), atrazine and polycyclic aromatic hydrocarbons), matter cycling (methane, nitrogen and sulfur), and inorganic ion and mineral metabolites. This study can help enhance our understanding of the composition of the microbial assemblages and its implications as an environmental indicator in an aquifer affected by saltwater intrusion.}, }
@article {pmid30470746, year = {2018}, author = {Emiola, A and Oh, J}, title = {High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4956}, doi = {10.1038/s41467-018-07240-8}, pmid = {30470746}, issn = {2041-1723}, support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; }, abstract = {We developed Growth Rate InDex (GRiD) for estimating in situ growth rates of ultra-low coverage (>0.2×) and de novo-assembled metagenomes. Applying GRiD to human and environmental metagenomic datasets to demonstrate its versatility, we uncovered new associations with previously uncharacterized bacteria whose growth rates were associated with several disease characteristics or environmental interactions. In addition, with GRiD-MG (metagenomic), a high-throughput implementation of GRiD, we estimated growth dynamics of 1756 bacteria species from a healthy skin metagenomic dataset and identified a new Staphylococcus-Corynebacterium antagonism likely mediated by antimicrobial production in the skin. GRiD-MG significantly increases the ability to extract growth rate inferences from complex metagenomic data with minimal input from the user.}, }
@article {pmid30470230, year = {2018}, author = {San Martín, C and van Raaij, MJ}, title = {The so far farthest reaches of the double jelly roll capsid protein fold.}, journal = {Virology journal}, volume = {15}, number = {1}, pages = {181}, doi = {10.1186/s12985-018-1097-1}, pmid = {30470230}, issn = {1743-422X}, support = {BFU2014-53425-P//Spanish Ministry of Economy, Industry and Competitiveness/International ; BFU2016-74868-P//Spanish Ministry of Economy, Industry and Competitiveness/International ; BIO2015-68990-REDT//Spanish Ministry of Economy, Industry and Competitiveness/International ; }, abstract = {BACKGROUND: During the last two decades, structural biology analyses have shown that viruses infecting hosts far apart in evolution share similar architectural features, prompting a new virus classification based on structural lineages. Until recently, only a few prokaryotic viruses had been described for one of the lineages, whose main characteristic is a capsid protein with a perpendicular double jelly roll.<br><br>MAIN BODY: Metagenomics analyses are showing that the variety of prokaryotic viruses encoding double jelly roll capsid proteins is much larger than previously thought. The newly discovered viruses have novel genome organisations with interesting implications for virus structure, function and evolution. There are also indications of their having a significant ecological impact.<br><br>CONCLUSION: Viruses with double jelly roll capsid proteins that infect prokaryotic hosts form a large part of the virosphere that had so far gone unnoticed. Their discovery by metagenomics is only a first step towards many more exciting findings. Work needs to be invested in isolating these viruses and their hosts, characterizing the structure and function of the proteins their genomes encode, and eventually access the wealth of biological information they may hold.}, }
@article {pmid30470178, year = {2018}, author = {Griffith, BC and Weiss, BL and Aksoy, E and Mireji, PO and Auma, JE and Wamwiri, FN and Echodu, R and Murilla, G and Aksoy, S}, title = {Analysis of the gut-specific microbiome from field-captured tsetse flies, and its potential relevance to host trypanosome vector competence.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {146}, doi = {10.1186/s12866-018-1284-7}, pmid = {30470178}, issn = {1471-2180}, support = {D43 TW007391/TW/FIC NIH HHS/United States ; R01 AI051584/AI/NIAID NIH HHS/United States ; R01 AI068932/AI/NIAID NIH HHS/United States ; U01 AI115648/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: The tsetse fly (Glossina sp.) midgut is colonized by maternally transmitted and environmentally acquired bacteria. Additionally, the midgut serves as a niche in which pathogenic African trypanosomes reside within infected flies. Tsetse's bacterial microbiota impacts many aspects of the fly's physiology. However, little is known about the structure of tsetse's midgut-associated bacterial communities as they relate to geographically distinct fly habitats in east Africa and their contributions to parasite infection outcomes. We utilized culture dependent and independent methods to characterize the taxonomic structure and density of bacterial communities that reside within the midgut of tsetse flies collected at geographically distinct locations in Kenya and Uganda.<br><br>RESULTS: Using culture dependent methods, we isolated 34 strains of bacteria from four different tsetse species (G. pallidipes, G. brevipalpis, G. fuscipes and G. fuscipleuris) captured at three distinct locations in Kenya. To increase the depth of this study, we deep sequenced midguts from individual uninfected and trypanosome infected G. pallidipes captured at two distinct locations in Kenya and one in Uganda. We found that tsetse's obligate endosymbiont, Wigglesworthia, was the most abundant bacterium present in the midgut of G. pallidipes, and the density of this bacterium remained largely consistent regardless of whether or not its tsetse host was infected with trypanosomes. These fly populations also housed the commensal symbiont Sodalis, which was found at significantly higher densities in trypanosome infected compared to uninfected flies. Finally, midguts of field-captured G. pallidipes were colonized with distinct, low density communities of environmentally acquired microbes that differed in taxonomic structure depending on parasite infection status and the geographic location from which the flies were collected.<br><br>CONCLUSIONS: The results of this study will enhance our understanding of the tripartite relationship between tsetse, its microbiota and trypanosome vector competence. This information may be useful for developing novel disease control strategies or enhancing the efficacy of those already in use.}, }
@article {pmid30469432, year = {2018}, author = {Hwang, H and Lee, JH}, title = {Characterization of Arginine Catabolism by Lactic Acid Bacteria Isolated from Kimchi.}, journal = {Molecules (Basel, Switzerland)}, volume = {23}, number = {11}, pages = {}, doi = {10.3390/molecules23113049}, pmid = {30469432}, issn = {1420-3049}, support = {KE1801-2//World Institute of Kimchi/ ; }, abstract = {Kimchi fermentation depends on diverse lactic acid bacteria, which convert raw materials into numerous metabolites that contribute to the taste of food. Amino acids and saccharides are important primary metabolites. Arginine is nearly exhausted during kimchi fermentation, whereas the concentrations of other amino acids are reported not to increase or decrease dramatically. These phenomena could imply that arginine is an important nutritional component among the amino acids during kimchi fermentation. In this study, we investigated the arginine-catabolism pathway of seven lactic acid bacteria isolated from kimchi and evaluated the products of arginine catabolism (citrulline and ornithine) associated with the bacteria. The arginine content dramatically decreased in cultures of Lactobacillus brevis and Weissella confusa from 300 μg/mL of arginine to 0.14 ± 0.19 and 1.3 ± 0.01 μg/mL, respectively, after 6 h of cultivation. Citrulline and ornithine production by L. brevis and W. confusa showed a pattern that was consistent with arginine catabolism. Interestingly, Pediococcus pentosaceus, Lactobacillus plantarum, Leuconostoc mesenteroides, and Leuconostoc lactis did not show increased citrulline levels after arginine was added. The ornithine contents were higher in all bacteria except for L. lactis after adding arginine to the culture. These results were consistent with the absence of the arginine deiminase gene among the lactic acid bacteria. Arginine consumption and ornithine production were monitored and compared with lactic acid bacteria by metagenomics analysis, which showed that the increment of ornithine production correlated positively with lactic acid bacteria growth.}, }
@article {pmid30465678, year = {2018}, author = {Shao, Y and Wang, Z}, title = {Changes in the nutrients of camels' milk alter the functional features of the intestine microbiota.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/c8fo00812d}, pmid = {30465678}, issn = {2042-650X}, abstract = {Heat treatment alters the nutritive quality of camels' milk and thus the intestine microbiota, but the effect of heat treatment-induced nutrient loss on the functional features of the intestine microbiota is unknown. In this study, the influence of two heat treatments of camels' milk on the intestine microbiota was investigated to establish the correlations between milk nutrients and the functional features of the intestine microbiota. Camels' milk, heat treated at low (65 °C) or high (100 °C) temperatures, was administered to mice (LM = low; HM = high); control mice received sterile distilled water (CW = control). Intestine microbiota were compared in the three groups using metagenomic-based 16S rRNA gene high throughput sequencing. The results showed that the relative abundance of probiotic genera (Akkermansia, Bifidobacterium and Lactobacillus) was significantly higher in the LM group mice than in the HM group mice, due to the high-temperature degradation of the nutrients of camels' milk. The diversity of the intestine microbiota in mice receiving milk was lower than in the control group because of the intrinsically high antimicrobial components (lactoferrin and lysozyme) detected in camels' milk. Carbohydrate digestion/absorption, and cysteine and methionine metabolism were significantly higher in the intestine microbiota of the LM group mice than in the HM group mice owing to the corresponding degradation of lactose, cysteine and methionine in camels' milk at high temperatures. Changes in the nutrients of camels' milk affected the changes in the functional features of the intestine microbiota. This research suggests that low temperature heat treatment achieves nutrient preservation, but also encourages probiotic genera.}, }
@article {pmid30465105, year = {2018}, author = {Maffioli, SI and Sosio, M and Ebright, RH and Donadio, S}, title = {Discovery, properties, and biosynthesis of pseudouridimycin, an antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10295-018-2109-2}, pmid = {30465105}, issn = {1476-5535}, support = {GM041376//National Institutes of Health/ ; AI104660//National Institutes of Health/ ; 30190679//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, abstract = {Pseudouridimycin (PUM) is a novel pseudouridine-containing peptidyl-nucleoside antibiotic that inhibits bacterial RNA polymerase (RNAP) through a binding site and mechanism different from those of clinically approved RNAP inhibitors of the rifamycin and lipiarmycin (fidaxomicin) classes. PUM was discovered by screening microbial fermentation extracts for RNAP inhibitors. In this review, we describe the discovery and characterization of PUM. We also describe the RNAP-inhibitory and antibacterial properties of PUM. Finally, we review available information on the gene cluster and pathway for PUM biosynthesis and on the potential for discovering additional novel pseudouridine-containing nucleoside antibiotics by searching bacterial genome and metagenome sequences for sequences similar to pumJ, the pseudouridine-synthase gene of the PUM biosynthesis gene cluster.}, }
@article {pmid30464766, year = {2018}, author = {Purahong, W and Orrù, L and Donati, I and Perpetuini, G and Cellini, A and Lamontanara, A and Michelotti, V and Tacconi, G and Spinelli, F}, title = {Plant Microbiome and Its Link to Plant Health: Host Species, Organs and Pseudomonas syringae pv. actinidiae Infection Shaping Bacterial Phyllosphere Communities of Kiwifruit Plants.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1563}, doi = {10.3389/fpls.2018.01563}, pmid = {30464766}, issn = {1664-462X}, abstract = {Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of the bacterial canker, the most devastating disease of kiwifruit vines. Before entering the host tissues, this pathogen has an epiphytic growth phase on kiwifruit flowers and leaves, thus the ecological interactions within epiphytic bacterial community may greatly influence the onset of the infection process. The bacterial community associated to the two most important cultivated kiwifruit species, Actinidia chinensis and Actinidia deliciosa, was described both on flowers and leaves using Illumina massive parallel sequencing of the V3 and V4 variable regions of the 16S rRNA gene. In addition, the effect of plant infection by Psa on the epiphytic bacterial community structure and biodiversity was investigated. Psa infection affected the phyllosphere microbiome structures in both species, however, its impact was more pronounced on A. deliciosa leaves, where a drastic drop in microbial biodiversity was observed. Furthermore, we also showed that Psa was always present in syndemic association with Pseudomonas syringae pv. syringae and Pseudomonas viridiflava, two other kiwifruit pathogens, suggesting the establishment of a pathogenic consortium leading to a higher pathogenesis capacity. Finally, the analyses of the dynamics of bacterial populations provided useful information for the screening and selection of potential biocontrol agents against Psa.}, }
@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 = {}, doi = {10.1128/mSphereDirect.00588-18}, pmid = {30463925}, issn = {2379-5042}, 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 {pmid30462578, year = {2018}, author = {Miao, J and Shi, Y and Zeng, D and Wu, G}, title = {Enhanced shortcut nitrogen removal and metagenomic analysis of functional microbial communities in a double sludge system treating ammonium-rich wastewater.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-37}, doi = {10.1080/09593330.2018.1551432}, pmid = {30462578}, issn = {0959-3330}, abstract = {Biological nitrogen removal processes based on partial nitrification are promising for ammonium-rich wastewater treatment. In this study, a partial nitrification-denitrification double sludge system was applied to treat synthetic ammonium-rich wastewater. Metagenomic analysis of functional genes and metabolic pathways was conducted, also with the evaluation of system performance and nitrous oxide (N2O) emission. In the nitrifying sequencing batch reactor (SBRPN), the removal percentage of ammonium nitrogen reached to 99.98% with a high nitritation efficiency of 93.24%, and the N2O emission factor was 0.88%. In the denitrifying sequencing batch reactor (SBRDN), there was almost no nitrate nitrogen and nitrite nitrogen in the effluent, and the maximum N2O emission was 0.078 mg N/L. The dominant ammonia oxidizing bacteria was Nitrosomonas in SBRPN (13.6%), and the main potential denitrifiers in SBRDN were Thauera (14.6%), an uncultured genus in the Comamonadaceae family (4.0%), an uncultured genus in Rhodocyclaceae family (2.4%) and Comamonas (1.1%). Metagenomic analysis revealed that amo mainly distributed in Nitrosomonas eutropha (38.3%), Nitrosomonas europaea (27.1%), Nitrosomonas sp. GH22 (20.5%) and Nitrosomonas sp. TK794 (15.0%), and Bacteroidetes had the N2O reduction potential in SBRPN.}, }
@article {pmid30462168, year = {2018}, author = {Baldini, F and Heinken, A and Heirendt, L and Magnusdottir, S and Fleming, RMT and Thiele, I}, title = {The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/bty941}, pmid = {30462168}, issn = {1367-4811}, abstract = {Motivation: The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes.<br><br>Results: To address this gap, we created a comprehensive toolbox to model i) microbe-microbe and host-microbe metabolic interactions, and ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the COBRA Toolbox.<br><br>Availability: The Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.}, }
@article {pmid30461157, year = {2018}, author = {James, AK and Kelly, LW and Nelson, CE and Wilbanks, EG and Carlson, CA}, title = {Elevated pCO2 Alters Marine Heterotrophic Bacterial Community Composition and Metabolic Potential in Response to a Pulse of Phytoplankton Organic Matter.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14484}, pmid = {30461157}, issn = {1462-2920}, abstract = {Factors that affect the respiration of organic carbon by marine bacteria can alter the extent to which the oceans act as a sink of atmospheric carbon dioxide. We designed seawater dilution experiments to assess the effect of pCO2 enrichment on heterotrophic bacterial community composition and metabolic potential in response to a pulse of phytoplankton-derived organic carbon. Experiments included treatments of elevated (1000 ppm) and low (250 ppm) pCO2 , amended with 10 μmol L-1 dissolved organic carbon from Emiliana huxleyi lysates, and were conducted using surface-seawater collected from the South Pacific Subtropical Gyre. To assess differences in community composition and metabolic potential, shotgun metagenomic libraries were sequenced from low and elevated pCO2 treatments collected at the start of the experiment and following exponential growth. Our results indicate bacterial communities changed markedly in response to the organic matter pulse over time and was significantly affected by pCO2 enrichment. Elevated pCO2 also had disproportionate effects on the abundance of sequences related to proton pumps, carbohydrate metabolism, modifications of the phospholipid bilayer, resistance to toxic compounds and conjugative transfer. These results contribute to a growing understanding of the effects of elevated pCO2 on bacteria-mediated carbon cycling during phytoplankton bloom conditions in the marine environment. This article is protected by copyright. All rights reserved.}, }
@article {pmid30459724, year = {2018}, author = {Wang, M and Xiong, W and Liu, P and Xie, X and Zeng, J and Sun, Y and Zeng, Z}, title = {Metagenomic Insights Into the Contribution of Phages to Antibiotic Resistance in Water Samples Related to Swine Feedlot Wastewater Treatment.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2474}, doi = {10.3389/fmicb.2018.02474}, pmid = {30459724}, issn = {1664-302X}, abstract = {In this study, we examined the types of antibiotic resistance genes (ARGs) possessed by bacteria and bacteriophages in swine feedlot wastewater before and after treatment using a metagenomics approach. We found that the relative abundance of ARGs in bacterial DNA in all water samples was significantly higher than that in phages DNA (>10.6-fold), and wastewater treatment did not significantly change the relative abundance of bacterial- or phage-associated ARGs. We further detected the distribution and diversity of the different types of ARGs according to the class of antibiotics to which they confer resistance, the tetracycline resistance genes were the most abundant resistance genes and phages were more likely to harbor ATP-binding cassette transporter family and ribosomal protection genes. Moreover, the colistin resistance gene mcr-1 was also detected in the phage population. When assessing the contribution of phages in spreading different groups of ARGs, β-lactamase resistance genes had a relatively high spreading ability even though the abundance was low. These findings possibly indicated that phages not only could serve as important reservoir of ARG but also carry particular ARGs in swine feedlot wastewater, and this phenomenon is independent of the environment.}, }
@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}, doi = {10.1038/s41467-018-07343-2}, pmid = {30459421}, issn = {2041-1723}, 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 {pmid30459334, year = {2018}, author = {Jersie-Christensen, RR and Lanigan, LT and Lyon, D and Mackie, M and Belstrøm, D and Kelstrup, CD and Fotakis, AK and Willerslev, E and Lynnerup, N and Jensen, LJ and Cappellini, E and Olsen, JV}, title = {Quantitative metaproteomics of medieval dental calculus reveals individual oral health status.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4744}, doi = {10.1038/s41467-018-07148-3}, pmid = {30459334}, issn = {2041-1723}, abstract = {The composition of ancient oral microbiomes has recently become accessible owing to advanced biomolecular methods such as metagenomics and metaproteomics, but the utility of metaproteomics for such analyses is less explored. Here, we use quantitative metaproteomics to characterize the dental calculus associated with the remains of 21 humans retrieved during the archeological excavation of the medieval (ca. 1100-1450 CE) cemetery of Tjærby, Denmark. We identify 3671 protein groups, covering 220 bacterial species and 81 genera across all medieval samples. The metaproteome profiles of bacterial and human proteins suggest two distinct groups of archeological remains corresponding to health-predisposed and oral disease-susceptible individuals, which is supported by comparison to the calculus metaproteomes of healthy living individuals. Notably, the groupings identified by metaproteomics are not apparent from the bioarchaeological analysis, illustrating that quantitative metaproteomics has the potential to provide additional levels of molecular information about the oral health status of individuals from archeological contexts.}, }
@article {pmid30459201, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Ruffin, MT and Koumpouras, CC and Schloss, PD}, title = {Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, doi = {10.1128/mBio.02248-18}, pmid = {30459201}, issn = {2150-7511}, abstract = {Human viruses (those that infect human cells) have been associated with many cancers, largely due to their mutagenic and functionally manipulative abilities. Despite this, cancer microbiome studies have focused almost exclusively on bacteria instead of viruses. We began evaluating the cancer virome by focusing on colorectal cancer, a primary cause of morbidity and mortality throughout the world and a cancer linked to altered colonic bacterial community compositions but with an unknown association with the gut virome. We used 16S rRNA gene, whole shotgun metagenomic, and purified virus metagenomic sequencing of stool to evaluate the differences in human colorectal cancer virus and bacterial community composition. Through random forest modeling, we identified differences in the healthy and colorectal cancer viromes. The cancer-associated virome consisted primarily of temperate bacteriophages that were also predicted to be bacterium-virus community network hubs. These results provide foundational evidence that bacteriophage communities are associated with colorectal cancer and potentially impact cancer progression by altering the bacterial host communities.IMPORTANCE Colorectal cancer is a leading cause of cancer-related death in the United States and worldwide. Its risk and severity have been linked to colonic bacterial community composition. Although human-specific viruses have been linked to other cancers and diseases, little is known about colorectal cancer virus communities. We addressed this knowledge gap by identifying differences in colonic virus communities in the stool of colorectal cancer patients and how they compared to bacterial community differences. The results suggested an indirect role for the virome in impacting colorectal cancer by modulating the associated bacterial community. These findings both support the idea of a biological role for viruses in colorectal cancer and provide a new understanding of basic colorectal cancer etiology.}, }
@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}, doi = {10.1186/s12866-018-1331-4}, 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 {pmid30457937, year = {2018}, author = {Cruz, YWG and Vieira, YA and Vilar, DS and Torres, NH and Aguiar, MM and Cavalcanti, EB and Américo-Pinheiro, JHP and Soriano, RN and Bharagava, RN and Lima, ÁS and Ferreira, LFR}, title = {Pulp wash: a new source for production of ligninolytic enzymes and biomass and its toxicological evaluation after biological treatment.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-28}, doi = {10.1080/09593330.2018.1551428}, pmid = {30457937}, issn = {0959-3330}, abstract = {Pulp wash was used as substrate for the activity of ligninolytic enzymes of the fungus Pleurotus sajor-caju. Activity of laccase (Lac) and manganese peroxidase (MnP) as well as fungal biomass occurred under four conditions: different pulp wash concentrations, pH variation at the optimal pulp wash concentration, different glucose concentrations, and different concentrations of ammonium nitrate. The best enzyme activity and biomass production were obtained with in natura pulp wash and pH corrected to 5.0 (4884 IU/L Lac; 82 IU/L MnP; 25 g/100 mL biomass). However, glucose and ammonium nitrate addition to the pulp wash were not necessary for increasing the enzyme activity and biomass production. Efficient removal of pulp wash chemical oxygen demand (COD) (99.66%) and biochemical oxygen demand (BOD) (83.27%) occurred after the mycoremediation with P. sajor-caju in the optimized conditions. Lactuca sativa L. seeds germination bioassay showed a four-fold reduction in the residue toxicity (EC50 28.72%) after the treatment with the fungus. Our findings are consistent with the notion that pulp wash is an excellent substrate for inducing the activity of ligninolytic enzymes and producing fungal biomass, and that the biological treatment is efficient to reduce effluent toxicity.}, }
@article {pmid30455068, year = {2018}, author = {Music, MS and Samarzija, I and Hogenhout, SA and Haryono, M and Cho, ST and Kuo, CH}, title = {The genome of 'Candidatus Phytoplasma solani' strain SA-1 is highly dynamic and prone to adopting foreign sequences.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.syapm.2018.10.008}, pmid = {30455068}, issn = {1618-0984}, abstract = {Bacteria of the genus 'Candidatus Phytoplasma' are uncultivated intracellular plant pathogens transmitted by phloem-feeding insects. They have small genomes lacking genes for essential metabolites, which they acquire from either plant or insect hosts. Nonetheless, some phytoplasmas, such as 'Ca. P. solani', have broad plant host range and are transmitted by several polyphagous insect species. To understand better how these obligate symbionts can colonize such a wide range of hosts, the genome of 'Ca. P. solani' strain SA-1 was sequenced from infected periwinkle via a metagenomics approach. The de novo assembly generated a draft genome with 19 contigs totalling 821,322bp, which corresponded to more than 80% of the estimated genome size. Further completion of the genome was challenging due to the high occurrence of repetitive sequences. The majority of repeats consisted of gene arrangements characteristic of phytoplasma potential mobile units (PMUs). These regions showed variation in gene orders intermixed with genes of unknown functions and lack of similarity to other phytoplasma genes, suggesting that they were prone to rearrangements and acquisition of new sequences via recombination. The availability of this high-quality draft genome also provided a foundation for genome-scale genotypic analysis (e.g., average nucleotide identity and average amino acid identity) and molecular phylogenetic analysis. Phylogenetic analyses provided evidence of horizontal transfer for PMU-like elements from various phytoplasmas, including distantly related ones. The 'Ca. P. solani' SA-1 genome also contained putative secreted protein/effector genes, including a homologue of SAP11, found in many other phytoplasma species.}, }
@article {pmid30453904, year = {2018}, author = {Salazar, JK and Carstens, CK and Ramachandran, P and Shazer, AG and Narula, SS and Reed, E and Ottesen, A and Schill, KM}, title = {Metagenomics of pasteurized and unpasteurized gouda cheese using targeted 16S rDNA sequencing.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {189}, doi = {10.1186/s12866-018-1323-4}, pmid = {30453904}, issn = {1471-2180}, support = {U19 FD005322/FD/FDA HHS/United States ; U19FD005322//U.S. Food and Drug Administration/ ; }, abstract = {BACKGROUND: The microbiome of cheese is diverse, even within a variety. The metagenomics of cheese is dependent on a vast array of biotic and abiotic factors. Biotic factors include the population of microbiota and their resulting cellular metabolism. Abiotic factors, including the pH, water activity, fat, salt, and moisture content of the cheese matrix, as well as environmental conditions (temperature, humidity, and location of aging), influence the biotic factors. This study assessed the metagenomics of commercial Gouda cheese prepared using pasteurized or unpasteurized cow milk or pasteurized goat milk via 16S rDNA sequencing.<br><br>RESULTS: Results were analyzed and compared based on milk pasteurization and source, spatial variability (core, outer, and under the rind), and length of aging (2-4 up to 12-18 months). The dominant organisms in the Gouda cheeses, based on percentage of sequence reads identified at the family or genus levels, were Bacillaceae, Lactococcus, Lactobacillus, Streptococcus, and Staphylococcus. More genus- or family-level (e.g. Bacillaceae) identifications were observed in the Gouda cheeses prepared with unpasteurized cow milk (120) compared with those prepared with pasteurized cow milk (92). When assessing influence of spatial variability on the metagenomics of the cheese, more pronounced differences in bacterial genera were observed in the samples taken under the rind; Brachybacterium, Pseudoalteromonas, Yersinia, Klebsiella, and Weissella were only detected in these samples. Lastly, the aging length of the cheese greatly influenced the number of organisms observed. Twenty-seven additional genus-level identifications were observed in Gouda cheese aged for 12-18 months compared with cheese only aged 2-4 months.<br><br>CONCLUSIONS: Collectively, the results of this study are important in determining the typical microbiota associated with Gouda cheese and how the microbiome plays a role in safety and quality.}, }
@article {pmid30453603, year = {2018}, author = {Ogunade, I and Schweickart, H and Andries, K and Lay, J and Adeyemi, J}, title = {Monensin Alters the Functional and Metabolomic Profile of Rumen Microbiota in Beef Cattle.}, journal = {Animals : an open access journal from MDPI}, volume = {8}, number = {11}, pages = {}, doi = {10.3390/ani8110211}, pmid = {30453603}, issn = {2076-2615}, support = {Evans-Allen project 1008985//National Institute of Food and Agriculture/ ; }, abstract = {To identify differences in rumen function as a result of feeding monensin to beef cattle, rumen fluid metagenomics and metabolomics analyses were used to evaluate the functional attributes and metabolites of rumen microbiota in beef steers fed no or 200 mg/d of monensin. Eight rumen-fistulated steers were used in the study for a period of 53 days. Rumen fluid samples were collected on the last day of the experiment. Monensin increased the relative abundance of Selenomonas sp. ND2010, Prevotella dentalis, Hallella seregens, Parabacteroides distasonis, Propionispira raffinosivorans, and Prevotella brevis, but reduced the relative abundance of Robinsoniella sp. KNHs210, Butyrivibrio proteoclasticus, Clostridium botulinum, Clostridium symbiosum, Burkholderia sp. LMG29324, and Clostridium butyricum. Monensin increased the relative abundance of functional genes involved in amino acid metabolism and lipid metabolism. A total of 245 metabolites were identified. Thirty-one metabolites were found to be differentially expressed. Pathway analysis of the differentially expressed metabolites revealed upregulated metabolic pathways associated with metabolism of linoleic acid and some amino acids. These findings confirm that monensin affects rumen fermentation of forage-fed beef cattle by modulating the rumen microbiome, and by reducing amino acid degradation and biohydrogenation of linoleic acid in the rumen.}, }
@article {pmid30453276, year = {2018}, author = {Zhang, X and Tang, S and Wang, M and Sun, W and Xie, Y and Peng, H and Zhong, A and Liu, H and Zhang, X and Yu, H and Giesy, JP and Hecker, M}, title = {Acid mine drainage affects the diversity and metal resistance gene profile of sediment bacterial community along a river.}, journal = {Chemosphere}, volume = {217}, number = {}, pages = {790-799}, doi = {10.1016/j.chemosphere.2018.10.210}, pmid = {30453276}, issn = {1879-1298}, abstract = {Acid mine drainage (AMD) is one of the most hazardous byproducts of some types of mining. However, research on how AMD affects the bacterial community structure of downstream riverine ecosystems and the distribution of metal resistance genes (MRGs) along pollution gradient is limited. Comprehensive geochemical and high-throughput next-generation sequencing analyses can be integrated to characterize spatial distributions and MRG profiles of sediment bacteria communities along the AMD-contaminated Hengshi River. We found that (1) diversities of bacterial communities significantly and gradually increased along the river with decreasing contamination, suggesting community composition reflected changes in geochemical conditions; (2) relative abundances of phyla Proteobacteria and genus Halomonas and Planococcaceae that function in metal reduction decreased along the AMD gradient; (3) low levels of sediment salinity, sulfate, aquatic lead (Pb), and cadmium (Cd) were negatively correlated with bacterial diversity despite pH was in a positive manner with diversity; and (4) arsenic (As) and copper (Cu) resistance genes corresponded to sediment concentrations of As and Cu, respectively. Altogether, our findings offer initial insight into the distribution patterns of sediment bacterial community structure, diversity and MRGs along a lotic ecosystem contaminated by AMD, and the factors that affect them.}, }
@article {pmid30453138, year = {2018}, author = {Chen, H and Chen, R and Jing, L and Bai, X and Teng, Y}, title = {A metagenomic analysis framework for characterization of antibiotic resistomes in river environment: Application to an urban river in Beijing.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {245}, number = {}, pages = {398-407}, doi = {10.1016/j.envpol.2018.11.024}, pmid = {30453138}, issn = {1873-6424}, abstract = {River is considered generally as a natural reservoir of antibiotic resistance genes (ARGs) in environments. For the prevention and control of ARG risks, it is critical to comprehensively characterize the antibiotic resistomes and their associations in riverine systems. In this study, we proposed a metagenomic framework for identifying antibiotic resistomes in river sediments from multiple categories, including ARG potential, ARG hosts, pathogenicity potential, co-selection potential and gene transfer potential, and applied it to understand the presence, hosts, and co-occurrence of ARGs in the sediments of an urban river in Beijing. Results showed that a total of 203 ARG subtypes belonging to 21 ARG types were detected in the river sediments with an abundance range of 107.7-1004.1×/Gb, dominated by multidrug, macrolide-lincosamide-streptogramin, bacitracin, quinolone and sulfonamide resistance genes. Host-tracking analysis identified Dechloromonas, Pseudoxanthomonas, Arenimonas, Lysobacter and Pseudomonas as the major hosts of ARGs. A number of ARG-carrying contigs (ACCs) were annotated as fragments of pathogenic bacteria and carried multiple multidrug-ARGs. In addition, various biocide/metal resistance genes (B/MRGs) and mobile genetic elements (MGEs), including prophages, plasmids, integrons and transposons, were detected in the river sediments. More importantly, the co-occurrence analysis via ACCs showed a strong association of ARGs with B/MRGs and MGEs, indicating high potential of co-selection and active horizontal transmission for ARGs in the river environment, likely driven by the frequent impact of anthropogenic activities in that area.}, }
@article {pmid30452938, year = {2018}, author = {Bilal, T and Malik, B and Hakeem, KR}, title = {Metagenomic analysis of uncultured microorganisms and their enzymatic attributes.}, journal = {Journal of microbiological methods}, volume = {155}, number = {}, pages = {65-69}, doi = {10.1016/j.mimet.2018.11.014}, pmid = {30452938}, issn = {1872-8359}, abstract = {Although second generation biofuel technology is a sustainable route for bioethanol production it is not currently a robust technology because of certain hindrances viz., unavailability of potential enzyme resources, low efficiency of enzymes and restricted availability of potent enzymes that work under harsh conditions in industrial processes. Therefore, bioprospecting of extremophilic microorganisms using metagenomics is a promising alternative to discover novel microbes and enzymes with efficient tolerance to unfavourable conditions and thus could revolutionize the energy sector. Metagenomics a recent field in &quot;omics&quot; technology enables the genomic study of uncultured microorganisms with the goal of better understanding microbial dynamics. Metagenomics in conjunction with NextGen Sequencing technology facilitates the sequencing of microbial DNA directly from environmental samples and has expanded, and transformed our knowledge of the microbial world. However, filtering the meaningful information from the millions of genomic sequences offers a serious challenge to bioinformaticians. The current review holds the opinion tool 'know- how' to unravel the secrets of nature while expediting the bio-industrial world. We also discuss the novel biocatalytic agents discovered through metagenomics and how bioengineering plays a pivotal role to enhance their efficiency.}, }
@article {pmid30451857, year = {2018}, author = {Schulz, F and Alteio, L and Goudeau, D and Ryan, EM and Yu, FB and Malmstrom, RR and Blanchard, J and Woyke, T}, title = {Hidden diversity of soil giant viruses.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4881}, doi = {10.1038/s41467-018-07335-2}, pmid = {30451857}, issn = {2041-1723}, abstract = {Known giant virus diversity is currently skewed towards viruses isolated from aquatic environments and cultivated in the laboratory. Here, we employ cultivation-independent metagenomics and mini-metagenomics on soils from the Harvard Forest, leading to the discovery of 16 novel giant viruses, chiefly recovered by mini-metagenomics. The candidate viruses greatly expand phylogenetic diversity of known giant viruses and either represented novel lineages or are affiliated with klosneuviruses, Cafeteria roenbergensis virus or tupanviruses. One assembled genome with a size of 2.4 Mb represents the largest currently known viral genome in the Mimiviridae, and others encode up to 80% orphan genes. In addition, we find more than 240 major capsid proteins encoded on unbinned metagenome fragments, further indicating that giant viruses are underexplored in soil ecosystems. The fact that most of these novel viruses evaded detection in bulk metagenomes suggests that mini-metagenomics could be a valuable approach to unearth viral giants.}, }
@article {pmid30451355, year = {2018}, author = {Liu, Y and Brandt, D and Ishino, S and Ishino, Y and Koonin, EV and Kalinowski, J and Krupovic, M and Prangishvili, D}, title = {New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14479}, pmid = {30451355}, issn = {1462-2920}, abstract = {Viruses infecting hyperthermophilic archaea of the phylum Crenarchaeota display enormous morphological and genetic diversity, and are classified into 12 families. Eight of these families include only one or two species, indicating sparse sampling of the crenarchaeal virus diversity. In an attempt to expand the crenarchaeal virome, we explored virus diversity in the acidic, hot spring Umi Jigoku in Beppu, Japan. Environmental samples were used to establish enrichment cultures under conditions favoring virus replication. The host diversity in the enrichment cultures was restricted to members of the order Sulfolobales. Metagenomic sequencing of the viral communities yielded 7 complete or near-complete double-stranded DNA virus genomes. Six of these genomes could be attributed to polyhedral and filamentous viruses that were observed by electron microscopy in the enrichment cultures. Two icosahedral viruses represented species in the family Portogloboviridae. Among the filamentous viruses, two were identified as new species in the families Rudiviridae and Lipothrixviridae, whereas two other formed a group seemingly distinct from the known virus genera. No particle morphotype could be unequivocally assigned to the seventh viral genome, which apparently represents a new virus type. Our results suggest that filamentous viruses are globally distributed and are prevalent virus types in extreme geothermal environments. This article is protected by copyright. All rights reserved.}, }
@article {pmid30450395, year = {2018}, author = {Johny, TK and Saidumohamed, BE and Sasidharan, RS and Bhat, SG}, title = {Metabarcoding data of bacterial diversity of the deep sea shark, Centroscyllium fabricii.}, journal = {Data in brief}, volume = {21}, number = {}, pages = {1029-1032}, doi = {10.1016/j.dib.2018.10.062}, pmid = {30450395}, issn = {2352-3409}, abstract = {This data article describes the bacterial diversity of the deep sea shark, Centroscyllium fabricii. The data was acquired by metabarcoding using 16S rDNA. Centroscyllium fabricii, a deep sea shark found at depths below 275 m was sampled during Sagar Sampada cruise no 305 in the Indian Ocean and metagenomic DNA was isolated from the gut contents using QIAamp DNA stool minikit. V3 region of 16S rDNA region was amplified and the amplicons were sequenced on Illumina MiSeq system using 151 bp × 2 paired end reads. The data of this metagenome is available in the BioSample Submission Portal as Bio-Project PRJNA431407and Sequence Read Archive (SRA) accession number SRR6507004.}, }
@article {pmid30450139, year = {2018}, author = {Najafi, A and Moradinasab, M and Seyedabadi, M and Haghighi, MA and Nabipour, I}, title = {First Molecular Identification of Symbiotic Archaea in a Sponge Collected from the Persian Gulf, Iran.}, journal = {The open microbiology journal}, volume = {12}, number = {}, pages = {323-332}, doi = {10.2174/1874285801812010323}, pmid = {30450139}, issn = {1874-2858}, abstract = {Background: Marine sponges are associated with numerically vast and phylogenetically diverse microbial communities at different geographical locations. However, little is known about the archaeal diversity of sponges in the Persian Gulf. The present study was aimed to identify the symbiotic archaea with a sponge species gathered from the Persian Gulf, Iran.<br><br>Methods: Sponge sample was collected from a depth of 3 m offshore Bushehr, Persian Gulf, Iran. Metagenomic DNA was extracted using a hexadecyl trimethyl ammonium bromide (CTAB) method. The COI mtDNA marker was used for molecular taxonomy identification of sponge sample. Also, symbiotic archaea were identified using the culture-independent analysis of the 16S rRNA gene and PCR- cloning.<br><br>Results: In this study, analysis of multilocus DNA marker and morphological characteristics revealed that the sponge species belonged to Chondrilla australiensis isolate PG_BU4. PCR cloning and sequencing showed that all of the sequences of archaeal 16S rRNA gene libraries clustered into the uncultured archaeal group.<br><br>Conclusion: The present study is the first report of the presence of the genus of Chondrilla in the Persian Gulf. Traditional taxonomy methods, when used along with molecular techniques, could play a significant role in the accurate taxonomy of sponges. Also, the uncultured archaea may promise a potential source for bioactive compounds. Further functional studies are needed to explore the role of the sponge-associated uncultured archaea as a part of the marine symbiosis.}, }
@article {pmid30450127, year = {2018}, author = {Efimova, D and Tyakht, A and Popenko, A and Vasilyev, A and Altukhov, I and Dovidchenko, N and Odintsova, V and Klimenko, N and Loshkarev, R and Pashkova, M and Elizarova, A and Voroshilova, V and Slavskii, S and Pekov, Y and Filippova, E and Shashkova, T and Levin, E and Alexeev, D}, title = {Knomics-Biota - a system for exploratory analysis of human gut microbiota data.}, journal = {BioData mining}, volume = {11}, number = {}, pages = {25}, doi = {10.1186/s13040-018-0187-3}, pmid = {30450127}, issn = {1756-0381}, abstract = {Background: Metagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for investigating experimental data are of high interest to researchers.<br><br>Results: Knomics-Biota is a web-based resource for exploratory analysis of human gut metagenomes. Users can generate and share analytical reports corresponding to common experimental schemes (like case-control study or paired comparison). Interactive visualizations and statistical analysis are provided in association with the external factors and in the context of thousands of publicly available datasets arranged into thematic collections. The web-service is available at https://biota.knomics.ru.<br><br>Conclusions: Knomics-Biota web service is a comprehensive tool for interactive metagenomic data analysis.}, }
@article {pmid30449316, year = {2018}, author = {Guerin, E and Shkoporov, A and Stockdale, SR and Clooney, AG and Ryan, FJ and Sutton, TDS and Draper, LA and Gonzalez-Tortuero, E and Ross, RP and Hill, C}, title = {Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut.}, journal = {Cell host &amp; microbe}, volume = {24}, number = {5}, pages = {653-664.e6}, doi = {10.1016/j.chom.2018.10.002}, pmid = {30449316}, issn = {1934-6069}, abstract = {CrAssphages represent the most abundant virus in the human gut microbiota, but the lack of available genome sequences for comparison has kept them enigmatic. Recently, sequence-based classification of distantly related crAss-like phages from multiple environments was reported, leading to a proposed familial-level taxonomic group. Here, we assembled the metagenomic sequencing reads from 702 human fecal virome/phageome samples and analyzed 99 complete circular crAss-like phage genomes and 150 contigs ≥70 kb. In silico comparative genomics and taxonomic analysis enabled a classification scheme of crAss-like phages from human fecal microbiomes into four candidate subfamilies composed of ten candidate genera. Laboratory analysis was performed on fecal samples from an individual harboring seven distinct crAss-like phages. We achieved crAss-like phage propagation in ex vivo human fecal fermentations and visualized short-tailed podoviruses by electron microscopy. Mass spectrometry of a crAss-like phage capsid protein could be linked to metagenomic sequencing data, confirming crAss-like phage structural annotations.}, }
@article {pmid30449244, year = {2018}, author = {Sterlin, D and Fieschi, C and Malphettes, M and Larsen, M and Gorochov, G and Fadlallah, J}, title = {Immune/microbial interface perturbation in human IgA deficiency.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-5}, doi = {10.1080/19490976.2018.1546520}, pmid = {30449244}, issn = {1949-0984}, abstract = {In a recently published article we report the metagenomic analysis of human gut microbiomes evolved in the absence of immunoglobulin A (IgA). We show that human IgA deficiency is not associated with massive quantitative perturbations of gut microbial ecology. While our study underlines a rather expected pathobiont expansion, we at the same time highlight a less expected depletion in some typically beneficial symbionts. We also show that IgM partially supply IgA deficiency, explaining the relatively mild clinical phenotype associated with the early steps of this condition. Microbiome studies in patients should consider potential issues such as cohort size, human genetic polymorphism and treatments. In this commentary, we discuss how such issues were taken into account in our own study.}, }
@article {pmid30448738, year = {2018}, author = {Rehman, ZU and Ali, M and Iftikhar, H and Leiknes, T}, title = {Genome-resolved metagenomic analysis reveals roles of microbial community members in full-scale seawater reverse osmosis plant.}, journal = {Water research}, volume = {149}, number = {}, pages = {263-271}, doi = {10.1016/j.watres.2018.11.012}, pmid = {30448738}, issn = {1879-2448}, abstract = {Biofouling of Reverse Osmosis (RO) membrane is a significant issue for the water treatment industry. In this study, we apply the metagenomic shot-gun sequencing technology to characterise the composition and functional potential of the microbial community in a full-scale RO plant, at different stages of seawater treatment. We find Proteobacteria, Bacteroidetes and Planctomycetes to be the most abundant bacterial phyla. The genetic potential of the RO membrane microbial community shows the enrichment of genes involved in biofilm formation, representing the selective pressure of the biofilm formation process. We recover 31 metagenome-assembled genomes (MAGs) from intake (raw seawater), fouled RO membranes (leading and middle RO module) and brine reject water. A total of 25 MAGs are recovered from the biofilm samples (leading and middle RO modules), with 9 of them (36%) belonging to Planctomycetes. We investigate all 25 MAGs for genes (pili, flagella, quorum sensing, quorum quenching and nitrate reduction) that play an important role in biofilm formation and sustenance of cells. We show that Planctomycetes contain genes for the formation of flagella and pili, and the reduction of nitrate. Although genes for quorum sensing are not detected, quorum quenching genes are identified in the biofilm MAGs. Our results show that Planctomycetes, along with other microbes, play an important role in the formation and sustenance of biofilms on seawater RO membranes.}, }
@article {pmid30447983, year = {2018}, 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 = {}, number = {}, pages = {}, doi = {10.3168/jds.2018-15062}, pmid = {30447983}, issn = {1525-3198}, 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 {pmid30447151, year = {2018}, author = {Zhang, F and Shan, A and Luan, Y}, title = {A novel method to accurately calculate statistical significance of local similarity analysis for high-throughput time series.}, journal = {Statistical applications in genetics and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1515/sagmb-2018-0019}, pmid = {30447151}, issn = {1544-6115}, abstract = {In recent years, a large number of time series microbial community data has been produced in molecular biological studies, especially in metagenomics. Among the statistical methods for time series, local similarity analysis is used in a wide range of environments to capture potential local and time-shifted associations that cannot be distinguished by traditional correlation analysis. Initially, the permutation test is popularly applied to obtain the statistical significance of local similarity analysis. More recently, a theoretical method has also been developed to achieve this aim. However, all these methods require the assumption that the time series are independent and identically distributed. In this paper, we propose a new approach based on moving block bootstrap to approximate the statistical significance of local similarity scores for dependent time series. Simulations show that our method can control the type I error rate reasonably, while theoretical approximation and the permutation test perform less well. Finally, our method is applied to human and marine microbial community datasets, indicating that it can identify potential relationship among operational taxonomic units (OTUs) and significantly decrease the rate of false positives.}, }
@article {pmid30445993, year = {2018}, author = {Breitwieser, FP and Baker, DN and Salzberg, SL}, title = {KrakenUniq: confident and fast metagenomics classification using unique k-mer counts.}, journal = {Genome biology}, volume = {19}, number = {1}, pages = {198}, doi = {10.1186/s13059-018-1568-0}, pmid = {30445993}, issn = {1474-760X}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R01-HG006677//National Human Genome Research Institute (US)/ ; R01-GM118568//National Institute of General Medical Sciences/ ; R01 GM083873/GM/NIGMS NIH HHS/United States ; W911NF-14-1-0490//Army Research Office (US)/ ; R01 GM118568/GM/NIGMS NIH HHS/United States ; R01-GM083873//National Institute of General Medical Sciences/ ; }, abstract = {False-positive identifications are a significant problem in metagenomics classification. We present KrakenUniq, a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory. KrakenUniq is freely available at https://github.com/fbreitwieser/krakenuniq .}, }
@article {pmid30445181, year = {2018}, author = {Starke, R and Jehmlich, N and Bastida, F}, title = {Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics.}, journal = {Journal of proteomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jprot.2018.11.011}, pmid = {30445181}, issn = {1876-7737}, abstract = {Metaproteomics was established to analyse both the structure and the function of microbial communities and, particularly in soils, their contribution to ecosystem services. In this review, we provide an overview on how the study of the soil metaproteome can provide fundamental information on the role of microbial communities in soil ecosystem services. We further discuss the strengths and weaknesses of soil metaproteomics in comparison to other culture-independent OMIC techniques. We critically review its bottlenecks but also provide strategies to mitigate and possible directions for future research as the direct link of structure and function is advantageous and complementary to metagenomics, metatranscriptomics and metametabolomics.}, }
@article {pmid30444087, year = {2018}, author = {Tokarz-Deptuła, B and Czupryńska, P and Poniewierska-Baran, A and Deptuła, W}, title = {Characteristics of virophages and giant viruses.}, journal = {Acta biochimica Polonica}, volume = {}, number = {}, pages = {}, doi = {10.18388/abp.2018_2631}, pmid = {30444087}, issn = {1734-154X}, abstract = {Five years after being discovered in 2003, some giant viruses were demonstrated to play a role of the hosts for virophages, their parasites, setting out a novel and yet unknown regulatory mechanism of the giant viruses presence in an aqueous. So far, 20 virophages have been registered and 13 of them have been described as a metagenomic material, which indirectly impacts the number of single- and multi-cell organisms, the environment where giant viruses replicate.}, }
@article {pmid30443861, year = {2018}, author = {Zhang, QY and Gui, JF}, title = {Diversity, evolutionary contribution and ecological roles of aquatic viruses.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11427-018-9414-7}, pmid = {30443861}, issn = {1869-1889}, abstract = {Aquatic viruses include infected viruses in aquatic animals, plants and microorganisms, and free-floating viruses (virioplankton) in water environments. In the last three decades, a huge number of aquatic viruses, especially diverse free-floating viruses, including cyanophages, phycoviruses, archaea viruses, giant viruses, and even virophages, have been identified by virological experiments and metagenomic analyses. Based on a comprehensive introduction of aquatic virus classification and their morphological and genetic diversity, here, we summarize and outline main virus species, their evolutionary contribution to aquatic communities through horizontal gene transfer, and their ecological roles for cyanobacterial bloom termination and global biogeochemical cycling in freshwater and marine ecosystems. Thereby, some novel insights of aquatic viruses and virus-host interactions, especially their evolutionary contribution and ecological rolesin diverse aquatic communities and ecosystems, are highlighted in this review.}, }
@article {pmid30443602, year = {2018}, author = {Hillmann, B and Al-Ghalith, GA and Shields-Cutler, RR and Zhu, Q and Gohl, DM and Beckman, KB and Knight, R and Knights, D}, title = {Evaluating the Information Content of Shallow Shotgun Metagenomics.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00069-18}, pmid = {30443602}, issn = {2379-5077}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 AI121383/AI/NIAID NIH HHS/United States ; }, abstract = {Although microbial communities are associated with human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes in such communities. While deep whole-metagenome shotgun (WMS) sequencing provides high taxonomic and functional resolution, it is often prohibitively expensive for large-scale studies. The prevailing alternative, 16S rRNA gene amplicon (16S) sequencing, often does not resolve taxonomy past the genus level and provides only moderately accurate predictions of the functional profile; thus, there is currently no widely accepted approach to affordable, high-resolution, taxonomic, and functional microbiome analysis. To address this technology gap, we evaluated the information content of shallow shotgun sequencing with as low as 0.5 million sequences per sample as an alternative to 16S sequencing for large human microbiome studies. We describe a library preparation protocol enabling shallow shotgun sequencing at approximately the same per-sample cost as 16S sequencing. We analyzed multiple real and simulated biological data sets, including two novel human stool samples with ultradeep sequencing of 2.5 billion sequences per sample, and found that shallow shotgun sequencing recovers more-accurate species-level taxonomic and functional profiles of the human microbiome than 16S sequencing. We discuss the inherent limitations of shallow shotgun sequencing and note that 16S sequencing remains a valuable and important method for taxonomic profiling of novel environments. Although deep WMS sequencing remains the gold standard for high-resolution microbiome analysis, we recommend that researchers consider shallow shotgun sequencing as a useful alternative to 16S sequencing for large-scale human microbiome research studies where WMS sequencing may be cost-prohibitive. IMPORTANCE A common refrain in recent microbiome-related academic meetings is that the field needs to move away from broad taxonomic surveys using 16S sequencing and toward more powerful longitudinal studies using shotgun sequencing. However, performing deep shotgun sequencing in large longitudinal studies remains prohibitively expensive for all but the most well-funded research labs and consortia, which leads many researchers to choose 16S sequencing for large studies, followed by deep shotgun sequencing on a subset of targeted samples. Here, we show that shallow- or moderate-depth shotgun sequencing may be used by researchers to obtain species-level taxonomic and functional data at approximately the same cost as amplicon sequencing. While shallow shotgun sequencing is not intended to replace deep shotgun sequencing for strain-level characterization, we recommend that microbiome scientists consider using shallow shotgun sequencing instead of 16S sequencing for large-scale human microbiome studies.}, }
@article {pmid30442907, year = {2018}, author = {Zhou, W and Chow, KH and Fleming, E and Oh, J}, title = {Selective colonization ability of human fecal microbes in different mouse gut environments.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0312-9}, pmid = {30442907}, issn = {1751-7370}, support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; 1 DP2 GM126893-01//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; ACS-RSG-16-255-01-MPC//American Cancer Society (American Cancer Society, Inc.)/ ; }, abstract = {Mammalian hosts constantly interact with diverse exogenous microbes, but only a subset of the microbes manage to colonize due to selective colonization resistance exerted by host genetic factors as well as the native microbiota of the host. An important question in microbial ecology and medical science is if such colonization resistance can discriminate closely related microbial species, or even closely related strains of the same species. Using human-mouse fecal microbiota transplantation and metagenomic shotgun sequencing, we reconstructed colonization patterns of human fecal microbes in mice with different genotypes (C57BL6/J vs. NSG) and with or without an intact gut microbiota. We found that mouse genotypes and the native mouse gut microbiota both exerted different selective pressures on exogenous colonizers: human fecal Bacteroides successfully established in the mice gut, however, different species of Bacteroides selectively enriched under different gut conditions, potentially due to a multitude of functional differences, ranging from versatility in nutrient acquisition to stress responses. Additionally, different clades of Bacteroides cellulosilyticus strains were selectively enriched in different gut conditions, suggesting that the fitness of conspecific microbial strains in a novel host environment could differ.}, }
@article {pmid30441786, year = {2018}, author = {Bal, A and Sarkozy, C and Josset, L and Cheynet, V and Oriol, G and Becker, J and Vilchez, G and Sesques, P and Mallet, F and Pachot, A and Morfin, F and Lina, B and Salles, G and Reynier, F and Trouillet-Assant, S and Brengel-Pesce, K}, title = {Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management.}, journal = {Viruses}, volume = {10}, number = {11}, pages = {}, doi = {10.3390/v10110633}, pmid = {30441786}, issn = {1999-4915}, abstract = {Over recent years, there has been increasing interest in the use of the anelloviruses, the major component of the human virome, for the prediction of post-transplant complications such as severe infections. Due to an important diversity, the comprehensive characterization of this viral family over time has been poorly studied. To overcome this challenge, we used a metagenomic next-generation sequencing (mNGS) approach with the aim of determining the individual anellovirus profile of autologous stem cell transplant (ASCT) patients. We conducted a prospective pilot study on a homogeneous patient cohort regarding the chemotherapy regimens that included 10 ASCT recipients. A validated viral mNGS workflow was used on 108 plasma samples collected at 11 time points from diagnosis to 90 days post-transplantation. A complex interindividual variability in terms of abundance and composition was noticed. In particular, a strong sex effect was found and confirmed using quantitative PCR targeting torque teno virus, the most abundant anellovirus. Interestingly, an important turnover in the anellovirus composition was observed during the course of the disease revealing a strong intra-individual variability. Although more studies are needed to better understand anellovirus dynamics, these findings are of prime importance for their future use as biomarkers of immune competence.}, }
@article {pmid30440884, year = {2018}, author = {Gao, Z and Chen, KY and Mueller, O and Zhang, H and Rakhilin, N and Chen, J and Shen, X}, title = {Microbiota of Inflammatory Bowel Disease Models.}, journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, volume = {2018}, number = {}, pages = {2374-2377}, doi = {10.1109/EMBC.2018.8512848}, pmid = {30440884}, issn = {1557-170X}, abstract = {Gut microbiome plays an important role in inflammatory bowel disease (IBD), a group of intestinal chronic inflammation conditions that affect a large population. The animal models of IBD have long been established on basis of pathological features, but their ability to recapitulate patient gut microbiota is unknown. We investigated and compared the composition and biodiversity of bacterial population in the fecal samples from rat models of the two IBD subtypes, and compared them with patient samples. Our analyses revealed that inflammation reduces overall microbiome diversity and increased variation between individuals. We identified specific microbial signatures associated with the two IBD subtypes that were consistent between the animal models and human IBD patients, suggesting that the animal models can partially recapitulate the microbiota in human diseases. Furthermore, metagenome prediction analysis suggested microbial functions that were likely altered by host-microbiota interactions in IBD models.}, }
@article {pmid30440633, year = {2018}, author = {Ariza-Jimenez, L and Quintero, OL and Pinel, N}, title = {Unsupervised fuzzy binning of metagenomic sequence fragments on three-dimensional Barnes-Hut t-Stochastic Neighbor Embeddings.}, journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference}, volume = {2018}, number = {}, pages = {1315-1318}, doi = {10.1109/EMBC.2018.8512529}, pmid = {30440633}, issn = {1557-170X}, abstract = {Shotgun metagenomic studies attempt to reconstruct population genome sequences from complex microbial communities. In some traditional genome demarcation approaches, high-dimensional sequence data are embedded into two-dimensional spaces and subsequently binned into candidate genomic populations. One such approach uses a combination of the Barnes-Hut approximation and the $t -$Stochastic Neighbor Embedding (BH-SNE) algorithm for dimensionality reduction of DNA sequence data pentamer profiles; and demarcation of groups based on Gaussian mixture models within humanimposed boundaries. We found that genome demarcation from three-dimensional BH-SNE embeddings consistently results in more accurate binnings than 2-D embeddings. We further addressed the lack of a priori population number information by developing an unsupervised binning approach based on the Subtractive and Fuzzy c-means (FCM) clustering algorithms combined with internal clustering validity indices. Lastly, we addressed the subject of shared membership of individual data objects in a mixed community by assigning a degree of membership to individual objects using the FCM algorithm, and discriminated between confidently binned and uncertain sequence data objects from the community for subsequent biological interpretation. The binning of metagenome sequence fragments according to thresholds in the degree of membership opens the door for the identification of horizontally transferred elements and other genomic regions of uncertain assignment in which biologically meaningful information resides. The reported approach improves the unsupervised genome demarcation of populations within complex communities, increases the confidence in the coherence of the binned elements, and enables the identification of evolutionary processes ignored in hard-binning approaches in shotgun metagenomic studies.}, }
@article {pmid30440093, year = {2018}, author = {Park, CH and Lee, AR and Lee, YR and Eun, CS and Lee, SK and Han, DS}, title = {Evaluation of gastric microbiome and metagenomic function in patients with intestinal metaplasia using 16S rRNA gene sequencing.}, journal = {Helicobacter}, volume = {}, number = {}, pages = {e12547}, doi = {10.1111/hel.12547}, pmid = {30440093}, issn = {1523-5378}, support = {//National Research Foundation of Korea (NRF)/ ; NRF-2017R1C1B5015928//Korea government (MSIP; Ministry of Science, ICT &amp; Future Planning)/ ; }, abstract = {BACKGROUND: Despite recent advances in studies on the gastric microbiome, the role of the non-Helicobacter pylori gastric microbiome in gastric carcinogenesis remains unclear. We evaluated the characteristics of the gastric microbiome and metagenomic functions in patients with IM.<br><br>METHODS: Participants were classified into six groups according to disease status (chronic superficial gastritis [CSG], intestinal metaplasia [IM], and cancer) and H. pylori- infection status (H. pylori-positive and H. pylori-negative). The gastric microbiome was analyzed in mucosal tissues at the gastric antrum by 16S rRNA gene sequencing. Moreover, we assessed the metagenome including the type IV secretion system (T4SS) gene, as T4SS proteins are essential for transferring CagA from H. pylori- into the human gastric epithelium.<br><br>RESULTS: Among the 138 included patients, 48, 9, 23, 14, 12, and 32 were classified into the H. pylori-negative CSG, H. pylori-negative IM, H. pylori-negative cancer, H. pylori-positive CSG, H. pylori-positive IM, and H. pylori-positive cancer groups, respectively. Cyanobacteria were predominant in the H. pylori-negative CSG group compared to in the H. pylori-negative IM and H. pylori-negative cancer groups (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 14.0% vs 4.2% vs 0.04%, P < 0.001). In contrast, Rhizobiales were commonly observed in the H. pylori-negative IM group (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 1.9% vs 15.4% vs 2.8%, P < 0.001). The relative abundance of Rhizobiales increased as H. pylori-infected stomachs progressed from gastritis to IM. In the H. pylori-negative IM group, genes encoding T4SS were prevalent among the metagenome. Additionally, after H. pylori- eradication therapy, the gastric microbiome was similar to the microbiome observed after spontaneous clearance of H. pylori-.<br><br>CONCLUSIONS: The relative abundance of Rhizobiales was higher in patients with H. pylori-negative IM than in those with H. pylori-negative CSG or cancer. Additionally, T4SS genes were highly observed in the metagenome of patients with IM. Highly abundant T4SS proteins in these patients may promote gastric carcinogenesis.}, }
@article {pmid30430271, year = {2018}, author = {Zhang, B and Xu, X and Zhu, L}, title = {Activated sludge bacterial communities of typical wastewater treatment plants: distinct genera identification and metabolic potential differential analysis.}, journal = {AMB Express}, volume = {8}, number = {1}, pages = {184}, doi = {10.1186/s13568-018-0714-0}, pmid = {30430271}, issn = {2191-0855}, support = {51478416//National Natural Science Foundation of China/ ; }, abstract = {To investigate the differences in activated sludge microbial communities of different wastewater treatment plants (WWTPs) and understand their metabolic potentials, we sampled sludge from every biological treatment unit of 5 full-scale waste water treatment systems in 3 typical Chinese municipal WWTPs. The microbial communities and overall metabolic patterns were not only affected by influent characteristics but also varied between different biological treatment units. Distinct genera in different wastewater treatment systems were identified. The important microorganisms in domestic sewage treatment systems were unclassified SHA-20, Caldilinea, Dechloromonas, and unclassified genera from Rhodospirilaceae and Caldilineaceae. The important microorganisms in dyeing wastewater treatment systems were Nitrospira, Sphingobacteriales, Thiobacillus, Sinobacteraceae and Comamonadaceae. Compared with the obvious differences in microbial community composition, the metabolic potential showed no significant differences.}, }
@article {pmid30429253, year = {2018}, author = {Yan, Q and Wi, YM and Thoendel, MJ and Raval, YS and Greenwood-Quaintance, KE and Abdel, MP and Jeraldo, PR and Chia, N and Patel, R}, title = {Evaluation of the CosmosID Bioinformatics Platform for Prosthetic Joint-Associated Sonicate Fluid Shotgun Metagenomic Data Analysis.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JCM.01182-18}, pmid = {30429253}, issn = {1098-660X}, abstract = {We previously demonstrated that shotgun metagenomic sequencing can detect bacteria in sonicate fluid, providing a diagnosis of prosthetic joint infection (PJI). A limitation of the approach we used is that data analysis was time consuming and specialized bioinformatics expertise was required, both barriers to routine clinical use. Fortunately, automated commercial analytic platforms that can &quot;interpret&quot; shotgun metagenomic data are emerging. In this study, we evaluated the CosmosID bioinformatics platform using shotgun metagenomic sequencing data derived from 408 sonicate fluids from our prior study, with the goal of evaluating the platform vis-à-vis bacterial detection and antibiotic resistance gene detection for predicting staphylococcal antibacterial susceptibility. Samples were divided into a derivation set and a validation set, each consisting of 204 samples; results from the derivation set were used to establish cutoffs which were then tested in the validation set for identifying pathogens and predicting staphylococcal antibacterial resistance. Metagenomic analysis detected bacteria in 94.8% (109/115) of sonicate culture-positive PJIs and 37.8% (37/98) of sonicate culture-negative PJIs. Metagenomic analysis showed sensitivities ranging from 65.7 to 85.0% for predicting staphylococcal antibacterial resistance. In conclusion, the CosmosID platform has the potential to provide fast, reliable bacterial detection and identification from metagenomic shotgun sequencing data derived from sonicate fluid for diagnosis of PJI. Strategies for metagenomic detection of antibiotic resistance genes for predicting staphylococcal antibacterial resistance need further development.}, }
@article {pmid30427852, year = {2018}, author = {Brito, TL and Campos, AB and Bastiaan von Meijenfeldt, FA and Daniel, JP and Ribeiro, GB and Silva, GGZ and Wilke, DV and de Moraes, DT and Dutilh, BE and Meirelles, PM and Trindade-Silva, AE}, title = {The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0200437}, doi = {10.1371/journal.pone.0200437}, pmid = {30427852}, issn = {1932-6203}, abstract = {Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae &quot;clade I&quot; strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills' metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.}, }
@article {pmid30427574, year = {2018}, author = {Barnes, RC and Kim, H and Fang, C and Bennett, W and Nemec, M and Sirven, MA and Suchodolski, JS and Deutz, N and Britton, RA and Mertens-Talcott, SU and Talcott, ST}, title = {Body Mass Index as a Determinant of Systemic Exposure to Gallotannin Metabolites during 6-Week Consumption of Mango (Mangifera indica L.) and Modulation of Intestinal Microbiota in Lean and Obese Individuals.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e1800512}, doi = {10.1002/mnfr.201800512}, pmid = {30427574}, issn = {1613-4133}, support = {//National Mango Board/ ; }, abstract = {SCOPE: This human clinical pilot trial investigated pharmacokinetics of gallotannin-metabolites and modulation of intestinal microbiota in healthy lean and obese individuals after 6 weeks of daily mango consumption.<br><br>METHODS AND RESULTS: Participants are divided into three groups: Lean Mango (LM: n = 12; BMI = 22.9 kg m-2), Obese Mango (OM: n = 9; BMI = 34.6 kg m-2), and Lean Control (LC: n = 11; BMI = 22.1 kg m-2). LM and OM consumed 400 g of mango per day for 6 weeks. LC consumed mango only on Days 0 and 42. After 6 weeks, LM experienced increased systemic exposure (AUC0-8h) to gallotannin-metabolites, 1.4-fold (p = 0.043). The greatest increase is 4-O-methyl-gallic acid, 3.3-fold (p = 0.0026). Cumulative urinary excretion of gallotannin-metabolites significantly increased in LM and OM, but not LC. For OM, qPCR data show increased levels of tannase-producing Lactococcus lactis and decreased levels of Clostridium leptum and Bacteroides thetaiotaomicron, bacteria associated with obesity. LM experienced an increased trend of fecal levels of butyric (1.3-fold; p = 0.09) and valeric acids (1.5-fold; p = 0.056). Plasma endotoxins showed a decreased trend in LM and OM.<br><br>CONCLUSION: Continuous mango intake significantly increased systemic exposure to gallotannin- metabolites and induced an increased trend for fecal short-chain fatty acids in lean but not obese individuals. This pharmacokinetic discrepancy may result in BMI-associated reduced gallotannin-derived health benefits.}, }
@article {pmid30425894, year = {2018}, author = {Ornelas-García, P and Pajares, S and Sosa-Jiménez, VM and Rétaux, S and Miranda-Gamboa, RA}, title = {Microbiome differences between river-dwelling and cave-adapted populations of the fish Astyanax mexicanus (De Filippi, 1853).}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5906}, doi = {10.7717/peerj.5906}, pmid = {30425894}, issn = {2167-8359}, abstract = {Symbiotic relationships between host and microbiome can play a major role in local adaptation. Previous studies with freshwater organisms have shown that microbiome performs numerous important biochemical functions for the host, playing a key role in metabolism, physiology or health. Experimental studies in fish groups have found an effect of enzymatic activity of gut microbiota on a variety of metabolic processes. The goal of this study was to compare stomach microbiome from cave and surface Astyanax mexicanus, in order to evaluate the potential response of microbiota to contrasting environmental conditions and physiological adaptations of the host. Stomach microbiota was obtained from three different populations: Pachón cave, and two surface rivers (Rascón and Micos rivers). The stomach microbiome was analyzed using the Ion 16S Metagenomic kit considering seven variable regions: V2, V3, V4, V6-7, V8 and V9. A high diversity was observed across samples, including 16 phyla, 120 families and 178 genera. Gammaproteobacteria, Firmicutes, Bacteroidetes and Betaproteobacteria were the most abundant phyla across the samples. Although the relative abundance of the core OTUs at genus level were highly contrasting among populations, we did not recover differences in stomach microbiome between contrasting habitats (cave vs. surface rivers). Rather, we observed a consistent association between β-diversity and dissolved oxygen concentration in water. Therefore, and unexpectedly, the microbiota of A. mexicanus is not linked with the contrasting conditions of the habitat considered here but is related to water parameters.}, }
@article {pmid30425704, year = {2018}, author = {Jäger, T and Hembach, N and Elpers, C and Wieland, A and Alexander, J and Hiller, C and Krauter, G and Schwartz, T}, title = {Reduction of Antibiotic Resistant Bacteria During Conventional and Advanced Wastewater Treatment, and the Disseminated Loads Released to the Environment.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2599}, doi = {10.3389/fmicb.2018.02599}, pmid = {30425704}, issn = {1664-302X}, abstract = {The occurrence of new chemical and microbiological contaminants in the aquatic environment has become an issue of increasing environmental concern. Thus, wastewater treatment plants (WWTPs) play an important part in the distribution of so-called new emerging pathogens and antibiotic resistances. Therefore, the daily loads released by the WWTP were calculated including a model system for the distribution of these loads within the receiving water body. UV-, as well as ozone-treatment in separate or in combination for wastewater treatment were under investigation aiming at the reduction of these loads. Here, the impact of these treatments on the DNA integrity via antibody staining and PCR efficiencies experiments were included. All three facultative pathogenic bacteria [enterococci (23S rRNA), Pseudomonas aeruginosa (ecfX), and Escherichia coli (yccT)] and seven clinically relevant antibiotic resistance genes (ARGs) (mecA (methicillin resistance gene), ctx-M32 (β- lactame resistance gene), ermB (erythromycine resistance gene), blaTEM (β- lactame resistance gene), sul1 (sulfonamide resistance gene), vanA (vancomycin resistance gene), and intI1 (Integrase1 gene) associated with mobile genetic elements were detected in wastewaters. Different reduction efficiencies were analyzed during advanced wastewater treatments. ARGs were still found to be present in the effluents under the parameters of 1.0 g ozone per g dissolved organic carbon (DOC) and 400 J/m2, like ctx-M32, ermB, blaTEM, sul1, and intI1. Especially UV radiation induced thymidine dimerization which was analyzed via antibody mediated detection in the metagenome of the natural wastewater population. These specific DNA alterations were not observed during ozone treatment and combinations of UV/ozone treatment. The dimerization or potential other DNA alterations during UV treatment might be responsible for a decreased PCR efficiency of the 16S rRNA amplicons (176, 490, and 880 bp fragments) from natural metagenomes compared to the untreated sample. This impact on PCR efficiencies was also observed for the combination of ozone and UV treatment.}, }
@article {pmid30425690, year = {2018}, author = {Fang, X and Monk, JM and Nurk, S and Akseshina, M and Zhu, Q and Gemmell, C and Gianetto-Hill, C and Leung, N and Szubin, R and Sanders, J and Beck, PL and Li, W and Sandborn, WJ and Gray-Owen, SD and Knight, R and Allen-Vercoe, E and Palsson, BO and Smarr, L}, title = {Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2559}, doi = {10.3389/fmicb.2018.02559}, pmid = {30425690}, issn = {1664-302X}, support = {U01 AI124316/AI/NIAID NIH HHS/United States ; }, abstract = {Dysbiosis of the gut microbiome, including elevated abundance of putative leading bacterial triggers such as E. coli in inflammatory bowel disease (IBD) patients, is of great interest. To date, most E. coli studies in IBD patients are focused on clinical isolates, overlooking their relative abundances and turnover over time. Metagenomics-based studies, on the other hand, are less focused on strain-level investigations. Here, using recently developed bioinformatic tools, we analyzed the abundance and properties of specific E. coli strains in a Crohns disease (CD) patient longitudinally, while also considering the composition of the entire community over time. In this report, we conducted a pilot study on metagenomic-based, strain-level analysis of a time-series of E. coli strains in a left-sided CD patient, who exhibited sustained levels of E. coli greater than 100X healthy controls. We: (1) mapped out the composition of the gut microbiome over time, particularly the presence of E. coli strains, and found that the abundance and dominance of specific E. coli strains in the community varied over time; (2) performed strain-level de novo assemblies of seven dominant E. coli strains, and illustrated disparity between these strains in both phylogenetic origin and genomic content; (3) observed that strain ST1 (recovered during peak inflammation) is highly similar to known pathogenic AIEC strains NC101 and LF82 in both virulence factors and metabolic functions, while other strains (ST2-ST7) that were collected during more stable states displayed diverse characteristics; (4) isolated, sequenced, experimentally characterized ST1, and confirmed the accuracy of the de novo assembly; and (5) assessed growth capability of ST1 with a newly reconstructed genome-scale metabolic model of the strain, and showed its potential to use substrates found abundantly in the human gut to outcompete other microbes. In conclusion, inflammation status (assessed by the blood C-reactive protein and stool calprotectin) is likely correlated with the abundance of a subgroup of E. coli strains with specific traits. Therefore, strain-level time-series analysis of dominant E. coli strains in a CD patient is highly informative, and motivates a study of a larger cohort of IBD patients.}, }
@article {pmid30425689, year = {2018}, author = {Spini, G and Spina, F and Poli, A and Blieux, AL and Regnier, T and Gramellini, C and Varese, GC and Puglisi, E}, title = {Molecular and Microbiological Insights on the Enrichment Procedures for the Isolation of Petroleum Degrading Bacteria and Fungi.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2543}, doi = {10.3389/fmicb.2018.02543}, pmid = {30425689}, issn = {1664-302X}, abstract = {Autochthonous bioaugmentation, by exploiting the indigenous microorganisms of the contaminated environment to be treated, can represent a successful bioremediation strategy. In this perspective, we have assessed by molecular methods the evolution of bacterial and fungal communities during the selective enrichment on different pollutants of a soil strongly polluted by mixtures of aliphatic and polycyclic hydrocarbons. Three consecutive enrichments were carried out on soil samples from different soil depths (0-1, 1-2, 2-3 m), and analyzed at each step by means of high-throughput sequencing of bacterial and fungal amplicons biomarkers. At the end of the enrichments, bacterial and fungal contaminants degrading strains were isolated and identified in order to (i) compare the composition of enriched communities by culture-dependent and culture-independent molecular methods and to (ii) obtain a collection of hydrocarbon degrading microorganisms potentially exploitable for soil bioremediation. Molecular results highlighted that for both bacteria and fungi the pollutant had a partial shaping effect on the enriched communities, with paraffin creating distinct enriched bacterial community from oil, and polycyclic aromatic hydrocarbons generally overlapping; interestingly neither the soil depth or the enrichment step had significant effects on the composition of the final enriched communities. Molecular analyses well-agreed with culture-dependent analyses in terms of most abundant microbial genera. A total of 95 bacterial and 94 fungal strains were isolated after selective enrichment procedure on different pollutants. On the whole, isolated bacteria where manly ascribed to Pseudomonas genus followed by Sphingobacterium, Bacillus, Stenothrophomonas, Achromobacter, and Serratia. As for fungi, Fusarium was the most abundant genus followed by Trichoderma and Aspergillus. The species comprising more isolates, such as Pseudomonas putida, Achromobacter xylosoxidans and Ochromobactrum anthropi for bacteria, Fusarium oxysporum and Fusarium solani for fungi, were also the dominant OTUs assessed in Illumina.}, }
@article {pmid30424933, year = {2018}, author = {Castillo-Álvarez, F and Marzo-Sola, ME}, title = {Disease of the holobiont, the example of multiple sclerosis.}, journal = {Medicina clinica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.medcli.2018.08.019}, pmid = {30424933}, issn = {1578-8989}, abstract = {In recent years there has been a revolution regarding the role of the microbiota in different diseases, most of them within the spectrum of inflammatory and autoimmune diseases, associated with the development of metagenomics and the concept of holobiont, a large organism together with its microbiota. Specifically, in Multiple Sclerosis, multiple evidence points to the role of the microbiota in experimental autoimmune encephalomyelitis, animal model of the disease, and several articles have been published in recent years about differences in intestinal microbiota among patients with multiple sclerosis and control subjects. We review in this article the concept of holobiont and the gut microbiota functions, as well as the evidence accumulated about the role of the microbiota in experimental autoimmune encephalomyelitis and multiple sclerosis. Nowadays, there is a lot of evidence showing the role of the microbiota in the genesis, prevention and treatment of experimental autoimmune encephalomyelitis based mainly on three immunological pillars, the Th1-Th17 / Th2 balance, the Treg cells and the humoral immunity. It is also well documented that there are differences in the microbiota of patients with MS that are associated with a different expression of genes related to inflammation.}, }
@article {pmid30424821, year = {2018}, author = {Singh, NK and Wood, JM and Karouia, F and Venkateswaran, K}, title = {Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {204}, doi = {10.1186/s40168-018-0585-2}, pmid = {30424821}, issn = {2049-2618}, support = {19-12829-26//2012 Space Biology NNH12ZTT001N/ ; }, abstract = {BACKGROUND: The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms.<br><br>RESULTS: The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii, and Aspergillus lentulus. Even though Rhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3. The AMR signatures associated with β-lactam, cationic antimicrobial peptide, and vancomycin were detected. Prominent virulence factors were cobalt-zinc-cadmium resistance and multidrug-resistance efflux pumps.<br><br>CONCLUSIONS: There was an increase in AMR and virulence gene factors detected over the period sampled, and metagenome sequences of human pathogens persisted over time. Comparative analysis of the microbial compositions of ISS with Earth analogs revealed that the ISS environmental surfaces were different in microbial composition. Metagenomics coupled with PMA treatment would help future space missions to estimate problematic risk group microbial pathogens. Cataloging AMR/virulence characteristics, succession, accumulation, and persistence of microorganisms would facilitate the development of suitable countermeasures to reduce their presence in the closed built environment.}, }
@article {pmid30423107, year = {2018}, author = {García-Jiménez, B and de la Rosa, T and Wilkinson, MD}, title = {MDPbiome: microbiome engineering through prescriptive perturbations.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {17}, pages = {i838-i847}, doi = {10.1093/bioinformatics/bty562}, pmid = {30423107}, issn = {1367-4811}, abstract = {Motivation: Recent microbiome dynamics studies highlight the current inability to predict the effects of external perturbations on complex microbial populations. To do so would be particularly advantageous in fields such as medicine, bioremediation or industrial scenarios.<br><br>Results: MDPbiome statistically models longitudinal metagenomics samples undergoing perturbations as a Markov Decision Process (MDP). Given a starting microbial composition, our MDPbiome system suggests the sequence of external perturbation(s) that will engineer that microbiome to a goal state, for example, a healthier or more performant composition. It also estimates intermediate microbiome states along the path, thus making it possible to avoid particularly undesirable/unhealthy states. We demonstrate MDPbiome performance over three real and distinct datasets, proving its flexibility, and the reliability and universality of its output 'optimal perturbation policy'. For example, an MDP created using a vaginal microbiome time series, with a goal of recovering from bacterial vaginosis, suggested avoidance of perturbations such as lubricants or sex toys; while another MDP provided a quantitative explanation for why salmonella vaccine accelerates gut microbiome maturation in chicks. This novel analytical approach has clear applications in medicine, where it could suggest low-impact clinical interventions that will lead to achievement or maintenance of a healthy microbial population, or alternately, the sequence of interventions necessary to avoid strongly negative microbiome states.<br><br>Code (https://github.com/beatrizgj/MDPbiome) and result files (https://tomdelarosa.shinyapps.io/MDPbiome/) are available online.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30423080, year = {2018}, author = {Dadi, TH and Siragusa, E and Piro, VC and Andrusch, A and Seiler, E and Renard, BY and Reinert, K}, title = {DREAM-Yara: an exact read mapper for very large databases with short update time.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {17}, pages = {i766-i772}, doi = {10.1093/bioinformatics/bty567}, pmid = {30423080}, issn = {1367-4811}, abstract = {Motivation: Mapping-based approaches have become limited in their application to very large sets of references since computing an FM-index for very large databases (e.g. >10 GB) has become a bottleneck. This affects many analyses that need such index as an essential step for approximate matching of the NGS reads to reference databases. For instance, in typical metagenomics analysis, the size of the reference sequences has become prohibitive to compute a single full-text index on standard machines. Even on large memory machines, computing such index takes about 1 day of computing time. As a result, updates of indices are rarely performed. Hence, it is desirable to create an alternative way of indexing while preserving fast search times.<br><br>Results: To solve the index construction and update problem we propose the DREAM (Dynamic seaRchablE pArallel coMpressed index) framework and provide an implementation. The main contributions are the introduction of an approximate search distributor via a novel use of Bloom filters. We combine several Bloom filters to form an interleaved Bloom filter and use this new data structure to quickly exclude reads for parts of the databases where they cannot match. This allows us to keep the databases in several indices which can be easily rebuilt if parts are updated while maintaining a fast search time. The second main contribution is an implementation of DREAM-Yara a distributed version of a fully sensitive read mapper under the DREAM framework.<br><br>https://gitlab.com/pirovc/dream_yara/.}, }
@article {pmid30423069, year = {2018}, author = {Andrusch, A and Dabrowski, PW and Klenner, J and Tausch, SH and Kohl, C and Osman, AA and Renard, BY and Nitsche, A}, title = {PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {17}, pages = {i715-i721}, doi = {10.1093/bioinformatics/bty595}, pmid = {30423069}, issn = {1367-4811}, abstract = {Motivation: Next generation sequencing (NGS) has provided researchers with a powerful tool to characterize metagenomic and clinical samples in research and diagnostic settings. NGS allows an open view into samples useful for pathogen detection in an unbiased fashion and without prior hypothesis about possible causative agents. However, NGS datasets for pathogen detection come with different obstacles, such as a very unfavorable ratio of pathogen to host reads. Alongside often appearing false positives and irrelevant organisms, such as contaminants, tools are often challenged by samples with low pathogen loads and might not report organisms present below a certain threshold. Furthermore, some metagenomic profiling tools are only focused on one particular set of pathogens, for example bacteria.<br><br>Results: We present PAIPline, a bioinformatics pipeline specifically designed to address problems associated with detecting pathogens in diagnostic samples. PAIPline particularly focuses on userfriendliness and encapsulates all necessary steps from preprocessing to resolution of ambiguous reads and filtering up to visualization in a single tool. In contrast to existing tools, PAIPline is more specific while maintaining sensitivity. This is shown in a comparative evaluation where PAIPline was benchmarked along other well-known metagenomic profiling tools on previously published well-characterized datasets. Additionally, as part of an international cooperation project, PAIPline was applied to an outbreak sample of hemorrhagic fevers of then unknown etiology. The presented results show that PAIPline can serve as a robust, reliable, user-friendly, adaptable and generalizable stand-alone software for diagnostics from NGS samples and as a stepping stone for further downstream analyses.<br><br>PAIPline is freely available under https://gitlab.com/rki_bioinformatics/paipline.}, }
@article {pmid30423048, year = {2018}, author = {Miao, Q and Ma, Y and Wang, Q and Pan, J and Zhang, Y and Jin, W and Yao, Y and Su, Y and Huang, Y and Wang, M and Li, B and Li, H and Zhou, C and Li, C and Ye, M and Xu, X and Li, Y and Hu, B}, title = {Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {67}, number = {suppl_2}, pages = {S231-S240}, doi = {10.1093/cid/ciy693}, pmid = {30423048}, issn = {1537-6591}, abstract = {Background: Metagenomic next-generation sequencing (mNGS) was suggested to potentially replace traditional microbiological methodology because of its comprehensiveness. However, clinical experience with application of the test is relatively limited.<br><br>Methods: From April 2017 to December 2017, 511 specimens were collected, and their retrospective diagnoses were classified into infectious disease (347 [67.9%]), noninfectious disease (119 [23.3%]), and unknown cases (45 [8.8%]). The diagnostic performance of pathogens was compared between mNGS and culture. The effect of antibiotic exposure on detection rate was also assessed.<br><br>Results: The sensitivity and specificity of mNGS for diagnosing infectious disease were 50.7% and 85.7%, respectively, and these values outperformed those of culture, especially for Mycobacterium tuberculosis (odds ratio [OR], 4 [95% confidence interval {CI}, 1.7-10.8]; P < .01), viruses (mNGS only; P < .01), anaerobes (OR, ∞ [95% CI, 1.71-∞]; P < .01) and fungi (OR, 4.0 [95% CI, 1.6-10.3]; P < .01). Importantly, for mNGS-positive cases where the conventional method was inconclusive, 43 (61%) cases led to diagnosis modification, and 41 (58%) cases were not covered by empirical antibiotics. For cases where viruses were identified, broad-spectrum antibiotics were commonly administered (14/27), and 10 of 27 of these cases were suspected to be inappropriate. Interestingly, the sensitivity of mNGS was superior to that of culture (52.5% vs 34.2%; P < .01) in cases with, but not without, antibiotic exposure.<br><br>Conclusions: mNGS could yield a higher sensitivity for pathogen identification and is less affected by prior antibiotic exposure, thereby emerging as a promising technology for detecting infectious diseases.}, }
@article {pmid30422704, year = {2018}, author = {Yue, SJ and Liu, J and Wang, AT and Meng, XT and Yang, ZR and Peng, C and Guan, HS and Wang, CY and Yan, D}, title = {Berberine alleviates insulin resistance by reducing peripheral branched-chain amino acids.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpendo.00256.2018}, pmid = {30422704}, issn = {1522-1555}, abstract = {Increased circulating branched-chain amino acids (BCAAs) have been involved in the pathogenesis of obesity and insulin resistance (IR). However, evidence relating berberine (BBR), gut microbiota, BCAAs and IR is limited. Here, we showed that BBR could effectively rectify steatohepatitis and glucose intolerance in high-fat diet (HFD)-fed mice. BBR reorganized gut microbiota populations under both the normal chow diet (NCD) and HFD. Particularly, BBR noticeably decreased the relative abundance of BCAA-producing bacteria, including order Clostridiales, families Streptococcaceae, Clostridiaceae and Prevotellaceae, and genera Streptococcus and Prevotella. Compared with the HFD group, predictive metagenomics indicated a reduction in the proportion of gut microbiota genes involved in BCAA biosynthesis, but the enrichment genes for BCAA degradation and transport by BBR treatment. Accordingly, the elevated serum BCAAs of HFD group were significantly decreased by BBR. Furthermore, the Western blotting results implied that BBR could promote the BCAA catabolism in the liver and epididymal white adipose tissues of HFD-fed mice by activation of the multienzyme branched-chain α-ketoacid dehydrogenase complex (BCKDC), whereas by inhibition of the phosphorylation state of BCKDHA (E1α subunit) and branched-chain α-ketoacid dehydrogenase kinase (BCKDK). The ex vivo assay further confirmed that BBR could increase BCAA catabolism in both AML12 hepatocytes and 3T3-L1 adipocytes. Finally, data from healthy subjects and diabetics confirmed that BBR could improve glycemic control and modulate circulating BCAAs. Together, our findings clarified BBR improving IR associated not only with gut microbiota alteration in BCAA biosynthesis, but also with BCAA catabolism in liver and adipose tissues.}, }
@article {pmid30421297, year = {2018}, author = {Shah, A and Morrison, M and Holtmann, GJ}, title = {Gastroduodenal &quot;Dysbiosis&quot;: a New Clinical Entity.}, journal = {Current treatment options in gastroenterology}, volume = {16}, number = {4}, pages = {591-604}, doi = {10.1007/s11938-018-0207-x}, pmid = {30421297}, issn = {1092-8472}, abstract = {PURPOSE OF REVIEW: Like the rest of the gastrointestinal tract, the small intestine is colonised by microbes, but how this &quot;microbiome&quot; affects the immune system and digestive functions has largely been overlooked, especially in the &quot;omics&quot; era. Here, we present recent findings that show that the diversity, density and interactions of these microbes in the small intestine can play an important role in the pathogenesis of a number of gastrointestinal and extraintestinal disorders.<br><br>RECENT FINDINGS: Changes in the small intestinal mucosa-associated microbiota (SI-MAM) have been shown to occur with inflammatory bowel diseases, functional gastrointestinal disorders, metabolic disorders such as obesity and type 2 diabetes. More recently, there is emerging evidence that small intestinal dysbiosis can be a driver for the progression of chronic liver disease. Initially believed that small intestinal dysbiosis (e.g. SIBO) is mainly due to alterations of luminal conditions (e.g. after surgical resections of the ileocecal valve), there is now enough evidence to conclude that small intestinal dysbiosis can occur without underlying structural abnormalities. Alterations of the SI-MAM appear to play a key role for the manifestation and progression of inflammatory and metabolic disorders.}, }
@article {pmid30420843, year = {2018}, author = {Alves, LF and Meleiro, LP and Silva, RN and Westmann, CA and Guazzaroni, ME}, title = {Novel Ethanol- and 5-Hydroxymethyl Furfural-Stimulated β-Glucosidase Retrieved From a Brazilian Secondary Atlantic Forest Soil Metagenome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2556}, doi = {10.3389/fmicb.2018.02556}, pmid = {30420843}, issn = {1664-302X}, abstract = {Beta-glucosidases are key enzymes involved in lignocellulosic biomass degradation for bioethanol production, which complete the final step during cellulose hydrolysis by converting cellobiose into glucose. Currently, industry requires enzymes with improved catalytic performance or tolerance to process-specific parameters. In this sense, metagenomics has become a powerful tool for accessing and exploring the biochemical biodiversity present in different natural environments. Here, we report the identification of a novel β-glucosidase from metagenomic DNA isolated from soil samples enriched with decaying plant matter from a Secondary Atlantic Forest region. For this, we employed a functional screening approach using an optimized and synthetic broad host-range vector for library production. The novel β-glucosidase - named Lfa2 - displays three GH3-family conserved domains and conserved catalytic amino acids D283 and E487. The purified enzyme was most active in pH 5.5 and at 50°C, and showed hydrolytic activity toward several pNP synthetic substrates containing β-glucose, β-galactose, β-xylose, β-fucose, and α-arabinopyranose, as well as toward cellobiose. Lfa2 showed considerable glucose tolerance, exhibiting an IC50 of 300 mM glucose and 30% of remaining activity in 600 mM glucose. In addition, Lfa2 retained full or slightly enhanced activity in the presence of several metal ions. Further, β-glucosidase activity was increased by 1.7-fold in the presence of 10% (v/v) ethanol, a concentration that can be reached in conventional fermentation processes. Similarly, Lfa2 showed 1.7-fold enhanced activity at high concentrations of 5-hydroxymethyl furfural, one of the most important cellulase inhibitors in pretreated sugarcane bagasse hydrolysates. Moreover, the synergistic effect of Lfa2 on Bacillus subtilis GH5-CBM3 endoglucanase activity was demonstrated by the increased production of glucose (1.6-fold). Together, these results indicate that β-glucosidase Lfa2 is a promissory enzyme candidate for utilization in diverse industrial applications, such as cellulosic biomass degradation or flavor enhancement in winemaking and grape processing.}, }
@article {pmid30420838, year = {2018}, author = {Li, W and Yuan, Y and Xia, Y and Sun, Y and Miao, Y and Ma, S}, title = {A Cross-Scale Neutral Theory Approach to the Influence of Obesity on Community Assembly of Human Gut Microbiome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2320}, doi = {10.3389/fmicb.2018.02320}, pmid = {30420838}, issn = {1664-302X}, abstract = {Background: The implications of gut microbiome to obesity have been extensively investigated in recent years although the exact mechanism is still unclear. The question whether or not obesity influences gut microbiome assembly has not been addressed. The question is significant because it is fundamental for investigating the diversity maintenance and stability of gut microbiome, and the latter should hold a key for understanding the etiological implications of gut microbiome to obesity. Methods: In this study, we adopt a dual neutral theory modeling strategy to address this question from both species and community perspectives, with both discrete and continuous neutral theory models. The first neutral theory model we apply is Hubbell's neutral theory of biodiversity that has been extensively tested in macro-ecology of plants and animals, and the second we apply is Sloan's neutral theory model that was developed particularly for microbial communities based on metagenomic sequencing data. Both the neutral models are complementary to each other and integrated together offering a comprehensive approach to more accurately revealing the possible influence of obesity on gut microbiome assembly. This is not only because the focus of both neutral theory models is different (community vs. species), but also because they adopted two different modeling strategies (discrete vs. continuous). Results: We test both the neutral theory models with datasets from Turnbaugh et al. (2009). Our tests showed that the species abundance distributions of more than ½ species (59-69%) in gut microbiome satisfied the prediction of Sloan's neutral theory, although at the community level, the number of communities satisfied the Hubbell's neutral theory was negligible (2 out of 278). Conclusion: The apparently contradictory findings above suggest that both stochastic neutral effects and deterministic environmental (host) factors play important roles in shaping the assembly and diversity of gut microbiome. Furthermore, obesity may just be one of the host factors, but its influence may not be strong enough to tip the balance between stochastic and deterministic forces that shape the community assembly. Finally, the apparent contradiction from both the neutral theories should not be surprising given that there are still near 30-40% species that do not obey the neutral law.}, }
@article {pmid30420687, year = {2018}, author = {Gao, Y and Li, H}, title = {Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41592-018-0182-0}, pmid = {30420687}, issn = {1548-7105}, support = {R01 GM123056/GM/NIGMS NIH HHS/United States ; R01 GM129781/GM/NIGMS NIH HHS/United States ; }, abstract = {The accurate quantification of microbial growth dynamics for species without complete genome sequences is biologically important, but computationally challenging in metagenomics. Here we present dynamic estimator of microbial communities (DEMIC; https://sourceforge.net/projects/demic/), a multi-sample algorithm based on contigs and coverage values, to infer the relative distances of contigs from the replication origin and to accurately compare bacterial growth rates between samples. We demonstrate robust performances of DEMIC for various sample sizes and assembly qualities using multiple synthetic and real datasets.}, }
@article {pmid30420263, year = {2018}, author = {Lamprecht, P and Fischer, N and Huang, J and Burkhardt, L and Lütgehetmann, M and Arndt, F and Rolfs, I and Kerstein, A and Iking-Konert, C and Laudien, M}, title = {Changes in the composition of the upper respiratory tract microbial community in granulomatosis with polyangiitis.}, journal = {Journal of autoimmunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaut.2018.10.005}, pmid = {30420263}, issn = {1095-9157}, abstract = {Dysbiosis¸ i.e. changes in microbial composition at a mucosal interface, is implicated in the pathogenesis of many chronic inflammatory and autoimmune diseases. To assess the composition of the microbial upper respiratory tract (URT) community in patients with granulomatosis with polyangiitis (GPA), we used culture-independent high-throughput methods. In this prospective clinical study, nasal swabs were collected from patients with GPA, patients with rheumatoid arthritis (RA, disease control), and healthy controls. Nasal bacterial taxa were assessed using V3-V4 region 16S rRNA amplicon sequencing. Staphylococcus aureus, Haemophilus influenza, and entero- and rhinoviruses were detected using qPCR. Unbiased metagenomic RNA sequencing (UMERS) was performed in a subset of samples to determine the relative abundance of bacterial, fungal, and viral species. A trend toward reduced microbiome diversity was detected in GPA samples compared with healthy controls. The abundance of bacterial taxa and microbial richness were significantly decreased in GPA samples compared with RA samples. The relative abundance of bacterial families shifted, with increased Planococcaceae and decreased Moraxellaceae, Tissierellaceae, Staphylococcaceae, and Propionibacteriaceae in GPA and RA. Further, decreased abundance of Corynebacteriaceae, and Aerococcaceae was observed in GPA samples. Significantly more colonization of S. aureus was seen in the nasal microbiome of GPA compared with RA and healthy control samples. H. influenzae colonization was also observed in GPA samples. UMERS detected the presence of rhinoviral sequences in some GPA samples. Thus, our study uncovered changes in the URT microbial composition in patients with GPA and RA, suggesting that both immunosuppression and disease background affect the URT microbiome. Complex alterations of host-microbiome interactions in the URT could influence chronic endonasal inflammation in GPA.}, }
@article {pmid30419949, year = {2018}, author = {Silverman, JD and Durand, HK and Bloom, RJ and Mukherjee, S and David, LA}, title = {Dynamic linear models guide design and analysis of microbiota studies within artificial human guts.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {202}, doi = {10.1186/s40168-018-0584-3}, pmid = {30419949}, issn = {2049-2618}, support = {IIS-1320357//National Science Foundation (US)/ ; DMS1613261//National Science Foundation (US)/ ; DMS-1418261//National Science Foundation/ ; IIS-1546331//National Science Foundation/ ; R01 DK116187/DK/NIDDK NIH HHS/United States ; 1R01DK116187//National Institutes of Health/ ; None//University of North Carolina Center for Gastrointestinal Biology and Disease/ ; T32 GM007171/GM/NIGMS NIH HHS/United States ; NNX16AO69A//Translational Research Institute/ ; None//Hartwell Foundation/ ; DMS-1045153//National Science Foundation (US)/ ; }, abstract = {BACKGROUND: Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models' fundamental biology include the timescales on which microbiota vary and the factors that drive such change. Answering these questions though requires overcoming analytical obstacles like estimating the effects of technical variation on observed microbiota dynamics, as well as the lack of appropriate benchmark datasets.<br><br>RESULTS: To address these obstacles, we created a modeling framework based on multinomial logistic-normal dynamic linear models (MALLARDs) and performed dense longitudinal sampling of four replicate artificial human guts over the course of 1 month. The resulting analyses revealed how the ratio of biological variation to technical variation from sample processing depends on sampling frequency. In particular, we find that at hourly sampling frequencies, 76% of observed variation could be ascribed to technical sources, which could also skew the observed covariation between taxa. We also found that the artificial guts demonstrated replicable trajectories even after a recovery from a transient feed disruption. Additionally, we observed irregular sub-daily oscillatory dynamics associated with the bacterial family Enterobacteriaceae within all four replicate vessels.<br><br>CONCLUSIONS: Our analyses suggest that, beyond variation due to sequence counting, technical variation from sample processing can obscure temporal variation from biological sources in artificial gut studies. Our analyses also supported hypotheses that human gut microbiota fluctuates on sub-daily timescales in the absence of a host and that microbiota can follow replicable trajectories in the presence of environmental driving forces. Finally, multiple aspects of our approach are generalizable and could ultimately be used to facilitate the design and analysis of longitudinal microbiota studies in vivo.}, }
@article {pmid30419782, year = {2018}, author = {Dąbkowski, D and Tabaszewski, P and Górecki, P}, title = {Minimizing the deep coalescence cost.}, journal = {Journal of bioinformatics and computational biology}, volume = {16}, number = {5}, pages = {1840021}, doi = {10.1142/S0219720018400218}, pmid = {30419782}, issn = {1757-6334}, abstract = {Metagenomic studies identify the species present in an environmental sample usually by using procedures that match molecular sequences, e.g. genes, with the species taxonomy. Here, we first formulate the problem of gene-species matching in the parsimony framework using binary phylogenetic gene and species trees under the deep coalescence cost and the assumption that each gene is paired uniquely with one species. In particular, we solve the problem in the cases when one of the trees is a caterpillar. Next, we propose a dynamic programming algorithm, which solves the problem exactly, however, its time and space complexity is exponential. Next, we generalize the problem to include non-binary trees and show the solution for caterpillar trees. We then propose time and space-efficient heuristic algorithms for solving the gene-species matching problem for any input trees. Finally, we present the results of computational experiments on simulated and empirical datasets consisting of binary tree pairs.}, }
@article {pmid30418610, year = {2018}, author = {Huerta-Cepas, J and Szklarczyk, D and Heller, D and Hernández-Plaza, A and Forslund, SK and Cook, H and Mende, DR and Letunic, I and Rattei, T and Jensen, LJ and von Mering, C and Bork, P}, title = {eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gky1085}, pmid = {30418610}, issn = {1362-4962}, abstract = {eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. In total, 4.4M orthologous groups (OGs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, HMM models and functional descriptors. Precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each OG. Our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. All precomputed data are publicly available for downloading or via API queries at http://eggnog.embl.de.}, }
@article {pmid30418481, year = {2018}, author = {Stewart, RD and Auffret, M and Snelling, TJ and Roehe, R and Watson, M}, title = {MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs).}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/bty905}, pmid = {30418481}, issn = {1367-4811}, abstract = {Motivation: Metagenomics is a powerful tool for assaying the DNA from every genome present in an environment. Recent advances in bioinformatics have enabled the rapid assembly of near complete metagenome-assembled genomes (MAGs), and there is a need for reproducible pipelines that can annotate and characterise thousands of genomes simultaneously, to enable identification and functional characterisation.<br><br>Results: Here we present MAGpy, a scalable and reproducible pipeline that takes multiple genome assemblies as FASTA and compares them to several public databases, checks quality, suggests a taxonomy and draws a phylogenetic tree.<br><br>Availability: MAGpy is available on github: https://github.com/WatsonLab/MAGpy.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30417889, year = {2018}, author = {Hyeon, JY and Mann, DA and Townsend, AM and Deng, X}, title = {Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {140}, pages = {}, doi = {10.3791/58612}, pmid = {30417889}, issn = {1940-087X}, abstract = {Quasi-metagenomics sequencing refers to the sequencing-based analysis of modified microbiomes of food and environmental samples. In this protocol, microbiome modification is designed to concentrate genomic DNA of a target foodborne pathogen contaminant to facilitate the detection and subtyping of the pathogen in a single workflow. Here, we explain and demonstrate the sample preparation steps for the quasi-metagenomics analysis of Salmonella enterica from representative food and environmental samples including alfalfa sprouts, ground black pepper, ground beef, chicken breast and environmental swabs. Samples are first subjected to the culture enrichment of Salmonella for a shortened and adjustable duration (4-24 h). Salmonella cells are then selectively captured from the enrichment culture by immunomagnetic separation (IMS). Finally, multiple displacement amplification (MDA) is performed to amplify DNA from IMS-captured cells. The DNA output of this protocol can be sequenced by high throughput sequencing platforms. An optional quantitative PCR analysis can be performed to replace sequencing for Salmonella detection or assess the concentration of Salmonella DNA before sequencing.}, }
@article {pmid30417114, year = {2018}, author = {Huang, SK and Ye, KT and Huang, WF and Ying, BH and Su, X and Lin, LH and Li, JH and Chen, YP and Li, JL and Bao, XL and Hu, JZ}, title = {Influence of Feeding Type and Nosema ceranae Infection on the Gut Microbiota of Apis cerana Workers.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00177-18}, pmid = {30417114}, issn = {2379-5077}, abstract = {The gut microbiota plays an essential role in the health of bees. To elucidate the effect of feed and Nosema ceranae infection on the gut microbiota of honey bee (Apis cerana), we used 16S rRNA sequencing to survey the gut microbiota of honey bee workers fed with sugar water or beebread and inoculated with or without N. ceranae. The gut microbiota of A. cerana is dominated by Serratia, Snodgrassella, and Lactobacillus genera. The overall gut microbiota diversity was show to be significantly differential by feeding type. N. ceranae infection significantly affects the gut microbiota only in bees fed with sugar water. Higher abundances of Lactobacillus, Gluconacetobacter, and Snodgrassella and lower abundances of Serratia were found in bees fed with beebread than in those fed with sugar water. N. ceranae infection led to a higher abundance of Snodgrassella and a lower abundance of Serratia in sugar-fed bees. Imputed bacterial Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed the significant metagenomics functional differences by feeding and N. ceranae infections. Furthermore, A. cerana workers fed with sugar water showed lower N. ceranae spore loads but higher mortality than those fed with beebread. The cumulative mortality was strongly positive correlated (rho = 0.61) with the changes of overall microbiota dissimilarities by N. ceranae infection. Both feeding types and N. ceranae infection significantly affect the gut microbiota in A. cerana workers. Beebread not only provides better nutrition but also helps establish a more stable gut microbiota and therefore protects bees in response to N. ceranae infection. IMPORTANCE The gut microbiota plays an essential role in the health of bees. Scientific evidence suggests that diet and infection can affect the gut microbiota and modulate the health of the gut; however, the interplay between those two factors and the bee gut microbiota is not well known. In this study, we used a high-throughput sequencing method to monitor the changes of gut microbiota associated with both feeding types and Nosema ceranae infection. Our results showed that the gut microbiota composition and diversity of Asian honey bee were significantly associated with both feeding types and the N. ceranae infection. More interestingly, bees fed with beebread showed higher microbiota stability and lower mortality rates than those fed with sugar water when infected by N. ceranae. Those data suggest that beebread has the potential not only to provide better nutrition but also help to establish a more stable gut microbiota to protect bees against N. ceranae infection.}, }
@article {pmid30417110, year = {2018}, author = {Wei, ST and Wu, YW and Lee, TH and Huang, YS and Yang, CY and Chen, YL and Chiang, YR}, title = {Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSystems.00113-18}, pmid = {30417110}, issn = {2379-5077}, abstract = {The 2,3-seco pathway, the pathway for anaerobic cholesterol degradation, has been established in the denitrifying betaproteobacterium Sterolibacterium denitrificans. However, knowledge of how microorganisms respond to cholesterol at the community level is elusive. Here, we applied mesocosm incubation and 16S rRNA sequencing to reveal that, in denitrifying sludge communities, three betaproteobacterial operational taxonomic units (OTUs) with low (94% to 95%) 16S rRNA sequence similarity to Stl. denitrificans are cholesterol degraders and members of the rare biosphere. Metatranscriptomic and metabolite analyses show that these degraders adopt the 2,3-seco pathway to sequentially catalyze the side chain and sterane of cholesterol and that two molybdoenzymes-steroid C25 dehydrogenase and 1-testosterone dehydrogenase/hydratase-are crucial for these bioprocesses, respectively. The metatranscriptome further suggests that these betaproteobacterial degraders display chemotaxis and motility toward cholesterol and that FadL-like transporters may be the key components for substrate uptake. Also, these betaproteobacteria are capable of transporting micronutrients and synthesizing cofactors essential for cellular metabolism and cholesterol degradation; however, the required cobalamin is possibly provided by cobalamin-de novo-synthesizing gamma-, delta-, and betaproteobacteria via the salvage pathway. Overall, our results indicate that the ability to degrade cholesterol in sludge communities is reserved for certain rare biosphere members and that C25 dehydrogenase can serve as a biomarker for sterol degradation in anoxic environments. IMPORTANCE Steroids are ubiquitous and abundant natural compounds that display recalcitrance. Biodegradation via sludge communities in wastewater treatment plants is the primary removal process for steroids. To date, compared to studies for aerobic steroid degradation, the knowledge of anaerobic degradation of steroids has been based on only a few model organisms. Due to the increase of anthropogenic impacts, steroid inputs may affect microbial diversity and functioning in ecosystems. Here, we first investigated microbial functional responses to cholesterol, the most abundant steroid in sludge, at the community level. Our metagenomic and metatranscriptomic analyses revealed that the capacities for cholesterol approach, uptake, and degradation are unique traits of certain low-abundance betaproteobacteria, indicating the importance of the rare biosphere in bioremediation. Apparent expression of genes involved in cofactor de novo synthesis and salvage pathways suggests that these micronutrients play important roles for cholesterol degradation in sludge communities.}, }
@article {pmid30417108, year = {2018}, author = {Ren, L and Zhang, R and Rao, J and Xiao, Y and Zhang, Z and Yang, B and Cao, D and Zhong, H and Ning, P and Shang, Y and Li, M and Gao, Z and Wang, J}, title = {Transcriptionally Active Lung Microbiome and Its Association with Bacterial Biomass and Host Inflammatory Status.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSystems.00199-18}, pmid = {30417108}, issn = {2379-5077}, abstract = {Alteration of the lung microbiome has been observed in several respiratory tract diseases. However, most previous studies were based on 16S ribosomal RNA and shotgun metagenome sequencing; the viability and functional activity of the microbiome, as well as its interaction with host immune systems, have not been well studied. To characterize the active lung microbiome and its associations with host immune response and clinical features, we applied metatranscriptome sequencing to bronchoalveolar lavage fluid (BALF) samples from 25 patients with chronic obstructive pulmonary disease (COPD) and from nine control cases without known pulmonary disease. Community structure analyses revealed three distinct microbial compositions, which were significantly correlated with bacterial biomass, human Th17 immune response, and COPD exacerbation frequency. Specifically, samples with transcriptionally active Streptococcus, Rothia, or Pseudomonas had bacterial loads 16 times higher than samples enriched for Escherichia and Ralstonia. These high-bacterial-load samples also tended to undergo a stronger Th17 immune response. Furthermore, an increased proportion of lymphocytes was found in samples with active Pseudomonas. In addition, COPD patients with active Streptococcus or Rothia infections tended to have lower rates of exacerbations than patients with active Pseudomonas and patients with lower bacterial biomass. Our results support the idea of a stratified structure of the active lung microbiome and a significant host-microbe interaction. We speculate that diverse lung microbiomes exist in the population and that their presence and activities could either influence or reflect different aspects of lung health. IMPORTANCE Recent studies of the microbiome proposed that resident microbes play a beneficial role in maintaining human health. Although lower respiratory tract disease is a leading cause of sickness and mortality, how the lung microbiome interacts with human health remains largely unknown. Here we assessed the association between the lung microbiome and host gene expression, cytokine concentration, and over 20 clinical features. Intriguingly, we found a stratified structure of the active lung microbiome which was significantly associated with bacterial biomass, lymphocyte proportion, human Th17 immune response, and COPD exacerbation frequency. These observations suggest that the microbiome plays a significant role in lung homeostasis. Not only microbial composition but also active functional elements and host immunity characteristics differed among different individuals. Such diversity may partially account for the variation in susceptibility to particular diseases.}, }
@article {pmid30416839, year = {2018}, author = {Chu, H and Williams, B and Schnabl, B}, title = {Gut microbiota, fatty liver disease, and hepatocellular carcinoma.}, journal = {Liver research}, volume = {2}, number = {1}, pages = {43-51}, doi = {10.1016/j.livres.2017.11.005}, pmid = {30416839}, issn = {2096-2878}, support = {I01 BX002213/BX/BLRD VA/United States ; R01 AA020703/AA/NIAAA NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; }, abstract = {Intestinal bacteria contribute to the pathogenesis of non-alcoholic fatty liver disease (NAFLD). Recently developed microbial profiling techniques are beginning to shed light on the nature of the changes in the gut microbiota that accompany NAFLD and non-alcoholic steatohepatitis (NASH). In this review, we summarize the role of gut microbiota in the development of NAFLD, NASH, and hepatocellular carcinoma (HCC). We highlight the mechanisms by which gut microbiota contribute to NAFLD/NASH, including through alterations in gut epithelial permeability, choline metabolism, endogenous alcohol production, release of inflammatory cytokines, regulation of hepatic Toll-like receptor (TLR), and bile acid metabolism. In addition, we analyze possible mechanisms for enhanced hepatic carcinogenesis, including alterations in bile acid metabolism, release of inflammatory cytokines, and expression of TLR-4. Finally, we describe therapeutic approaches for NAFLD/NASH and preventive strategies for HCC involving modulation of the intestinal microbiota or affected host pathways. Although recent studies have provided useful information, large-scale prospective studies are required to better characterize the intestinal microbiota and metabolome, in order to demonstrate a causative role for changes in the gut microbiota in the etiology of NAFLD/NASH, to identify new therapeutic strategies for NAFLD/NASH, and to develop more effective methods of preventing HCC.}, }
@article {pmid30416642, year = {2017}, author = {Thaker, VV}, title = {GENETIC AND EPIGENETIC CAUSES OF OBESITY.}, journal = {Adolescent medicine: state of the art reviews}, volume = {28}, number = {2}, pages = {379-405}, pmid = {30416642}, issn = {1934-4287}, support = {K23 DK110539/DK/NIDDK NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; }, abstract = {Obesity is a complex, heritable trait influenced by the interplay of genetics, epigenetics, metagenomics and the environment. With the increasing access to high precision diagnostic tools for genetic investigations, numerous genes influencing the phenotype have been identified, especially in early onset severe obesity. This review summarizes the current knowledge on the known genetic causes of obesity and the available therapeutic options. Furthermore, we discuss the role and potential mechanism of epigenetic changes that may be involved as mediators of the environmental influences and that may provide future opportunities for intervention.}, }
@article {pmid30416499, year = {2018}, author = {Hendrickson, HL and Poole, AM}, title = {Manifold Routes to a Nucleus.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2604}, doi = {10.3389/fmicb.2018.02604}, pmid = {30416499}, issn = {1664-302X}, abstract = {It is widely assumed that there is a clear distinction between eukaryotes, with cell nuclei, and prokaryotes, which lack nuclei. This suggests the evolution of nuclear compartmentation is a singular event. However, emerging knowledge of the diversity of bacterial internal cell structures suggests the picture may not be as black-and-white as previously thought. For instance, some members of the bacterial PVC superphylum appear to have nucleus-like compartmentation, where transcription and translation are physically separated, and some jumbophages have recently been shown to create nucleus-like structures within their Pseudomonad hosts. Moreover, there is also tantalizing metagenomic identification of new Archaea that carry homologs of genes associated with internal cell membrane structure in eukaryotes. All these cases invite comparison with eukaryote cell biology. While the bacterial cases of genetic compartmentation are likely convergent, and thus viewed by many as not germane to the question of eukaryote origins, we argue here that, in addressing the broader question of the evolution of compartmentation, other instances are at least as important: they provide us with a point of comparison which is critical for a more general understanding of both the conditions favoring the emergence of intracellular compartmentation of DNA and the evolutionary consequences of such cellular architecture. Finally, we consider three classes of explanation for the emergence of compartmentation: physical protection, crosstalk avoidance and nonadaptive origins.}, }
@article {pmid30416492, year = {2018}, author = {Annavajhala, MK and Kapoor, V and Santo-Domingo, J and Chandran, K}, title = {Structural and Functional Interrogation of Selected Biological Nitrogen Removal Systems in the United States, Denmark, and Singapore Using Shotgun Metagenomics.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2544}, doi = {10.3389/fmicb.2018.02544}, pmid = {30416492}, issn = {1664-302X}, abstract = {Conventional biological nitrogen removal (BNR), comprised of nitrification and denitrification, is traditionally employed in wastewater treatment plants (WWTPs) to prevent eutrophication in receiving water bodies. More recently, the combination of selective ammonia to nitrite oxidation (nitritation) and autotrophic anaerobic ammonia oxidation (anammox), collectively termed deammonification, has also emerged as a possible energy- and cost-effective BNR alternative. Herein, we analyzed microbial diversity and functional potential within 13 BNR processes in the United States, Denmark, and Singapore operated with varying reactor configuration, design, and operational parameters. Using next-generation sequencing and metagenomics, gene-coding regions were aligned against a custom protein database expanded to include all published aerobic ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB), anaerobic ammonia oxidizing bacteria (AMX), and complete ammonia oxidizing bacteria (CMX). Overall contributions of these N-cycle bacteria to the total functional potential of each reactor was determined, as well as that of several organisms associated with denitrification and/or structural integrity of microbial aggregates (biofilm or granules). The potential for these engineered processes to foster a broad spectrum of microbial catabolic, anabolic, and carbon assimilation transformations was elucidated. Seeded sidestream DEMON® deammonification systems and single-stage nitritation-anammox moving bed biofilm reactors (MBBRs) and a mainstream Cleargreen reactor designed to enrich in AOB and AMX showed lower enrichment in AMX functionality than an enriched two-stage nitritation-anammox MBBR system treating mainstream wastewater. Conventional BNR systems in Singapore and the United States had distinct metagenomes, especially relating to AOB. A hydrocyclone process designed to recycle biomass granules for mainstream BNR contained almost identical structural and functional characteristics in the overflow, underflow, and inflow of mixed liquor (ALT) rather than the expected selective enrichment of specific nitrifying or AMX organisms. Inoculum used to seed a sidestream deammonification process unexpectedly contained <10% of total coding regions assigned to AMX. These results suggest the operating conditions of engineered bioprocesses shape the resident microbial structure and function far more than the bioprocess configuration itself. We also highlight the advantage of a systems- and metagenomics-based interrogation of both the microbial structure and potential function therein over targeting of individual populations or specific genes.}, }
@article {pmid30416489, year = {2018}, author = {Stamps, BW and Leddy, MB and Plumlee, MH and Hasan, NA and Colwell, RR and Spear, JR}, title = {Characterization of the Microbiome at the World's Largest Potable Water Reuse Facility.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2435}, doi = {10.3389/fmicb.2018.02435}, pmid = {30416489}, issn = {1664-302X}, abstract = {Conventional water resources are not sufficient in many regions to meet the needs of growing populations. Due to cyclical weather cycles, drought, and climate change, water stress has increased worldwide including in Southern California, which serves as a model for regions that integrate reuse of wastewater for both potable and non-potable use. The Orange County Water District (OCWD) Advanced Water Purification Facility (AWPF) is a highly engineered system designed to treat and produce up to 100 million gallons per day (MGD) of purified water from a municipal wastewater source for potable reuse. Routine facility microbial water quality analysis is limited to standard indicators at this and similar facilities. Given recent advances in high throughput DNA sequencing techniques, complete microbial profiling of communities in water samples is now possible. By using 16S/18S rRNA gene sequencing, metagenomic and metatranscriptomic sequencing coupled to a highly accurate identification method along with 16S rRNA gene qPCR, we describe a detailed view of the total microbial community throughout the facility. The total bacterial load of the water at stages of the treatment train ranged from 3.02 × 106 copies in source, unchlorinated wastewater feed to 5.49 × 101 copies of 16S rRNA gene/mL after treatment (consisting of microfiltration, reverse osmosis, and ultraviolet/advanced oxidation). Microbial diversity and load decreased by several orders of magnitude after microfiltration and reverse osmosis treatment, falling to almost non-detectable levels that more closely resembled controls of molecular grade laboratory water than the biomass detected in the source water. The presence of antibiotic resistance genes and viruses was also greatly reduced. Overall, system design performance was achieved, and comprehensive microbial community analysis was found to enable a more complete characterization of the water/wastewater microbial signature.}, }
@article {pmid30415264, year = {2018}, author = {Samra, M and Nam, SK and Lim, DH and Kim, DH and Yang, J and Kim, YK and Kim, JH}, title = {Urine Bacteria-Derived Extracellular Vesicles and Allergic Airway Diseases in Children.}, journal = {International archives of allergy and immunology}, volume = {}, number = {}, pages = {1-9}, doi = {10.1159/000492677}, pmid = {30415264}, issn = {1423-0097}, abstract = {BACKGROUND: Microbiota and human allergic airway diseases have been proven to be interrelated. Bacteria-derived extracellular vesicle (EV)s are known to play important roles in interbacterial and human-bacteria communications, but their relationship with allergies has not been examined yet. Urine EVs were investigated to determine whether they could be used as biomarkers for monitoring allergic airway diseases in children.<br><br>METHODS: Subjects were 4 groups of chronic rhinitis (CR), allergic rhinitis (AR), atopic asthma (AS) and healthy controls. Single voided urine samples were collected. Urine EVs were isolated and their DNA was extracted for 16S-rDNA pyrosequencing.<br><br>RESULTS: A total of 118 children participated in this study; 27, 39, 19, and 33 were in the CR, AR, AS, and control group, respectively. The AR had a significantly high Chao-1 index than that of controls. Principal component analysis revealed dysbiosis in the CR, AR, and AS compared to the controls. One phylum and 19 families and genera were significantly enriched or depleted in the disease groups compared to the controls; the Actinobacteria phylum and the Sphingomonadaceae family were more abundant in the AS and CR, the Comamonadaceae family, the Propionibacteraceae family, Propionibacterium and Enhydrobacter were more enriched in the CR, and the Methylobacteriaceae family and Methylobacterium were more abundant in each disease group, while the Enterobacteriaceae family was depleted in each disease group.<br><br>CONCLUSIONS: CR, AR, and AS had a distinct composition of urine EVs. Urine EVs could be an indicator for assessing allergic airway diseases in children.}, }
@article {pmid30414312, year = {2018}, author = {Magnusson, AO and Szekrenyi, A and Joosten, HJ and Finnigan, J and Charnock, S and Fessner, WD}, title = {nanoDSF as screening tool for enzyme libraries and biotechnology development.}, journal = {The FEBS journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/febs.14696}, pmid = {30414312}, issn = {1742-4658}, abstract = {Enzymes are attractive tools for synthetic applications. To be viable for industrial use enzymes need sufficient stability towards the desired reaction conditions such as high substrate and cosolvent concentration, non-neutral pH and elevated temperatures. Thermal stability is an attractive feature not only because it allows for protein purification by thermal treatment and higher process temperatures, but also due to the associated higher stability against other destabilising factors. Therefore, high-throughput screening methods are desirable for the identification of thermostable biocatalysts by discovery from nature or by protein engineering but current methods have low throughput and require time-demanding purification of protein samples. We found that nanoscale differential scanning fluorimetry (nanoDSF) is a valuable tool to rapidly and reliably determine melting points of native proteins. To avoid intrinsic problems posed by crude protein extracts, hypotonic extraction of over-expressed protein from bacterial host cells resulted in higher sample quality and accurate manual determination of several hundred melting temperatures per day. We have probed the use of nanoDSF for high-throughput screening of a phylogenetically diverse aldolase library to identify novel thermostable enzymes from metagenomic sources and for the rapid measurements of variants from saturation mutagenesis. The feasibility of nanoDSF for the screening of synthetic reaction conditions was proved by studies of co-solvent tolerance, which showed protein melting temperature to decrease linearly with increasing cosolvent concentration for all combinations of six enzymes and eight water-miscible cosolvents investigated, and of substrate affinity, which showed stabilization of hexokinase by sugars in the absence of ATP cofactor. This article is protected by copyright. All rights reserved.}, }
@article {pmid30413677, year = {2018}, author = {Franzo, G and Kekarainen, T and Llorens, A and Correa-Fiz, F and Segalés, J}, title = {Exploratory metagenomic analyses of periweaning failure-to-thrive syndrome-affected pigs.}, journal = {The Veterinary record}, volume = {}, number = {}, pages = {}, doi = {10.1136/vr.105125}, pmid = {30413677}, issn = {2042-7670}, abstract = {Modern pig farming is characterised by the emergence of several syndromes whose aetiology is unclear or has a multifactorial origin, including periweaning failure-to-thrive syndrome (PFTS). In fact, its specific aetiology remains elusive, although several causes have been investigated over time. The present study aimed to investigate the potential role of viral agents in PFTS-affected and healthy animals by evaluating the virome composition of different organs using a metagenomic approach. This analysis allowed demonstrating a higher abundance of Porcine parvovirus 6 (PPV6) in healthy subjects while Ungulate bocaparvovirus 2 (BoPV2), Ungulate protoparvovirus 1 (PPV) and Porcine circovirus 3 (PCV-3) were increased in pigs with PFTS. No differential abundance of RNA viruses was found between PFTS-affected and control pigs. Remarkably, this is the first molecular characterisation of PPV6 and BoPV2 in Spain and one of the few all around the world, supporting their apparent widespread circulation. Interestingly, PCV-3 has been recently identified in several clinical-pathological conditions as well as in healthy pigs, while BoPV2 pathogenic potential is unknown. Although obtained results must be taken as preliminary, they open the door for further studies on the potential role of these viruses or their combination as predisposing factor/s for PFTS occurrence.}, }
@article {pmid30412889, year = {2018}, author = {Nathani, NM and Mootapally, C and Dave, BP}, title = {Antibiotic resistance genes allied to the pelagic sediment microbiome in the Gulf of Khambhat and Arabian Sea.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {446-454}, doi = {10.1016/j.scitotenv.2018.10.409}, pmid = {30412889}, issn = {1879-1026}, abstract = {Antibiotics have been widely spread in the environments, imposing profound stress on the resistome of the residing microbes. Marine microbiomes are well established large reservoirs of novel antibiotics and corresponding resistance genes. The Gulf of Khambhat is known for its extreme tides and complex sedimentation process. We performed high throughput sequencing and applied bioinformatics techniques on pelagic sediment microbiome across four coordinates of the Gulf of Khambhat to assess the marine resistome, its corresponding bacterial community and compared with the open Arabian Sea sample. We identified a total of 2354 unique types of resistance genes, with most abundant and diverse gene profile in the area that had anthropogenic activities being carried out on-shore. The genes with >1% abundance in all samples included carA, macB, sav1866, tlrC, srmB, taeA, tetA, oleC and bcrA which belonged to the macrolides, glycopeptides and peptide drug classes. ARG enriched phyla distribution was quite varying between all the sites, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes among the dominant phyla. Based on the outcomes, we also propose potential biomarker candidates Desulfovibrio, Thermotaga and Pelobacter for antibiotic monitoring in the two of the Gulf samples probable contamination prone environments, and genera Nitrosocccus, Marinobacter and Streptomyces in the rest of the three studied samples. Outcomes support the concept that ARGs naturally originate in environments and human activities contribute to the dissemination of antibiotic resistance.}, }
@article {pmid30412190, year = {2018}, author = {Goordial, J and Ronholm, J}, title = {Metagenomics meets read clouds.}, journal = {Nature biotechnology}, volume = {36}, number = {11}, pages = {1049-1051}, doi = {10.1038/nbt.4284}, pmid = {30412190}, issn = {1546-1696}, }
@article {pmid30412047, year = {2018}, author = {Charles, J and Tangudu, CS and Hurt, SL and Tumescheit, C and Firth, AE and Garcia-Rejon, JE and Machain-Williams, C and Blitvich, BJ}, title = {Detection of novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico using metagenomics and characterization of their in vitro host ranges.}, journal = {The Journal of general virology}, volume = {}, number = {}, pages = {}, doi = {10.1099/jgv.0.001165}, pmid = {30412047}, issn = {1465-2099}, abstract = {A metagenomics approach was used to detect novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico. A total of 1359 mosquitoes of 7 species and 5 genera (Aedes, Anopheles, Culex, Mansonia and Psorophora) were sorted into 37 pools, homogenized and inoculated onto monolayers of Aedes albopictus (C6/36) cells. A second blind passage was performed and then total RNA was extracted and analysed by RNA-seq. Two novel viruses, designated Uxmal virus and Mayapan virus, were identified. Uxmal virus was isolated from three pools of Aedes (Ochlerotatus) taeniorhynchus and phylogenetic data indicate that it should be classified within the recently proposed taxon Negevirus. Mayapan virus was recovered from two pools of Psorophora ferox and is most closely related to unclassified Nodaviridae-like viruses. Two recognized viruses were also detected: Culex flavivirus (family Flaviviridae) and Houston virus (family Mesoniviridae), with one and two isolates being recovered, respectively. The in vitro host ranges of all four viruses were determined by assessing their replicative abilities in cell lines of avian, human, monkey, hamster, murine, lepidopteran and mosquito (Aedes, Anopheles and Culex) origin, revealing that all viruses possess vertebrate replication-incompetent phenotypes. In conclusion, we report the isolation of both novel and recognized RNA viruses from mosquitoes collected in Mexico, and add to the growing plethora of viruses discovered recently through the use of metagenomics.}, }
@article {pmid30409177, year = {2018}, author = {Zhu, Q and Dupont, CL and Jones, MB and Pham, KM and Jiang, ZD and DuPont, HL and Highlander, SK}, title = {Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {201}, doi = {10.1186/s40168-018-0579-0}, pmid = {30409177}, issn = {2049-2618}, support = {R21 DK099573/DK/NIDDK NIH HHS/United States ; R21DK099573//National Institute of Diabetes and Digestive and Kidney Diseases/ ; }, abstract = {BACKGROUND: Travelers' diarrhea (TD) is often caused by enterotoxigenic Escherichia coli, enteroaggregative E. coli, other bacterial pathogens, Norovirus, and occasionally parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 40% of TD patients. It is predicted that new pathogens may be causative agents of the disease.<br><br>RESULTS: We performed a comprehensive amplicon and whole genome shotgun (WGS) metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers, all of which were negative for the known etiologic agents of TD based on standard microbiological and immunological assays. Abnormal and diverse taxonomic profiles in TD samples were revealed. WGS reads were assembled and the resulting contigs were visualized using multiple query types. A semi-manual workflow was applied to isolate independent genomes from metagenomic pools. A total of 565 genome bins were extracted, 320 of which were complete enough to be characterized as cellular genomes; 160 were viral genomes. We made predictions of the etiology of disease for many of the individual subjects based on the properties and features of the recovered genomes. Multiple patients with low-diversity metagenomes were predominated by one to several E. coli strains. Functional annotation allowed prediction of pathogenic type in many cases. Five patients were co-infected with E. coli and other members of Enterobacteriaceae, including Enterobacter, Klebsiella, and Citrobacter; these may represent blooms of organisms that appear following secretory diarrhea. New &quot;dark matter&quot; microbes were observed in multiple samples. In one, we identified a novel TM7 genome that phylogenetically clustered with a sludge isolate; it carries genes encoding potential virulence factors. In multiple samples, we observed high proportions of putative novel viral genomes, some of which form clusters with the ubiquitous gut virus, crAssphage. The total relative abundance of viruses was significantly higher in healthy travelers versus TD patients.<br><br>CONCLUSION: Our study highlights the strength of assembly-based metagenomics, especially the manually curated, visualization-assisted binning of contigs, in resolving unusual and under-characterized pathogenic profiles of human-associated microbiomes. Results show that TD may be polymicrobial, with multiple novel cellular and viral strains as potential players in the diarrheal disease.}, }
@article {pmid30408669, year = {2018}, author = {You, Y and Wang, Z and Xu, W and Wang, C and Zhao, X and Su, Y}, title = {Phthalic acid esters disturbed the genetic information processing and improved the carbon metabolism in black soils.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {212-222}, doi = {10.1016/j.scitotenv.2018.10.355}, pmid = {30408669}, issn = {1879-1026}, abstract = {Phthalic acid esters (PAEs), such as dimethyl phthalate (DMP) and dibutyl phthalate (DBP), are widely distributed as environmental pollutants. In this study, the effects of these chemicals were investigated in black soils using a metagenomics approach. The results clearly showed that DMP or DBP increased the abundance of genes involved in transcription, replication and repair in black soils. In addition, the abundances of genes associated with metabolic functions was improved following treatment with DMP or DBP, including those involved in lipid transport and metabolism, carbohydrate transport and metabolism, and energy production and conversion. There could be many reasons for these observed changes. First, the DMP or DBP treatments increased the abundances of genes associated with the LuxR family, the UvrABC repair system, DNA replication pathways, the RNA polymerase complex and base excision repair. Second, the abundances of genes associated with isocitrate lyase regulator (IclR) family transcriptional regulators, lipid metabolism and carbohydrate active enzymes (CAZys) were altered by the DMP or DBP treatments. Finally, the DMP or DBP treatments also increased the emission load of CO2 and altered the fluorescence intensity of humic acid. Therefore, the results of this study suggested that DMP and DBP contamination altered the abundances of genes associated with genetic information processing and improved the carbon metabolism in black soils.}, }
@article {pmid30406643, year = {2018}, author = {Gao, B and Chi, L and Tu, P and Gao, N and Lu, K}, title = {The carbamate aldicarb altered the gut microbiome, metabolome and lipidome of C57BL/6J mice.}, journal = {Chemical research in toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.chemrestox.8b00179}, pmid = {30406643}, issn = {1520-5010}, abstract = {The gut microbiome is highly involved in numerous aspects of host physiology, from energy harvest to stress response, and can confer many benefits to the host. The gut microbiome development could be affected by genetic and environmental factors, including the pesticides. The carbamate insecticide aldicarb has been extensively used in agriculture, which raises serious public health concern. However, the impact of aldicarb on the gut microbiome, host metabolome and lipidome has not been well studied yet. Herein, we use multi-omics approaches, including16S rRNA sequencing, shotgun metagenomics sequencing, metabolomics and lipidomics, to elucidate aldicarb-induced toxicity in the gut microbiome and the host metabolic homeostasis. We demonstrated that aldicarb perturbed the gut microbiome development trajectory, enhanced gut bacterial pathogenicity, altered complex lipid profile, induced oxidative stress, protein degradation and DNA damage. The brain metabolism was also disturbed by the aldicarb exposure. These findings may provide a novel understanding of the toxicity of carbamate insecticides.}, }
@article {pmid30406048, year = {2018}, author = {Oechslin, CP and Lenz, N and Liechti, N and Ryter, S and Agyeman, P and Bruggmann, R and Leib, SL and Beuret, CM}, title = {Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {375}, doi = {10.3389/fcimb.2018.00375}, pmid = {30406048}, issn = {2235-2988}, abstract = {The etiologic cause of encephalitis, meningitis or meningo-encephalitis is unknown in up to 70% of cases. Clinical shotgun metagenomics combined with host depletion is a promising technique to identify infectious etiologies of central nervous system (CNS) infections. We developed a straightforward eukaryotic host nucleic acid depletion method that preserves intact viruses and bacteria for subsequent shotgun metagenomics screening of clinical samples, focusing on cerebrospinal fluid (CSF). A surrogate CSF sample for a CNS infection paradigm was used to evaluate the proposed depletion method consisting of selective host cell lysis, followed by enzymatic degradation of the liberated genomic DNA for final depletion with paramagnetic beads. Extractives were subjected to reverse transcription, followed by whole genome amplification and next generation sequencing. The effectiveness of the host depletion method was demonstrated in surrogate CSF samples spiked with three 1:100 dilutions of Influenza A H3N2 virus (qPCR Ct-values 20.7, 28.8, >42/negative). Compared to the native samples, host depletion increased the amount of the virus subtype reads by factor 7127 and 132, respectively, while in the qPCR negative sample zero vs. 31 (1.4E-4 %) virus subtype reads were detected (native vs. depleted). The workflow was applied to thirteen CSF samples of patients with meningo-/encephalitis (two bacterial, eleven viral etiologies), a serum of an Andes virus infection and a nose swab of a common cold patient. Unlike surrogate samples, host depletion of the thirteen human CSF samples and the nose swab did not result in more reads indicating presence of damaged pathogens due to, e.g., host immune response. Nevertheless, previously diagnosed pathogens in the human CSF samples (six viruses, two bacteria), the serum, and the nose swab (Human rhinovirus A31) were detected in the depleted and/or the native samples. Unbiased evaluation of the taxonomic profiles supported the diagnosed pathogen in two native CSF samples and the native and depleted serum and nose swab, while detecting various contaminations that interfered with pathogen identification at low concentration levels. In summary, damaged pathogens and contaminations complicated analysis and interpretation of clinical shotgun metagenomics data. Still, proper consideration of these issues may enable future application of metagenomics for clinical diagnostics.}, }
@article {pmid30406041, year = {2018}, author = {Xiao, P and Li, C and Zhang, Y and Han, J and Guo, X and Xie, L and Tian, M and Li, Y and Wang, M and Liu, H and Ren, J and Zhou, H and Lu, H and Jin, N}, title = {Metagenomic Sequencing From Mosquitoes in China Reveals a Variety of Insect and Human Viruses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {364}, doi = {10.3389/fcimb.2018.00364}, pmid = {30406041}, issn = {2235-2988}, abstract = {We collected 8,700 mosquitoes in three sites in China, which belonged to seven species. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The abundant viral sequences were detected and annotated belonging to more than 50 viral taxonomic families. The results were verified by PCR, followed by phylogenetic analysis. In the present study, we identified partial viral genes of dengue virus (DENV), a novel circovirus (CCV), densovirus (DNV), Japanese encephalitis virus (JEV), and Wuhan mosquito virus (WMV) in mosquitoes. Metagenomic analysis and PCR amplification revealed three DENV sequences, which were as homologous to the NS3 gene of DENV from Singapore isolated in 2005, with at least 91% nucleotide (nt) identity. Seven fragments of JEV encoding structural proteins were identified belonging to genotype I. They all shared high homology with structural protein genes of JEV isolated from Laos in 2009. The production of infectious virus particles of the newly isolated virus YunnanJEV2017-4 increased after passage from the BHK-21 cell line to the Vero cell line. Novel circovirus-related genes were identified and as being related to an unnamed gene of a mosquito circovirus (MCCV) sequence from the USA isolated in 2011, with at least 41% nt identity: this distant relationship suggests that the parent virus might belong to a novel circovirus genus. Additionally, numerous known viruses and some unknown viruses were also detected in mosquitoes from Yunnan province, China, which will be tested for propagation.}, }
@article {pmid30406038, year = {2018}, author = {Xiao, P and Han, J and Zhang, Y and Li, C and Guo, X and Wen, S and Tian, M and Li, Y and Wang, M and Liu, H and Ren, J and Zhou, H and Lu, H and Jin, N}, title = {Metagenomic Analysis of Flaviviridae in Mosquito Viromes Isolated From Yunnan Province in China Reveals Genes From Dengue and Zika Viruses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {359}, doi = {10.3389/fcimb.2018.00359}, pmid = {30406038}, issn = {2235-2988}, abstract = {More than 6,000 mosquitoes of six species from six sites were collected and tested for their virome using metagenomics sequencing and bioinformatic analysis. The identified viral sequences belonged to more than 50 viral families. The results were verified by PCR of selected viruses in all mosquitoes, followed by phylogenetic analysis. In the present study, we identified the partial dengue virus (DENV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV) sequences in mosquitoes. Metagenomic analysis and the PCR amplification revealed three DENV sequences, one of which encodes a partial envelope protein. Two ZIKV sequences both encoding partial nonstructural protein 3 and one JEV sequence encoding the complete envelope protein were identified. There was variability in the viral titers of the newly isolated virus JEV-China/YN2016-1 of different passage viruses. The newly identified Zika virus gene from ZIKV-China/YN2016-1 was an Asian genotype and shared the highest nucleotide sequence identity (97.1%) with a ZIKV sequence from Thailand isolated in 2004. Phylogenetic analysis of ZIKV-China/YN2016-1 and ZIKV-China/YN2016-2 with known Flavivirus genes indicated that ZIKV has propagated in Yunnan province, China.}, }
@article {pmid30405973, year = {2018}, author = {Castro, JC and Rodriguez-R, LM and Harvey, WT and Weigand, MR and Hatt, JK and Carter, MQ and Konstantinidis, KT}, title = {imGLAD: accurate detection and quantification of target organisms in metagenomes.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5882}, doi = {10.7717/peerj.5882}, pmid = {30405973}, issn = {2167-8359}, abstract = {Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting from inadequate identification of regions of the genome that are either too highly conserved to be diagnostic (e.g., rRNA genes) or prone to frequent horizontal genetic exchange (e.g., mobile elements) remains unknown. To overcome these limitations, we introduce imGLAD, which aims to detect (target) genomic sequences in metagenomic datasets. imGLAD achieves high accuracy because it uses the sequence-discrete population concept for discriminating between metagenomic reads originating from the target organism compared to reads from co-occurring close relatives, masks regions of the genome that are not informative using the MyTaxa engine, and models both the sequencing breadth and depth to determine relative abundance and limit of detection. We validated imGLAD by analyzing metagenomic datasets derived from spinach leaves inoculated with the enteric pathogen Escherichia coli O157:H7 and showed that its limit of detection can be comparable to that of PCR-based approaches for these samples (∼1 cell/gram).}, }
@article {pmid30405597, year = {2018}, author = {Goldbeck, O and Eck, AW and Seibold, GM}, title = {Real Time Monitoring of NADPH Concentrations in Corynebacterium glutamicum and Escherichia coli via the Genetically Encoded Sensor mBFP.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2564}, doi = {10.3389/fmicb.2018.02564}, pmid = {30405597}, issn = {1664-302X}, abstract = {Analyses of intracellular NADPH concentrations are prerequisites for the design of microbial production strains and process optimization. mBFP was described as metagenomics derived, blue fluorescent protein showing NADPH-dependent fluorescence. Characterization of mBFP showed a high specificity for binding of NADPH (KD 0.64 mM) and no binding of NADH, the protein exclusively amplified fluorescence of NADPH. mBFP catalyzed the NADPH-dependent reduction of benzaldehyde and further aldehydes, which fits to its classification as short chain dehydrogenase. For in vivo NADPH analyses a codon-optimized gene for mBFP was introduced into Corynebacterium glutamicum WT and the phosphoglucoisomerase-deficient strain C. glutamicum Δpgi, which accumulates high levels of NADPH. For determination of intracellular NADPH concentrations by mBFP a calibration method with permeabilized cells was developed. By this means an increase of intracellular NADPH concentrations within seconds after the addition of glucose to nutrient-starved cells of both C. glutamicum WT and C. glutamicum Δpgi was observed; as expected the internal NADPH concentration was significantly higher for C. glutamicum Δpgi (0.31 mM) when compared to C. glutamicum WT (0.19 mM). Addition of paraquat to E. coli cells carrying mBFP led as expected to an immediate decrease of intracellular NADPH concentrations, showing the versatile use of mBFP as intracellular sensor.}, }
@article {pmid30405589, year = {2018}, author = {Jarvis, KG and Daquigan, N and White, JR and Morin, PM and Howard, LM and Manetas, JE and Ottesen, A and Ramachandran, P and Grim, CJ}, title = {Microbiomes Associated With Foods From Plant and Animal Sources.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2540}, doi = {10.3389/fmicb.2018.02540}, pmid = {30405589}, issn = {1664-302X}, abstract = {Food microbiome composition impacts food safety and quality. The resident microbiota of many food products is influenced throughout the farm to fork continuum by farming practices, environmental factors, and food manufacturing and processing procedures. Currently, most food microbiology studies rely on culture-dependent methods to identify bacteria. However, advances in high-throughput DNA sequencing technologies have enabled the use of targeted 16S rRNA gene sequencing to profile complex microbial communities including non-culturable members. In this study we used 16S rRNA gene sequencing to assess the microbiome profiles of plant and animal derived foods collected at two points in the manufacturing process; post-harvest/pre-retail (cilantro) and retail (cilantro, masala spice mixes, cucumbers, mung bean sprouts, and smoked salmon). Our findings revealed microbiome profiles, unique to each food, that were influenced by the moisture content (dry spices, fresh produce), packaging methods, such as modified atmospheric packaging (mung bean sprouts and smoked salmon), and manufacturing stage (cilantro prior to retail and at retail). The masala spice mixes and cucumbers were comprised mainly of Proteobacteria, Firmicutes, and Actinobacteria. Cilantro microbiome profiles consisted mainly of Proteobacteria, followed by Bacteroidetes, and low levels of Firmicutes and Actinobacteria. The two brands of mung bean sprouts and the three smoked salmon samples differed from one another in their microbiome composition, each predominated by either by Firmicutes or Proteobacteria. These data demonstrate diverse and highly variable resident microbial communities across food products, which is informative in the context of food safety, and spoilage where indigenous bacteria could hamper pathogen detection, and limit shelf life.}, }
@article {pmid30405577, year = {2018}, author = {Bertelli, C and Courtois, S and Rosikiewicz, M and Piriou, P and Aeby, S and Robert, S and Loret, JF and Greub, G}, title = {Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2520}, doi = {10.3389/fmicb.2018.02520}, pmid = {30405577}, issn = {1664-302X}, abstract = {In drinking water distribution systems (DWDS), a disinfectant residual is usually applied to limit bacterial regrowth. However, delivering water with no or reduced chlorine residual could potentially decrease the selection for antimicrobial resistant microorganisms, favor bacterial regrowth and result in changes in bacterial populations. To evaluate the feasibility of water reduction in local DWDS while ensuring water safety, water quality was measured over 2 months in two different networks, each of them harboring sub-areas with normal and reduced chlorine. Water quality remained good in chlorine reduced samples, with limited development of total flora and absence of coliforms. Furthermore, 16S rRNA amplicon-based metagenomics was used to investigate the diversity and the composition of microbial communities in the sub-networks. Taxonomic classification of sequence reads showed a reduced bacterial diversity in sampling points with higher chlorine residuals. Chlorine disinfection created more homogeneous bacterial population, dominated by Pseudomonas, a genus that contains some major opportunistic pathogens such as P. aeruginosa. In the absence of chlorine, a larger and unknown biodiversity was unveiled, also highlighted by a decreased rate of taxonomic classification to the genus and species level. Overall, this experiment in a functional DWDS will facilitate the move toward potable water delivery systems without residual disinfectants and will improve water taste for consumers.}, }
@article {pmid30405551, year = {2018}, author = {Sasaki, N and Katagiri, S and Komazaki, R and Watanabe, K and Maekawa, S and Shiba, T and Udagawa, S and Takeuchi, Y and Ohtsu, A and Kohda, T and Tohara, H and Miyasaka, N and Hirota, T and Tamari, M and Izumi, Y}, title = {Endotoxemia by Porphyromonas gingivalis Injection Aggravates Non-alcoholic Fatty Liver Disease, Disrupts Glucose/Lipid Metabolism, and Alters Gut Microbiota in Mice.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2470}, doi = {10.3389/fmicb.2018.02470}, pmid = {30405551}, issn = {1664-302X}, abstract = {Many risk factors related to the development of non-alcoholic fatty liver disease (NAFLD) have been proposed, including the most well-known of diabetes and obesity as well as periodontitis. As periodontal pathogenic bacteria produce endotoxins, periodontal treatment can result in endotoxemia. The aim of this study was to investigate the effects of intravenous, sonicated Porphyromonas gingivalis (Pg) injection on glucose/lipid metabolism, liver steatosis, and gut microbiota in mice. Endotoxemia was induced in C57BL/6J mice (8 weeks old) by intravenous injection of sonicated Pg; Pg was deactivated but its endotoxin remained. The mice were fed a high-fat diet and administered sonicated Pg (HFPg) or saline (HFco) injections for 12 weeks. Liver steatosis, glucose metabolism, and gene expression in the liver were evaluated. 16S rRNA gene sequencing with metagenome prediction was performed on the gut microbiota. Compared to HFco mice, HFPg mice exhibited impaired glucose tolerance and insulin resistance along with increased liver steatosis. Liver microarray analysis demonstrated that 1278 genes were differentially expressed between HFco and HFPg mice. Gene set enrichment analysis showed that fatty acid metabolism, hypoxia, and TNFα signaling via NFκB gene sets were enriched in HFPg mice. Although sonicated Pg did not directly reach the gut, it changed the gut microbiota and decreased bacterial diversity in HFPg mice. Metagenome prediction in the gut microbiota showed enriched citrate cycle and carbon fixation pathways in prokaryotes. Overall, intravenous injection of sonicated Pg caused impaired glucose tolerance, insulin resistance, and liver steatosis in mice fed high-fat diets. Thus, blood infusion of Pg contributes to NAFLD and alters the gut microbiota.}, }
@article {pmid30405201, year = {2018}, author = {Wankhade, UD and Zhong, Y and Kang, P and Alfaro, M and Chintapalli, SV and Piccolo, BD and Mercer, KE and Andres, A and Thakali, KM and Shankar, K}, title = {Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16502}, doi = {10.1038/s41598-018-34453-0}, pmid = {30405201}, issn = {2045-2322}, support = {6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; }, abstract = {The contributions of maternal diet and obesity in shaping offspring microbiome remain unclear. Here we employed a mouse model of maternal diet-induced obesity via high-fat diet feeding (HFD, 45% fat calories) for 12 wk prior to conception on offspring gut microbial ecology. Male and female offspring were provided access to control or HFD from weaning until 17 wk of age. Maternal HFD-associated programming was sexually dimorphic, with male offspring from HFD dams showing hyper-responsive weight gain to postnatal HFD. Likewise, microbiome analysis of offspring cecal contents showed differences in α-diversity, β-diversity and higher Firmicutes in male compared to female mice. Weight gain in offspring was significantly associated with abundance of Lachnospiraceae and Clostridiaceae families and Adlercreutzia, Coprococcus and Lactococcus genera. Sex differences in metagenomic pathways relating to lipid metabolism, bile acid biosynthesis and immune response were also observed. HFD-fed male offspring from HFD dams also showed worse hepatic pathology, increased pro-inflammatory cytokines, altered expression of bile acid regulators (Cyp7a1, Cyp8b1 and Cyp39a1) and serum bile acid concentrations. These findings suggest that maternal HFD alters gut microbiota composition and weight gain of offspring in a sexually dimorphic manner, coincident with fatty liver and a pro-inflammatory state in male offspring.}, }
@article {pmid30405065, year = {2018}, author = {Aučynaitė, A and Rutkienė, R and Tauraitė, D and Meškys, R and Urbonavičius, J}, title = {Identification of a 2'-O-Methyluridine Nucleoside Hydrolase Using the Metagenomic Libraries.}, journal = {Molecules (Basel, Switzerland)}, volume = {23}, number = {11}, pages = {}, doi = {10.3390/molecules23112904}, pmid = {30405065}, issn = {1420-3049}, support = {SEN-07/2015//Lietuvos Mokslo Taryba/ ; }, abstract = {Ribose methylation is among the most ubiquitous modifications found in RNA. 2'-O-methyluridine is found in rRNA, snRNA, snoRNA and tRNA of Archaea, Bacteria, and Eukaryota. Moreover, 2'-O-methylribonucleosides are promising starting materials for the production of nucleic acid-based drugs. Despite the countless possibilities of practical use for the metabolic enzymes associated with methylated nucleosides, there are very few reports regarding the metabolic fate and enzymes involved in the metabolism of 2'-O-alkyl nucleosides. The presented work focuses on the cellular degradation of 2'-O-methyluridine. A novel enzyme was found using a screening strategy that employs Escherichia coli uracil auxotroph and the metagenomic libraries. A 2'-O-methyluridine hydrolase (RK9NH) has been identified together with an aldolase (RK9DPA)-forming a part of a probable gene cluster that is involved in the degradation of 2'-O-methylated nucleosides. The RK9NH is functional in E. coli uracil auxotroph and in vitro. The RK9NH nucleoside hydrolase could be engineered to enzymatically produce 2'-O-methylated nucleosides that are of great demand as raw materials for production of nucleic acid-based drugs. Moreover, RK9NH nucleoside hydrolase converts 5-fluorouridine, 5-fluoro-2'-deoxyuridine and 5-fluoro-2'-O-methyluridine into 5-fluorouracil, which suggests it could be employed in cancer therapy.}, }
@article {pmid30404941, year = {2018}, author = {Morand, A and Cornu, F and Dufour, JC and Tsimaratos, M and Lagier, JC and Raoult, D}, title = {Human bacterial repertoire of the urinary tract: a potential paradigm shift.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JCM.00675-18}, pmid = {30404941}, issn = {1098-660X}, abstract = {The aim of this article is to review the human repertoire of bacteria already described by culture and metagenomic techniques in urine, and published in the literature. Our study led us to compare this repertoire with other human repertoires available.We followed automatic and manual bibliographical methods and found 562 bacterial species reported in the literature as part of the human urinary microbiota. Of the 562 species, 322 were described only by culture, 101 by both culture and metagenomics, and 139 only by metagenomic. Three hundred and fifty-two species (62.6%) have been associated with at least one case report of human infection, of which 225 (40.0%) have been described as causative agents of urinary tract infection. The urinary tract bacterial repertoire contains 21.4% of the known prokaryotic diversity associated with human beings (464 in common) and share 23.6% species with the human gut microbiota (350 in common, 62.3% of the urine species). Urinary repertoire shares a significant difference in aero-intolerant species compared with gut microbiota (100/562; 17.8% and 505/1484; 34.0% respectively; p<0.001; OR=9.0 [7.0-11.4]). Studies using high-throughput sequencing show a higher proportion of aero-intolerant bacteria in urine (74/240, 30.8%).Most pathogenic bacteria are part of the commensal human urinary tract bacteria and their pathogenicity may occur following any imbalance of this microbiota. The restoration of urinary tract health can occur following a fecal transplantation. The potential gut origin of the human bacterial microbiota has to be explored.}, }
@article {pmid30404810, year = {2018}, author = {Harvey, E and Rose, K and Eden, JS and Lo, N and Abeyasuriya, T and Shi, M and Doggett, SL and Holmes, EC}, title = {Extensive Diversity of RNA Viruses in Australian Ticks.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JVI.01358-18}, pmid = {30404810}, issn = {1098-5514}, abstract = {Understanding the microbiome of ticks in Australia is of considerable interest given the ongoing debate over whether Lyme disease, and its causative agent the bacterium Borrelia burgdorferi sensu lato, are present in Australia. The diversity of bacteria infecting Australian ticks has been studied using both culture and metagenomics based techniques. However, little is known about the virome of Australian ticks, including whether this includes viruses with the potential to infect mammals. We used a meta-transcriptomics approach to reveal the diversity and evolution of viruses from Australian ticks collected from two locations on the central-east coast of Australia, including metropolitan Sydney. From this we identified 19 novel RNA viruses belonging to 12 families, as well as one previously described RNA virus. The majority of these viruses were related to arthropod-associated viruses suggesting that they do not utilize mammalian hosts. However, two novel viruses discovered in ticks feeding on bandicoot marsupials clustered closely within the mammalian-associated hepacivirus and pestivirus groups (family Flaviviridae). Another bandicoot tick yielded a novel coltivirus (family Reoviridae) - a group of largely tick-associated viruses containing the known human pathogen Colorado tick fever virus and its relative Eyach virus. Importantly, our transcriptomic data provided no evidence for the presence of B. burgdorferi s.l. in any tick sample, providing further evidence against the presence of Lyme Disease in Australia. In sum, this study reveals that Australian ticks harbor a diverse virome, including some viruses that merit additional screening in the context of emerging infectious disease.IMPORTANCE Each year a growing number of individuals along the east coast of Australia experience debilitating disease following tick bites. As there is no evidence for the presence of the causative agent of Lyme disease, Borrelia Burgdorferi sensu lato, in Australian ticks, the etiological basis of this disease syndrome remains controversial. To characterize the viruses associated with Australian ticks, particularly those that might be associated with mammalian infection, we performed unbiased RNA sequencing on 146 ticks collected across two locations along the coast of New South Wales, Australia. This revealed 19 novel RNA viruses from a diverse set of families. Notably, three of these viruses clustered with known mammalian viruses, including a novel coltivirus that was related to the human pathogen Colorado tick fever virus.}, }
@article {pmid30404694, year = {2018}, author = {Ma, LK and Xue, Y and He, TC and Zhang, YM}, title = {[Associations of Socioeconomic Factors,Nutrients Intake,and Gut Microbiota of Healthy Pregnant Women in the Third Trimester with Gestational Weight Gain].}, journal = {Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae}, volume = {40}, number = {5}, pages = {630-636}, doi = {10.3881/j.issn.1000-503X.10505}, pmid = {30404694}, issn = {1000-503X}, abstract = {Objective To investigate the associations of socioeconomic factors,nutrients intake,and gut microbiota of healthy pregnant women in the third trimester with gestational weight gain (GWG).Methods We recruited 98 pregnant women in the third trimester who had received antenatal care in the Department of Obstetrics Gynecology,Peking Union Medical College Hospital from October,2015 to May,2016. We collected socioeconomic information through a structured questionnaire covering age,ethnicity,height,pre-pregnancy weight,and education. Nutritional status of these pregnant women was assessed by a 24-hour dietary intake recall. The participants were provided with collective tubes for faecal sample collection at home;their weight before the delivery was recorded. The pre-pregnancy weight and GWG were classified according to World Health Organization body mass index (BMI) standard for adults and the Institute of Medicine GWG guidelines (2009),respectively. The gut microbiota of the participants were analyzed using a whole-metagenome shotgun sequencing method.Results Insufficient and excessive GWG accounted for 15.3% and 50.0% of the cohort,respectively. Appropriate GWG level was associated with intakes of fat (F=3.113,P=0.049),carbohydrates (F=3.750,P=0.027),and dietary fiber (F=4.499,P=0.014) but not with age (F=2.495,P=0.088),ethnicity (Χ 2=0.065,P=0.968),education (Χ 2=0.827,P=0.661),or pre-pregnancy BMI (F=0.121,P=0.887). Compared with the participants with appropriate GWG,those with excessive GWG had significantly higher abundance of Akkermansia muciniphila,Atopobium parvulum,and Alistipes indistinctus as well as lower abundance of Lactobacillus rhamnosus,Weissella unclassified,Eubacterium ventriosum,Ruminococcus torques,and Bacteroides uniformis. Compared with the participants with appropriate GWG,those with insufficient GWG had significantly higher abundance of Dialister invisus,Alistipes unclassified,Peptoniphilus harei,Escherichia unclassified,Parvimonas unclassified,Campylobacter ureolyticus,Lactobacillus crispatus,and Fusobacterium nucleatum and lower abundance of Eubacterium ventriosum.Conclusions Abnormal GWG is common in pregnant women. GWG is significantly associated with gut microbiota as well as with nutritional factors including fat,carbohydrate,and dietary fiber intake.}, }
@article {pmid30403636, year = {2018}, author = {Sokolovska, N and Permiakova, O and Forslund, K and Zucker, JD}, title = {Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1109/TCBB.2018.2879504}, pmid = {30403636}, issn = {1557-9964}, abstract = {An important question in microbiology is whether treatment causes changes in gut flora, and whether it also affects metabolism. The reconstruction of causal relations purely from non-temporal observational data is challenging. We address the problem of causal inference in a bivariate case, where the joint distribution of two variables is observed. In this contribution, we introduce a novel method of causality discovering which is based on the widely used assumption that if X causes Y, then P(X) and P(Y|X) are independent. We propose to explore a semi-supervised approach where P(Y|X) and P(X) are estimated from labeled and unlabeled data respectively, whereas the marginal probability is estimated potentially from much more unlabeled data than the conditional distribution. We illustrate by experiments on several benchmarks of biological network reconstruction that the proposed approach is very competitive in terms of computational time and accuracy compared to the state-of-the-art methods. Finally, we apply the proposed method to an original medical task where we study whether drugs confound human metagenome.}, }
@article {pmid30401779, year = {2018}, author = {Bratburd, JR and Keller, C and Vivas, E and Gemperline, E and Li, L and Rey, FE and Currie, CR}, title = {Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, doi = {10.1128/mBio.02032-18}, pmid = {30401779}, issn = {2150-7511}, support = {U19 AI109673/AI/NIAID NIH HHS/United States ; R56 DK071801/DK/NIDDK NIH HHS/United States ; R01 DK108259/DK/NIDDK NIH HHS/United States ; S10 RR029531/RR/NCRR NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; R01 DK071801/DK/NIDDK NIH HHS/United States ; }, abstract = {The gut microbiota confers resistance to pathogens of the intestinal ecosystem, yet the dynamics of pathogen-microbiome interactions and the metabolites involved in this process remain largely unknown. Here, we use gnotobiotic mice infected with the virulent pathogen Salmonella enterica serovar Typhimurium or the opportunistic pathogen Candida albicans in combination with metagenomics and discovery metabolomics to identify changes in the community and metabolome during infection. To isolate the role of the microbiota in response to pathogens, we compared mice monocolonized with the pathogen, uninfected mice &quot;humanized&quot; with a synthetic human microbiome, or infected humanized mice. In Salmonella-infected mice, by 3 days into infection, microbiome community structure and function changed substantially, with a rise in Enterobacteriaceae strains and a reduction in biosynthetic gene cluster potential. In contrast, Candida-infected mice had few microbiome changes. The LC-MS metabolomic fingerprint of the cecum differed between mice monocolonized with either pathogen and humanized infected mice. Specifically, we identified an increase in glutathione disulfide, glutathione cysteine disulfide, inosine 5'-monophosphate, and hydroxybutyrylcarnitine in mice infected with Salmonella in contrast to uninfected mice and mice monocolonized with Salmonella These metabolites potentially play a role in pathogen-induced oxidative stress. These results provide insight into how the microbiota community members interact with each other and with pathogens on a metabolic level.IMPORTANCE The gut microbiota is increasingly recognized for playing a critical role in human health and disease, especially in conferring resistance to both virulent pathogens such as Salmonella, which infects 1.2 million people in the United States every year (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, et al., Emerg Infect Dis 17:7-15, 2011, https://doi.org/10.3201/eid1701.P11101), and opportunistic pathogens like Candida, which causes an estimated 46,000 cases of invasive candidiasis each year in the United States (Centers for Disease Control and Prevention, Antibiotic Resistance Threats in the United States, 2013, 2013). Using a gnotobiotic mouse model, we investigate potential changes in gut microbial community structure and function during infection using metagenomics and metabolomics. We observe that changes in the community and in biosynthetic gene cluster potential occur within 3 days for the virulent Salmonella enterica serovar Typhimurium, but there are minimal changes with a poorly colonizing Candida albicans In addition, the metabolome shifts depending on infection status, including changes in glutathione metabolites in response to Salmonella infection, potentially in response to host oxidative stress.}, }
@article {pmid30401770, year = {2018}, author = {Smith, GJ and Angle, JC and Solden, LM and Borton, MA and Morin, TH and Daly, RA and Johnston, MD and Stefanik, KC and Wolfe, R and Gil, B and Wrighton, KC}, title = {Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, doi = {10.1128/mBio.00815-18}, pmid = {30401770}, issn = {2150-7511}, abstract = {Microbial carbon degradation and methanogenesis in wetland soils generate a large proportion of atmospheric methane, a highly potent greenhouse gas. Despite their potential to mitigate greenhouse gas emissions, knowledge about methane-consuming methanotrophs is often limited to lower-resolution single-gene surveys that fail to capture the taxonomic and metabolic diversity of these microorganisms in soils. Here our objective was to use genome-enabled approaches to investigate methanotroph membership, distribution, and in situ activity across spatial and seasonal gradients in a freshwater wetland near Lake Erie. 16S rRNA gene analyses demonstrated that members of the methanotrophic Methylococcales were dominant, with the dominance largely driven by the relative abundance of four taxa, and enriched in oxic surface soils. Three methanotroph genomes from assembled soil metagenomes were assigned to the genus Methylobacter and represented the most abundant methanotrophs across the wetland. Paired metatranscriptomes confirmed that these Old Woman Creek (OWC) Methylobacter members accounted for nearly all the aerobic methanotrophic activity across two seasons. In addition to having the capacity to couple methane oxidation to aerobic respiration, these new genomes encoded denitrification potential that may sustain energy generation in soils with lower dissolved oxygen concentrations. We further show that Methylobacter members that were closely related to the OWC members were present in many other high-methane-emitting freshwater and soil sites, suggesting that this lineage could participate in methane consumption in analogous ecosystems. This work contributes to the growing body of research suggesting that Methylobacter may represent critical mediators of methane fluxes in freshwater saturated sediments and soils worldwide.IMPORTANCE Here we used soil metagenomics and metatranscriptomics to uncover novel members within the genus Methylobacter We denote these closely related genomes as members of the lineage OWC Methylobacter Despite the incredibly high microbial diversity in soils, here we present findings that unexpectedly showed that methane cycling was primarily mediated by a single genus for both methane production (&quot;Candidatus Methanothrix paradoxum&quot;) and methane consumption (OWC Methylobacter). Metatranscriptomic analyses revealed that decreased methanotrophic activity rather than increased methanogenic activity possibly contributed to the greater methane emissions that we had previously observed in summer months, findings important for biogeochemical methane models. Although members of this Methylococcales order have been cultivated for decades, multi-omic approaches continue to illuminate the methanotroph phylogenetic and metabolic diversity harbored in terrestrial and marine ecosystems.}, }
@article {pmid30400812, year = {2018}, author = {Kumar, MS and Slud, EV and Okrah, K and Hicks, SC and Hannenhalli, S and Corrada Bravo, H}, title = {Analysis and correction of compositional bias in sparse sequencing count data.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {799}, doi = {10.1186/s12864-018-5160-5}, pmid = {30400812}, issn = {1471-2164}, support = {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 ; }, 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 {pmid30398115, year = {2018}, author = {Hazra, S and Patra, S}, title = {Alleviating the Neglected Tropical Diseases: Recent Developments in Diagnostics and Detection.}, journal = {Current topics in medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/1568026618666181106124015}, pmid = {30398115}, issn = {1873-4294}, abstract = {Background Neglected tropical diseases (NTDs) are communicable diseases caused by a group of bacteria, viruses, protozoa and helminths prevalent in more than 145 countries that affect the world's poverty stricken populations. WHO enlists 18 NTDs amongst people living in endemic areas having inaccessibility to preventive measures. Steps to reduce the global disease burden of the NTDs need attention at multi-factorial levels. Control programmes, mass drug administrations, transmission checks, eradication surveillances and diagnoses are some of them. The foremost in this list is confirmatory diagnosis. A comprehensive summary of the innovative, high-impact, multiplexed, low-cost diagnostic tools developed in the last decade that helped to meet the needs of users can depict a holistic approach to further evaluate potential technologies and reagents currently in research. Major advancements A literature survey based on developing nano-biotechnological platforms to meet the diagnostic challenges in NTDs towards development of a useful point-of-care (POC) unit is reported. However, in order to pave the way for complete eradication more sensitive tools are required that are user-friendly and applicable for use in endemic and low-resource settings. There are various novel research progresses/advancements made for qualitative and quantitative measurement of infectious load in some diseases like dengue, Chagas disease and leishmaniasis; though further improvements on the specificity and sensitivity front are still awaited. Strategies to combat the problem of antimicrobial drug resistance in diagnosis of NTDs have also been put forward by various research groups and organizations. Moreover, the state-of-the-art &quot;omics&quot; approaches like metabolomics and metagenomics have also started to contribute constructively towards diagnosis and prevention of the NTDs. Conclusion A concrete solution towards a single specimen based common biomarker detection platform for NTDs is lacking. Identifying robust biomarkers and implementing them on simple diagnostic tools to ease the process of pathogen detection can help us understand the obstacles in current diagnostic measures of the NTDs.}, }
@article {pmid30398110, year = {2018}, author = {Wang, L and Yu, X and Zhang, C and Zeng, T}, title = {Detecting personalized determinates during drug treatment from omics big data.}, journal = {Current pharmaceutical design}, volume = {}, number = {}, pages = {}, doi = {10.2174/1381612824666181106102111}, pmid = {30398110}, issn = {1873-4286}, abstract = {BACKGROUNDS: The targeted therapy is the foundation of personalized medicine in cancer, which is often understood as the right patient using the right drug. Thinking from the viewpoint of determinates during personalized drug treatment, the genetics, epigenetics and metagenomics would provide individual-specific biological elements to characterize the personalized responses for therapy.<br><br>METHODS: Such personalized determinates should be not extremely understood as specificity for only one person, while they should have certain replicate observations in a group of individuals but no all, which actually provide more credible and reproducible personalized biological features. And the requirement of detecting personalized determinates is well supported by novel high-throughput sequencing technologies and newly temporal-spatial experimental protocols, which quickly produce the omics big data.<br><br>RESULTS: In this mini-review, we would like to give a brief introduction firstly on the advanced drug or drug-like therapy with genetics, epigenetics and metagenomics respectively from the viewpoint of personalized determinates; then summarize the computational methods helpful to analyze the corresponding omics data under the consideration of personalized biological context; and particularly focus on the metagenomics to discuss current data, method, and opportunity for personalized medicine.<br><br>CONCLUSIONS: Totally, detecting personalized determinates during drug treatment from omics big data will bring the precision medicine or personalized medicine from concept to application. More and more inspiring bio-technologies, data resources, and analytic approaches will benefit All of US in the near future.}, }
@article {pmid30397794, year = {2018}, author = {Lau, NS and Zarkasi, KZ and Md Sah, ASR and Shu-Chien, AC}, title = {Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1283-0}, pmid = {30397794}, issn = {1432-184X}, abstract = {Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.}, }
@article {pmid30397546, year = {2018}, author = {Md Zoqratt, MZH and Eng, WWH and Thai, BT and Austin, CM and Gan, HM}, title = {Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5826}, doi = {10.7717/peerj.5826}, pmid = {30397546}, issn = {2167-8359}, abstract = {Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3-V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.}, }
@article {pmid30397357, year = {2018}, author = {Tirosh, O and Conlan, S and Deming, C and Lee-Lin, SQ and Huang, X and ,  and Su, HC and Freeman, AF and Segre, JA and Kong, HH}, title = {Expanded skin virome in DOCK8-deficient patients.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41591-018-0211-7}, pmid = {30397357}, issn = {1546-170X}, abstract = {Human microbiome studies have revealed the intricate interplay of host immunity and bacterial communities to achieve homeostatic balance. Healthy skin microbial communities are dominated by bacteria with low viral representation1-3, mainly bacteriophage. Specific eukaryotic viruses have been implicated in both common and rare skin diseases, but cataloging skin viral communities has been limited. Alterations in host immunity provide an opportunity to expand our understanding of microbial-host interactions. Primary immunodeficient patients manifest with various viral, bacterial, fungal, and parasitic infections, including skin infections4. Dedicator of cytokinesis 8 (DOCK8) deficiency is a rare primary human immunodeficiency characterized by recurrent cutaneous and systemic infections, as well as atopy and cancer susceptibility5. DOCK8, encoding a guanine nucleotide exchange factor highly expressed in lymphocytes, regulates actin cytoskeleton, which is critical for migration through collagen-dense tissues such as skin6. Analyzing deep metagenomic sequencing data from DOCK8-deficient skin samples demonstrated a notable increase in eukaryotic viral representation and diversity compared with healthy volunteers. De novo assembly approaches identified hundreds of novel human papillomavirus genomes, illuminating microbial dark matter. Expansion of the skin virome in DOCK8-deficient patients underscores the importance of immune surveillance in controlling eukaryotic viral colonization and infection.}, }
@article {pmid30397356, year = {2018}, author = {Sun, L and Xie, C and Wang, G and Wu, Y and Wu, Q and Wang, X and Liu, J and Deng, Y and Xia, J and Chen, B and Zhang, S and Yun, C and Lian, G and Zhang, X and Zhang, H and Bisson, WH and Shi, J and Gao, X and Ge, P and Liu, C and Krausz, KW and Nichols, RG and Cai, J and Rimal, B and Patterson, AD and Wang, X and Gonzalez, FJ and Jiang, C}, title = {Gut microbiota and intestinal FXR mediate the clinical benefits of metformin.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41591-018-0222-4}, pmid = {30397356}, issn = {1546-170X}, abstract = {The anti-hyperglycemic effect of metformin is believed to be caused by its direct action on signaling processes in hepatocytes, leading to lower hepatic gluconeogenesis. Recently, metformin was reported to alter the gut microbiota community in humans, suggesting that the hyperglycemia-lowering action of the drug could be the result of modulating the population of gut microbiota. However, the critical microbial signaling metabolites and the host targets associated with the metabolic benefits of metformin remained elusive. Here, we performed metagenomic and metabolomic analysis of samples from individuals with newly diagnosed type 2 diabetes (T2D) naively treated with metformin for 3 d, which revealed that Bacteroides fragilis was decreased and the bile acid glycoursodeoxycholic acid (GUDCA) was increased in the gut. These changes were accompanied by inhibition of intestinal farnesoid X receptor (FXR) signaling. We further found that high-fat-diet (HFD)-fed mice colonized with B. fragilis were predisposed to more severe glucose intolerance, and the metabolic benefits of metformin treatment on glucose intolerance were abrogated. GUDCA was further identified as an intestinal FXR antagonist that improved various metabolic endpoints in mice with established obesity. Thus, we conclude that metformin acts in part through a B. fragilis-GUDCA-intestinal FXR axis to improve metabolic dysfunction, including hyperglycemia.}, }
@article {pmid30397237, year = {2018}, author = {Souza, WM and Fumagalli, MJ and Torres Carrasco, AO and Romeiro, MF and Modha, S and Seki, MC and Gheller, JM and Daffre, S and Nunes, MRT and Murcia, PR and Acrani, GO and Figueiredo, LTM}, title = {Viral diversity of Rhipicephalus microplus parasitizing cattle in southern Brazil.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16315}, doi = {10.1038/s41598-018-34630-1}, pmid = {30397237}, issn = {2045-2322}, support = {MC_UU_120/14/9//Medical Research Council (MRC)/ ; }, abstract = {Ticks are ectoparasites spread worldwide and are well known as vectors of many viruses of great importance to human and animal health. However, the viral diversity in ticks is still poorly understood, particularly in South America. Here we characterized the viral diversity present in Rhipicephalus microplus parasitizing cattle in the southern region of Brazil using metagenomics. Our study revealed the presence of viruses that had not been previously described in the region, including lihan tick virus (Phenuiviridae family) and wuhan tick virus 2 (Chuviridae family), as well as expands the biogeography of jingmen tick virus (Flaviviridae family) in Brazil. Also, we described three novel tymoviruses (Tymovirales order), named guarapuava tymovirus-like 1 to 3. We described the genomic and phylogenetic characterization of these viruses. Our study sheds light on the viral diversity of Rhipicephalus microplus in South America, and also expands the biogeography of tick viruses that were previously described only in Asia.}, }
@article {pmid30396371, year = {2018}, author = {Meisel, JS and Nasko, DJ and Brubach, B and Cepeda-Espinoza, V and Chopyk, J and Corrada-Bravo, H and Fedarko, M and Ghurye, J and Javkar, K and Olson, ND and Shah, N and Allard, SM and Bazinet, AL and Bergman, NH and Brown, A and Caporaso, JG and Conlan, S and DiRuggiero, J and Forry, SP and Hasan, NA and Kralj, J and Luethy, PM and Milton, DK and Ondov, BD and Preheim, S and Ratnayake, S and Rogers, SM and Rosovitz, MJ and Sakowski, EG and Schliebs, NO and Sommer, DD and Ternus, KL and Uritskiy, G and Zhang, SX and Pop, M and Treangen, TJ}, title = {Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {197}, doi = {10.1186/s40168-018-0582-5}, pmid = {30396371}, issn = {2049-2618}, support = {R01-AI-100947//National Institutes of Health/ ; U54CA143924//National Institutes of Health/ ; U54CA143925//National Institutes of Health/ ; IIS-1513615//National Science Foundation (US)/ ; 1565100//National Science Foundation (US)/ ; DEB1556574//National Science Foundation (US)/ ; W911NF-17-2-0089//Intelligence Advanced Research Projects Activity (US)/ ; R01 GM114267//National Institutes of Health (US)/ ; HSHQDC-15-C-00064//Science and Technology Directorate/ ; }, abstract = {The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.}, }
@article {pmid30396006, year = {2018}, author = {Velikonja, A and Lipoglavšek, L and Zorec, M and Orel, R and Avguštin, G}, title = {Alterations in gut microbiota composition and metabolic parameters after dietary intervention with barley beta glucans in patients with high risk for metabolic syndrome development.}, journal = {Anaerobe}, volume = {55}, number = {}, pages = {67-77}, doi = {10.1016/j.anaerobe.2018.11.002}, pmid = {30396006}, issn = {1095-8274}, abstract = {Metabolic syndrome is a complex disease that is exponentially increasing in the western world, and diet is one of the possible ways to improve the metabolic status of patients. Barley beta glucans are dietary fibres that show promise for improvement cholesterol levels and postprandial glucose response, but they have been rarely investigated in human trials with concurrent focus on gut microbiota. A double-blind, placebo-controlled, randomised clinical trial was conducted with 43 volunteers with high risk for metabolic syndrome development or with diagnosed metabolic syndrome. During a four-week intervention study, participants consumed experimental bread containing 6 g of barley beta glucans or equal bread but without beta glucans. After dietary intervention, total plasma cholesterol decreased in the test group (-0.26 ± 0.54, p = 0.019), but not in the control group. Short chain fatty acids (SCFA) composition in faeces significantly changed with increase of propionic acid in test group (43.2%, p = 0.045) and with decrease of acetic acid in control group (41.8%, p = 0.011). The microbiome analysis based on Illumina paired end sequencing of 16S rRNA genes showed a decrease in microbial diversity and richness in the test group. The pre-intervention gut microbiota composition showed higher abundance of health associated Bifidobacterium spp. and Akkermansia municiphila within cholesterol-responsive group, showing that diet-induced metabolic response is possibly dependent on individual gut microbiota composition.}, }
@article {pmid30395567, year = {2018}, author = {Koehler, JW and Douglas, CE and Minogue, TD}, title = {A highly multiplexed broad pathogen detection assay for infectious disease diagnostics.}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {11}, pages = {e0006889}, doi = {10.1371/journal.pntd.0006889}, pmid = {30395567}, issn = {1935-2735}, abstract = {Rapid pathogen identification during an acute febrile illness is a critical first step for providing appropriate clinical care and patient isolation. Primary screening using sensitive and specific assays, such as real-time PCR and ELISAs, can rapidly test for known circulating infectious diseases. If the initial testing is negative, potentially due to a lack of developed diagnostic assays or an incomplete understanding of the pathogens circulating within a geographic region, additional testing would be required including highly multiplexed assays and metagenomic next generation sequencing. To bridge the gap between rapid point of care diagnostics and sequencing, we developed a highly multiplexed assay designed to detect 164 different viruses, bacteria, and parasites using the NanoString nCounter platform. Included in this assay were high consequence pathogens such as Ebola virus, highly endemic organisms including several Plasmodium species, and a large number of less prevalent pathogens to ensure a broad coverage of potential human pathogens. Evaluation of this panel resulted in positive detection of 113 (encompassing 98 different human pathogen types) of the 126 organisms available to us including the medically important Ebola virus, Lassa virus, dengue virus serotypes 1-4, Chikungunya virus, yellow fever virus, and Plasmodium falciparum. Overall, this assay could improve infectious disease diagnostics and biosurveillance efforts as a quick, highly multiplexed, and easy to use pathogen screening tool.}, }
@article {pmid30394652, year = {2018}, author = {Borton, MA and Daly, RA and O'Banion, B and Hoyt, DW and Marcus, DN and Welch, S and Hastings, SS and Meulia, T and Wolfe, RA and Booker, AE and Sharma, S and Cole, DR and Wunch, K and Moore, JD and Darrah, TH and Wilkins, MJ and Wrighton, KC}, title = {Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14467}, pmid = {30394652}, issn = {1462-2920}, abstract = {About 60% of natural gas production in the United States comes from hydraulic fracturing of unconventional reservoirs, such as shales or organic-rich micrites. This process inoculates and enriches for halotolerant microorganisms in these reservoirs over time, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of methanogens across unconventional reservoirs, and report that members of genus Methanohalophilus are recovered from every hydraulically fractured unconventional reservoir sampled by metagenomics. We provide the first genomic sequencing of three isolate genomes, as well as two metagenome assembled genomes. Utilizing six other previously sequenced genomes, we perform comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in CRISPR-Cas systems of Methanohalophilus, with genomes from geographically distinct unconventional reservoirs sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic methane production in hydraulically fractured unconventional reservoirs. This article is protected by copyright. All rights reserved.}, }
@article {pmid30394313, year = {2018}, author = {Wang, M and Zhou, J and He, F and Cai, C and Wang, H and Wang, Y and Lin, Y and Rong, H and Cheng, G and Xu, R and Zhou, W}, title = {Alteration of gut microbiota-associated epitopes in children with autism spectrum disorders.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2018.10.006}, pmid = {30394313}, issn = {1090-2139}, abstract = {BACKGROUND: Autism spectrum disorder (ASD) affects 1% of children and has no cure. Gastrointestinal (GI) problems are common in children with ASD, and although gut microbiota is known to play an important role in ASD through the gut-brain axis, the specific mechanism is unknown. Recent evidence suggests that gut microbiota may participate in the pathogenesis of ASD through immune- and inflammation-mediated pathways. Here, we identified potentially immunogenic epitopes derived from gut microbiota in stool samples from ASD children with and without GI problems and typically developing (TD) children.<br><br>METHODS: Candidate gut microbiota-associated epitopes (MEs) were identified by blast shotgun metagenomic sequencing of fecal samples from 43 ASD children (19 with and 24 without GI involvement) and 31 sex- and age-matched typically developing (TD) children. Potentially immunogenic epitopes were screened against a predictive human Immune Epitope Database. The composition and abundance of candidate MEs were compared between the three groups of children.<br><br>RESULTS: MEs identified in ASD children with GI problems were significantly more diverse than those in TD children. ME composition could discriminate between the three groups of children. We identified 34 MEs that were significantly more or less abundant in ASD children than TD children, most (29/34) of the differences in MEs were reduced in ASD and associated with abnormal gut IgA level and altered gut microbiota composition, these MEs were limited effected by clinical factors such as age, gender, and GI problems, of which eleven MEs were pathogenic microorganisms peptides with strong T or B cell response, nine MEs showed high homology to peptides from human self proteins associated with autoimmune disease occurrence, eliciting immune attack against hematopoietic stem cells and inhibition antigen binding. We also found that the abundance of five MEs were increased in ASD, including three human self proteins, gap junction alpha-1 (GJA1), paired box protein Pax-3 (PAX3) and eyes absent homolog 1 isoform 4 (EYA1) which associated with cancer, and a ME with homology to a Listeriolysin O peptide from the pathogenic bacterium Listeria monocytogenes was significantly increased in ASD children compared with TD children.<br><br>CONCLUSIONS: Our findings demonstrate the abnormal of MEs composition in the gut of children with ASD, moreover, the abnormality in MEs composition was associated with abnormal gut IgA levels and altered gut microbiota composition, this abnormality also suggests that there may be abnormalities in intestinal immunity in children with ASD; In all, thirty-four MEs identified were potential biomarker of ASD, andalterations in MEs may contribute to abnormalities in gut immunity and/or homeostasis in ASD children. Further study of the MEs identified here may advance our understanding of the pathogenesis of ASD.}, }
@article {pmid30392911, year = {2018}, author = {Zhang, Y and Weng, Y and Gan, H and Zhao, X and Zhi, F}, title = {Streptococcus gallolyticus conspires myeloid cells to promote tumorigenesis of inflammatory bowel disease.}, journal = {Biochemical and biophysical research communications}, volume = {506}, number = {4}, pages = {907-911}, doi = {10.1016/j.bbrc.2018.10.136}, pmid = {30392911}, issn = {1090-2104}, abstract = {Metagenomic analyses indicate that streptococcus gallolyticus is enriched at carcinoma in colitis associated colorectal cancer compared with sporadic colorectal cancer. But the particular mechanism of streptococcus gallolyticus in Inflammatory Bowel Disease malignant progression remains undefined yet. We aim to explore the biological carcinogenesis efficacy of streptococcus gallolyticus and its potential mechanism in azoxymethane and dextran sodium sulphate-induced colitis associated colorectal cancer in mice. Oral pretreatment of streptococcus gallolyticus was adopted to evaluate its detrimental effect. The colorectums of experimental C57BL/6 mice were collected and examined for the degree of tumorigenesis. Comparative 16S rRNA sequencing was carried out to observe streptococcus gallolyticus alterations in abundance. We found that streptococcus gallolyticus are enriched in colonic carcinoma compared to adenoma and healthy mice. Pretreatment of Streptococcus gallolyticus aggravated tumor formation, with more colonic obstruction, larger number and diameter of tumor node. Furthermore, Streptococcus gallolyticus selectively recruits tumor-infiltrating myeloid cells but not mast cells, including marrow-derived suppressor cells, tumor-associated macrophages and dendritic cells, which can inhibit competence of T cells. Moreover, several myeloid-cell-derived proinflammatory cytokines (IL-6, IL-1β, IL-8, CCL2, COX-2, TNF-α) were increased with the formation of carcinoma in IBD. Collectively, these data suggest that, through recruitment of tumor-infiltrating immune cells, Streptococcus gallolyticus generate an immune suppressive microenvironment that is conducive for neoplasia progression of Inflammatory Bowel Disease.}, }
@article {pmid30392727, year = {2018}, author = {Wang, L and Ravichandran, V and Yin, Y and Yin, J and Zhang, Y}, title = {Natural Products from Mammalian Gut Microbiota.}, journal = {Trends in biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibtech.2018.10.003}, pmid = {30392727}, issn = {1879-3096}, abstract = {The mammalian gut has a remarkable abundance of microbes. These microbes have strong potential to biosynthesize distinct metabolites that are promising drugs, and many more bioactive compounds have yet to be explored as potential drug candidates. These small bioactive molecules often mediate important host-microbe and microbe-microbe interactions. In this review, we provide perspectives on and challenges associated with three mining strategies - culture-based, (meta)genomics-based, and metabolomics-based mining approaches - for discovering natural products derived from biosynthetic gene clusters (BGCs) in mammalian gut microbiota. In addition, we comprehensively summarize the structures, biological functions, and BGCs of these compounds. Improving these techniques, including by using combinatorial approaches, may accelerate drug discovery from gut microbes.}, }
@article {pmid30390805, year = {2018}, author = {Wang, Q and Yang, F and Jia, H}, title = {Mining the Microbiome for Drug Targets.}, journal = {Methods in enzymology}, volume = {610}, number = {}, pages = {59-72}, doi = {10.1016/bs.mie.2018.09.014}, pmid = {30390805}, issn = {1557-7988}, abstract = {The human microbiome is our &quot;other genome.&quot; Implicated in a growing list of complex diseases, for which genomic studies typically explain a portion of the disease susceptibility, the human gut microbiome has been at the spotlight for our understanding of human diseases. As the microbiome is intrinsically more variable than the human genome, it is important to take careful considerations at each step of a study. Here, we put forward our recommendations, which we envision would facilitate identification of true drug targets in the human microbiome in the colon as well as at other body sites.}, }
@article {pmid30390617, year = {2018}, author = {Kwak, J and Park, J}, title = {What we can see from very small size sample of metagenomic sequences.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {399}, doi = {10.1186/s12859-018-2431-8}, pmid = {30390617}, issn = {1471-2105}, abstract = {BACKGROUND: Since the analysis of a large number of metagenomic sequences costs heavy computing resources and takes long time, we examined a selected small part of metagenomic sequences as &quot;sample&quot;s of the entire full sequences, both for a mock community and for 10 different existing metagenomics case studies. A mock community with 10 bacterial strains was prepared, and their mixed genome were sequenced by Hiseq. The hits of BLAST search for reference genome of each strain were counted. Each of 176 different small parts selected from these sequences were also searched by BLAST and their hits were also counted, in order to compare them to the original search results from the full sequences. We also prepared small parts of sequences which were selected from 10 publicly downloadable research data of MG-RAST service, and analyzed these samples with MG-RAST.<br><br>RESULTS: Both the BLAST search tests of the mock community and the results from the publicly downloadable researches of MG-RAST show that sampling an extremely small part from sequence data is useful to estimate brief taxonomic information of the original metagenomic sequences. For 9 cases out of 10, the most annotated classes from the MG-RAST analyses of the selected partial sample sequences are the same as the ones from the originals.<br><br>CONCLUSIONS: When a researcher wants to estimate brief information of a metagenome's taxonomic distribution with less computing resources and within shorter time, the researcher can analyze a selected small part of metagenomic sequences. With this approach, we can also build a strategy to monitor metagenome samples of wider geographic area, more frequently.}, }
@article {pmid30390509, year = {2019}, author = {Leng, L and Nobu, MK and Narihiro, T and Yang, P and Amy Tan, GY and Lee, PH}, title = {Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: Pathways and mechanisms.}, journal = {Water research}, volume = {148}, number = {}, pages = {281-291}, doi = {10.1016/j.watres.2018.10.063}, pmid = {30390509}, issn = {1879-2448}, abstract = {Glycerol is presently being generated in surplus with the rapid growth of the biodiesel industry and seeks ways to be upcycled, rather than to be treated with costs. Glycerol for the co-production of 1,3-propanediol (1,3-PDO) and caproate has a great prospect. Yet, its technical difficulty lies in the enhancement of caproate productivity, which requires the presence of ethanol as a co-substrate and necessitates the co-existence of functional microbes for glycerol fermentation and chain elongation. This study successfully achieved 6.38 mM C 1,3-PDO d-1 and 2.95 mM C caproate d-1 in a 2-L mixed-cultured semi-continuous fermenter with a glycerol-ethanol-acetate stoichiometric ratio of 4:3:1. Such conversions were mainly facilitated by a microbial community of Eubacterium limosum, Clostridium kluyveri and Massilibacterium senegalense. With such a synergistic microbiome, the co-production of 1,3-PDO and caproate was achieved from glycerol without ethanol addition. Based on metagenomics, E. limosum is capable of converting glycerol to 1,3-PDO, ethanol and H2, and also redirecting the electron potential of H2 into acetate via the Wood-Ljungdahl pathway, which is then used for chain elongation. C. kluyveri worked synergistically with E. limosum by consuming ethanol and acetate for caproate production. M. senegalense encodes for ethanol oxidation to acetate and butyrate, facilitating the generation of these intermediates for C. kluyveri elongation to caproate. During the transition between fermentation and elongation, an unexpected observation of poly-β-hydroxybutyrate (PHB) formation and reutilization by M. senegalense may be associated with butyrate formation for further caproate generation. The knowledge gleaned from the substrate constitute, microbial consortium and their synergetic metabolism demonstrates a resource upgrade potential for crude glycerol or glycerol-containing wastewater generated from the biodiesel industry.}, }
@article {pmid30388523, year = {2019}, author = {Zhang, Y and Hua, ZS and Lu, H and Oehmen, A and Guo, J}, title = {Elucidating functional microorganisms and metabolic mechanisms in a novel engineered ecosystem integrating C, N, P and S biotransformation by metagenomics.}, journal = {Water research}, volume = {148}, number = {}, pages = {219-230}, doi = {10.1016/j.watres.2018.10.061}, pmid = {30388523}, issn = {1879-2448}, abstract = {Denitrifying sulfur conversion-associated enhanced biological phosphorous removal (DS-EBPR) system is not only a novel wastewater treatment process, but also an ideal model for microbial ecology in a community context. However, it exists the knowledge gap on the roles and interactions of functional microorganisms in the DS-EBPR system for carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) bioconversions. We use genome-resolved metagenomics to build up an ecological model of microbial communities in a lab-scale DS-EBPR system with stable operation for more than 400 days. Our results yield 11 near-complete draft genomes that represent a substantial portion of the microbial community (39.4%). Sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB) promote complex metabolic processes and interactions for C, N, P and S conversions. Bins 1-4 and 10 are considered as new potential polyphosphate-accumulating organisms (PAOs), in which Bins 1-4 can be considered as S-related PAOs (S-PAOs) with no previously cultivated or reported members. Our findings give an insight into a new ecological system with C, N, P and S simultaneous bioconversions and improve the understanding of interactions among SRB, SOB, denitrifiers and PAOs within a community context.}, }
@article {pmid30388453, year = {2018}, author = {Vangay, P and Johnson, AJ and Ward, TL and Al-Ghalith, GA and Shields-Cutler, RR and Hillmann, BM and Lucas, SK and Beura, LK and Thompson, EA and Till, LM and Batres, R and Paw, B and Pergament, SL and Saenyakul, P and Xiong, M and Kim, AD and Kim, G and Masopust, D and Martens, EC and Angkurawaranon, C and McGready, R and Kashyap, PC and Culhane-Pera, KA and Knights, D}, title = {US Immigration Westernizes the Human Gut Microbiome.}, journal = {Cell}, volume = {175}, number = {4}, pages = {962-972.e10}, doi = {10.1016/j.cell.2018.10.029}, pmid = {30388453}, issn = {1097-4172}, abstract = {Many US immigrant populations develop metabolic diseases post immigration, but the causes are not well understood. Although the microbiome plays a role in metabolic disease, there have been no studies measuring the effects of US immigration on the gut microbiome. We collected stool, dietary recalls, and anthropometrics from 514 Hmong and Karen individuals living in Thailand and the United States, including first- and second-generation immigrants and 19 Karen individuals sampled before and after immigration, as well as from 36 US-born European American individuals. Using 16S and deep shotgun metagenomic DNA sequencing, we found that migration from a non-Western country to the United States is associated with immediate loss of gut microbiome diversity and function in which US-associated strains and functions displace native strains and functions. These effects increase with duration of US residence and are compounded by obesity and across generations.}, }
@article {pmid30388112, year = {2018}, author = {Jiang, ZD and Jenq, RR and Ajami, NJ and Petrosino, JF and Alexander, AA and Ke, S and Iqbal, T and DuPont, AW and Muldrew, K and Shi, Y and Peterson, C and Do, KA and DuPont, HL}, title = {Safety and preliminary efficacy of orally administered lyophilized fecal microbiota product compared with frozen product given by enema for recurrent Clostridium difficile infection: A randomized clinical trial.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0205064}, doi = {10.1371/journal.pone.0205064}, pmid = {30388112}, issn = {1932-6203}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) via colonoscopy or enema has become a commonly used treatment of recurrent C. difficile infection (CDI).<br><br>AIMS: To compare the safety and preliminary efficacy of orally administered lyophilized microbiota product compared with frozen product by enema.<br><br>METHODS: In a single center, adults with ≥ 3 episodes of recurrent CDI were randomized to receive encapsulated lyophilized fecal microbiota from 100-200 g of donor feces (n = 31) or frozen FMT from 100 g of donor feces (n = 34) by enema. Safety during the three months post FMT was the primary study objective. Prevention of CDI recurrence during the 60 days after FMT was a secondary objective. Fecal microbiome changes were examined in first 39 subjects studied.<br><br>RESULTS: Adverse experiences were commonly seen in equal frequency in both groups and did not appear to relate to the route of delivery of FMT. CDI recurrence was prevented in 26 of 31 (84%) subjects randomized to capsules and in 30 of 34 (88%) receiving FMT by enema (p = 0.76). Both products normalized fecal microbiota diversity while the lyophilized orally administered product was less effective in repleting Bacteroidia and Verrucomicrobia classes compared to frozen product via enema.<br><br>CONCLUSIONS: The route of delivery, oral or rectal, did not influence adverse experiences in FMT. In preliminary evaluation, both routes appeared to show equivalent efficacy, although the dose may need to be higher for lyophilized product. Spore-forming bacteria appear to be the most important engrafting organisms in FMT by the oral route using lyophilized product.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT02449174.}, }
@article {pmid30386778, year = {2018}, author = {Ferrandi, EE and Sayer, C and De Rose, SA and Guazzelli, E and Marchesi, C and Saneei, V and Isupov, MN and Littlechild, JA and Monti, D}, title = {New Thermophilic α/β Class Epoxide Hydrolases Found in Metagenomes From Hot Environments.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {6}, number = {}, pages = {144}, doi = {10.3389/fbioe.2018.00144}, pmid = {30386778}, issn = {2296-4185}, abstract = {Two novel epoxide hydrolases (EHs), Sibe-EH and CH65-EH, were identified in the metagenomes of samples collected in hot springs in Russia and China, respectively. The two α/β hydrolase superfamily fold enzymes were cloned, over-expressed in Escherichia coli, purified and characterized. The new EHs were active toward a broad range of substrates, and in particular, Sibe-EH was excellent in the desymmetrization of cis-2,3-epoxybutane producing the (2R,3R)-diol product with ee exceeding 99%. Interestingly these enzymes also hydrolyse (4R)-limonene-1,2-epoxide with Sibe-EH being specific for the trans isomer. The Sibe-EH is a monomer in solution whereas the CH65-EH is a dimer. Both enzymes showed high melting temperatures with the CH65-EH being the highest at 85°C retaining 80% of its initial activity after 3 h thermal treatment at 70°C making it the most thermal tolerant wild type epoxide hydrolase described. The Sibe-EH and CH65-EH have been crystallized and their structures determined to high resolution, 1.6 and 1.4 Å, respectively. The CH65-EH enzyme forms a dimer via its cap domains with different relative orientation of the monomers compared to previously described EHs. The entrance to the active site cavity is located in a different position in CH65-EH and Sibe-EH in relation to other known bacterial and mammalian EHs.}, }
@article {pmid30386437, year = {2018}, author = {Deutsch-Nagy, L and Urbán, P and Tóth, Z and Bihari, Z and Kocsis, B and Fekete, C and Kilár, F}, title = {Genome sequence of Shigella sonnei 4303.}, journal = {Gut pathogens}, volume = {10}, number = {}, pages = {47}, doi = {10.1186/s13099-018-0274-5}, pmid = {30386437}, issn = {1757-4749}, abstract = {Background: Shigella spp. are Gram-negative intracellular pathogenic bacteria belonging to the family Enterobacteriaceae and can cause bacterial dysentery, a severe diarrheal disease. The pathophysiological impact of the Gram-negative bacteria is highly related to the composition and structural variability of lipopolysaccharides, the major lipoid components of the outer membrane. Out of the 114 genes involved in the lipopolysaccharide biosynthesis pathway, 47 genes are specific to Shigella spp. Changes in the specific genes can lead to loss of the O polysaccharide side chain, resulting in rough (R) type bacteria with increased sensitivity to temperature, or hydrophobic antibiotics. The formation of various different lipopolysaccharides or lipooligosaccharides has been observed previously in a mutant line showing altered biological properties, but the genetic background has not been investigated in detail.<br><br>Results: The parental strain of the mutant line, Shigella sonnei 4303, was subjected to whole genome sequencing to gain a better insight into the structure and biosynthesis of lipopolysaccharides. The sequencing revealed a 4,546,505 bp long genome including chromosomal and plasmid DNA, and the lipopolysaccharide biosynthesis genes were also identified. A comparison of the genome was performed with the phylogenetically closely related, wild type, well characterized, highly virulent strain, S. sonnei 53G.<br><br>Conclusion: Analysis of the lipopolysaccharide biosynthetic genes helped us to get more insight into the pathogenicity and virulence of the bacteria. The genome revealed high similarities with S. sonnei 53G, which can be used as a standard in characterizing the S. sonnei 4303's R-type isogenic derivatives.}, }
@article {pmid30386306, year = {2018}, author = {Gao, X and Huynh, BT and Guillemot, D and Glaser, P and Opatowski, L}, title = {Inference of Significant Microbial Interactions From Longitudinal Metagenomics Data.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2319}, doi = {10.3389/fmicb.2018.02319}, pmid = {30386306}, issn = {1664-302X}, abstract = {Data of next-generation sequencing (NGS) and their analysis have been facilitating advances in our understanding of microbial ecosystems such as human gut microbiota. However, inference of microbial interactions occurring within an ecosystem is still a challenge mainly due to sequencing data (e.g., 16S rDNA sequences) providing relative abundance of microbes instead of absolute cell count. In order to describe growtth dynamics of microbial communities and estimate the involved microbial interactions, we introduce a procedure by integrating generalized Lotka-Volterra equations, forward stepwise regression and bootstrap aggregation. First, we successfully identify experimentally confirmed microbial interactions based on relative abundance data of a cheese microbial community. Then, we apply the procedure to time-series of 16S rDNA sequences of gut microbiomes of children who were progressing to Type 1 diabetes (T1D progressors), and compare their gut microbial interactions to a healthy control group. Our results suggest that the number of inferred microbial interactions increased over time during the first 3 years of life. More microbial interactions are found in the gut flora of healthy children than that of T1D progressors. The inhibitory effects from Actinobacteria and Bacilli to Bacteroidia, from Bacteroidia to Clostridia, and the beneficial effect from Clostridia to Bacteroidia are shared between healthy children and T1D progressors. An inhibition of Clostridia by Gammaproteobacteria is found in healthy children that maintains through their first 3 years of life. This suppression appears in T1D progressors during the first year of life, which transforms to a commensalism relationship at the age of 3 years old. Gammaproteobacteria is found exerting an inhibition on Bacteroidia in the T1D progressors, which is not identified in the healthy controls.}, }
@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}, 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 {pmid30384205, year = {2018}, author = {Duan, Y and Awasthi, SK and Chen, H and Liu, T and Zhang, Z and Zhang, L and Awasthi, MK and Taherzadeh, MJ}, title = {Evaluating the impact of bamboo biochar on the fungal community succession during chicken manure composting.}, journal = {Bioresource technology}, volume = {272}, number = {}, pages = {308-314}, doi = {10.1016/j.biortech.2018.10.045}, pmid = {30384205}, issn = {1873-2976}, abstract = {The objective of this study was to investigate the fungal community succession and variations in chicken manure (CM) compost with different concentration of bamboo biochar (BB) as additive via the using of metagenomics method. The consequent obviously revealed that Chytridiomycota, Mucoromycota, Ascomycota and Basidiomycota were the dominant phylum, while Batrachochytrium, Funneliformis, Mucor, Phizophagus and Pyronema were the pre-dominant genera in each treatment. Redundancy analyses indicated that higher dosage of biochar applied treatments has significant correlation between fungal communities and environmental factors. The diversity of fungal community was analogous but the relative abundance (RA) was inconsistent among the all treatments. In addition, the principal component analysis was also confirmed that T5 and T6 treatments have considerably correlation than other treatments. However, the mean value of RA remained maximum in higher dosage of biochar blended treatments. Ultimately, the RA of different fungal genus and species were influenced in CM compost by the BB amendment.}, }
@article {pmid30382616, year = {2018}, 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 = {}, number = {}, pages = {}, doi = {10.1111/jam.14147}, pmid = {30382616}, issn = {1365-2672}, support = {//Agencia Nacional de Promoción Científica y Tecnológica (MINCyT)/ ; }, 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 {pmid30382566, year = {2018}, author = {Goh, HH and Ng, CL and Loke, KK}, title = {Functional Genomics.}, journal = {Advances in experimental medicine and biology}, volume = {1102}, number = {}, pages = {11-30}, doi = {10.1007/978-3-319-98758-3_2}, pmid = {30382566}, issn = {0065-2598}, abstract = {Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery. An overview of transcriptomics workflow and experimental considerations is also introduced. Lastly, we present an in-house case study of transcriptomics analysis of an aromatic herbal plant to understand the effect of elicitation on the biosynthesis of volatile organic compounds.}, }
@article {pmid30381486, year = {2018}, author = {Piantadosi, A and Freije, CA and Gosmann, C and Ye, S and Park, D and Schaffner, SF and Tully, DC and Allen, TM and Dong, KL and Sabeti, PC and Kwon, DS}, title = {Metagenomic sequencing of HIV-1 in the blood and female genital tract reveals little quasispecies diversity during acute infection.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JVI.00804-18}, pmid = {30381486}, issn = {1098-5514}, abstract = {Heterosexual transmission of human immunodeficiency virus-1 (HIV-1) is associated with a significant bottleneck in the viral quasispecies population, yet the timing of that bottleneck is poorly understood. We characterized HIV-1 diversity in the blood and female genital tract (FGT) within two weeks after detection of infection in three women enrolled in a unique prospective cohort in South Africa. We assembled full-length HIV-1 genomes from matched samples of cervicovaginal lavage (CVL) and plasma. Deep sequencing allowed us to identify intrahost single nucleotide variants (iSNVs) and characterize within-sample HIV-1 diversity.Our results demonstrated very little HIV-1 diversity in the FGT and plasma by the time of detectable viremia. Within each subject, the consensus HIV-1 sequences were identical in plasma and CVL. No iSNV was present at >6% frequency. One subject had 77 low-frequency iSNVs across both CVL and plasma; another subject had 14 iSNVs in only CVL from the earliest time point; and the third subject had no iSNVs in CVL or plasma. Overall, the small amount of diversity that we detected was higher in the FGT than plasma and declined over the first two weeks after detectable viremia, compatible with a very early HIV-1 transmission bottleneck. To our knowledge, our study represents the earliest genomic analysis of HIV-1 in the FGT after transmission. Further, the use of metagenomic sequencing allowed us to characterize other organisms in the FGT, including commensal bacteria and sexually transmitted infections, highlighting the utility of this method to sequence both HIV-1 and its metagenomic environment.IMPORTANCE Due to error-prone replication, HIV-1 generates a diverse population of viruses within a chronically infected individual. When HIV-1 is transmitted to a new individual, one or a few viruses establish the new infection, leading to a genetic bottleneck in the virus population. Understanding the timing and nature of this bottleneck may provide insight into HIV-1 vaccine design and other preventative strategies. We examined the HIV-1 population in three women enrolled in a unique prospective cohort in South Africa, who were followed closely during the earliest stages of HIV-1 infection. We found very little HIV-1 diversity in the blood and female genital tract during the first two weeks after virus was detected in the bloodstream. These results are compatible with a very early HIV-1 population bottleneck, suggesting the need to study the HIV-1 population in the female genital tract before virus is detectable in the bloodstream.}, }
@article {pmid30379893, year = {2018}, author = {Bovo, S and Ribani, A and Utzeri, VJ and Schiavo, G and Bertolini, F and Fontanesi, L}, title = {Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0205575}, doi = {10.1371/journal.pone.0205575}, pmid = {30379893}, issn = {1932-6203}, abstract = {Honey bees are considered large-scale monitoring tools due to their environmental exploration and foraging activities. Traces of these activities can be recovered in the honey that also may reflect the hive ecological micro-conditions in which it has been produced. This study applied a next generation sequencing platform (Ion Torrent) for shotgun metagenomic analysis of honey environmental DNA (eDNA). The study tested a methodological framework to interpret DNA sequence information useful to describe the complex ecosystems of the honey bee colony superorganism, its pathosphere and the heterogeneity of the agroecological environments and environmental sources that left DNA marks in the honey. Analysis of two honeys reported sequence reads from five main organism groups (kingdoms or phyla): arthropods (that mainly included reads from Apis mellifera, several other members of the Hymenotpera, in addition to members of the Diptera, Coleoptera and Lepidoptera, as well as aphids and mites), plants (that clearly confirmed the botanical origin of the two honeys, i.e. orange tree blossom and eucalyptus tree blossom honeys), fungi and bacteria (including common hive and honey bee gut microorganisms, honey bee pathogens and plant pathogens), and viruses (which accounted for the largest number of reads in both honeys, mainly assigned to Apis mellifera filamentous virus). The shotgun metagenomic approach that was used in this study can be applied in large scale experiments that might have multiple objectives according to the multi-kingdom derived eDNA that is contained in the honey.}, }
@article {pmid30379272, year = {2018}, author = {Luvizotto, DM and Araujo, JE and Silva, MCP and Dias, ACF and Kraft, B and Tegetmeye, H and Strous, M and Andreote, FD}, title = {The rates and players of denitrification, dissimilatory nitrate reduction to ammonia (DNRA) and anaerobic ammonia oxidation (anammox) in mangrove soils.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {}, number = {}, pages = {0}, doi = {10.1590/0001-3765201820180373}, pmid = {30379272}, issn = {1678-2690}, abstract = {Mangroves are ecosystems located in the transition zone between land and sea, characterized by periodic flooding that confer to its unique characteristics. Little is known about the transformation of nutrients that occur during the organic matter degradation in this system. In this study, we monitor the nitrogen transformations in soils from three mangroves with distinct levels of contamination using labeled 15NO3-. We also screened the mangroves metagenomes for the presence of genes that encode enzymes involved in denitrification (nirS, nirK, nosZ, norB and narG), anaerobic oxidation of ammonia (anammox) (hh, hao and hzo) and dissimilatory nitrate reduction to ammonium (DNRA) (nrfA). The transformations of 15NO3- indicated the balance of denitrification over anammox and DNRA in all three mangroves, with lower rates of processes in the mangrove affected by oil contamination. The metagenomic analysis detected 56 sequences related to denitrification, 19 with anammox and 6 with DNRA. Genes related with denitrification were phylogenetically distributed among several groups of bacteria (mainly Gammaproteobacteria). Anammox and DNRA related sequences were affiliated with Planctomycetes and Gammaproteobacteria, respectively. Thus, metagenomic and functional approaches supported the description of denitrification, anammox and DNRA rates in mangrove soils, and identified the major bacterial groups involved in these processes.}, }
@article {pmid30377376, year = {2018}, author = {Franzosa, EA and McIver, LJ and Rahnavard, G and Thompson, LR and Schirmer, M and Weingart, G and Lipson, KS and Knight, R and Caporaso, JG and Segata, N and Huttenhower, C}, title = {Species-level functional profiling of metagenomes and metatranscriptomes.}, journal = {Nature methods}, volume = {15}, number = {11}, pages = {962-968}, doi = {10.1038/s41592-018-0176-y}, pmid = {30377376}, issn = {1548-7105}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, abstract = {Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types.}, }
@article {pmid30376898, year = {2018}, author = {Leiby, JS and McCormick, K and Sherrill-Mix, S and Clarke, EL and Kessler, LR and Taylor, LJ and Hofstaedter, CE and Roche, AM and Mattei, LM and Bittinger, K and Elovitz, MA and Leite, R and Parry, S and Bushman, FD}, title = {Lack of detection of a human placenta microbiome in samples from preterm and term deliveries.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {196}, doi = {10.1186/s40168-018-0575-4}, pmid = {30376898}, issn = {2049-2618}, support = {P30 AI045008//National Institute of Allergy and Infectious Diseases/ ; T32 AI007632//National Institute of Allergy and Infectious Diseases/ ; T32 AI007324//National Institute of Allergy and Infectious Diseases/ ; }, abstract = {BACKGROUND: Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is colonized with bacteria. For example, analysis of DNA from placenta samples yielded small proportions of microbial sequences which were proposed to represent normal bacterial colonization. However, an analysis by our group showed no distinction between background negative controls and placenta samples. Also supporting the idea that the womb is sterile is the observation that germ-free mammals can be generated by sterile delivery of neonates into a sterile isolator, after which neonates remain germ-free, which would seem to provide strong data in support of sterility of the womb.<br><br>RESULTS: To probe this further and to investigate possible placental colonization associated with spontaneous preterm birth, we carried out another study comparing microbiota in placenta samples from 20 term and 20 spontaneous preterm deliveries. Both 16S rRNA marker gene sequencing and shotgun metagenomic sequencing were used to characterize placenta and control samples. We first quantified absolute amounts of bacterial 16S rRNA gene sequences using 16S rRNA gene quantitative PCR (qPCR). As in our previous study, levels were found to be low in the placenta samples and indistinguishable from negative controls. Analysis by DNA sequencing did not yield a placenta microbiome distinct from negative controls, either using marker gene sequencing as in our previous work, or with shotgun metagenomic sequencing. Several types of artifacts, including erroneous read classifications and barcode misattribution, needed to be identified and removed from the data to clarify this point.<br><br>CONCLUSIONS: Our findings do not support the existence of a consistent placental microbiome, in either placenta from term deliveries or spontaneous preterm births.}, }
@article {pmid30373891, year = {2018}, author = {Bhatt, S and Egan, M and Critelli, B and Kouse, A and Kalman, D and Upreti, C}, title = {The Evasive Enemy: Insights into the Virulence and Epidemiology of the Emerging Attaching and Effacing Pathogen, Escherichia albertii.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1128/IAI.00254-18}, pmid = {30373891}, issn = {1098-5522}, abstract = {The diarrheic attaching and effacing (A/E) pathogen Escherichia albertii was first isolated from infants in Bangladesh in 1991, although the bacterium was initially classified as Hafnia alvei Subsequent genetic and biochemical interrogation of these isolates raised concerns about their initial taxonomic placement. It was not until 2003 that these isolates were reassigned to the novel taxon Escherichia albertii because they were genetically more closely related to E. coli, although they had diverged sufficiently to warrant a novel species name. Unfortunately, new isolates continue to be mistyped as enteropathogenic E. coli (EPEC) or enterohemorrhagic E. coli (EHEC) owing to shared traits, most notably the ability to form A/E lesions. Consequently, E. albertii remains an underappreciated A/E pathogen, despite multiple reports demonstrating that many provisional EPEC and EHEC isolates incriminated in disease outbreaks are actually E. albertii. Metagenomic studies on dozens of E. albertii isolates reveal a genetic architecture that boasts an arsenal of candidate virulence factors to rival that of its better-characterized cousins, EPEC and EHEC. Beyond these computational comparisons, studies addressing the regulation, structure, function, and mechanism of action of its repertoire of virulence factors are lacking. Thus, the paucity of knowledge about the epidemiology, virulence, and antibiotic resistance of E. albertii, coupled to its misclassification and its ability to develop multidrug resistance in a single step, highlight the challenges in combatting this emerging pathogen. This review seeks to synthesize our current, but yet incomplete, understanding of the biology of E. albertii.}, }
@article {pmid30373669, year = {2018}, author = {Nasko, DJ and Koren, S and Phillippy, AM and Treangen, TJ}, title = {RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification.}, journal = {Genome biology}, volume = {19}, number = {1}, pages = {165}, doi = {10.1186/s13059-018-1554-6}, pmid = {30373669}, issn = {1474-760X}, abstract = {In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes. These results suggest a need for new classification approaches specially adapted for large databases.}, }
@article {pmid30373533, year = {2018}, author = {Yao, Y and Jin, Z and Lee, JH}, title = {An improved statistical model for taxonomic assignment of metagenomics.}, journal = {BMC genetics}, volume = {19}, number = {1}, pages = {98}, doi = {10.1186/s12863-018-0680-1}, pmid = {30373533}, issn = {1471-2156}, support = {R03 AG054186/AG/NIA NIH HHS/United States ; R56 AG051876/AG/NIA NIH HHS/United States ; AG054186//National Institutes of Health/ ; AG051876//National Institute on Aging/ ; }, abstract = {BACKGROUND: With the advances in the next-generation sequencing technologies, researchers can now rapidly examine the composition of samples from humans and their surroundings. To enhance the accuracy of taxonomy assignments in metagenomic samples, we developed a method that allows multiple mismatch probabilities from different genomes.<br><br>RESULTS: We extended the algorithm of taxonomic assignment of metagenomic sequence reads (TAMER) by developing an improved method that can set a different mismatch probability for each genome rather than imposing a single parameter for all genomes, thereby obtaining a greater degree of accuracy. This method, which we call TADIP (Taxonomic Assignment of metagenomics based on DIfferent Probabilities), was comprehensively tested in simulated and real datasets. The results support that TADIP improved the performance of TAMER especially in large sample size datasets with high complexity.<br><br>CONCLUSIONS: TADIP was developed as a statistical model to improve the estimate accuracy of taxonomy assignments. Based on its varying mismatch probability setting and correlated variance matrix setting, its performance was enhanced for high complexity samples when compared with TAMER.}, }
@article {pmid30373528, year = {2018}, author = {Bal, A and Pichon, M and Picard, C and Casalegno, JS and Valette, M and Schuffenecker, I and Billard, L and Vallet, S and Vilchez, G and Cheynet, V and Oriol, G and Trouillet-Assant, S and Gillet, Y and Lina, B and Brengel-Pesce, K and Morfin, F and Josset, L}, title = {Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow.}, journal = {BMC infectious diseases}, volume = {18}, number = {1}, pages = {537}, doi = {10.1186/s12879-018-3446-5}, pmid = {30373528}, issn = {1471-2334}, abstract = {BACKGROUND: In recent years, metagenomic Next-Generation Sequencing (mNGS) has increasingly been used for an accurate assumption-free virological diagnosis. However, the systematic workflow evaluation on clinical respiratory samples and implementation of quality controls (QCs) is still lacking.<br><br>METHODS: A total of 3 QCs were implemented and processed through the whole mNGS workflow: a no-template-control to evaluate contamination issues during the process; an internal and an external QC to check the integrity of the reagents, equipment, the presence of inhibitors, and to allow the validation of results for each sample. The workflow was then evaluated on 37 clinical respiratory samples from patients with acute respiratory infections previously tested for a broad panel of viruses using semi-quantitative real-time PCR assays (28 positive samples including 6 multiple viral infections; 9 negative samples). Selected specimens included nasopharyngeal swabs (n = 20), aspirates (n = 10), or sputums (n = 7).<br><br>RESULTS: The optimal spiking level of the internal QC was first determined in order to be sufficiently detected without overconsumption of sequencing reads. According to QC validation criteria, mNGS results were validated for 34/37 selected samples. For valid samples, viral genotypes were accurately determined for 36/36 viruses detected with PCR (viral genome coverage ranged from 0.6 to 100%, median = 67.7%). This mNGS workflow allowed the detection of DNA and RNA viruses up to a semi-quantitative PCR Ct value of 36. The six multiple viral infections involving 2 to 4 viruses were also fully characterized. A strong correlation between results of mNGS and real-time PCR was obtained for each type of viral genome (R2 ranged from 0.72 for linear single-stranded (ss) RNA viruses to 0.98 for linear ssDNA viruses).<br><br>CONCLUSIONS: Although the potential of mNGS technology is very promising, further evaluation studies are urgently needed for its routine clinical use within a reasonable timeframe. The approach described herein is crucial to bring standardization and to ensure the quality of the generated sequences in clinical setting. We provide an easy-to-use single protocol successfully evaluated for the characterization of a broad and representative panel of DNA and RNA respiratory viruses in various types of clinical samples.}, }
@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}, 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 character