@article {pmid30649062, year = {2019}, author = {Sessa, L and Reddel, S and Manno, E and Quagliariello, A and Cotugno, N and Del Chierico, F and Amodio, D and Capponi, C and Leone, F and Bernardi, S and Rossi, P and Putignani, L and Palma, P}, title = {Distinct gut microbiota profile in ART-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.}, journal = {AIDS (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1097/QAD.0000000000002131}, pmid = {30649062}, issn = {1473-5571}, abstract = {OBJECTIVE: Persistent inflammation and higher risk to develop cardiovascular diseases (CVDs) still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota (GM) profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART.<br><br>DESIGN: Cross-sectional study including sixty-one ART-treated PHIV (age range 3-30 years old) and seventy-one age-matched healthy controls (CTRL). Blood and stool sample were collected at the same time and analyzed for GM composition and plasma biomarkers.<br><br>METHODS: GM composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, SI and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4+ and CD8+T-cells.<br><br>RESULTS: We identified two distinct GM profiles (group A and B) among PHIV. No different clinical parameters (age, sex, ethnicity, clinical class), dietary and sexual habits were found between the groups. The group A showed a relative dominance of Akkermansia muciniphila (A.muciniphila), whereas GM of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of sE-selectin (p = 0.0296), ICAM-1 (p = 0.0028), VCAM-1 (p = 0.0230), IL-6 (p = 0.0247) and sCD14 (p = 0.0142) in group A compared to group B.<br><br>CONCLUSIONS: Distinctive GM profiles are differently associated with inflammation, MT and VEA. Future studies are needed in order to understand the role of A.muciniphila and risk to develop CVDs in PHIV.}, }
@article {pmid30648011, year = {2019}, author = {Susi, H and Filloux, D and Frilander, MJ and Roumagnac, P and Laine, AL}, title = {Diverse and variable virus communities in wild plant populations revealed by metagenomic tools.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6140}, doi = {10.7717/peerj.6140}, pmid = {30648011}, issn = {2167-8359}, abstract = {Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.}, }
@article {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 {pmid28702706, year = {2018}, author = {Espínola, F and Dionisi, HM and Borglin, S and Brislawn, CJ and Jansson, JK and Mac Cormack, WP and Carroll, J and Sjöling, S and Lozada, M}, title = {Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {123-139}, pmid = {28702706}, issn = {1432-184X}, support = {CSP proposal ID 328//Joint Genome Institute/ ; ANPCyT PICT2008 Nº 0468//National Agency for the Promotion of Science and Technology of Argentina/ ; 112-200801-01736//CONICET/ ; UBA 20020100100378//Secretaria de Ciencia y Tecnica, Universidad de Buenos Aires/ ; grant No. 228107//Research Council of Norway/ ; DE-AC05-76RL01830//Laboratory Directed Research and Development Program at PNNL/ ; }, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Cold Climate ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Hydrocarbons/*metabolism ; Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.}, }
@article {pmid28647755, year = {2018}, author = {Scola, V and Ramond, JB and Frossard, A and Zablocki, O and Adriaenssens, EM and Johnson, RM and Seely, M and Cowan, DA}, title = {Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {193-203}, pmid = {28647755}, issn = {1432-184X}, support = {N00113-95565//National Research Foundation of South Africa/ ; }, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; Desert Climate ; *Microbiota ; Namibia ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The hyperarid Namib desert is a coastal desert in southwestern Africa and one of the oldest and driest deserts on the planet. It is characterized by a west/east increasing precipitation gradient and by regular coastal fog events (extending up to 75 km inland) that can also provide soil moisture. In this study, we evaluated the role of this natural aridity and xeric gradient on edaphic microbial community structure and function in the Namib desert. A total of 80 individual soil samples were collected at 10-km intervals along a 190-km transect from the fog-dominated western coastal region to the eastern desert boundary. Seventeen physicochemical parameters were measured for each soil sample. Soil parameters reflected the three a priori defined climatic/xeric zones along the transect (&quot;fog,&quot; &quot;low rain,&quot; and &quot;high rain&quot;). Microbial community structures were characterized by terminal restriction fragment length polymorphism fingerprinting and shotgun metaviromics, and their functional capacities were determined by extracellular enzyme activity assays. Both microbial community structures and activities differed significantly between the three xeric zones. The deep sequencing of surface soil metavirome libraries also showed shifts in viral composition along the xeric transect. While bacterial community assembly was influenced by soil chemistry and stochasticity along the transect, variations in community &quot;function&quot; were apparently tuned by xeric stress.}, }
@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 {pmid30250208, year = {2018}, author = {Pärnänen, K and Karkman, A and Hultman, J and Lyra, C and Bengtsson-Palme, J and Larsson, DGJ and Rautava, S and Isolauri, E and Salminen, S and Kumar, H and Satokari, R and Virta, M}, title = {Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3891}, pmid = {30250208}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/*adverse effects ; Antibiotic Prophylaxis/adverse effects ; Breast Feeding ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Humans ; Infant ; Interspersed Repetitive Sequences/*genetics ; Maternal Inheritance ; Metagenomics ; Milk, Human/*microbiology ; Phylogeny ; Time Factors ; }, abstract = {The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers. MGEs in mothers' breast milk are also shared with their own infants. Termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers, which have the potential to affect microbial community composition, are associated with higher abundances of specific ARGs, the composition of which is largely shaped by bacterial phylogeny in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but microbiota composition still strongly impacts the overall resistance load.}, }
@article {pmid30143202, year = {2018}, author = {Shikata, A and Sermsathanaswadi, J and Thianheng, P and Baramee, S and Tachaapaikoon, C and Waeonukul, R and Pason, P and Ratanakhanokchai, K and Kosugi, A}, title = {Characterization of an Anaerobic, Thermophilic, Alkaliphilic, High Lignocellulosic Biomass-Degrading Bacterial Community, ISHI-3, Isolated from Biocompost.}, journal = {Enzyme and microbial technology}, volume = {118}, number = {}, pages = {66-75}, doi = {10.1016/j.enzmictec.2018.07.001}, pmid = {30143202}, issn = {1879-0909}, mesh = {Alkalies/chemistry ; Animals ; Bacteria, Anaerobic/growth &amp; development ; *Biomass ; Cattle ; *Composting ; Lignin/*metabolism ; Metagenome ; *Microbial Consortia ; Oryza/*metabolism/microbiology ; Phylogeny ; Temperature ; Zea mays/*metabolism/microbiology ; }, abstract = {The generation of a complex microbial consortium is a promising approach for efficient biomass decomposition. An anaerobic thermophilic alkaliphilic microbial consortium with efficient degradation ability was screened from bovine manure compost using non-pretreated milling corn stover (CS) and rice straw (RS). A stable microbial consortium ISHI-3 with high degradation ability for CS and RS was isolated by the roll tube technique. ISHI-3 comprised Herbivorax saccincola and bacteria belonging to the classes Pelotomaculum, Tepidanaerobacter, and Tepidimicrobium, as determined by DGGE of the PCR-generated 16S rRNA genes. Furthermore, metagenomics analysis using a 16S rRNA library was carried out to determine the bacterial distribution during degradation of CS and RS. H. saccincola and bacteria belonging to Pelotomaculum were relatively abundant in the beginning to middle periods of culture with CS and RS whereas bacteria belonging to Tepidanaerobacter and Tepidimicrobium gradually increased in the population during the later stages. To understand the role of non-cellulolytic bacteria in the consortium, novel strains ET1 and GL4, which were most closely related to Tepidimicrobium ferriphilum and Tepidanaerobacter acetatoxydans, were isolated from ISHI-3. Based on their carbon source usage, morphology, and phylogenetic analysis, we propose that strains ET1 and GL4 should be classified as a novel genus or species. Bacteria ET1 and GL4 can utilize different organic compounds as carbon and energy sources such as organic acids, alcohols, sugars, and amino acids, showing a preference for organic acids and alcohols rather than sugars such as glucose and cellobiose. These results indicated that ET1 and GL4 help to accelerate efficient lignocellulose degradation of H. saccincola.}, }
@article {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 {pmid30036363, year = {2018}, author = {Chai, H and Jiang, H and Lin, L and Liu, L}, title = {A marginalized two-part Beta regression model for microbiome compositional data.}, journal = {PLoS computational biology}, volume = {14}, number = {7}, pages = {e1006329}, pmid = {30036363}, issn = {1553-7358}, mesh = {Animals ; Colony Count, Microbial ; Likelihood Functions ; *Logistic Models ; Metagenomics ; Mice ; *Microbiota ; Skin/*microbiology ; }, abstract = {In microbiome studies, an important goal is to detect differential abundance of microbes across clinical conditions and treatment options. However, the microbiome compositional data (quantified by relative abundance) are highly skewed, bounded in [0, 1), and often have many zeros. A two-part model is commonly used to separate zeros and positive values explicitly by two submodels: a logistic model for the probability of a specie being present in Part I, and a Beta regression model for the relative abundance conditional on the presence of the specie in Part II. However, the regression coefficients in Part II cannot provide a marginal (unconditional) interpretation of covariate effects on the microbial abundance, which is of great interest in many applications. In this paper, we propose a marginalized two-part Beta regression model which captures the zero-inflation and skewness of microbiome data and also allows investigators to examine covariate effects on the marginal (unconditional) mean. We demonstrate its practical performance using simulation studies and apply the model to a real metagenomic dataset on mouse skin microbiota. We find that under the proposed marginalized model, without loss in power, the likelihood ratio test performs better in controlling the type I error than those under conventional methods.}, }
@article {pmid30017197, year = {2018}, author = {He, F and Liu, D and Zhai, J and Zhang, L and Ma, Y and Xu, Y and Rong, K and Ma, J}, title = {Metagenomic analysis revealed the effects of goat milk feeding and breast feeding on the gut microbiome of Amur tiger cubs.}, journal = {Biochemical and biophysical research communications}, volume = {503}, number = {4}, pages = {2590-2596}, doi = {10.1016/j.bbrc.2018.07.020}, pmid = {30017197}, issn = {1090-2104}, mesh = {Animals ; Animals, Newborn ; Bacteria/isolation &amp; purification ; Feeding Behavior ; *Gastrointestinal Microbiome ; *Goats/microbiology ; Metagenomics/*methods ; *Milk ; *Tigers/microbiology ; }, abstract = {BACKGROUND: Ingredients in breast milk can help establish a healthy community of microorganisms in the infant gut, but no research exists regarding the effects of goat milk feeding and breast feeding on the gut microbiome of the Amur tiger, which is one of the most endangered species in the world.<br><br>METHODS: In this study, we used whole-metagenome shotgun sequencing to analyze the effects of two different feeding patterns, goat milk feeding and breast feeding, on the composition and functional structures of gut microbiota in Amur tiger cubs.<br><br>RESULTS: Goat milk-fed cubs have fewer beneficial bacteria and more pathogenic bacteria and a higher microbial diversity in their gut than breastfed cubs. A total of 15 genera showed statistically significant differences; the relative abundances of Streptomyces scabiei, Streptomyces avermitilis and Streptomyces davawensis were significantly decreased, whereas those of Niabella soli, Aeromonas media and Brochothrix thermosphacta were significantly increased in the goat milk-fed group compared with those in the breastfed group. At the functional level, carbohydrate metabolism, translation and replication and repair decreased, and amino acid metabolism, membrane transport and metabolism of cofactors and vitamins increased in the gut microbiota of goat milk-fed cubs compared with breastfed cubs.<br><br>CONCLUSION: Our results indicate for the first time that the different milk feeding patterns of goat milk feeding and breast feeding can change the composition and functional structures of gut microbiota in Amur tiger cubs and that breastfed tiger cubs and goat milk-fed tiger cubs have distinct microbiotas in their guts.}, }
@article {pmid29890228, year = {2018}, author = {Poussin, C and Sierro, N and Boué, S and Battey, J and Scotti, E and Belcastro, V and Peitsch, MC and Ivanov, NV and Hoeng, J}, title = {Interrogating the microbiome: experimental and computational considerations in support of study reproducibility.}, journal = {Drug discovery today}, volume = {23}, number = {9}, pages = {1644-1657}, doi = {10.1016/j.drudis.2018.06.005}, pmid = {29890228}, issn = {1878-5832}, mesh = {Animals ; Computational Biology/*methods ; Crowdsourcing ; Data Accuracy ; Humans ; *Metagenome/genetics ; Metagenomics/*methods ; *Microbiota/genetics ; Reproducibility of Results ; *Research Design ; Workflow ; }, abstract = {The microbiome is an important factor in human health and disease and is investigated to develop novel therapeutics. Metagenomics leverages advances in sequencing technologies and computational analysis to identify and quantify the microorganisms present in a sample. This field has, however, not yet reached maturity and the international metagenomics community, aware of the current limitations and of the necessity for standardization, has started investigating sources of variability in experimental and computational workflows. The first studies have already resulted in the identification of crucial steps and factors affecting metagenomics data quality, quantification and interpretation. This review summarizes experimental and computational considerations for interrogating the microbiome and establishing reproducible and robust analysis workflows.}, }
@article {pmid29554948, year = {2018}, author = {Walsh, AM and Crispie, F and O'Sullivan, O and Finnegan, L and Claesson, MJ and Cotter, PD}, title = {Species classifier choice is a key consideration when analysing low-complexity food microbiome data.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {50}, pmid = {29554948}, issn = {2049-2618}, support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; 11/PI/1137//Science Foundation Ireland/Ireland ; 13/SIRG/2160//Science Foundation Ireland/Ireland ; }, mesh = {Bacteria/classification/*genetics ; Base Sequence/genetics ; Computational Biology/methods ; DNA, Bacterial/*genetics ; Food Microbiology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with respect to choice of species classification tool, platform, or sequencing depth. Here, we benchmarked the performances of three high-throughput short-read sequencing platforms, the Illumina MiSeq, NextSeq 500, and Ion Proton, for shotgun metagenomics of food microbiota. Briefly, we sequenced six kefir DNA samples and a mock community DNA sample, the latter constructed by evenly mixing genomic DNA from 13 food-related bacterial species. A variety of bioinformatic tools were used to analyse the data generated, and the effects of sequencing depth on these analyses were tested by randomly subsampling reads.<br><br>RESULTS: Compositional analysis results were consistent between the platforms at divergent sequencing depths. However, we observed pronounced differences in the predictions from species classification tools. Indeed, PERMANOVA indicated that there was no significant differences between the compositional results generated by the different sequencers (p = 0.693, R2 = 0.011), but there was a significant difference between the results predicted by the species classifiers (p = 0.01, R2 = 0.127). The relative abundances predicted by the classifiers, apart from MetaPhlAn2, were apparently biased by reference genome sizes. Additionally, we observed varying false-positive rates among the classifiers. MetaPhlAn2 had the lowest false-positive rate, whereas SLIMM had the greatest false-positive rate. Strain-level analysis results were also similar across platforms. Each platform correctly identified the strains present in the mock community, but accuracy was improved slightly with greater sequencing depth. Notably, PanPhlAn detected the dominant strains in each kefir sample above 500,000 reads per sample. Again, the outputs from functional profiling analysis using SUPER-FOCUS were generally accordant between the platforms at different sequencing depths. Finally, and expectedly, metagenome assembly completeness was significantly lower on the MiSeq than either on the NextSeq (p = 0.03) or the Proton (p = 0.011), and it improved with increased sequencing depth.<br><br>CONCLUSIONS: Our results demonstrate a remarkable similarity in the results generated by the three sequencing platforms at different sequencing depths, and, in fact, the choice of bioinformatics methodology had a more evident impact on results than the choice of sequencer did.}, }
@article {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 {pmid29482639, year = {2018}, author = {Marotz, CA and Sanders, JG and Zuniga, C and Zaramela, LS and Knight, R and Zengler, K}, title = {Improving saliva shotgun metagenomics by chemical host DNA depletion.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {42}, pmid = {29482639}, issn = {2049-2618}, support = {R21 AR071731/AR/NIAMS NIH HHS/United States ; AR071731/AR/NIAMS NIH HHS/United States ; n/a//Center for Microbiome Innovation/International ; }, mesh = {Azides/*chemistry ; Bacteria/genetics ; DNA/*chemistry ; Fungi/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Propidium/*analogs &amp; derivatives/chemistry ; Saliva/*microbiology ; Sequence Analysis, DNA ; Viruses/genetics ; }, abstract = {BACKGROUND: Shotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencing approaches that assess taxonomy but not function and are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in microbial populations because few DNA sequence reads are from the microbial component. We developed and optimized a novel method for enriching microbial DNA from human oral samples and compared its efficiency and potential taxonomic bias with commercially available kits.<br><br>RESULTS: Three commercially available host depletion kits were directly compared with size filtration and a novel method involving osmotic lysis and treatment with propidium monoazide (lyPMA) in human saliva samples. We evaluated the percentage of shotgun metagenomic sequencing reads aligning to the human genome, and taxonomic biases of those not aligning, compared to untreated samples. lyPMA was the most efficient method of removing host-derived sequencing reads compared to untreated sample (8.53 ± 0.10% versus 89.29 ± 0.03%). Furthermore, lyPMA-treated samples exhibit the lowest taxonomic bias compared to untreated samples.<br><br>CONCLUSION: Osmotic lysis followed by PMA treatment is a cost-effective, rapid, and robust method for enriching microbial sequence data in shotgun metagenomics from fresh and frozen saliva samples and may be extensible to other host-derived sample types.}, }
@article {pmid29469169, year = {2018}, author = {Fountain, MT and Bennett, J and Cobo-Medina, M and Conde Ruiz, R and Deakin, G and Delgado, A and Harrison, R and Harrison, N}, title = {Alimentary microbes of winter-form Drosophila suzukii.}, journal = {Insect molecular biology}, volume = {27}, number = {3}, pages = {383-392}, doi = {10.1111/imb.12377}, pmid = {29469169}, issn = {1365-2583}, mesh = {Animals ; DNA, Ribosomal Spacer/analysis ; Drosophila/*microbiology ; England ; *Gastrointestinal Microbiome ; *Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seasons ; }, abstract = {Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a damaging pest of fruit. Reproductively diapausing adults overwinter in woodlands and remain active on warmer winter days. It is unknown if this adult phase of the lifecycle feeds during the winter period, and what the food source may be. This study characterized the flora in the digestive tract of D. suzukii using a metagenomics approach. Live D. suzukii were trapped in four woodlands in the south of England and their guts dissected for DNA extraction and amplicon-based metagenomics sequencing (internal transcribed spacer and 16S rRNA). Analysis at genus and family taxonomic levels showed high levels of diversity with no differences in digestive tract bacterial or fungal biota between woodland sites of winter-form D. suzukii. Female D. suzukii at one site appeared to have higher bacterial diversity in the alimentary canal than males, but there was a site, sex interaction. Many of the biota were associated with cold, wet climatic conditions and decomposition. This study provides the first evidence that winter-form D. suzukii may be opportunistic feeders during the winter period and are probably exploiting food sources associated with moisture on decomposing vegetation during this time. A core gut microbiome has been identified for winter-form D. suzukii.}, }
@article {pmid28866243, year = {2018}, author = {Heeney, DD and Gareau, MG and Marco, ML}, title = {Intestinal Lactobacillus in health and disease, a driver or just along for the ride?.}, journal = {Current opinion in biotechnology}, volume = {49}, number = {}, pages = {140-147}, pmid = {28866243}, issn = {1879-0429}, support = {R01 AT009365/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Behavior ; Biodiversity ; Cognition ; *Disease ; *Health ; Humans ; Intestines/*microbiology ; Lactobacillus/*physiology ; }, abstract = {Metagenomics and related methods have led to significant advances in our understanding of the human microbiome. Members of the genus Lactobacillus, although best understood for essential roles in food fermentations and applications as probiotics, have also come to the fore in a number of untargeted gut microbiome studies in humans and animals. Even though Lactobacillus is only a minor member of the human colonic microbiota, the proportions of those bacteria are frequently either positively or negatively correlated with human disease and chronic conditions. Recent findings on Lactobacillus species in human and animal microbiome research, together with the increased knowledge on probiotic and other ingested lactobacilli, have resulted in new perspectives on the importance of this genus to human health.}, }
@article {pmid29793542, year = {2018}, author = {Li, LG and Yin, X and Zhang, T}, title = {Tracking antibiotic resistance gene pollution from different sources using machine-learning classification.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {93}, pmid = {29793542}, issn = {2049-2618}, support = {172099/14E//Hong Kong General Research Fund/International ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; China ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Machine Learning ; Metagenomics ; Sewage/*microbiology ; Soil Microbiology ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) has been a worldwide public health concern. Current widespread AMR pollution has posed a big challenge in accurately disentangling source-sink relationship, which has been further confounded by point and non-point sources, as well as endogenous and exogenous cross-reactivity under complicated environmental conditions. Because of insufficient capability in identifying source-sink relationship within a quantitative framework, traditional antibiotic resistance gene (ARG) signatures-based source-tracking methods would hardly be a practical solution.<br><br>RESULTS: By combining broad-spectrum ARG profiling with machine-learning classification SourceTracker, here we present a novel way to address the question in the era of high-throughput sequencing. Its potential in extensive application was firstly validated by 656 global-scale samples covering diverse environmental types (e.g., human/animal gut, wastewater, soil, ocean) and broad geographical regions (e.g., China, USA, Europe, Peru). Its potential and limitations in source prediction as well as effect of parameter adjustment were then rigorously evaluated by artificial configurations with representative source proportions. When applying SourceTracker in region-specific analysis, excellent performance was achieved by ARG profiles in two sample types with obvious different source compositions, i.e., influent and effluent of wastewater treatment plant. Two environmental metagenomic datasets of anthropogenic interference gradient further supported its potential in practical application. To complement general-profile-based source tracking in distinguishing continuous gradient pollution, a few generalist and specialist indicator ARGs across ecotypes were identified in this study.<br><br>CONCLUSION: We demonstrated for the first time that the developed source-tracking platform when coupling with proper experiment design and efficient metagenomic analysis tools will have significant implications for assessing AMR pollution. Following predicted source contribution status, risk ranking of different sources in ARG dissemination will be possible, thereby paving the way for establishing priority in mitigating ARG spread and designing effective control strategies.}, }
@article {pmid29793532, year = {2018}, author = {Bilen, M and Dufour, JC and Lagier, JC and Cadoret, F and Daoud, Z and Dubourg, G and Raoult, D}, title = {The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {94}, pmid = {29793532}, issn = {2049-2618}, mesh = {Actinobacteria/isolation &amp; purification ; Archaea/*classification/genetics/*isolation &amp; purification ; Bacteria/*classification/genetics/*isolation &amp; purification ; Bacteroidetes/isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Firmicutes/isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics ; Proteobacteria/isolation &amp; purification ; }, abstract = {After a decade of research and metagenomic analyses, our knowledge of the human microbiota appears to have reached a plateau despite promising results. In many studies, culture has proven to be essential in describing new prokaryotic species and filling metagenomic gaps. In 2015, only 2172 different prokaryotic species were reported to have been isolated at least once from the human body as pathogens or commensals. In this review, we update the previous repertoire by reporting the different species isolated from the human body to date, increasing it by 28% to reach a total of 2776 species associated with human beings. They have been classified into 11 different phyla, mostly the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Finally, culturomics contributed up to 66.2% towards updating this repertoire by reporting 400 species, of which 288 were novel. This demonstrates the need to continue the culturing work, which seems essential in order to decipher the hidden human microbial content.}, }
@article {pmid29789015, year = {2018}, author = {Panebianco, C and Andriulli, A and Pazienza, V}, title = {Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {92}, pmid = {29789015}, issn = {2049-2618}, support = {RC1703GA31//Ministero della Salute/International ; RC1503GA40//Ministero della Salute/International ; }, mesh = {Antineoplastic Agents/*metabolism/*therapeutic use ; Bacteria/*metabolism ; Dysbiosis/*chemically induced ; Gastrointestinal Microbiome/*physiology ; Humans ; Intestines/microbiology ; Neoplasms/*drug therapy/microbiology ; Prebiotics ; Probiotics/*therapeutic use ; Synbiotics ; }, abstract = {Cancer is a major health burden worldwide, and despite continuous advances in medical therapies, resistance to standard drugs and adverse effects still represent an important cause of therapeutic failure. There is a growing evidence that gut bacteria can affect the response to chemo- and immunotherapeutic drugs by modulating either efficacy or toxicity. Moreover, intratumor bacteria have been shown to modulate chemotherapy response. At the same time, anticancer treatments themselves significantly affect the microbiota composition, thus disrupting homeostasis and exacerbating discomfort to the patient. Here, we review the existing knowledge concerning the role of the microbiota in mediating chemo- and immunotherapy efficacy and toxicity and the ability of these therapeutic options to trigger dysbiotic condition contributing to the severity of side effects. In addition, we discuss the use of probiotics, prebiotics, synbiotics, postbiotics, and antibiotics as emerging strategies for manipulating the microbiota in order to improve therapeutic outcome or at least ensure patients a better quality of life all along of anticancer treatments.}, }
@article {pmid29636439, year = {2018}, author = {Brown, CT and Xiong, W and Olm, MR and Thomas, BC and Baker, R and Firek, B and Morowitz, MJ and Hettich, RL and Banfield, JF}, title = {Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.}, journal = {mBio}, volume = {9}, number = {2}, pages = {}, pmid = {29636439}, issn = {2150-7511}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R01 GM103600/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*chemistry/classification/genetics ; Biota ; Enterocolitis, Necrotizing/microbiology/pathology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; *Hospitalization ; Humans ; Infant, Newborn ; *Infant, Premature ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Proteome/*analysis ; Proteomics ; }, abstract = {During the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC), a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants. In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context.IMPORTANCE Humans are colonized by microbes at birth, a process that is important to health and development. However, much remains to be known about the fine-scale microbial dynamics that occur during the colonization period. We conducted a genome-resolved study of microbial community composition, replication rates, and proteomes during the first 3 months of life of both healthy and sick premature infants. Infants were found to be colonized by similar microbes, but each underwent a distinct colonization trajectory. Interestingly, related microbes colonizing different infants were found to have distinct proteomes, indicating that microbiome function is not only driven by which organisms are present, but also largely depends on microbial responses to the unique set of physiological conditions in the infant gut.}, }
@article {pmid28730353, year = {2018}, author = {Vieira, FR and Pecchia, JA}, title = {An Exploration into the Bacterial Community under Different Pasteurization Conditions during Substrate Preparation (Composting-Phase II) for Agaricus bisporus Cultivation.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {318-330}, pmid = {28730353}, issn = {1432-184X}, support = {005707/2012-05//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Agaricus/*growth &amp; development/metabolism ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Composting ; Culture Media/*chemistry/metabolism ; DNA, Bacterial/genetics ; Hot Temperature ; Pasteurization/instrumentation/*methods ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Substrate preparation (i.e., composting) for Agaricus bisporus cultivation is the most critical point of mushroom production. Among many factors involved in the composting process, the microbial ecology of the system is the underlying drive of composting and can be influenced by composting management techniques. Pasteurization temperature at the beginning of phase II, in theory, may influence the bacterial community and subsequently the &quot;selectivity&quot; and nutrition of the final substrate. Therefore, this hypothesis was tested by simulation in bioreactors under different pasteurization conditions (57 °C/6 h, 60 °C/2 h, and 68 °C/2 h), simulating conditions adopted by many producers. Bacterial diversity, based on 16S ribosomal RNA obtained by high-throughput sequencing and classified in operational taxonomic units (OTUs), was greater than previously reported using culture-dependent methods. Alpha diversity estimators show a lower diversity of OTUs under a high-temperature pasteurization condition. Bacillales order shows a relatively higher OTU abundance under a high-pasteurization temperature, which also was related to high ammonia emission measurements. On the other hand, beta diversity analysis showed no significantly changes in the bacterial community structure under different conditions. Agaricus bisporus mycelium growth during a standard spawn run period was significantly slower in the compost pasteurized at high temperature. Since the bacterial community structure was not greatly affected by different pasteurization conditions but by-products left (e.g., ammonia) at the end of compost conditioning varied, further studies need to be conducted to determine the functional role of the microbial communities found during substrate preparation for Agaricus bisporus cultivation.}, }
@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 {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 {pmid30342053, year = {2018}, author = {Vallianou, NG and Stratigou, T and Tsagarakis, S}, title = {Microbiome and diabetes: Where are we now?.}, journal = {Diabetes research and clinical practice}, volume = {146}, number = {}, pages = {111-118}, doi = {10.1016/j.diabres.2018.10.008}, pmid = {30342053}, issn = {1872-8227}, mesh = {Animals ; Diabetes Mellitus, Type 2/*microbiology ; Dysbiosis/*microbiology ; Fecal Microbiota Transplantation/*methods ; Gastrointestinal Microbiome/*genetics ; Humans ; Mice ; Prebiotics/*microbiology ; Probiotics/*metabolism ; }, abstract = {Alterations in the diversity or structure of gut microbiota known as dysbiosis, may affect metabolic activities, resulting in metabolic disorders, such as obesity and diabetes. The development of more sophisticated methods, such as metagenomics sequencing, PCR-denaturing gradient gel electrophoresis, microarrays and fluorescence in situ hybridization, has expanded our knowledge on gut microbiome. Dysbiosis has been related to increased plasma concentrations of gut microbiota-derived lipopolysaccharide (LPS), which triggers the production of a variety of cytokines and the recruitment of inflammatory cells. Metabolomics have demonstrated that butyrate and propionate suppress weight gain in mice with high fat diet-induced obesity, and acetate has been proven to reduce food intake in healthy mice. The role of prebiotics, probiotics, genetically modified bacteria and fecal microbiota transplantation, as potential therapeutic challenges for type 2 diabetes will be discussed in this review.}, }
@article {pmid28659635, year = {2017}, author = {Hosomi, K and Ohno, H and Murakami, H and Natsume-Kitatani, Y and Tanisawa, K and Hirata, S and Suzuki, H and Nagatake, T and Nishino, T and Mizuguchi, K and Miyachi, M and Kunisawa, J}, title = {Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4339}, pmid = {28659635}, issn = {2045-2322}, mesh = {Adult ; Bacteria/classification/genetics ; *Biodiversity ; Feces/microbiology ; Female ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Metagenomic analysis based on the 16S rRNA gene is generally performed to examine the diversity and abundance of commensal bacteria in feces, which is now recognized to be associated with human health and diseases. Guanidine thiocyanate (GuSCN) solution is used as a less onerous way compared with a frozen method to transport and stock fecal samples at room temperature for DNA analysis; however, optimal methods to measure fecal bacterial composition in GuSCN solution remain to be investigated. Here, we examined the influence of various factors such as pretreatment (e.g., removing GuSCN solution and washing feces with phosphate-buffered saline (PBS) before mechanical lysis), fecal concentration in the GuSCN solution, storage time, and position of fecal subsampling on the 16S rRNA-based analysis of fecal bacteria in GuSCN solution. We found that pretreatment and fecal concentration affected the bacterial composition, and a little change was noted with subsampling position. Based on these results, we propose a basic protocol, including fecal sampling, sample storage, and DNA extraction, for the 16S rRNA-based analysis of bacterial composition in feces suspended in GuSCN solution.}, }
@article {pmid30240699, year = {2018}, author = {Harris, L and van Zyl, LJ and Kirby-McCullough, BM and Damelin, LH and Tiemessen, CT and Trindade, M}, title = {Identification and sequence analysis of two novel cryptic plasmids isolated from the vaginal mucosa of South African women.}, journal = {Plasmid}, volume = {98}, number = {}, pages = {56-62}, doi = {10.1016/j.plasmid.2018.09.008}, pmid = {30240699}, issn = {1095-9890}, mesh = {DNA, Bacterial/*genetics ; Female ; Humans ; Lactobacillus/classification/*genetics/*isolation &amp; purification/metabolism ; Microbiota ; Mucous Membrane/*microbiology ; Phylogeny ; Plasmids/chemistry/*genetics ; Sequence Analysis, DNA ; South Africa/epidemiology ; Vagina/*microbiology ; Vaginosis, Bacterial/epidemiology/*microbiology ; }, abstract = {The vaginal mucosa is dominated by Gram positive, rod shaped lactobacilli which serve as a natural barrier against infection. In both healthy- and bacterial vaginosis (BV)-infected women Lactobacillus crispatus and Lactobacillus jensenii have been found to be the predominant Lactobacillus species. Many studies have been conducted to assess factors influencing lactobacilli dominance in the vaginal microbiome. In the present study two plasmids, pLc4 and pLc17, isolated from vaginal Lactobacillus strains of both healthy and BV-infected women were characterized. The smaller plasmid, pLc4 (4224 bp), was detected in both L. crispatus and L. jensenii strains, while pLc17 was only detected in L. crispatus. Based on its nucleotide sequence pLc4 appears highly novel, with its replication protein having 44% identity to the replication initiation protein of pSMQ173b_03. Phylogenetic analysis with other Rolling Circle Replication plasmids confirmed that pLc4 shows a low degree of similarity to these plasmids. Plasmid pLc17 (16,663 bp) appears to carry both a RCR replicon and a theta replicon, which is rare in naturally occurring plasmids. pLc4 was maintained at a high copy number of 29, while pLc17 appears to be a medium copy number plasmid maintained at 11 copies per chromosome. While sequence analysis is a valuable tool to study cryptic plasmids, further function-based analysis will be required in order to fully elucidate the role of these plasmids within the vaginal milieu.}, }
@article {pmid30309375, year = {2018}, author = {Zepeda Mendoza, ML and Roggenbuck, M and Manzano Vargas, K and Hansen, LH and Brunak, S and Gilbert, MTP and Sicheritz-Pontén, T}, title = {Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.}, journal = {Acta veterinaria Scandinavica}, volume = {60}, number = {1}, pages = {61}, pmid = {30309375}, issn = {1751-0147}, support = {R52-A5062//Lundbeckfonden/ ; }, mesh = {Adaptation, Biological ; Animals ; Animals, Wild/microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Falconiformes/*microbiology/physiology ; *Feeding Behavior ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Skin/*microbiology ; }, abstract = {BACKGROUND: Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut.<br><br>RESULTS: We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut.<br><br>CONCLUSIONS: Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.}, }
@article {pmid30091981, year = {2018}, author = {Bradley, PH and Nayfach, S and Pollard, KS}, title = {Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.}, journal = {PLoS computational biology}, volume = {14}, number = {8}, pages = {e1006242}, pmid = {30091981}, issn = {1553-7358}, support = {T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Gastrointestinal Microbiome/*genetics/physiology ; Gene Expression Regulation, Bacterial/genetics ; Genes, Microbial/genetics ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; }, abstract = {The mechanisms by which different microbes colonize the healthy human gut versus other body sites, the gut in disease states, or other environments remain largely unknown. Identifying microbial genes influencing fitness in the gut could lead to new ways to engineer probiotics or disrupt pathogenesis. We approach this problem by measuring the statistical association between a species having a gene and the probability that the species is present in the gut microbiome. The challenge is that closely related species tend to be jointly present or absent in the microbiome and also share many genes, only a subset of which are involved in gut adaptation. We show that this phylogenetic correlation indeed leads to many false discoveries and propose phylogenetic linear regression as a powerful solution. To apply this method across the bacterial tree of life, where most species have not been experimentally phenotyped, we use metagenomes from hundreds of people to quantify each species' prevalence in and specificity for the gut microbiome. This analysis reveals thousands of genes potentially involved in adaptation to the gut across species, including many novel candidates as well as processes known to contribute to fitness of gut bacteria, such as acid tolerance in Bacteroidetes and sporulation in Firmicutes. We also find microbial genes associated with a preference for the gut over other body sites, which are significantly enriched for genes linked to fitness in an in vivo competition experiment. Finally, we identify gene families associated with higher prevalence in patients with Crohn's disease, including Proteobacterial genes involved in conjugation and fimbria regulation, processes previously linked to inflammation. These gene targets may represent new avenues for modulating host colonization and disease. Our strategy of combining metagenomics with phylogenetic modeling is general and can be used to identify genes associated with adaptation to any environment.}, }
@article {pmid30504906, year = {2018}, author = {Wampach, L and Heintz-Buschart, A and Fritz, JV and Ramiro-Garcia, J and Habier, J and Herold, M and Narayanasamy, S and Kaysen, A and Hogan, AH and Bindl, L and Bottu, J and Halder, R and Sjöqvist, C and May, P and Andersson, AF and de Beaufort, C and Wilmes, P}, title = {Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5091}, doi = {10.1038/s41467-018-07631-x}, pmid = {30504906}, issn = {2041-1723}, mesh = {Cesarean Section ; Delivery, Obstetric ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; In Vitro Techniques ; Infant, Newborn ; Infectious Disease Transmission, Vertical ; Interleukin-18/metabolism ; Lipopolysaccharides/metabolism ; Metagenomics/methods ; Pregnancy ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {The rate of caesarean section delivery (CSD) is increasing worldwide. It remains unclear whether disruption of mother-to-neonate transmission of microbiota through CSD occurs and whether it affects human physiology. Here we perform metagenomic analysis of earliest gut microbial community structures and functions. We identify differences in encoded functions between microbiomes of vaginally delivered (VD) and CSD neonates. Several functional pathways are over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis. We link these enriched functions to individual-specific strains, which are transmitted from mothers to neonates in case of VD. The stimulation of primary human immune cells with LPS isolated from early stool samples of VD neonates results in higher levels of tumour necrosis factor (TNF-α) and interleukin 18 (IL-18). Accordingly, the observed levels of TNF-α and IL-18 in neonatal blood plasma are higher after VD. Taken together, our results support that CSD disrupts mother-to-neonate transmission of specific microbial strains, linked functional repertoires and immune-stimulatory potential during a critical window for neonatal immune system priming.}, }
@article {pmid30459421, year = {2018}, author = {Xu, J and Zhang, Y and Zhang, P and Trivedi, P and Riera, N and Wang, Y and Liu, X and Fan, G and Tang, J and Coletta-Filho, HD and Cubero, J and Deng, X and Ancona, V and Lu, Z and Zhong, B and Roper, MC and Capote, N and Catara, V and Pietersen, G and Vernière, C and Al-Sadi, AM and Li, L and Yang, F and Xu, X and Wang, J and Yang, H and Jin, T and Wang, N}, title = {The structure and function of the global citrus rhizosphere microbiome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4894}, pmid = {30459421}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics ; Citrus/*microbiology ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/genetics ; Metagenome/genetics ; Metagenomics/classification/methods ; Microbiota/*genetics ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.}, }
@article {pmid30308248, year = {2018}, author = {Hessler, T and Harrison, STL and Huddy, RJ}, title = {Stratification of microbial communities throughout a biological sulphate reducing up-flow anaerobic packed bed reactor, revealed through 16S metagenomics.}, journal = {Research in microbiology}, volume = {169}, number = {10}, pages = {543-551}, doi = {10.1016/j.resmic.2018.09.003}, pmid = {30308248}, issn = {1769-7123}, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Bioreactors/*microbiology ; DNA, Bacterial/genetics ; Genome, Bacterial ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sulfur Compounds/*metabolism ; }, abstract = {Biological sulphate reduction (BSR) is a promising low-cost treatment of acid rock drainage effluents. In this paper, the system performance and microbial ecology of a lactate supplemented BSR up-flow anaerobic packed bed reactor (UAPBR) are evaluated across reactor height and compared to a continuous stirred tank reactor (CSTR). The biomass concentrations of planktonic and biofilm communities were quantified and subsequently characterised by 16S rRNA gene amplicon sequencing. The defined microbial communities were shown to correlate with differing availability of lactate, volatile fatty acids produced from lactate degradation and sulphate concentration. The UAPBR was able to achieve near complete sulphate conversion at a 4-day hydraulic residence time (HRT) at a sulphate feed concentration of 10.41 mM (1 g/L). The high volumetric sulphate reduction rate of 0.184 mM/L.h achieved in the first third of the reactor was attributed to OTUs present in the planktonic and biofilm communities. While the scavenging of sulphate within the final third of the UAPBR was attributed to an acetate oxidising genus of SRB which was not detected in the lactate-fed CSTR. The detailed analyses of the microbial communities throughout the UAPBR and CSTR contribute to the growing understanding of the impact of the microbial communities of BSR reactors on system performance.}, }
@article {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 {pmid30479342, year = {2018}, author = {Ramani, S and Stewart, CJ and Laucirica, DR and Ajami, NJ and Robertson, B and Autran, CA and Shinge, D and Rani, S and Anandan, S and Hu, L and Ferreon, JC and Kuruvilla, KA and Petrosino, JF and Venkataram Prasad, BV and Bode, L and Kang, G and Estes, MK}, title = {Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5010}, pmid = {30479342}, issn = {2041-1723}, support = {R01 AI036040/AI/NIAID NIH HHS/United States ; R01 AI105101/AI/NIAID NIH HHS/United States ; R37 AI036040/AI/NIAID NIH HHS/United States ; }, mesh = {Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Milk, Human/*chemistry/*microbiology ; Oligosaccharides/*metabolism ; Rotavirus/pathogenicity ; Rotavirus Infections/immunology/*microbiology ; Rotavirus Vaccines/immunology ; }, abstract = {Neonatal rotavirus infections are predominantly asymptomatic. While an association with gastrointestinal symptoms has been described in some settings, factors influencing differences in clinical presentation are not well understood. Using multidisciplinary approaches, we show that a complex interplay between human milk oligosaccharides (HMOs), milk microbiome, and infant gut microbiome impacts neonatal rotavirus infections. Validating in vitro studies where HMOs are not decoy receptors for neonatal strain G10P[11], population studies show significantly higher levels of Lacto-N-tetraose (LNT), 2'-fucosyllactose (2'FL), and 6'-siallylactose (6'SL) in milk from mothers of rotavirus-positive neonates with gastrointestinal symptoms. Further, these HMOs correlate with abundance of Enterobacter/Klebsiella in maternal milk and infant stool. Specific HMOs also improve the infectivity of a neonatal strain-derived rotavirus vaccine. This study provides molecular and translational insight into host factors influencing neonatal rotavirus infections and identifies maternal components that could promote the performance of live, attenuated rotavirus vaccines.}, }
@article {pmid30478343, year = {2018}, author = {Regan, T and Barnett, MW and Laetsch, DR and Bush, SJ and Wragg, D and Budge, GE and Highet, F and Dainat, B and de Miranda, JR and Watson, M and Blaxter, M and Freeman, TC}, title = {Characterisation of the British honey bee metagenome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4995}, pmid = {30478343}, issn = {2041-1723}, mesh = {Animals ; Bees/*genetics/microbiology ; Contig Mapping ; Genetic Variation ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; Symbiosis/genetics ; United Kingdom ; }, abstract = {The European honey bee (Apis mellifera) plays a major role in pollination and food production. Honey bee health is a complex product of the environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of these factors will help manage modern challenges to bee health. Here we used DNA sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from across Britain. Low heterozygosity was observed in many Scottish colonies which had high similarity to the native dark bee. Colonies exhibited high diversity in composition and relative abundance of individual microbiome taxa. Most non-bee sequences were derived from known honey bee commensal bacteria or pathogens. However, DNA was also detected from additional fungal, protozoan and metazoan species. To classify cobionts lacking genomic information, we developed a novel network analysis approach for clustering orphan DNA contigs. Our analyses shed light on microbial communities associated with honey bees and demonstrate the power of high-throughput, directed metagenomics for identifying novel biological threats in agroecosystems.}, }
@article {pmid29902201, year = {2018}, author = {Li, X and Naser, SA and Khaled, A and Hu, H and Li, X}, title = {When old metagenomic data meet newly sequenced genomes, a case study.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0198773}, pmid = {29902201}, issn = {1932-6203}, support = {R15 GM123407/GM/NIGMS NIH HHS/United States ; }, mesh = {Colitis/genetics/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; *Metagenomics ; *Whole Genome Sequencing ; }, abstract = {Dozens of computational methods are developed to identify species present in a metagenomic dataset. Many of these computational methods depend on available sequenced microbial species, which are still far from being representative. To see how newly sequenced genomes affect the analysis results, we re-analyzed a shotgun metagenomic dataset composed of twelve colitis free metagenomic samples and ten colitis-related metagenomic samples. Unexpectedly, we identified at least two new phyla that may relate to colitis development in patients, together with the phylum identified previously. Compared with the previously identified phylum that differed between the two types of samples, the differences associated with the two new phyla are statistically more significant. Moreover, the abundance of the two new phyla correlates more with the severity of colitis. Surprisingly, even by repeating the analyses implemented in the previous study, we found that at least one main conclusion in the previous study is not supported. Our study indicates the importance of re-analysis of the generated metagenomic datasets and the necessity of considering multiple updated tools in metagenomic studies. It also sheds light on the limitations of the popular tools used currently and the importance to infer the presence of taxa without relying upon available sequenced genomes.}, }
@article {pmid29899081, year = {2019}, author = {Aron-Wisnewsky, J and Prifti, E and Belda, E and Ichou, F and Kayser, BD and Dao, MC and Verger, EO and Hedjazi, L and Bouillot, JL and Chevallier, JM and Pons, N and Le Chatelier, E and Levenez, F and Ehrlich, SD and Dore, J and Zucker, JD and Clément, K}, title = {Major microbiota dysbiosis in severe obesity: fate after bariatric surgery.}, journal = {Gut}, volume = {68}, number = {1}, pages = {70-82}, doi = {10.1136/gutjnl-2018-316103}, pmid = {29899081}, issn = {1468-3288}, mesh = {Adult ; *Bariatric Surgery ; Biomarkers/blood ; Chromatography, Liquid ; Comorbidity ; Dysbiosis/*etiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Mass Spectrometry ; Metagenomics ; Obesity, Morbid/*microbiology/*surgery ; Phenotype ; Prospective Studies ; Risk Factors ; }, abstract = {OBJECTIVES: Decreased gut microbial gene richness (MGR) and compositional changes are associated with adverse metabolism in overweight or moderate obesity, but lack characterisation in severe obesity. Bariatric surgery (BS) improves metabolism and inflammation in severe obesity and is associated with gut microbiota modifications. Here, we characterised severe obesity-associated dysbiosis (ie, MGR, microbiota composition and functional characteristics) and assessed whether BS would rescue these changes.<br><br>DESIGN: Sixty-one severely obese subjects, candidates for adjustable gastric banding (AGB, n=20) or Roux-en-Y-gastric bypass (RYGB, n=41), were enrolled. Twenty-four subjects were followed at 1, 3 and 12 months post-BS. Gut microbiota and serum metabolome were analysed using shotgun metagenomics and liquid chromatography mass spectrometry (LC-MS). Confirmation groups were included.<br><br>RESULTS: Low gene richness (LGC) was present in 75% of patients and correlated with increased trunk-fat mass and comorbidities (type 2 diabetes, hypertension and severity). Seventy-eight metagenomic species were altered with LGC, among which 50% were associated with adverse body composition and metabolic phenotypes. Nine serum metabolites (including glutarate, 3-methoxyphenylacetic acid and L-histidine) and functional modules containing protein families involved in their metabolism were strongly associated with low MGR. BS increased MGR 1 year postsurgery, but most RYGB patients remained with low MGR 1 year post-BS, despite greater metabolic improvement than AGB patients.<br><br>CONCLUSIONS: We identified major gut microbiota alterations in severe obesity, which include decreased MGR and related functional pathways linked with metabolic deteriorations. The lack of full rescue post-BS calls for additional strategies to improve the gut microbiota ecosystem and microbiome-host interactions in severe obesity.<br><br>TRIAL REGISTRATION NUMBER: NCT01454232.}, }
@article {pmid29690922, year = {2018}, author = {Jaenicke, S and Albaum, SP and Blumenkamp, P and Linke, B and Stoye, J and Goesmann, A}, title = {Flexible metagenome analysis using the MGX framework.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {76}, pmid = {29690922}, issn = {2049-2618}, mesh = {*Database Management Systems ; *Metagenome ; Metagenomics/*methods ; Microbiota ; Reproducibility of Results ; User-Computer Interface ; Workflow ; }, abstract = {BACKGROUND: The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as metagenomics; in particular, the recent advances in sequencing technologies have enabled researchers to study even the most complex communities. Metagenome analysis, the assignment of sequences to taxonomic and functional entities, however, remains a tedious task: large amounts of data need to be processed. There are a number of approaches addressing particular aspects, but scientific questions are often too specific to be answered by a general-purpose method.<br><br>RESULTS: We present MGX, a flexible and extensible client/server-framework for the management and analysis of metagenomic datasets; MGX features a comprehensive set of adaptable workflows required for taxonomic and functional metagenome analysis, combined with an intuitive and easy-to-use graphical user interface offering customizable result visualizations. At the same time, MGX allows to include own data sources and devise custom analysis pipelines, thus enabling researchers to perform basic as well as highly specific analyses within a single application.<br><br>CONCLUSIONS: With MGX, we provide a novel metagenome analysis platform giving researchers access to the most recent analysis tools. MGX covers taxonomic and functional metagenome analysis, statistical evaluation, and a wide range of visualizations easing data interpretation. Its default taxonomic classification pipeline provides equivalent or superior results in comparison to existing tools.}, }
@article {pmid29685174, year = {2018}, author = {Fan, X and Peters, BA and Jacobs, EJ and Gapstur, SM and Purdue, MP and Freedman, ND and Alekseyenko, AV and Wu, J and Yang, L and Pei, Z and Hayes, RB and Ahn, J}, title = {Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {59}, pmid = {29685174}, issn = {2049-2618}, support = {R01 CA159036/CA/NCI NIH HHS/United States ; U01CA182370/CA/NCI NIH HHS/United States ; R21CA183887/CA/NCI NIH HHS/United States ; Pancreas Cancer Action Network Career Development Award//American Association for Cancer Research/International ; P30CA016087/CA/NCI NIH HHS/United States ; R03CA159414/CA/NCI NIH HHS/United States ; R01CA159036/CA/NCI NIH HHS/United States ; R01CA164964/CA/NCI NIH HHS/United States ; R01 CA164964/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; *Alcohol Drinking ; Female ; Humans ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Public Health Surveillance ; RNA, Ribosomal, 16S/genetics ; United States ; }, abstract = {BACKGROUND: Dysbiosis of the oral microbiome can lead to local oral disease and potentially to cancers of the head, neck, and digestive tract. However, little is known regarding exogenous factors contributing to such microbial imbalance.<br><br>RESULTS: We examined the impact of alcohol consumption on the oral microbiome in a cross-sectional study of 1044 US adults. Bacterial 16S rRNA genes from oral wash samples were amplified, sequenced, and assigned to bacterial taxa. We tested the association of alcohol drinking level (non-drinker, moderate drinker, or heavy drinker) and type (liquor, beer, or wine) with overall microbial composition and individual taxon abundance. The diversity of oral microbiota and overall bacterial profiles differed between heavy drinkers and non-drinkers (α-diversity richness p = 0.0059 and β-diversity unweighted UniFrac p = 0.0036), and abundance of commensal order Lactobacillales tends to be decreased with higher alcohol consumption (fold changes = 0.89 and 0.94 for heavy and moderate drinkers, p trend = 0.005 [q = 0.064]). Additionally, certain genera were enriched in subjects with higher alcohol consumption, including Actinomyces, Leptotrichia, Cardiobacterium, and Neisseria; some of these genera contain oral pathogens, while Neisseria can synthesize the human carcinogen acetaldehyde from ethanol. Wine drinkers may differ from non-drinkers in microbial diversity and profiles (α-diversity richness p = 0.048 and β-diversity unweighted UniFrac p = 0.059) after controlling for drinking amount, while liquor and beer drinkers did not. All significant differences between drinkers and non-drinkers remained after exclusion of current smokers.<br><br>CONCLUSIONS: Our results, from a large human study of alcohol consumption and the oral microbiome, indicate that alcohol consumption, and heavy drinking in particular, may influence the oral microbiome composition. These findings may have implications for better understanding the potential role that oral bacteria play in alcohol-related diseases.}, }
@article {pmid29684865, year = {2018}, author = {Kurokawa, S and Kishimoto, T and Mizuno, S and Masaoka, T and Naganuma, M and Liang, KC and Kitazawa, M and Nakashima, M and Shindo, C and Suda, W and Hattori, M and Kanai, T and Mimura, M}, title = {The effect of fecal microbiota transplantation on psychiatric symptoms among patients with irritable bowel syndrome, functional diarrhea and functional constipation: An open-label observational study.}, journal = {Journal of affective disorders}, volume = {235}, number = {}, pages = {506-512}, doi = {10.1016/j.jad.2018.04.038}, pmid = {29684865}, issn = {1573-2517}, mesh = {Adult ; Anxiety Disorders/*psychology ; Constipation/psychology/*therapy ; Depressive Disorder/*psychology ; Diarrhea/psychology/*therapy ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; Gastrointestinal Diseases ; Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/psychology/*therapy ; Male ; Middle Aged ; }, abstract = {BACKGROUNDS: The intestinal microbiota is considered as a potential common underpinning pathophysiology of Functional Gastrointestinal Disorders (FGIDs) and psychiatric disorders such as depression and anxiety. Fecal Microbiota Transplantation (FMT) has been reported to have therapeutic effects on diseases related to dysbiosis, but few studies have evaluated its effect on psychiatric symptoms.<br><br>METHODS: We followed 17 patients with either Irritable Bowel Syndrome (IBS), Functional Diarrhea (FDr) or Functional Constipation (FC) who underwent FMT for the treatment of gastrointestinal symptoms and observation of psychiatric symptoms. Changes in Hamilton Rating Scale for Depression (HAM-D) and subscale of sleep-related items, Hamilton Rating Scale for Anxiety (HAM-A) and Quick Inventory for Depressive Symptoms (QIDS) between baseline and 4 weeks after FMT, and relationship with the intestinal microbiota were measured.<br><br>RESULTS: At baseline, 12 out of 17 patients were rated with HAM-D ≥ 8. Significant improvement in HAM-D total and sleep subscale score, HAM-A and QIDS were observed (p = 0.007, p = 0.007, p = 0.01, p = 0.007, respectively). Baseline Shannon index indicated that microbiota showed lower diversity in patients with HAM-D ≥ 8 compared to those of healthy donors and patients with HAM-D < 8. There was a significant correlation between baseline Shannon index and HAM-D score, and a correlation between Shannon index change and HAM-D improvement after FMT.<br><br>LIMITATIONS: The small sample size with no control group.<br><br>CONCLUSIONS: Our results suggest that depression and anxiety symptoms may be improved by FMT regardless of gastrointestinal symptom change in patients with IBS, FDr and FC, and the increase of microbiota diversity may help to improve patient's mood.}, }
@article {pmid29669589, year = {2018}, author = {Coelho, LP and Kultima, JR and Costea, PI and Fournier, C and Pan, Y and Czarnecki-Maulden, G and Hayward, MR and Forslund, SK and Schmidt, TSB and Descombes, P and Jackson, JR and Li, Q and Bork, P}, title = {Similarity of the dog and human gut microbiomes in gene content and response to diet.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {72}, pmid = {29669589}, issn = {2049-2618}, support = {686070//Horizon 2020 Framework Programme (BE)/International ; }, mesh = {Animals ; *Diet ; Dogs ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; Mice ; *Microbiota ; Obesity ; Swine ; }, abstract = {BACKGROUND: Gut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metagenomics to investigate the relationship between the gut metagenomes of dogs, humans, mice, and pigs.<br><br>RESULTS: We present a dog gut microbiome gene catalog containing 1,247,405 genes (based on 129 metagenomes and a total of 1.9 terabasepairs of sequencing data). Based on this catalog and taxonomic abundance profiling, we show that the dog microbiome is closer to the human microbiome than the microbiome of either pigs or mice. To investigate this similarity in terms of response to dietary changes, we report on a randomized intervention with two diets (high-protein/low-carbohydrate vs. lower protein/higher carbohydrate). We show that diet has a large and reproducible effect on the dog microbiome, independent of breed or sex. Moreover, the responses were in agreement with those observed in previous human studies.<br><br>CONCLUSIONS: We conclude that findings in dogs may be predictive of human microbiome results. In particular, a novel finding is that overweight or obese dogs experience larger compositional shifts than lean dogs in response to a high-protein diet.}, }
@article {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 {pmid29642940, year = {2018}, author = {Dai, Z and Coker, OO and Nakatsu, G and Wu, WKK and Zhao, L and Chen, Z and Chan, FKL and Kristiansen, K and Sung, JJY and Wong, SH and Yu, J}, title = {Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {70}, pmid = {29642940}, issn = {2049-2618}, support = {766613, 14106145, 14111216//RGC-GRF/International ; 2016YFC1303200//135 Program Project China/International ; 2013CB531401//973 Program China/International ; 2014BAI09B05//National Key Technology R&amp;D Program/International ; }, mesh = {Aged ; Bacteria/*classification/*genetics ; Cell Transformation, Neoplastic ; Colorectal Neoplasms/diagnosis/*etiology ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Gene Ontology ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; }, abstract = {BACKGROUND: Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort the structure of microbial dysbiosis in CRC and lead to inconsistent results among studies. In this regard, our study targeted at exploring changes in gut microbiota that are universal across populations at species level.<br><br>RESULTS: Based on the combined analysis of 526 metagenomic samples from Chinese, Austrian, American, and German and French cohorts, seven CRC-enriched bacteria (Bacteroides fragilis, Fusobacterium nucleatum, Porphyromonas asaccharolytica, Parvimonas micra, Prevotella intermedia, Alistipes finegoldii, and Thermanaerovibrio acidaminovorans) have been identified across populations. The seven enriched bacterial markers classified cases from controls with an area under the receiver-operating characteristics curve (AUC) of 0.80 across the different populations. Abundance correlation analysis demonstrated that CRC-enriched and CRC-depleted bacteria respectively formed their own mutualistic networks, in which the latter was disjointed in CRC. The CRC-enriched bacteria have been found to be correlated with lipopolysaccharide and energy biosynthetic pathways.<br><br>CONCLUSIONS: Our study identified potential diagnostic bacterial markers that are robust across populations, indicating their potential universal use for non-invasive CRC diagnosis. We also elucidated the ecological networks and functional capacities of CRC-associated microbiota.}, }
@article {pmid29631628, year = {2018}, author = {Mason, MR and Chambers, S and Dabdoub, SM and Thikkurissy, S and Kumar, PS}, title = {Characterizing oral microbial communities across dentition states and colonization niches.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {67}, pmid = {29631628}, issn = {2049-2618}, support = {T32-DE014320/DE/NIDCR NIH HHS/United States ; R01 DE022579/DE/NIDCR NIH HHS/United States ; F30- DE024940/DE/NIDCR NIH HHS/United States ; F30 DE024940/DE/NIDCR NIH HHS/United States ; T32 DE014320/DE/NIDCR NIH HHS/United States ; R01-DE022579/DE/NIDCR NIH HHS/United States ; }, mesh = {Biodiversity ; Cross-Sectional Studies ; *Dentition ; Gingiva/microbiology ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; }, abstract = {METHODS: The present study aimed to identify patterns and processes in acquisition of oral bacteria and to characterize the microbiota of different dentition states and habitats. Mucosal, salivary, supragingival, and subgingival biofilm samples were collected from orally and systemically healthy children and mother-child dyads in predentate, primary, mixed, and permanent dentitions. 16S rRNA gene sequences were compared to the Human Oral Microbiome Database (HOMD). Functional potential was inferred using PICRUSt.<br><br>RESULTS: Unweighted and weighted UniFrac distances were significantly smaller between each mother-predentate dyad than infant-unrelated female dyads. Predentate children shared a median of 85% of species-level operational taxonomic units (s-OTUs) and 100% of core s-OTUs with their mothers. Maternal smoking, but not gender, mode of delivery, feeding habits, or type of food discriminated between predentate microbial profiles. The primary dentition demonstrated expanded community membership, structure, and function when compared to the predentate stage, as well as significantly lower similarity between mother-child dyads. The primary dentition also included 85% of predentate core s-OTUs. Subsequent dentitions exhibited over 90% similarity to the primary dentition in phylogenetic and functional structure. Species from the predentate mucosa as well as new microbial assemblages were identified in the primary supragingival and subgingival microbiomes. All individuals shared 65% of species between supragingival and subgingival habitats; however, the salivary microbiome exhibited less than 35% similarity to either habitat.<br><br>CONCLUSIONS: Within the limitations of a cross-sectional study design, we identified two definitive stages in oral bacterial colonization: an early predentate imprinting and a second wave with the eruption of primary teeth. Bacterial acquisition in the oral microbiome is influenced by the maternal microbiome. Personalization begins with the eruption of primary teeth; however, this is limited to phylogeny; functionally, individuals exhibit few differences, suggesting that microbial assembly may follow a defined schematic that is driven by the functional requirements of the ecosystem. This early microbiome forms the foundation upon which newer communities develop as more colonization niches emerge, and expansion of biodiversity is attributable to both introduction of new species and increase in abundance of predentate organisms.}, }
@article {pmid29631623, year = {2018}, author = {Shkoporov, AN and Ryan, FJ and Draper, LA and Forde, A and Stockdale, SR and Daly, KM and McDonnell, SA and Nolan, JA and Sutton, TDS and Dalmasso, M and McCann, A and Ross, RP and Hill, C}, title = {Reproducible protocols for metagenomic analysis of human faecal phageomes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {68}, pmid = {29631623}, issn = {2049-2618}, support = {SFI/14/SP APC/B3032//Science Foundation Ireland/Ireland ; SFI/12/RC/2273//Science Foundation Ireland/Ireland ; N/A//Janssen Biotech, Inc/International ; }, mesh = {Bacteria/classification/genetics ; Bacteriophages/*genetics ; Feces/*virology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {BACKGROUND: Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing. The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing.<br><br>RESULTS: Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at + 4 °C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples.<br><br>CONCLUSIONS: The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results.}, }
@article {pmid29615108, year = {2018}, author = {Cornuault, JK and Petit, MA and Mariadassou, M and Benevides, L and Moncaut, E and Langella, P and Sokol, H and De Paepe, M}, title = {Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {65}, pmid = {29615108}, issn = {2049-2618}, mesh = {Animals ; Bacteriophages/*physiology/ultrastructure ; Biodiversity ; Colitis/etiology ; DNA Damage ; Dysbiosis ; Faecalibacterium prausnitzii/*virology ; *Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Inflammatory Bowel Diseases/etiology ; Metagenome ; Metagenomics/methods ; Mice ; Retroelements ; Symbiosis ; }, abstract = {BACKGROUND: Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases.<br><br>METHODS: We identified 18 prophages in 15 genomes of F. prausnitzii, used comparative genomics to define eight phage clades, and annotated the genome of the type phage of each clade. For two of the phages, we studied prophage induction in vitro and in vivo in mice. Finally, we aligned reads from already published viral metagenomic data onto the newly identified phages.<br><br>RESULTS: We show that each phage clade represents a novel viral genus and that a surprisingly large fraction of them (10 of the 18 phages) codes for a diversity-generating retroelement, which could contribute to their adaptation to the digestive tract environment. We obtained either experimental or in silico evidence of activity for at least one member of each genus. In addition, four of these phages are either significantly more prevalent or more abundant in stools of IBD patients than in those of healthy controls.<br><br>CONCLUSION: Since IBD patients generally have less F. prausnitzii in their microbiota than healthy controls, the higher prevalence or abundance of some of its phages may indicate that they are activated during disease. This in turn suggests that phages could trigger or aggravate F. prausnitzii depletion in patients. Our results show that prophage detection in sequenced strains of the microbiota can usefully complement viral metagenomic studies.}, }
@article {pmid29609653, year = {2018}, author = {De Vrieze, J and Pinto, AJ and Sloan, WT and Ijaz, UZ}, title = {The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {63}, pmid = {29609653}, issn = {2049-2618}, support = {NE/L011956/1//Natural Environment Research Council/International ; EP/M016811/1//Engineering and Physical Sciences Research Council/International ; }, mesh = {*Anaerobiosis ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing.<br><br>RESULTS: A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles.<br><br>CONCLUSIONS: In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion.}, }
@article {pmid29587880, year = {2018}, author = {Gasc, C and Peyret, P}, title = {Hybridization capture reveals microbial diversity missed using current profiling methods.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {61}, pmid = {29587880}, issn = {2049-2618}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; *Metagenome ; *Metagenomics/methods ; *Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Soil Microbiology ; }, abstract = {BACKGROUND: Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method has resulted in the discovery of many unexpected evolutionary lineages. However, amplicon sequencing is subject to numerous biases, with some taxa being missed, and is limited by the read length of second-generation sequencing platforms, which drastically reduces the phylogenetic resolution.<br><br>RESULTS: Here, we describe a hybridization capture strategy that allows the enrichment of 16S rRNA genes from metagenomic samples and enables an exhaustive identification and a complete reconstruction of the biomarker. Applying this approach to a microbial mock community and a soil sample, we demonstrated that hybridization capture is able to reveal greater microbial diversity than 16S rDNA amplicon sequencing and shotgun sequencing. The reconstruction of full-length 16S rRNA genes facilitated the improvement of phylogenetic resolution and the discovery of novel prokaryotic taxa.<br><br>CONCLUSIONS: Our results demonstrate that hybridization capture can lead to major breakthroughs in our understanding of microbial diversity, overcoming the limitations of conventional 16S rRNA gene studies. If applied to a broad range of environmental samples, this innovative approach could reveal the undescribed diversity of the still underexplored microbial communities and could provide a better understanding of ecosystem function.}, }
@article {pmid29106455, year = {2018}, author = {Maarala, AI and Bzhalava, Z and Dillner, J and Heljanko, K and Bzhalava, D}, title = {ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {6}, pages = {928-935}, doi = {10.1093/bioinformatics/btx702}, pmid = {29106455}, issn = {1367-4811}, mesh = {Algorithms ; Computers ; *Genome, Viral ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods ; *Software ; Viruses/*genetics ; }, abstract = {Motivation: Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and cheaper than ever before. However, the traditional sequential genome analysis algorithms, tools, and platforms are inefficient for performing large-scale metagenomic studies on ever-growing sample data volumes. Currently, there is an urgent need for scalable analysis pipelines that enable harnessing all the power of parallel computation in computing clusters and in cloud computing environments. We propose ViraPipe, a scalable metagenome analysis pipeline that is able to analyze thousands of human microbiomes in parallel in tolerable time. The pipeline is tuned for analyzing viral metagenomes and the software is applicable for other metagenomic analyses as well. ViraPipe integrates parallel BWA-MEM read aligner, MegaHit De novo assembler, and BLAST and HMMER3 sequence search tools. We show the scalability of ViraPipe by running experiments on mining virus related genomes from NGS datasets in a distributed Spark computing cluster.<br><br>Results: ViraPipe analyses 768 human samples in 210 minutes on a Spark computing cluster comprising 23 nodes and 1288 cores in total. The speedup of ViraPipe executed on 23 nodes was 11x compared to the sequential analysis pipeline executed on a single node. The whole process includes parallel decompression, read interleaving, BWA-MEM read alignment, filtering and normalizing of non-human reads, De novo contigs assembling, and searching of sequences with BLAST and HMMER3 tools.<br><br>Contact: ilari.maarala@aalto.fi.<br><br>https://github.com/NGSeq/ViraPipe.}, }
@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 {pmid30258040, year = {2018}, author = {Taft, DH and Liu, J and Maldonado-Gomez, MX and Akre, S and Huda, MN and Ahmad, SM and Stephensen, CB and Mills, DA}, title = {Bifidobacterial Dominance of the Gut in Early Life and Acquisition of Antimicrobial Resistance.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30258040}, issn = {2379-5042}, support = {S10 RR029668/RR/NCRR NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; F32 HD093185/HD/NICHD NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; R01 AT007079/AT/NCCIH NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bangladesh ; Bifidobacterium/genetics/*physiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; Probiotics/therapeutic use ; Regression Analysis ; }, abstract = {Bifidobacterium species are important commensals capable of dominating the infant gut microbiome, in part by producing acids that suppress growth of other taxa. Bifidobacterium species are less prone to possessing antimicrobial resistance (AMR) genes (ARGs) than other taxa that may colonize infants. Given that AMR is a growing public health crisis and ARGs are present in the gut microbiome of humans from early life, this study examines the correlation between a Bifidobacterium-dominated infant gut microbiome and AMR levels, measured by a culture-independent metagenomic approach both in early life and as infants become toddlers. In general, Bifidobacterium dominance is associated with a significant reduction in AMR in a Bangladeshi cohort, both in the number of acquired AMR genes present and in the abundance of AMR genes. However, by year 2, Bangladeshi infants had no significant differences in AMR related to their early-life Bifidobacterium levels. A generalized linear model including all infants in a previously published Swedish cohort found a significant negative association between log-transformed total AMR and Bifidobacterium levels, thus confirming the relationship between Bifidobacterium levels and AMR. In both cohorts, there was no change between early-life and later-life AMR abundance in high-Bifidobacterium infants but a significant reduction in AMR abundance in low-Bifidobacterium infants. These results support the hypothesis that early Bifidobacterium dominance of the infant gut microbiome may help reduce colonization by taxa containing ARGs.IMPORTANCE Infants are vulnerable to an array of infectious diseases, and as the gut microbiome may serve as a reservoir of AMR for pathogens, reducing the levels of AMR in infants is important to infant health. This study demonstrates that high levels of Bifidobacterium are associated with reduced levels of AMR in early life and suggests that probiotic interventions to increase infant Bifidobacterium levels have the potential to reduce AMR in infants. However, this effect is not sustained at year 2 of age in Bangladeshi infants, underscoring the need for more detailed studies of the biogeography and timing of infant AMR acquisition.}, }
@article {pmid30232167, year = {2018}, author = {Ingala, MR and Simmons, NB and Perkins, SL}, title = {Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30232167}, issn = {2379-5042}, mesh = {Animals ; Chiroptera/*microbiology ; *Diet ; Ecology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; *Metagenomics ; Phylogeny ; }, abstract = {Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome.}, }
@article {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 {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 {pmid29092015, year = {2018}, author = {Olekhnovich, EI and Vasilyev, AT and Ulyantsev, VI and Kostryukova, ES and Tyakht, AV}, title = {MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {3}, pages = {434-444}, doi = {10.1093/bioinformatics/btx681}, pmid = {29092015}, issn = {1367-4811}, mesh = {Algorithms ; Bacteria/*genetics ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics/*methods ; *Software ; }, abstract = {Motivation: Antibiotic resistance is an important global public health problem. Human gut microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens.<br><br>Results: We developed MetaCherchant-an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph. The algorithm was validated on a number of simulated and published datasets, as well as applied to new 'shotgun' metagenomes of gut microbiota from patients with Helicobacter pylori who underwent antibiotic therapy. Genomic context was reconstructed for several major resistance genes. Taxonomic annotation of the context suggests that within a single metagenome, the resistance genes can be contained in genomes of multiple species. MetaCherchant allows reconstruction of mobile elements with resistance genes within the genomes of bacteria using metagenomic data. Application of MetaCherchant in differential mode produced specific graph structures suggesting the evidence of possible resistance gene transmission within a mobile element that occurred as a result of the antibiotic therapy. MetaCherchant is a promising tool giving researchers an opportunity to get an insight into dynamics of resistance transmission in vivo basing on metagenomic data.<br><br>Source code and binaries are freely available for download at https://github.com/ctlab/metacherchant. The code is written in Java and is platform-independent.<br><br>Cotanct: ulyantsev@rain.ifmo.ru.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid28968799, year = {2018}, author = {Äijö, T and Müller, CL and Bonneau, R}, title = {Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {3}, pages = {372-380}, pmid = {28968799}, issn = {1367-4811}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; *Models, Statistical ; RNA, Ribosomal, 16S/*analysis ; Sequence Analysis, DNA/methods ; }, abstract = {Motivation: The number of microbial and metagenomic studies has increased drastically due to advancements in next-generation sequencing-based measurement techniques. Statistical analysis and the validity of conclusions drawn from (time series) 16S rRNA and other metagenomic sequencing data is hampered by the presence of significant amount of noise and missing data (sampling zeros). Accounting uncertainty in microbiome data is often challenging due to the difficulty of obtaining biological replicates. Additionally, the compositional nature of current amplicon and metagenomic data differs from many other biological data types adding another challenge to the data analysis.<br><br>Results: To address these challenges in human microbiome research, we introduce a novel probabilistic approach to explicitly model overdispersion and sampling zeros by considering the temporal correlation between nearby time points using Gaussian Processes. The proposed Temporal Gaussian Process Model for Compositional Data Analysis (TGP-CODA) shows superior modeling performance compared to commonly used Dirichlet-multinomial, multinomial and non-parametric regression models on real and synthetic data. We demonstrate that the nonreplicative nature of human gut microbiota studies can be partially overcome by our method with proper experimental design of dense temporal sampling. We also show that different modeling approaches have a strong impact on ecological interpretation of the data, such as stationarity, persistence and environmental noise models.<br><br>A Stan implementation of the proposed method is available under MIT license at https://github.com/tare/GPMicrobiome.<br><br>Contact: taijo@flatironinstitute.org or rb113@nyu.edu.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@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 {pmid30138419, year = {2018}, author = {Oliveira, JL and Cury, JC and Gurgel-Gonçalves, R and Bahia, AC and Monteiro, FA}, title = {Field-collected Triatoma sordida from central Brazil display high microbiota diversity that varies with regard to developmental stage and intestinal segmentation.}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {8}, pages = {e0006709}, pmid = {30138419}, issn = {1935-2735}, mesh = {Animals ; Bacteria/*classification ; Brazil ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Male ; Nymph ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Triatoma/growth &amp; development/*microbiology ; }, abstract = {BACKGROUND/METHODOLOGY: Triatomine bugs are the vectors of Trypanosoma cruzi, the agent of Chagas disease. Vector control has for decades relied upon insecticide spraying, but insecticide resistance has recently emerged in several triatomine populations. One alternative strategy to reduce T. cruzi transmission is paratransgenesis, whereby symbiotic bacteria are genetically engineered to produce T. cruzi-killing proteins in the vector's gut. This approach requires in-depth knowledge of the vectors' natural gut microbiota. Here, we use metagenomics (16S rRNA 454 pyrosequencing) to describe the gut microbiota of field-caught Triatoma sordida-likely the most common peridomestic triatomine in Brazil. For large nymphs (4th and 5th stage) and adults, we also studied separately the three main digestive-tract segments-anterior midgut, posterior midgut, and hindgut.<br><br>PRINCIPAL FINDINGS: Bacteria of four phyla (12 genera) were present in both nymphs (all five stages) and adults, thus defining T. sordida's 'bacterial core': Actinobacteria (Brevibacterium, Corynebacterium, Dietzia, Gordonia, Nitriliruptor, Nocardia, Nocardiopsis, Rhodococcus, and Williamsia), Proteobacteria (Pseudomonas and Sphingobium), and Firmicutes (Staphylococcus). We found some clear differences in bacterial composition and relative abundance among development stages; overall, Firmicutes and Proteobacteria increased, but Actinobacteria decreased, through development. Finally, the bacterial microbiotas of the bugs' anterior midgut, posterior midgut, and hindgut were sharply distinct.<br><br>CONCLUSIONS/SIGNIFICANCE: Our results identify the 'bacterial core set' of T. sordida and reveal important gut microbiota differences among development stages-particularly between 1st-3rd stage nymphs and adults. Further, we show that, within any given development stage, the vectors' gut cannot be regarded as a single homogeneous environment. Cultivable, non-pathogenic 'core' bacterial species may now be tested as candidates for paratransgenic control of T. cruzi transmission by T. sordida.}, }
@article {pmid29667264, year = {2018}, author = {Xu, Y and Jia, YH and Chen, L and Huang, WM and Yang, DQ}, title = {Metagenomic analysis of oral microbiome in young children aged 6-8 years living in a rural isolated Chinese province.}, journal = {Oral diseases}, volume = {24}, number = {6}, pages = {1115-1125}, doi = {10.1111/odi.12871}, pmid = {29667264}, issn = {1601-0825}, mesh = {Child ; China ; Dentition, Mixed ; Female ; Humans ; Male ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; *Rural Population ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The mixed dentition is an important transition period from primary teeth to permanent teeth. However, the caries prevalence of first permanent molar in mixed dentitions was about 30%, which almost represent the caries rate of permanent teeth in this period of time. Therefore, we assessed the oral bacterial profiles in young children (age 6-8) with mixed dentition with or without first molar caries for providing the research basis of caries etiology.<br><br>METHODS: We collected samples of supragingival plaque and saliva from the children living in Guizhou, a rural isolated province in China. Then, we performed DNA extraction and purification followed by 454 pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA and compared our results with those of previous research.<br><br>RESULTS: (i) We analyzed 48,320 unique sequences that represented 18 phyla, 29 classes, 44 orders, 74 families, 129 genera, 15,003 species-level OUT in plaque and saliva samples; (ii) longitudinally, there was the &quot;healthy core microbiome&quot; between healthy deciduous dentition and early mixed dentition, for example, Neisseria, Porphyromonas, Selenomonas etc.; (iii) horizontally, there also existed the &quot;healthy core microbiome&quot; in early mixed dentition, for example, Neisseria, Streptococcus, Prevotella etc.; (iv) the dominant bacteria detected by Lefse in caries group including Actinomycetaceae, Streptobacillus (p < 0.05) and those in caries-free group including Gammaproteobacteria, Pasteurellaceae, Aggregatibacter, Chloroflexi, (p < 0.05).<br><br>CONCLUSIONS: The oral cavity is a highly heterogeneous ecosystem with the &quot;healthy core microbiome&quot; in children, although microbial composition shifts along with aging. In addition, the abundance and diversity of microbiota vary between caries and caries-free groups verify the ecological plaque hypothesis.}, }
@article {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 {pmid28083919, year = {2018}, author = {Ishihara, K}, title = {New approach for studying mobile genes using metagenomic analysis.}, journal = {Oral diseases}, volume = {24}, number = {4}, pages = {494-496}, doi = {10.1111/odi.12640}, pmid = {28083919}, issn = {1601-0825}, mesh = {Bacteria/*genetics ; Drug Resistance, Bacterial/genetics ; Fiji ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Humans ; *Metagenome ; Metagenomics ; Mouth/*microbiology ; Mouth Diseases/*microbiology ; North America ; }, }
@article {pmid29227468, year = {2018}, author = {Beaulaurier, J and Zhu, S and Deikus, G and Mogno, I and Zhang, XS and Davis-Richardson, A and Canepa, R and Triplett, EW and Faith, JJ and Sebra, R and Schadt, EE and Fang, G}, title = {Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.}, journal = {Nature biotechnology}, volume = {36}, number = {1}, pages = {61-69}, pmid = {29227468}, issn = {1546-1696}, support = {R01 GM114472/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/genetics ; Cluster Analysis ; DNA Methylation/*genetics ; Environmental Microbiology ; Genome, Bacterial/genetics ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Plasmids/genetics ; Sequence Analysis, DNA ; }, abstract = {Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing. Our method takes advantage of these endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins. We validate our method using synthetic and real microbiome sequences. In addition to genome binning, we show that our method links plasmids and other mobile genetic elements to their host species in a real microbiome sample. Incorporation of DNA methylation information into shotgun metagenomics analyses will complement existing methods to enable more accurate sequence binning.}, }
@article {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 {pmid30048915, year = {2018}, author = {Milanović, V and Osimani, A and Garofalo, C and De Filippis, F and Ercolini, D and Cardinali, F and Taccari, M and Aquilanti, L and Clementi, F}, title = {Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE.}, journal = {International journal of food microbiology}, volume = {286}, number = {}, pages = {66-74}, doi = {10.1016/j.ijfoodmicro.2018.07.022}, pmid = {30048915}, issn = {1879-3460}, mesh = {Acetic Acid/*analysis ; Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; Fermentation ; Metagenomics ; Microbiota/genetics ; Molecular Typing ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Wine/*microbiology ; }, abstract = {The production of traditional vinegar is usually carried out using the so-called &quot;seed vinegar&quot; or &quot;mother of vinegar&quot; that is composed of an undefined and complex pool of microorganisms deriving from a previous vinegar production. To date, there have been relatively few studies on the microbiota of seed vinegars. The present study was carried out to discover the bacterial biota of seed vinegar samples used in the homemade production of local vinegars obtained from the acetic fermentation of white wine. The seed vinegar samples were subjected to viable counting and advanced molecular analyses, namely, Illumina sequencing and PCR-DGGE. The adopted polyphasic approach allowed the bacterial diversity of the analyzed samples to be profiled, thus revealing the presence of acetic acid bacteria ascribed to the genera Acetobacter, Gluconacetobacter, Gluconobacter and Komagataeibacter. Moreover, other microbial genera as Pseudomonas, Bacillus and Clostridium were abundantly found in almost all the samples, together with other minority genera. The results of viable counting confirmed the well-acknowledged limitations inherent with acetic acid bacteria recovery on plate growth media. The overall results confirmed that seed vinegars have a complex and heterogeneous biodiversity, thus encouraging their exploitation for the isolation and future technological characterization of cultures to be selected for the manufacture of mixed starter cultures.}, }
@article {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 {pmid29133882, year = {2018}, author = {Yutin, N and Makarova, KS and Gussow, AB and Krupovic, M and Segall, A and Edwards, RA and Koonin, EV}, title = {Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {38-46}, pmid = {29133882}, issn = {2058-5276}, support = {Z01 LM000073-12/NULL/Intramural NIH HHS/United States ; }, mesh = {Bacteriophages/*classification/*genetics ; Bacteroidetes/virology ; Databases, Protein ; Gastrointestinal Microbiome/*genetics ; Genome, Viral/genetics ; *Genomics ; Humans ; *Metagenomics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, Protein ; Viral Proteins/chemistry/genetics ; }, abstract = {Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery 1-3 . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome 4 . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study. Here we combine a comprehensive search of genomic and metagenomic databases with sensitive methods for protein sequence analysis to identify an expansive, diverse group of bacteriophages related to crAssphage and predict the functions of the majority of phage proteins, in particular those that comprise the structural, replication and expression modules. Most, if not all, of the crAss-like phages appear to be associated with diverse bacteria from the phylum Bacteroidetes, which includes some of the most abundant bacteria in the human gut microbiome and that are also common in various other habitats. These findings provide for experimental characterization of the most abundant but poorly understood members of the human-associated virome.}, }
@article {pmid29109478, year = {2018}, author = {Kolinko, S and Wu, YW and Tachea, F and Denzel, E and Hiras, J and Gabriel, R and Bäcker, N and Chan, LJG and Eichorst, SA and Frey, D and Chen, Q and Azadi, P and Adams, PD and Pray, TR and Tanjore, D and Petzold, CJ and Gladden, JM and Simmons, BA and Singer, SW}, title = {A bacterial pioneer produces cellulase complexes that persist through community succession.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {99-107}, doi = {10.1038/s41564-017-0052-z}, pmid = {29109478}, issn = {2058-5276}, support = {S10 OD018530/OD/NIH HHS/United States ; }, mesh = {Bacteria/*classification/*enzymology/metabolism ; Bacterial Proteins/analysis/isolation &amp; purification ; Biological Evolution ; Cellulase/*analysis/isolation &amp; purification ; Cellulose/*metabolism ; Composting ; Genome, Bacterial/genetics ; Glycoside Hydrolases/analysis/isolation &amp; purification ; Glycosylation ; Heterotrophic Processes ; Metagenomics ; Microbial Consortia/*physiology ; Models, Biological ; Multienzyme Complexes/*analysis/isolation &amp; purification ; *Phylogeny ; Soil Microbiology ; }, abstract = {Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.}, }
@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 {pmid28588199, year = {2017}, author = {Gomez-Arango, LF and Barrett, HL and McIntyre, HD and Callaway, LK and Morrison, M and Nitert, MD}, title = {Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2860}, pmid = {28588199}, issn = {2045-2322}, mesh = {Adult ; Biomarkers ; Female ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Mouth/*microbiology ; Obesity/*etiology ; Overweight/*etiology ; Phylogeny ; Placenta/*microbiology ; Pregnancy ; *Pregnancy Complications ; }, abstract = {A distinct bacterial signature of the placenta was reported, providing evidence that the fetus does not develop in a sterile environment. The oral microbiome was suggested as a possible source of the bacterial DNA present in the placenta based on similarities to the oral non-pregnant microbiome. Here, the possible origin of the placental microbiome was assessed, examining the gut, oral and placental microbiomes from the same pregnant women. Microbiome profiles from 37 overweight and obese pregnant women were examined by 16SrRNA sequencing. Fecal and oral contributions to the establishment of the placental microbiome were evaluated. Core phylotypes between body sites and metagenome predictive functionality were determined. The placental microbiome showed a higher resemblance and phylogenetic proximity with the pregnant oral microbiome. However, similarity decreased at lower taxonomic levels and microbiomes clustered based on tissue origin. Core genera: Prevotella, Streptococcus and Veillonella were shared between all body compartments. Pathways encoding tryptophan, fatty-acid metabolism and benzoate degradation were highly enriched specifically in the placenta. Findings demonstrate that the placental microbiome exhibits a higher resemblance with the pregnant oral microbiome. Both oral and gut microbiomes contribute to the microbial seeding of the placenta, suggesting that placental colonization may have multiple niche sources.}, }
@article {pmid28584301, year = {2017}, author = {Pootakham, W and Mhuantong, W and Yoocha, T and Putchim, L and Sonthirod, C and Naktang, C and Thongtham, N and Tangphatsornruang, S}, title = {High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2774}, pmid = {28584301}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/*genetics ; Biodiversity ; *Metagenomics/methods ; *Microbiota ; Phylogeny ; Phylogeography ; *RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Thailand ; }, abstract = {Coral reefs are a complex ecosystem consisting of coral animals and a vast array of associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their fundamental roles in fitness and survival of the host animal. The scleractinian coral Porites lutea is one of the dominant reef-builders in the Indo-West Pacific. Currently, very little is known about the composition and structure of bacterial communities across P. lutea reefs. The purpose of this study is twofold: to demonstrate the advantages of using PacBio circular consensus sequencing technology in microbial community studies and to investigate the diversity and structure of P. lutea-associated microbiome in the Indo-Pacific. This is the first metagenomic study of marine environmental samples that utilises the PacBio sequencing system to capture full-length 16S rRNA sequences. We observed geographically distinct coral-associated microbial profiles between samples from the Gulf of Thailand and Andaman Sea. Despite the geographical and environmental impacts on the coral-host interactions, we identified a conserved community of bacteria that were present consistently across diverse reef habitats. Finally, we demonstrated the superior performance of full-length 16S rRNA sequences in resolving taxonomic uncertainty of coral associates at the species level.}, }
@article {pmid28536449, year = {2017}, author = {Choi, S and Song, H and Tripathi, BM and Kerfahi, D and Kim, H and Adams, JM}, title = {Effect of experimental soil disturbance and recovery on structure and function of soil community: a metagenomic and metagenetic approach.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2260}, pmid = {28536449}, issn = {2045-2322}, mesh = {Biodiversity ; *Biota ; Ecosystem ; *Metagenome ; *Metagenomics/methods ; Microbiota ; *Soil ; *Soil Microbiology ; }, abstract = {There has been little study of effects of disturbance on soil biota combining closely controlled experimental conditions and DNA-based methods. We sampled pots of soil at varying times following an initial simulated mass mortality event. Soil DNA was extracted at intervals up to 24 weeks after the event, and shotgun metagenomes sequenced using NextSeq. Compared to initial conditions, we found: consistent, sequential changes in functional metagenome and community structure over time, indicating successional niche differentiation amongst soil biota. As predicted, early successional systems had greater abundance of genes associated with motility, but fewer genes relating to DNA/RNA/protein metabolism, cell division and cell cycle. Contrary to predictions, there were no significant differences in cell signaling, virulence and defense-related genes. Also, stress related genes were less abundant in later succession. The early successional system had lower taxonomic diversity but higher functional gene diversity. Over time, community characteristics changed progressively, but by the end of the experiment had not returned to the 'original' state of the system before disturbance. Results indicated a predictable sequence of gene functions and taxa following disturbance, analogous to ecosystem succession for large organisms. It is unclear if and when the system would return to its pre-disturbance state.}, }
@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 {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 {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 {pmid29551526, year = {2018}, author = {Santos, JC and Tarvin, RD and O'Connell, LA and Blackburn, DC and Coloma, LA}, title = {Diversity within diversity: Parasite species richness in poison frogs assessed by transcriptomics.}, journal = {Molecular phylogenetics and evolution}, volume = {125}, number = {}, pages = {40-50}, doi = {10.1016/j.ympev.2018.03.015}, pmid = {29551526}, issn = {1095-9513}, mesh = {Animals ; Anura/*genetics/*parasitology ; Biodiversity ; *Gene Expression Profiling ; Genetic Speciation ; Host-Parasite Interactions/genetics ; Parasites/*physiology ; Phylogeny ; Poisons ; Species Specificity ; Transcriptome/genetics ; }, abstract = {Symbionts (e.g., endoparasites and commensals) play an integral role in their host's ecology, yet in many cases their diversity is likely underestimated. Although endoparasites are traditionally characterized using morphology, sequences of conserved genes, and shotgun metagenomics, host transcriptomes constitute an underused resource to identify these organisms' diversity. By isolating non-host transcripts from host transcriptomes, individual host tissues can now simultaneously reveal their endoparasite species richness (i.e., number of different taxa) and provide insights into parasite gene expression. These approaches can be used in host taxa whose endoparasites are mostly unknown, such as those of tropical amphibians. Here, we focus on the poison frogs (Dendrobatidae) as hosts, which are a Neotropical clade known for their bright coloration and defensive alkaloids. These toxins are an effective protection against vertebrate predators (e.g., snakes and birds), bacteria, and skin-biting ectoparasites (e.g., mosquitoes); however, little is known about their deterrence against eukaryotic endoparasites. With de novo transcriptomes of dendrobatids, we developed a bioinformatics pipeline for endoparasite identification that uses host annotated RNA-seq data and set of a priori parasite taxonomic terms, which are used to mine for specific endoparasites. We found a large community of helminths and protozoans that were mostly restricted to the digestive tract and a few systemic parasites (e.g., Trypanosoma). Contrary to our expectations, all dendrobatid frogs regardless of the presence of alkaloid defenses have endoparasites, with their highest species richness located in the frog digestive tract. Some of these organisms (e.g., roundworms) might prove to be generalists, as they were not found to be co-diversifying with their frog hosts. We propose that endoparasites may escape poison frogs' chemical defenses by colonizing tissues with fewer alkaloids than the frog's skin, where most toxins are stored.}, }
@article {pmid29396546, year = {2018}, author = {Gonzalez-Martinez, A and Sihvonen, M and Muñoz-Palazon, B and Rodriguez-Sanchez, A and Mikola, A and Vahala, R}, title = {Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2208}, pmid = {29396546}, issn = {2045-2322}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Arctic Regions ; Bacteria/classification/genetics/*isolation &amp; purification ; Bioreactors/*microbiology ; *Biota ; Finland ; Fungi/classification/genetics/*isolation &amp; purification ; Metagenomics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/microbiology ; Waste Water/*microbiology ; Water Purification ; }, abstract = {Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.}, }
@article {pmid29395346, year = {2018}, author = {Limborg, MT and Alberdi, A and Kodama, M and Roggenbuck, M and Kristiansen, K and Gilbert, MTP}, title = {Applied Hologenomics: Feasibility and Potential in Aquaculture.}, journal = {Trends in biotechnology}, volume = {36}, number = {3}, pages = {252-264}, doi = {10.1016/j.tibtech.2017.12.006}, pmid = {29395346}, issn = {1879-3096}, mesh = {Animals ; *Aquaculture ; Epigenomics ; *Feasibility Studies ; Fishes/*microbiology ; Food Industry ; Gastrointestinal Microbiome/genetics/immunology ; Genome, Microbial/genetics/immunology ; Humans ; Immune System/immunology/microbiology ; *Metagenomics ; Proteomics ; Transcriptome ; }, abstract = {Aquaculture will play an essential role in feeding a growing human population, but several biological challenges impede sustainable growth of production. Emerging evidence across all areas of life has revealed the importance of the intimate biological interactions between animals and their associated gut microbiota. Based on challenges in aquaculture, we leverage current knowledge in molecular biology and host microbiota interactions to propose an applied holo-omic framework that integrates molecular data including genomes, transcriptomes, epigenomes, proteomes, and metabolomes for analyzing fish and their gut microbiota as interconnected and coregulated systems. With an eye towards aquaculture, we discuss the feasibility and potential of our holo-omic framework to improve growth, health, and sustainability in any area of food production, including livestock and agriculture.}, }
@article {pmid29330424, year = {2018}, author = {Cui, X and Ye, L and Li, J and Jin, L and Wang, W and Li, S and Bao, M and Wu, S and Li, L and Geng, B and Zhou, X and Zhang, J and Cai, J}, title = {Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {635}, pmid = {29330424}, issn = {2045-2322}, mesh = {Adult ; Aged ; Bacteria/*classification/genetics/isolation &amp; purification ; Butyrates/analysis ; Dysbiosis/*diagnosis ; Female ; Gastrointestinal Microbiome ; Heart Failure/*complications ; Humans ; Male ; Metabolomics/*methods ; Metagenomics/*methods ; Methylamines/analysis ; Middle Aged ; Phylogeny ; }, abstract = {Previous studies suggested a possible gut microbiota dysbiosis in chronic heart failure (CHF). However, direct evidence was lacking. In this study, we investigated the composition and metabolic patterns of gut microbiota in CHF patients to provide direct evidence and comprehensive understanding of gut microbiota dysbiosis in CHF. We enrolled 53 CHF patients and 41 controls. Metagenomic analyses of faecal samples and metabolomic analyses of faecal and plasma samples were then performed. We found that the composition of gut microbiota in CHF was significantly different from controls. Faecalibacterium prausnitzii decrease and Ruminococcus gnavus increase were the essential characteristics in CHF patients' gut microbiota. We also observed an imbalance of gut microbes involved in the metabolism of protective metabolites such as butyrate and harmful metabolites such as trimethylamine N-oxide in CHF patients. Metabolic features of both faecal and plasma samples from CHF patients also significantly changed. Moreover, alterations in faecal and plasma metabolic patterns correlated with gut microbiota dysbiosis in CHF. Taken together, we found that CHF was associated with distinct gut microbiota dysbiosis and pinpointed the specific core bacteria imbalance in CHF, along with correlations between changes in certain metabolites and gut microbes.}, }
@article {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 {pmid29040406, year = {2018}, author = {Pericard, P and Dufresne, Y and Couderc, L and Blanquart, S and Touzet, H}, title = {MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {4}, pages = {585-591}, doi = {10.1093/bioinformatics/btx644}, pmid = {29040406}, issn = {1367-4811}, mesh = {Algorithms ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metagenome ; Metagenomics/methods ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {Motivation: Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution.<br><br>Results: We designed MATAM, a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. The method implements a stepwise process based on construction and analysis of a read overlap graph. It is applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes. We show that MATAM outperforms other available methods in terms of low error rates and recovered fractions and is suitable to provide improved assemblies for precise taxonomic assignments.<br><br>https://github.com/bonsai-team/matam.<br><br>Contact: pierre.pericard@gmail.com or helene.touzet@univ-lille1.fr.<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 {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 {pmid30394652, year = {2018}, author = {Borton, MA and Daly, RA and O'Banion, B and Hoyt, DW and Marcus, DN and Welch, S and Hastings, SS and Meulia, T and Wolfe, RA and Booker, AE and Sharma, S and Cole, DR and Wunch, K and Moore, JD and Darrah, TH and Wilkins, MJ and Wrighton, KC}, title = {Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale.}, journal = {Environmental microbiology}, volume = {20}, number = {12}, pages = {4596-4611}, doi = {10.1111/1462-2920.14467}, pmid = {30394652}, issn = {1462-2920}, support = {1342701//National Science Foundation Dimensions of Biodiversity/ ; FE0024297//Department of Energy's National Energy Technology Laboratory/ ; //U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//Office of Science of the U.S. Department of Energy/ ; }, abstract = {About 60% of natural gas production in the United States comes from hydraulic fracturing of unconventional reservoirs, such as shales or organic-rich micrites. This process inoculates and enriches for halotolerant microorganisms in these reservoirs over time, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of methanogens across unconventional reservoirs, and report that members of genus Methanohalophilus are recovered from every hydraulically fractured unconventional reservoir sampled by metagenomics. We provide the first genomic sequencing of three isolate genomes, as well as two metagenome assembled genomes (MAGs). Utilizing six other previously sequenced isolate genomes and MAGs, we perform comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in CRISPR-Cas systems of Methanohalophilus, with genomes from geographically distinct unconventional reservoirs sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic methane production in hydraulically fractured unconventional reservoirs.}, }
@article {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 {pmid29668334, year = {2018}, author = {Amrane, S and Raoult, D and Lagier, JC}, title = {Metagenomics, culturomics, and the human gut microbiota.}, journal = {Expert review of anti-infective therapy}, volume = {16}, number = {5}, pages = {373-375}, doi = {10.1080/14787210.2018.1467268}, pmid = {29668334}, issn = {1744-8336}, mesh = {Culture Techniques/*methods ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; }, }
@article {pmid30384903, year = {2018}, author = {Huang, X and Zhu, J and Cai, Z and Lao, Y and Jin, H and Yu, K and Zhang, B and Zhou, J}, title = {Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach.}, journal = {Microbiological research}, volume = {217}, number = {}, pages = {1-13}, doi = {10.1016/j.micres.2018.08.015}, pmid = {30384903}, issn = {1618-0623}, mesh = {Acyltransferases/genetics/metabolism ; Bacteria/classification/*genetics/*metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Carbon-Sulfur Lyases/genetics/metabolism ; China ; Dinoflagellida/growth &amp; development/*microbiology ; Eutrophication/physiology ; Marine Biology ; Metagenomics/*methods ; Microbiota/*genetics/*physiology ; Phylogeny ; Proteobacteria/genetics/metabolism ; Quorum Sensing/*genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis ; Sequence Analysis, Protein ; Sequence Homology ; Symbiosis ; Transcription Factors/genetics/metabolism ; }, abstract = {The complicated relationships among environmental microorganisms are regulated by quorum sensing (QS). Understanding QS-based signals could shed light on the interactions between microbial communities in certain environments. Although QS characteristics have been widely discussed, few studies have been conducted on the role of QS in phycospheric microorganisms. Here, we used metagenomics to examine the profile of AI-1 (AinS, HdtS, LuxI) and AI-2 (LuxS) autoinducers from a deeply sequenced microbial database, obtained from a complete dinoflagellate bloom. A total of 3001 putative AI-1 homologs and 130 AI-2 homologs were identified. The predominant member among the AI groups was HdtS. The abundance of HdtS, AinS, and LuxS increased as the bloom developed, whereas the abundance of LuxI showed the opposite trend. Phylogenetic analysis suggested that HdtS and LuxI synthase originated mainly from alpha-, beta-, and gamma-Proteobacteria, whereas AinS synthase originated solely from Vibrionales. In comparison to AI-1, the sequences related to AI-2 (LuxS) demonstrated a much wider taxonomic coverage. Some significant correlations were found between dominant species and QS signals. In addition to the QS, we also performed parallel analysis of the quorum quenching (QQ) sequences. In comparison to QS, the relative abundance of QQ signals was lower; however, an obvious frequency correlation was observed. These results suggested that QS and QQ signals co-participate in regulating microbial communities during an algal bloom. These data helped to reveal the characteristic behavior of algal symbiotic bacteria, and facilitated a better understanding of microbial dynamics during an algal bloom event from a chemical ecological perspective.}, }
@article {pmid27188959, year = {2016}, author = {Angelakis, E and Bachar, D and Henrissat, B and Armougom, F and Audoly, G and Lagier, JC and Robert, C and Raoult, D}, title = {Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26276}, pmid = {27188959}, issn = {2045-2322}, mesh = {Bacteria/genetics ; DNA, Bacterial/genetics/*isolation &amp; purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Kwashiorkor/microbiology ; *Metagenomics ; Obesity/microbiology ; Polysaccharides/*chemistry ; Polysaccharides, Bacterial/chemistry ; Protein-Energy Malnutrition/microbiology ; }, abstract = {Exopolysaccharides produced by bacterial species and present in feces are extremely inhibitory to DNA restriction and can cause discrepancies in metagenomic studies. We determined the effects of different DNA extraction methods on the apparent composition of the gut microbiota using Illumina MiSeq deep sequencing technology. DNA was extracted from the stool from an obese female using 10 different methods and the choice of DNA extraction method affected the proportional abundance at the phylum level, species richness (Chao index, 227 to 2,714) and diversity (non parametric Shannon, 1.37 to 4.4). Moreover DNA was extracted from stools obtained from 83 different individuals by the fastest extraction assay and by an extraction assay that degradated exopolysaccharides. The fastest extraction method was able to detect 68% to 100% genera and 42% to 95% species whereas the glycan degradation extraction method was able to detect 56% to 93% genera and 25% to 87% species. To allow a good liberation of DNA from exopolysaccharides commonly presented in stools, we recommend the mechanical lysis of stools plus glycan degradation, used here for the first time. Caution must be taken in the interpretation of current metagenomic studies, as the efficiency of DNA extraction varies widely among stool samples.}, }
@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 {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 {pmid30372979, year = {2019}, author = {Park, SE and Seo, SH and Kim, EJ and Byun, S and Na, CS and Son, HS}, title = {Changes of microbial community and metabolite in kimchi inoculated with different microbial community starters.}, journal = {Food chemistry}, volume = {274}, number = {}, pages = {558-565}, doi = {10.1016/j.foodchem.2018.09.032}, pmid = {30372979}, issn = {1873-7072}, mesh = {Bacteria/metabolism ; Brassica/metabolism/*microbiology ; *Fermentation ; Fermented Foods/*microbiology ; *Food Microbiology ; *Microbiota ; }, abstract = {Gas chromatography mass spectrometry-based metabolomics and next generation sequencing-based metagenomics were applied to investigate the effect of different microbial community starters (MCSs) on kimchi fermentation. Profiles of metabolites and microbial community in kimchi were remarkably different from those on the first day of fermentation according to MCS used. Kimchi inoculated with MCS5 or MCS10 had relatively higher levels of lactic acid, leucine, propanedioic acid, serine, glycerol, erythritol, and sorbitol but lower levels of butanedioic acid, glyceric acid, myo-inositol, xylose, fructose, and talose compared to control kimchi or kimchi inoculated with MCS1. Microbial communities of kimchi inoculated with MCS1, MCS5, and MCS10 were characterized by high ratios of Leuconostoc, Lactobacillus plantarum, and Lactobacillus brevis, respectively. The microbial community of kimchi formed on the first day of fermentation was stable for 50 days, suggesting that microbial communities containing multiple microorganisms can be used as starters to obtain desired quality of kimchi.}, }
@article {pmid30173738, year = {2018}, author = {Stroebel, C and Alexander, T and Workentine, ML and Timsit, E}, title = {Effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of recently weaned beef cattle.}, journal = {Veterinary microbiology}, volume = {223}, number = {}, pages = {126-133}, doi = {10.1016/j.vetmic.2018.08.007}, pmid = {30173738}, issn = {1873-2542}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; Bovine Respiratory Disease Complex/*microbiology ; Cattle ; DNA, Bacterial/chemistry/genetics ; Female ; *Metagenomics ; *Microbiota ; Moraxella/genetics/isolation &amp; purification ; Mycoplasma/genetics/isolation &amp; purification ; Nasopharynx/microbiology ; RNA, Ribosomal, 16S/chemistry/genetics ; Trachea/microbiology ; Transportation ; Weaning ; }, abstract = {The objective was to study effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of feedlot cattle. Two groups of 30 Angus-cross heifers were studied from weaning to 28 d after arrival at a feedlot. For each group, half the heifers were either transported directly to a feedlot after weaning (RANC) or transported to and co-mingled at an auction market for 24 h before being placed in a feedlot (AUCT). Deep nasal swabs (DNS) and trans-tracheal aspirates (TTA) were collected at weaning (d0) and at on-arrival processing at the feedlot (d2). At 7 (d9) and 28 d (d30) after arrival, DNS were repeated. The DNA was extracted from DNS and TTA and the V4 region of the 16S rRNA gene sequenced (MiSeq). Alpha diversity analysis did not reveal differences between AUCT and RANC. However, bacterial diversity decreased over time in the nasopharynx, especially at d9. Although beta-diversity was not different between AUCT and RANC, interval after arrival and feedlot where heifers were placed affected composition of the nasopharyngeal bacterial communities. In both groups, a large increase in Mycoplasma was observed after arrival; in one group, Mycoplasma bovis was dominant at d9 and remained dominant until d30. However, in the other group, Mycoplasma dispar dominated at d9 and was replaced by Moraxella at d30. We concluded that transportation to and co-mingling at an auction market for 24 h did not significantly influence diversity or composition of nasopharyngeal or tracheal bacterial communities.}, }
@article {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 {pmid29980232, year = {2018}, author = {Hani, J and Abdel Nour, G and Matta, J and Jazzar, B and Pfaffl, MW and Hanna-Wakim, L and Abdel Nour, AM}, title = {Shisha microbiota: the good, the bad and the not so ugly.}, journal = {BMC research notes}, volume = {11}, number = {1}, pages = {446}, pmid = {29980232}, issn = {1756-0500}, mesh = {Adult ; Bacteria/genetics/*isolation &amp; purification ; Equipment Contamination ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S ; Smoking ; Smoking Water Pipes/*microbiology ; Tobacco ; }, abstract = {OBJECTIVE: Over the last decade, there has been a rapid expansion of the trendy water pipe smoking around the world especially among younger adults. The initial objective of this study was to identify the microbiota of the shisha, which may either be of no harm for the smoker or enhance the threat on his well-being. The total DNA for the metagenomics study was conducted on three different shishas from three different delivery shops in Jounieh, Lebanon. The microbiota in two solid parts of the shisha, shaft and hose, were analysed including the fresh tobacco and the water in the bowl. All samples were analysed using high-throughput sequencing of 16S rRNA gene amplicons.<br><br>RESULTS: Overall, more than 40 bacterial genera were found in the three investigated shishas, some are commensal others are pathogenic. All three shishas showed similar microbial content regarding the bacteria inhabiting in water, shaft, or hose. From the results of this study it appears that a very large quantity of bacteria was found in the water pipes, some are harmful and others beneficial. We assume that the presence of gut dependent microbiota is related to the loose hygienic conditions in which the shisha is prepared.}, }
@article {pmid29974156, year = {2018}, author = {Sharma, S and Grewal, S and Vakhlu, J}, title = {Phylogenetic diversity and metabolic potential of microbiome of natural healing clay from Chamliyal (J&amp;K).}, journal = {Archives of microbiology}, volume = {200}, number = {9}, pages = {1333-1343}, doi = {10.1007/s00203-018-1549-4}, pmid = {29974156}, issn = {1432-072X}, support = {38(1269)/10/EMR-II//Council of Scientific and Industrial Research/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Clay/*analysis/*chemistry ; Fungi/classification/*isolation &amp; purification/*metabolism ; Humans ; India ; Iron/metabolism ; Metagenome ; Microbiota/*physiology ; Molecular Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Skin Diseases/therapy ; Sulfur/metabolism ; }, abstract = {Clay therapy for skin disease treatment is an ancient practice popular worldwide as a cheap alternative to pharmaceutical products. Effectiveness of clay against skin problems has been linked to its mineral composition and to microbial activity. The clay-water paste of a holy shrine Chamliyal in the Jammu region of J&amp;K, India is used as an ointment to treat different skin disorders particularly psoriasis. Using the 16 SrDNA amplicon pyrosequencing and whole-metagenome direct shotgun Illumina sequencing, microbial phylogeny and potential metabolic functions were catalogued for Chamliyal's clay. Microbial diversity profile of the Chamliyal's clay is similar to other medicinal clays, particularly Dead Sea; there is some uniqueness as well. Although Proteobacteria, Actinomycetes and Firmicutes are common inhabitants of all the clay types, sulphur- and iron-reducing bacteria like Deferribacterales are particular to clays used for skin healing. In the present study it is proposed that healing properties of clay may be due to the microbes and microbial genes associated with metabolism of minerals like iron and sulphur, that lead to mineral acquisition in the Chamliyal's clay.}, }
@article {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 {pmid29940835, year = {2018}, author = {Devlin, JC and Battaglia, T and Blaser, MJ and Ruggles, KV}, title = {WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {493}, pmid = {29940835}, issn = {1471-2164}, support = {U01 AI22285//Foundation for the National Institutes of Health/ ; }, mesh = {Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research.<br><br>RESULTS: We developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics.<br><br>CONCLUSIONS: WHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets.}, }
@article {pmid29866485, year = {2018}, author = {Garin-Fernandez, A and Pereira-Flores, E and Glöckner, FO and Wichels, A}, title = {The North Sea goes viral: Occurrence and distribution of North Sea bacteriophages.}, journal = {Marine genomics}, volume = {41}, number = {}, pages = {31-41}, doi = {10.1016/j.margen.2018.05.004}, pmid = {29866485}, issn = {1876-7478}, mesh = {Bacteriophages/classification/*physiology ; *Biodiversity ; Metagenomics ; North Sea ; Water Movements ; }, abstract = {Marine viruses are dominated by phages and have an enormous influence on microbial population dynamics, due to lysis and horizontal gene transfer. The aim of this study is to analyze the occurrence and diversity of phages in the North Sea, considering the virus-host interactions and biogeographic factors. The virus community of four sampling stations were described using virus metagenomics (viromes). The results show that the virus community was not evenly distributed throughout the North Sea. The dominant phage members were identified as unclassified phage group, followed by Caudovirales order. Myoviridae was the dominant phage family in the North Sea, which occurrence decreased from the coast to the open sea. In contrast, the occurrence of Podoviridae increased and the occurrence of Siphoviridae was low throughout the North Sea. The occurrence of other groups such as Phycodnaviridae decreased from the coast to the open sea. The coastal virus community was genetically more diverse than the open sea community. The influence of riverine inflow and currents, for instance the English Channel flow affects the genetic virus diversity with the community carrying genes from a variety of metabolic pathways and other functions. The present study offers the first insights in the virus community in the North Sea using viromes and shows the variation in virus diversity and the genetic information moved from coastal to open sea areas.}, }
@article {pmid29790949, year = {2018}, author = {Salas-Mani, A and Jeusette, I and Castillo, I and Manuelian, CL and Lionnet, C and Iraculis, N and Sanchez, N and Fernández, S and Vilaseca, L and Torre, C}, title = {Fecal microbiota composition changes after a BW loss diet in Beagle dogs.}, journal = {Journal of animal science}, volume = {96}, number = {8}, pages = {3102-3111}, pmid = {29790949}, issn = {1525-3163}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Body Composition ; Body Weight ; Caloric Restriction/*veterinary ; Diet, Fat-Restricted/*veterinary ; Dietary Fiber ; Dogs/*physiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; *Metagenomics ; Obesity/prevention &amp; control/veterinary ; }, abstract = {In developed countries, dogs and cats frequently suffer from obesity. Recently, gut microbiota composition in humans has been related to obesity and metabolic diseases. This study aimed to evaluate changes in body composition, and gut microbiota composition in obese Beagle dogs after a 17-wk BW loss program. A total of six neutered adult Beagle dogs with an average initial BW of 16.34 ± 1.52 kg and BCS of 7.8 ± 0.1 points (9-point scale) were restrictedly fed with a hypocaloric, low-fat and high-fiber dry-type diet. Body composition was assessed with dual-energy X-ray absorptiometry scan, before (T0) and after (T1) BW loss program. Individual stool samples were collected at T0 and T1 for the 16S rRNA analyses of gut microbiota. Taxonomic analysis was done with amplicon-based metagenomic results, and functional analysis of the metabolic potential of the microbial community was done with shotgun metagenomic results. All dogs reached their ideal BW at T1, with an average weekly proportion of BW loss of -1.07 ± 0.03% of starting BW. Body fat (T0, 7.02 ± 0.76 kg) was reduced by half (P < 0.001), while bone (T0, 0.56 ± 0.06 kg) and muscle mass (T0, 8.89 ± 0.80 kg) remained stable (P > 0.05). The most abundant identified phylum was Firmicutes (T0, 74.27 ± 0.08%; T1, 69.38 ± 0.07%), followed by Bacteroidetes (T0, 12.68 ± 0.08%; T1, 16.68 ± 0.05%), Fusobacteria (T0, 7.45 ± 0.02%; T1, 10.18 ± 0.03%), Actinobacteria (T0, 4.53 ± 0.02%; T1, 3.34 ± 0.01%), and Proteobacteria (T0, 1.06 ± 0.01%; T1, 1.40 ± 0.00%). At genus level, the presence of Clostridium, Lactobacillus, and Dorea, at T1 decreased (P = 0.028), while Allobaculum increased (P = 0.046). Although the microbiota communities at T0 and T1 showed a low separation level when compared (Anosim's R value = 0.39), they were significantly biodiverse (P = 0.01). Those differences on microbiota composition could be explained by 13 genus (α = 0.05, linear discriminant analysis (LDA) score > 2.0). Additionally, differences between both communities could also be explained by the expression of 18 enzymes and 27 pathways (α = 0.05, LDA score > 2.0). In conclusion, restricted feeding of a low-fat and high-fiber dry-type diet successfully modifies gut microbiota in obese dogs, increasing biodiversity with a different representation of microbial genus and metabolic pathways.}, }
@article {pmid29564487, year = {2018}, author = {Pulikkan, J and Maji, A and Dhakan, DB and Saxena, R and Mohan, B and Anto, MM and Agarwal, N and Grace, T and Sharma, VK}, title = {Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1102-1114}, pmid = {29564487}, issn = {1432-184X}, mesh = {Adolescent ; Autism Spectrum Disorder/*microbiology ; Bacteria/classification/isolation &amp; purification ; Biomarkers/analysis ; Child ; Child, Preschool ; DNA, Bacterial/analysis ; Dysbiosis/*epidemiology/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; India/epidemiology ; Male ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; }, abstract = {Autism spectrum disorder (ASD) is a term associated with a group of neurodevelopmental disorders. The etiology of ASD is not yet completely understood; however, a disorder in the gut-brain axis is emerging as a prominent factor leading to autism. To identify the taxonomic composition and markers associated with ASD, we compared the fecal microbiota of 30 ASD children diagnosed using Childhood Autism Rating Scale (CARS) score, DSM-5 approved AIIMS-modified INCLEN Diagnostic Tool for Autism Spectrum Disorder (INDT-ASD), and Indian Scale for Assessment of Autism (ISAA) tool, with family-matched 24 healthy children from Indian population using next-generation sequencing (NGS) of 16S rRNA gene amplicon. Our study showed prominent dysbiosis in the gut microbiome of ASD children, with higher relative abundances of families Lactobacillaceae, Bifidobacteraceae, and Veillonellaceae, whereas the gut microbiome of healthy children was dominated by the family Prevotellaceae. Comparative meta-analysis with a publicly available dataset from the US population consisting of 20 ASD and 20 healthy control samples from children of similar age, revealed a significantly high abundance of genus Lactobacillus in ASD children from both the populations. The results reveal the microbial dysbiosis and an association of selected Lactobacillus species with the gut microbiome of ASD children.}, }
@article {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 {pmid29425888, year = {2018}, author = {Rajpoot, M and Sharma, AK and Sharma, A and Gupta, GK}, title = {Understanding the microbiome: Emerging biomarkers for exploiting the microbiota for personalized medicine against cancer.}, journal = {Seminars in cancer biology}, volume = {52}, number = {Pt 1}, pages = {1-8}, doi = {10.1016/j.semcancer.2018.02.003}, pmid = {29425888}, issn = {1096-3650}, mesh = {*Biomarkers, Tumor ; Genetic Variation ; Humans ; Metagenomics/methods/trends ; Microbiota/*genetics ; Neoplasms/*diagnosis/*microbiology ; Precision Medicine/*methods/trends ; Sequence Analysis, DNA/methods ; }, abstract = {The human body is a home to more than 1 trillion microbes with a diverse variety of commensal microbes that play a crucial role towards the health of the individual. These microbes occupy different habitats such as gut, skin, vagina, oral etc. Not only the types and abundance of microbes are different in different organs, but also these may differ in different individuals. The genome of these microbiota and their ecosystem constitute to form a microbiome. Factors such as diet, environment, host genetics etc. may be the reason behind the wide microbial diversity. A number of studies performed on human microbiome have revealed that microbiota present in healthy and diseased individuals are distinct. Altered microbiome is many a times the reason behind the overexpression of genes which may cause complex diseases including cancer. Manipulation of the human microbiome can be done by microbial supplements such as probiotics or synbiotics, diet or prebiotics and microbial suppression strategies using antibiotics. Recent advances in genome sequencing technologies and metagenomic analysis provide us the broader understanding of these commensal microbes and highlighting the distinctive features of microbiome during healthy and disease states. Molecular pathological epidemiology (MPE) studies have been very helpful in providing insights into the pathological process behind disease evolution and progression by determining the specific etiological factors. New emerging field of research targets the microbiome for therapeutic purposes by which personalized medicines can be made for treating various types of tumors. Screening programmes might be helpful in identifying patients who are at the verge of developing cancer and in delivering appropriate approaches according to individual risk modes so that disease could be prevented.}, }
@article {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 {pmid29367606, year = {2018}, author = {Shangpliang, HNJ and Rai, R and Keisam, S and Jeyaram, K and Tamang, JP}, title = {Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1532}, pmid = {29367606}, issn = {2045-2322}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cultured Milk Products/*microbiology ; High-Throughput Nucleotide Sequencing ; India ; Metagenomics ; }, abstract = {Naturally fermented milk (NFM) products are popular ethnic fermented foods in Arunachal Pradesh and Sikkim states of India. The present study is the first to have documented the bacterial community in 54 samples of NFM products viz. chhurpi, churkam, dahi and gheu/mar by high-throughput Illumina amplicon sequencing. Metagenomic investigation showed that Firmicutes (Streptococcaceae, Lactobacillaceae) and Proteobacteria (Acetobacteraceae) were the two predominant members of the bacterial communities in these products. Lactococcus lactis and Lactobacillus helveticus were the predominant lactic acid bacteria while Acetobacter spp. and Gluconobacter spp. were the predominant acetic acid bacteria present in these products.}, }
@article {pmid29362424, year = {2018}, author = {Verma, MK and Ahmed, V and Gupta, S and Kumar, J and Pandey, R and Mandhan, V and Chauhan, NS}, title = {Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1397}, pmid = {29362424}, issn = {2045-2322}, mesh = {Bacterial Proteins/*genetics ; Bacteroidetes/genetics/*isolation &amp; purification ; Cloning, Molecular ; Gastrointestinal Microbiome ; Gene Expression Regulation, Bacterial ; Humans ; Metagenomics/*methods ; Phylogeny ; *Salt Tolerance ; }, abstract = {Every niche in the biosphere is touched by the seemingly endless capacity of microbes to transform the world around them by adapting swiftly and flexibly to the environmental changes, likewise the gastrointestinal tract is no exception. The ability to cope with rapid changes in external osmolarity is an important aspect of gut microbes for their survival and colonization. Identification of these survival mechanisms is a pivotal step towards understanding genomic suitability of a symbiont for successful human gut colonization. Here we highlight our recent work applying functional metagenomics to study human gut microbiome to identify candidate genes responsible for the salt stress tolerance. A plasmid borne metagenomic library of Bacteroidetes enriched human fecal metagenomic DNA led to identification of unique salt osmotolerance clones SR6 and SR7. Subsequent gene analysis combined with functional studies revealed that TLSRP1 within pSR7 and TMSRP1 and ABCTPP of pSR6 are the active loci responsible for osmotolerance through an energy dependent mechanism. Our study elucidates the novel genetic machinery involved in bestowing osmotolerance in Prevotella and Bacteroidetes, the predominant microbial groups in a North Indian population. This study unravels an alternative method for imparting ionic stress tolerance, which may be prevalent in the human gut microbiome.}, }
@article {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 {pmid29297282, year = {2017}, author = {Tran, Q and Pham, DT and Phan, V}, title = {Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities.}, journal = {BMC bioinformatics}, volume = {18}, number = {Suppl 14}, pages = {499}, pmid = {29297282}, issn = {1471-2105}, mesh = {Algorithms ; Bacteria/*genetics/*isolation &amp; purification ; Genetic Markers ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Quantification and identification of microbial genomes based on next-generation sequencing data is a challenging problem in metagenomics. Although current methods have mostly focused on analyzing bacteria whose genomes have been sequenced, such analyses are, however, complicated by the presence of unknown bacteria or bacteria whose genomes have not been sequence.<br><br>RESULTS: We propose a method for detecting unknown bacteria in environmental samples. Our approach is unique in its utilization of short reads only from 16S rRNA genes, not from entire genomes. We show that short reads from 16S rRNA genes retain sufficient information for detecting unknown bacteria in oral microbial communities.<br><br>CONCLUSION: In our experimentation with bacterial genomes from the Human Oral Microbiome Database, we found that this method made accurate and robust predictions at different read coverages and percentages of unknown bacteria. Advantages of this approach include not only a reduction in experimental and computational costs but also a potentially high accuracy across environmental samples due to the strong conservation of the 16S rRNA gene.}, }
@article {pmid29277868, year = {2018}, author = {Maltez Thomas, A and Prata Lima, F and Maria Silva Moura, L and Maria da Silva, A and Dias-Neto, E and Setubal, JC}, title = {Comparative Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1704}, number = {}, pages = {243-260}, doi = {10.1007/978-1-4939-7463-4_8}, pmid = {29277868}, issn = {1940-6029}, mesh = {Computational Biology ; Humans ; Metagenomics/*methods ; *Microbiota ; Mouth Mucosa/*microbiology ; Sequence Analysis, DNA/methods ; Software ; Tongue/*microbiology ; }, abstract = {Thanks in large part to newer, better, and cheaper DNA sequencing technologies, an enormous number of metagenomic sequence datasets have been and continue to be generated, covering a huge variety of environmental niches, including several different human body sites. Comparing these metagenomes and identifying their commonalities and differences is a challenging task, due not only to the large amounts of data, but also because there are several methodological considerations that need to be taken into account to ensure an appropriate and sound comparison between datasets. In this chapter, we describe current techniques aimed at comparing metagenomes generated by 16S ribosomal RNA and shotgun DNA sequencing, emphasizing methodological issues that arise in these comparative studies. We provide a detailed case study to illustrate some of these techniques using data from the Human Microbiome Project comparing the microbial communities from ten buccal mucosa samples with ten tongue dorsum samples in terms of alpha diversity, beta diversity, and their taxonomic and functional profiles.}, }
@article {pmid29208946, year = {2018}, author = {Mehrshad, M and Rodriguez-Valera, F and Amoozegar, MA and López-García, P and Ghai, R}, title = {The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {655-668}, pmid = {29208946}, issn = {1751-7370}, support = {322669//European Research Council/International ; }, mesh = {Chloroflexi/classification/genetics/*isolation &amp; purification/*metabolism ; Genomics ; Metagenome ; Metagenomics ; Microbiota ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; Sulfur/*metabolism ; }, abstract = {The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.}, }
@article {pmid29157743, year = {2018}, author = {Cocolin, L and Mataragas, M and Bourdichon, F and Doulgeraki, A and Pilet, MF and Jagadeesan, B and Rantsiou, K and Phister, T}, title = {Next generation microbiological risk assessment meta-omics: The next need for integration.}, journal = {International journal of food microbiology}, volume = {287}, number = {}, pages = {10-17}, doi = {10.1016/j.ijfoodmicro.2017.11.008}, pmid = {29157743}, issn = {1879-3460}, mesh = {*Computational Biology ; Food Microbiology/*trends ; Metabolomics ; Metagenomics ; Microbiota ; Proteomics ; Risk Assessment/trends ; }, abstract = {The development of a multi-omics approach has provided a new approach to the investigation of microbial communities allowing an integration of data, which can be used to better understand the behaviour of and interactions between community members. Metagenomics, metatranscriptomics, metaproteomics and metabolomics have the potential of producing a large amount of data in a very short time, however an important challenge is how to exploit and interpret these data to assist risk managers in food safety and quality decisions. This can be achieved by integrating multi-omics data in microbiological risk assessment. In this paper we identify limitations and challenges of the multi-omics approach, underlining promising potentials, but also identifying gaps, which should be addressed for its full exploitation. A view on how this new way of investigation will impact the traditional microbiology schemes in the food industry is also presented.}, }
@article {pmid28533514, year = {2017}, author = {Yohda, M and Ikegami, K and Aita, Y and Kitajima, M and Takechi, A and Iwamoto, M and Fukuda, T and Tamura, N and Shibasaki, J and Koike, S and Komatsu, D and Miyagi, S and Nishimura, M and Uchino, Y and Shiroma, A and Shimoji, M and Tamotsu, H and Ashimine, N and Shinzato, M and Ohki, S and Nakano, K and Teruya, K and Satou, K and Hirano, T and Yagi, O}, title = {Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2230}, pmid = {28533514}, issn = {2045-2322}, mesh = {Chloroflexi/classification/*genetics/metabolism ; Ethylene Dichlorides/metabolism ; Ethylenes/metabolism ; *Gene Rearrangement ; *Genome, Bacterial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Microbial Consortia ; Vinyl Chloride/metabolism ; }, abstract = {We have developed and characterized a bacterial consortium that reductively dechlorinates trichloroethene to ethene. Quantitative PCR analysis for the 16S rRNA and reductive dehalogenase genes showed that the consortium is highly enriched with Dehalococcoides spp. that have two vinyl chloride reductive dehalogenase genes, bvcA and vcrA, and a trichloroethene reductive dehalogenase gene, tceA. The metagenome analysis of the consortium by the next generation sequencer SOLiD 3 Plus suggests that a Dehalococcoides sp. that is highly homologous to D. mccartyi 195 and equipped with vcrA and tceA exists in the consortium. We isolated this Dehalococcoides sp. and designated it as D. mccartyi UCH-ATV1. As the growth of D. mccartyi UCH-ATV1 is too slow under isolated conditions, we constructed a consortium by mixing D. mccartyi UCH-ATV1 with several other bacteria and performed metagenomic sequencing using the single molecule DNA sequencer PacBio RS II. We successfully determined the complete genome sequence of D. mccartyi UCH-ATV1. The strain is equipped with vcrA and tceA, but lacks bvcA. Comparison with tag sequences of SOLiD 3 Plus from the original consortium shows a few differences between the sequences. This suggests that a genome rearrangement of Dehalococcoides sp. occurred during culture.}, }
@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 {pmid28345673, year = {2017}, author = {Xie, G and Wang, X and Zhao, A and Yan, J and Chen, W and Jiang, R and Ji, J and Huang, F and Zhang, Y and Lei, S and Ge, K and Zheng, X and Rajani, C and Alegado, RA and Liu, J and Liu, P and Nicholson, J and Jia, W}, title = {Sex-dependent effects on gut microbiota regulate hepatic carcinogenic outcomes.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45232}, pmid = {28345673}, issn = {2045-2322}, support = {P30 CA071789/CA/NCI NIH HHS/United States ; U01 CA188387/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; Bile Acids and Salts/metabolism ; Carcinoma, Hepatocellular/chemically induced/drug therapy/genetics/*microbiology ; Cholestyramine Resin/pharmacology/therapeutic use ; Diet, High-Fat/*adverse effects ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/drug effects ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Incidence ; Liver Neoplasms/chemically induced/genetics/*microbiology ; Male ; Metagenomics/*methods ; Mice ; MicroRNAs/genetics ; Non-alcoholic Fatty Liver Disease/drug therapy/etiology/metabolism/*microbiology ; Sex Factors ; Streptozocin/*adverse effects ; }, abstract = {Emerging evidence points to a strong association between sex and gut microbiota, bile acids (BAs), and gastrointestinal cancers. Here, we investigated the mechanistic link between microbiota and hepatocellular carcinogenesis using a streptozotocin-high fat diet (STZ-HFD) induced nonalcoholic steatohepatitis-hepatocellular carcinoma (NASH-HCC) murine model and compared results for both sexes. STZ-HFD feeding induced a much higher incidence of HCC in male mice with substantially increased intrahepatic retention of hydrophobic BAs and decreased hepatic expression of tumor-suppressive microRNAs. Metagenomic analysis showed differences in gut microbiota involved in BA metabolism between normal male and female mice, and such differences were amplified when mice of both sexes were exposed to STZ-HFD. Treating STZ-HFD male mice with 2% cholestyramine led to significant improvement of hepatic BA retention, tumor-suppressive microRNA expressions, microbial gut communities, and prevention of HCC. Additionally the sex-dependent differences in BA profiles in the murine model can be correlated to the differential BA profiles between men and women during the development of HCC. These results uncover distinct male and female profiles for gut microbiota, BAs, and microRNAs that may contribute to sex-based disparity in liver carcinogenesis, and suggest new possibilities for preventing and controlling human obesity-related gastrointestinal cancers that often exhibit sex differences.}, }
@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 {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 {pmid30121535, year = {2019}, author = {Bedoya, K and Coltell-Simon, O and Cabarcas, F and Alzate, JF}, title = {Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia.}, journal = {The Science of the total environment}, volume = {648}, number = {}, pages = {572-581}, doi = {10.1016/j.scitotenv.2018.08.119}, pmid = {30121535}, issn = {1879-1026}, mesh = {Colombia ; *Metagenome ; Methane/*biosynthesis ; *Microbiota/genetics ; Solid Waste/*analysis ; *Waste Disposal, Fluid ; Waste Water/*microbiology ; }, abstract = {Abundance and diversity of microbial communities in biosolids are variable and poorly studied in the tropics, and it is known that rainfall is one of the events that could affect the phylogenetic and functional microbial structure. In the present study, using NGS technics, we studied the microbial diversity as well as the methanogenesis pathway in one of the largest WWTP in Colombia. Besides, we sampled and analyzed biosolids from rainy season and dry season. Phylogenetic classification showed a predominance of bacteria in both samples and difference in the dominant groups depending on the rainfall season. Whereas Pseudomonas was the dominant bacteria in the dry season, Coprothermobacter was in the rainy season. Archaea abundance was higher in the rainy season (11.5%) doubling dry season proportion. The bioreactor biogas production and total solids content showed similar results between rainy and dry season at the sampling dates. The most abundant Archaea related with methanogenesis was Methanosaeta, which is a methanogenic microorganism that exclusively uses acetate to produce methane. Moreover, annotation of the methanogenic pathway in the metagenome showed abundance in genes encoding Acetyl-CoA synthetases (ACSS), an enzyme that catalyzes acetate activation. Our results suggest that the microbial diversity was stable among the two time points tested, rainy season and dry season; and, although there were changes in the microbial abundance of dominant bacterial species, anaerobic digester performance is not affected.}, }
@article {pmid29806626, year = {2018}, author = {Mihara, T and Koyano, H and Hingamp, P and Grimsley, N and Goto, S and Ogata, H}, title = {Taxon Richness of &quot;Megaviridae&quot; Exceeds those of Bacteria and Archaea in the Ocean.}, journal = {Microbes and environments}, volume = {33}, number = {2}, pages = {162-171}, doi = {10.1264/jsme2.ME17203}, pmid = {29806626}, issn = {1347-4405}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; Databases, Genetic ; Evolution, Molecular ; Giant Viruses/*classification/genetics ; Metagenomics ; *Oceans and Seas ; *Phylogeny ; RNA Polymerase II/genetics ; }, abstract = {Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family &quot;Megaviridae&quot;, suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean. In the present study, we compared the taxon richness and phylogenetic diversity of Megaviridae, Bacteria, and Archaea using DNA-dependent RNA polymerase as a common marker gene. By leveraging existing microbial metagenomic data, we found higher richness and phylogenetic diversity in this single viral family than in the two prokaryotic domains. We also obtained results showing that the evolutionary rate alone cannot account for the observed high diversity of Megaviridae lineages. These results suggest that the Megaviridae family has a deep co-evolutionary history with diverse marine protists since the early &quot;Big-Bang&quot; radiation of the eukaryotic tree of life.}, }
@article {pmid29794413, year = {2018}, author = {Hu, Y and Bai, C and Cai, J and Dai, J and Shao, K and Tang, X and Gao, G}, title = {Co-occurrence Network Reveals the Higher Fragmentation of the Bacterial Community in Kaidu River Than Its Tributaries in Northwestern China.}, journal = {Microbes and environments}, volume = {33}, number = {2}, pages = {127-134}, doi = {10.1264/jsme2.ME17170}, pmid = {29794413}, issn = {1347-4405}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; China ; Computational Biology ; DNA, Bacterial ; Ecosystem ; Metagenomics ; *Microbial Interactions ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; *Water Microbiology ; }, abstract = {Rivers and their tributaries sculpt the earth's surface, and play an important role in substance circulation and energy flow. Bacteria are involved in most biogeochemical processes in the fluvial ecosystem; however, their pattern distribution in a river and its tributaries has not yet been investigated in detail. In the present study, high-throughput sequencing was employed to examine bacterial communities and their co-occurrence networks between Kaidu River and its nine tributaries in northwestern China. The results obtained demonstrated that both bacterial communities shared a similar dominant sub-community, mainly consisting of Actinobacteria, Bacteroidetes, and Proteobacteria, with Limnohabitans and Variovorax as the dominant genera. In spite of these commonalities, bacterial community structures still significantly differed between these two habitats, which may be related to the distance-related dispersal limitation. Their co-occurrence networks were generally both positively structured. The structural analysis showed that OTUs from the same phyla were more likely to co-occur. Although the keystone genera were taxonomically different between Kaidu River and its tributaries, they both shared common trophic properties in exploiting niches under oligotrophic conditions. We noted that their relative abundances were less than 1%, indicating the over-proportional roles of rare genera in the bacterial community. In addition, the inferred networks showed less nodes and edges, but higher modularity in Kaidu River than its tributaries, suggesting the higher fragmentation of the bacterial community in the mainstream.}, }
@article {pmid29783653, year = {2018}, author = {Li, H and Liu, X and Chen, F and Zuo, K and Wu, C and Yan, Y and Chen, W and Lin, W and Xie, Q}, title = {Avian Influenza Virus Subtype H9N2 Affects Intestinal Microbiota, Barrier Structure Injury, and Inflammatory Intestinal Disease in the Chicken Ileum.}, journal = {Viruses}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/v10050270}, pmid = {29783653}, issn = {1999-4915}, mesh = {Animals ; Chickens/*virology ; Cytokines/genetics/metabolism ; DNA, Bacterial/genetics ; Enteritis/metabolism ; Escherichia coli/metabolism ; *Gastrointestinal Microbiome ; Influenza A Virus, H9N2 Subtype/*physiology ; Influenza in Birds/immunology/metabolism/*microbiology ; Intestinal Mucosa/*injuries ; Metagenomics ; RNA, Messenger/metabolism ; RNA, Ribosomal, 16S/genetics ; Specific Pathogen-Free Organisms ; }, abstract = {Avian influenza virus subtype H9N2 (H9N2 AIV) has caused significant losses to the poultry industry due to the high mortality associated with secondary infections attributable to E. coli. This study tries to address the underlying secondary mechanisms after H9N2 AIV infection. Initially, nine day-old specific pathogen-free chickens were assigned to control (uninfected) and H9N2-infected groups, respectively. Using Illumina sequencing, histological examination, and quantitative real-time PCR, it was found that H9N2 AIV caused intestinal microbiota disorder, injury, and inflammatory damage to the intestinal mucosa. Notably, the genera Escherichia, especially E. coli, significantly increased (p < 0.01) at five days post-infection (dpi), while Lactobacillus, Enterococcus, and other probiotic organisms were significantly reduced (p < 0.01). Simultaneously, the mRNA expression of tight junction proteins (ZO-1, claudin 3, and occludin), TFF2, and Muc2 were significantly reduced (p < 0.01), indicating the destruction of the intestinal epithelial cell tight junctions and the damage of mucin layer construction. Moreover, the mRNA expression of proinflammatory cytokines IFN-γ, IL-22, IFN-α, and IL-17A in intestinal epithelial cells were significantly upregulated, resulting in the inflammatory response and intestinal injury. Our findings may provide a theoretical basis for observed gastroenteritis-like symptoms such as diarrhea and secondary E. coli infection following H9N2 AIV infection.}, }
@article {pmid29681561, year = {2018}, author = {Tandon, K and Yang, SH and Wan, MT and Yang, CC and Baatar, B and Chiu, CY and Tsai, JW and Liu, WC and Tang, SL}, title = {Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan.}, journal = {Microbes and environments}, volume = {33}, number = {2}, pages = {120-126}, doi = {10.1264/jsme2.ME17148}, pmid = {29681561}, issn = {1347-4405}, mesh = {*Air Microbiology ; Bacteria/*classification/genetics ; *Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spatio-Temporal Analysis ; Taiwan ; *Water Microbiology ; }, abstract = {Very few studies have attempted to profile the microbial communities in the air above freshwater bodies, such as lakes, even though freshwater sources are an important part of aquatic ecosystems and airborne bacteria are the most dispersible microorganisms on earth. In the present study, we investigated microbial communities in the waters of two high mountain sub-alpine montane lakes-located 21 km apart and with disparate trophic characteristics-and the air above them. Although bacteria in the lakes had locational differences, their community compositions remained constant over time. However, airborne bacterial communities were diverse and displayed spatial and temporal variance. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria were dominant in both lakes, with different relative abundances between lakes, and Parcubacteria (OD1) was dominant in air samples for all sampling times, except two. We also identified certain shared taxa between lake water and the air above it. The results obtained on these communities in the present study provide putative candidates to study how airborne communities shape lake water bacterial compositions and vice versa.}, }
@article {pmid29311639, year = {2018}, author = {Segobola, J and Adriaenssens, E and Tsekoa, T and Rashamuse, K and Cowan, D}, title = {Exploring Viral Diversity in a Unique South African Soil Habitat.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {111}, doi = {10.1038/s41598-017-18461-0}, pmid = {29311639}, issn = {2045-2322}, mesh = {Bacteriophages/classification/genetics ; *Biodiversity ; Computational Biology/methods ; Genome, Viral ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Soil Microbiology ; South Africa ; Viruses/*classification/genetics/ultrastructure ; }, abstract = {The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.}, }
@article {pmid29293960, year = {2018}, author = {Fang, C and Zhong, H and Lin, Y and Chen, B and Han, M and Ren, H and Lu, H and Luber, JM and Xia, M and Li, W and Stein, S and Xu, X and Zhang, W and Drmanac, R and Wang, J and Yang, H and Hammarström, L and Kostic, AD and Kristiansen, K and Li, J}, title = {Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.}, journal = {GigaScience}, volume = {7}, number = {3}, pages = {1-8}, doi = {10.1093/gigascience/gix133}, pmid = {29293960}, issn = {2047-217X}, support = {T32 HG002295/HG/NHGRI NIH HHS/United States ; T32 GM074897/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Computational Biology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Background: More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of 2 Illumina platforms.<br><br>Findings: Using fecal samples from 20 healthy individuals, we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform vs the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the 2 Illumina platforms against each other. By a newly developed overall accuracy quality control method, an average of 82.45 million high-quality reads (96.06% of raw reads) per sample, with 90.56% of bases scoring Q30 and above, was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02%-3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias toward genes with higher GC content being enriched on the HiSeq platforms.<br><br>Conclusions: Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.}, }
@article {pmid30301312, year = {2018}, author = {Yu, YC and Yum, SJ and Jeon, DY and Jeong, HG}, title = {Analysis of the Microbiota on Lettuce (Lactuca sativa L.) Cultivated in South Korea to Identify Foodborne Pathogens.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {8}, pages = {1318-1331}, doi = {10.4014/jmb.1803.03007}, pmid = {30301312}, issn = {1738-8872}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; *Food Microbiology ; Foodborne Diseases/*microbiology ; Geography ; Lettuce/*microbiology ; Metagenomics ; Microbial Interactions ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; }, abstract = {Lettuce (Lactuca sativa L.) is a major ingredient used in many food recipes in South Korea. Lettuce samples were collected during their maximum production period between April and July in order to investigate the microbiota of lettuce during different seasons. 16S rRNA gene-based sequencing was conducted using Illumina MiSeq, and real-time PCR was performed for quantification. The number of total bacterial was greater in lettuce collected in July than in that collected in April, albeit with reduced diversity. The bacterial compositions varied according to the site and season of sample collection. Potential pathogenic species such as Bacillus spp., Enterococcus casseliflavus, Klebsiella pneumoniae, and Pseudomonas aeruginosa showed season-specific differences. Results of the network co-occurrence analysis with core genera correlations showed characteristics of bacterial species in lettuce, and provided clues regarding the role of different microbes, including potential pathogens, in this microbiota. Although further studies are needed to determine the specific effects of regional and seasonal characteristics on the lettuce microbiota, our results imply that the 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria in lettuce.}, }
@article {pmid29705728, year = {2018}, author = {Ticinesi, A and Milani, C and Guerra, A and Allegri, F and Lauretani, F and Nouvenne, A and Mancabelli, L and Lugli, GA and Turroni, F and Duranti, S and Mangifesta, M and Viappiani, A and Ferrario, C and Dodi, R and Dall'Asta, M and Del Rio, D and Ventura, M and Meschi, T}, title = {Understanding the gut-kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers.}, journal = {Gut}, volume = {67}, number = {12}, pages = {2097-2106}, doi = {10.1136/gutjnl-2017-315734}, pmid = {29705728}, issn = {1468-3288}, mesh = {Adult ; Aged ; Bacteria/classification/isolation &amp; purification ; Bacterial Typing Techniques ; Biodiversity ; Calcium Oxalate/analysis ; Case-Control Studies ; DNA, Bacterial/analysis ; Energy Intake/physiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; Nephrolithiasis/metabolism/*microbiology ; Oxalates/metabolism ; RNA, Ribosomal, 16S/analysis ; Recurrence ; Young Adult ; }, abstract = {OBJECTIVES: The involvement of the gut microbiota in the pathogenesis of calcium nephrolithiasis has been hypothesised since the discovery of the oxalate-degrading activity of Oxalobacter formigenes, but never comprehensively studied with metagenomics. The aim of this case-control study was to compare the faecal microbiota composition and functionality between recurrent idiopathic calcium stone formers (SFs) and controls.<br><br>DESIGN: Faecal samples were collected from 52 SFs and 48 controls (mean age 48±11). The microbiota composition was analysed through 16S rRNA microbial profiling approach. Ten samples (five SFs, five controls) were also analysed with deep shotgun metagenomics sequencing, with focus on oxalate-degrading microbial metabolic pathways. Dietary habits, assessed through a food-frequency questionnaire, and 24-hour urinary excretion of prolithogenic and antilithogenic factors, including calcium and oxalate, were compared between SFs and controls, and considered as covariates in the comparison of microbiota profiles.<br><br>RESULTS: SFs exhibited lower faecal microbial diversity than controls (Chao1 index 1460±363vs 1658±297, fully adjusted p=0.02 with stepwise backward regression analysis). At multivariate analyses, three taxa (Faecalibacterium, Enterobacter, Dorea) were significantly less represented in faecal samples of SFs. The Oxalobacter abundance was not different between groups. Faecal samples from SFs exhibited a significantly lower bacterial representation of genes involved in oxalate degradation, with inverse correlation with 24-hour oxalate excretion (r=-0.87, p=0.002). The oxalate-degrading genes were represented in several bacterial species, whose cumulative abundance was inversely correlated with oxaluria (r=-0.85, p=0.02).<br><br>CONCLUSIONS: Idiopathic calcium SFs exhibited altered gut microbiota composition and functionality that could contribute to nephrolithiasis physiopathology.}, }
@article {pmid29272899, year = {2017}, author = {Shah, A and Shanahan, E and Macdonald, GA and Fletcher, L and Ghasemi, P and Morrison, M and Jones, M and Holtmann, G}, title = {Systematic Review and Meta-Analysis: Prevalence of Small Intestinal Bacterial Overgrowth in Chronic Liver Disease.}, journal = {Seminars in liver disease}, volume = {37}, number = {4}, pages = {388-400}, doi = {10.1055/s-0037-1608832}, pmid = {29272899}, issn = {1098-8971}, mesh = {Bacteria/*growth &amp; development ; Disease Progression ; *Dysbiosis ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Intestine, Small/*microbiology ; Liver Diseases/diagnosis/epidemiology/*microbiology ; Prevalence ; Prognosis ; Risk Factors ; }, abstract = {The authors conducted a meta-analysis of the prevalence of small intestinal bacterial overgrowth (SIBO) in patients with chronic liver disease (CLD) and controls. Using the search terms &quot;small intestinal bacterial overgrowth (SIBO)&quot; and &quot;chronic liver disease (CLD)&quot; or &quot;cirrhosis,&quot; 19 case-control studies were identified. Utilizing breath tests, the prevalence of SIBO in CLD was 35.80% (95% CI, 32.60-39.10) compared with 8.0% (95% CI, 5.70-11.00) in controls. Using culture techniques, the prevalence was 68.31% (95% CI, 59.62-76.00) in CLD patients as compared with 7.94% (95% CI, 3.44-12.73) in controls. No difference between cirrhotic and noncirrhotic patients was found. SIBO is significantly more frequent in CLD patients as compared with controls. The association of SIBO and CLD was not confined to patients with advanced CLD, suggesting that SIBO is not a consequence of advanced liver disease but may play a role in the progression of CLD.}, }
@article {pmid29243150, year = {2018}, author = {Naik, OA and Shashidhar, R and Rath, D and Bandekar, JR and Rath, A}, title = {Characterization of multiple antibiotic resistance of culturable microorganisms and metagenomic analysis of total microbial diversity of marine fish sold in retail shops in Mumbai, India.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {7}, pages = {6228-6239}, doi = {10.1007/s11356-017-0945-7}, pmid = {29243150}, issn = {1614-7499}, support = {2012/37B/50/BRNS//Board of Research in Nuclear Sciences/ ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/genetics ; Biodiversity ; Drug Resistance, Multiple, Bacterial/*genetics ; Fishes/*microbiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; India ; Integrons/genetics ; *Metagenomics ; Microbial Sensitivity Tests ; Plasmids/genetics ; }, abstract = {Marine fish species were analyzed for culturable and total metagenomic microbial diversity, antibiotic resistance (AR) pattern, and horizontal gene transfer in culturable microorganisms. We observed a high AR microbial load of 3 to 4 log CFU g-1. Many fish pathogens like Providencia, Staphylococcus, Klebsiella pneumoniae, Enterobacter, Vagococcus, and Aeromonas veronii were isolated. Photobacterium and Vibrio were two major fish and human pathogens which were identified in the fish metagenome. Other pathogens that were identified were Shewanella, Acinetobacter, Psychrobacter, and Flavobacterium. Most of these pathogens were resistant to multiple antibiotics such as erythromycin, kanamycin, neomycin, streptomycin, penicillin, cefotaxime, bacitracin, rifampicin, trimethoprim, ciprofloxacin, and doxycycline with a high multiple antibiotic resistance index of 0.54-0.77. The fish microflora showed high prevalence of AR genes like bla TEM, Class I integron, tetA, aph(3')-IIIa, ermB, aadA, and sul1. Nineteen of 26 AR isolates harbored Class I integrons showing high co-resistance to trimethoprim, kanamycin, doxycycline, and cefotaxime. Mobile R-plasmids from 6 of the 12 AR pathogens were transferred to recipient E. coli after conjugation. The transconjugants harbored the same R-plasmid carrying bla CTX-M, dfr1, tetA, bla TEM, and cat genes. This study confirms that fish is a potential carrier of AR pathogens which can enter the human gut via food chain. To the best of our knowledge, this is the first study in the Indian subcontinent reporting a direct evidence of spread of AR pathogens to humans from specific marine fish consumption.}, }
@article {pmid28436439, year = {2017}, author = {Song, C and Wang, B and Tan, J and Zhu, L and Lou, D}, title = {Discovery of tauroursodeoxycholic acid biotransformation enzymes from the gut microbiome of black bears using metagenomics.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45495}, doi = {10.1038/srep45495}, pmid = {28436439}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/enzymology/isolation &amp; purification ; Bile Acids and Salts/chemistry/metabolism ; Cloning, Molecular ; DNA, Bacterial/isolation &amp; purification/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Hydroxysteroid Dehydrogenases/chemistry/genetics/*metabolism ; Kinetics ; *Metagenomics ; Protein Stability ; Recombinant Proteins/biosynthesis/isolation &amp; purification ; Sequence Alignment ; Stereoisomerism ; Taurochenodeoxycholic Acid/*metabolism ; Ursidae ; }, abstract = {Tauroursodeoxycholic acid (TUDCA) has been used to treat many diseases effectively. 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 7β-hydroxysteroid dehydrogenase (7β-HSDH) are two key enzymes that drive the efficient biosynthesis of TUDCA from taurochenodeoxycholic acid (TCDCA) in vitro. In this study, a metagenomic approach was used to isolate 7α- and 7β-HSDHs from fecal samples of black bears. Five new 7α-HSDHs and one new 7β-HSDH enzyme were discovered and identified from the gut microbiota of black bears, and four of them presented good enzymatic properties. Our data also suggest cooperation in the biotransformation of TUDCA by the gut microbiota in black bears. In conclusion, this work expands the natural enzyme bank of HSDHs, provides promising candidate enzymes for application in the biosynthesis TUDCA and the epimerization reaction of bile acids at the C-7 position, and provides a data set for the discovery of novel enzymes in the gut micriobiome of black bears.}, }
@article {pmid29759899, year = {2018}, author = {Belgini, DRB and Siqueira, VM and Oliveira, DM and Fonseca, SG and Piccin-Santos, V and Dias, RS and Quartaroli, L and Souza, RS and Torres, APR and Sousa, MP and Silva, CM and Silva, CC and De Paula, SO and Oliveira, VM}, title = {Integrated diversity analysis of the microbial community in a reverse osmosis system from a Brazilian oil refinery.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {5}, pages = {473-486}, doi = {10.1016/j.syapm.2018.03.007}, pmid = {29759899}, issn = {1618-0984}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biodiversity ; Biofilms/growth &amp; development ; Brazil ; Fungi/*classification/genetics/isolation &amp; purification/physiology ; Metagenomics ; *Microbial Consortia ; *Oil and Gas Industry ; Osmosis ; Waste Water/*microbiology ; Water Purification/*methods ; }, abstract = {Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality. In this study, the microbial diversity of feedwater and reverse osmosis membranes was investigated using a combination of culture-dependent and culture-independent methods in order to characterize the microorganisms colonizing and deteriorating the membranes. In total, 37 bacterial isolates, 17 filamentous fungi and approximately 400 clones were obtained and analyzed. Among the bacterial genera identified, the most represented were Sphingobium, Acidovorax, Microbacterium, Rhizobium and Shinella. The results revealed genera that acted as candidate key players in initial biofilm formation in membrane systems, and provided important information concerning the microbial ecology of oligotrophic aquatic systems.}, }
@article {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 {pmid29636446, year = {2018}, author = {Zhou, X and Guang, X and Sun, D and Xu, S and Li, M and Seim, I and Jie, W and Yang, L and Zhu, Q and Xu, J and Gao, Q and Kaya, A and Dou, Q and Chen, B and Ren, W and Li, S and Zhou, K and Gladyshev, VN and Nielsen, R and Fang, X and Yang, G}, title = {Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1276}, doi = {10.1038/s41467-018-03722-x}, pmid = {29636446}, issn = {2041-1723}, mesh = {Adaptation, Biological ; Animals ; Biological Evolution ; China ; Chromosome Mapping ; *Genome ; *Metagenomics ; *Phylogeny ; Porpoises/classification/*genetics ; Reproductive Isolation ; Rivers ; Seawater ; Water-Electrolyte Balance ; }, abstract = {Cetaceans (whales, dolphins, and porpoises) are a group of mammals adapted to various aquatic habitats, from oceans to freshwater rivers. We report the sequencing, de novo assembly and analysis of a finless porpoise genome, and the re-sequencing of an additional 48 finless porpoise individuals. We use these data to reconstruct the demographic history of finless porpoises from their origin to the occupation into the Yangtze River. Analyses of selection between marine and freshwater porpoises identify genes associated with renal water homeostasis and urea cycle, such as urea transporter 2 and angiotensin I-converting enzyme 2, which are likely adaptations associated with the difference in osmotic stress between ocean and rivers. Our results strongly suggest that the critically endangered Yangtze finless porpoises are reproductively isolated from other porpoise populations and harbor unique genetic adaptations, supporting that they should be considered a unique incipient species.}, }
@article {pmid29311667, year = {2018}, author = {Trosvik, P and Rueness, EK and de Muinck, EJ and Moges, A and Mekonnen, A}, title = {Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {20}, doi = {10.1038/s41598-017-18435-2}, pmid = {29311667}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Cercopithecinae ; Chloroplasts/genetics ; *Ecology ; *Gastrointestinal Microbiome ; Geography ; Metagenomics/methods ; Microbiota ; RNA, Ribosomal, 16S ; Seasons ; }, abstract = {Human activities can cause habitat degradation that may alter the types and quality of available food resources and thus influence the microbiomes of wild animal populations. Furthermore, seasonal shifts in food availability may cause adaptive responses in the gut microbiome to meet the need for different metabolic capabilities. Here, we demonstrate local-scale population structure in the gastrointestinal microbiotas of Chlorocebus monkeys, in southern Ethiopia, in response to varying degrees of human encroachment. We further provide evidence of adaptation to ecological conditions associated with the dry and wet seasons, and show seasonal effects to be more pronounced in areas with limited human activity. Finally, we report species-level microbiota differences between the endemic Ethiopian Bale monkey, an ecological specialist, and generalist Chlorocebus species from the same geographical region.}, }
@article {pmid29115058, year = {2018}, author = {Randle-Boggis, RJ and Ashton, PD and Helgason, T}, title = {Increasing flooding frequency alters soil microbial communities and functions under laboratory conditions.}, journal = {MicrobiologyOpen}, volume = {7}, number = {1}, pages = {}, doi = {10.1002/mbo3.548}, pmid = {29115058}, issn = {2045-8827}, mesh = {Archaea/*classification/*growth &amp; development ; Bacteria/*classification/*growth &amp; development ; *Biota ; *Floods ; Metabolic Networks and Pathways/genetics ; Metabolism ; Models, Theoretical ; *Soil Microbiology ; }, abstract = {The impacts of increased flooding frequency on soil microbial communities and potential functions, in line with predicted environmental changes, were investigated in a laboratory-controlled environment. More frequent flooding events altered microbial community composition and significantly increased the resolved species alpha-diversity (Shannon index). The Bacteria:Archaea ratio was greater at the end of the experiment than at the start, more-so after only one flood. Significant changes in taxa and functional gene abundances were identified and quantified. These include genes related to the reduction and oxidation of substances associated with anoxia, for example, those involved in nitrogen and sulfur cycling. No significant changes were observed in the methanogenesis pathway, another function associated with anoxia and which contributes to the emission of greenhouse gases.}, }
@article {pmid30249182, year = {2018}, author = {Cavalcanti, GS and Shukla, P and Morris, M and Ribeiro, B and Foley, M and Doane, MP and Thompson, CC and Edwards, MS and Dinsdale, EA and Thompson, FL}, title = {Rhodoliths holobionts in a changing ocean: host-microbes interactions mediate coralline algae resilience under ocean acidification.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {701}, doi = {10.1186/s12864-018-5064-4}, pmid = {30249182}, issn = {1471-2164}, mesh = {Biodiversity ; Hydrogen-Ion Concentration ; Metagenome ; *Microbiota/genetics ; Oceans and Seas ; Photosynthesis ; Rhodophyta/metabolism/*microbiology/physiology ; Seawater/chemistry/microbiology ; Stress, Physiological ; }, abstract = {BACKGROUND: Life in the ocean will increasingly have to contend with a complex matrix of concurrent shifts in environmental properties that impact their physiology and control their life histories. Rhodoliths are coralline red algae (Corallinales, Rhodophyta) that are photosynthesizers, calcifiers, and ecosystem engineers and therefore represent important targets for ocean acidification (OA) research. Here, we exposed live rhodoliths to near-future OA conditions to investigate responses in their photosynthetic capacity, calcium carbonate production, and associated microbiome using carbon uptake, decalcification assays, and whole genome shotgun sequencing metagenomic analysis, respectively. The results from our live rhodolith assays were compared to similar manipulations on dead rhodolith (calcareous skeleton) biofilms and water column microbial communities, thereby enabling the assessment of host-microbiome interaction under climate-driven environmental perturbations.<br><br>RESULTS: Under high pCO2 conditions, live rhodoliths exhibited positive physiological responses, i.e. increased photosynthetic activity, and no calcium carbonate biomass loss over time. Further, whereas the microbiome associated with live rhodoliths remained stable and resembled a healthy holobiont, the microbial community associated with the water column changed after exposure to elevated pCO2.<br><br>CONCLUSIONS: Our results suggest that a tightly regulated microbial-host interaction, as evidenced by the stability of the rhodolith microbiome recorded here under OA-like conditions, is important for host resilience to environmental stress. This study extends the scarce comprehension of microbes associated with rhodolith beds and their reaction to increased pCO2, providing a more comprehensive approach to OA studies by assessing the host holobiont.}, }
@article {pmid30021874, year = {2018}, author = {Glassman, SI and Martiny, JBH}, title = {Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units.}, journal = {mSphere}, volume = {3}, number = {4}, pages = {}, doi = {10.1128/mSphere.00148-18}, pmid = {30021874}, issn = {2379-5042}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Environmental Microbiology ; Fungi/*classification/*genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Recent discussion focuses on the best method for delineating microbial taxa, based on either exact sequence variants (ESVs) or traditional operational taxonomic units (OTUs) of marker gene sequences. We sought to test if the binning approach (ESVs versus 97% OTUs) affected the ecological conclusions of a large field study. The data set included sequences targeting all bacteria (16S rRNA) and fungi (internal transcribed spacer [ITS]), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all α and β diversity metrics were highly positively correlated (r > 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Furthermore, ESVs only moderately increased the genetic resolution of fungal and bacterial diversity (1.3 and 2.1 times OTU richness, respectively). We conclude that for broadscale (e.g., all bacteria or all fungi) α and β diversity analyses, ESV or OTU methods will often reveal similar ecological results. Thus, while there are good reasons to employ ESVs, we need not question the validity of results based on OTUs.IMPORTANCE Microbial ecologists have made exceptional improvements in our understanding of microbiomes in the last decade due to breakthroughs in sequencing technologies. These advances have wide-ranging implications for fields ranging from agriculture to human health. Due to limitations in databases, the majority of microbial ecology studies use a binning approach to approximate taxonomy based on DNA sequence similarity. There remains extensive debate on the best way to bin and approximate this taxonomy. Here we examine two popular approaches using a large field-based data set examining both bacteria and fungi and conclude that there are not major differences in the ecological outcomes. Thus, it appears that standard microbial community analyses are not overly sensitive to the particulars of binning approaches.}, }
@article {pmid29976643, year = {2018}, author = {Chaudhary, A and Kauser, I and Ray, A and Poretsky, R}, title = {Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community.}, journal = {mSphere}, volume = {3}, number = {4}, pages = {}, doi = {10.1128/mSphere.00194-18}, pmid = {29976643}, issn = {2379-5042}, mesh = {*Biota ; Chicago ; Cluster Analysis ; *Cyclonic Storms ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Urban streams are susceptible to stormwater and sewage inputs that can impact their ecological health and water quality. Microbial communities in streams play important functional roles, and their composition and metabolic potential can help assess ecological state and water quality. Although these environments are highly heterogenous, little is known about the influence of isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, we examined the microbial community composition and diversity in an urban stream during dry and wet weather conditions with both 16S rRNA gene sequencing across multiple years and shotgun metagenomics to more deeply analyze a single storm flow event. Metagenomics was used to assess population-level dynamics as well as shifts in the microbial community taxonomic profile and functional potential before and after a substantial rainfall. The results demonstrated general trends present in the stream under storm flow versus base flow conditions and also highlighted the influence of increased effluent flow following rain in shifting the stream microbial community from abundant freshwater taxa to those more associated with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to changes in functional gene content, particularly for transmembrane transport and organic substance biosynthesis. We also observed an increase in relative abundance of genes encoding degradation of organic pollutants and antibiotic resistance after rain. Overall, this study highlighted some differences in the microbial community of an urban stream under storm flow conditions and showed the impact of a storm flow event on the microbiome from an environmental and public health perspective.IMPORTANCE Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced storm flow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high-rainfall event, with potential environment and public health implications. Previous work in this area has focused on specific genes/organisms or has not assessed immediate storm flow impact.}, }
@article {pmid29738477, year = {2018}, author = {Klimenko, NS and Tyakht, AV and Popenko, AS and Vasiliev, AS and Altukhov, IA and Ischenko, DS and Shashkova, TI and Efimova, DA and Nikogosov, DA and Osipenko, DA and Musienko, SV and Selezneva, KS and Baranova, A and Kurilshikov, AM and Toshchakov, SM and Korzhenkov, AA and Samarov, NI and Shevchenko, MA and Tepliuk, AV and Alexeev, DG}, title = {Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project.}, journal = {Nutrients}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/nu10050576}, pmid = {29738477}, issn = {2072-6643}, mesh = {Bacteroidetes/genetics/isolation &amp; purification ; Bifidobacterium/genetics/isolation &amp; purification ; Clostridium/genetics/isolation &amp; purification ; Cluster Analysis ; *Diet ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Methanobrevibacter/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sample Size ; Sequence Analysis, DNA ; }, abstract = {Personalized nutrition is of increasing interest to individuals actively monitoring their health. The relations between the duration of diet intervention and the effects on gut microbiota have yet to be elucidated. Here we examined the associations of short-term dietary changes, long-term dietary habits and lifestyle with gut microbiota. Stool samples from 248 citizen-science volunteers were collected before and after a self-reported 2-week personalized diet intervention, then analyzed using 16S rRNA sequencing. Considerable correlations between long-term dietary habits and gut community structure were detected. A higher intake of vegetables and fruits was associated with increased levels of butyrate-producing Clostridiales and higher community richness. A paired comparison of the metagenomes before and after the 2-week intervention showed that even a brief, uncontrolled intervention produced profound changes in community structure: resulting in decreased levels of Bacteroidaceae, Porphyromonadaceae and Rikenellaceae families and decreased alpha-diversity coupled with an increase of Methanobrevibacter, Bifidobacterium, Clostridium and butyrate-producing Lachnospiraceae- as well as the prevalence of a permatype (a bootstrapping-based variation of enterotype) associated with a higher diversity of diet. The response of microbiota to the intervention was dependent on the initial microbiota state. These findings pave the way for the development of an individualized diet.}, }
@article {pmid30217078, year = {2018}, author = {Li, Y and Hingamp, P and Watai, H and Endo, H and Yoshida, T and Ogata, H}, title = {Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters.}, journal = {Viruses}, volume = {10}, number = {9}, pages = {}, doi = {10.3390/v10090496}, pmid = {30217078}, issn = {1999-4915}, support = {203143100025//Canon Foundation for Scientific Research/International ; 16KT0020//Japan Society for the Promotion of Science/International ; 17H03850//Japan Society for the Promotion of Science/International ; 26430184//Japan Society for the Promotion of Science/International ; 2016-28//Institute for Chemical Research, Kyoto University/International ; 2017-25//Institute for Chemical Research, Kyoto University/International ; ANR-11-BTBR-0008//French Investments for the Future program/International ; }, mesh = {*Biodiversity ; Computational Biology/methods ; Genome, Viral ; Giant Viruses/*classification/*genetics ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Polymerase Chain Reaction/methods ; Seawater/*virology ; *Water Microbiology ; }, abstract = {&quot;Megaviridae&quot; is a proposed family of giant viruses infecting unicellular eukaryotes. These viruses are ubiquitous in the sea and have impact on marine microbial community structure and dynamics through their lytic infection cycle. However, their diversity and biogeography have been poorly characterized due to the scarce detection of Megaviridae sequences in metagenomes, as well as the limitation of reference sequences used to design specific primers for this viral group. Here, we propose a set of 82 degenerated primers (referred to as MEGAPRIMER), targeting DNA polymerase genes (polBs) of Megaviridae. MEGAPRIMER was designed based on 921 Megaviridae polBs from sequenced genomes and metagenomes. By applying this primer set to environmental DNA meta-barcoding of a coastal seawater sample, we report 5595 non-singleton operational taxonomic units (OTUs) of Megaviridae at 97% nucleotide sequence identity. The majority of the OTUs were found to form diverse clades, which were phylogenetically distantly phylogenetically related to known viruses such as Mimivirus. The Megaviridae OTUs detected in this study outnumber the giant virus OTUs identified in previous individual studies by more than an order of magnitude. Hence, MEGAPRIMER represents a useful tool to study the diversity of Megaviridae at the population level in natural environments.}, }
@article {pmid29790941, year = {2018}, author = {Batut, B and Gravouil, K and Defois, C and Hiltemann, S and Brugère, JF and Peyretaillade, E and Peyret, P}, title = {ASaiM: a Galaxy-based framework to analyze microbiota data.}, journal = {GigaScience}, volume = {7}, number = {6}, pages = {}, doi = {10.1093/gigascience/giy057}, pmid = {29790941}, issn = {2047-217X}, mesh = {Base Sequence ; Metagenomics ; *Microbiota ; *Software ; *Statistics as Topic ; }, abstract = {Background: New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies.<br><br>Findings: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore, and visualize microbiota information from raw metataxonomic, metagenomic, or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io).<br><br>Conclusions: Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation, and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible, and shareable.}, }
@article {pmid29321640, year = {2018}, author = {Ehsani, E and Hernandez-Sanabria, E and Kerckhof, FM and Props, R and Vilchez-Vargas, R and Vital, M and Pieper, DH and Boon, N}, title = {Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {340}, doi = {10.1038/s41598-017-18668-1}, pmid = {29321640}, issn = {2045-2322}, mesh = {*Biodiversity ; *Ecosystem ; Metagenome ; Metagenomics/methods ; *Microbiota ; Models, Theoretical ; Phenotype ; }, abstract = {The effect of initial evenness on the temporal trajectory of synthetic communities in comprehensive, low-volume microcosm studies remains unknown. We used flow cytometric fingerprinting and 16S rRNA gene amplicon sequencing to assess the impact of time on community structure in one hundred synthetic ecosystems of fixed richness but varying initial evenness. Both methodologies uncovered a similar reduction in diversity within synthetic communities of medium and high initial evenness classes. However, the results of amplicon sequencing showed that there were no significant differences between and within the communities in all evenness groups at the end of the experiment. Nevertheless, initial evenness significantly impacted the cell density of the community after five medium transfers. Highly even communities retained the highest cell densities at the end of the experiment. The relative abundances of individual species could be associated to particular evenness groups, suggesting that their presence was dependent on the initial evenness of the synthetic community. Our results reveal that using synthetic communities for testing ecological hypotheses requires prior assessment of initial evenness, as it impacts temporal dynamics.}, }
@article {pmid29311585, year = {2018}, author = {Odamaki, T and Bottacini, F and Kato, K and Mitsuyama, E and Yoshida, K and Horigome, A and Xiao, JZ and van Sinderen, D}, title = {Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {85}, doi = {10.1038/s41598-017-18391-x}, pmid = {29311585}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Bifidobacterium longum/*classification/*genetics ; Child ; Child, Preschool ; Gastrointestinal Microbiome ; Gene Order ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Infant ; Infant, Newborn ; Japan ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; Multigene Family ; Phylogeny ; Young Adult ; }, abstract = {Bifidobacterium longum subsp. longum represents one of the most prevalent bifidobacterial species in the infant, adult and elderly (human) gut. In the current study, we performed a comparative genome analysis involving 145 B. longum representatives, including 113 B. longum subsp. longum strains obtained from healthy Japanese subjects aged between 0 and 98 years. Although MCL clustering did not reveal any correlation between isolated strains and subject age, certain characteristics appear to be more prevalent among strains corresponding to specific host ages, such as genes involved in carbohydrate metabolism and environmental response. Remarkably, a substantial number of strains appeared to have been transmitted across family members, a phenomenon that was shown not to be confined to mother-infant pairs. This suggests that the ubiquitous distribution of B. longum subsp. longum across the human lifespan is at least partly due to extensive transmission between relatives. Our findings form a foundation for future research aimed at unraveling the mechanisms that allow B. longum strains to successfully transfer between human hosts, where they then colonize and persist in the gut environment throughout the host's lifespan.}, }
@article {pmid28397879, year = {2017}, author = {Chen, SY and Tsai, CN and Lee, YS and Lin, CY and Huang, KY and Chao, HC and Lai, MW and Chiu, CH}, title = {Intestinal microbiome in children with severe and complicated acute viral gastroenteritis.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {46130}, doi = {10.1038/srep46130}, pmid = {28397879}, issn = {2045-2322}, mesh = {Acute Disease ; Biodiversity ; Caliciviridae Infections/microbiology ; Case-Control Studies ; Child ; Gastroenteritis/*microbiology/*virology ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; Rotavirus Infections/microbiology ; Sequence Analysis, RNA ; *Severity of Illness Index ; }, abstract = {The aim of the present study was to evaluate the microbiota of children with severe or complicated acute viral gastroenteritis (AGE). To that end, next-generation sequencing (NGS) technology was used to sequence the 16S ribosomal RNA (16S rRNA) gene in 20 hospitalized pediatric patients with severe or complicated AGE and a further 20 otherwise healthy children; the fecal microbiome was then assessed. Comparative metagenomics data were analyzed by a Wilcoxon rank-sum test and hierarchical clustering analysis of bacterial reads. The statistical analyses showed a significantly decreased Shannon diversity index (entropy score) of the intestinal microbiota in patients with severe AGE compared with normal controls (P = 0.017) and patients with mild-to-moderate AGE (P = 0.011). The intestinal microbiota score of the 5 patients with rotavirus AGE was significantly lower than that of those with norovirus infection (P = 0.048). Greater richness in Campylobacteraceae (P = 0.0003), Neisseriaceae (P = 0.0115), Methylobacteriaceae (P = 0.0004), Sphingomonadaceae (P = 0.0221), and Enterobacteriaceae (P = 0.0451) was found in patients with complicated AGE compared with normal controls. The data suggest a significant reduction in intestinal microbial diversity in patients with severe AGE, particularly those with rotavirus infection.}, }
@article {pmid27613488, year = {2017}, author = {Häfner, S}, title = {The last of the organs.}, journal = {Microbes and infection}, volume = {19}, number = {1}, pages = {1-4}, doi = {10.1016/j.micinf.2016.08.006}, pmid = {27613488}, issn = {1769-714X}, mesh = {Clostridium Infections/immunology/microbiology ; Clostridium difficile/isolation &amp; purification ; *Gastrointestinal Tract/immunology/microbiology ; Humans ; Hypersensitivity, Immediate/immunology/microbiology ; *Metagenome ; Metagenomics ; *Microbiota ; }, }
@article {pmid29705928, year = {2018}, author = {Bonilla, JO and Kurth, DG and Cid, FD and Ulacco, JH and Gil, RA and Villegas, LB}, title = {Prokaryotic and eukaryotic community structure affected by the presence of an acid mine drainage from an abandoned gold mine.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {5}, pages = {699-711}, doi = {10.1007/s00792-018-1030-y}, pmid = {29705928}, issn = {1433-4909}, support = {PICT 2013 No. 3170//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, mesh = {Acids/analysis ; Actinobacteria/isolation &amp; purification ; Diatoms/isolation &amp; purification ; *Extreme Environments ; Fungi/isolation &amp; purification ; Gammaproteobacteria/isolation &amp; purification ; Geologic Sediments/chemistry/*microbiology ; Gold/analysis ; Metagenome ; Metals, Heavy/analysis ; *Microbiota ; Mining ; }, abstract = {The acid mine drainage that originates in the abandoned gold mine in San Luis, Argentina, is released into La Carolina stream. The aim of this study was to determine the influence of this mine drainage on the physicochemical parameters of the area studied and on both prokaryotic and eukaryotic community structure. In addition, specific relationships between microbial taxonomic groups and physicochemical parameters were established. The drainage that flows into La Carolina stream acidifies the stream and increases its sulfate, Zn, Cd and Te concentrations. Microbial analysis showed that prokaryotic community structure is mainly affected by pH values. Actinobacteria and Gammaproteobacteria were abundant in samples characterized by low pH values, while Nitrospirae, Chloroflexi, Deltaproteobacteria, Thaumarchaeota and Euryarchaeota were associated with high concentrations of heavy metals. Otherwise, Alphaproteobacteria was present in samples taken in sunlit areas. Regarding eukaryotic community structure, the sunlight had the greatest impact. Inside the mine, in the absence of light, fungi and protists members were the most abundant microorganisms, while those samples taken in the presence of light displayed algae (green algae and diatoms) as the most abundant ones. After receiving the mine drainage, the stream showed a decrease in the diatom abundance and green algae predominated.}, }
@article {pmid30110928, year = {2018}, author = {Wu, L and Wang, J and Wu, H and Chen, J and Xiao, Z and Qin, X and Zhang, Z and Lin, W}, title = {Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture.}, journal = {International journal of molecular sciences}, volume = {19}, number = {8}, pages = {}, doi = {10.3390/ijms19082394}, pmid = {30110928}, issn = {1422-0067}, mesh = {*Bacteria/classification/genetics/growth &amp; development ; *Metagenome ; Microbial Consortia/*physiology ; Rehmannia/*microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Consecutive monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive monoculture. The results showed R. glutinosa monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive monoculture.}, }
@article {pmid29040451, year = {2018}, author = {Chen, J and King, E and Deek, R and Wei, Z and Yu, Y and Grill, D and Ballman, K and Stegle, O}, title = {An omnibus test for differential distribution analysis of microbiome sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {4}, pages = {643-651}, doi = {10.1093/bioinformatics/btx650}, pmid = {29040451}, issn = {1367-4811}, mesh = {Arthritis, Rheumatoid/microbiology ; Humans ; Inflammatory Bowel Diseases/microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; *Models, Statistical ; *Software ; }, abstract = {Motivation: One objective of human microbiome studies is to identify differentially abundant microbes across biological conditions. Previous statistical methods focus on detecting the shift in the abundance and/or prevalence of the microbes and treat the dispersion (spread of the data) as a nuisance. These methods also assume that the dispersion is the same across conditions, an assumption which may not hold in presence of sample heterogeneity. Moreover, the widespread outliers in the microbiome sequencing data make existing parametric models not overly robust. Therefore, a robust and powerful method that allows covariate-dependent dispersion and addresses outliers is still needed for differential abundance analysis.<br><br>Results: We introduce a novel test for differential distribution analysis of microbiome sequencing data by jointly testing the abundance, prevalence and dispersion. The test is built on a zero-inflated negative binomial regression model and winsorized count data to account for zero-inflation and outliers. Using simulated data and real microbiome sequencing datasets, we show that our test is robust across various biological conditions and overall more powerful than previous methods.<br><br>R package is available at https://github.com/jchen1981/MicrobiomeDDA.<br><br>Contact: chen.jun2@mayo.edu or zhiwei@njit.edu.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid28322295, year = {2017}, author = {Li, TH and Qin, Y and Sham, PC and Lau, KS and Chu, KM and Leung, WK}, title = {Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {44935}, doi = {10.1038/srep44935}, pmid = {28322295}, issn = {2045-2322}, mesh = {Biodiversity ; *Cell Transformation, Neoplastic ; Female ; Gastric Mucosa/*microbiology/*physiology ; Helicobacter Infections/*complications/*microbiology ; *Helicobacter pylori ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Microbiota ; Stomach Neoplasms/*etiology/*pathology ; }, abstract = {The role of bacteria other than Helicobacter pylori (HP) in the stomach remains elusive. We characterized the gastric microbiota in individuals with different histological stages of gastric carcinogenesis and after receiving HP eradication therapy. Endoscopic gastric biopsies were obtained from subjects with HP gastritis, gastric intestinal metaplasia (IM), gastric cancer (GC) and HP negative controls. Gastric microbiota was characterized by Illumina MiSeq platform targeting the 16 S rDNA. Apart from dominant H. pylori, we observed other Proteobacteria including Haemophilus, Serratia, Neisseria and Stenotrophomonas as the major components of the human gastric microbiota. Although samples were largely converged according to the relative abundance of HP, a clear separation of GC and other samples was recovered. Whilst there was a strong inverse association between HP relative abundance and bacterial diversity, this association was weak in GC samples which tended to have lower bacterial diversity compared with other samples with similar HP levels. Eradication of HP resulted in an increase in bacterial diversity and restoration of the relative abundance of other bacteria to levels similar to individuals without HP. In conclusion, HP colonization results in alterations of gastric microbiota and reduction in bacterial diversity, which could be restored by antibiotic treatment.}, }
@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 {pmid30346155, year = {2018}, author = {Pérez-Burillo, S and Pastoriza, S and Jiménez-Hernández, N and D'Auria, G and Francino, MP and Rufián-Henares, JA}, title = {Effect of Food Thermal Processing on the Composition of the Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {43}, pages = {11500-11509}, doi = {10.1021/acs.jafc.8b04077}, pmid = {30346155}, issn = {1520-5118}, mesh = {Bacteria/classification ; *Cooking ; Edible Grain ; Fabaceae ; Fatty Acids, Volatile/analysis ; Fermentation ; Fruit ; Furaldehyde/analogs &amp; derivatives/analysis ; *Gastrointestinal Microbiome ; *Hot Temperature ; Humans ; Lysine/analogs &amp; derivatives/analysis ; Maillard Reaction ; Meat ; RNA, Ribosomal, 16S/genetics ; Vegetables ; }, abstract = {Cooking modifies food composition due to chemical reactions. Additionally, food composition shapes the human gut microbiota. Thus, the objective of this research was to unravel the effect of different food cooking methods on the structure and functionality of the gut microbiota. Common culinary techniques were applied to five foods, which were submitted to in vitro digestion-fermentation. Furosine, 5-(hydroxymethyl)furfural, and furfural were used as Maillard reaction indicators to control the heat treatment. Short-chain fatty acids production was quantified as indicator of healthy metabolic output. Gut microbial community structure was analyzed through 16S rRNA. Both food composition and cooking methods modified the microbiota composition and released short-chain fatty acids. In general, intense cooking technologies (roasting and grilling) increased the abundance of beneficial bacteria like Ruminococcus spp. or Bifidobacterium spp. compared to milder treatments (boiling). However, for some foods (banana or bread), intense cooking decreased the levels of healthy bacteria.}, }
@article {pmid29788417, year = {2018}, author = {Patil, RD and Ellison, MJ and Wolff, SM and Shearer, C and Wright, AM and Cockrum, RR and Austin, KJ and Lamberson, WR and Cammack, KM and Conant, GC}, title = {Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes.}, journal = {Journal of animal science}, volume = {96}, number = {6}, pages = {2113-2124}, doi = {10.1093/jas/sky096}, pmid = {29788417}, issn = {1525-3163}, mesh = {Animal Feed/*analysis ; Animals ; Female ; *Gastrointestinal Microbiome ; *Metabolic Networks and Pathways ; *Metagenomics ; Rumen/metabolism/microbiology ; Sheep/microbiology/*physiology ; }, abstract = {Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not. We conducted shotgun sequencing of microbial DNA from the rumen contents of 16 sheep that differed in their residual feed intake (RFI), a measure of feed efficiency. Metagenomic reads from each sheep were mapped onto a database-derived microbial metabolic network, which was linked to the sheep metabolic network by interface metabolites (metabolites transferred from microbes to host). No single enzyme was identified as being significantly different in abundance between the low and high RFI animals (P > 0.05, Wilcoxon test). However, when we analyzed the metabolic network as a whole, we found several differences between efficient and inefficient animals. Microbes from low RFI (efficient) animals use a suite of enzymes closer in network space to the host's reactions than those of the high RFI (inefficient) animals. Similarly, low RFI animals have microbial metabolic networks that, on average, contain reactions using shorter carbon chains than do those of high RFI animals, potentially allowing the host animals to extract metabolites more efficiently. Finally, the efficient animals possess community networks with greater Shannon diversity among their enzymes than do inefficient ones. Thus, our system approach to the ruminal microbiome identified differences attributable to feed efficiency in the structure of the microbes' community metabolic network that were undetected at the level of individual microbial taxa or reactions.}, }
@article {pmid28349946, year = {2017}, author = {Yan, W and Sun, C and Yuan, J and Yang, N}, title = {Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45308}, doi = {10.1038/srep45308}, pmid = {28349946}, issn = {2045-2322}, mesh = {Amino Acids/metabolism ; Animal Feed ; Animals ; Bacteria/genetics/isolation &amp; purification ; Biodiversity ; Cecum/microbiology ; Chickens ; Duodenum/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Lactobacillus/genetics/*isolation &amp; purification ; *Metagenomics ; Phenotype ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Interactions between the host and gut microbiota can affect gut metabolism. In this study, the individual performances of 252 hens were recorded to evaluate feed efficiency. Hens with contrasting feed efficiencies (14 birds per group) were selected to investigate their duodenal, cecal and fecal microbial composition by sequencing the 16S rRNA gene V4 region. The results showed that the microbial community in the cecum was quite different from those in the duodenum and feces. The highest biodiversity and all differentially abundant taxa between the different efficiency groups were observed in the cecal microbial community with false discovery rate (FDR) <0.05. Of these differentially abundant cecal microbes, Lactobacillus accounted for a greater proportion than the others. The abundances of Lactobacillus and Akkermansia were significantly higher while that of Faecalibacterium was lower (FDR < 0.05) in the better feed efficiency (BFE) group. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis revealed that the functions relating to glycometabolism and amino acid metabolism were enriched in the cecal microbiota of the BFE group. These results indicated the prominent role of cecal microbiota in the feed efficiency of chickens and suggested plausible uses of Lactobacillus to improve the feed efficiency of host.}, }
@article {pmid28112173, year = {2017}, author = {Ji, P and Zhang, Y and Wang, J and Zhao, F}, title = {MetaSort untangles metagenome assembly by reducing microbial community complexity.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {14306}, doi = {10.1038/ncomms14306}, pmid = {28112173}, issn = {2041-1723}, mesh = {Bacteria/*genetics ; Computational Biology ; Genome, Bacterial ; Genome, Microbial ; Kelp/*microbiology ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities.}, }
@article {pmid30205462, year = {2018}, author = {Hidalgo-Cantabrana, C and Sanozky-Dawes, R and Barrangou, R}, title = {Insights into the Human Virome Using CRISPR Spacers from Microbiomes.}, journal = {Viruses}, volume = {10}, number = {9}, pages = {}, doi = {10.3390/v10090479}, pmid = {30205462}, issn = {1999-4915}, support = {support//North Carolina Agricultural Foundation/International ; internal support//North Carolina State University/International ; }, mesh = {*Biodiversity ; Clustered Regularly Interspaced Short Palindromic Repeats ; Humans ; Metagenomics ; *Microbiota ; Viruses/*classification/genetics/*isolation &amp; purification ; }, abstract = {Due to recent advances in next-generation sequencing over the past decade, our understanding of the human microbiome and its relationship to health and disease has increased dramatically. Yet, our insights into the human virome, and its interplay with important microbes that impact human health, is relatively limited. Prokaryotic and eukaryotic viruses are present throughout the human body, comprising a large and diverse population which influences several niches and impacts our health at various body sites. The presence of prokaryotic viruses like phages, has been documented at many different body sites, with the human gut being the richest ecological niche. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated proteins constitute the adaptive immune system of bacteria, which prevents attack by invasive nucleic acid. CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing.}, }
@article {pmid28696003, year = {2018}, author = {Malanoski, AP and Lin, B and Eddie, BJ and Wang, Z and Hervey, WJ and Glaven, SM}, title = {Relative abundance of 'Candidatus Tenderia electrophaga' is linked to cathodic current in an aerobic biocathode community.}, journal = {Microbial biotechnology}, volume = {11}, number = {1}, pages = {98-111}, doi = {10.1111/1751-7915.12757}, pmid = {28696003}, issn = {1751-7915}, mesh = {*Bioelectric Energy Sources ; *Biota ; Carbon Dioxide/metabolism ; Chromatiaceae/classification/genetics/*isolation &amp; purification/*metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrodes/*microbiology ; Metagenomics ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Biocathode microbial communities are proposed to catalyse a range of useful reactions. Unlike bioanodes, model biocathode organisms have not yet been successfully cultivated in isolation highlighting the need for culture-independent approaches to characterization. Biocathode MCL (Marinobacter, Chromatiaceae, Labrenzia) is a microbial community proposed to couple CO2 fixation to extracellular electron transfer and O2 reduction. Previous metagenomic analysis of a single MCL bioelectrochemical system (BES) resulted in resolution of 16 bin genomes. To further resolve bin genomes and compare community composition across replicate MCL BES, we performed shotgun metagenomic and 16S rRNA gene (16S) sequencing at steady-state current. Clustering pooled reads from replicate BES increased the number of resolved bin genomes to 20, over half of which were > 90% complete. Direct comparison of unassembled metagenomic reads and 16S operational taxonomic units (OTUs) predicted higher community diversity than the assembled/clustered metagenome and the predicted relative abundances did not match. However, when 16S OTUs were mapped to bin genomes and genome abundance was scaled by 16S gene copy number, estimated relative abundance was more similar to metagenomic analysis. The relative abundance of the bin genome representing 'Ca. Tenderia electrophaga' was correlated with increasing current, further supporting the hypothesis that this organism is the electroautotroph.}, }
@article {pmid30122883, year = {2018}, author = {Zhao, Y and Mao, YF and Tang, YS and Ni, MZ and Liu, QH and Wang, Y and Feng, Q and Peng, JH and Hu, YY}, title = {Altered oral microbiota in chronic hepatitis B patients with different tongue coatings.}, journal = {World journal of gastroenterology}, volume = {24}, number = {30}, pages = {3448-3461}, doi = {10.3748/wjg.v24.i30.3448}, pmid = {30122883}, issn = {2219-2840}, mesh = {Adult ; Bacteria/genetics/*isolation &amp; purification/metabolism ; Case-Control Studies ; DNA, Viral/isolation &amp; purification ; Female ; Gastrointestinal Microbiome/*physiology ; Healthy Volunteers ; Hepatitis B virus/genetics/*isolation &amp; purification ; Hepatitis B, Chronic/diagnosis/metabolism/*microbiology ; Humans ; Male ; Medicine, Chinese Traditional/methods ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Tongue/*microbiology ; }, abstract = {AIM: To elucidate tongue coating microbiota and metabolic differences in chronic hepatitis B (CHB) patients with yellow or white tongue coatings.<br><br>METHODS: Tongue coating samples were collected from 53 CHB patients (28 CHB yellow tongue coating patients and 25 CHB white tongue coating patients) and 22 healthy controls. Microbial DNA was extracted from the tongue samples, and the bacterial 16S ribosomal RNA gene V3 region was amplified from all samples and sequenced with the Ion Torrent PGM™ sequencing platform according to the standard protocols. The metabolites in the tongue coatings were evaluated using a liquid chromatography-mass spectrometry (LC-MS) platform. Statistical analyses were then performed.<br><br>RESULTS: The relative compositions of the tongue coating microbiotas and metabolites in the CHB patients were significantly different from those of the healthy controls, but the tongue coating microbiota abundances and diversity levels were not significantly different. Compared with the CHB white tongue coating patients, the CHB yellow tongue coating patients had higher hepatitis B viral DNA (HBV-DNA) titers (median 21210 vs 500, respectively, P = 0.03) and a significantly lower level of Bacteroidetes (20.14% vs 27.93%, respectively, P = 0.013) and higher level of Proteobacteria (25.99% vs 18.17%, respectively, P = 0.045) in the microbial compositions at the phylum level. The inferred metagenomic pathways enriched in the CHB yellow tongue coating patients were mainly those involved in amino acid metabolism, which was consistent with the metabolic disorder. The abundances of bacteria from Bacteroidales at the order level were higher in the CHB white tongue coating patients (19.2% vs 27.22%, respectively, P = 0.011), whereas Neisseriales were enriched in the yellow tongue coating patients (21.85% vs 13.83%, respectively, P = 0.029). At the family level, the abundance of Neisseriaceae in the yellow tongue patients was positively correlated with the HBV-DNA level but negatively correlated with the S-adenosyl-L-methionine level.<br><br>CONCLUSION: This research illustrates specific clinical features and bacterial structures in CHB patients with different tongue coatings, which facilitates understanding of the traditional tongue diagnosis.}, }
@article {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 {pmid28255158, year = {2017}, author = {Jandhyala, SM and Madhulika, A and Deepika, G and Rao, GV and Reddy, DN and Subramanyam, C and Sasikala, M and Talukdar, R}, title = {Altered intestinal microbiota in patients with chronic pancreatitis: implications in diabetes and metabolic abnormalities.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43640}, doi = {10.1038/srep43640}, pmid = {28255158}, issn = {2045-2322}, mesh = {Adult ; Biodiversity ; Case-Control Studies ; Diabetes Mellitus, Type 2/diagnosis/*etiology ; Disease Progression ; *Dysbiosis ; Energy Metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolic Diseases/diagnosis/*etiology ; Metagenome ; Metagenomics/methods ; Middle Aged ; Pancreatitis, Chronic/*complications/diagnosis ; }, abstract = {Intestinal dysbiosis and its functional implications in chronic pancreatitis (CP) have not been elaborately studied. We evaluated the taxonomic and functional alterations in intestinal microbiota in 30 well-characterised patients with CP (16 without, 14 with diabetes) and 10 healthy controls. The patients with CP and diabetes had significantly longer disease duration and greater degree of malnutrition. There was increase in plasma endotoxin concentrations from controls to CP non-diabetics to CP diabetics. We observed significant differences in richness and alpha diversity between the groups. We also observed increase in the Firmicutes:Bacteroidetes ratio in CP patients without and with diabetes. There was reduction in abundance of Faecalibacterium prausnitzii and Ruminococcus bromii from controls to CP non-diabetics to CP diabetics. On the other hand, there was increase in LPS (endotoxin) synthetic pathways (KEGG orthology) in the groups. Faecalibacterium prausnitzii abundance correlated negatively with plasma endotoxin and glycemic status; while plasma endotoxin correlated positively with blood glucose and negatively with plasma insulin. Our results have important implications for future studies exploring mechanistic insights on secondary diabetes in CP.}, }
@article {pmid28240318, year = {2017}, author = {Lee, ST and Davy, SK and Tang, SL and Kench, PS}, title = {Water flow buffers shifts in bacterial community structure in heat-stressed Acropora muricata.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43600}, doi = {10.1038/srep43600}, pmid = {28240318}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology/*physiology ; Bacteria/*classification/genetics ; *Biodiversity ; Environment ; *Hot Temperature ; Metagenome ; Metagenomics/methods ; Seasons ; Seawater ; *Stress, Physiological ; *Symbiosis ; Temperature ; Vibrio/classification/genetics ; }, abstract = {Deterioration of coral health and associated change in the coral holobiont's bacterial community are often a result of different environmental stressors acting synergistically. There is evidence that water flow is important for a coral's resistance to elevated seawater temperature, but there is no information on how water flow affects the coral-associated bacterial community under these conditions. In a laboratory cross-design experiment, Acropora muricata nubbins were subjected to interactive effects of seawater temperature (27 °C to 31 °C) and water flow (0.20 m s-1 and 0.03 m s-1). In an in situ experiment, water flow manipulation was conducted with three colonies of A. muricata during the winter and summer, by partially enclosing each colony in a clear plastic mesh box. 16S rRNA amplicon pyrosequencing showed an increase in the relative abundance of Flavobacteriales and Rhodobacterales in the laboratory experiment, and Vibrio spp. in the in situ experiment when corals were exposed to elevated temperature and slow water flow. In contrast, corals that were exposed to faster water flow under laboratory and in situ conditions had a stable bacterial community. These findings indicate that water flow plays an important role in the maintenance of specific coral-bacteria associations during times of elevated thermal stress.}, }
@article {pmid29076296, year = {2017}, author = {de la Calle, F}, title = {Marine microbiome as source of natural products.}, journal = {Microbial biotechnology}, volume = {10}, number = {6}, pages = {1293-1296}, doi = {10.1111/1751-7915.12882}, pmid = {29076296}, issn = {1751-7915}, mesh = {Biological Products/*metabolism ; Biotechnology/methods ; Data Mining/methods ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Seawater/*microbiology ; }, }
@article {pmid30041354, year = {2018}, author = {Tiralerdpanich, P and Sonthiphand, P and Luepromchai, E and Pinyakong, O and Pokethitiyook, P}, title = {Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis.}, journal = {Marine pollution bulletin}, volume = {133}, number = {}, pages = {595-605}, doi = {10.1016/j.marpolbul.2018.06.015}, pmid = {30041354}, issn = {1879-3363}, mesh = {Alkanes/*metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Gasoline ; Geologic Sediments/*microbiology ; Metagenomics/methods ; Microbial Consortia/genetics/*physiology ; Phenanthrenes/*metabolism ; RNA, Ribosomal, 16S/metabolism ; Thailand ; Wetlands ; }, abstract = {Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg-1 sediment day-1, respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.}, }
@article {pmid28252037, year = {2017}, author = {Aoki, R and Kamikado, K and Suda, W and Takii, H and Mikami, Y and Suganuma, N and Hattori, M and Koga, Y}, title = {A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43522}, doi = {10.1038/srep43522}, pmid = {28252037}, issn = {2045-2322}, mesh = {Acetates/*metabolism ; Animals ; Bifidobacterium/*metabolism ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Glucose Intolerance/metabolism/therapy ; Male ; Metabolic Diseases/etiology/*metabolism/therapy ; Metagenome ; Metagenomics/methods ; Mice ; *Probiotics ; }, abstract = {The gut microbiota is an important contributor to the worldwide prevalence of metabolic syndrome (MS), which includes obesity and diabetes. The anti-MS effects exerted by Bifidobacterium animalis ssp. lactis GCL2505 (BlaG), a highly proliferative Bifidobacterium strain in the gut, and B. longum ssp. longum JCM1217T (BloJ) were comparatively examined. BlaG treatment reduced visceral fat accumulation and improved glucose tolerance, whereas BloJ had no effect on these parameters. Gut microbial analysis revealed that BlaG exerted stronger effects on the overall bacterial structure of the gut microbiota than BloJ, including enrichment of the genus Bifidobacterium. The levels of acetate and glucagon-like peptide-1 were increased by BlaG treatment in both the gut and plasma, but not by BloJ treatment. Correlation analysis suggested that the elevation of gut acetate levels by BlaG treatment plays a pivotal role in the BlaG-induced anti-MS effects. These findings indicated that BlaG, a highly viable and proliferative probiotic, improves metabolic disorders by modulating gut microbiota, which results in the elevation of SCFAs, especially acetate.}, }
@article {pmid30166168, year = {2018}, author = {Li, Z and Feng, C and Luo, X and Yao, H and Zhang, D and Zhang, T}, title = {Revealing the influence of microbiota on the quality of Pu-erh tea during fermentation process by shotgun metagenomic and metabolomic analysis.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {405-415}, doi = {10.1016/j.fm.2018.07.001}, pmid = {30166168}, issn = {1095-9998}, mesh = {Aspergillus/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Camellia sinensis/chemistry/*microbiology ; Fermentation ; Flavoring Agents/chemistry/metabolism ; Metabolomics ; Metagenomics ; *Microbiota ; Phenols/chemistry/metabolism ; Quality Control ; Tea/*chemistry/microbiology ; }, abstract = {Multispecies microbial community in natural solid-state fermentation (SSF) is crucial for the formation of Chinese Pu-erh tea's unique quality. However, the association between microbiota and tea quality are still poorly understood. Herein, shotgun metagenomic and metabolomic analysis showed that significant variations in composition of microbiota, collective functional genes, and flavour compounds occurred during SSF process. Furthermore, the formation pathways of the dominant flavours including theabrownin, methoxy-phenolic compound, alcohol and carvone were proposed. Moreover, biological interaction networks analysis among functional core microbiota, functional genes, and dominant flavours indicated Aspergillus was the main flavour-producing microorganism in the early SSF, while many other genera including Bacillus, Rasamsonia, Lichtheimia, Debaryomyces were determined as the functional core microorganism for flavours production in the late SSF. This study provides a perspective for bridging the gap between the microbiota and quality in Pu-erh tea, and benefited for further optimizing production efficiency and product quality.}, }
@article {pmid29471863, year = {2018}, author = {Petrosino, JF}, title = {The microbiome in precision medicine: the way forward.}, journal = {Genome medicine}, volume = {10}, number = {1}, pages = {12}, doi = {10.1186/s13073-018-0525-6}, pmid = {29471863}, issn = {1756-994X}, support = {R01 AI108588/AI/NIAID NIH HHS/United States ; HHSN267200700014C/DK/NIDDK NIH HHS/United States ; R01 MH112356/MH/NIMH NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Disease ; Humans ; *Microbiota ; Phenotype ; *Precision Medicine ; }, abstract = {Novel associations between the human microbiome and health and disease are routinely emerging, and important host-microbiome interactions are targets for new diagnostics and therapeutics. Understanding how broadly host-microbe associations are maintained across populations is revealing individualized host-microbiome phenotypes that can be integrated with other 'omics' data sets to enhance precision medicine.}, }
@article {pmid28396267, year = {2017}, author = {Puehler, A and Kalinowski, J}, title = {Microbial genomics and metagenomics in human health and disease.}, journal = {Journal of biotechnology}, volume = {250}, number = {}, pages = {1}, doi = {10.1016/j.jbiotec.2017.04.007}, pmid = {28396267}, issn = {1873-4863}, mesh = {Bacteria/genetics ; Bacterial Infections/*genetics ; Bacteriophages/genetics ; *Genome, Bacterial ; Genomics ; Humans ; Microbiota ; Sequence Analysis, DNA ; }, }
@article {pmid28785417, year = {2016}, author = {Jameson, E and Doxey, AC and Airs, R and Purdy, KJ and Murrell, JC and Chen, Y}, title = {Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems.}, journal = {Microbial genomics}, volume = {2}, number = {9}, pages = {e000080}, doi = {10.1099/mgen.0.000080}, pmid = {28785417}, issn = {2057-5858}, mesh = {Actinobacteria/enzymology/*genetics ; *Data Mining ; *Ecosystem ; Gastrointestinal Microbiome/*genetics ; Geologic Sediments/microbiology ; Humans ; *Metagenomics ; Methylamines/*metabolism ; Oxidoreductases, N-Demethylating/genetics ; Proteobacteria/enzymology/*genetics ; }, abstract = {Existing metagenome datasets from many different environments contain untapped potential for understanding metabolic pathways and their biological impact. Our interest lies in the formation of trimethylamine (TMA), a key metabolite in both human health and climate change. Here, we focus on bacterial degradation pathways for choline, carnitine, glycine betaine and trimethylamine N-oxide (TMAO) to TMA in human gut and marine metagenomes. We found the TMAO reductase pathway was the most prevalent pathway in both environments. Proteobacteria were found to contribute the majority of the TMAO reductase pathway sequences, except in the stressed gut, where Actinobacteria dominated. Interestingly, in the human gut metagenomes, a high proportion of the Proteobacteria hits were accounted for by the genera Klebsiella and Escherichia. Furthermore Klebsiella and Escherichia harboured three of the four potential TMA-production pathways (choline, carnitine and TMAO), suggesting they have a key role in TMA cycling in the human gut. In addition to the intensive TMAO-TMA cycling in the marine environment, our data suggest that carnitine-to-TMA transformation plays an overlooked role in aerobic marine surface waters, whereas choline-to-TMA transformation is important in anaerobic marine sediments. Our study provides new insights into the potential key microbes and metabolic pathways for TMA formation in two contrasting environments.}, }
@article {pmid28211884, year = {2017}, author = {Li, Z and Lu, L and Guo, J and Yang, J and Zhang, J and He, B and Xu, L}, title = {Responses of spatial-temporal dynamics of bacterioplankton community to large-scale reservoir operation: a case study in the Three Gorges Reservoir, China.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42469}, doi = {10.1038/srep42469}, pmid = {28211884}, issn = {2045-2322}, mesh = {*Bacteroidetes ; *Biodiversity ; China ; Chlorophyll/analysis ; Environment ; Geography ; Metagenome ; Metagenomics/methods ; *Plankton ; Rivers/*microbiology ; Spatio-Temporal Analysis ; *Water Microbiology ; }, abstract = {Large rivers are commonly regulated by damming, yet the effects of such disruption on bacterioplankton community structures have not been adequately studied. The aim of this study was to explore the biogeographical patterns present under dam regulation and to uncover the major drivers structuring bacterioplankton communities. Bacterioplankton assemblages in the Three Gorges Reservoir (TGR) were analyzed using Illumina Miseq sequencing by comparing seven sites located within the TGR before and after impoundment. This approach revealed ecological and spatial-temporal variations in bacterioplankton community composition along the longitudinal axis. The community was dynamic and dominated by Proteobacteria and Actinobacteria phyla, encompassing 39.26% and 37.14% of all sequences, respectively, followed by Bacteroidetes (8.67%) and Cyanobacteria (3.90%). The Shannon-Wiener index of the bacterioplankton community in the flood season (August) was generally higher than that in the impoundment season (November). Principal Component Analysis of the bacterioplankton community compositions showed separation between different seasons and sampling sites. Results of the relationship between bacterioplankton community compositions and environmental variables highlighted that ecological processes of element cycling and large dam disturbances are of prime importance in driving the assemblages of riverine bacterioplankton communities.}, }
@article {pmid28198425, year = {2017}, author = {Leite, MF and Pan, Y and Bloem, J and Berge, HT and Kuramae, EE}, title = {Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42634}, doi = {10.1038/srep42634}, pmid = {28198425}, issn = {2045-2322}, mesh = {Bacteria ; Carbon/chemistry/metabolism ; Fungi ; Metagenome ; Metagenomics/methods ; Microbiota ; Nitrogen/*chemistry/*metabolism ; *Soil Microbiology ; }, abstract = {Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.}, }
@article {pmid28198423, year = {2017}, author = {Montella, S and Ventorino, V and Lombard, V and Henrissat, B and Pepe, O and Faraco, V}, title = {Discovery of genes coding for carbohydrate-active enzyme by metagenomic analysis of lignocellulosic biomasses.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42623}, doi = {10.1038/srep42623}, pmid = {28198423}, issn = {2045-2322}, mesh = {Biodegradation, Environmental ; *Biomass ; Biotransformation ; Carbohydrate Metabolism/*genetics ; Cellulases/*genetics/*metabolism ; Computational Biology/methods ; Crops, Agricultural ; Gene Expression Profiling ; Glycoside Hydrolases/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrolysis ; Lignin/*metabolism ; *Metagenome ; *Metagenomics/methods ; Microbiota ; Open Reading Frames ; Polysaccharides/metabolism ; }, abstract = {In this study, a high-throughput sequencing approach was applied to discover novel biocatalysts for lignocellulose hydrolysis from three dedicated energy crops, Arundo donax, Eucalyptus camaldulensis and Populus nigra, after natural biodegradation. The microbiomes of the three lignocellulosic biomasses were dominated by bacterial species (approximately 90%) with the highest representation by the Streptomyces genus both in the total microbial community composition and in the microbial diversity related to GH families of predicted ORFs. Moreover, the functional clustering of the predicted ORFs showed a prevalence of poorly characterized genes, suggesting these lignocellulosic biomasses are potential sources of as yet unknown genes. 1.2%, 0.6% and 3.4% of the total ORFs detected in A. donax, E. camaldulensis and P. nigra, respectively, were putative Carbohydrate-Active Enzymes (CAZymes). Interestingly, the glycoside hydrolases abundance in P. nigra (1.8%) was higher than that detected in the other biomasses investigated in this study. Moreover, a high percentage of (hemi)cellulases with different activities and accessory enzymes (mannanases, polygalacturonases and feruloyl esterases) was detected, confirming that the three analyzed samples were a reservoir of diversified biocatalysts required for an effective lignocellulose saccharification.}, }
@article {pmid29660711, year = {2018}, author = {Kotoky, R and Rajkumari, J and Pandey, P}, title = {The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil.}, journal = {Journal of environmental management}, volume = {217}, number = {}, pages = {858-870}, doi = {10.1016/j.jenvman.2018.04.022}, pmid = {29660711}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; Hydrocarbons/*metabolism ; Microbiota ; Plant Roots ; *Rhizosphere ; Soil ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.}, }
@article {pmid29032502, year = {2018}, author = {Santoro, A and Ostan, R and Candela, M and Biagi, E and Brigidi, P and Capri, M and Franceschi, C}, title = {Gut microbiota changes in the extreme decades of human life: a focus on centenarians.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {75}, number = {1}, pages = {129-148}, doi = {10.1007/s00018-017-2674-y}, pmid = {29032502}, issn = {1420-9071}, mesh = {Aged ; Aged, 80 and over ; Aging/genetics/*physiology ; *Diet ; Female ; Gastrointestinal Microbiome/*physiology ; Genetics, Population ; Humans ; Longevity/genetics/*physiology ; Male ; }, abstract = {The gut microbiota (GM) is a complex, evolutionarily molded ecological system, which contributes to a variety of physiological functions. The GM is highly dynamic, being sensitive to environmental stimuli, and its composition changes over the host's entire lifespan. However, the basic question of how much these changes may be ascribed to variables such as population, diet, genetics and gender, and/or to the aging process per se is still largely unanswered. We argue that comparison among studies on centenarians-the best model of healthy aging and longevity-recruited from different geographical areas/populations (different genetics and dietary habits) can help to disentangle the contribution of aging and non-aging-related variables to GM remodeling with age. The current review focuses on the role of population, gender and host genetics as possible drivers of GM modification along the human aging process. The feedback impact of age-associated GM variation on the GM-brain axis and GM metabolomics is also discussed. We likewise address the role of GM in neurodegenerative diseases such as Parkinson's and Alzheimer's, and its possible therapeutic use, taking advantage of the fact that centenarians are characterized by an extreme (healthy) phenotype versus patients suffering from age-related pathologies. Finally, it is argued that longitudinal studies combining metagenomics sequencing and in-depth phylogenetic analysis with a comprehensive phenotypic characterization of centenarians and patients using up-to-date omics (metabolomics, transcriptomics and meta-transcriptomics) are urgently needed.}, }
@article {pmid28983638, year = {2018}, author = {Turroni, F and Milani, C and Duranti, S and Ferrario, C and Lugli, GA and Mancabelli, L and van Sinderen, D and Ventura, M}, title = {Bifidobacteria and the infant gut: an example of co-evolution and natural selection.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {75}, number = {1}, pages = {103-118}, doi = {10.1007/s00018-017-2672-0}, pmid = {28983638}, issn = {1420-9071}, mesh = {Bifidobacterium/genetics/*physiology ; Evolution, Molecular ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; Infant ; Microbial Interactions/genetics/*physiology ; Polysaccharides/metabolism ; Selection, Genetic ; Time Factors ; }, abstract = {Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut. Among the most abundant members of the infant microbiota are species belonging to the Bifidobacterium genus, which are believed to confer beneficial effects upon their host. Bifidobacteria may be acquired directly from the mother by vertical transmission and their persistence in the infant gut is associated with their saccharolytic activity toward glycans that are abundant in the infant gut. Here, we discuss the establishment of the infant gut microbiota and the contribution of bifidobacteria to this early life microbial consortium.}, }
@article {pmid28176868, year = {2017}, author = {Yergeau, E and Michel, C and Tremblay, J and Niemi, A and King, TL and Wyglinski, J and Lee, K and Greer, CW}, title = {Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42242}, doi = {10.1038/srep42242}, pmid = {28176868}, issn = {2045-2322}, mesh = {Arctic Regions ; Canada ; Databases, Genetic ; Geography ; Ice Cover/*microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {Climate change has resulted in an accelerated decline of Arctic sea ice since 2001 resulting in primary production increases and prolongation of the ice-free season within the Northwest Passage. The taxonomic and functional microbial community composition of the seawater and sea ice of the Canadian Arctic is not very well known. Bacterial communities from the bottom layer of sea ice cores and surface water from 23 locations around Cornwallis Island, NU, Canada, were extensively screened. The bacterial 16S rRNA gene was sequenced for all samples while shotgun metagenomics was performed on selected samples. Bacterial community composition showed large variation throughout the sampling area both for sea ice and seawater. Seawater and sea ice samples harbored significantly distinct microbial communities, both at different taxonomic levels and at the functional level. A key difference between the two sample types was the dominance of algae in sea ice samples, as visualized by the higher relative abundance of algae and photosynthesis-related genes in the metagenomic datasets and the higher chl a concentrations. The relative abundance of various OTUs and functional genes were significantly correlated with multiple environmental parameters, highlighting many potential environmental drivers and ecological strategies.}, }
@article {pmid28169321, year = {2017}, author = {Xu, J and Wei, Y and Jia, H and Xiao, L and Gong, D}, title = {A new perspective on studying burial environment before archaeological excavation: analyzing bacterial community distribution by high-throughput sequencing.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41691}, doi = {10.1038/srep41691}, pmid = {28169321}, issn = {2045-2322}, mesh = {*Archaeology ; Bacteria/classification/genetics ; Biodiversity ; *Burial ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; Microbiota ; Phylogeny ; Salinity ; Soil/chemistry ; *Soil Microbiology ; Water/chemistry ; }, abstract = {Burial conditions play a crucial role in archaeological heritage preservation. Especially, the microorganisms were considered as the leading causes which incurred degradation and vanishment of historic materials. In this article, we analyzed bacterial diversity and community structure from M1 of Wangshanqiao using 16 S rRNA gene amplicon sequencing. The results indicated that microbial communities in burial conditions were diverse among four different samples. The samples from the robber hole varied most obviously in community structure both in Alpha and Beta diversity. In addition, the dominant phylum in different samples were Proteobacteria, Actinobacteria and Bacteroidetes, respectively. Moreover, the study implied that historical materials preservation conditions had connections with bacterial community distribution. At the genus level, Acinetobacter might possess high ability in degrading organic culture heritage in burial conditions, while Bacteroides were associated closely with favorable preservation conditions. This method contributes to fetch information which would never recover after excavation, and it will help to explore microbial degradation on precious organic culture heritage and further our understanding of archaeological burial environment. The study also indicates that robbery has a serious negative impact on burial remains.}, }
@article {pmid28150710, year = {2017}, author = {Nguyen, D and Boberg, J and Cleary, M and Bruelheide, H and Hönig, L and Koricheva, J and Stenlid, J}, title = {Foliar fungi of Betula pendula: impact of tree species mixtures and assessment methods.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41801}, doi = {10.1038/srep41801}, pmid = {28150710}, issn = {2045-2322}, mesh = {Betula/classification/*microbiology ; Biodiversity ; Ecosystem ; Fungi/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Plant Leaves/microbiology ; }, abstract = {Foliar fungi of silver birch (Betula pendula) in an experimental Finnish forest were investigated across a gradient of tree species richness using molecular high-throughput sequencing and visual macroscopic assessment. We hypothesized that the molecular approach detects more fungal taxa than visual assessment, and that there is a relationship among the most common fungal taxa detected by both techniques. Furthermore, we hypothesized that the fungal community composition, diversity, and distribution patterns are affected by changes in tree diversity. Sequencing revealed greater diversity of fungi on birch leaves than the visual assessment method. One species showed a linear relationship between the methods. Species-specific variation in fungal community composition could be partially explained by tree diversity, though overall fungal diversity was not affected by tree diversity. Analysis of specific fungal taxa indicated tree diversity effects at the local neighbourhood scale, where the proportion of birch among neighbouring trees varied, but not at the plot scale. In conclusion, both methods may be used to determine tree diversity effects on the foliar fungal community. However, high-throughput sequencing provided higher resolution of the fungal community, while the visual macroscopic assessment detected functionally active fungal species.}, }
@article {pmid28139751, year = {2017}, author = {Jia, HR and Dai, PL and Geng, LL and Jack, CJ and Li, YH and Wu, YY and Diao, QY and Ellis, JD}, title = {No effect of Bt Cry1Ie toxin on bacterial diversity in the midgut of the Chinese honey bees, Apis cerana cerana (Hymenoptera, Apidae).}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41688}, doi = {10.1038/srep41688}, pmid = {28139751}, issn = {2045-2322}, mesh = {Animals ; Bacillus thuringiensis ; Bacterial Toxins/*pharmacology ; Bees/*drug effects/*microbiology ; *Biodiversity ; Cluster Analysis ; Gastrointestinal Microbiome/*drug effects ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cry1Ie protein derived from Bacillus thuringiensis (Bt) has been proposed as a promising candidate for the development of a new Bt-maize variety to control maize pests in China. We studied the response of the midgut bacterial community of Apis cerana cerana to Cry1Ie toxin under laboratory conditions. Newly emerged bees were fed one of the following treatments for 15 and 30 days: three concentrations of Cry1Ie toxin (20 ng/mL, 200 ng/mL, and 20 μg/mL) in sugar syrup, pure sugar syrup as a negative control and 48 ng/mL imidacloprid as a positive control. The relative abundance of 16S rRNA genes was measured by Quantitative Polymerase Chain Reaction and no apparent differences were found among treatments for any of these counts at any time point. Furthermore, the midgut bacterial structure and compositions were determined using high-throughput sequencing targeting the V3-V4 regions of the 16S rDNA. All core honey bee intestinal bacterial genera such as Lactobacillus, Bifidobacterium, Snodgrassella, and Gilliamella were detected, and no significant changes were found in the species diversity and richness for any bacterial taxa among treatments at different time points. These results suggest that Cry1Ie toxin may not affect gut bacterial communities of Chinese honey bees.}, }
@article {pmid28091525, year = {2017}, author = {Patrascu, O and Béguet-Crespel, F and Marinelli, L and Le Chatelier, E and Abraham, AL and Leclerc, M and Klopp, C and Terrapon, N and Henrissat, B and Blottière, HM and Doré, J and Béra-Maillet, C}, title = {A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40248}, doi = {10.1038/srep40248}, pmid = {28091525}, issn = {2045-2322}, support = {322820//European Research Council/International ; }, mesh = {Bacteroides/metabolism ; Carbohydrate Metabolism ; Carboxymethylcellulose Sodium/metabolism ; Chromosome Mapping ; Clostridiales/metabolism ; Dietary Fiber/*metabolism/*microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology ; Metagenome ; Metagenomics ; Xylans/metabolism ; }, abstract = {The digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres. Eleven positive clones revealed a broad range of CAZyme encoding genes from Bacteroides and Clostridiales species, as well as Polysaccharide Utilization Loci (PULs). The functional glycoside hydrolase genes were identified, and oligosaccharide break-down products examined from different polysaccharides including mixed-linkage β-glucans. CAZymes and PULs were also examined for their prevalence in human gut microbiome. Several clusters of genes of low prevalence in fecal microbiome suggested they belong to unidentified strains rather specifically established upstream the colon, in the ileum. Thus, the ileal mucosa-associated microbiota encompasses the enzymatic potential for PCW polysaccharide degradation in the small intestine.}, }
@article {pmid29439741, year = {2018}, author = {Xiong, W and Wang, Y and Sun, Y and Ma, L and Zeng, Q and Jiang, X and Li, A and Zeng, Z and Zhang, T}, title = {Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {34}, doi = {10.1186/s40168-018-0419-2}, pmid = {29439741}, issn = {2049-2618}, support = {31702290//the National Natural Science Foundation of China/International ; 31672608//the National Natural Science Foundation of China/International ; GRF7201/11E//Hong Kong/International ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*classification/drug effects/genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; Bifidobacterium/classification/drug effects/genetics/isolation &amp; purification ; Chickens ; Chlortetracycline/pharmacology ; *Drug Resistance, Bacterial ; Escherichia/classification/drug effects/genetics/isolation &amp; purification ; Feces/*microbiology ; Gene Regulatory Networks ; Klebsiella/classification/drug effects/genetics/isolation &amp; purification ; Metagenomics ; Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels.<br><br>RESULTS: The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline.<br><br>CONCLUSIONS: We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.}, }
@article {pmid29347966, year = {2018}, author = {Zhou, W and Gay, N and Oh, J}, title = {ReprDB and panDB: minimalist databases with maximal microbial representation.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {15}, doi = {10.1186/s40168-018-0399-2}, pmid = {29347966}, issn = {2049-2618}, support = {K22 AI119231/AI/NIAID NIH HHS/United States ; }, mesh = {Access to Information ; Algorithms ; Computational Biology/methods ; *Databases, Genetic ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*methods ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {BACKGROUND: Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes.<br><br>RESULTS: We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets.<br><br>CONCLUSIONS: reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.}, }
@article {pmid29298732, year = {2018}, author = {Luna, PN and Hasegawa, K and Ajami, NJ and Espinola, JA and Henke, DM and Petrosino, JF and Piedra, PA and Sullivan, AF and Camargo, CA and Shaw, CA and Mansbach, JM}, title = {The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {2}, doi = {10.1186/s40168-017-0385-0}, pmid = {29298732}, issn = {2049-2618}, support = {R01 AI-114552/NH/NIH HHS/United States ; UG3 OD-023253/NH/NIH HHS/United States ; R01 AI-108588/NH/NIH HHS/United States ; R01 AI108588/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; U01 AI-087881/NH/NIH HHS/United States ; }, mesh = {Bronchiolitis/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Hospitalization ; Humans ; Infant ; Longitudinal Studies ; Male ; Microbiota ; Nasal Cavity/*microbiology ; Nasopharynx/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Staphylococcus/classification/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: The airway microbiome is a subject of great interest for the study of respiratory disease. Anterior nare samples are more accessible than samples from deeper within the nasopharynx. However, the correlation between the microbiota found in the anterior nares and the microbiota found within the nasopharynx is unknown. We assessed the anterior nares and nasopharyngeal microbiota to determine (1) the relation of the microbiota from these two upper airway sites and (2) if associations were maintained between the microbiota from these two sites and two bronchiolitis severity outcomes.<br><br>RESULTS: Among 815 infants hospitalized at 17 US centers for bronchiolitis with optimal 16S rRNA gene sequence reads from both nasal swab and nasopharyngeal aspirate samples, there were strong intra-individual correlations in the microbial communities between the two sample types, especially relating to Haemophilus and Moraxella genera. By contrast, we found a high abundance of Staphylococcus genus in the nasal swabs-a pattern not found in the nasopharyngeal samples and not informative when predicting the dominant nasopharyngeal genera. While these disparities may have been due to sample processing differences (i.e., nasal swabs were mailed at ambient temperature to emulate processing of future parent collected swabs while nasopharyngeal aspirates were mailed on dry ice), a previously reported association between Haemophilus-dominant nasopharyngeal microbiota and the increased severity of bronchiolitis was replicated utilizing the nasal swab microbiota and the same outcome measures: intensive care use (adjusted OR 6.43; 95% CI 2.25-20.51; P < 0.001) and hospital length-of-stay (adjusted OR 4.31; 95% CI, 1.73-11.11; P = 0.002). Additionally, Moraxella-dominant nasopharyngeal microbiota was previously identified as protective against intensive care use, a result that was replicated when analyzing the nasal swab microbiota (adjusted OR 0.30; 95% CI, 0.11-0.64; P = 0.01).<br><br>CONCLUSIONS: While the microbiota of the anterior nares and the nasopharynx are distinct, there is considerable overlap between the bacterial community compositions from these two anatomic sites. Despite processing differences between the samples, these results indicate that microbiota severity associations from the nasopharynx are recapitulated in the anterior nares, suggesting that nasal swab samples not only are effective sample types, but also can be used to detect microbial risk markers.}, }
@article {pmid28323391, year = {2018}, author = {Martinez-Sañudo, I and Simonato, M and Squartini, A and Mori, N and Marri, L and Mazzon, L}, title = {Metagenomic analysis reveals changes of the Drosophila suzukii microbiota in the newly colonized regions.}, journal = {Insect science}, volume = {25}, number = {5}, pages = {833-846}, doi = {10.1111/1744-7917.12458}, pmid = {28323391}, issn = {1744-7917}, support = {613678//European Union's Seventh Framework Programme/ ; }, mesh = {*Animal Distribution ; Animals ; Bacteria/*classification ; China ; Drosophila/*microbiology ; Europe ; *Gastrointestinal Microbiome ; *Introduced Species ; Japan ; *Metagenome ; Metagenomics ; United States ; }, abstract = {The spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a highly polyphagous pest of a wide variety of wild or cultivated berry and stone fruit. Originating from Southeast Asia, it has recently invaded a wide range of regions in Europe and North America. It is well known that insect microbiotas may significantly influence several aspects of the host biology and play an important role in invasive species introduction into new areas. However, in spite of the great economic importance of D. suzukii, a limited attention has been given so far to its microbiota. In this study, we present the first in-depth characterization of gut bacterial diversity from field (native and invasive range) and lab-reared populations of this insect. The gut bacterial communities of field insects were dominated, regardless of their origin, by 2 families of the phylum Proteobacteria: Acetobacteraceae and Enterobacteriaceae, while Firmicutes, mainly represented by the family Staphylococcaceae, prevailed in lab-reared population. Locality was the most significant factor in shaping the microbiota of wild flies. Moreover, a negative correlation between diversity and abundance of Enterobacteriaceae and the time elapsed since the establishment of D. suzukii in a new region was observed. Altogether our results indicate that habitat, food resources as well as the colonization phase of a new region contribute to shape the bacterial communities of the invasive species which, in turn, by evolving more quickly, could influence host adaptation in a new environment.}, }
@article {pmid30356699, year = {2018}, author = {Weißbecker, C and Wubet, T and Lentendu, G and Kühn, P and Scholten, T and Bruelheide, H and Buscot, F}, title = {Experimental Evidence of Functional Group-Dependent Effects of Tree Diversity on Soil Fungi in Subtropical Forests.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2312}, doi = {10.3389/fmicb.2018.02312}, pmid = {30356699}, issn = {1664-302X}, abstract = {Deconvoluting the relative contributions made by specific biotic and abiotic drivers to soil fungal community compositions facilitates predictions about the functional responses of ecosystems to environmental changes, such as losses of plant diversity, but it is hindered by the complex interactions involved. Experimental assembly of tree species allows separation of the respective effects of plant community composition (biotic components) and soil properties (abiotic components), enabling much greater statistical power than can be achieved in observational studies. We therefore analyzed these contributions by assessing, via pyrotag sequencing of the internal transcribed spacer (ITS2) rDNA region, fungal communities in young subtropical forest plots included in a large experiment on the effects of tree species richness. Spatial variables and soil properties were the main drivers of soil fungal alpha and beta-diversity, implying strong early-stage environmental filtering and dispersal limitation. Tree related variables, such as tree community composition, significantly affected arbuscular mycorrhizal and pathogen fungal community structure, while differences in tree host species and host abundance affected ectomycorrhizal fungal community composition. At this early stage of the experiment, only a limited amount of carbon inputs (rhizodeposits and leaf litter) was being provided to the ecosystem due to the size of the tree saplings, and persisting legacy effects were observed. We thus expect to find increasing tree related effects on fungal community composition as forest development proceeds.}, }
@article {pmid29555111, year = {2018}, author = {Pandit, RJ and Hinsu, AT and Patel, SH and Jakhesara, SJ and Koringa, PG and Bruno, F and Psifidi, A and Shah, SV and Joshi, CG}, title = {Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {4}, pages = {374-385}, doi = {10.1016/j.syapm.2018.02.002}, pmid = {29555111}, issn = {1618-0984}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/*classification/genetics ; Cattle ; *Diet ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/genetics ; Rumen/*microbiology ; }, abstract = {Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.}, }
@article {pmid28134326, year = {2017}, author = {Liu, H and Carvalhais, LC and Schenk, PM and Dennis, PG}, title = {Effects of jasmonic acid signalling on the wheat microbiome differ between body sites.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41766}, doi = {10.1038/srep41766}, pmid = {28134326}, issn = {2045-2322}, mesh = {Biodiversity ; Biomass ; Cyclopentanes/*metabolism ; Metagenome ; Metagenomics/methods ; Microbiota/*genetics ; Oxylipins/*metabolism ; Plant Roots/metabolism/microbiology ; Plant Shoots/metabolism/microbiology ; Rhizosphere ; *Signal Transduction ; Soil Microbiology ; Triticum/genetics/*metabolism/*microbiology ; }, abstract = {Jasmonic acid (JA) signalling helps plants to defend themselves against necrotrophic pathogens and herbivorous insects and has been shown to influence the root microbiome of Arabidopsis thaliana. In this study, we determined whether JA signalling influences the diversity and functioning of the wheat (Triticum aestivum) microbiome and whether these effects are specific to particular parts of the plant. Activation of the JA pathway was achieved via exogenous application of methyl jasmonate and was confirmed by significant increases in the abundance of 10 JA-signalling-related gene transcripts. Phylogenetic marker gene sequencing revealed that JA signalling reduced the diversity and changed the composition of root endophytic but not shoot endophytic or rhizosphere bacterial communities. The total enzymatic activity and substrate utilisation profiles of rhizosphere bacterial communities were not affected by JA signalling. Our findings indicate that the effects of JA signalling on the wheat microbiome are specific to individual plant compartments.}, }
@article {pmid28134269, year = {2017}, author = {Zhou, X and Zhang, J and Gao, D and Gao, H and Guo, M and Li, L and Zhao, M and Wu, F}, title = {Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41502}, doi = {10.1038/srep41502}, pmid = {28134269}, issn = {2045-2322}, mesh = {Agriculture ; Biodiversity ; *Fungi/classification/genetics ; Helianthus/growth &amp; development/*microbiology ; Metagenome ; Metagenomics/methods ; *Soil Microbiology ; *Triticum/growth &amp; development/microbiology ; }, abstract = {Understanding soil microbial communities in agroecosystems has the potential to contribute to the improvement of agricultural productivity and sustainability. Effects of conversion from long-term wheat plantation to Jerusalem artichoke (JA) plantation on soil fungal communities were determined by amplicon sequencing of total fungal ITS regions. Quantitative PCR and PCR-denaturing gradient gel electrophoresis were also used to analyze total fungal and Trichoderma spp. ITS regions and Fusarium spp. Ef1α genes. Results showed that soil organic carbon was higher in the first cropping of JA and Olsen P was lower in the third cropping of JA. Plantation conversion changed soil total fungal and Fusarium but not Trichoderma spp. community structures and compositions. The third cropping of JA had the lowest total fungal community diversity and Fusarium spp. community abundance, but had the highest total fungal and Trichoderma spp. community abundances. The relative abundances of potential fungal pathogens of wheat were higher in the wheat field. Fungal taxa with plant growth promoting, plant pathogen or insect antagonistic potentials were enriched in the first and second cropping of JA. Overall, short-term conversion from wheat to JA plantation changed soil fungal communities, which is related to changes in soil organic carbon and Olsen P contents.}, }
@article {pmid29273717, year = {2017}, author = {Albanese, D and Donati, C}, title = {Strain profiling and epidemiology of bacterial species from metagenomic sequencing.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {2260}, doi = {10.1038/s41467-017-02209-5}, pmid = {29273717}, issn = {2041-1723}, mesh = {Bacteria/*genetics ; Bifidobacterium longum/genetics ; *Computational Biology ; Databases, Genetic ; Enterococcus faecalis/genetics ; Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Neisseria meningitidis/genetics ; Polymorphism, Single Nucleotide ; Propionibacterium acnes/genetics ; Staphylococcus aureus/genetics ; Staphylococcus epidermidis/genetics ; Streptococcus pneumoniae/genetics ; }, abstract = {Microbial communities are often composed by complex mixtures of multiple strains of the same species, characterized by a wide genomic and phenotypic variability. Computational methods able to identify, quantify and classify the different strains present in a sample are essential to fully exploit the potential of metagenomic sequencing in microbial ecology, with applications that range from the epidemiology of infectious diseases to the characterization of the dynamics of microbial colonization. Here we present a computational approach that uses the available genomic data to reconstruct complex strain profiles from metagenomic sequencing, quantifying the abundances of the different strains and cataloging them according to the population structure of the species. We validate the method on synthetic data sets and apply it to the characterization of the strain distribution of several important bacterial species in real samples, showing how its application provides novel insights on the structure and complexity of the microbiota.}, }
@article {pmid29950381, year = {2018}, author = {Jenior, ML and Leslie, JL and Young, VB and Schloss, PD}, title = {Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSphere.00261-18}, pmid = {29950381}, issn = {2379-5042}, mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage/adverse effects ; Cecum/*chemistry/*microbiology ; Clostridium Infections/*microbiology ; Clostridium difficile/*growth &amp; development ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Metabolomics ; Metagenomics ; Mice ; }, abstract = {Susceptibility to Clostridium difficile infection (CDI) is primarily associated with previous exposure to antibiotics, which compromise the structure and function of the gut bacterial community. Specific antibiotic classes correlate more strongly with recurrent or persistent C. difficile infection. As such, we utilized a mouse model of infection to explore the effect of distinct antibiotic classes on the impact that infection has on community-level transcription and metabolic signatures shortly following pathogen colonization and how those changes may associate with persistence of C. difficile Untargeted metabolomic analysis revealed that C. difficile infection had significantly larger impacts on the metabolic environment across cefoperazone- and streptomycin-pretreated mice, which became persistently colonized compared to clindamycin-pretreated mice, where infection quickly became undetectable. Through metagenome-enabled metatranscriptomics, we observed that transcripts for genes associated with carbon and energy acquisition were greatly reduced in infected animals, suggesting that those niches were instead occupied by C. difficile Furthermore, the largest changes in transcription were seen in the least abundant species, indicating that C. difficile may &quot;attack the loser&quot; in gut environments where sustained infection occurs more readily. Overall, our results suggest that C. difficile is able to restructure the nutrient-niche landscape in the gut to promote persistent infection.IMPORTANCEClostridium difficile has become the most common single cause of hospital-acquired infection over the last decade in the United States. Colonization resistance to the nosocomial pathogen is primarily provided by the gut microbiota, which is also involved in clearing the infection as the community recovers from perturbation. As distinct antibiotics are associated with different risk levels for CDI, we utilized a mouse model of infection with 3 separate antibiotic pretreatment regimens to generate alternative gut microbiomes that each allowed for C. difficile colonization but varied in clearance rate. To assess community-level dynamics, we implemented an integrative multi-omics approach that revealed that infection significantly changed many aspects of the gut community. The degree to which the community changed was inversely correlated with clearance during the first 6 days of infection, suggesting that C. difficile differentially modifies the gut environment to promote persistence. This is the first time that metagenome-enabled metatranscriptomics have been employed to study the behavior of a host-associated microbiota in response to an infection. Our results allow for a previously unseen understanding of the ecology associated with C. difficile infection and provide the groundwork for identification of context-specific probiotic therapies.}, }
@article {pmid29898983, year = {2018}, author = {Zhu, L and Yang, Z and Yao, R and Xu, L and Chen, H and Gu, X and Wu, T and Yang, X}, title = {Potential Mechanism of Detoxification of Cyanide Compounds by Gut Microbiomes of Bamboo-Eating Pandas.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSphere.00229-18}, pmid = {29898983}, issn = {2379-5042}, mesh = {Ailuridae/*microbiology/*physiology ; Animals ; Bacteria/classification/genetics/metabolism ; Biotransformation ; Cyanides/*metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; Ursidae/*microbiology/*physiology ; }, abstract = {Gut microbes can enhance the ability of hosts to consume secondary plant compounds and, therefore, expand the dietary niche breadth of mammalian herbivores. The giant and red pandas are bamboo-eating specialists within the mammalian order Carnivora. Bamboo contains abundant plant secondary metabolites (e.g., cyanide-containing compounds). However, Carnivora species, including the giant panda, have deficient levels of rhodanese (one of the essential cyanide detoxification enzymes) in their tissues compared with the same tissues of herbivores. Here, we make a comparative analysis of 94 gut metagenomes, including 25 from bamboo-eating pandas (19 from giant pandas and 6 from red pandas), 30 from Père David's deer, and 39 from published data for other mammals. The bamboo-eating pandas' gut microbiomes had some common features, such as high proportions of Pseudomonas bacteria. The results revealed that bamboo-eating pandas' gut microbiomes were significantly enriched in putative genes coding for enzymes related to cyanide degradation (e.g., rhodanese) compared with the gut microbiomes of typical herbivorous mammals, which might have coevolved with their special bamboo diets. The enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet.IMPORTANCE The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), two obligate bamboo feeders, have distinct phylogenetic positions in the order Carnivora. Bamboo is extraordinarily rich in plant secondary metabolites, such as allied phenolic and polyphenolic compounds and even toxic cyanide compounds. Here, the enrichment of putative cyanide-digesting gut microbes, in combination with adaptations related to morphology (e.g., pseudothumbs) and genomic signatures, show that the giant panda and red panda have evolved some common traits to adapt to their bamboo diet. Thus, here is another story of diet-driven gut microbiota in nature.}, }
@article {pmid29848762, year = {2018}, author = {Garcia, SL and Buck, M and Hamilton, JJ and Wurzbacher, C and Grossart, HP and McMahon, KD and Eiler, A}, title = {Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSphere.00202-18}, pmid = {29848762}, issn = {2379-5042}, mesh = {Bacteria/*metabolism ; Fresh Water/*microbiology ; *Metabolism ; *Microbial Consortia ; Microbial Interactions ; }, abstract = {Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.}, }
@article {pmid29687353, year = {2018}, author = {Allali, I and Boukhatem, N and Bouguenouch, L and Hardi, H and Boudouaya, HA and Cadenas, MB and Ouldim, K and Amzazi, S and Azcarate-Peril, MA and Ghazal, H}, title = {Gut microbiome of Moroccan colorectal cancer patients.}, journal = {Medical microbiology and immunology}, volume = {207}, number = {3-4}, pages = {211-225}, doi = {10.1007/s00430-018-0542-5}, pmid = {29687353}, issn = {1432-1831}, mesh = {Adult ; Aged ; Cluster Analysis ; Colorectal Neoplasms/*complications/*microbiology ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Fatty Acids/analysis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Morocco ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Surveys and Questionnaires ; Young Adult ; }, abstract = {Although colorectal cancer is the third leading cause of death in Morocco, there are no studies of the microbiome changes associated with the disease in the Moroccan population. The aim of our study was to compare the stool microbiome of Moroccan cancer patients with healthy individuals. We analyzed the microbiome composition of samples from 11 CRC patients and 12 healthy individuals by 16S rRNA amplicon sequencing. Principal coordinate analysis of samples revealed defined cancer versus healthy clusters. Our findings showed that cancer samples had higher proportions of Firmicutes (T = 50.5%; N = 28.4%; p = 0.04), specifically of Clostridia (T = 48.3%; N = 19.0%; p = 0.002), and Fusobacteria (T = 0.1%; N = 0.0%; p = 0.02), especially of Fusobacteriia (T = 0.1%; N = 0.0%; p = 0.02), while Bacteroidetes were enriched in healthy samples (T = 35.1%; N = 62.8%; p = 0.06), particularly the class Bacteroidia (T = 35.1%; N = 62.6%; p = 0.06). Porphyromonas, Clostridium, Ruminococcus, Selenomonas, and Fusobacterium were significantly overrepresented in diseased patients, similarly to other studies. Predicted functional information showed that bacterial motility proteins, flagellar assembly, and fatty acid biosynthesis metabolism were significantly overrepresented in cancer patients, while amino acid metabolism and glycan biosynthesis were overrepresented in controls. This suggests that involvement of these functional metagenomes is similar and relevant in the carcinogenesis process, independent of the origin of the samples. Results from this study allowed identification of bacterial taxa relevant to the Moroccan population and encourages larger studies to facilitate population-directed therapeutic approaches.}, }
@article {pmid29079861, year = {2018}, author = {Velásquez-Mejía, EP and de la Cuesta-Zuluaga, J and Escobar, JS}, title = {Impact of DNA extraction, sample dilution, and reagent contamination on 16S rRNA gene sequencing of human feces.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {1}, pages = {403-411}, doi = {10.1007/s00253-017-8583-z}, pmid = {29079861}, issn = {1432-0614}, mesh = {DNA/genetics/*isolation &amp; purification ; *DNA Contamination ; DNA, Bacterial/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Indicators and Reagents ; Metagenomics/methods ; Microbial Consortia/genetics ; Microbiota/genetics ; RNA, Ribosomal, 16S/chemistry/*genetics ; Sequence Analysis, DNA ; }, abstract = {Culture-independent methods have granted the possibility to study microbial diversity in great detail, but technical issues pose a threat to the accuracy of new findings. Biases introduced during DNA extraction can result in erroneous representations of the microbial community, particularly in samples with low microbial biomass. We evaluated the DNA extraction method, initial sample biomass, and reagent contamination on the assessment of the human gut microbiota. Fecal samples of 200 mg were subjected to 1:10 serial dilutions; total DNA was obtained using two commercial kits and the microbiota assessed by 16S ribosomal RNA (rRNA) gene sequencing. In addition, we sequenced multiple technical controls. The two kits were efficient in extracting DNA from samples with as low as 2 mg of feces. However, in instances of lower biomass, only one kit performed well. The number of reads from negative controls was negligible. Both DNA extraction kits allowed inferring microbial consortia with similar membership but different abundances. Furthermore, we found differences in the taxonomic profile of the microbial community. Unexpectedly, the effect of sample dilution was moderate and did not introduce severe bias into the microbial inference. Indeed, the microbiota inferred from fecal samples was distinguishable from that of negative controls. In most cases, samples as low as 2 mg did not result in a dissimilar representation of the microbial community compared with the undiluted sample. Our results indicate that the gut microbiota inference is not much affected by contamination with laboratory reagents but largely impacted by the protocol to extract DNA.}, }
@article {pmid27530840, year = {2016}, author = {Jitwasinkul, T and Suriyaphol, P and Tangphatsornruang, S and Hansen, MA and Hansen, LH and Sørensen, SJ and Permpikul, C and Rongrungruang, Y and Tribuddharat, C}, title = {Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients.}, journal = {Journal of global antimicrobial resistance}, volume = {6}, number = {}, pages = {57-66}, doi = {10.1016/j.jgar.2016.03.001}, pmid = {27530840}, issn = {2213-7173}, mesh = {Animals ; Anti-Bacterial Agents ; Cattle ; Drug Resistance, Multiple, Bacterial/*genetics ; *Gastrointestinal Microbiome ; *Genes, Bacterial ; Humans ; Inpatients ; Metagenomics ; Microbial Sensitivity Tests ; Plasmids/*genetics ; Sequence Analysis, DNA ; Thailand ; }, abstract = {Antibiotic resistance genes are rapidly spread between pathogens and the normal flora, with plasmids playing an important role in their circulation. This study aimed to investigate antibiotic resistance plasmids in the gut microbiome of hospitalised patients. Stool samples were collected from seven inpatients at Siriraj Hospital (Bangkok, Thailand) and were compared with a sample from a healthy volunteer. Plasmids from the gut microbiomes extracted from the stool samples were subjected to high-throughput DNA sequencing (GS Junior). Newbler-assembled DNA reads were categorised into known and unknown sequences (using >80% alignment length as the cut-off), and ResFinder was used to classify the antibiotic resistance gene pools. Plasmid replicon modules were used for plasmid typing. Forty-six genes conferring resistance to several classes of antibiotics were identified in the stool samples. Several antibiotic resistance genes were shared by the patients; interestingly, most were reported previously in food animals and healthy humans. Four antibiotic resistance genes were found in the healthy subject. One gene (aph3-III) was identified in the patients and the healthy subject and was related to that in cattle. Uncommon genes of hospital origin such as blaTEM-124-like and fosA, which confer resistance to extended-spectrum β-lactams and fosfomycin, respectively, were identified. The resistance genes did not match the patients' drug treatments. In conclusion, several plasmid types were identified in the gut microbiome; however, it was difficult to link these to the antibiotic resistance genes identified. That the antibiotic resistance genes came from hospital and community environments is worrying.}, }
@article {pmid29934497, year = {2018}, author = {Ji, Y and Zhang, F and Zhang, R and Shen, Y and Liu, L and Wang, J and Yang, J and Tang, Q and Xun, J and Qi, T and Wang, Z and Song, W and Tang, Y and Chen, J and Lu, H}, title = {Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count.}, journal = {Emerging microbes &amp; infections}, volume = {7}, number = {1}, pages = {113}, doi = {10.1038/s41426-018-0117-y}, pmid = {29934497}, issn = {2222-1751}, support = {81571977//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Adult ; Antiretroviral Therapy, Highly Active ; Biodiversity ; Biomarkers ; *CD4 Lymphocyte Count ; CD4-CD8 Ratio ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome/drug effects ; HIV Infections/drug therapy/*immunology/virology ; HIV-1/*immunology ; Humans ; Male ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Viral Load ; }, abstract = {The roles of immunodeficiency and combined antiretroviral therapy (cART) in shaping the gut microbiota in HIV-1-infected subjects (HISs) have not been described thoroughly by time-series investigations. In this study, 36 antiretroviral-naïve HISs were enrolled to prospectively assess alterations in the fecal microbiota and plasma markers of microbial translocation and inflammation with cART. At baseline, the species α-diversity of the fecal microbiota was significantly lower in HISs with a CD4+ T cell count <300/mm3 than in HISs with a CD4+ T cell count >300/mm3 (Shannon index: Median 2.557 vs. 2.981, P = 0.006; Simpson index: Median 0.168 vs. 0.096, P = 0.004). Additionally, the baseline α-diversity indices correlated with CD4+ T cell counts (Shannon index: r = 0.474, P = 0.004; Simpson index: r = -0.467, P = 0.004) and the specific plasma biomarkers for microbial translocation and inflammation. After cART introduction, the species α-diversity of fecal microbiota in HISs with CD4+ T cell counts <300/mm3 was significantly restored (Shannon index: Median 2.557 vs. 2.791, P = 0.007; Simpson index: Median 0.168 vs. 0.112, P = 0.004), while the variances were insignificant among HISs with CD4+ T cell counts >300/mm3 (Shannon index: Median 2.981 vs. 2.934, P = 0.179; Simpson index: Median 0.096 vs. 0.119, P = 0.082). Meanwhile, with cART introduction, alterations in the gut microbial composition were more significant in the subgroup with CD4+ T cell counts >300/mm3, corresponding to increases in the specific plasma inflammatory markers. These findings implicated the interactive roles of immunodeficiency and cART for affecting gut microbiota in HIV-1-infected individuals, providing new insights into intestinal microbiome dysbiosis related to HIV-1 infection.}, }
@article {pmid29800328, year = {2018}, author = {Birkl, P and Bharwani, A and Kjaer, JB and Kunze, W and McBride, P and Forsythe, P and Harlander-Matauschek, A}, title = {Differences in cecal microbiome of selected high and low feather-pecking laying hens.}, journal = {Poultry science}, volume = {97}, number = {9}, pages = {3009-3014}, doi = {10.3382/ps/pey167}, pmid = {29800328}, issn = {1525-3171}, mesh = {*Aggression ; Animals ; Bacteria/classification ; Cecum/*microbiology ; Chickens/genetics/*microbiology/*physiology ; Feathers ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Selection, Genetic ; Sequence Analysis, RNA/veterinary ; }, abstract = {In mammals, it has become increasingly clear that the gut microbiota influences not only gastrointestinal physiology but also modulates behavior. In domestic birds, ceca have the greatest gastrointestinal microbial population. Feather-pecking (FP) behavior in laying hens is one of the most important unsolved behavioral issues in modern agriculture. The aim of the present study was to assess the cecal microbial community of divergently selected high (HFP; n = 20) and low (LFP; n = 20) feather-pecking birds at 60 wk of age. The cecal samples were subjected to community profiling of 16S rRNA and in silico metagenomics using a modified bar-coded Illumina sequencing method on a MiSeq Illumina sequencer. Our results revealed that compared to HFP birds, LFP birds are characterized by an increased overall microbial diversity (beta diversity) shown by a difference in the Bray-Curtis index (R2 = 0.171, P < 0.05). Furthermore, operational taxonomic unit comparisons showed an increased presence of Clostridiae and decreased presence of Lactobaccillacae in HFP birds when compared to LFP birds (False Discovery Rate < 0.05, Mann-Whitney comparisons). Our data indicate that there may be differences in the cecal profile between these 2 lines of laying hens. More research, building on this first study using sequencing technology for profiling the chicken cecal microbiome, will be needed in order to reveal if and how there exists a functional link between the performance of FP and the cecal microbial community.}, }
@article {pmid28094284, year = {2017}, author = {Murphy, K and Curley, D and O'Callaghan, TF and O'Shea, CA and Dempsey, EM and O'Toole, PW and Ross, RP and Ryan, CA and Stanton, C}, title = {The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40597}, doi = {10.1038/srep40597}, pmid = {28094284}, issn = {2045-2322}, mesh = {Biodiversity ; Feces/*microbiology ; Humans ; Infant ; Infant, Newborn ; Metagenome ; Metagenomics/methods ; *Microbiota ; Milk, Human/*microbiology ; Pilot Projects ; }, abstract = {Human milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70-88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine.}, }
@article {pmid29028897, year = {2018}, author = {Guo, X and Li, Z and Yao, Q and Mueller, RS and Eng, JK and Tabb, DL and Hervey, WJ and Pan, C}, title = {Sipros Ensemble improves database searching and filtering for complex metaproteomics.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {5}, pages = {795-802}, doi = {10.1093/bioinformatics/btx601}, pmid = {29028897}, issn = {1367-4811}, abstract = {Motivation: Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased discrimination of true identifications from false identifications by database searching and filtering algorithms in metaproteomics.<br><br>Results: Sipros Ensemble was developed here for metaproteomics using an ensemble approach. Three diverse scoring functions from MyriMatch, Comet and the original Sipros were incorporated within a single database searching engine. Supervised classification with logistic regression was used to filter database searching results. Benchmarking with soil and marine microbial communities demonstrated a higher number of peptide and protein identifications by Sipros Ensemble than MyriMatch/Percolator, Comet/Percolator, MS-GF+/Percolator, Comet &amp; MyriMatch/iProphet and Comet &amp; MyriMatch &amp; MS-GF+/iProphet. Sipros Ensemble was computationally efficient and scalable on supercomputers.<br><br>Freely available under the GNU GPL license at http://sipros.omicsbio.org.<br><br>Contact: cpan@utk.edu.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30325092, year = {2018}, author = {Zhang, SY and Tsementzi, D and Hatt, JK and Bivins, A and Khelurkar, N and Brown, J and Tripathi, SN and Konstantinidis, KT}, title = {Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14439}, pmid = {30325092}, issn = {1462-2920}, abstract = {Little is known about microbial communities in the Ganges River, India and how they respond to intensive anthropogenic inputs. Here we applied shotgun metagenomics sequencing to study microbial community dynamics and function in planktonic samples collected along a ~700 km river transect, including urban cities and rural settings in upstream waters, before and after the monsoon rainy season. Our results showed that 11-32% of the microbes represented terrestrial, sewage and human inputs (allochthonous). Sewage inputs significantly contributed to the higher abundance, by 13-fold of human gut microbiome (HG) associated sequences and 2-fold of antibiotic resistance genes (ARGs) in the Ganges relative to other riverine ecosystems in Europe, North and South America. Metagenome-assembled genome sequences (MAGs) representing allochthonous populations were detectable and tractable across the river after 1-2 days of (downstream) transport (>200 km apart). Only ~8% of these MAGs were abundant in U.S. freshwater ecosystems, revealing distinct biodiversity for the Ganges. Microbial communities in the rainy season exhibited increased alpha-diversity and spatial heterogeneity and showed significantly weaker distance-decay patterns compared to the dry season. These results advance our understanding of the Ganges microbial communities and how they respond to anthropogenic pollution. This article is protected by copyright. All rights reserved.}, }
@article {pmid29524068, year = {2018}, author = {Wang, C and Li, Q and Li, J}, title = {Gut microbiota and its implications in small bowel transplantation.}, journal = {Frontiers of medicine}, volume = {12}, number = {3}, pages = {239-248}, doi = {10.1007/s11684-018-0617-0}, pmid = {29524068}, issn = {2095-0225}, mesh = {Biomarkers ; *Gastrointestinal Microbiome ; Graft Rejection/*immunology ; Humans ; Immunity, Mucosal ; Intestine, Small/*microbiology/*transplantation ; Metagenomics ; Transplantation Tolerance/*immunology ; }, abstract = {The gut microbiota is mainly composed of a diverse population of commensal bacterial species and plays a pivotal role in the maintenance of intestinal homeostasis, immune modulation and metabolism. The influence of the gut microbiota on solid organ transplantation has recently been recognized. In fact, several studies indicated that acute and chronic allograft rejection in small bowel transplantation (SBT) is closely associated with the alterations in microbial patterns in the gut. In this review, we focused on the recent findings regarding alterations in the microbiota following SBTand the potential roles of these alterations in the development of acute and chronic allograft rejection. We also reviewed important advances with respect to the interplays between the microbiota and host immune systems in SBT. Furthermore, we explored the potential of the gut microbiota as a microbial marker and/or therapeutic target for the predication and intervention of allograft rejection and chronic dysfunction. Given that current research on the gut microbiota has become increasingly sophisticated and comprehensive, large cohort studies employing metagenomic analysis and multivariate linkage should be designed for the characterization of host-microbe interaction and causality between microbiota alterations and clinical outcomes in SBT. The findings are expected to provide valuable insights into the role of gut microbiota in the development of allograft rejection and other transplant-related complications and introduce novel therapeutic targets and treatment approaches in clinical practice.}, }
@article {pmid29433401, year = {2018}, author = {Alex, CE and Kubiski, SV and Li, L and Sadeghi, M and Wack, RF and McCarthy, MA and Pesavento, JB and Delwart, E and Pesavento, PA}, title = {Amdoparvovirus Infection in Red Pandas (Ailurus fulgens).}, journal = {Veterinary pathology}, volume = {55}, number = {4}, pages = {552-561}, doi = {10.1177/0300985818758470}, pmid = {29433401}, issn = {1544-2217}, mesh = {Ailuridae/*virology ; Animals ; Endangered Species ; Feces/virology ; Female ; *Genetic Variation ; Genome, Viral/*genetics ; In Situ Hybridization/veterinary ; Male ; Metagenomics ; Microscopy, Electron/veterinary ; Parvoviridae Infections/diagnostic imaging/pathology/*veterinary/virology ; Parvovirinae/genetics/*isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Virus Shedding ; }, abstract = {Aleutian mink disease virus is the type species in the genus Amdoparvovirus, and in mink and other Mustelidae can cause either subclinical disease or fatal chronic immune stimulation and immune complex disease. The authors describe a novel amdoparvovirus in the endangered red panda (Ailurus fulgens), discovered using viral metagenomics. The authors analyzed the prevalence, tissue distribution, and disease association by PCR, in situ hybridization, electron microscopy, and histology in a group of 6 red pandas from a single zoological collection. The study incorporates a fecal shedding survey and analysis of tissues from 4 necropsied animals over a 12-year span. The tentatively named red panda amdoparvovirus (RpAPV) was detected in the feces and/or tissues of all animals tested. At necropsy of 1 geriatric animal, infection was associated with pyogranulomatous peritonitis, pancreatitis, and myocarditis. Other animals had detectable low-level viral nucleic acid in lymph nodes and both oral and intestinal epithelium at the time of necropsy. Full-length genome sequences of RpAPV strains from 2 animals had 12% sequence divergence, demonstrating genetic diversity even among in-contact animals. RpAPV is a persistent infection in this cohort of red pandas, and has variable clinical expression.}, }
@article {pmid29346588, year = {2018}, author = {Cridland, JM and Ramirez, SR and Dean, CA and Sciligo, A and Tsutsui, ND}, title = {Genome Sequencing of Museum Specimens Reveals Rapid Changes in the Genetic Composition of Honey Bees in California.}, journal = {Genome biology and evolution}, volume = {10}, number = {2}, pages = {458-472}, doi = {10.1093/gbe/evy007}, pmid = {29346588}, issn = {1759-6653}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bees/*genetics ; California ; Chromosome Mapping ; *Evolution, Molecular ; Genetics, Population ; *Genome, Insect ; Introduced Species ; Metagenomics ; Pollination ; Polymorphism, Single Nucleotide ; Population Dynamics ; }, abstract = {The western honey bee, Apis mellifera, is an enormously influential pollinator in both natural and managed ecosystems. In North America, this species has been introduced numerous times from a variety of different source populations in Europe and Africa. Since then, feral populations have expanded into many different environments across their broad introduced range. Here, we used whole genome sequencing of historical museum specimens and newly collected modern populations from California (USA) to analyze the impact of demography and selection on introduced populations during the past 105 years. We find that populations from both northern and southern California exhibit pronounced genetic changes, but have changed in different ways. In northern populations, honey bees underwent a substantial shift from western European to eastern European ancestry since the 1960s, whereas southern populations are dominated by the introgression of Africanized genomes during the past two decades. Additionally, we identify an isolated island population that has experienced comparatively little change over a large time span. Fine-scale comparison of different populations and time points also revealed SNPs that differ in frequency, highlighting a number of genes that may be important for recent adaptations in these introduced populations.}, }
@article {pmid29242367, year = {2017}, author = {Costea, PI and Coelho, LP and Sunagawa, S and Munch, R and Huerta-Cepas, J and Forslund, K and Hildebrand, F and Kushugulova, A and Zeller, G and Bork, P}, title = {Subspecies in the global human gut microbiome.}, journal = {Molecular systems biology}, volume = {13}, number = {12}, pages = {960}, pmid = {29242367}, issn = {1744-4292}, mesh = {Escherichia coli/physiology ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; *Microbiota/genetics ; Phenotype ; Phylogeography ; Species Specificity ; }, abstract = {Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies-specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro-inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.}, }
@article {pmid28079128, year = {2017}, author = {Jing, G and Sun, Z and Wang, H and Gong, Y and Huang, S and Ning, K and Xu, J and Su, X}, title = {Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40371}, doi = {10.1038/srep40371}, pmid = {28079128}, issn = {2045-2322}, support = {R34 AA021502/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; Base Sequence ; Biodiversity ; Biomarkers/metabolism ; Child ; Computer Simulation ; Databases, Genetic ; Humans ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Time Factors ; }, abstract = {The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing. Application of Parallel-META 3 on 5,337 samples with 1,117,555,208 sequences from diverse studies and platforms showed it could produce similar results as QIIME and PICRUSt with much faster speed and lower memory usage, which demonstrates its ability to unravel the taxonomical and functional dynamics patterns across large datasets and elucidate ecological links between microbiome and the environment. Parallel-META 3 is implemented in C/C++ and R, and integrated into an executive package for rapid installation and easy access under Linux and Mac OS X. Both binary and source code packages are available at http://bioinfo.single-cell.cn/parallel-meta.html.}, }
@article {pmid30308887, year = {2019}, author = {Coble, AA and Flinders, CA and Homyack, JA and Penaluna, BE and Cronn, RC and Weitemier, K}, title = {eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications.}, journal = {The Science of the total environment}, volume = {649}, number = {}, pages = {1157-1170}, doi = {10.1016/j.scitotenv.2018.08.370}, pmid = {30308887}, issn = {1879-1026}, abstract = {Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our objectives are to describe potential applications of eDNA across the wood products supply chain extending from regenerating forests, harvesting, and wood transport, to manufacturing facilities, and to review the current state of the science in this context. To meet our second objective, we summarize the taxa examined with targeted (PCR, qPCR or ddPCR) or metagenomic eDNA methods (eDNA metabarcoding), evaluate how estimated species richness compares between traditional field sampling and eDNA metabarcoding approaches, and compare the geographical representation of prior eDNA studies in freshwater ecosystems to global wood baskets. Potential applications of eDNA include evaluating the effects of forestry and forest manufacturing activities on aquatic biota, delineating fish-bearing versus non fish-bearing reaches, evaluating effectiveness of constructed road crossings for freshwater organism passage, and determining the presence of at-risk species. Studies using targeted eDNA approaches focused on fish, amphibians, and invertebrates, while metagenomic studies focused on fish, invertebrates, and microorganisms. Rare, threatened, or endangered species received the least attention in targeted eDNA research, but are arguably of greatest interest to sustainable forestry and forest manufacturing that seek to preserve freshwater biodiversity. Ultimately, using eDNA methods will enable forestry and forest manufacturing managers to have data-driven prioritization for conservation actions for all freshwater species.}, }
@article {pmid29476620, year = {2018}, author = {Chappell, CR and Fukami, T}, title = {Nectar yeasts: a natural microcosm for ecology.}, journal = {Yeast (Chichester, England)}, volume = {35}, number = {6}, pages = {417-423}, doi = {10.1002/yea.3311}, pmid = {29476620}, issn = {1097-0061}, mesh = {Animals ; Bacteria ; Biota ; Flowers ; Models, Biological ; *Plant Nectar ; Pollination ; *Social Behavior ; *Social Environment ; *Yeasts ; }, abstract = {The species of yeasts that colonize floral nectar can modify the mutualistic relationships between plants and pollinators by changing the chemical properties of nectar. Recent evidence supporting this possibility has led to increased interest among ecologists in studying these fungi as well as the bacteria that interact with them in nectar. Although not fully explored, nectar yeasts also constitute a promising natural microcosm that can be used to facilitate development of general ecological theory. We discuss the methodological and conceptual advantages of using nectar yeasts from this perspective, including simplicity of communities, tractability of dispersal, replicability of community assembly, and the ease with which the mechanisms of species interactions can be studied in complementary experiments conducted in the field and the laboratory. To illustrate the power of nectar yeasts as a study system, we discuss several topics in community ecology, including environmental filtering, priority effects, and metacommunity dynamics. An exciting new direction is to integrate metagenomics and comparative genomics into nectar yeast research to address these fundamental ecological topics.}, }
@article {pmid29773467, year = {2018}, author = {Daliri, EB and Tango, CN and Lee, BH and Oh, DH}, title = {Human microbiome restoration and safety.}, journal = {International journal of medical microbiology : IJMM}, volume = {308}, number = {5}, pages = {487-497}, doi = {10.1016/j.ijmm.2018.05.002}, pmid = {29773467}, issn = {1618-0607}, mesh = {Anti-Bacterial Agents ; Bacteria/classification/isolation &amp; purification ; Diet ; Dysbiosis/*therapy ; Fecal Microbiota Transplantation/*adverse effects/methods ; Gastrointestinal Microbiome/*physiology ; Humans ; Probiotics/*administration &amp; dosage ; }, abstract = {The human gut microbiome consists of many bacteria which are in symbiotic relationship with human beings. The gut microbial metabolism, as well as the microbial-host co-metabolism, has been found to greatly influence health and disease. Factors such as diet, antibiotic use and lifestyle have been associated with alterations in the gut microbial community and may result in several pathological conditions. For this reason, several strategies including fecal microbiota transplant and probiotic administration have been applied and proven to be feasible and effective in restoring the gut microbiota in humans. Yet, safety concerns such as potential health risks that may arise from such interventions and how these strategies are regulated need to be addressed. Also, it will be important to know if these microbiome restoration strategies can have a profound impact on health. This review provides an overview of our current knowledge of the microbiome restoration strategies and safety issues on how these strategies are regulated.}, }
@article {pmid29588360, year = {2018}, author = {Corvelo, A and Clarke, WE and Robine, N and Zody, MC}, title = {taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time.}, journal = {Genome research}, volume = {28}, number = {5}, pages = {751-758}, doi = {10.1101/gr.225276.117}, pmid = {29588360}, issn = {1549-5469}, mesh = {Bacteria/classification/genetics ; Computational Biology/*methods ; Databases, Nucleic Acid ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Reproducibility of Results ; Rivers/microbiology ; *Software ; Species Specificity ; Water Microbiology ; }, abstract = {High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classification tool. Using a combination of simulated and real metagenomics data sets, we demonstrate that taxMaps is more sensitive and more precise than widely used taxonomic classifiers and is capable of delivering classification accuracy comparable to that of BLASTN, but at up to three orders of magnitude less computational cost.}, }
@article {pmid29083504, year = {2018}, author = {Puri, P and Liangpunsakul, S and Christensen, JE and Shah, VH and Kamath, PS and Gores, GJ and Walker, S and Comerford, M and Katz, B and Borst, A and Yu, Q and Kumar, DP and Mirshahi, F and Radaeva, S and Chalasani, NP and Crabb, DW and Sanyal, AJ and , }, title = {The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis.}, journal = {Hepatology (Baltimore, Md.)}, volume = {67}, number = {4}, pages = {1284-1302}, doi = {10.1002/hep.29623}, pmid = {29083504}, issn = {1527-3350}, support = {U01 AA021883/AA/NIAAA NIH HHS/United States ; U01 AA021840/AA/NIAAA NIH HHS/United States ; R01 AA021171/AA/NIAAA NIH HHS/United States ; U01 AA021788/AA/NIAAA NIH HHS/United States ; K23 AA021179/AA/NIAAA NIH HHS/United States ; U01 AA021891/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; Alcohol Drinking/adverse effects ; DNA, Bacterial/*blood/genetics ; Endotoxins/blood ; Female ; Hepatitis, Alcoholic/*microbiology ; Humans ; Liver/microbiology/pathology ; Liver Diseases, Alcoholic/*microbiology ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; Monocytes/pathology ; }, abstract = {Intestinal dysbiosis is implicated in alcoholic hepatitis (AH). However, changes in the circulating microbiome, its association with the presence and severity of AH, and its functional relevance in AH is unknown. Qualitative and quantitative assessment of changes in the circulating microbiome were performed by sequencing bacterial DNA in subjects with moderate AH (MAH) (n = 18) or severe AH (SAH) (n = 19). These data were compared with heavy drinking controls (HDCs) without obvious liver disease (n = 19) and non-alcohol-consuming controls (NACs, n = 20). The data were related to endotoxin levels and markers of monocyte activation. Linear discriminant analysis effect size (LEfSe) analysis, inferred metagenomics, and predictive functional analysis using PICRUSt were performed. There was a significant increase in 16S copies/ng DNA both in MAH (P < 0.01) and SAH (P < 0.001) subjects. Compared with NACs, the relative abundance of phylum Bacteroidetes was significantly decreased in HDCs, MAH, and SAH (P < 0.001). In contrast, all alcohol-consuming groups had enrichment with Fusobacteria; this was greatest for HDCs and decreased progressively in MAH and SAH. Subjects with SAH had significantly higher endotoxemia (P = 0.01). Compared with alcohol-consuming groups, predictive functional metagenomics indicated an enrichment of bacteria with genes related to methanogenesis and denitrification. Furthermore, both HDCs and SAH showed activation of a type III secretion system that has been linked to gram-negative bacterial virulence. Metagenomics in SAH versus NACs predicted increased isoprenoid synthesis via mevalonate and anthranilate degradation, known modulators of gram-positive bacterial growth and biofilm production, respectively.<br><br>CONCLUSION: Heavy alcohol consumption appears to be the primary driver of changes in the circulating microbiome associated with a shift in its inferred metabolic functions. (Hepatology 2018;67:1284-1302).}, }
@article {pmid28232956, year = {2017}, author = {Marbouty, M and Baudry, L and Cournac, A and Koszul, R}, title = {Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay.}, journal = {Science advances}, volume = {3}, number = {2}, pages = {e1602105}, doi = {10.1126/sciadv.1602105}, pmid = {28232956}, issn = {2375-2548}, mesh = {Animals ; *Bacteria/genetics/metabolism/virology ; *Bacteriophages/genetics/metabolism ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; *Genome, Viral ; Male ; Mice ; }, abstract = {The biochemical activities of microbial communities, or microbiomes, are essential parts of environmental and animal ecosystems. The dynamics, balance, and effects of these communities are strongly influenced by phages present in the population. Being able to characterize bacterium-phage relationships is therefore essential to investigate these ecosystems to the full extent of their complexity. However, this task is currently limited by (i) the ability to characterize complete bacterial and viral genomes from a complex mix of species and (ii) the difficulty to assign phage sequences to their bacterial hosts. We show that both limitations can be circumvented using meta3C, an experimental and computational approach that exploits the physical contacts between DNA molecules to infer their proximity. In a single experiment, dozens of bacterial and phage genomes present in a complex mouse gut microbiota were assembled and scaffolded de novo. The phage genomes were then assigned to their putative bacterial hosts according to the physical contacts between the different DNA molecules, opening new perspectives for a comprehensive picture of the genomic structure of the gut flora. Therefore, this work holds far-reaching implications for human health studies aiming to bridge the virome to the microbiome.}, }
@article {pmid30149004, year = {2018}, author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS}, title = {Intestinal fluke Metagonimus yokogawai infection increases probiotic Lactobacillus in mouse cecum.}, journal = {Experimental parasitology}, volume = {193}, number = {}, pages = {45-50}, doi = {10.1016/j.exppara.2018.08.002}, pmid = {30149004}, issn = {1090-2449}, mesh = {Animals ; Bacteria/classification/growth &amp; development ; Cecum/*microbiology ; Fish Diseases/parasitology ; Gastrointestinal Microbiome ; Heterophyidae/*physiology ; *Lactobacillus ; Mice ; Mice, Inbred ICR ; Osmeriformes/parasitology ; *Probiotics ; Trematode Infections/*microbiology ; }, abstract = {Helminth infection can alleviate immune-mediated disorders such as allergies and autoimmune diseases, by altering the gut microbiome. However, changes in gut microbiome due to intestinal trematodes remain unelucidated. Here, we evaluated the changes in the gut microbiome of ICR mice infected with Metagonimus yokogawai, a hypo-virulent intestinal trematode. Four weeks after infection, mouse cecal content was analyzed by 16S rRNA amplicon analysis. Although there was no apparent difference in species richness and diversity, the microbiome composition was different in the infected and control groups. Furthermore, several Lactobacillus species with known immunomodulatory role in immune-mediated diseases were increased in the infected group.}, }
@article {pmid29654556, year = {2018}, author = {Jung, DH and Seo, DH and Kim, GY and Nam, YD and Song, EJ and Yoon, S and Park, CS}, title = {The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {11}, pages = {4927-4936}, doi = {10.1007/s00253-018-8971-z}, pmid = {29654556}, issn = {1432-0614}, support = {no. 2017R1A2B4004218//National Research Foundation of Korea/ ; }, mesh = {Animals ; Bacteria/isolation &amp; purification/metabolism ; Cattle ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Humans ; Rumen/*microbiology ; Starch/*metabolism/*pharmacology ; }, abstract = {Resistant starch (RS) in the diet reaches the large intestine without degradation, where it is decomposed by the commensal microbiota. The fermentation of RS produces secondary metabolites including short-chain fatty acids (SCFAs), which have been linked to a variety of physiological and health effects. Therefore, the availability of RS as a prebiotic is a current issue. The objectives of this study were (1) to use metagenomics to observe microbial flora changes in Bos taurus coreanae rumen fluid in the presence of RS and (2) to isolate RS-degrading microorganisms. The major microbial genus in a general rumen fluid was Succiniclasticum sp., whereas Streptococcus sp. immediately predominated after the addition of RS into the culture medium and was then drastically replaced by Lactobacillus sp. The presence of Bifidobacterium sp. was also observed continuously. Several microorganisms with high RS granule-degrading activity were identified and isolated, including B. choerinum FMB-1 and B. pseudolongum FMB-2. B. choerinum FMB-1 showed the highest RS-hydrolyzing activity and degraded almost 60% of all substrates tested. Coculture experiments demonstrated that Lactobacillus brevis ATCC 14869, which was isolated from human feces, could grow using reducing sugars generated from RS by B. choerinum FMB-1. These results suggest that Bifidobacterium spp., especially B. choerinum FMB-1, are the putative primary degrader of RS in rumen microbial flora and could be further studied as probiotic candidates.}, }
@article {pmid30271256, year = {2018}, author = {Anslan, S and Nilsson, RH and Wurzbacher, C and Baldrian, P and Leho Tedersoo,  and Bahram, M}, title = {Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding.}, journal = {MycoKeys}, volume = {}, number = {39}, pages = {29-40}, doi = {10.3897/mycokeys.39.28109}, pmid = {30271256}, issn = {1314-4049}, abstract = {Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.}, }
@article {pmid30165813, year = {2018}, author = {Rotimi, AM and Pierneef, R and Reva, ON}, title = {Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {309}, doi = {10.1186/s12859-018-2320-1}, pmid = {30165813}, issn = {1471-2105}, support = {93664//National Research Foundation/ ; }, mesh = {Algorithms ; Bacteria/*genetics ; Base Sequence ; DNA Barcoding, Taxonomic/*methods ; *Genes, Bacterial ; Genetic Markers ; Humans ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; ROC Curve ; Reproducibility of Results ; Sample Size ; *Software ; Species Specificity ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant level of genetic heterogeneity on the species level. It has become apparent that patterns of superior bioactivity of bacteria applicable in biotechnology as well as the enhanced virulence of pathogens often requires distinguishing between closely related species or sub-species. Current methods for binning of metagenomic reads usually do not allow for identification below the genus level and generally stops at the family level.<br><br>RESULTS: In this work, an attempt was made to improve metagenomic binning resolution by creating genome specific barcodes based on the core and accessory genomes. This protocol was implemented in novel software tools available for use and download from http://bargene.bi.up.ac.za /. The most abundant barcode genes from the core genomes were found to encode for ribosomal proteins, certain central metabolic genes and ABC transporters. Performance of metabarcode sequences created by this package was evaluated using artificially generated and publically available metagenomic datasets. Furthermore, a program (Barcoding 2.0) was developed to align reads against barcode sequences and thereafter calculate various parameters to score the alignments and the individual barcodes. Taxonomic units were identified in metagenomic samples by comparison of the calculated barcode scores to set cut-off values. In this study, it was found that varying sample sizes, i.e. number of reads in a metagenome and metabarcode lengths, had no significant effect on the sensitivity and specificity of the algorithm. Receiver operating characteristics (ROC) curves were calculated for different taxonomic groups based on the results of identification of the corresponding genomes in artificial metagenomic datasets. The reliability of distinguishing between species of the same genus or family by the program was nearly perfect.<br><br>CONCLUSIONS: The results showed that the novel online tool BarcodeGenerator (http://bargene.bi.up.ac.za /) is an efficient approach for generating barcode sequences from a set of complete genomes provided by users. Another program, Barcoder 2.0 is available from the same resource to enable an efficient and practical use of metabarcodes for visualization of the distribution of organisms of interest in environmental and clinical samples.}, }
@article {pmid30128756, year = {2018}, author = {Mukhtar, S and Mirza, BS and Mehnaz, S and Mirza, MS and Mclean, J and Malik, KA}, title = {Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {34}, number = {9}, pages = {136}, doi = {10.1007/s11274-018-2509-5}, pmid = {30128756}, issn = {1573-0972}, support = {Project # HEC (FD/2012/1843)//Higher Education Commission, Pakistan/ ; Project # 5-9/PAS/2012/969//Pakistan Academy of Sciences/ ; }, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Bacterial ; Ecosystem ; Metagenomics ; Microbiota/genetics/*physiology ; Pakistan ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Salinity ; Salt-Tolerant Plants/classification/*microbiology ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The rhizosphere microbiome plays a significant role in the life of plants in promoting plant survival under adverse conditions. However, limited information is available about microbial diversity in saline environments. In the current study, we compared the composition of the rhizosphere microbiomes of the halophytes Urochloa, Kochia, Salsola, and Atriplex living in moderate and high salinity environments (Khewra salt mines; Pakistan) with that of the non-halophyte Triticum. Soil microbiomes analysis using pyrosequencing of 16S rRNA gene indicated that Actinobacteria were dominant in saline soil samples whereas Proteobacteria predominated in non-saline soil samples. Firmicutes, Acidobacteria, Bacteriodetes and Thaumarchaeota were predominant phyla in saline and non-saline soils, whereas Cyanobacteria, Verrucomicrobia, Gemmatimonadetes and the unclassified WPS-2 were less abundant. Sequences from Euryarchaeota, Ignavibacteriae, and Nanohaloarchaeota were identified only from the rhizosphere of halophytes. Dominant halophilic bacteria and archaea identified in this study included Agrococcus, Armatimonadetes gp4, Halalkalicoccus, Haloferula and Halobacterium. Our analysis showed that increases in soil salinity correlated with significant differences in the alpha and beta diversity of the microbial communities across saline and non-saline soil samples. Having a complete inventory of the soil bacteria from different saline environments in Pakistan will help in the discovery of potential inoculants for crops growing on salt-affected land.}, }
@article {pmid29704757, year = {2018}, author = {Campanaro, S and Treu, L and Kougias, PG and Luo, G and Angelidaki, I}, title = {Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants.}, journal = {Water research}, volume = {140}, number = {}, pages = {123-134}, doi = {10.1016/j.watres.2018.04.043}, pmid = {29704757}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Biofuels ; Bioreactors/*microbiology ; Manure ; *Metagenome ; Metagenomics/methods ; Microbiota/*physiology ; Sewage/microbiology ; Waste Disposal, Fluid ; Waste Water ; }, abstract = {The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome. Canonical correspondence analysis was used to determine the influence of biotic and environmental factors on MAGs abundance and to investigate the methanogenic performance of the biogas plants. Prediction of the functional properties of MAGs was obtained analyzing their KEGG pathways and their carbohydrate active domains. Network analysis allowed investigation of species-species associations and shed light on syntrophic interactions between members belonging to the anaerobic digestion dark matter (phylum Fermentibacteria). By stratifying and comparing different levels of information, it was predicted that some MAGs have a crucial role in the manure-supplemented thermophilic biogas plants and it was highlighted the importance of the glycine cleavage system in complementing the &quot;truncated&quot; Wood-Ljungdahl pathway.}, }
@article {pmid29676472, year = {2018}, author = {Hao, DC and Zhang, CR and Xiao, PG}, title = {The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing.}, journal = {Journal of basic microbiology}, volume = {58}, number = {6}, pages = {501-512}, doi = {10.1002/jobm.201700663}, pmid = {29676472}, issn = {1521-4028}, mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Biodegradation, Environmental ; Environmental Pollutants/adverse effects ; Fungi/classification/genetics/isolation &amp; purification ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Genes, Viral/genetics ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Plant Roots/*microbiology ; *Rhizosphere ; *Soil Microbiology ; Taxus/*microbiology ; Viruses/classification/genetics/isolation &amp; purification ; }, abstract = {In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539). KEGG analysis predicted numerous functional genes; 7101 Unigenes belong to &quot;Xenobiotics biodegradation and metabolism.&quot; A total of 12,040 Unigenes involved in defense mechanisms (e.g., xenobiotic metabolism) were annotated by eggNOG. Talaromyces addition could influence not only the diversity and structure of microbial communities of Taxus rhizosphere, but also the relative abundance of functional genes, including metabolic genes, antibiotic resistant genes, and genes involved in pathogen-host interaction, bacterial virulence, and bacterial secretion system. The structure and function of rhizosphere microbiome could be sensitive to non-native microbe addition, which could impact on the pollutant degradation. This study, complementary to the amplicon sequencing, more objectively reflects the native microbiome of Taxus rhizosphere and its response to environmental pressure, and lays a foundation for potential combination of phytoremediation and bioaugmentation.}, }
@article {pmid29567298, year = {2018}, author = {Stensvold, CR and van der Giezen, M}, title = {Associations between Gut Microbiota and Common Luminal Intestinal Parasites.}, journal = {Trends in parasitology}, volume = {34}, number = {5}, pages = {369-377}, doi = {10.1016/j.pt.2018.02.004}, pmid = {29567298}, issn = {1471-5007}, mesh = {Blastocystis/*physiology ; Dientamoeba/*physiology ; *Environmental Biomarkers ; Gastrointestinal Microbiome/*physiology ; Host-Parasite Interactions/*physiology ; Humans ; Intestinal Diseases, Parasitic/*microbiology ; Intestines/microbiology/parasitology ; }, abstract = {The development and integration of DNA-based methods in research and clinical microbiology laboratories have enabled standardised and comprehensive detection and differentiation of the microbes colonising our guts. For instance, the single-celled parasites Blastocystis and Dientamoeba appear to be much more common than previously thought, especially so in healthy individuals. While increasing evidence appears to suggest limited pathogenicity of these parasites, next-generation-sequencing-based studies have helped us to appreciate links between parasite colonisation and certain host phenotypical characteristics and gut microbial profiles. The fundamental question remains as to whether such parasites are merely indicators or active manipulators of gut microbiota structure and function. In this article, we collate existing evidence that these parasites are, at minimum, indicators of intestinal microbiota structure.}, }
@article {pmid29500689, year = {2018}, author = {Xia, H and Wang, Y and Shi, C and Atoni, E and Zhao, L and Yuan, Z}, title = {Comparative Metagenomic Profiling of Viromes Associated with Four Common Mosquito Species in China.}, journal = {Virologica Sinica}, volume = {33}, number = {1}, pages = {59-66}, doi = {10.1007/s12250-018-0015-4}, pmid = {29500689}, issn = {1995-820X}, mesh = {Animals ; *Biodiversity ; China ; Culicidae/*virology ; Host Specificity ; *Metagenomics ; Mosquito Vectors/*virology ; Viral Tropism ; Viruses/*classification/genetics/*isolation &amp; purification ; }, abstract = {Vast viruses are thought to be associated with mosquitoes. Anopheles sinensis, Armigeres subalbatus, Culex quinquefasciatus, and Culex tritaeniorhynchus are very common mosquito species in China, and whether the virome structure in each species is species-specific has not been evaluated. In this study, a total of 2222 mosquitoes were collected from the same geographic location, and RNAs were sequenced using the Illumina Miseq platform. After querying to the Refseq database, a total of 3,435,781, 2,223,509, 5,727,523, and 6,387,867 paired-end reads were classified under viral sequences from An. sinensis, Ar. subalbatus, Cx. quinquefasciatus, and Cx. tritaeniorhynchus, respectively, with the highest prevalence of virus-associated reads being observed in Cx. quinquefasciatus. The metagenomic comparison analysis showed that the virus-related reads were distributed across 26 virus families, together with an unclassified group of viruses. Anelloviridae, Circoviridae, Genomoviridae, Iridoviridae, Mesoniviridae, Microviridae, Myoviridae, Parvoviridae, Phenuiviridae, and Podoviridae were the top ten significantly different viral families among the four species. Further analysis reveals that the virome is species-specific in four mosquito samples, and several viral sequences which maybe belong to novel viruses are discovered for the first time in those mosquitoes. This investigation provides a basis for a comprehensive knowledge on the mosquito virome status in China.}, }
@article {pmid29171095, year = {2018}, author = {Barko, PC and McMichael, MA and Swanson, KS and Williams, DA}, title = {The Gastrointestinal Microbiome: A Review.}, journal = {Journal of veterinary internal medicine}, volume = {32}, number = {1}, pages = {9-25}, doi = {10.1111/jvim.14875}, pmid = {29171095}, issn = {1939-1676}, mesh = {Animals ; Dysbiosis/*veterinary ; *Gastrointestinal Microbiome ; Mammals ; Metabolomics ; Metagenomics ; }, abstract = {The gastrointestinal microbiome is a diverse consortium of bacteria, archaea, fungi, protozoa, and viruses that inhabit the gut of all mammals. Studies in humans and other mammals have implicated the microbiome in a range of physiologic processes that are vital to host health including energy homeostasis, metabolism, gut epithelial health, immunologic activity, and neurobehavioral development. The microbial genome confers metabolic capabilities exceeding those of the host organism alone, making the gut microbiome an active participant in host physiology. Recent advances in DNA sequencing technology and computational biology have revolutionized the field of microbiomics, permitting mechanistic evaluation of the relationships between an animal and its microbial symbionts. Changes in the gastrointestinal microbiome are associated with diseases in humans and animals including inflammatory bowel disease, asthma, obesity, metabolic syndrome, cardiovascular disease, immune-mediated conditions, and neurodevelopmental conditions such as autism spectrum disorder. While there remains a paucity of data regarding the intestinal microbiome in small animals, recent studies have helped to characterize its role in host animal health and associated disease states. This review is intended to familiarize small animal veterinarians with recent advances in the field of microbiomics and to prime them for a future in which diagnostic tests and therapies will incorporate these developments into clinical practice.}, }
@article {pmid28891744, year = {2018}, author = {Fraumene, C and Manghina, V and Cadoni, E and Marongiu, F and Abbondio, M and Serra, M and Palomba, A and Tanca, A and Laconi, E and Uzzau, S}, title = {Caloric restriction promotes rapid expansion and long-lasting increase of Lactobacillus in the rat fecal microbiota.}, journal = {Gut microbes}, volume = {9}, number = {2}, pages = {104-114}, doi = {10.1080/19490976.2017.1371894}, pmid = {28891744}, issn = {1949-0984}, mesh = {Animals ; Bacteria/classification/genetics/*growth &amp; development ; *Caloric Restriction ; Cluster Analysis ; DNA, Bacterial/genetics ; Diet ; Feces/*microbiology ; Gastrointestinal Microbiome/*physiology ; Lactobacillus/classification/*growth &amp; development ; Models, Animal ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Inbred F344 ; }, abstract = {Previous studies indicated that caloric restricted diet enables to lower significantly the risk of cardiovascular and metabolic diseases. In experimental animal models, life-long lasting caloric restriction (CR) was demonstrated to induce changes of the intestinal microbiota composition, regardless of fat content and/or exercise. To explore the potential impact of short and long-term CR treatment on the gut microbiota, we conducted an analysis of fecal microbiota composition in young and adult Fisher 344 rats treated with a low fat feed under ad libitum (AL) or CR conditions (70%). We report here significant changes of the rat fecal microbiota that arise rapidly in young growing animals after short-term administration of a CR diet. In particular, Lactobacillus increased significantly after 8 weeks of CR treatment and its relative abundance was significantly higher in CR vs AL fed animals after 36 weeks of dietary intervention. Taken together, our data suggest that Lactobacillus intestinal colonization is hampered in AL fed young rats compared to CR fed ones, while health-promoting CR diet intervention enables the expansion of this genus rapidly and persistently up to adulthood.}, }
@article {pmid29453765, year = {2018}, author = {Mahajan, R and Attri, S and Sharma, K and Singh, N and Sharma, D and Goel, G}, title = {Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples.}, journal = {Molecular biology reports}, volume = {45}, number = {3}, pages = {297-308}, doi = {10.1007/s11033-018-4162-3}, pmid = {29453765}, issn = {1573-4978}, support = {INT/RUS/RFBR/P-175//Department of Science and Technology, Ministry of Science and Technology/ ; }, mesh = {Animals ; DNA/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Feces/chemistry ; Humans ; Metagenomics/methods ; Microbiota/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Soil/chemistry ; }, abstract = {Cost-effectiveness, quality, time-effectiveness and ease of the methodology are the most crucial factors in isolating quality DNA from wide variety of samples. Thus, research efforts focusing on the development of an efficient DNA extraction protocol is the need of the hour. The present study therefore, focuses on development of an efficient, rapid and free of inhibitory substances based methodology for extracting metagenomic DNA from diverse environmental samples viz. anaerobic biogas digesta, ruminant stomach, human feces, soil, and microbial starter cultures used for preparation of fermented food. PCR-DGGE based analysis and quality metagenomic library preparation, using DNA extraction methodology, validates the developed protocol. The developed protocol is cost effective, capable of isolating DNA from small sample size (100-1000 µl), time efficient (1.5-2.0 h protocol) and results in significantly higher DNA yield (4-8 times increased yield) when compared to previously available DNA extraction method and a commercial DNA extraction kit. The DNA extracted from the samples using different protocols was evaluated based on its ability to identify diverse microbial species using PCR-DGGE profiles targeting variable region within the 16S rRNA gene. The results of microbial community analysis revealed comparability of the developed protocol to commercial kits, in effectively identifying dominant representatives of the microbial community in different samples. Using the DNA extracted from the presented methodology, metagenomic libraries were prepared, which were found suitable for sequencing on Illumina platform.}, }
@article {pmid28612429, year = {2017}, author = {Tanner, K and Vilanova, C and Porcar, M}, title = {Bioprospecting challenges in unusual environments.}, journal = {Microbial biotechnology}, volume = {10}, number = {4}, pages = {671-673}, doi = {10.1111/1751-7915.12723}, pmid = {28612429}, issn = {1751-7915}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Bioprospecting/*trends ; Biotechnology ; *Environmental Microbiology ; Metagenomics ; }, }
@article {pmid29858829, year = {2018}, author = {Gupta, SK and Shin, H and Han, D and Hur, HG and Unno, T}, title = {Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {56}, number = {6}, pages = {408-415}, doi = {10.1007/s12275-018-8195-z}, pmid = {29858829}, issn = {1976-3794}, mesh = {Anti-Bacterial Agents/*toxicity ; Bacteria/*classification/drug effects/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Metals, Heavy/*toxicity ; Microbial Consortia/genetics ; Phylogeny ; Republic of Korea ; Sequence Analysis ; Sewage/microbiology ; Waste Water/*microbiology ; Water Purification ; }, abstract = {The increased antibiotic resistance among microorganisms has resulted into growing interest for investigating the wastewater treatment plants (WWTPs) as they are reported to be the major source in the dissemination of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment. In this study, we investigated the prevalence and persistence of ARGs and HMRGs as well as bacterial diversity and mobile genetic elements (MGEs) in influent and effluent at the WWTP in Gwangju, South Korea, using high-throughput sequencing based metagenomic approach. A good number of broad-spectrum of resistance genes (both ARG and HMRG) were prevalent and likely persistent, although large portion of them were successfully removed at the wastewater treatment process. The relative abundance of ARGs and MGEs was higher in effluent as compared to that of influent. Our results suggest that the resistance genes with high abundance and bacteria harbouring ARGs and MGEs are likely to persist more through the treatment process. On analyzing the microbial community, the phylum Proteobacteria, especially potentially pathogenic species belonging to the genus Acinetobacter, dominated in WWTP. Overall, our study demonstrates that many ARGs and HMRGs may persist the treatment processes in WWTPs and their association to MGEs may contribute to the dissemination of resistance genes among microorganisms in the environment.}, }
@article {pmid29587819, year = {2018}, author = {Dickson, LB and Ghozlane, A and Volant, S and Bouchier, C and Ma, L and Vega-Rúa, A and Dusfour, I and Jiolle, D and Paupy, C and Mayanja, MN and Kohl, A and Lutwama, JJ and Duong, V and Lambrechts, L}, title = {Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {207}, doi = {10.1186/s13071-018-2780-1}, pmid = {29587819}, issn = {1756-3305}, support = {ANR-16-CE35-0004-01//Agence Nationale de la Recherche/International ; ANR-17-ERC2-0016-01//Agence Nationale de la Recherche/International ; ANR-10-LABX-62-IBEID//Investissement d'Avenir program Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases/International ; 734584//European Union's Horizon 2020 research and innovation programme under ZikaPLAN/International ; 2015-FED-192//Programme Opérationnel FEDER-Guadeloupe-Conseil Régional/International ; MC_UU_12014//Medical Research Council/United Kingdom ; ANR10-INBS-09-08//France Génomique consortium/International ; }, mesh = {Aedes/*microbiology ; Animals ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Host-associated microbes, collectively known as the microbiota, play an important role in the biology of multicellular organisms. In mosquito vectors of human pathogens, the gut bacterial microbiota influences vectorial capacity and has become the subject of intense study. In laboratory studies of vector biology, genetic effects are often inferred from differences between geographically and genetically diverse colonies of mosquitoes that are reared in the same insectary. It is unclear, however, to what extent genetic effects can be confounded by uncontrolled differences in the microbiota composition among mosquito colonies. To address this question, we used 16S metagenomics to compare the midgut bacterial microbiome of six laboratory colonies of Aedes aegypti recently derived from wild populations representing the geographical range and genetic diversity of the species.<br><br>RESULTS: We found that the diversity, abundance, and community structure of the midgut bacterial microbiome was remarkably similar among the six different colonies of Ae. aegypti, regardless of their geographical origin. We also confirmed the relatively low complexity of bacterial communities inhabiting the mosquito midgut.<br><br>CONCLUSIONS: Our finding that geographically diverse colonies of Ae. aegypti reared in the same insectary harbor a similar gut bacterial microbiome supports the conclusion that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype. Thus, uncontrolled differences in microbiota composition are unlikely to represent a significant confounding factor in genetic studies of vector biology.}, }
@article {pmid29497869, year = {2018}, author = {Tan, Z and Wang, Y and Yang, T and Ao, H and Chen, S and Xing, K and Zhang, F and Zhao, X and Liu, J and Wang, C}, title = {Differences in gut microbiota composition in finishing Landrace pigs with low and high feed conversion ratios.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {9}, pages = {1673-1685}, doi = {10.1007/s10482-018-1057-1}, pmid = {29497869}, issn = {1572-9699}, support = {BAIC02-2016//Beijing Innovation Consortium of Agriculture Research System/ ; }, mesh = {Amino Acids/metabolism ; Animal Feed/*analysis ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Carbohydrate Metabolism ; Cecum/microbiology ; Colon/microbiology ; DNA, Bacterial/genetics ; Discriminant Analysis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Intestine, Small/microbiology ; Metabolic Networks and Pathways ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Swine ; }, abstract = {The goal of this study was to evaluate the microbial communities in the gut and feces from female finishing Landrace pigs with high and low feed conversion ratio (FCR) by 16S rRNA gene amplicon sequencing. Many potential biomarkers can distinguish between high and low FCR groups in the duodenum, ileum, cecum, colon, and rectum, according to linear discriminant analysis effect sizes. The relative abundance of microbes were tested by Mann-Whitney test between the high and low FCR groups in different organs: Campylobacter, Prevotella and Sphaerochaeta were different in the duodenum (P < 0.05); Sanguibacter, Kingella and Anaeroplasma in jejunum; Anaeroplasma, Arthrobacter, Kingella, Megasphaera and SMB53 in the ileum; Butyricicoccus, Campylobacter, Mitsuokella, and Coprobacillus in the cecum; Lactococcus and Peptococcus in the colon; Staphylococcus in the rectum; and Rothia in feces. The prevalence of microbial genera in certain locations could potentially be used as biomarkers to distinguish between high and low FCR. Functional prediction clustering analysis suggested that bacteria in the hindgut mainly participated in carbohydrate metabolism and amino acid metabolism, and different in the relative abundance of metabolic pathways, as predicted from the microbial taxa present, were identified by comparing the high and low groups of each location. The results may provide insights for the alteration of the intestinal microbial communities to improve the growth rate of pigs.}, }
@article {pmid29268781, year = {2017}, author = {Carda-Diéguez, M and Ghai, R and Rodríguez-Valera, F and Amaro, C}, title = {Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {162}, doi = {10.1186/s40168-017-0376-1}, pmid = {29268781}, issn = {2049-2618}, support = {BES-2012-052361//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; AGL2014-58933-P (cofunded with FEDER funds)//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; 17-04828S//Grantová Agentura České Republiky/International ; CGL2016-76273-P [AEI/FEDER, EU]//AEI/FEDER/EU/International ; CGL2015-71523-REDC (Acciones de dinamización &quot;REDES DE EXCELENCIA&quot; CONSOLIDER)//Dirección General de Investigación Científica y Técnica/International ; Prometeo II/2014/012 &quot;AQUAMET&quot;//Generalitat Valenciana/International ; }, mesh = {Anguilla/anatomy &amp; histology/*microbiology ; Animals ; Animals, Wild/microbiology ; Bacteria/genetics/isolation &amp; purification/*pathogenicity ; DNA, Bacterial ; Evolution, Molecular ; Genomic Islands ; Genomics ; Humans ; Metagenomics ; Microbiota/*genetics ; Mucus/*microbiology ; Skin/*microbiology ; Vibrio/genetics/isolation &amp; purification/pathogenicity ; *Water Microbiology ; }, abstract = {BACKGROUND: Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host.<br><br>RESULTS: Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibrio vulnificus and Vibrio cholerae/Vibrio metoecus being the most abundant ones in SMS from estuary and lake, respectively. Functions encoded in the SMS-microbiome differed significantly from those in the W-microbiome and allowed us to predict that successful mucus colonizers should have specific genes for (i) attachment (mainly by forming biofilms), (ii) bacterial competence and communication, and (iii) resistance to mucosal innate immunity, predators (amoeba), and heavy metals/drugs. In addition, we found several mobile genetic elements (mainly integrative conjugative elements) as well as a series of evidences suggesting that bacteria exchange DNA in SMS. Further, we isolated and sequenced a V. metoecus strain from SMS. This isolate shares pathogenicity islands with V. cholerae O1 from intestinal infections that are absent in the rest of sequenced V. metoecus strains, all of them from water and extra-intestinal infections.<br><br>CONCLUSIONS: We have obtained metagenomic and genomic evidence in favor of the hypothesis on the role of fish mucosal surfaces as a specialized habitat selecting microbes capable of colonizing and persisting on other comparable mucosal surfaces, e.g., the human intestine.}, }
@article {pmid29246178, year = {2017}, author = {Razavi, M and Marathe, NP and Gillings, MR and Flach, CF and Kristiansson, E and Joakim Larsson, DG}, title = {Discovery of the fourth mobile sulfonamide resistance gene.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {160}, doi = {10.1186/s40168-017-0379-y}, pmid = {29246178}, issn = {2049-2618}, support = {942-2015-750//Svenska Forskningsrådet Formas/ ; 521-2013-8633//Vetenskapsrådet/ ; 2015-02492//Vetenskapsrådet (SE)/ ; }, mesh = {Aminoglycosides/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Bioprospecting ; Cross Infection/microbiology ; Dihydropteroate Synthase/genetics/isolation &amp; purification ; Drug Resistance, Microbial/*genetics ; Escherichia coli/drug effects/genetics ; Genes, Bacterial ; Humans ; India ; *Integrons/genetics ; Metagenomics ; Microbial Consortia/genetics ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Sulfonamides/*pharmacology ; beta-Lactams/pharmacology ; }, abstract = {BACKGROUND: Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long- and short-read technologies to maintain both accuracy and context.<br><br>RESULTS: Up to 89% of identified open reading frames encode known resistance genes, or variations thereof (> 1000). We identified putative novel ARGs to aminoglycosides, beta-lactams, trimethoprim, rifampicin, and chloramphenicol, including several novel OXA variants, providing reduced susceptibility to carbapenems. One dihydropteroate synthase gene, with less than 34% amino acid identity to the three known mobile sulfonamide resistance genes (sul1-3), provided complete resistance when expressed in Escherichia coli. The mobilized gene, here named sul4, is the first mobile sulfonamide resistance gene discovered since 2003. Analyses of adjacent DNA suggest that sul4 has been decontextualized from a set of chromosomal genes involved in folate synthesis in its original host, likely within the phylum Chloroflexi. The presence of an insertion sequence common region element could provide mobility to the entire integron. Screening of 6489 metagenomic datasets revealed that sul4 is already widespread in seven countries across Asia and Europe.<br><br>CONCLUSIONS: Our findings show that exploring integrons from environmental communities with a history of antibiotic exposure can provide an efficient way to find novel, mobile resistance genes. The mobilization of a fourth sulfonamide resistance gene is likely to provide expanded opportunities for sulfonamide resistance to spread, with potential impacts on both human and animal health.}, }
@article {pmid29228991, year = {2017}, author = {Auffret, MD and Dewhurst, RJ and Duthie, CA and Rooke, JA and John Wallace, R and Freeman, TC and Stewart, R and Watson, M and Roehe, R}, title = {The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {159}, doi = {10.1186/s40168-017-0378-z}, pmid = {29228991}, issn = {2049-2618}, support = {BB/N01720X/1 and BB/N016742/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animal Feed/adverse effects/*analysis ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteriocins/pharmacology ; Bacteroidetes/drug effects/genetics/pathogenicity ; Cattle/*microbiology ; Chloramphenicol/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Firmicutes/drug effects/genetics/pathogenicity ; *Genes, Bacterial ; Humans ; Metagenomics/methods ; *Microbiota ; Proteobacteria/drug effects/genetics/pathogenicity ; Red Meat/analysis ; Rumen/*microbiology ; Virulence ; }, abstract = {BACKGROUND: The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate.<br><br>RESULTS: Two hundred and four genes associated with antimicrobial resistance (AMR), colonisation, communication or pathogenicity functions were identified from 4966 metagenomic genes using KEGG identification. Both the diversity and abundance of these genes were higher in concentrate-fed animals. Chloramphenicol and microcin resistance genes were dominant in samples from forage-fed animals (P < 0.001), while aminoglycoside and streptomycin resistances were enriched in concentrate-fed animals. The concentrate-based diet also increased the relative abundance of Proteobacteria, which includes many animal and zoonotic pathogens. A high ratio of Proteobacteria to (Firmicutes + Bacteroidetes) was confirmed as a good indicator for rumen dysbiosis, with eight cases all from concentrate-fed animals. Finally, network analysis demonstrated that the resistance/pathogenicity genes are potentially useful as biomarkers for health risk assessment of the ruminal microbiome.<br><br>CONCLUSIONS: Diet has important effects on the complement of AMR genes in the rumen microbial community, with potential implications for human and animal health.}, }
@article {pmid29197424, year = {2017}, author = {Cheng, K and Ning, Z and Zhang, X and Li, L and Liao, B and Mayne, J and Stintzi, A and Figeys, D}, title = {MetaLab: an automated pipeline for metaproteomic data analysis.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {157}, doi = {10.1186/s40168-017-0375-2}, pmid = {29197424}, issn = {2049-2618}, support = {217066//Natural Sciences and Engineering Research Council of Canada/ ; 9408//Genome Canada/Ontario Genomics/ ; }, mesh = {*Computational Biology ; Databases, Protein ; Gastrointestinal Microbiome ; *Metagenomics ; Microbiota ; *Proteomics ; *Software ; Statistics as Topic ; }, abstract = {BACKGROUND: Research involving microbial ecosystems has drawn increasing attention in recent years. Studying microbe-microbe, host-microbe, and environment-microbe interactions are essential for the understanding of microbial ecosystems. Currently, metaproteomics provide qualitative and quantitative information of proteins, providing insights into the functional changes of microbial communities. However, computational analysis of large-scale data generated in metaproteomic studies remains a challenge. Conventional proteomic software have difficulties dealing with the extreme complexity and species diversity present in microbiome samples leading to lower rates of peptide and protein identification. To address this issue, we previously developed the MetaPro-IQ approach for highly efficient microbial protein/peptide identification and quantification.<br><br>RESULT: Here, we developed an integrated software platform, named MetaLab, providing a complete and automated, user-friendly pipeline for fast microbial protein identification, quantification, as well as taxonomic profiling, directly from mass spectrometry raw data. Spectral clustering adopted in the pre-processing step dramatically improved the speed of peptide identification from database searches. Quantitative information of identified peptides was used for estimating the relative abundance of taxa at all phylogenetic ranks. Taxonomy result files exported by MetaLab are fully compatible with widely used metagenomics tools. Herein, the potential of MetaLab is evaluated by reanalyzing a metaproteomic dataset from mouse gut microbiome samples.<br><br>CONCLUSION: MetaLab is a fully automatic software platform enabling an integrated data-processing pipeline for metaproteomics. The function of sample-specific database generation can be very advantageous for searching peptides against huge protein databases. It provides a seamless connection between peptide determination and taxonomic profiling; therefore, the peptide abundance is readily used for measuring the microbial variations. MetaLab is designed as a versatile, efficient, and easy-to-use tool which can greatly simplify the procedure of metaproteomic data analysis for researchers in microbiome studies.}, }
@article {pmid29036588, year = {2018}, author = {Liu, X and Yu, Y and Liu, J and Elliott, CF and Qian, C and Liu, J}, title = {A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {1}, pages = {171-178}, doi = {10.1093/bioinformatics/btx432}, pmid = {29036588}, issn = {1367-4811}, support = {P30 CA177558/CA/NCI NIH HHS/United States ; R01 HG006272/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/genetics ; *Genome, Microbial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Motivation: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand.<br><br>Results: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads. The algorithm employs a novel data structure, called l-Othello, to support efficient querying of a taxon using its k-mer signatures. MetaOthello is an order-of-magnitude faster than the current state-of-the-art algorithms Kraken and Clark, and requires only one-third of the RAM. In comparison to Kaiju, a metagenomic classification tool using protein sequences instead of genomic sequences, MetaOthello is three times faster and exhibits 20-30% higher classification sensitivity. We report comparative analyses of both scalability and accuracy using a number of simulated and empirical datasets.<br><br>MetaOthello is a stand-alone program implemented in C ++. The current version (1.0) is accessible via https://doi.org/10.5281/zenodo.808941.<br><br>Contact: liuj@cs.uky.edu.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid28597254, year = {2017}, author = {Gopal, M and Bhute, SS and Gupta, A and Prabhu, SR and Thomas, GV and Whitman, WB and Jangid, K}, title = {Changes in structure and function of bacterial communities during coconut leaf vermicomposting.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {10}, pages = {1339-1355}, doi = {10.1007/s10482-017-0894-7}, pmid = {28597254}, issn = {1572-9699}, support = {BT/PR/0054/NDB/52/94/2007//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Animals ; Bacteria/classification/genetics ; Bacterial Proteins/metabolism ; *Biodiversity ; *Cocos ; *Composting ; DNA, Bacterial/genetics ; Metagenomics/methods ; *Microbiota ; Oligochaeta/*metabolism/microbiology ; Plant Leaves/*metabolism ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {To understand bacterial community dynamics during the vermicomposting of lignin-rich coconut leaves using an indigenous isolate of an epigeic earthworm, Eudrilus sp., we employed amplicon-based pyrosequencing of the V1 to V3 region of the 16S rRNA genes. Total community DNA was isolated from two separate vermicomposting tanks in triplicate at four different stages of the process: pre-decomposition (15th day), initial vermicomposting (45th day), 50-70% vermicomposting (75th day) and mature vermicompost (105th day). Alpha diversity measurements revealed an increase in bacterial diversity till the 75th day, which then declined in the mature vermicompost. Beta diversity comparisons showed formation of distinct, stage-specific communities. In terms of relative abundance, the Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, Planctomycetes, TM7 and WS3 groups increased until the 50-70% vermicomposting stage (p = 0.05). During the same time, the abundance of Bacteroidetes and Proteobacteria decreased. In contrast, the levels of Firmicutes increased throughout the 105-day vermicomposting process. The distribution of the most abundant OTUs revealed that each stage of the vermicomposting process possessed its own unique microbiome. Predictions based on the OTUs present by PICRUSt suggested a functional shift in the microbiome during vermicomposting. Enzymes and pathways of lipid and lignin metabolism were predicted to be initially abundant, but by the end of the process, biosynthesis of secondary metabolites and plant beneficial properties were enriched. The study revealed that bacterial communities undergo a continuous change throughout the vermicomposting process and that certain OTUs associated with specific stages could be targets for further improvements in the process.}, }
@article {pmid29540507, year = {2018}, author = {Succurro, A and Ebenhöh, O}, title = {Review and perspective on mathematical modeling of microbial ecosystems.}, journal = {Biochemical Society transactions}, volume = {46}, number = {2}, pages = {403-412}, doi = {10.1042/BST20170265}, pmid = {29540507}, issn = {1470-8752}, mesh = {*Ecosystem ; Metagenomics ; *Microbiota ; *Models, Biological ; }, abstract = {Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial 'who is there?'<br><br>QUESTION: An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment. Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act. Differential equation models and constraint-based stoichiometric models are deterministic approaches that can successfully provide a macroscopic description of the outcome from microscopic behaviors. In this mini-review, we present classical and recent applications of these modeling methods and illustrate the potential of their integration. Indeed, approaches that can capture multiple scales are needed in order to understand emergent patterns in ecosystems and their dynamics regulated by different spatio-temporal phenomena. We finally discuss promising examples of methods proposing the integration of differential equations with constraint-based stoichiometric models and argue that more work is needed in this direction.}, }
@article {pmid30242595, year = {2018}, author = {Hemmat-Jou, MH and Safari-Sinegani, AA and Mirzaie-Asl, A and Tahmourespour, A}, title = {Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach.}, journal = {Ecotoxicology (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10646-018-1981-x}, pmid = {30242595}, issn = {1573-3017}, abstract = {Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.}, }
@article {pmid30240114, year = {2018}, author = {Bergner, LM and Orton, RJ and da Silva Filipe, A and Shaw, AE and Becker, DJ and Tello, C and Biek, R and Streicker, DG}, title = {Using non-invasive metagenomics to characterize viral communities from wildlife.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.12946}, pmid = {30240114}, issn = {1755-0998}, abstract = {Microbial communities play an important role in organismal and ecosystem health. While high throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses present and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from non-invasively collected fecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in fetal bovine serum, we recommend storing swabs in RNALater or another non-biological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNAse treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time. This article is protected by copyright. All rights reserved.}, }
@article {pmid30231921, year = {2018}, author = {Vavourakis, CD and Andrei, AS and Mehrshad, M and Ghai, R and Sorokin, DY and Muyzer, G}, title = {A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {168}, doi = {10.1186/s40168-018-0548-7}, pmid = {30231921}, issn = {2049-2618}, support = {322551//European Research Council/International ; 322551//European Research Council/International ; L200961651//Czech Academy of Science/ ; 16-14-00121//Russian Science Support Foundation/ ; 24002002//Dutch Ministry of Education and Science/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 17-04828S//Grant Agency of the Czech Republic/ ; }, abstract = {BACKGROUND: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.<br><br>RESULTS: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.<br><br>CONCLUSIONS: Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.}, }
@article {pmid29180750, year = {2017}, author = {Brooks, B and Olm, MR and Firek, BA and Baker, R and Thomas, BC and Morowitz, MJ and Banfield, JF}, title = {Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1814}, doi = {10.1038/s41467-017-02018-w}, pmid = {29180750}, issn = {2041-1723}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Cross Infection/*microbiology ; Environmental Exposure ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/microbiology/*physiology ; Humans ; Infant ; Infant, Newborn ; Infant, Premature/*physiology ; *Intensive Care Units, Neonatal ; Metagenomics/methods ; }, abstract = {Preterm infants exhibit different microbiome colonization patterns relative to full-term infants, and it is speculated that the hospital room environment may contribute to infant microbiome development. Here, we present a genome-resolved metagenomic study of microbial genotypes from the gastrointestinal tracts of infants and from the neonatal intensive care unit (NICU) room environment. Some strains detected in hospitalized infants also occur in sinks and on surfaces, and belong to species such as Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa, and Klebsiella pneumoniae, which are frequently implicated in nosocomial infection and preterm infant gut colonization. Of the 15 K. pneumoniae strains detected in the study, four were detected in both infant gut and room samples. Time series experiments showed that nearly all strains associated with infant gut colonization can be detected in the room after, and often before, detection in the gut. Thus, we conclude that a component of premature infant gut colonization is the cycle of microbial exchange between the room and the occupant.}, }
@article {pmid29404836, year = {2018}, author = {Boers, SA and de Zeeuw, M and Jansen, R and van der Schroeff, MP and van Rossum, AMC and Hays, JP and Verhaegh, SJC}, title = {Characterization of the nasopharyngeal and middle ear microbiota in gastroesophageal reflux-prone versus gastroesophageal reflux non-prone children.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {37}, number = {5}, pages = {851-857}, doi = {10.1007/s10096-017-3178-2}, pmid = {29404836}, issn = {1435-4373}, mesh = {Bacterial Typing Techniques ; Biodiversity ; Child ; Child, Preschool ; Ear, Middle/*microbiology ; Female ; Gastroesophageal Reflux/*complications ; Humans ; Infant ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Nasopharyngitis/diagnosis/*etiology ; Nasopharynx/*microbiology ; Otitis Media/diagnosis/*etiology ; RNA, Ribosomal, 16S ; }, abstract = {Otitis media (OM) is one of the most common pediatric infections worldwide, but the complex microbiology associated with OM is poorly understood. Previous studies have shown an association between OM and gastroesophageal reflux (GER) in children. Therefore, in order to bridge the gap in our current understanding of the interaction between GER and OM, we investigated the nasopharyngeal and middle ear microbiota of children suffering from GER-associated OM and OM only, using culture-independent 16S rRNA gene sequencing. Middle ear fluid, nasopharyngeal swabs, and clinical data were collected as part of a prospective pilot study conducted at the Department of Otorhinolaryngology of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands. A total of 30 children up to 12 years of age who suffered from recurrent acute otitis media (AOM) (5), chronic otitis media with effusion (OME) (23), or both (2), and who were listed for tympanostomy tube placement, were included in the study. Nine children were included in the GER-associated OM cohort and 21 in the OM-only cohort. We found no obvious effect of GER on the nasopharyngeal and middle ear microbiota between the two groups of children. However, our results highlight the need to assess the true role of Alloiococcus spp. and Turicella spp. in children presenting with a high prevalence of recurrent AOM and chronic OME.}, }
@article {pmid29340898, year = {2018}, author = {Mirande, C and Bizine, I and Giannetti, A and Picot, N and van Belkum, A}, title = {Epidemiological aspects of healthcare-associated infections and microbial genomics.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {37}, number = {5}, pages = {823-831}, doi = {10.1007/s10096-017-3170-x}, pmid = {29340898}, issn = {1435-4373}, mesh = {Bacteria/classification/genetics ; Bacterial Typing Techniques/methods ; Cross Infection/*epidemiology/*microbiology/prevention &amp; control ; Disease Outbreaks ; Genome, Bacterial ; Humans ; *Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; Molecular Epidemiology ; Whole Genome Sequencing ; }, abstract = {Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determinants. This renders correct and rapid species identification and antibiotic susceptibility testing (AST) important and underscores the relevance of bacterial epidemiological typing. The latter is needed for the sensitive detection and exact tracing of nosocomial spread of these potentially multidrug-resistant microorganisms (MDRO). Many microbial typing technologies have been developed and put to some level of executive practice, but it seems that the continued evolution in methodology has currently reached an apex: there is likely to be scientific and practical consensus on the ultimate typing potential of bacterial whole-genome sequencing (WGS). The possibility to perform pan-genomic nucleotide-to-nucleotide comparisons between strains belonging to a single species and to detect even minute changes in nucleotide order will identify closely related organisms, while upon accumulation of such mutations, independent descend can be assumed. Calibration of difference levels [i.e. number of single nucleotide polymorphisms (SNPs)] into categories of inter-strain relatedness needs to be performed in order to generate robust, portable typing schemes. Here, we will briefly discuss the state of affairs regarding bacterial epidemiology based upon WGS, its relatedness with the nomenclature of former typing approaches and the continuing need for a global typing language.}, }
@article {pmid29334978, year = {2018}, author = {Wang, H and Li, S and Mahmood, A and Yang, S and Wang, X and Shen, Q and Shan, T and Deng, X and Li, J and Hua, X and Cui, L and Delwart, E and Zhang, W}, title = {Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes.}, journal = {Virology journal}, volume = {15}, number = {1}, pages = {11}, doi = {10.1186/s12985-018-0923-9}, pmid = {29334978}, issn = {1743-422X}, mesh = {Animals ; Biodiversity ; Cattle ; Cattle Diseases/*virology ; DNA Viruses/*genetics ; *DNA, Circular ; *DNA, Viral ; Forests ; *Genetic Variation ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Phylogeny ; Sequence Analysis, DNA ; *Viral Load ; Virus Diseases/*veterinary ; }, abstract = {BACKGROUND: Free-range cattle are common in the Northeast China area, which have close contact with farmers and may carry virus threatening to cattle and farmers.<br><br>METHODS: Using viral metagenomics we analyzed the virome in plasma samples collected from 80 cattle from the forested region of Northeast China.<br><br>RESULTS: The virome of cattle plasma is composed of the viruses belonging to the families including Parvoviridae, Papillomaviridae, Picobirnaviridae, and divergent viral genomes showing sequence similarity to circular Rep-encoding single stranded (CRESS) DNA viruses. Five such CRESS-DNA genomes were full characterized, with Rep sequences related to circovirus and gemycircularvirus. Three bovine parvoviruses belonging to two different genera were also characterized.<br><br>CONCLUSION: The virome in plasma samples of cattle from the forested region of Northeast China was revealed, which further characterized the diversity of viruses in cattle plasma.}, }
@article {pmid28442730, year = {2017}, author = {Wang, S and Hou, X and Su, H}, title = {Exploration of the relationship between biogas production and microbial community under high salinity conditions.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1149}, doi = {10.1038/s41598-017-01298-y}, pmid = {28442730}, issn = {2045-2322}, mesh = {Biofuels/*microbiology ; Biota/*drug effects ; Carbon Dioxide/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Metagenomics ; Methane/*metabolism ; *Salinity ; Sewage/*microbiology ; Sodium Chloride/metabolism ; }, abstract = {High salinity frequently causes inhibition and even failure in anaerobic digestion. To explore the impact of increasing NaCl concentrations on biogas production, and reveal the microbial community variations in response to high salinity stress, the Illumina high-throughput sequencing technology was employed. The results showed that a NaCl concentration of 20 g/L (H group) exhibited a similar level of VFAs and specific CO2 production rate with that in the blank group, thus indicating that the bacterial activity in acidogenesis might not be inhibited. However, the methanogenic activity in the H group was significantly affected compared with that in the blank group, causing a 42.2% decrease in CH4 production, a 37.12% reduction in the specific CH4 generation rate and a lower pH value. Illumina sequencing revealed that microbial communities between the blank and H groups were significantly different. Bacteroides, Clostridium and BA021 uncultured were the dominant species in the blank group while some halotolerant genera, such as Thermovirga, Soehngenia and Actinomyces, dominated and complemented the hydrolytic and acidogenetic abilities in the H group. Additionally, the most abundant archaeal species included Methanosaeta, Methanolinea, Methanospirillum and Methanoculleus in both groups, but hydrogenotrophic methanogens showed a lower resistance to high salinity than aceticlastic methanogens.}, }
@article {pmid30213145, year = {2018}, author = {Gómez-Villegas, P and Vigara, J and León, R}, title = {Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain).}, journal = {Marine drugs}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/md16090332}, pmid = {30213145}, issn = {1660-3397}, support = {0055_ALGARED_PLUS_5_E//INTERREG VA España-Portugal (POCTEP) 2014-2020 Cooperation Program/ ; }, abstract = {The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown.}, }
@article {pmid29526926, year = {2018}, author = {Do, TH and Le, NG and Dao, TK and Nguyen, TMP and Le, TL and Luu, HL and Nguyen, KHV and Nguyen, VL and Le, LA and Phung, TN and van Straalen, NM and Roelofs, D and Truong, NH}, title = {Metagenomic insights into lignocellulose-degrading genes through Illumina-based de novo sequencing of the microbiome in Vietnamese native goats' rumen.}, journal = {The Journal of general and applied microbiology}, volume = {64}, number = {3}, pages = {108-116}, doi = {10.2323/jgam.2017.08.004}, pmid = {29526926}, issn = {1349-8037}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/classification/*enzymology/*genetics ; Base Sequence ; DNA, Bacterial/genetics ; Databases, Genetic ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/genetics ; Glycoside Hydrolases/*genetics/metabolism ; Goats/*microbiology ; Lignin/metabolism ; Metagenome/*genetics ; Metagenomics ; Open Reading Frames ; Rumen/*microbiology ; Vietnam ; }, abstract = {The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats' rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes' modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.}, }
@article {pmid30209011, year = {2018}, author = {Shade, A and Dunn, RR and Blowes, SA and Keil, P and Bohannan, BJM and Herrmann, M and Küsel, K and Lennon, JT and Sanders, NJ and Storch, D and Chase, J}, title = {Macroecology to Unite All Life, Large and Small.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2018.08.005}, pmid = {30209011}, issn = {1872-8383}, abstract = {Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. Research in microbial ecology and macroecology have long been detached. Here, we argue that it is time to bridge the gap, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity. Microbial ecology and macroecology will mutually benefit from a unified research agenda and shared datasets that span the entirety of the biodiversity of life and the geographic expanse of the Earth.}, }
@article {pmid28686571, year = {2017}, author = {Chistoserdova, L}, title = {Application of Omics Approaches to Studying Methylotrophs and Methylotroph Comunities.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {119-142}, doi = {10.21775/cimb.024.119}, pmid = {28686571}, issn = {1467-3045}, mesh = {Aerobiosis ; Anaerobiosis ; Bacteria/*metabolism ; Metabolomics/methods ; Metagenomics/*methods ; Methane/chemistry/*metabolism ; Methanol/chemistry/*metabolism ; *Microbial Consortia ; Proteomics/methods ; }, abstract = {This review covers some recent advances in application of omics technologies to studying methylotrophs, with special reference to their activities in natural environments. Some of the developments highlighted in this review are the new outlook at the role of the XoxF-type, lanthanum-dependent methanol dehydrogenase in natural habitats, new mechanistic details of methane oxidation through the reverse methanogenesis pathway, propensity of 'aerobic' methanotrophs to thrive in hypoxic environments and potential connection of this process to denitrification, and a novel outlook at methane oxidation as a community function.}, }
@article {pmid28686567, year = {2017}, author = {Sudarikov, K and Tyakht, A and Alexeev, D}, title = {Methods for The Metagenomic Data Visualization and Analysis.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {37-58}, doi = {10.21775/cimb.024.037}, pmid = {28686567}, issn = {1467-3045}, mesh = {Bacteria/*genetics ; *Computer Graphics ; Databases, Genetic ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; }, abstract = {Surveys of environmental microbial communities using metagenomic approach produce vast volumes of multidimensional data regarding the phylogenetic and functional composition of the microbiota. Faced with such complex data, a metagenomic researcher needs to select the means for data analysis properly. Data visualization became an indispensable part of the exploratory data analysis and serves a key to the discoveries. While the molecular-genetic analysis of even a single bacterium presents multiple layers of data to be properly displayed and perceived, the studies of microbiota are significantly more challenging. Here we present a review of the state-of-art methods for the visualization of metagenomic data in a multi-level manner: from the methods applicable to an in-depth analysis of a single metagenome to the techniques appropriate for large-scale studies containing hundreds of environmental samples.}, }
@article {pmid28686566, year = {2017}, author = {Odintsova, V and Tyakht, A and Alexeev, D}, title = {Guidelines to Statistical Analysis of Microbial Composition Data Inferred from Metagenomic Sequencing.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {17-36}, doi = {10.21775/cimb.024.017}, pmid = {28686566}, issn = {1467-3045}, mesh = {Algorithms ; Computational Biology/*methods ; Data Interpretation, Statistical ; *Guidelines as Topic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; *Microbiota ; *Software ; }, abstract = {Metagenomics, the application of high-throughput DNA sequencing for surveys of environmental samples, has revolutionized our view on the taxonomic and genetic composition of complex microbial communities. An enormous richness of microbiota keeps unfolding in the context of various fields ranging from biomedicine and food industry to geology. Primary analysis of metagenomic reads allows to infer semi-quantitative data describing the community structure. However, such compositional data possess statistical specific properties that are important to be considered during preprocessing, hypothesis testing and interpreting the results of statistical tests. Failure to account for these specifics may lead to essentially wrong conclusions as a result of the survey. Here we present a researcher introduced to the field of metagenomics with the basic properties of microbial compositional data including statistical power and proposed distribution models, perform a review of the publicly available software tools developed specifically for such data and outline the recommendations for the application of the methods.}, }
@article {pmid28686565, year = {2017}, author = {Marco, D}, title = {Integration of Ecology and Environmental Metagenomics Conceptual and Methodological Frameworks.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {1-16}, doi = {10.21775/cimb.024.001}, pmid = {28686565}, issn = {1467-3045}, mesh = {*Biodiversity ; Computational Biology/*methods ; Ecology/*methods ; Ecosystem ; Environment ; Humans ; Metagenomics/*methods ; Models, Theoretical ; }, abstract = {Although from its origin metagenomics was concerned with composition of communities of microbial OTUs (Operational Taxonomic Units) living in a given habitat and their diversity and functional heterogeneity (concepts already well rooted in ecology), the new field was more 'environmentally' than 'ecologically' oriented. Probably by circumstantial reasons, metagenomics and ecology followed rather independent trajectories and conceptual and methodological gaps appeared. Recently, calls for the need of integrating the theoretical basis and methodologies coming from metagenomics (and other meta-omics) and ecology have been made. Here I will address some of the principles and methods of field ecology that, although useful in the context of environmental metagenomic studies, have been rather disregarded. In particular, I will emphasize the contribution of some well established concepts and methods of field ecology to a an appropriate field sampling and experimental design of environmental metagenomic studies.}, }
@article {pmid27572648, year = {2016}, author = {Jansson, JK and Baker, ES}, title = {A multi-omic future for microbiome studies.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {16049}, doi = {10.1038/nmicrobiol.2016.49}, pmid = {27572648}, issn = {2058-5276}, mesh = {*Gene Expression Profiling ; Humans ; *Metabolomics ; *Metagenomics ; *Microbiota ; *Proteomics ; }, }
@article {pmid29941576, year = {2018}, author = {Borton, MA and Hoyt, DW and Roux, S and Daly, RA and Welch, SA and Nicora, CD and Purvine, S and Eder, EK and Hanson, AJ and Sheets, JM and Morgan, DM and Wolfe, RA and Sharma, S and Carr, TR and Cole, DR and Mouser, PJ and Lipton, MS and Wilkins, MJ and Wrighton, KC}, title = {Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {28}, pages = {E6585-E6594}, doi = {10.1073/pnas.1800155115}, pmid = {29941576}, issn = {1091-6490}, mesh = {Bacteria/classification/*metabolism ; *Hydraulic Fracking ; Microbial Consortia/*physiology ; Natural Gas/*microbiology ; United States ; }, abstract = {Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth's surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and metabolite findings from the laboratory were then corroborated using regression-based modeling performed on metagenomic and metabolite data from more than 40 produced fluids from five hydraulically fractured shale wells. Collectively, our findings show that Halanaerobium, Geotoga, and Methanohalophilus strain abundances predict a significant fraction of nitrogen and carbon metabolites in the field. Our laboratory findings also exposed cryptic predatory, cooperative, and competitive interactions that impact microorganisms across fractured shales. Scaling these results from the laboratory to the field identified mechanisms underpinning biogeochemical reactions, yielding knowledge that can be harnessed to potentially increase energy yields and inform management practices in hydraulically fractured shales.}, }
@article {pmid29500976, year = {2018}, author = {Tang, X and Guo, Y and Jiang, B and Liu, S}, title = {Metagenomic approaches to understanding bacterial communication during the anammox reactor start-up.}, journal = {Water research}, volume = {136}, number = {}, pages = {95-103}, doi = {10.1016/j.watres.2018.02.054}, pmid = {29500976}, issn = {1879-2448}, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Bioreactors/*microbiology ; Metagenomics ; Nitrogen/chemistry ; Waste Water/chemistry/*microbiology ; }, abstract = {Increasing attention has been paid to the anammox community for its significant function in high-efficiency wastewater treatment. However, bacterial interaction in terms of bacterial communication is still elusive. This study firstly explored the intra- and interspecific communication of bacteria in the anammox community using metagenomic sequence data obtained during bioreactor operation. We verified the existence of multiple bacterial communication gene (BCG) subtypes by alignment with the constructed BCG database containing 11 identified gene subtypes. Bacterial communication was more active at the initial start-up than in the high loading-rate phase, and was correlated with the gradually decreasing bacterial diversity. Hdts, one of the key genes that produced the intraspecific signaling molecule AHL, and RpfF, the key gene that produced the intra- and interspecific signaling molecule DSF, were the primary communication engines in the anammox community because of their high abundance. Anammox bacteria mainly used Hdts genes to communicate with others, while RpfF gene played a core role characterized by their multiple correlations with other BCG subtypes. Interestingly, bacteria with abundant BCGs were more inclined to interact with the bacteria with the same functional traits, indicating the potential communication-related interaction among these bacteria in addition to the frequently reported substrate co-utilization. This highlights the primary importance of AHL and DSF for the anammox community, and thereby hints at a potential strategy for the target regulation of the signals to improve anammox viability and competitive capacity in wastewater treatment.}, }
@article {pmid29729565, year = {2018}, author = {Chen, L and Hu, C and Lok-Shun Lai, N and Zhang, W and Hua, J and Lam, PKS and Lam, JCW and Zhou, B}, title = {Acute exposure to PBDEs at an environmentally realistic concentration causes abrupt changes in the gut microbiota and host health of zebrafish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {240}, number = {}, pages = {17-26}, doi = {10.1016/j.envpol.2018.04.062}, pmid = {29729565}, issn = {1873-6424}, mesh = {Animals ; Bacteria ; Female ; Gastrointestinal Microbiome/*drug effects ; Halogenated Diphenyl Ethers/metabolism/*toxicity ; Intestines/metabolism ; Liver/metabolism ; Male ; Metagenomics ; Water Pollutants, Chemical/*toxicity ; Zebrafish/microbiology/*physiology ; }, abstract = {Contamination from lower brominated PBDEs is ubiquitous in the environments. However, their effects on gut microbiota and intestinal health have not yet been investigated. This study exposed adult zebrafish to an environmentally realistic concentration of pentaBDE mixture (DE-71) at 5.0 ng/L for 7 days, after which metagenomic sequencing of the intestinal microbiome was conducted and host physiological activities in the intestine and liver were also examined. The results showed that acute exposure to DE-71 significantly shifted the gut microbial community in a sex-specific manner. Certain genera (e.g., Mycoplasma, Ruminiclostridium, unclassified Firmicutes sensu stricto, and Fusobacterium) disappeared from the DE-71-exposed intestines, resulting in decreased bacterial diversity. Bacterial metabolic functions in guts were also affected by DE-71, namely those covering energy metabolism, virulence, respiration, cell division, cell signaling, and stress response. In addition, measurement of diverse sensitive biomarkers showed that the health of male intestines was remarkably compromised by the DE-71 exposure, as indicated by the disruption to its neural signaling (serotonin), epithelial barrier integrity (tight junction protein 2), inflammatory response (interleukin 1β), oxidative stress and antioxidant capacity, as well as detoxifying potential (ethoxyresorufin-O-deethylase activity). However, female intestines maintained intact physiological activities. Compared to the direct impact on intestines, a latent effect of DE-71 was observed in livers. Co-occurrence network analysis demonstrated that the gut bacteria vigorously interacted to establish the fittest community under DE-71 stress by promoting the reproduction of favorable genera, while diminishing the survival of unfavorable ones. Significant correlations between the zebrafish gut microbiota and physiological activities (e.g., oxidative stress, detoxification, neurotransmission, and epithelial integrity) were also observed. Overall, this study has demonstrated, for the first time, the high susceptibility of gut microbiota and intestinal health of zebrafish to DE-71, thus warranting more work to reveal its mode of toxicity.}, }
@article {pmid27262209, year = {2018}, author = {Tsai, CY and Tang, CY and Tan, TS and Chen, KH and Liao, KH and Liou, ML}, title = {Subgingival microbiota in individuals with severe chronic periodontitis.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {51}, number = {2}, pages = {226-234}, doi = {10.1016/j.jmii.2016.04.007}, pmid = {27262209}, issn = {1995-9133}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Base Sequence ; Biodiversity ; Chronic Periodontitis/*microbiology ; Gingiva/*microbiology ; Humans ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Taiwan ; }, abstract = {BACKGROUND/PURPOSE: Subgingival microorganisms are potentially associated with periodontal diseases. However, the correlation between the variance in the periodontal microbiome and the prevalence and severity of periodontitis remains unclear. The aim of this study was to determine the subgingival microbiota in Taiwanese individuals with severe chronic periodontitis (SP).<br><br>METHODS: The composition of the subgingival microbiota in healthy and diseased individuals was compared using a 16S rRNA metagenomic approach and quantitative polymerase chain reaction (qPCR). A total of 20 samples, including 10 from healthy individuals and 10 from SP patients, were analyzed.<br><br>RESULTS: We found high microbial diversity, with an average of 774 classified phylotypes per sample and a total of six bacterial phyla across all samples. Cluster analysis by principal component analysis and heat map showed that the bacterial communities were different in the two groups. Streptococcus dominated across all the healthy samples, whereas Prevotella, Porphyromonas, and Treponema were highly abundant across all diseased samples. At least 13 bacterial genera were conserved among all the samples. Only eight genera, including Lautropia, Parvimonas, Actinomyces, Capnocytophaga, Paludibacter, Streptococcus, Haemophilus, and Corynebacterium, were significantly enriched in the healthy group, and six genera, including Porphyromonas, Treponema, Tannerella, Aggregatibacter, Peptostreptococcus, and Filifactor, were significantly enriched in the diseased group. Furthermore, a trend of abundance of bacteria at the species level measured by qPCR in all samples was consistent with the 16S rRNA metagenomics results.<br><br>CONCLUSION: This study is the first in Taiwan to provide a picture of the microbiome in SP via 16S rRNA metagenomics.}, }
@article {pmid29568746, year = {2018}, author = {Wu, H and Cai, L and Li, D and Wang, X and Zhao, S and Zou, F and Zhou, K}, title = {Metagenomics Biomarkers Selected for Prediction of Three Different Diseases in Chinese Population.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {2936257}, doi = {10.1155/2018/2936257}, pmid = {29568746}, issn = {2314-6141}, mesh = {Algorithms ; Arthritis, Rheumatoid/*microbiology ; Asian Continental Ancestry Group/*genetics ; Biomarkers/*metabolism ; Diabetes Mellitus, Type 2/*microbiology ; Dysbiosis/genetics ; Female ; Humans ; Liver Cirrhosis/*microbiology ; Male ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; ROC Curve ; }, abstract = {The dysbiosis of human microbiome has been proven to be associated with the development of many human diseases. Metagenome sequencing emerges as a powerful tool to investigate the effects of microbiome on diseases. Identification of human gut microbiome markers associated with abnormal phenotypes may facilitate feature selection for multiclass classification. Compared with binary classifiers, multiclass classification models deploy more complex discriminative patterns. Here, we developed a pipeline to address the challenging characterization of multilabel samples. In this study, a total of 300 biomarkers were selected from the microbiome of 806 Chinese individuals (383 controls, 170 with type 2 diabetes, 130 with rheumatoid arthritis, and 123 with liver cirrhosis), and then logistic regression prediction algorithm was applied to those markers as the model intrinsic features. The estimated model produced an F1 score of 0.9142, which was better than other popular classification methods, and an average receiver operating characteristic (ROC) of 0.9475 showed a significant correlation between these selected biomarkers from microbiome and corresponding phenotypes. The results from this study indicate that machine learning is a vital tool in data mining from microbiome in order to identify disease-related biomarkers, which may contribute to the application of microbiome-based precision medicine in the future.}, }
@article {pmid29576590, year = {2018}, author = {Okamoto, H and Koizumi, S and Shimizu, H and Cho, O and Sugita, T}, title = {Characterization of the Axillary Microbiota of Japanese Male Subjects with Spicy and Milky Odor Types by Pyrosequencing.}, journal = {Biocontrol science}, volume = {23}, number = {1}, pages = {1-5}, doi = {10.4265/bio.23.1}, pmid = {29576590}, issn = {1884-0205}, mesh = {Adult ; Axilla/*microbiology ; Bacteria/classification/genetics ; Biodiversity ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Japan ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; *Odorants ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Malodorants in the human axilla are produced from human biogenic precursors by axillary bacterial enzymes. In the present study, we used pyrosequencing analysis to identify the axillary bacterial microbiota of 13 Japanese male subjects with cumin-like, spicy body odor (C type), and 9 with milky, skin-based body odor (M type). Anaerococcus, Corynebacterium, and Staphylococcus predominated in both C- and M-type subjects, followed by Moraxella and Peptoniphilus. These genera accounted for 96.2-99.9% of the total bacterial population, except in the microbiota of one C-type subject. However, the axillary bacteria in C-type subjects were more abundant than that in M-type subjects. These results suggest that the level of colonization by axillary bacteria is important for the production of malodorants.}, }
@article {pmid29432849, year = {2018}, author = {Joshi, A and Lanjekar, V and Dhakephalkar, PK and Dagar, SS}, title = {Cultivation of multiple genera of hydrogenotrophic methanogens from different environmental niches.}, journal = {Anaerobe}, volume = {50}, number = {}, pages = {64-68}, doi = {10.1016/j.anaerobe.2018.02.001}, pmid = {29432849}, issn = {1095-8274}, mesh = {Animals ; *Environmental Microbiology ; Feces/microbiology ; Geologic Sediments/microbiology ; Hydrogen/*metabolism ; Metagenome ; Metagenomics/methods ; Methane/*metabolism ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Rumen/microbiology ; }, abstract = {Six genera of hydrogenotrophic methanogens, namely Methanobrevibacter, Methanobacterium, Methanocorpusculum, Methanothermobacter, Methanoculleus, and Methanospirillum were cultivated from diverse environmental niches like rumen, feces, gut, and sediments using BY medium. We also report a putative novel genus and two novel species of methanogens isolated from termite, Indian star tortoise, and green iguana.}, }
@article {pmid29330119, year = {2018}, author = {Jin, W and Wang, Y and Li, Y and Cheng, Y and Zhu, W}, title = {Temporal changes of the bacterial community colonizing wheat straw in the cow rumen.}, journal = {Anaerobe}, volume = {50}, number = {}, pages = {1-8}, doi = {10.1016/j.anaerobe.2018.01.004}, pmid = {29330119}, issn = {1095-8274}, mesh = {Animal Feed/*microbiology ; Animals ; *Bacteria/classification/ultrastructure ; Biodiversity ; Biomass ; Cattle ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Rumen/*microbiology ; Triticum/*microbiology ; }, abstract = {This study used Miseq pyrosequencing and scanning electron microscopy to investigate the temporal changes in the bacterial community tightly attached to wheat straw in the cow rumen. The wheat straw was incubated in the rumens and samples were recovered at various times. The wheat straw degradation exhibited three phases: the first degradation phase occurred within 0.5 h, and the second degradation phase occurred after 6 h, with a stalling phase occurring between 0.5 and 6 h. Scanning electron microscopy revealed the colonization of the microorganisms on the wheat straw over time. The bacterial communities at 0.5, 6, 24, and 72 h were determined, corresponding to the degradation phases. Firmicutes and Bacteroidetes were the two most dominant phyla in the bacterial communities at the four time points. Principal coordinate analysis (PCoA) showed that the bacterial communities at the four time points were distinct from each other. The wheat straw-associated bacteria stabilized at the phylum level after 0.5 h of rumen incubation, and only modest phylum-level and family-level changes were observed for most taxa between 0.5 h and 72 h. The relative abundance of the dominant genera, Butyrivibrio, Coprococcus, Ruminococcus, Succiniclasticum, Clostridium, Prevotella, YRC22, CF231, and Treponema, changed significantly over time (P < .05). However, at the genus level, unclassified taxa accounted for 70.3% ± 6.1% of the relative abundance, indicating their probable importance in the degradation of wheat straw as well as in the temporal changes of the bacterial community. Thus, understanding the function of these unclassified taxa is of great importance for targeted improvement of forage use efficiency in ruminants. Collectively, our results revealed distinct degradation phases of wheat straw and corresponding changes in the colonized bacterial community.}, }
@article {pmid29182421, year = {2018}, author = {McKenney, EA and O'Connell, TM and Rodrigo, A and Yoder, AD}, title = {Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs.}, journal = {Gut microbes}, volume = {9}, number = {3}, pages = {202-217}, doi = {10.1080/19490976.2017.1408762}, pmid = {29182421}, issn = {1949-0984}, support = {S10 OD018164/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Biodiversity ; *Diet ; Feces/chemistry/microbiology ; Feeding Methods/veterinary ; Fermentation ; Fruit/chemistry/metabolism ; Gastrointestinal Tract/*microbiology/physiology ; Lemur/metabolism/*microbiology ; Metabolic Networks and Pathways ; *Metagenome ; Microbiota/genetics/*physiology ; Plant Leaves/chemistry/metabolism ; Species Specificity ; Strepsirhini/metabolism/microbiology ; }, abstract = {Many studies have demonstrated the effects of host diet on gut microbial membership, metagenomics, and fermentation individually; but few have attempted to interpret the relationship among these biological phenomena with respect to host features (e.g. gut morphology). We quantitatively compare the fecal microbial communities, metabolic pathways, and fermentation products associated with the nutritional intake of frugivorous (fruit-eating) and folivorous (leaf-eating) lemurs. Our results provide a uniquely multidimensional and comparative perspective on the adaptive dynamics between host and microbiome. Shotgun metagenomic sequencing revealed significant differential taxonomic and metabolic pathway enrichment, tailored to digest and detoxify different diets. Frugivorous metagenomes feature pathways to degrade simple carbohydrates and host-derived glycosaminoglycans, while folivorous metagenomes are equipped to break down phytic acid and other phytochemical compounds in an anaerobic environment. We used nuclear magnetic resonance based metabolic profiling of fecal samples to link metabolic pathways to fermentation products, confirming that the dissimilar substrates provided in each diet select for specific microbial functions. Fecal samples from frugivorous lemurs contained significantly different profiles of short chain fatty acids, alcohol fermentation products, amino acids, glucose, and glycerol compared to folivorous lemurs. We present the relationships between these datasets as an integrated visual framework, which we refer to as microbial geometry. We use microbial geometry to compare empirical gut microbial profiles across different feeding strategies, and suggest additional utility as a tool for hypothesis-generation.}, }
@article {pmid27739431, year = {2016}, author = {Bagnoud, A and Chourey, K and Hettich, RL and de Bruijn, I and Andersson, AF and Leupin, OX and Schwyn, B and Bernier-Latmani, R}, title = {Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12770}, doi = {10.1038/ncomms12770}, pmid = {27739431}, issn = {2041-1723}, mesh = {*Aluminum Silicates ; Autotrophic Processes ; Bacteria/classification/genetics/metabolism ; Carbon Cycle ; Ecosystem ; Geography ; Heterotrophic Processes ; Hydrogen/*metabolism ; *Metabolic Networks and Pathways ; Metagenomics/*methods ; *Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; Radioactive Waste ; *Soil Microbiology ; Switzerland ; }, abstract = {The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.}, }
@article {pmid30177919, year = {2018}, author = {Lin, JD and Lemay, MA and Parfrey, LW}, title = {Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1914}, doi = {10.3389/fmicb.2018.01914}, pmid = {30177919}, issn = {1664-302X}, abstract = {Bacteria are integral to marine carbon cycling. They transfer organic carbon to higher trophic levels and remineralise it into inorganic forms. Kelp forests are among the most productive ecosystems within the global oceans, yet the diversity and metabolic capacity of bacteria that transform kelp carbon is poorly understood. Here, we use 16S amplicon and metagenomic shotgun sequencing to survey bacterial communities associated with the surfaces of the giant kelp Macrocystis pyrifera and assess the capacity of these bacteria for carbohydrate metabolism. We find that Macrocystis-associated communities are distinct from the water column, and that they become more diverse and shift in composition with blade depth, which is a proxy for tissue age. These patterns are also observed in metagenomic functional profiles, though the broader functional groups-carbohydrate active enzyme families-are largely consistent across samples and depths. Additionally, we assayed more than 250 isolates cultured from Macrocystis blades and the surrounding water column for the ability to utilize alginate, the primary polysaccharide in Macrocystis tissue. The majority of cultured bacteria (66%) demonstrated this capacity; we find that alginate utilization is patchily distributed across diverse genera in the Bacteroidetes and Proteobacteria, yet can also vary between isolates with identical 16S rRNA sequences. The genes encoding enzymes involved in alginate metabolism were detected in metagenomic data across taxonomically diverse bacterial communities, further indicating this capacity is likely widespread amongst bacteria in kelp forests. Overall, the M. pyrifera epibiota shifts across a depth gradient, demonstrating a connection between bacterial assemblage and host tissue state.}, }
@article {pmid30177915, year = {2018}, author = {Wu, YT and Yang, CY and Chiang, PW and Tseng, CH and Chiu, HH and Saeed, I and Baatar, B and Rogozin, D and Halgamuge, S and Degermendzhi, A and Tang, SL}, title = {Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1763}, doi = {10.3389/fmicb.2018.01763}, pmid = {30177915}, issn = {1664-302X}, abstract = {Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2-5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.}, }
@article {pmid29760079, year = {2018}, author = {Wang, GD and Zhang, BL and Zhou, WW and Li, YX and Jin, JQ and Shao, Y and Yang, HC and Liu, YH and Yan, F and Chen, HM and Jin, L and Gao, F and Zhang, Y and Li, H and Mao, B and Murphy, RW and Wake, DB and Zhang, YP and Che, J}, title = {Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {22}, pages = {E5056-E5065}, doi = {10.1073/pnas.1716257115}, pmid = {29760079}, issn = {1091-6490}, mesh = {Animals ; Anura/*genetics/*physiology ; Gene Flow/*genetics ; *Genetic Speciation ; Hybridization, Genetic ; Metagenomics ; Phylogeny ; Selection, Genetic ; Tibet ; }, abstract = {Tibetan frogs, Nanorana parkeri, are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome. Selection accounts for 579 broadly scattered, highly divergent regions (HDRs) of the genome, which involve 365 genes. These genes fall into 51 gene ontology (GO) functional classes, 14 of which are likely to be important in driving reproductive isolation. GO enrichment analyses of E reveal many overrepresented functional categories associated with adaptation to high elevations, including blood circulation, response to hypoxia, and UV radiation. Four genes, including DNAJC8 in the brain, TNNC1 and ADORA1 in the heart, and LAMB3 in the lung, differ in levels of expression between low- and high-elevation populations. High-altitude adaptation plays an important role in maintaining and driving continuing divergence and reproductive isolation. Use of total genomes enabled recognition of selection and adaptation in and between populations, as well as documentation of evolution along a stepped cline toward speciation.}, }
@article {pmid29058768, year = {2018}, author = {Hernandez-Rodriguez, J and Arandjelovic, M and Lester, J and de Filippo, C and Weihmann, A and Meyer, M and Angedakin, S and Casals, F and Navarro, A and Vigilant, L and Kühl, HS and Langergraber, K and Boesch, C and Hughes, D and Marques-Bonet, T}, title = {The impact of endogenous content, replicates and pooling on genome capture from faecal samples.}, journal = {Molecular ecology resources}, volume = {18}, number = {2}, pages = {319-333}, doi = {10.1111/1755-0998.12728}, pmid = {29058768}, issn = {1755-0998}, support = {U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; DNA/*genetics/*isolation &amp; purification ; Feces/*chemistry ; Gabon ; Genetics, Population/*methods ; Metagenomics/*methods ; Pan troglodytes ; Sampling Studies ; Uganda ; }, abstract = {Target-capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off-target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.}, }
@article {pmid28439121, year = {2017}, author = {Mukherjee, A and Chettri, B and Langpoklakpam, JS and Basak, P and Prasad, A and Mukherjee, AK and Bhattacharyya, M and Singh, AK and Chattopadhyay, D}, title = {Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1108}, doi = {10.1038/s41598-017-01126-3}, pmid = {28439121}, issn = {2045-2322}, mesh = {Bacteria/classification/*drug effects ; Biota/*drug effects ; Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Environmental Pollutants/*metabolism ; Metagenomics/*methods ; Petroleum/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.}, }
@article {pmid28285978, year = {2017}, author = {Raoult, D}, title = {The study of microbiota needs both microbiologists and medical doctors.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {23}, number = {8}, pages = {500-501}, doi = {10.1016/j.cmi.2017.03.002}, pmid = {28285978}, issn = {1469-0691}, mesh = {Bacteria, Aerobic/classification/growth &amp; development ; Bacteria, Anaerobic/classification/growth &amp; development ; Colon/microbiology ; Feces/microbiology ; Humans ; Metagenomics/methods ; *Microbiology/education/trends ; *Microbiota ; *Physicians ; }, }
@article {pmid28787780, year = {2017}, author = {Noronha, MF and Lacerda Júnior, GV and Gilbert, JA and de Oliveira, VM}, title = {Taxonomic and functional patterns across soil microbial communities of global biomes.}, journal = {The Science of the total environment}, volume = {609}, number = {}, pages = {1064-1074}, doi = {10.1016/j.scitotenv.2017.07.159}, pmid = {28787780}, issn = {1879-1026}, mesh = {Biodiversity ; Classification ; *Ecosystem ; Metagenomics ; Soil ; *Soil Microbiology ; }, }
@article {pmid29567068, year = {2018}, author = {Górska, A and Peter, S and Willmann, M and Autenrieth, I and Schlaberg, R and Huson, DH}, title = {Dynamics of the human gut phageome during antibiotic treatment.}, journal = {Computational biology and chemistry}, volume = {74}, number = {}, pages = {420-427}, doi = {10.1016/j.compbiolchem.2018.03.011}, pmid = {29567068}, issn = {1476-928X}, mesh = {Anti-Bacterial Agents/administration &amp; dosage/*pharmacology ; Ciprofloxacin/administration &amp; dosage/*pharmacology ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/*drug effects/microbiology ; Healthy Volunteers ; Humans ; Metagenomics ; }, abstract = {Bacterial viruses contribute to the dynamics of the microbiome communities, as they are involved in the horizontal gene transfer. Previously we studied changes in the gut microbiome of the two healthy individuals over the course of a 6-days antibiotics treatment and subsequent 28 days recovery time (Willmann et al., 2015). Now, from the same samples, the virus-like particles were isolated and sequenced. As the phage sequences are currently poorly represented in reference databases, the reads had to be assembled, annotated and their abundance had to be evaluated via reads mapping. We analyzed and compared patterns of changes in abundance of the phage scaffolds and scaffolds with antibiotics resistant genes, in both phage and whole-genome metagenomic sets. We observed an increase in abundance of scaffolds carrying antibiotic-resistant genes in response to the treatment.}, }
@article {pmid29899109, year = {2018}, author = {Russo, AG and Eden, JS and Enosi Tuipulotu, D and Shi, M and Selechnik, D and Shine, R and Rollins, LA and Holmes, EC and White, PA}, title = {Viral Discovery in the Invasive Australian Cane Toad (Rhinella marina) Using Metatranscriptomic and Genomic Approaches.}, journal = {Journal of virology}, volume = {92}, number = {17}, pages = {}, doi = {10.1128/JVI.00768-18}, pmid = {29899109}, issn = {1098-5514}, mesh = {Animals ; Bufo marinus/*virology ; Gene Expression Profiling ; Metagenomics ; Proviruses/*classification/genetics/*isolation &amp; purification ; Viruses/*classification/genetics/*isolation &amp; purification ; Western Australia ; }, abstract = {Cane toads are a notorious invasive species, inhabiting over 1.2 million km2 of Australia and threatening native biodiversity. The release of pathogenic cane toad viruses is one possible biocontrol strategy yet is currently hindered by the poorly described cane toad virome. Metatranscriptomic analysis of 16 cane toad livers revealed the presence of a novel and full-length picornavirus, Rhimavirus A (RhiV-A), a member of a reptile- and amphibian-specific cluster of the Picornaviridae basal to the Kobuvirus-like group. In the combined liver transcriptome, we also identified a complete genome sequence of a distinct epsilonretrovirus, Rhinella marina endogenous retrovirus (RMERV). The recently sequenced cane toad genome contains 8 complete RMERV proviruses as well as 21 additional truncated insertions. The oldest full-length RMERV provirus was estimated to have inserted 1.9 million years ago (MYA). To screen for these viral sequences in additional toads, we analyzed publicly available transcriptomes from six diverse Australian locations. RhiV-A transcripts were identified in toads sampled from three locations across 1,000 km of Australia, stretching to the current Western Australia (WA) invasion front, while RMERV transcripts were observed at all six sites. Finally, we scanned the cane toad genome for nonretroviral endogenous viral elements, finding three sequences related to small DNA viruses in the family Circoviridae This shows ancestral circoviral infection with subsequent genomic integration. The identification of these current and past viral infections enriches our knowledge of the cane toad virome, an understanding of which will facilitate future work on infection and disease in this important invasive species.IMPORTANCE Cane toads are poisonous amphibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study samples cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol.}, }
@article {pmid29495531, year = {2018}, author = {Chen, H and Wu, H and Yan, B and Zhao, H and Liu, F and Zhang, H and Sheng, Q and Miao, F and Liang, Z}, title = {Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism?.}, journal = {International journal of molecular sciences}, volume = {19}, number = {3}, pages = {}, doi = {10.3390/ijms19030672}, pmid = {29495531}, issn = {1422-0067}, mesh = {Biodiversity ; Genetic Variation ; Metagenome ; Metagenomics/methods ; *Microbiota ; Plants, Medicinal/classification/genetics/metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics ; Salvia miltiorrhiza/classification/genetics/metabolism/*microbiology ; Seeds/metabolism/*microbiology ; }, abstract = {Seed microbiome includes special endophytic or epiphytic microbial taxa associated with seeds, which affects seed germination, plant growth, and health. Here, we analyzed the core microbiome of 21 Salvia miltiorrhiza seeds from seven different geographic origins using 16S rDNA and ITS amplicon sequencing, followed by bioinformatics analysis. The whole bacterial microbiome was classified into 17 microbial phyla and 39 classes. Gammaproteobacteria (67.6%), Alphaproteobacteria (15.6%), Betaproteobacteria (2.6%), Sphingobacteria (5.0%), Bacilli (4.6%), and Actinobacteria (2.9%) belonged to the core bacterial microbiome. Dothideomycetes comprised 94% of core fungal microbiome in S. miltiorrhiza seeds, and another two dominant classes were Leotiomycetes (3.0%) and Tremellomycetes (2.0%). We found that terpenoid backbone biosynthesis, degradation of limonene, pinene, and geraniol, and prenyltransferases, were overrepresented in the core bacterial microbiome using phylogenetic examination of communities by reconstruction of unobserved states (PICRUSt) software. We also found that the bacterial genera Pantoea, Pseudomonas, and Sphingomonas were enriched core taxa and overlapped among S. miltiorrhiza, maize, bean, and rice, while a fungal genus, Alternaria, was shared within S. miltiorrhiza, bean, and Brassicaceae families. These findings highlight that seed-associated microbiomeis an important component of plant microbiomes, which may be a gene reservoir for secondary metabolism in medicinal plants.}, }
@article {pmid28393285, year = {2018}, author = {Rowland, I and Gibson, G and Heinken, A and Scott, K and Swann, J and Thiele, I and Tuohy, K}, title = {Gut microbiota functions: metabolism of nutrients and other food components.}, journal = {European journal of nutrition}, volume = {57}, number = {1}, pages = {1-24}, doi = {10.1007/s00394-017-1445-8}, pmid = {28393285}, issn = {1436-6215}, mesh = {Bacteria/enzymology/*metabolism ; Bile Acids and Salts/metabolism ; Diet ; Dietary Carbohydrates/metabolism ; Dietary Proteins/metabolism ; Fatty Acids/metabolism ; *Food ; Gastrointestinal Microbiome/*physiology ; *Health Promotion ; Humans ; Metagenomics ; Models, Theoretical ; Phytochemicals/metabolism ; Plants, Edible/chemistry/metabolism ; Polyphenols/metabolism ; Proteomics ; Vitamins/biosynthesis ; }, abstract = {The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays.}, }
@article {pmid29405134, year = {2017}, author = {Desikan, P}, title = {Our microbial signatures.}, journal = {Indian journal of medical microbiology}, volume = {35}, number = {4}, pages = {443-444}, doi = {10.4103/ijmm.IJMM_17_250}, pmid = {29405134}, issn = {1998-3646}, mesh = {Biological Variation, Individual ; *Dysbiosis ; Healthy Volunteers ; Humans ; Metagenomics ; *Microbiota ; }, }
@article {pmid29108974, year = {2018}, author = {Yasir, M}, title = {Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {49}, number = {2}, pages = {248-257}, doi = {10.1016/j.bjm.2017.08.005}, pmid = {29108974}, issn = {1678-4405}, mesh = {*Antibiosis ; Bacteria/*classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Euryarchaeota/classification/genetics/growth &amp; development/isolation &amp; purification ; Metagenomics ; Pakistan ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.}, }
@article {pmid28336973, year = {2017}, author = {Wang, R and Zhang, H and Sun, L and Qi, G and Chen, S and Zhao, X}, title = {Microbial community composition is related to soil biological and chemical properties and bacterial wilt outbreak.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {343}, doi = {10.1038/s41598-017-00472-6}, pmid = {28336973}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/classification/genetics/*isolation &amp; purification ; Hydrogen-Ion Concentration ; Metagenomics ; Phosphorus/analysis ; Phylogeny ; Plant Diseases/*microbiology ; Potassium/analysis ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil microbes play important roles in plant growth and health. Little is known about the differences of soil microbes between healthy and bacterial wilt infected soils with Ralstonia solanacearum. By Illumina-MiSeq sequencing of 16S rRNA and 18S rRNA gene amplicons, we found the soil microbial composition and diversity were distinct between healthy and bacterial wilt infected soils. Soil microbial community varied at different plant growth stages due to changes of root exudates composition and soil pH. Healthy soils exhibited higher microbial diversity than the bacterial wilt infected soils. More abundant beneficial microbes including Bacillus, Agromyces, Micromonospora, Pseudonocardia, Acremonium, Lysobacter, Mesorhizobium, Microvirga, Bradyrhizobium, Acremonium and Chaetomium were found in the healthy soils rather than the bacterial wilt infected soils. Compared to bacterial wilt infected soils, the activities of catalase, invertase and urease, as well as soil pH, available phosphorous and potassium content, were all significantly increased in the healthy soils. In a conclusion, the higher abundance of beneficial microbes are positively related the higher soil quality, including better plant growth, lower disease incidence, and higher nutrient contents, soil enzyme activities and soil pH.}, }
@article {pmid29380873, year = {2018}, author = {Bapatla, KG and Singh, A and Yeddula, S and Patil, RH}, title = {Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua.}, journal = {Journal of basic microbiology}, volume = {58}, number = {3}, pages = {217-226}, doi = {10.1002/jobm.201700462}, pmid = {29380873}, issn = {1521-4028}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastrointestinal Tract/microbiology ; Helianthus/parasitology ; High-Throughput Nucleotide Sequencing ; Lepidoptera/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soybeans/parasitology ; }, abstract = {The insect gut has been the house of many taxonomically and physiologically diverse groups of microbial colonizers as symbionts and commensals, which are evolving to support the physiological requirement of insects. Lepidoptera is one of the important family of class hexapoda, comprising agriculture insect pest Spodoptera litura and Spilosoma obliqua. Information on gut microbiota and their functional role in these insects was meager to elucidate the wide-ranging survivalist mechanisms. In this context, we analyzed the composition, diversity and functional role of gut bacteria in S. litura and S. obliqua collected from soybean and sunflower crops, respectively, using Next Generation Sequencing of 16S rRNA. A total of 3427 and 206 Operation Taxonomic Units (OTUs) were identified in S. litura and S. obliqua gut metagenome, respectively. Highest number of sequences were annotated to unclassified bacteria (34%), followed by Proteobacteria (27%), and Chlorobi (14%) in S. litura, while S. obliqua has significant representation of Firmicutes (48%), followed by Bacteroidetes (20%), and unclassified bacteria (11%). Functionality of both metagenomes revealed, high abundance of ammonia oxidizers (20.1 58.0%) followed by relative abundance of detoxifying processes - dehalogenation (17.4-41.2%) and aromatic hydrocarbons degradation (1.1-3.1%). This study highlights the significance of the inherent microbiome of two defoliators in shaping the metagenome for nutrition and detoxifying the chemical molecules, and opens an avenue for exploring role of insect gut bacteria in host selection, metabolic endurance of insecticides and synergistic or agonistic mechanisms inside gut of insects feeding on insect-resistant biotech crops.}, }
@article {pmid29129355, year = {2018}, author = {Li, J and Fu, R and Yang, Y and Horz, HP and Guan, Y and Lu, Y and Lou, H and Tian, L and Zheng, S and Liu, H and Shi, M and Tang, K and Wang, S and Xu, S}, title = {A metagenomic approach to dissect the genetic composition of enterotypes in Han Chinese and two Muslim groups.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {1}, pages = {1-12}, doi = {10.1016/j.syapm.2017.09.006}, pmid = {29129355}, issn = {1618-0984}, mesh = {Asian Continental Ancestry Group ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ethnic Groups ; *Gastrointestinal Microbiome ; Genetic Association Studies ; Healthy Volunteers ; Humans ; Islam ; Lysophospholipase/genetics ; *Metagenomics ; *Microbiota ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Distinct enterotypes have been observed in the human gut but little is known about the genetic basis of the microbiome. Moreover, it is not clear how many genetic differences exist between enterotypes within or between populations. In this study, both the 16S rRNA gene and the metagenomes of the gut microbiota were sequenced from 48 Han Chinese, 48 Kazaks, and 96 Uyghurs, and taxonomies were assigned after de novo assembly. Single nucleotide polymorphisms were also identified by referring to data from the Human Microbiome Project. Systematic analysis of the gut communities in terms of their abundance and genetic composition was also performed, together with a genome-wide association study of the host genomes. The gut microbiota of 192 subjects was clearly classified into two enterotypes (Bacteroides and Prevotella). Interestingly, both enterotypes showed a clear genetic differentiation in terms of their functional catalogue of genes, especially for genes involved in amino acid and carbohydrate metabolism. In addition, several differentiated genera and genes were found among the three populations. Notably, one human variant (rs878394) was identified that showed significant association with the abundance of Prevotella, which is linked to LYPLAL1, a gene associated with body fat distribution, the waist-hip ratio and insulin sensitivity. Taken together, considerable differentiation was observed in gut microbes between enterotypes and among populations that was reflected in both the taxonomic composition and the genetic makeup of their functional genes, which could have been influenced by a variety of factors, such as diet and host genetic variation.}, }
@article {pmid29415902, year = {2018}, author = {Kishida, S and Kato-Mori, Y and Hagiwara, K}, title = {Influence of changes in the intestinal microflora on the immune function in mice.}, journal = {The Journal of veterinary medical science}, volume = {80}, number = {3}, pages = {440-446}, doi = {10.1292/jvms.17-0485}, pmid = {29415902}, issn = {1347-7439}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Concanavalin A/metabolism ; Cytokines/metabolism ; Flow Cytometry ; Gastrointestinal Microbiome/drug effects/*immunology ; Immunity/immunology/*physiology ; Mice/immunology/microbiology ; Mice, Inbred BALB C/immunology/microbiology ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; Spleen/cytology ; T-Lymphocyte Subsets/immunology/physiology ; }, abstract = {The composition of the intestinal microbiota is related to the health and immune function of the host. Administration of antibiotics affects the composition of the intestinal microbiota. However, the effects of immune function on the composition of the intestinal microbiota are still unclear. In this study, we investigated the lymphocyte composition and determined the relationships between lymphocyte function and the intestinal microbiota following antibiotic treatment in mice. To change the composition of the intestinal microbiota, mice were treated with or without antibiotics. Analysis of intestinal microbiota was performed by metagenomic analysis targeting 16S rRNA. Lymphocyte subsets of splenocytes were measured by flow cytometry. For functional analysis of T cells, splenocytes were stimulated with concanavalin (Con A), and cytokine gene expression was measured by real-time polymerase chain reaction. Firmicutes were predominant in the control group, whereas Bacteroidetes predominated in the antibiotic-treated group, as determined by metagenomic analysis. The diversity of the microbiota decreased in the antibiotic-treated group. Analysis of lymphocyte subsets showed that CD3+ cells decreased, whereas CD19+ cells increased in the antibiotic-treated group. All cytokine genes in splenocytes treated with Con A were downregulated in the antibiotic-treated group; in particular, genes encoding interferon-γ, interleukin (IL)-6, and IL-13 significantly decreased. Taken together, these results revealed that changes in the composition of the intestinal microbiota by antibiotic treatment influenced the population of lymphocytes in splenocytes and affected the immune response.}, }
@article {pmid28640714, year = {2017}, author = {Wen, SW and Wong, CHY}, title = {An unexplored brain-gut microbiota axis in stroke.}, journal = {Gut microbes}, volume = {8}, number = {6}, pages = {601-606}, doi = {10.1080/19490976.2017.1344809}, pmid = {28640714}, issn = {1949-0984}, mesh = {Animals ; Bacteria/classification ; *Bacterial Physiological Phenomena ; Bacterial Translocation ; *Disease Models, Animal ; Dysbiosis/etiology/*microbiology ; Escherichia coli/physiology ; Gastrointestinal Tract/microbiology ; *Host-Pathogen Interactions ; Humans ; Lung/microbiology ; Mice ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Specific Pathogen-Free Organisms ; Stroke/complications/*microbiology ; }, abstract = {Microbiota research, in particular that of the gut, has recently gained much attention in medical research owing to technological advances in metagenomics and metabolomics. Despite this, much of the research direction has focused on long-term or chronic effects of microbiota manipulation on health and disease. In this addendum, we reflect on our recent publication that reported findings addressing a rather unconventional hypothesis. Bacterial pneumonia is highly prevalent and is one of the leading contributors to stroke morbidity and mortality worldwide. However, microbiological cultures of samples taken from stroke patient with a suspected case of pneumonia often return with a negative result. Therefore, we proposed that post-stroke infection may be due to the presence of anaerobic bacteria, possibly those originated from the host gut microbiota. Supporting this, we showed that stroke promotes intestinal barrier breakdown and robust microbiota changes, and the subsequent translocation of selective bacterial strain from the host gut microbiota to peripheral tissues (i.e. lung) induces post-stroke infections. Our findings were further supported by various elegant studies published in the past 12 months. Here, we discuss and provide an overview of our key findings, supporting studies, and the implications for future advances in stroke research.}, }
@article {pmid27352007, year = {2016}, author = {Jangi, S and Gandhi, R and Cox, LM and Li, N and von Glehn, F and Yan, R and Patel, B and Mazzola, MA and Liu, S and Glanz, BL and Cook, S and Tankou, S and Stuart, F and Melo, K and Nejad, P and Smith, K and Topçuolu, BD and Holden, J and Kivisäkk, P and Chitnis, T and De Jager, PL and Quintana, FJ and Gerber, GK and Bry, L and Weiner, HL}, title = {Alterations of the human gut microbiome in multiple sclerosis.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12015}, doi = {10.1038/ncomms12015}, pmid = {27352007}, issn = {2041-1723}, support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI126880/AI/NIAID NIH HHS/United States ; R01 NS087226/NS/NINDS NIH HHS/United States ; R21 NS087867/NS/NINDS NIH HHS/United States ; }, mesh = {Adult ; Breath Tests ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome ; Genes, Bacterial ; Humans ; Immunomodulation ; Male ; Methane/analysis ; Middle Aged ; Monocytes/metabolism ; Multiple Sclerosis, Relapsing-Remitting/immunology/*microbiology/therapy ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; T-Lymphocytes/metabolism ; }, abstract = {The gut microbiome plays an important role in immune function and has been implicated in several autoimmune disorders. Here we use 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=60) and healthy controls (n=43). Microbiome alterations in MS include increases in Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signalling and NF-kB signalling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of Prevotella and Sutterella, and decreased Sarcina, compared with untreated patients. MS patients of a second cohort show elevated breath methane compared with controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis.}, }
@article {pmid30123190, year = {2018}, author = {Roscini, L and Tristezza, M and Corte, L and Colabella, C and Perrotta, C and Rampino, P and Robert, V and Vu, D and Cardinali, G and Grieco, F}, title = {Early Ongoing Speciation of Ogataea uvarum Sp. Nov. Within the Grape Ecosystem Revealed by the Internal Variability Among the rDNA Operon Repeats.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1687}, doi = {10.3389/fmicb.2018.01687}, pmid = {30123190}, issn = {1664-302X}, abstract = {A yeast strain was isolated during a study on vineyard-associated yeast strains from Apulia in Southern Italy. ITS and LSU D1/D2 rDNA sequences showed this strain not to belong to any known species and was described as the type strain of Ogataea uvarum sp. nov., a close relative of O. philodendri. Several secondary peaks appeared in the sequences, suggesting internal heterogeneity among the copies of the rDNA. This hypothesis was tested by sequencing single clones of the marker region. The analyses showed different levels of variability throughout the operon with differences between the rRNA encoding genes and the internally transcribed regions. O. uvarum and O. philodendri share high frequency variants, i.e., variants frequently found in many clones, whereas there is a large variability of the low frequency polymorphisms, suggesting that the mechanism of homogenization is more active with the former than with the latter type of variation. These findings indicate that low frequency variants are detected in Sanger sequencing as secondary peaks whereas in Next Generation Sequencing (NGS) of metagenomics DNA would lead to an overestimate of the alpha diversity. For the first time in our knowledge, this investigation shed light on the variation of the copy number of the rDNA cistron during the yeast speciation process. These polymorphisms can be used to investigate on the processes occurring in these taxonomic markers during the separation of fungal species, it being a genetic process highly frequent in the complex microbial ecosystem existing in grape, must and wine.}, }
@article {pmid29169222, year = {2018}, author = {Kim, D and Hong, S and Kim, YT and Ryu, S and Kim, HB and Lee, JH}, title = {Metagenomic Approach to Identifying Foodborne Pathogens on Chinese Cabbage.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {2}, pages = {227-235}, doi = {10.4014/jmb.1710.10021}, pmid = {29169222}, issn = {1738-8872}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; Brassica/*microbiology ; DNA, Bacterial/genetics ; Foodborne Diseases/*microbiology ; *Metagenomics ; Microbial Consortia ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {Foodborne illness represents a major threat to public health and is frequently attributed to pathogenic microorganisms on fresh produce. Recurrent outbreaks often come from vegetables that are grown close to or within the ground. Therefore, the first step to understanding the public health risk of microorganisms on fresh vegetables is to identify and describe microbial communities. We investigated the phyllospheres on Chinese cabbage (Brassica rapa subsp. pekinensis, N = 54). 16S rRNA gene amplicon sequencing targeting the V5-V6 region of 16S rRNA genes was conducted by employing the Illumina MiSeq system. Sequence quality was assessed, and phylogenetic assessments were performed using the RDP classifier implemented in QIIME with a bootstrap cutoff of 80%. Principal coordinate analysis was performed using a weighted Fast UniFrac matrix. The average number of sequence reads generated per sample was 34,584. At the phylum level, bacterial communities were composed primarily of Proteobacteria and Bacteroidetes. The most abundant genera on Chinese cabbages were Chryseobacterium, Aurantimonadaceae_g, Sphingomonas, and Pseudomonas. Diverse potential pathogens, such as Pantoea, Erwinia, Klebsiella, Yersinia, Bacillus, Staphylococcus, Salmonella, and Clostridium were also detected from the samples. Although further epidemiological studies will be required to determine whether the detected potential pathogens are associated with foodborne illness, our results imply that a metagenomic approach can be used to detect pathogenic bacteria on fresh vegetables.}, }
@article {pmid28766918, year = {2018}, author = {Sherwani, MA and Tufail, S and Muzaffar, AF and Yusuf, N}, title = {The skin microbiome and immune system: Potential target for chemoprevention?.}, journal = {Photodermatology, photoimmunology &amp; photomedicine}, volume = {34}, number = {1}, pages = {25-34}, doi = {10.1111/phpp.12334}, pmid = {28766918}, issn = {1600-0781}, mesh = {Animals ; Gastrointestinal Microbiome ; Humans ; *Microbiota/radiation effects ; Prebiotics ; Probiotics/pharmacology ; Skin/*immunology/*microbiology ; Skin Neoplasms/immunology/*microbiology/*prevention &amp; control ; Ultraviolet Rays ; Virus Diseases/complications ; Vitamin D/analogs &amp; derivatives/metabolism ; }, abstract = {There has been increasing interest in understanding the role of the human microbiome in skin diseases. Microbiome studies are being utilized in skin cancer research in numerous ways. Commensal bacteria are being studied as a potential tool to judge the biggest environmental risk of skin cancer, ultraviolet (UV) radiation. Owing to the recognized link of skin microbes in the process of inflammation, there have been theories linking commensal bacteria to skin cancer. Viral metagenomics has also provided insight into virus linked forms of skin cancers. Speculations can be drawn for skin microbiome that in a manner similar to gut microbiome, they can be involved in chemoprevention of skin cancer. Nonetheless, there are definitely huge gaps in our knowledge of the relationship of microbiome and skin cancers, especially in relation to chemoprevention. The utilization of microbiome in skin cancer research seems to be a promising field and may help yield novel skin cancer prevention and treatment options. This review focuses on recent utilization of the microbiome in skin cancer research, and it explores the potential of utilizing the microbiome in prevention, earlier diagnosis, and treatment of skin cancers.}, }
@article {pmid30117250, year = {2018}, author = {Cabello-Yeves, PJ and Picazo, A and Camacho, A and Callieri, C and Rosselli, R and Roda-Garcia, JJ and Coutinho, FH and Rodriguez-Valera, F}, title = {Ecological and genomic features of two widespread freshwater picocyanobacteria.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14377}, pmid = {30117250}, issn = {1462-2920}, }
@article {pmid27571981, year = {2016}, author = {Schimel, J}, title = {Microbial ecology: Linking omics to biogeochemistry.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {15028}, doi = {10.1038/nmicrobiol.2015.28}, pmid = {27571981}, issn = {2058-5276}, mesh = {*Ecology ; *Ecosystem ; Metagenomics ; Microbial Consortia ; Proteomics ; }, }
@article {pmid29878736, year = {2016}, author = {Lin, Z and Zu, XP and Xie, HS and Jin, HZ and Yang, N and Liu, XR and Zhang, WD}, title = {[Research progress in mechanism of intestinal microorganisms in human diseases].}, journal = {Yao xue xue bao = Acta pharmaceutica Sinica}, volume = {51}, number = {6}, pages = {843-852}, pmid = {29878736}, issn = {0513-4870}, mesh = {*Gastrointestinal Microbiome ; Humans ; Intestines/*microbiology ; *Metagenomics ; Symbiosis ; }, abstract = {The international cooperated research projects of the Human Microbiome Project (HMP) and Metagenomics of The Human Intestinal Tract (MetaHIT) were officially launched in 2007, which indicated the era of metagenomics research of microorganisms in human gastrointestinal tract had been coming. Each human body is a superorganism which is composed of 90% commensal microorganisms, especially the intestinal microorganisms. The intestinal microorganisms play an important role on health maintenance since they are involved in the absorption and metabolism of nutrients in the human bodies. Herein, we review the research progress in the mechanism of intestinal microorganisms in human diseases. Our purpose is to provide novel ideas on human health and therapeutic targets of diseases.}, }
@article {pmid28390093, year = {2018}, author = {Aw, W and Fukuda, S}, title = {Understanding the role of the gut ecosystem in diabetes mellitus.}, journal = {Journal of diabetes investigation}, volume = {9}, number = {1}, pages = {5-12}, doi = {10.1111/jdi.12673}, pmid = {28390093}, issn = {2040-1124}, mesh = {Animals ; Diabetes Mellitus, Type 1/metabolism/*microbiology ; Diabetes Mellitus, Type 2/metabolism/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; Metabolomics ; Metagenome ; }, abstract = {Diabetes mellitus is a type of metabolic disorder whereby patients are unable to regulate glycemia. It is currently a worldwide public health issue, and is a burden to society because of its disabling and common complications. Diabetes is multifactorial, and also induces the onset of other diseases. In the present report, we review the labyrinth encompassing the gut microbiota and gut microbiota-derived metabolites in type 1 diabetes and type 2 diabetes pathogenesis. There have been exceptional improvements in deoxyribonucleic acid sequencing and mass spectrometry technologies throughout these past years, and these have allowed the comprehensive collection of information on our unique gut ecosystem. We would like to advocate incorporating metagenome and metabolome information for a comprehensive perspective of the complex interrelationships between the gut environment, host metabolism and diabetes pathogenesis. We hope that with this improved understanding we would be able to provide exciting novel therapeutic approaches to engineer an ideal gut ecosystem for optimal health.}, }
@article {pmid29748902, year = {2018}, author = {Escudero, L and Oetiker, N and Gallardo, K and Tebes-Cayo, C and Guajardo, M and Nuñez, C and Davis-Belmar, C and Pueyo, JJ and Chong Díaz, G and Demergasso, C}, title = {A thiotrophic microbial community in an acidic brine lake in Northern Chile.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {8}, pages = {1403-1419}, doi = {10.1007/s10482-018-1087-8}, pmid = {29748902}, issn = {1572-9699}, support = {1100795//Fondecyt/ ; 32002137//BHP Minerals Americas/ ; }, mesh = {Bacteria/*classification/metabolism ; Biodiversity ; Carbon Cycle ; Chile ; DNA, Bacterial/genetics ; Energy Metabolism ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salts ; Sulfur/*metabolism ; }, abstract = {The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.}, }
@article {pmid29721711, year = {2018}, author = {Goodfellow, M and Nouioui, I and Sanderson, R and Xie, F and Bull, AT}, title = {Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {8}, pages = {1315-1332}, doi = {10.1007/s10482-018-1088-7}, pmid = {29721711}, issn = {1572-9699}, mesh = {Actinobacteria/*classification/genetics/isolation &amp; purification/metabolism ; Altitude ; Anti-Bacterial Agents/isolation &amp; purification ; *Biodiversity ; Chile ; *Desert Climate ; Ecosystem ; Metagenomics ; *Phylogeny ; *Soil Microbiology ; Species Specificity ; }, abstract = {An &quot;in house&quot; taxonomic approach to drug discovery led to the isolation of diverse actinobacteria from hyper-arid, extreme hyper-arid and very high altitude Atacama Desert soils. A high proportion of the isolates were assigned to novel taxa, with many showing activity in standard antimicrobial plug assays. The application of more advanced taxonomic and screening strategies showed that strains classified as novel species of Lentzea and Streptomyces synthesised new specialised metabolites thereby underpinning the premise that the extreme abiotic conditions in the Atacama Desert favour the development of a unique actinobacterial diversity which is the basis of novel chemistry. Complementary metagenomic analyses showed that the soils encompassed an astonishing degree of actinobacterial 'dark matter', while rank-abundance analyses showed them to be highly diverse habitats mainly composed of rare taxa that have not been recovered using culture-dependent methods. The implications of these pioneering studies on future bioprospecting campaigns are discussed.}, }
@article {pmid29396587, year = {2018}, author = {Mahony, J and Lugli, GA and van Sinderen, D and Ventura, M}, title = {Impact of gut-associated bifidobacteria and their phages on health: two sides of the same coin?.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {5}, pages = {2091-2099}, doi = {10.1007/s00253-018-8795-x}, pmid = {29396587}, issn = {1432-0614}, mesh = {Animals ; Bacteriophages/classification/genetics/isolation &amp; purification/*physiology ; Bifidobacterium/classification/genetics/*physiology/virology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology/*virology ; Humans ; }, abstract = {Bifidobacteria are among the first microbial colonisers of the human infant gut post-partum. Their early appearance and dominance in the human infant gut and the reported health-promoting or probiotic status of several bifidobacterial strains has culminated in intensive research efforts that focus on their activities as part of the gut microbiota and the concomitant implications for human health. In this mini-review, we evaluate current knowledge on the genomics of this diverse bacterial genus, and on the genetic and functional adaptations that have underpinned the success of bifidobacteria in colonising the infant gut. The growing interest in functional genomics of bifidobacteria has also created interest in the interactions of bifidobacteria and their (bacterio)phages. While virulent phages of bifidobacteria have yet to be isolated, the incidence of integrated (pro)phages in bifidobacterial genomes are widely reported and this mini-review considers the role of these so-called bifidoprophages in modulating bifidobacterial populations in the human gastrointestinal tract and the implications for existing and future development of probiotic therapies.}, }
@article {pmid29136413, year = {2017}, author = {Degois, J and Clerc, F and Simon, X and Bontemps, C and Leblond, P and Duquenne, P}, title = {First Metagenomic Survey of the Microbial Diversity in Bioaerosols Emitted in Waste Sorting Plants.}, journal = {Annals of work exposures and health}, volume = {61}, number = {9}, pages = {1076-1086}, doi = {10.1093/annweh/wxx075}, pmid = {29136413}, issn = {2398-7316}, mesh = {Aerosols/*analysis ; *Air Microbiology ; Bacteria/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Ribosomal/analysis ; Environmental Monitoring/*methods ; Feasibility Studies ; Fungi/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Occupational Exposure/analysis ; Proteobacteria/isolation &amp; purification ; Reproducibility of Results ; }, abstract = {Waste sorting activities are source of occupational bioaerosol exposures that are associated with several health disorders. New analytical tools, based on next-generation sequencing (NGS) technologies, provide powerful methods to assess the microbial composition of bioaerosols. The objectives of the study were (i) to assess the feasibility and the repeatability of NGS-based biodiversity measurements and (ii) to study the microbial biodiversity using NGS in bioaerosols emitted in a waste sorting plant (WSP). Three stationary parallel samples were collected in a sorting cabin using closed-face cassettes equipped with polycarbonate membranes. Bacterial and fungal diversity was assessed by sequencing 16S and 18S rDNA genes using either Illumina sequencing or 454 pyrosequencing methods. At sampling point, airborne bacteria were dominated by Proteobacteria, Firmicutes, and Actinobacteria with prevailing genera assigned to unclassified Enterobacteriaceae, Staphylococcus, Acinetobacter, Leuconostoc, Pseudomonas, and Lactobacillus. Airborne fungi were dominated by Ascomycota with prevailing genera assigned to Penicillium, Aspergillus, Rhizopus, Wallemia, and Hemicarpenteles. The NGS biodiversity measurements revealed a higher biodiversity bioaerosols that previously reported for WSP in studies carried out using culture methods followed by identification of microorganisms. These results provide the first survey about taxonomic biodiversity in bioaerosols from WSPs using high-throughput sequencing.}, }
@article {pmid28000755, year = {2016}, author = {Barnard, E and Shi, B and Kang, D and Craft, N and Li, H}, title = {The balance of metagenomic elements shapes the skin microbiome in acne and health.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39491}, doi = {10.1038/srep39491}, pmid = {28000755}, issn = {2045-2322}, support = {R01 GM099530/GM/NIGMS NIH HHS/United States ; UH2 AR057503/AR/NIAMS NIH HHS/United States ; }, mesh = {Acne Vulgaris/*microbiology ; Adolescent ; Adult ; Aged ; Bacteriophages/*isolation &amp; purification ; Case-Control Studies ; Cohort Studies ; Healthy Volunteers ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Propionibacterium acnes/*isolation &amp; purification/virology ; Sequence Analysis, DNA ; Skin/*microbiology ; Virulence ; Young Adult ; }, abstract = {Studies have emphasized the importance of disease-associated microorganisms in perturbed communities, however, the protective roles of commensals are largely under recognized and poorly understood. Using acne as a model disease, we investigated the determinants of the overall virulence property of the skin microbiota when disease- and health-associated organisms coexist in the community. By ultra-deep metagenomic shotgun sequencing, we revealed higher relative abundances of propionibacteria and Propionibacterium acnes phage in healthy skin. In acne patients, the microbiome composition at the species level and at P. acnes strain level was more diverse than in healthy individuals, with enriched virulence-associated factors and reduced abundance of metabolic synthesis genes. Based on the abundance profiles of the metagenomic elements, we constructed a quantitative prediction model, which classified the clinical states of the host skin with high accuracy in both our study cohort (85%) and an independent sample set (86%). Our results suggest that the balance between metagenomic elements, not the mere presence of disease-associated strains, shapes the overall virulence property of the skin microbiota. This study provides new insights into the microbial mechanism of acne pathogenesis and suggests probiotic and phage therapies as potential acne treatments to modulate the skin microbiota and to maintain skin health.}, }
@article {pmid29689266, year = {2018}, author = {Nakatsu, G and Zhou, H and Wu, WKK and Wong, SH and Coker, OO and Dai, Z and Li, X and Szeto, CH and Sugimura, N and Lam, TY and Yu, AC and Wang, X and Chen, Z and Wong, MC and Ng, SC and Chan, MTV and Chan, PKS and Chan, FKL and Sung, JJ and Yu, J}, title = {Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes.}, journal = {Gastroenterology}, volume = {155}, number = {2}, pages = {529-541.e5}, doi = {10.1053/j.gastro.2018.04.018}, pmid = {29689266}, issn = {1528-0012}, mesh = {Austria/epidemiology ; Biomarkers, Tumor/*analysis ; Case-Control Studies ; Cohort Studies ; Colonoscopy ; Colorectal Neoplasms/diagnostic imaging/mortality/pathology/*virology ; Cross-Sectional Studies ; Dysbiosis/diagnostic imaging/*virology ; Feces/virology ; Female ; France/epidemiology ; Gastrointestinal Microbiome/*genetics ; Germany/epidemiology ; Hong Kong/epidemiology ; Humans ; Male ; Metagenomics ; Middle Aged ; Sensitivity and Specificity ; Survival Analysis ; Viruses/*genetics ; }, abstract = {BACKGROUND &amp; AIMS: Patients with colorectal cancer (CRC) have a different gut microbiome signature than individuals without CRC. Little is known about the viral component of CRC-associated microbiome. We aimed to identify and validate viral taxonomic markers of CRC that might be used in detection of the disease or predicting outcome.<br><br>METHODS: We performed shotgun metagenomic analyses of viromes of fecal samples from 74 patients with CRC (cases) and 92 individuals without CRC (controls) in Hong Kong (discovery cohort). Viral sequences were classified by taxonomic alignment against an integrated microbial reference genome database. Viral markers associated with CRC were validated using fecal samples from 3 separate cohorts: 111 patients with CRC and 112 controls in Hong Kong, 46 patients with CRC and 63 controls in Austria, and 91 patients with CRC and 66 controls in France and Germany. Using abundance profiles of CRC-associated virome genera, we constructed random survival forest models to identify those associated with patient survival times.<br><br>RESULTS: The diversity of the gut bacteriophage community was significantly increased in patients with CRC compared with controls. Twenty-two viral taxa discriminated cases from controls with an area under the receiver operating characteristic curve of 0.802 in the discovery cohort. The viral markers were validated in 3 cohorts, with area under the receiver operating characteristic curves of 0.763, 0.736, and 0.715, respectively. Clinical subgroup analysis showed that dysbiosis of the gut virome was associated with early- and late-stage CRC. A combination of 4 taxonomic markers associated with reduced survival of patients with CRC (log-rank test, P = 8.1 × 10-6) independently of tumor stage, lymph node metastases, or clinical parameters. We found altered interactions between bacteriophages and oral bacterial commensals in fecal samples from patients with CRC compared with controls.<br><br>CONCLUSIONS: In a metagenomic analysis of fecal samples from patients and controls, we identified virome signatures associated with CRC. These data might be used to develop tools to identify individuals with CRC or predict outcomes.}, }
@article {pmid29438346, year = {2018}, author = {Wang, C and Zaheer, M and Bian, F and Quach, D and Swennes, AG and Britton, RA and Pflugfelder, SC and de Paiva, CS}, title = {Sjögren-Like Lacrimal Keratoconjunctivitis in Germ-Free Mice.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, doi = {10.3390/ijms19020565}, pmid = {29438346}, issn = {1422-0067}, support = {P30 CA125123/CA/NCI NIH HHS/United States ; T32 AI053831/AI/NIAID NIH HHS/United States ; P30 AI036211/AI/NIAID NIH HHS/United States ; P30 EY002520/EY/NEI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 EY026893/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; CD4-Positive T-Lymphocytes/immunology ; Fecal Microbiota Transplantation ; Female ; Germ-Free Life/*immunology ; Homeodomain Proteins/genetics/metabolism ; Immunity, Innate ; Interferon-gamma/metabolism ; Keratoconjunctivitis/immunology/*microbiology/therapy ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota ; }, abstract = {Commensal bacteria play an important role in the formation of the immune system but their role in the maintenance of immune homeostasis at the ocular surface and lacrimal gland remains poorly understood. This study investigated the eye and lacrimal gland phenotype in germ-free and conventional C57BL/6J mice. Our results showed that germ-free mice had significantly greater corneal barrier disruption, greater goblet cell loss, and greater total inflammatory cell and CD4⁺ T cell infiltration within the lacrimal gland compared to the conventionally housed group. A greater frequency of CD4⁺IFN-γ⁺ cells was observed in germ-free lacrimal glands. Females exhibited a more severe phenotype compared to males. Adoptive transfer of CD4⁺ T cells isolated from female germ-free mice into RAG1KO mice transferred Sjögren-like lacrimal keratoconjunctivitis. Fecal microbiota transplant from conventional mice reverted dry eye phenotype in germ-free mice and decreased CD4⁺IFN-γ⁺ cells to levels similar to conventional C57BL/6J mice. These findings indicate that germ-free mice have a spontaneous lacrimal keratoconjunctivitis similar to that observed in Sjögren syndrome patients and demonstrate that commensal bacteria function in maintaining immune homeostasis on the ocular surface. Thus, manipulation of intestinal commensal bacteria has the potential to become a novel therapeutic approach to treat Sjögren Syndrome.}, }
@article {pmid29191163, year = {2017}, author = {Ignasiak, K and Maxwell, A}, title = {Antibiotic-resistant bacteria in the guts of insects feeding on plants: prospects for discovering plant-derived antibiotics.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {223}, doi = {10.1186/s12866-017-1133-0}, pmid = {29191163}, issn = {1471-2180}, support = {BBS/E/J/00000201//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004561/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/chemistry/isolation &amp; purification/*pharmacology ; Bacteria/*drug effects/isolation &amp; purification ; Chromatography, High Pressure Liquid ; Chromatography, Liquid ; Drug Resistance, Bacterial/*drug effects ; Gastrointestinal Tract/microbiology ; Insecta/*microbiology ; Metagenomics ; Microbial Sensitivity Tests ; Microbiota ; Plant Extracts/chemistry/*pharmacology ; Plants/chemistry ; Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Although plants produce many secondary metabolites, currently none of these are commercial antibiotics. Insects feeding on specific plants can harbour bacterial strains resistant to known antibiotics suggesting that compounds in the plant have stimulated resistance development. We sought to determine whether the occurrence of antibiotic-resistant bacteria in insect guts was a widespread phenomenon, and whether this could be used as a part of a strategy to identify antibacterial compounds from plants.<br><br>RESULTS: Six insect/plant pairs were selected and the insect gut bacteria were identified and assessed for antibiotic susceptibilities compared with type strains from culture collections. We found that the gut strains could be more or less susceptible to antibiotics than the type strains, or show no differences. Evidence of antibacterial activity was found in the plant extracts from five of the six plants, and, in one case Catharanthus roseus (Madagascar Periwinkle), compounds with antibacterial activity were identified.<br><br>CONCLUSION: Bacterial strains isolated from insect guts show a range of susceptibilities to antibiotics suggesting a complex interplay between species in the insect gut microbiome. Extracts from selected plants can show antibacterial activity but it is not easy to isolate and identify the active components. We found that vindoline, present in Madagascar Periwinkle extracts, possessed moderate antibacterial activity. We suggest that plant-derived antibiotics are a realistic possibility given the advances in genomic and metabolomic methodologies.}, }
@article {pmid30086347, year = {2018}, author = {Miró-Abella, E and Torrell, H and Herrero, P and Canela, N and Arola, L and Borrull, F and Ras, R and Fontanals, N}, title = {Monitoring and evaluation of the interaction between deoxynivalenol and gut microbiota in Wistar rats by mass spectrometry-based metabolomics and next-generation sequencing.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fct.2018.08.006}, pmid = {30086347}, issn = {1873-6351}, abstract = {Published evidence has demonstrated the several toxic characteristics of mycotoxins and their considerable risk to human and animal health. One of the most common uncertainties regards whether if very low concentrations of the mycotoxin deoxynivalenol (DON), easily consumed within the Mediterranean Diet, can cause metabolic alterations; some of them produced by the interaction between DON and gut microbiota. Accordingly, faecal samples were collected from Wistar rats that had consumed the mycotoxin DON at low levels (60 and 120 μg kg-1 body weight of DON per day), and were analysed by ultra-high performance liquid chromatography coupled with tandem mass spectrometry detection, in order to monitor the mycotoxin DON and its metabolite de-epoxy deoxynivalenol (DOM-1). The obtained results showed an evolution in DON excretion and the metabolite DOM-1 which has less toxic properties, over the course of the days of the study. To elucidate whether intestinal microbiota had a role in the observed detoxification process, the changes in microbial gut biodiversity were explored through 16s rRNA high throughput sequencing. No main changes were detected but significant increase in Coprococcus genus relative abundance was found. Further studies are needed to confirm if intestinal microbiota composition and function are affected by low mycotoxin concentrations.}, }
@article {pmid29768437, year = {2018}, author = {Willmann, C and Mata, X and Hanghoej, K and Tonasso, L and Tisseyre, L and Jeziorski, C and Cabot, E and Chevet, P and Crubézy, E and Orlando, L and Esclassan, R and Thèves, C}, title = {Oral health status in historic population: Macroscopic and metagenomic evidence.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0196482}, doi = {10.1371/journal.pone.0196482}, pmid = {29768437}, issn = {1932-6203}, mesh = {DNA, Ancient/isolation &amp; purification ; DNA, Bacterial/genetics/history/isolation &amp; purification ; Dental Caries/history/microbiology/pathology ; Female ; France ; Health Status ; History, 18th Century ; Humans ; Male ; Metagenomics ; Microbiota/genetics ; Oral Health/*history ; Paleodontology ; Periodontitis/history/microbiology/pathology ; Rural Population/history ; }, abstract = {Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macroscopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces viscosus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olsenella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or periodontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual.}, }
@article {pmid29680562, year = {2018}, author = {Ribicic, D and Netzer, R and Hazen, TC and Techtmann, SM and Drabløs, F and Brakstad, OG}, title = {Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater.}, journal = {Marine pollution bulletin}, volume = {129}, number = {1}, pages = {370-378}, doi = {10.1016/j.marpolbul.2018.02.034}, pmid = {29680562}, issn = {1879-3363}, mesh = {Biodegradation, Environmental ; Environmental Monitoring/*methods ; *Metagenome ; Microbial Consortia/*genetics ; Norway ; Petroleum/*analysis ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {Oil biodegradation as a weathering process has been extensively investigated over the years, especially after the Deepwater Horizon blowout. In this study, we performed microcosm experiments at 5 °C with chemically dispersed oil in non-amended seawater. We link biodegradation processes with microbial community and metagenome dynamics and explain the succession based on substrate specialization. Reconstructed genomes and 16S rRNA gene analysis revealed that Bermanella and Zhongshania were the main contributors to initial n-alkane breakdown, while subsequent abundances of Colwellia and microorganisms closely related to Porticoccaceae were involved in secondary n‑alkane breakdown and beta‑oxidation. Cycloclasticus, Porticoccaceae and Spongiiabcteraceae were associated with degradation of mono- and poly-cyclic aromatics. Successional pattern of genes coding for hydrocarbon degrading enzymes at metagenome level, and reconstructed genomic content, revealed a high differentiation of bacteria involved in hydrocarbon biodegradation. A cooperation among oil degrading microorganisms is thus needed for the complete substrate transformation.}, }
@article {pmid29440402, year = {2018}, author = {Grébert, T and Doré, H and Partensky, F and Farrant, GK and Boss, ES and Picheral, M and Guidi, L and Pesant, S and Scanlan, DJ and Wincker, P and Acinas, SG and Kehoe, DM and Garczarek, L}, title = {Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {9}, pages = {E2010-E2019}, doi = {10.1073/pnas.1717069115}, pmid = {29440402}, issn = {1091-6490}, mesh = {*Acclimatization ; Chlorophyll/chemistry ; Color ; Computer Simulation ; Cyanobacteria/*genetics ; Ecosystem ; Ecotype ; Light ; Likelihood Functions ; Metagenome ; *Oceans and Seas ; Photosynthesis/physiology ; Phycobilisomes/*physiology ; Phylogeny ; Pigmentation ; Seawater/*microbiology ; Synechococcus/*genetics ; }, abstract = {Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined due to the lack of a single-genetic marker resolving all pigment types (PTs). Here, we developed and employed a robust method based on three distinct marker genes (cpcBA, mpeBA, and mpeW) to estimate the relative abundance of all known Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to reveal the global distribution of Synechococcus PTs and to define their environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified populations in which CA4 might be nonfunctional due to the lack of specific CA4 genes, notably in warm high-nutrient low-chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study provides important insights into the ecology of Synechococcus and highlights the complex interactions between vertical phylogeny, pigmentation, and environmental parameters that shape Synechococcus community structure and evolution.}, }
@article {pmid29103940, year = {2017}, author = {Nater, A and Mattle-Greminger, MP and Nurcahyo, A and Nowak, MG and de Manuel, M and Desai, T and Groves, C and Pybus, M and Sonay, TB and Roos, C and Lameira, AR and Wich, SA and Askew, J and Davila-Ross, M and Fredriksson, G and de Valles, G and Casals, F and Prado-Martinez, J and Goossens, B and Verschoor, EJ and Warren, KS and Singleton, I and Marques, DA and Pamungkas, J and Perwitasari-Farajallah, D and Rianti, P and Tuuga, A and Gut, IG and Gut, M and Orozco-terWengel, P and van Schaik, CP and Bertranpetit, J and Anisimova, M and Scally, A and Marques-Bonet, T and Meijaard, E and Krützen, M}, title = {Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species.}, journal = {Current biology : CB}, volume = {27}, number = {22}, pages = {3487-3498.e10}, doi = {10.1016/j.cub.2017.09.047}, pmid = {29103940}, issn = {1879-0445}, mesh = {Animals ; Behavior, Animal/physiology ; Biological Evolution ; Endangered Species ; Gene Flow/genetics ; *Genetic Speciation ; Genetic Variation ; Genome ; Genomics ; Hominidae/genetics ; Metagenomics/methods ; Phylogeny ; Pongo/classification/*genetics/physiology ; Pongo abelii/genetics ; Pongo pygmaeus/genetics ; }, abstract = {Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. VIDEO ABSTRACT.}, }
@article {pmid28844808, year = {2017}, author = {Torres-Fuentes, C and Schellekens, H and Dinan, TG and Cryan, JF}, title = {The microbiota-gut-brain axis in obesity.}, journal = {The lancet. Gastroenterology &amp; hepatology}, volume = {2}, number = {10}, pages = {747-756}, doi = {10.1016/S2468-1253(17)30147-4}, pmid = {28844808}, issn = {2468-1253}, mesh = {Affect ; Appetite Regulation ; Brain/*metabolism ; Diet, Reducing ; Energy Metabolism ; Fecal Microbiota Transplantation ; Feeding Behavior/psychology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Obesity/*metabolism/psychology/therapy ; Prebiotics ; Probiotics/therapeutic use ; Reward ; }, abstract = {Changes in microbial diversity and composition are increasingly associated with several disease states including obesity and behavioural disorders. Obesity-associated microbiota alter host energy harvesting, insulin resistance, inflammation, and fat deposition. Additionally, intestinal microbiota can regulate metabolism, adiposity, homoeostasis, and energy balance as well as central appetite and food reward signalling, which together have crucial roles in obesity. Moreover, some strains of bacteria and their metabolites might target the brain directly via vagal stimulation or indirectly through immune-neuroendocrine mechanisms. Therefore, the gut microbiota is becoming a target for new anti-obesity therapies. Further investigations are needed to elucidate the intricate gut-microbiota-host relationship and the potential of gut-microbiota-targeted strategies, such as dietary interventions and faecal microbiota transplantation, as promising metabolic therapies that help patients to maintain a healthy weight throughout life.}, }
@article {pmid26807926, year = {2016}, author = {Groah, SL and Pérez-Losada, M and Caldovic, L and Ljungberg, IH and Sprague, BM and Castro-Nallar, E and Chandel, NJ and Hsieh, MH and Pohl, HG}, title = {Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder Dysfunction.}, journal = {The Journal of urology}, volume = {196}, number = {2}, pages = {579-587}, doi = {10.1016/j.juro.2016.01.088}, pmid = {26807926}, issn = {1527-3792}, mesh = {Adult ; Biomarkers/urine ; Case-Control Studies ; Cross-Sectional Studies ; Female ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Phenotype ; Urinary Bladder, Neurogenic/diagnosis/*microbiology/physiopathology/urine ; Urine/*microbiology ; }, abstract = {PURPOSE: We used the PathoScope platform to perform species level analyses of publicly available, 16S rRNA pyrosequenced, asymptomatic urine data to determine relationships between microbiomes, and clinical and functional phenotypes.<br><br>MATERIALS AND METHODS: We reanalyzed previously reported, cross-sectionally acquired urine samples from 47 asymptomatic subjects, including 23 controls and 24 subjects with neuropathic bladder. Urine was originally collected by the usual method of bladder drainage and analyzed by urinalysis, culture and pyrosequencing. Urinalysis and culture values were stratified as leukocyte esterase (0, or 1 or greater), nitrite (positive or negative), pyuria (fewer than 5, or 5 or greater white blood cells per high power field), cloudy urine (positive or negative) and urine culture bacterial growth (less than 50,000, or 50,000 or greater cfu/ml). PathoScope was used for next generation sequencing alignment, bacterial classification and microbial diversity characterization.<br><br>RESULTS: Subjects with neuropathic bladder were significantly more likely to have positive leukocyte esterase and pyuria, cloudy urine and bacterial growth. Of 47 samples 23 showed bacterial growth on culture and in all samples bacteria were identified by pyrosequencing. Nonneuropathic bladder urine microbiomes included greater proportions of Lactobacillus crispatus in females and Staphylococcus haemolyticus in males. The Lactobacillus community differed significantly among females depending on bladder function. Irrespective of gender the subjects with neuropathic bladder had greater proportions of Enterococcus faecalis, Proteus mirabilis and Klebsiella pneumonia. In 4 subjects with neuropathic bladder Actinobaculum sp. was detected by sequencing and by PathoScope but not by cultivation and in all cases it was associated with pyuria.<br><br>CONCLUSIONS: Using PathoScope plus 16S pyrosequencing we were able to identify unique, phenotype dependent, species level microbes. Novel findings included absent L. crispatus in the urine of females with neuropathic bladder and the presence of Actinobaculum only in subjects with neuropathic bladder.}, }
@article {pmid30072968, year = {2018}, author = {Dittberner, H and Ohlmann, N and Acquisti, C}, title = {Stoichio-Metagenomics of Ocean Waters: A Molecular Evolution Approach to Trace the Dynamics of Nitrogen Conservation in Natural Communities.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1590}, doi = {10.3389/fmicb.2018.01590}, pmid = {30072968}, issn = {1664-302X}, abstract = {Nitrogen is crucially limiting in ocean surface waters, and its availability varies substantially with coastal regions typically richer in nutrients than open oceans. In a biological stoichiometry framework, a parsimonious strategy of nitrogen allocation predicts nitrogen content of proteins to be lower in communities adapted to open ocean than to coastal regions. To test this hypothesis we have directly interrogated marine microbial communities, using a series of metagenomics datasets with a broad geographical distribution from the Global Ocean Sampling Expedition. Analyzing over 20 million proteins, we document a ubiquitous signal of nitrogen conservation in open ocean communities, both in membrane and non-membrane proteins. Efficient nitrogen allocation is expected to specifically target proteins that are expressed at high rate in response to nitrogen starvation. Furthermore, in order to preserve protein functional efficiency, economic nitrogen allocation is predicted to target primarily the least functionally constrained regions of proteins. Contrasting the NtcA-induced pathway, typically up-regulated in response to nitrogen starvation, with the arginine anabolic pathway, which is instead up-regulated in response to nitrogen abundance, we show how both these predictions are fulfilled. Using evolutionary rates as an informative proxy of functional constraints, we show that variation in nitrogen allocation between open ocean and coastal communities is primarily localized in the least functionally constrained regions of the genes triggered by NtcA. As expected, such a pattern is not detectable in the genes involved in the arginine anabolic pathway. These results directly link environmental nitrogen availability to different adaptive strategies of genome evolution, and emphasize the relevance of the material costs of evolutionary change in natural ecosystems.}, }
@article {pmid29439665, year = {2018}, author = {Feng, G and Xie, T and Wang, X and Bai, J and Tang, L and Zhao, H and Wei, W and Wang, M and Zhao, Y}, title = {Metagenomic analysis of microbial community and function involved in cd-contaminated soil.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {11}, doi = {10.1186/s12866-018-1152-5}, pmid = {29439665}, issn = {1471-2180}, mesh = {Amino Acids/metabolism ; Bacteria/classification/*drug effects/genetics/metabolism ; Biodiversity ; Cadmium/metabolism/*toxicity ; China ; DNA, Bacterial ; Environmental Pollution ; Fatty Acids/metabolism ; Metabolic Networks and Pathways ; *Metagenomics ; Metals, Heavy/metabolism ; Microbial Consortia/*drug effects ; Nucleotides/metabolism ; Open Reading Frames ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/metabolism/*toxicity ; }, abstract = {BACKGROUND: Soil contaminated with the heavy metal Cadmium (Cd) is a widespread problem in many parts of the world. Based on metagenomic analysis, we investigated the functional potential and structural diversity of the microbial community in Cd-contaminated and non-contaminated soil samples and we explored the associated metabolic pathway network in cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG).<br><br>RESULTS: The results showed that microorganisms in these soils were quite abundant, and many of them possessed numerous physiological functions. However, Cd-contamination has the potential to reduce the microbial diversity and further alter the community structure in the soil. Notably, function analysis of the crucial microorganisms (e. g. Proteobacteria, Sulfuricella and Thiobacillus) indicated that these bacteria and their corresponding physiological functions were important for the community to cope with Cd pollution. The COG annotation demonstrated that the predominant category was the microbial metabolism cluster in both soil samples, while the relative abundance of metabolic genes was increased in the Cd-contaminated soil. The KEGG annotation results exhibited that the non-contaminated soil had more genes, pathways, modules, orthologies and enzymes involved in metabolic pathways of microbial communities than the Cd-contaminated soil. The relative abundance of some dominant KEGG pathways increased in the Cd contaminated soil, and they were mostly enriched to the metabolism, biosynthesis and degradation of amino acids, fatty acids and nucleotides, which was related to Cd tolerance of the microorganisms.<br><br>CONCLUSIONS: Cd-contamination can decrease the taxonomic species of microbes in soil and change the soil microbial composition. The functional pathways involved in the soil change with microbial structure variation, many of which are related to the heavy metal tolerance of soil microbes. The Cd-contaminated soil microbes is a potential resource for exploring cadmium resistant or tolerant bacteria.}, }
@article {pmid29153320, year = {2017}, author = {Dudek, NK and Sun, CL and Burstein, D and Kantor, RS and Aliaga Goltsman, DS and Bik, EM and Thomas, BC and Banfield, JF and Relman, DA}, title = {Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome.}, journal = {Current biology : CB}, volume = {27}, number = {24}, pages = {3752-3762.e6}, doi = {10.1016/j.cub.2017.10.040}, pmid = {29153320}, issn = {1879-0445}, mesh = {Animals ; Archaea/*classification ; Bacteria/*classification ; Bottle-Nosed Dolphin/*microbiology ; Female ; *Genome, Archaeal ; *Genome, Bacterial ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Mouth/microbiology ; }, abstract = {The vast majority of bacterial diversity lies within phylum-level lineages called &quot;candidate phyla,&quot; which lack isolated representatives and are poorly understood. These bacteria are surprisingly abundant in the oral cavity of marine mammals. We employed a genome-resolved metagenomic approach to recover and characterize genomes and functional potential from microbes in the oral gingival sulcus of two bottlenose dolphins (Tursiops truncatus). We detected organisms from 24 known bacterial phyla and one archaeal phylum. We also recovered genomes from two deep-branching, previously uncharacterized phylum-level lineages (here named &quot;Candidatus Delphibacteria&quot; and &quot;Candidatus Fertabacteria&quot;). The Delphibacteria lineage is found in both managed and wild dolphins; its metabolic profile suggests a capacity for denitrification and a possible role in dolphin health. We uncovered a rich diversity of predicted Cas9 proteins, including the two longest predicted Cas9 proteins to date. Notably, we identified the first type II CRISPR-Cas systems encoded by members of the Candidate Phyla Radiation. Using their spacer sequences, we subsequently identified and assembled a complete Saccharibacteria phage genome. These findings underscore the immense microbial diversity and functional potential that await discovery in previously unexplored environments.}, }
@article {pmid30069051, year = {2018}, author = {Bahram, M and Hildebrand, F and Forslund, SK and Anderson, JL and Soudzilovskaia, NA and Bodegom, PM and Bengtsson-Palme, J and Anslan, S and Coelho, LP and Harend, H and Huerta-Cepas, J and Medema, MH and Maltz, MR and Mundra, S and Olsson, PA and Pent, M and Põlme, S and Sunagawa, S and Ryberg, M and Tedersoo, L and Bork, P}, title = {Structure and function of the global topsoil microbiome.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-018-0386-6}, pmid = {30069051}, issn = {1476-4687}, abstract = {Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.}, }
@article {pmid29382070, year = {2018}, author = {D'Argenio, V}, title = {Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, doi = {10.3390/ijms19020383}, pmid = {29382070}, issn = {1422-0067}, mesh = {*Gastrointestinal Microbiome ; Genomics/*methods/standards ; Humans ; *Metagenome ; Transcriptome ; }, abstract = {The study of the human microbiome has become a very popular topic. Our microbial counterpart, in fact, appears to play an important role in human physiology and health maintenance. Accordingly, microbiome alterations have been reported in an increasing number of human diseases. Despite the huge amount of data produced to date, less is known on how a microbial dysbiosis effectively contributes to a specific pathology. To fill in this gap, other approaches for microbiome study, more comprehensive than 16S rRNA gene sequencing, i.e., shotgun metagenomics and metatranscriptomics, are becoming more widely used. Methods standardization and the development of specific pipelines for data analysis are required to contribute to and increase our understanding of the human microbiome relationship with health and disease status.}, }
@article {pmid29179769, year = {2017}, author = {Ma, L and Li, B and Jiang, XT and Wang, YL and Xia, Y and Li, AD and Zhang, T}, title = {Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {154}, doi = {10.1186/s40168-017-0369-0}, pmid = {29179769}, issn = {2049-2618}, support = {172057/15E//Hong Kong General Research Fund/ ; JCYJ20150831192847649//Shenzhen Knowledge Innovation Program-Basic Research Project/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; China ; Drinking Water/*analysis/*microbiology ; Drug Resistance, Microbial/*genetics ; Drug Resistance, Multiple/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Hong Kong ; Humans ; Metagenomics/methods ; Microbial Consortia/drug effects/genetics ; Public Health ; Surveys and Questionnaires ; United States ; Water Purification ; }, abstract = {BACKGROUND: Excesses of antibiotic resistance genes (ARGs), which are regarded as emerging environmental pollutants, have been observed in various environments. The incidence of ARGs in drinking water causes potential risks to human health and receives more attention from the public. However, ARGs harbored in drinking water remain largely unexplored. In this study, we aimed at establishing an antibiotic resistome catalogue in drinking water samples from a wide range of regions and to explore the potential hosts of ARGs.<br><br>RESULTS: A catalogue of antibiotic resistome in drinking water was established, and the host-tracking of ARGs was conducted through a large-scale survey using metagenomic approach. The drinking water samples were collected at the point of use in 25 cities in mainland China, Hong Kong, Macau, Taiwan, South Africa, Singapore and the USA. In total, 181 ARG subtypes belonging to 16 ARG types were detected with an abundance range of 2.8 × 10-2 to 4.2 × 10-1 copies of ARG per cell. The highest abundance was found in northern China (Henan Province). Bacitracin, multidrug, aminoglycoside, sulfonamide, and beta-lactam resistance genes were dominant in drinking water. Of the drinking water samples tested, 84% had a higher ARG abundance than typical environmental ecosystems of sediment and soil. Metagenomic assembly-based host-tracking analysis identified Acidovorax, Acinetobacter, Aeromonas, Methylobacterium, Methyloversatilis, Mycobacterium, Polaromonas, and Pseudomonas as the hosts of ARGs. Moreover, potential horizontal transfer of ARGs in drinking water systems was proposed by network and Procrustes analyses.<br><br>CONCLUSIONS: The antibiotic resistome catalogue compiled using a large-scale survey provides a useful reference for future studies on the global surveillance and risk management of ARGs in drinking water. .}, }
@article {pmid29179741, year = {2017}, author = {Anderson, CL and Sullivan, MB and Fernando, SC}, title = {Dietary energy drives the dynamic response of bovine rumen viral communities.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {155}, doi = {10.1186/s40168-017-0374-3}, pmid = {29179741}, issn = {2049-2618}, support = {2016-67011-24783//National Institute of Food and Agriculture/ ; 2012-68002-19823//National Institute of Food and Agriculture/ ; 3790.01//Gordon and Betty Moore Foundation/ ; }, mesh = {Animals ; Bacteriophages/genetics ; Cattle ; Cross-Over Studies ; DNA, Viral/genetics ; *Diet ; Food ; Metagenome ; Metagenomics/methods ; Microbiota/drug effects/*genetics ; Rumen/microbiology/*virology ; Sequence Analysis, DNA ; Viruses/classification/drug effects/*genetics/isolation &amp; purification ; Zinc/pharmacology ; }, abstract = {BACKGROUND: Rumen microbes play a greater role in host energy acquisition than that of gut-associated microbes in monogastric animals. Although genome-enabled advancements are providing access to the vast diversity of uncultivated microbes, our understanding of variables shaping rumen microbial communities is in its infancy. Viruses have been shown to impact microbial populations through a myriad of processes, including cell lysis and reprogramming of host metabolism. However, little is known about the processes shaping the distribution of rumen viruses or how viruses may modulate microbial-driven processes in the rumen. To this end, we investigated how rumen bacterial and viral community structure and function responded in five steers fed four randomized dietary treatments in a crossover design.<br><br>RESULTS: Total digestible nutrients (TDN), a measure of dietary energy, best explained the variation in bacterial and viral communities. Additional ecological drivers of viral communities included dietary zinc content and microbial functional diversity. Using partial least squares regression, we demonstrate significant associations between the abundances of 267 viral populations and variables driving the variation in rumen viral communities. While rumen viruses were dynamic, 14 near ubiquitous viral populations were identified, suggesting the presence of a core rumen virome largely comprised of novel viruses. Moreover, analysis of virally encoded auxiliary metabolic genes (AMGs) indicates rumen viruses have glycosidic hydrolases to potentially augment the breakdown of complex carbohydrates to increase energy production. Other AMGs identified have a role in redirecting carbon to the pentose phosphate pathway and one carbon pools by folate to boost viral replication.<br><br>CONCLUSIONS: We demonstrate that rumen bacteria and viruses have differing responses and ecological drivers to dietary perturbation. Our results show that rumen viruses have implications for understanding the structuring of the previously identified core rumen microbiota and impacting microbial metabolism through a vast array of AMGs. AMGs in the rumen appear to have consequences for microbial metabolism that are largely in congruence with the current paradigm established in marine systems. This study provides a foundation for future hypotheses regarding the dynamics of viral-mediated processes in the rumen.}, }
@article {pmid29178920, year = {2017}, author = {Nash, AK and Auchtung, TA and Wong, MC and Smith, DP and Gesell, JR and Ross, MC and Stewart, CJ and Metcalf, GA and Muzny, DM and Gibbs, RA and Ajami, NJ and Petrosino, JF}, title = {The gut mycobiome of the Human Microbiome Project healthy cohort.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {153}, doi = {10.1186/s40168-017-0373-4}, pmid = {29178920}, issn = {2049-2618}, support = {U54 HG003273/HG/NHGRI NIH HHS/United States ; 2 U54 HG003273//National Human Genome Research Institute/ ; }, mesh = {Candida/classification/genetics/isolation &amp; purification ; Cohort Studies ; DNA, Ribosomal Spacer/genetics ; Feces/microbiology ; Fungi/classification/genetics/*isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; *Healthy Volunteers ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Malassezia/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Microbiota ; *Mycobiome ; RNA, Ribosomal, 18S/genetics ; Saccharomyces/classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene.<br><br>RESULTS: Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents.<br><br>CONCLUSIONS: Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual's mycobiome is no more similar to itself over time than to another person's. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples.}, }
@article {pmid29083035, year = {2018}, author = {Laskar, F and Das Purkayastha, S and Sen, A and Bhattacharya, MK and Misra, BB}, title = {Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems.}, journal = {Journal of basic microbiology}, volume = {58}, number = {2}, pages = {101-119}, doi = {10.1002/jobm.201700341}, pmid = {29083035}, issn = {1521-4028}, mesh = {Archaea/*classification/genetics/growth &amp; development/*metabolism ; *Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water/*microbiology ; Geologic Sediments/microbiology ; Lakes/microbiology ; Metagenomics/*methods ; Methane/*metabolism ; Microbiological Techniques/*methods ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {About half of the global methane (CH4) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.}, }
@article {pmid28929212, year = {2018}, author = {Parmar, K and Dafale, N and Pal, R and Tikariha, H and Purohit, H}, title = {An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach.}, journal = {Current microbiology}, volume = {75}, number = {2}, pages = {132-141}, doi = {10.1007/s00284-017-1357-0}, pmid = {28929212}, issn = {1432-0991}, mesh = {Bacteriophages/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; *Ecosystem ; Metagenomics ; *Water Microbiology ; }, abstract = {Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called &quot;kill the winner&quot; suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses. Differential relative abundance of phage families-Siphoviridae (34%) and Myoviridae (26%) in WWTP, Myoviridae (30%) and Podoviridae (23%) in fresh water, and Myoviridae (41%) and Podoviridae (8%) in marine-was found to be a discriminating factor among four habitats while Rudiviridae (9%), Globuloviridae (8%), and Lipothrixviridae (1%) were exclusively observed in hot water spring. Subsequently, at genera level, Bpp-1-like virus, Chlorovirus, and T4-like virus were found abundant in WWTP, fresh, and marine habitat, respectively. PCA analysis revealed completely disparate composition of phage in hot water spring from other three ecosystems. Similar analysis of relative abundance of functional features corroborated observations from taxa analysis. Functional features corresponding to phage packaging machinery, replication, integration and excision, and gene transfer discriminated among four habitats. The comparative metagenomics approach exhibited genetically distinct phage communities among four habitats. Results revealed that selective distribution of phage communities would help in understanding the role of phages in food chains, nutrient cycling, and microbial ecology. Study of specific phages would also help in controlling environmental pathogens including MDR bacterial populations using phage therapy approach by selective mining and isolation of phages against specific pathogens persisting in a given environment.}, }
@article {pmid28910638, year = {2017}, author = {Verster, AJ and Ross, BD and Radey, MC and Bao, Y and Goodman, AL and Mougous, JD and Borenstein, E}, title = {The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition.}, journal = {Cell host &amp; microbe}, volume = {22}, number = {3}, pages = {411-419.e4}, doi = {10.1016/j.chom.2017.08.010}, pmid = {28910638}, issn = {1934-6069}, support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; R35 GM118159/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; R01 AI080609/AI/NIAID NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Bacteroides/classification/genetics/isolation &amp; purification/metabolism ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Middle Aged ; Phylogeny ; Type VI Secretion Systems/genetics/*metabolism ; Young Adult ; }, abstract = {Although gut microbiome composition is well defined, the mechanisms underlying community assembly remain poorly understood. Bacteroidales possess three genetic architectures (GA1-3) of the type VI secretion system (T6SS), an effector delivery pathway that mediates interbacterial competition. Here we define the distribution and role of GA1-3 in the human gut using metagenomic analysis. We find that adult microbiomes harbor limited effector and cognate immunity genes, suggesting selection for compatibility at the species (GA1 and GA2) and strain (GA3) levels. Bacteroides fragilis GA3 is known to mediate potent inter-strain competition, and we observe GA3 enrichment among strains colonizing infant microbiomes, suggesting competition early in life. Additionally, GA3 is associated with increased Bacteroides abundance, indicating that this system confers an advantage in Bacteroides-rich ecosystems. Collectively, these analyses uncover the prevalence of T6SS-dependent competition and reveal its potential role in shaping human gut microbial composition.}, }
@article {pmid30055354, year = {2018}, author = {Linard, B and Crampton-Platt, A and Moriniere, J and Timmermans, MJTN and Andujar, C and Arribas, P and Miller, KE and Lipecki, J and Favreau, E and Hunter, A and Gómez-Rodríguez, C and Barton, C and Nie, R and Gillett, CPDT and Breeschoten, T and Bocak, L and Vogler, AP}, title = {The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ympev.2018.07.008}, pmid = {30055354}, issn = {1095-9513}, abstract = {A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.}, }
@article {pmid29664968, year = {2018}, author = {Betiku, OC and Yeoman, CJ and Gaylord, TG and Americus, B and Olivo, S and Duff, GC and Sealey, WM}, title = {Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195967}, doi = {10.1371/journal.pone.0195967}, pmid = {29664968}, issn = {1932-6203}, mesh = {Animal Feed ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Oncorhynchus mykiss/*microbiology ; Vegetable Proteins ; *Water Microbiology ; }, abstract = {A two-phase feeding study evaluating performance of rainbow trout and comparing luminal and mucosal gastrointestinal tract (GIT) bacterial community compositions when fed two alternative protein diets in two rearing systems was conducted. Alternative protein diets (animal protein and plant protein diets) balanced with crystalline amino acids: lysine, methionine and threonine or unbalanced, were fed to rainbow trout in two separate water systems (recirculating (RR) and flow-through (FF)) for a period of 16 weeks. The four diets, each contained 38% digestible protein and 20% fats, were fed to rainbow trout with an average weight of 12.02 ± 0.61 g, and sorted at 30 fish/tank and 12 tanks per dietary treatment. Phase 1 lasted for 8 weeks after which fish from each tank were randomly divided, with one-half moved to new tanks of the opposing system (i.e. from RR to FF and vice versa). The remaining halves were retained in their initial tank and system, and fed their original diets for another 8 weeks (phase 2). After the 16th week, 3 fish/tank were sampled for each of proximate analysis, body indexes and 16S rRNA analysis of GIT microbiota. Fish weight (P = 0.0008, P = 0.0030, P<0.0010) and body fat (P = 0.0008, P = 0.0041, P = 0.0177) were significantly affected by diet, diet quality (balanced or unbalanced) and system, respectively. Feed intake (P = 0.0008) and body energy (P<0.0010) were altered by system. Body indexes were not affected by dietary treatment and water systems. Compositional dissimilarities existed between samples from the rearing water and GIT locations (ANOSIM: (R = 0.29, P = 0.0010), PERMANOVA: R = 0.39, P = 0.0010), but not in dietary samples (ANOSIM: R = 0.004, P = 0.3140, PERMANOVA: R = 0.008, P = 0.4540). Bacteria were predominantly from the phyla Proteobacteria, Firmicutes and Bacteroidetes. Their abundance differed with more dissimilarity in the luminal samples (ANOSIM: R = 0.40, P = 0.0010, PERMANOVA: R = 0.56, P = 0.0010) than those from the mucosal intestine (ANOSIM: R = 0.37, P = 0.0010, PERMANOVA: R = 0.41, P = 0.0010). Bacteria generally associated with carbohydrate and certain amino acids metabolism were observed in the mucosal intestine while rearing water appeared to serve as the main route of colonization of Aeromonas and Acinetobacter in the rainbow trout.}, }
@article {pmid29659617, year = {2018}, author = {Mohamed Ramli, N and Giatsis, C and Md Yusoff, F and Verreth, J and Verdegem, M}, title = {Resistance and resilience of small-scale recirculating aquaculture systems (RAS) with or without algae to pH perturbation.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195862}, doi = {10.1371/journal.pone.0195862}, pmid = {29659617}, issn = {1932-6203}, mesh = {Ammonia/chemistry ; *Aquaculture ; Bacteria/classification/genetics ; Biodiversity ; *Chlorophyta ; *Fresh Water ; *Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; Nitrogen/chemistry ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Water Quality ; }, abstract = {The experimental set-up of this study mimicked recirculating aquaculture systems (RAS) where water quality parameters such as dissolved oxygen, pH, temperature, and turbidity were controlled and wastes produced by fish and feeding were converted to inorganic forms. A key process in the RAS was the conversion of ammonia to nitrite and nitrite to nitrate through nitrification. It was hypothesized that algae inclusion in RAS would improve the ammonia removal from the water; thereby improving RAS water quality and stability. To test this hypothesis, the stability of the microbiota community composition in a freshwater RAS with (RAS+A) or without algae (RAS-A) was challenged by introducing an acute pH drop (from pH 7 to 4 during three hours) to the system. Stigeoclonium nanum, a periphytic freshwater microalga was used in this study. No significant effect of the algae presence was found on the resistance to the acute pH drop on ammonia conversion to nitrite and nitrite conversion to nitrate. Also the resilience of the ammonia conversion to the pH drop disruption was not affected by the addition of algae. This could be due to the low biomass of algae achieved in the RAS. However, with regard to the conversion step of nitrite to nitrate, RAS+A was significantly more resilient than RAS-A. In terms of overall bacterial communities, the composition and predictive function of the bacterial communities was significantly different between RAS+A and RAS-A.}, }
@article {pmid29187708, year = {2017}, author = {Hirai, M and Nishi, S and Tsuda, M and Sunamura, M and Takaki, Y and Nunoura, T}, title = {Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments.}, journal = {Microbes and environments}, volume = {32}, number = {4}, pages = {336-343}, doi = {10.1264/jsme2.ME17132}, pmid = {29187708}, issn = {1347-4405}, mesh = {Base Composition/genetics ; Base Sequence ; Biodiversity ; DNA, Archaeal/analysis/*genetics ; DNA, Bacterial/analysis/*genetics ; DNA, Protozoan/analysis/*genetics ; Gene Library ; Geologic Sediments/*microbiology/*parasitology ; Metagenome/*genetics ; Metagenomics/*methods ; Seawater/microbiology/parasitology ; Sequence Analysis, DNA ; }, abstract = {Shotgun metagenomics is a low biased technology for assessing environmental microbial diversity and function. However, the requirement for a sufficient amount of DNA and the contamination of inhibitors in environmental DNA leads to difficulties in constructing a shotgun metagenomic library. We herein examined metagenomic library construction from subnanogram amounts of input environmental DNA from subarctic surface water and deep-sea sediments using two library construction kits: the KAPA Hyper Prep Kit and Nextera XT DNA Library Preparation Kit, with several modifications. The influence of chemical contaminants associated with these environmental DNA samples on library construction was also investigated. Overall, shotgun metagenomic libraries were constructed from 1 pg to 1 ng of input DNA using both kits without harsh library microbial contamination. However, the libraries constructed from 1 pg of input DNA exhibited larger biases in GC contents, k-mers, or small subunit (SSU) rRNA gene compositions than those constructed from 10 pg to 1 ng DNA. The lower limit of input DNA for low biased library construction in this study was 10 pg. Moreover, we revealed that technology-dependent biases (physical fragmentation and linker ligation vs. tagmentation) were larger than those due to the amount of input DNA.}, }
@article {pmid29490093, year = {2018}, author = {Mulukutla, SN and Hsu, JW and Gaba, R and Bohren, KM and Guthikonda, A and Iyer, D and Ajami, NJ and Petrosino, JF and Hampe, CS and Ram, N and Jahoor, F and Balasubramanyam, A}, title = {Arginine Metabolism Is Altered in Adults with A-β + Ketosis-Prone Diabetes.}, journal = {The Journal of nutrition}, volume = {148}, number = {2}, pages = {185-193}, doi = {10.1093/jn/nxx032}, pmid = {29490093}, issn = {1541-6100}, support = {R01 DK101411/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Arginine/administration &amp; dosage/blood/*metabolism ; Blood Glucose/analysis ; Body Mass Index ; Diabetes Mellitus, Type 1/*metabolism/physiopathology ; Diabetes Mellitus, Type 2/physiopathology ; Female ; Gastrointestinal Microbiome/physiology ; Glucose/administration &amp; dosage ; Glucose Clamp Technique ; Humans ; Hyperglycemia ; Insulin/blood/secretion ; Insulin-Secreting Cells/*physiology ; Kinetics ; Male ; Metabolomics/methods ; Middle Aged ; Nitric Oxide/metabolism ; Ornithine/blood ; }, abstract = {Background: A-β + ketosis-prone diabetes (KPD) is a subset of type 2 diabetes in which patients have severe but reversible β cell dysfunction of unknown etiology. Plasma metabolomic analysis indicates that abnormal arginine metabolism may be involved.<br><br>Objective: The objective of this study was to determine the relation between gut microbiome and arginine metabolism and the relation between arginine availability and β cell function in KPD patients compared with control participants.<br><br>Methods: Kinetics of arginine and related metabolites were measured with stable isotope tracers, and insulin secretory responses to arginine and glucose were determined under euglycemic and hyperglycemic conditions in 6 KPD patients and 6 age-, gender-, and body mass index-matched control participants. Glucose potentiation of arginine-induced insulin secretion was performed in a different set of 6 KPD and 3 control participants.<br><br>Results: Arginine availability was higher in KPD patients during euglycemia [53.5 ± 4.3 (mean ± SEM) compared with 40.3 ± 2.4 μmol · kg lean body mass (LBM)-1 · h-1, P = 0.03] but declined more in response to hyperglycemia (Δ 10.15 ± 2.6 compared with Δ 3.20 ± 1.3 μmol · kg LBM-1 · h-1, P = 0.041). During hyperglycemia, ornithine flux was not different between groups but after an arginine bolus, plasma ornithine AUC trended higher in KPD patients (3360 ± 294 compared with 2584 ± 259 min · μmol · L-1, P = 0.08). In both euglycemia and hyperglycemia, the first-phase insulin responses to glucose stimulation were lower in KPD patients (euglycemic insulin AUC 282 ± 108 compared with 926 ± 257 min · μU · mL-1, P = 0.02; hyperglycemic insulin AUC 358 ± 79 compared with 866 ± 292 min · μU · mL-1, P = 0.05), but exogenous arginine restored first-phase insulin secretion in KPD patients to the level of control participants.<br><br>Conclusion: Compared with control participants, KPD patients have increased arginine availability in the euglycemic state, indicating a higher requirement. This is compromised during hyperglycemia, with an inadequate supply of arginine to sustain metabolic functions such as insulin secretion. Exogenous arginine administration restores a normal insulin secretory response.}, }
@article {pmid29189738, year = {2017}, author = {Ticinesi, A and Lauretani, F and Milani, C and Nouvenne, A and Tana, C and Del Rio, D and Maggio, M and Ventura, M and Meschi, T}, title = {Aging Gut Microbiota at the Cross-Road between Nutrition, Physical Frailty, and Sarcopenia: Is There a Gut-Muscle Axis?.}, journal = {Nutrients}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/nu9121303}, pmid = {29189738}, issn = {2072-6643}, mesh = {Aging/*physiology ; *Frailty ; *Gastrointestinal Microbiome ; Humans ; Muscle, Skeletal/*physiology ; *Nutritional Status ; *Sarcopenia ; }, abstract = {Inadequate nutrition and physical inactivity are the mainstays of primary sarcopenia-physiopathology in older individuals. Gut microbiota composition is strongly dependent on both of these elements, and conversely, can also influence the host physiology by modulating systemic inflammation, anabolism, insulin sensitivity, and energy production. The bacterial metabolism of nutrients theoretically influences skeletal muscle cell functionality through producing mediators that drive all of these systemic effects. In this study, we review the scientific literature supporting the concept of the involvement of gut microbiota in primary sarcopenia physiopathology. First, we examine studies associating fecal microbiota alterations with physical frailty, i.e., the loss of muscle performance and normal muscle mass. Then, we consider studies exploring the effects of exercise on gut microbiota composition. Finally, we examine studies demonstrating the possible effects of mediators produced by gut microbiota on skeletal muscle, and intervention studies considering the effects of prebiotic or probiotic administration on muscle function. Even if there is no evidence of a distinct gut microbiota composition in older sarcopenic patients, we conclude that the literature supports the possible presence of a &quot;gut-muscle axis&quot;, whereby gut microbiota may act as the mediator of the effects of nutrition on muscle cells.}, }
@article {pmid28973555, year = {2017}, author = {Chi, L and Bian, X and Gao, B and Tu, P and Ru, H and Lu, K}, title = {The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and Its Functional Metagenome.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {160}, number = {2}, pages = {193-204}, doi = {10.1093/toxsci/kfx174}, pmid = {28973555}, issn = {1096-0929}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 ES024950/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Arsenites/*toxicity ; Bacteria/classification/*drug effects/genetics ; Dysbiosis ; Environmental Pollutants/*toxicity ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Gene Expression Regulation, Bacterial ; Intestines/*drug effects/microbiology ; Metagenome/*drug effects/genetics ; Mice, Inbred C57BL ; Ribotyping ; Sodium Compounds/*toxicity ; Time Factors ; }, abstract = {Multiple environmental factors induce dysbiosis in the gut microbiome and cause a variety of human diseases. Previously, we have first demonstrated that arsenic alters the composition of the gut microbiome. However, the functional impact of arsenic on the gut microbiome has not been adequately assessed, particularly at environmentally relevant concentrations. In this study, we used 16S rRNA sequencing and metagenomics sequencing to investigate how exposure to 100 ppb arsenic for 13 weeks alters the composition and functional capacity of the gut microbiome in mice. Arsenic exposure altered the alpha and beta diversities as well as the composition profile of the gut microbiota. Metagenomics data revealed that the abundances of genes involved in carbohydrate metabolism, especially pyruvate fermentation, short-chain fatty acid synthesis, and starch utilization, and were significantly changed. Moreover, lipopolysaccharide biosynthesis genes, multiple stress response genes, and DNA repair genes were significantly increased in the gut microbiome of arsenic-exposed mice. The genes involved in the production or processing of multiple vitamins, including folic acid and vitamins B6, B12, and K2, were also enriched in arsenic-treated mice. In, addition, genes involved in multidrug resistance and conjugative transposon proteins were highly increased after treatment with arsenic. In conclusion, we demonstrate that arsenic exposure, at an environmentally relevant dose, not only perturbed the communal composition of the gut microbiome but also profoundly altered a variety of important bacterial functional pathways.}, }
@article {pmid29232848, year = {2017}, author = {Vernocchi, P and Del Chierico, F and Quagliariello, A and Ercolini, D and Lucidi, V and Putignani, L}, title = {A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics.}, journal = {Nutrients}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/nu9121342}, pmid = {29232848}, issn = {2072-6643}, mesh = {Bacteria/*genetics ; Case-Control Studies ; Child, Preschool ; Cystic Fibrosis/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics/*methods ; Phylogeny ; *Probiotics ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Cystic fibrosis (CF) is a life-limiting hereditary disorder that results in aberrant mucosa in the lungs and digestive tract, chronic respiratory infections, chronic inflammation, and the need for repeated antibiotic treatments. Probiotics have been demonstrated to improve the quality of life of CF patients. We investigated the distribution of gut microbiota (GM) bacteria to identify new potential probiotics for CF patients on the basis of GM patterns. Fecal samples of 28 CF patients and 31 healthy controls (HC) were collected and analyzed by 16S rRNA-based pyrosequencing analysis of GM, to produce CF-HC paired maps of the distribution of operational taxonomic units (OTUs), and by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) for Kyoto Encyclopedia of Genes and Genomes (KEGG) biomarker prediction. The maps were scanned to highlight the distribution of bacteria commonly claimed as probiotics, such as bifidobacteria and lactobacilli, and of butyrate-producing colon bacteria, such as Eubacterium spp. and Faecalibacterium prausnitzii. The analyses highlighted 24 OTUs eligible as putative probiotics. Eleven and nine species were prevalently associated with the GM of CF and HC subjects, respectively. Their KEGG prediction provided differential CF and HC pathways, indeed associated with health-promoting biochemical activities in the latter case. GM profiling and KEGG biomarkers concurred in the evaluation of nine bacterial species as novel putative probiotics that could be investigated for the nutritional management of CF patients.}, }
@article {pmid29196353, year = {2017}, author = {Moffatt, MF and Cookson, WO}, title = {The lung microbiome in health and disease.}, journal = {Clinical medicine (London, England)}, volume = {17}, number = {6}, pages = {525-529}, doi = {10.7861/clinmedicine.17-6-525}, pmid = {29196353}, issn = {1473-4893}, mesh = {Asthma/microbiology ; Bronchiectasis/microbiology ; Cystic Fibrosis/microbiology ; Humans ; Lung/*microbiology ; Lung Diseases/*microbiology ; Metagenomics ; *Microbiota/genetics ; Pulmonary Disease, Chronic Obstructive/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Human Microbiome Project began 10 years ago, leading to a significant growth in understanding of the role the human microbiome plays in health and disease. In this article, we explain with an emphasis on the lung, the origins of microbiome research. We discuss how 16S rRNA gene sequencing became the first major molecular tool to examine the bacterial communities present within the human body. We highlight the pitfalls of molecular-based studies, such as false findings resulting from contamination, and the limitations of 16S rRNA gene sequencing. Knowledge about the lung microbiome has evolved from initial scepticism to the realisation that it might have a significant influence on many illnesses. We also discuss the lung microbiome in the context of disease by giving examples of important respiratory conditions. In addition, we draw attention to the challenges for metagenomic studies of respiratory samples and the importance of systematic bacterial isolation to enable host-microbiome interactions to be understood. We conclude by discussing how knowledge of the lung microbiome impacts current clinical diagnostics.}, }
@article {pmid29301588, year = {2018}, author = {Greay, TL and Gofton, AW and Paparini, A and Ryan, UM and Oskam, CL and Irwin, PJ}, title = {Recent insights into the tick microbiome gained through next-generation sequencing.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {12}, doi = {10.1186/s13071-017-2550-5}, pmid = {29301588}, issn = {1756-3305}, support = {130100050//Australian Research Council/International ; 130100050//Bayer Australia Ltd/International ; 130100050//Bayer AG (Germany)/International ; }, mesh = {Animals ; High-Throughput Nucleotide Sequencing/*utilization ; Metagenomics/*methods ; *Microbiota ; Ticks/*microbiology ; }, abstract = {The tick microbiome comprises communities of microorganisms, including viruses, bacteria and eukaryotes, and is being elucidated through modern molecular techniques. The advent of next-generation sequencing (NGS) technologies has enabled the genes and genomes within these microbial communities to be explored in a rapid and cost-effective manner. The advantages of using NGS to investigate microbiomes surpass the traditional non-molecular methods that are limited in their sensitivity, and conventional molecular approaches that are limited in their scalability. In recent years the number of studies using NGS to investigate the microbial diversity and composition of ticks has expanded. Here, we provide a review of NGS strategies for tick microbiome studies and discuss the recent findings from tick NGS investigations, including the bacterial diversity and composition, influential factors, and implications of the tick microbiome.}, }
@article {pmid29284535, year = {2017}, author = {Pires, ACAM and Villegas, LEM and Campolina, TB and Orfanó, AS and Pimenta, PFP and Secundino, NFC}, title = {Bacterial diversity of wild-caught Lutzomyia longipalpis (a vector of zoonotic visceral leishmaniasis in Brazil) under distinct physiological conditions by metagenomics analysis.}, journal = {Parasites &amp; vectors}, volume = {10}, number = {1}, pages = {627}, doi = {10.1186/s13071-017-2593-7}, pmid = {29284535}, issn = {1756-3305}, support = {305512/2014-5//Brazilian Council for Scientific and Technological Development- CNPq- Research fellowship/International ; 308849/2015-9//Brazilian Council for Scientific and Technological Development- CNPq (Research fellowship)/International ; 00242-12//Fundação de Amparo à Pesquisa do Estado de Minas Gerais (BR) FAPEMIG/International ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; Brazil ; *Gastrointestinal Microbiome ; Insect Vectors/*microbiology ; Metagenomics ; Psychodidae/*microbiology ; }, abstract = {BACKGROUND: The leishmaniases are a group of diseases caused by protozoans of the genus Leishmania, which are transmitted by the bite of phlebotomine sand flies. In the New World, Lutzomyia longipalpis is the most important vector of visceral leishmaniasis and is a proven vector for Leishmania infantum chagasi in Brazil. During development within the vector, Leishmania can interact with a variety of microorganisms such as fungi and bacteria. The presence of bacteria in the midgut of sand flies can influence the development and survival of the parasite.<br><br>RESULTS: The bacteria-targeted metagenomic analysis revealed different community compositions between the distinct physiological stages of those tested. The amplicon-oriented metagenomic profiling revealed 64 bacterial genera and 46 families. By crossing the taxa indices from each experimental condition a core composed of 6 genera was identified (Enterobacter, Serratia, Stenotrophomonas, Enhydrobacter, Pseudomonas and Chryseobacterium).<br><br>CONCLUSIONS: The observed dynamic nature of the bacterial community expands the knowledge pertaining to the tripartite host-microbiota-pathogen interactions. Further studies addressing how laboratory and field collected communities differ are critical to successfully develop control strategies based on bacterial symbionts and paratransgenesis, as already tested in other arthropod vectors.}, }
@article {pmid29187243, year = {2017}, author = {Boynton, FDD and Ericsson, AC and Uchihashi, M and Dunbar, ML and Wilkinson, JE}, title = {Doxycycline induces dysbiosis in female C57BL/6NCrl mice.}, journal = {BMC research notes}, volume = {10}, number = {1}, pages = {644}, doi = {10.1186/s13104-017-2960-7}, pmid = {29187243}, issn = {1756-0500}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Disease Models, Animal ; Doxycycline/*pharmacology ; Dysbiosis/*chemically induced ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: This study aims to demonstrate the effect of oral doxycycline on fecal microbiota of mice. Doxycycline is a common effector for control of gene expression using the tet-inducible system in transgenic mice. The effect of oral doxycycline on murine gut microbiota has not been reported. We evaluated the effect of doxycycline treatment by sequencing the V4 hypervariable region of the 16S rRNA gene from fecal samples collected during a 4 week course of treatment at a dose of 2 mg/ml in the drinking water.<br><br>RESULTS: The fecal microbiota of treated animals were distinct from control animals; the decreased richness and diversity were characterized primarily by Bacteroides sp. enrichment. These effects persisted when the treatment was temporarily discontinued for 1 week. These data suggest that doxycycline treatment can induce significant dysbiosis, and its effects should be considered when used in animal models that are or maybe sensitive to perturbation of the gut microbiota.}, }
@article {pmid28562180, year = {2018}, author = {Gutleben, J and Chaib De Mares, M and van Elsas, JD and Smidt, H and Overmann, J and Sipkema, D}, title = {The multi-omics promise in context: from sequence to microbial isolate.}, journal = {Critical reviews in microbiology}, volume = {44}, number = {2}, pages = {212-229}, doi = {10.1080/1040841X.2017.1332003}, pmid = {28562180}, issn = {1549-7828}, mesh = {Metabolomics/*methods ; Metagenomics/*methods ; Microbiological Techniques/*methods ; *Microbiota ; Proteomics/*methods ; }, abstract = {The numbers and diversity of microbes in ecosystems within and around us is unmatched, yet most of these microorganisms remain recalcitrant to in vitro cultivation. Various high-throughput molecular techniques, collectively termed multi-omics, provide insights into the genomic structure and metabolic potential as well as activity of complex microbial communities. Nonetheless, pure or defined cultures are needed to (1) decipher microbial physiology and thus test multi-omics-based ecological hypotheses, (2) curate and improve database annotations and (3) realize novel applications in biotechnology. Cultivation thus provides context. In turn, we here argue that multi-omics information awaits integration into the development of novel cultivation strategies. This can build the foundation for a new era of omics information-guided microbial cultivation technology and reduce the inherent trial-and-error search space. This review discusses how information that can be extracted from multi-omics data can be applied for the cultivation of hitherto uncultured microorganisms. Furthermore, we summarize groundbreaking studies that successfully translated information derived from multi-omics into specific media formulations, screening techniques and selective enrichments in order to obtain novel targeted microbial isolates. By integrating these examples, we conclude with a proposed workflow to facilitate future omics-aided cultivation strategies that are inspired by the microbial complexity of the environment.}, }
@article {pmid30018874, year = {2018}, author = {Colabella, C and Corte, L and Roscini, L and Bassetti, M and Tascini, C and Mellor, JC and Meyer, W and Robert, V and Vu, D and Cardinali, G}, title = {NGS barcode sequencing in taxonomy and diagnostics, an application in &quot;Candida&quot; pathogenic yeasts with a metagenomic perspective.}, journal = {IMA fungus}, volume = {9}, number = {1}, pages = {91-105}, doi = {10.5598/imafungus.2018.09.01.07}, pmid = {30018874}, issn = {2210-6340}, abstract = {Species identification of yeasts and other Fungi is currently carried out with Sanger sequences of selected molecular markers, mainly from the ribosomal DNA operon, characterized by hundreds of tandem repeats of the 18S, ITS1, 5.8S, ITS2 and LSU loci. The ITS region has been recently proposed as a primary barcode marker making this region the most used one in taxonomy, phylogeny and diagnostics. The introduction of NGS is providing tools of high efficacy and relatively low cost to amplify two or more markers simultaneously with great sequencing depth. However, the presence of intra-genomic variability between the repeats requires specific analytical procedures and pipelines. In this study, 286 strains belonging to 11 pathogenic yeasts species were analysed with NGS of the region spanning from ITS1 to the D1/D2 domain of the LSU encoding ribosomal DNA. Results showed that relatively high heterogeneity can hamper the use of these sequences for the identification of single strains and even more of complex microbial mixtures. These observations point out that the metagenomics studies could be affected by species inflection at levels higher than currently expected.}, }
@article {pmid30003485, year = {2018}, author = {Li, M and Zhang, X and Yang, H and Li, X and Cui, Z}, title = {Soil sustainable utilization technology: mechanism of flavonols in resistance process of heavy metal.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-018-2485-1}, pmid = {30003485}, issn = {1614-7499}, abstract = {The soil ecosystem is critical for agricultural production, affecting many aspects of human health. Soil has more unknown biodiversity and edaphic parameters than any other ecosystem especially when polluted. Metagenomics and metatranscriptomics were applied to research on toxicological characteristics of Pb and resistance mechanism of flavonols. Rhizosphere microorganisms-plants system, a unified system closely related to soil environment was taken as research object. Results emphasize gene expression changes in different test groups. Gene ontology enrichment and eggNOG showed that Pb has a toxic effect on gene and protein function which concentrated on ATPase and ATP-dependent activity. Differentially expressed genes in the flavonols group indicated that flavonols regulate amino acid transport and other transportation process related to Pb stress. Kegg analysis represents that Pb interferences energy production process via not only the upstream like glycolysis and tricarboxylic acid (TCA) circle but also oxidative phosphorylation process, which can also produce reactive oxygen species and impact the eliminating process. Flavonols have shown the ability in alleviating toxic effect of Pb and improving the resistance of plants. Flavonols can recover the electronic transmission and other process in TCA and oxidative phosphorylation via ascorbic acid-glutathione metabolism. Flavonols activated antioxidative process and non-specific immunity via vitamins B2-B6 metabolism.}, }
@article {pmid29976249, year = {2018}, author = {Kayani, MUR and Doyle, SM and Sangwan, N and Wang, G and Gilbert, JA and Christner, BC and Zhu, TF}, title = {Metagenomic analysis of basal ice from an Alaskan glacier.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {123}, doi = {10.1186/s40168-018-0505-5}, pmid = {29976249}, issn = {2049-2618}, support = {2016YFC0206300//Ministry of Science and Technology of the People's Republic of China/ ; }, abstract = {BACKGROUND: Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on the microbial community structures and their metabolic potential is very limited. Here, we provide insights into the microbial lifestyle present at the base of the Matanuska Glacier, Alaska.<br><br>RESULTS: DNA and RNA were extracted from samples of the Matanuska Glacier basal ice. Using Illumina MiSeq and HiSeq sequencing, we investigated the microbial diversity with the metagenomic shotgun reads and 16S ribosomal RNA data. We further assembled 9 partial and draft bacterial genomes from the metagenomic assembly, and identified key metabolic pathways such as sulfur oxidation and nitrification. Collectively, our analyses suggest a prevalence of lithotrophic and heterotrophic metabolisms in the subglacial microbiome.<br><br>CONCLUSION: Our results present the first metagenomic assembly and bacterial draft genomes for a subglacial environment. These results extend our understanding of the chemical and biological processes in subglacial environments critically influenced by global climate change.}, }
@article {pmid29964641, year = {2017}, author = {Wang, BQ and Li, CY and Lu, W and Fan, H and Zhang, DZ and Wang, Z and Lü, C and Shen, FD}, title = {[Shift of Microbial Communities During the CO2-Brine-Sandstone Interaction Process].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {38}, number = {7}, pages = {2978-2987}, doi = {10.13227/j.hjkx.201612067}, pmid = {29964641}, issn = {0250-3301}, abstract = {In this study, the dynamic variation of the structure, functionality and biodiversity of indigenous microorganism during the CO2-brine-sandstone interaction process was investigated using MiSeq sequencing techniques. The results indicated that some kinds of indigenous microorganisms could grow well under the extreme condition induced by CO2-injection. After injection of CO2, the species of indigenous microorganisms tended to be single and the relative abundance of Proteobacteria reached up to 99.77% after 6 months. The dominant species varied as follows:Pseudomonas sp., Citrobacter sp. and Brevundimonas sp.. Meanwhile, some special genera such as Bacillus sp., Hydrogenophaga sp. and Rhizobium sp. with functionality of iron-reducing and denitrification were found in this study, which may have a potential effect on the capture and storage of CO2. In addition, the Shannon index decreased from 5.3302 to 1.9465 after injection of CO2, suggesting that the biodiversity reduced significantly. Function and main metabolites analysis of bacteria in the CO2-brine-sandstone interaction process showed that bacteria like Bacillus sp., Citrobacter sp. and Pseudomonas sp. could enhance CO2 solubility-trapping process. Bacteria metabolisms could accelerate the dissolution of feldspar and chlorites, and facilitate the formation of transition-state calcite and siderite. Otherwise, the great variation was mainly attributed to the change of condition driven by CO2-brine-sandstone interactions, such as pH and the chemical composition of brine water(anion and cation), etc.}, }
@article {pmid29915700, year = {2018}, author = {Carew, ME and Coleman, RA and Hoffmann, AA}, title = {Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4980}, doi = {10.7717/peerj.4980}, pmid = {29915700}, issn = {2167-8359}, abstract = {Background: High throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens identified by taxonomists are needed. This can be achieved through using DNA extraction methods that are not only suitable for metabarcoding but also for building reference DNA barcode libraries.<br><br>Methods: In this study, we test the suitability of a rapid non-destructive DNA extraction method for metabarcoding of freshwater invertebrate samples.<br><br>Results: This method resulted in detection of taxa from many taxonomic groups, comparable to results obtained with two other tissue-based extraction methods. Most taxa could also be successfully used for subsequent individual-based DNA barcoding and taxonomic identification. The method was successfully applied to field-collected invertebrate samples stored for taxonomic studies in 70% ethanol at room temperature, a commonly used storage method for freshwater samples.<br><br>Discussion: With further refinement and testing, non-destructive extraction has the potential to rapidly characterise species biodiversity in invertebrate samples, while preserving specimens for taxonomic investigation.}, }
@article {pmid29908593, year = {2018}, author = {Rastrojo, A and Alcamí, A}, title = {Viruses in Polar Lake and Soil Ecosystems.}, journal = {Advances in virus research}, volume = {101}, number = {}, pages = {39-54}, doi = {10.1016/bs.aivir.2018.02.002}, pmid = {29908593}, issn = {1557-8399}, abstract = {Viruses play an important role in the control of microbial communities, and it has been suggested that the influence of viruses in polar ecosystems, with low nutrients and under extreme environmental conditions, may be greater. Viral metagenomics allows the genetic characterization of complex viral communities without the need to isolate and grow viruses. Recent investigations in Antarctica and the Arctic are uncovering a great diversity of DNA viruses, including bacteriophages, circular single-stranded DNA viruses, algal-infecting phycodnaviruses, and virophages, adapted to these extreme environments. The limited sequence similarity between viruses in Antarctica and the Arctic suggests that viral communities in the two polar regions have evolved independently since the formation of the Antarctic continent, estimated to occur 25 million years ago. The community of RNA viruses in Antarctica is dominated by the order Picornavirales and their quasispecies composition suggests that higher genetic variability may correlate with viral adaptation to new environmental conditions.}, }
@article {pmid29874232, year = {2018}, author = {Higashi, K and Suzuki, S and Kurosawa, S and Mori, H and Kurokawa, K}, title = {Latent environment allocation of microbial community data.}, journal = {PLoS computational biology}, volume = {14}, number = {6}, pages = {e1006143}, doi = {10.1371/journal.pcbi.1006143}, pmid = {29874232}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; Databases, Genetic ; Environmental Microbiology ; Humans ; Metagenomics ; *Microbiota/genetics/physiology ; Models, Statistical ; Rivers/microbiology ; }, abstract = {As data for microbial community structures found in various environments has increased, studies have examined the relationship between environmental labels given to retrieved microbial samples and their community structures. However, because environments continuously change over time and space, mixed states of some environments and its effects on community formation should be considered, instead of evaluating effects of discrete environmental categories. Here we applied a hierarchical Bayesian model to paired datasets containing more than 30,000 samples of microbial community structures and sample description documents. From the training results, we extracted latent environmental topics that associate co-occurring microbes with co-occurring word sets among samples. Topics are the core elements of environmental mixtures and the visualization of topic-based samples clarifies the connections of various environments. Based on the model training results, we developed a web application, LEA (Latent Environment Allocation), which provides the way to evaluate typicality and heterogeneity of microbial communities in newly obtained samples without confining environmental categories to be compared. Because topics link words and microbes, LEA also enables to search samples semantically related to the query out of 30,000 microbiome samples.}, }
@article {pmid29800679, year = {2018}, author = {Feranchuk, S and Belkova, N and Potapova, U and Kuzmin, D and Belikov, S}, title = {Evaluating the use of diversity indices to distinguish between microbial communities with different traits.}, journal = {Research in microbiology}, volume = {169}, number = {4-5}, pages = {254-261}, doi = {10.1016/j.resmic.2018.03.004}, pmid = {29800679}, issn = {1769-7123}, abstract = {Several measures of biodiversity are commonly used to describe microbial communities, analyzed using 16S gene sequencing. A wide range of available experiments on 16S gene sequencing allows us to present a framework for a comparison of various diversity indices. The criterion for the comparison is the statistical significance of the difference in index values for microbial communities with different traits, within the same experiment. The results of the evaluation indicate that Shannon diversity is the most effective measure among the commonly used diversity indices. The results also indicate that, within the present framework, the Gini coefficient as a diversity index is comparable to Shannon diversity, despite the fact that the Gini coefficient, as a diversity estimator, is far less popular in microbiology than several other measures.}, }
@article {pmid29758429, year = {2018}, author = {Najar, IN and Sherpa, MT and Das, S and Das, S and Thakur, N}, title = {Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry.}, journal = {The Science of the total environment}, volume = {637-638}, number = {}, pages = {730-745}, doi = {10.1016/j.scitotenv.2018.05.037}, pmid = {29758429}, issn = {1879-1026}, abstract = {Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, pH, alkalinity, Ca2+, Mg2+, Cl2+, and sulfur were main environmental variables influencing the microbial community composition and diversity. Also the piper diagram suggested that the water of both the hot springs are Ca-HCO3- type and can be predicted as shallow fresh ground waters. This study has provided an insight into the ecological interaction of the diverse microbial communities and associated physicochemical parameters, which will help in determining the future studies on different biogeochemical pathways in these hot springs.}, }
@article {pmid29750384, year = {2018}, author = {Kosnicki, KL and Penprase, JC and Cintora, P and Torres, PJ and Harris, GL and Brasser, SM and Kelley, ST}, title = {Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome.}, journal = {Addiction biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/adb.12626}, pmid = {29750384}, issn = {1369-1600}, abstract = {Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans. The gut microbiota of rats voluntarily consuming a 20 percent ethanol solution, on alternate days, were compared with a non-exposed control group to identify differential taxonomic and functional profiles. Gut microbial diversity profiles were determined using culture-independent amplification, next-generation sequencing and bioinformatic analysis of bacterial 16S ribosomal RNA gene sequence libraries. Our results showed that, compared with controls, ethanol-consuming rats experienced a significant decline in the biodiversity of their gut microbiomes, a state generally associated with dysbiosis. We also observed significant shifts in the overall diversity of the gut microbial communities and a dramatic change in the relative abundance of particular microbes, such as the Lactobacilli. We also compared our results to human fecal microbiome data collected as part of the citizen science American Gut Project. In contrast to the rat data, human drinkers had significantly higher gut microbial biodiversity than non-drinkers. However, we also observed that microbes that differed among the human subjects displayed similar trends in the rat model, including bacteria implicated in metabolic disease.}, }
@article {pmid29740407, year = {2018}, author = {Nooij, S and Schmitz, D and Vennema, H and Kroneman, A and Koopmans, MPG}, title = {Overview of Virus Metagenomic Classification Methods and Their Biological Applications.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {749}, doi = {10.3389/fmicb.2018.00749}, pmid = {29740407}, issn = {1664-302X}, abstract = {Metagenomics poses opportunities for clinical and public health virology applications by offering a way to assess complete taxonomic composition of a clinical sample in an unbiased way. However, the techniques required are complicated and analysis standards have yet to develop. This, together with the wealth of different tools and workflows that have been proposed, poses a barrier for new users. We evaluated 49 published computational classification workflows for virus metagenomics in a literature review. To this end, we described the methods of existing workflows by breaking them up into five general steps and assessed their ease-of-use and validation experiments. Performance scores of previous benchmarks were summarized and correlations between methods and performance were investigated. We indicate the potential suitability of the different workflows for (1) time-constrained diagnostics, (2) surveillance and outbreak source tracing, (3) detection of remote homologies (discovery), and (4) biodiversity studies. We provide two decision trees for virologists to help select a workflow for medical or biodiversity studies, as well as directions for future developments in clinical viral metagenomics.}, }
@article {pmid29718202, year = {2018}, author = {Wu, L and McCluskey, K and Desmeth, P and Liu, S and Hideaki, S and Yin, Y and Moriya, O and Itoh, T and Kim, CY and Lee, JS and Zhou, Y and Kawasaki, H and Hazbón, MH and Robert, V and Boekhout, T and Lima, N and Evtushenko, L and Boundy-Mills, K and Bunk, B and Moore, ERB and Eurwilaichitr, L and Ingsriswang, S and Shah, H and Yao, S and Jin, T and Huang, J and Shi, W and Sun, Q and Fan, G and Li, W and Li, X and Kurtböke, I and Ma, J}, title = {The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species.}, journal = {GigaScience}, volume = {7}, number = {5}, pages = {}, doi = {10.1093/gigascience/giy026}, pmid = {29718202}, issn = {2047-217X}, abstract = {Genomic information is essential for taxonomic, phylogenetic, and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microorganisms. Hence, the GCM aims to promote research by deep-mining genomic data.}, }
@article {pmid29705130, year = {2018}, author = {Kudo, T and Kobiyama, A and Rashid, J and Reza, MS and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Segawa, S and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis.}, journal = {Gene}, volume = {665}, number = {}, pages = {174-184}, doi = {10.1016/j.gene.2018.04.072}, pmid = {29705130}, issn = {1879-0038}, mesh = {Animals ; *Bacteria/genetics/metabolism ; Bays/*microbiology ; *Genes, Bacterial ; Metagenomics/methods ; *Seasons ; Seawater/*microbiology ; Sulfonium Compounds/*metabolism ; *Water Microbiology ; }, abstract = {Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio Currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.}, }
@article {pmid29705129, year = {2018}, author = {Reza, MS and Kobiyama, A and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kudo, T and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay.}, journal = {Gene}, volume = {665}, number = {}, pages = {185-191}, doi = {10.1016/j.gene.2018.04.074}, pmid = {29705129}, issn = {1879-0038}, mesh = {*Archaea/genetics/growth &amp; development ; *Bacteria/genetics/growth &amp; development ; Bays/*microbiology ; Microbial Consortia/*physiology ; *Plankton/genetics/growth &amp; development ; *Seasons ; *Water Microbiology ; }, abstract = {The Ofunato Bay in the northeastern Pacific Ocean area of Japan possesses the highest biodiversity of marine organisms in the world and has attracted much attention due to its economic and environmental importance. We report here a shotgun metagenomic analysis of the year-round variation in free-living bacterioplankton collected across the entire length of the bay. Phylogenetic differences among spring, summer, autumn and winter bacterioplankton suggested that members of Proteobacteria tended to decrease at high water temperatures and increase at low temperatures. It was revealed that Candidatus Pelagibacter varied seasonally, reaching as much as 60% of all sequences at the genus level in the surface waters during winter. This increase was more evident in the deeper waters, where they reached up to 75%. The relative abundance of Planktomarina also rose during winter and fell during summer. A significant component of the winter bacterioplankton community was Archaea (mainly represented by Nitrosopumilus), as their relative abundance was very low during spring and summer but high during winter. In contrast, Actinobacteria and Cyanobacteria appeared to be higher in abundance during high-temperature periods. It was also revealed that Bacteroidetes constituted a significant component of the summer bacterioplankton community, being the second largest bacterial phylum detected in the Ofunato Bay. Its members, notably Polaribacter and Flavobacterium, were found to be high in abundance during spring and summer, particularly in the surface waters. Principal component analysis and hierarchal clustering analyses showed that the bacterial communities in the Ofunato Bay changed seasonally, likely caused by the levels of organic matter, which would be deeply mixed with surface runoff in the winter.}, }
@article {pmid29705124, year = {2018}, author = {Reza, MS and Kobiyama, A and Yamada, Y and Ikeda, Y and Ikeda, D and Mizusawa, N and Ikeo, K and Sato, S and Ogata, T and Jimbo, M and Kudo, T and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Mineta, K and Bajic, V and Gojobori, T and Watabe, S}, title = {Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay.}, journal = {Gene}, volume = {665}, number = {}, pages = {192-200}, doi = {10.1016/j.gene.2018.04.075}, pmid = {29705124}, issn = {1879-0038}, mesh = {*Archaea/classification/genetics/growth &amp; development ; *Bacteria/classification/genetics/growth &amp; development ; Bays/*microbiology ; Metagenomics ; Microbial Consortia/*physiology ; *Seasons ; *Water Microbiology ; }, abstract = {The Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias Coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 μm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 μm filters, targeting the free-living fraction only. From the 0.27-0.34 Gb WGS library, 0.9 × 106-1.2 × 106 reads from three sampling stations revealed 29 bacterial phyla (~80% of assigned reads), 3 archaeal phyla (~4%) and 59 eukaryotic phyla (~15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0-19.6% Planktomarina (Family Rhodobacteraceae) and 13.7-17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5-6.1%), Flavobacterium (1.8-2.6%), Sphingobacterium (1.4-1.6%) and Cellulophaga (1.4-2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8-15.2%, 3.6-4.9% and 2.1-3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.}, }
@article {pmid29694379, year = {2018}, author = {Garris, HW and Baldwin, SA and Taylor, J and Gurr, DB and Denesiuk, DR and Van Hamme, JD and Fraser, LH}, title = {Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0196032}, doi = {10.1371/journal.pone.0196032}, pmid = {29694379}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics/metabolism ; Biodiversity ; Hydrogen-Ion Concentration ; Metagenomics/*methods ; Mining ; Nitrates/metabolism ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Soil/chemistry ; Water/chemistry ; Wetlands ; }, abstract = {We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6 km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.}, }
@article {pmid29694348, year = {2018}, author = {Hoffman, KL and Hutchinson, DS and Fowler, J and Smith, DP and Ajami, NJ and Zhao, H and Scheet, P and Chow, WH and Petrosino, JF and Daniel, CR}, title = {Oral microbiota reveals signs of acculturation in Mexican American women.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0194100}, doi = {10.1371/journal.pone.0194100}, pmid = {29694348}, issn = {1932-6203}, support = {CA016672/NH/NIH HHS/United States ; R25CA057730/NH/NIH HHS/United States ; }, mesh = {*Acculturation ; Adult ; Aged ; Emigrants and Immigrants ; Female ; Fusobacterium/*isolation &amp; purification ; Humans ; *Mexican Americans ; Microbiota/*physiology ; Middle Aged ; Mouth/*microbiology ; Prevotella/*isolation &amp; purification ; Streptococcus/*isolation &amp; purification ; Young Adult ; }, abstract = {The oral microbiome has been linked to a number of chronic inflammatory conditions, including obesity, diabetes, periodontitis, and cancers of the stomach and liver. These conditions disproportionately affect Mexican American women, yet few studies have examined the oral microbiota in this at-risk group. We characterized the 16S rDNA oral microbiome in 369 non-smoking women enrolled in the MD Anderson Mano a Mano Mexican American Cohort Study. Lower bacterial diversity, a potential indicator of oral health, was associated with increased age and length of US residency among recent immigrants. Grouping women by overarching bacterial community type (e.g., &quot;Streptococcus,&quot; &quot;Fusobacterium,&quot; and &quot;Prevotella&quot; clusters), we observed differences across a number of acculturation-related variables, including nativity, age at immigration, time in the US, country of longest residence, and a multi-dimensional acculturation scale. Participants in the cluster typified by higher abundance of Streptococcus spp. exhibited the lowest bacterial diversity and appeared the most acculturated as compared to women in the &quot;Prevotella&quot; group. Computationally-predicted functional analysis suggested the Streptococcus-dominated bacterial community had greater potential for carbohydrate metabolism while biosynthesis of essential amino acids and nitrogen metabolism prevailed among the Prevotella-high group. Findings suggest immigration and adaption to life in the US, a well-established mediator of disease risk, is associated with differences in oral microbial profiles in Mexican American women. These results warrant further investigation into the joint and modifying effects of acculturation and oral bacteria on the health of Mexican American women and other immigrant populations. The oral microbiome presents an easily accessible biomarker of disease risk, spanning biological, behavioral, and environmental factors.}, }
@article {pmid29668682, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Koutra, D and Schloss, PD}, title = {Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.}, journal = {PLoS computational biology}, volume = {14}, number = {4}, pages = {e1006099}, doi = {10.1371/journal.pcbi.1006099}, pmid = {29668682}, issn = {1553-7358}, support = {T32AI007528/NH/NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; P30DK034933/NH/NIH HHS/United States ; U01AI124255/NH/NIH HHS/United States ; U19AI09087/NH/NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Bacteriophages/*genetics/*physiology ; Computational Biology ; Diet ; Humans ; Metagenomics ; Microbial Consortia/genetics/physiology ; Microbiota/*genetics/*physiology ; Models, Biological ; Phylogeography ; Skin/microbiology/virology ; }, abstract = {Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.}, }
@article {pmid29667329, year = {2018}, author = {Bista, I and Carvalho, GR and Tang, M and Walsh, K and Zhou, X and Hajibabaei, M and Shokralla, S and Seymour, M and Bradley, D and Liu, S and Christmas, M and Creer, S}, title = {Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.12888}, pmid = {29667329}, issn = {1755-0998}, abstract = {New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here, we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (three different amplicons) and shotgun mitogenome sequencing. Additionally, we used individual COI barcoding and de novo mitochondrial genome sequencing, to provide reference sequences for OTU assignment and metagenome mapping (mitogenome skimming), respectively. We found that, even though both methods occasionally failed to recover very low abundance species, metabarcoding was less consistent, by failing to recover some species with higher abundances, probably due to primer bias. Shotgun sequencing results provided highly significant correlations between read number and biomass in all but one species. Conversely, the read-biomass relationships obtained from metabarcoding varied across amplicons. Specifically, we found significant relationships for eight of 13 (amplicons B1FR-450 bp, FF130R-130 bp) or four of 13 (amplicon FFFR, 658 bp) species. Combining the results of all three COI amplicons (multiamplicon approach) improved the read-biomass correlations for some of the species. Overall, mitogenomic sequencing yielded more informative predictions of biomass content from bulk macroinvertebrate communities than metabarcoding. However, for large-scale ecological studies, metabarcoding currently remains the most commonly used approach for diversity assessment.}, }
@article {pmid29665523, year = {2018}, author = {Osimani, A and Milanović, V and Garofalo, C and Cardinali, F and Roncolini, A and Sabbatini, R and De Filippis, F and Ercolini, D and Gabucci, C and Petruzzelli, A and Tonucci, F and Clementi, F and Aquilanti, L}, title = {Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR.}, journal = {International journal of food microbiology}, volume = {276}, number = {}, pages = {54-62}, doi = {10.1016/j.ijfoodmicro.2018.04.013}, pmid = {29665523}, issn = {1879-3460}, mesh = {Animals ; *Biodiversity ; Denaturing Gradient Gel Electrophoresis ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Insecta/*microbiology ; *Metagenomics ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; *Real-Time Polymerase Chain Reaction ; Thailand ; }, abstract = {The present study aimed to identify the microbiota present in six species of processed edible insects produced in Thailand and marketed worldwide via the internet, namely, giant water bugs (Belostoma lutarium), black ants (Polyrhachis), winged termites (alates, Termitoidae), rhino beetles (Hyboschema contractum), mole crickets (Gryllotalpidae), and silkworm pupae (Bombyx mori). For each species, two samples of boiled, dried and salted insects were purchased. The microbial DNA was extracted from the insect samples and subjected to polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), high-throughput sequencing and qualitative real-time PCR assays. The microbiota of the analyzed samples were widely characterized by the presence of spore-forming bacteria mainly represented by the genera Bacillus and Clostridium. Moreover, the genera Anaerobacillus, Paenibacillus, Geobacillus, Pseudomonas, Stenotrophomonas, Massilia, Delftia, Lactobacillus, Staphylococcus, Streptococcus, Vagococcus, and Vibrio were also detected. Real-time PCR allowed for ascertainment of the absence of Coxiella burnetii, Shiga toxin-producing E. coli (STEC), and Pseudomonas aeruginosa in all samples. The results of this study confirm the importance of combining different molecular techniques to characterize the biodiversity of complex ecosystems such as edible insects. The presence of potential human pathogens suggests the need for a careful application of good manufacturing practices during insect processing. This study provides further data that will be useful in risk analyses of edible insects as a novel food source.}, }
@article {pmid29625974, year = {2018}, author = {Taboada, B and Isa, P and Gutiérrez-Escolano, AL and Del Ángel, RM and Ludert, JE and Vázquez, N and Tapia-Palacios, MA and Chávez, P and Garrido, E and Espinosa, AC and Eguiarte, LE and López, S and Souza, V and Arias, CF}, title = {The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, doi = {10.1128/AEM.00465-18}, pmid = {29625974}, issn = {1098-5336}, abstract = {The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare.IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its &quot;lost world&quot; status.}, }
@article {pmid29624889, year = {2018}, author = {Michał, B and Gagat, P and Jabłoński, S and Chilimoniuk, J and Gaworski, M and Mackiewicz, P and Marcin, Ł}, title = {PhyMet2 : a database and toolkit for phylogenetic and metabolic analyses of methanogens.}, journal = {Environmental microbiology reports}, volume = {10}, number = {3}, pages = {378-382}, doi = {10.1111/1758-2229.12648}, pmid = {29624889}, issn = {1758-2229}, abstract = {The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge of microbes stems from difficulties concerning their isolation and culture in laboratory conditions, which is necessary for describing their phenotype, among other things, for biotechnological purposes. An important component of the understudied ecosystems is methanogens, archaea producing a potent greenhouse-effect gas methane. Therefore, we created PhyMet2 , the first database that combines descriptions of methanogens and their culturing conditions with genetic information. The database contains a set of utilities that facilitate interactive data browsing, data comparison, phylogeny exploration and searching for sequence homologues. The most unique feature of the database is the web server MethanoGram, which can be used to significantly reduce the time and cost of searching for the optimal culturing conditions of methanogens by predicting them based on 16S RNA sequences. The database will aid many researchers in exploring the world of methanogens and their applications in biotechnological processes. PhyMet2 with the MethanoGram predictor is available at http://metanogen.biotech.uni.wroc.pl.}, }
@article {pmid29621268, year = {2018}, author = {Peoples, LM and Donaldson, S and Osuntokun, O and Xia, Q and Nelson, A and Blanton, J and Allen, EE and Church, MJ and Bartlett, DH}, title = {Vertically distinct microbial communities in the Mariana and Kermadec trenches.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195102}, doi = {10.1371/journal.pone.0195102}, pmid = {29621268}, issn = {1932-6203}, mesh = {Adaptation, Biological ; Biodiversity ; Geologic Sediments/*microbiology ; Hydrostatic Pressure ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Oceans and Seas ; *Water Microbiology ; }, abstract = {Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct microbial communities compared to those at shallower depths due to high hydrostatic pressures, topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of the communities present in the bottom waters of the Kermadec and Mariana trenches. Estimates of microbial protein production indicate active populations under in situ hydrostatic pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and size fraction are important drivers of microbial community structure. Many putative hadal bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter, are similar to members identified in other trenches. Most of the differences between the two trench microbiomes consists of taxa belonging to the Gammaproteobacteria whose distributions extend throughout the water column. Growth and survival estimates of representative isolates of these taxa under deep-sea conditions suggest that some members may descend from shallower depths and exist as a potentially inactive fraction of the hadal zone. We conclude that the distinct pelagic communities residing in these two trenches, and perhaps by extension other trenches, reflect both cosmopolitan hadal bathytypes and ubiquitous genera found throughout the water column.}, }
@article {pmid29609258, year = {2018}, author = {Shao, DT and Wei, WW}, title = {[Progress in research of human microbiota for upper gastrointestinal tumors and precancerous lesions].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {39}, number = {3}, pages = {382-386}, pmid = {29609258}, issn = {0254-6450}, mesh = {Esophageal Neoplasms/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Neoplasms/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Lactobacillus ; Metagenomics/methods/trends ; *Microbiota ; Precancerous Conditions/*microbiology ; Prognosis ; Research/*trends ; Risk Factors ; Stomach Neoplasms/microbiology ; }, abstract = {With the widely application of the metagenomics, the relationship between microbiota and disease has become a hot research topic. Understanding the potential association between upper gastrointestinal cancer or precancerous lesions and microbiota may play an important role in the early detection, clinical diagnosis and treatment, and prognostic evaluation of upper gastrointestinal cancer. Therefore, a literature retrieval was conducted by using PubMed, Embase and wanfang databases to summarize the latest research progress in the microbiota of upper gastrointestinal cancer, including oral, esophageal, gastric cancer and precancerous lesions. Lower microbial diversity or richness in esophageal cancer and precancerous lesions and specific prognostic biomarkers for esophageal cancer were found. Lactobacillus richness showed an increase trend during the process from gastritis to gastric cancer. This paper summarizes the progress in the research of potential biological etiology of upper gastrointestinal cancer from the perspective of metagenomics in order to provide evidence on the, prevention and control of upper gastrointestinal cancer.}, }
@article {pmid29596453, year = {2018}, author = {Konstantinou, D and Gerovasileiou, V and Voultsiadou, E and Gkelis, S}, title = {Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0195001}, doi = {10.1371/journal.pone.0195001}, pmid = {29596453}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Cyanobacteria/classification/genetics/*physiology ; Mediterranean Region ; Phylogeny ; Porifera/classification/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Sponge-cyanobacteria associations have attracted research interest from an ecological, evolutionary and biotechnological perspective. Current knowledge is, in its majority, &quot;hidden&quot; in metagenomics research studying the entire microbial communities of sponges, while knowledge on these associations is totally missing for certain geographic areas. In this study, we (a) investigated the occurrence of cyanobacteria in 18 sponge species, several of which are studied for the first time for their cyanobionts, from a previously unexplored eastern Mediterranean ecoregion, the Aegean Sea, (b) isolated sponge-associated cyanobacteria, and characterized them based on a polyphasic (morphological-morphometric and molecular phylogenetic analysis) approach, and (c) conducted a meta-analysis on the global diversity of sponge species hosting cyanobacteria, as well as the diversity of cyanobacterial symbionts. Our research provided new records for nine sponge species, previously unknown for this association, while the isolated cyanobacteria were found to form novel clades within Synechococcus, Leptolyngbyaceae, Pseudanabaenaceae, and Schizotrichaceae, whose taxonomic status requires further investigation; this is the first report of a Schizotrichaceae cyanobacterium associated with sponges. The extensive evaluation of the literature along with the new data from the Aegean Sea raised the number of sponge species known for hosting cyanobacteria to 320 and showed that the cyanobacterial diversity reported from sponges is yet underestimated.}, }
@article {pmid29591722, year = {2018}, author = {Wilson, JJ and Brandon-Mong, GJ and Gan, HM and Sing, KW}, title = {High-throughput terrestrial biodiversity assessments: mitochondrial metabarcoding, metagenomics or metatranscriptomics?.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {}, number = {}, pages = {1-8}, doi = {10.1080/24701394.2018.1455189}, pmid = {29591722}, issn = {2470-1408}, abstract = {Consensus on the optimal high-throughput sequencing (HTS) approach to examine biodiversity in mixed terrestrial arthropod samples has not been reached. Metatranscriptomics could increase the proportion of taxonomically informative mitochondrial reads in HTS outputs but has not been investigated for terrestrial arthropod samples. We compared the efficiency of 16S rRNA metabarcoding, metagenomics and metatranscriptomics for detecting species in a mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa). 16S rRNA metabarcoding and nuclear rRNA-depleted metatranscriptomics had the highest detection rate with 97% of input species detected. Based on cytochrome c oxidase I, metagenomics had the highest detection rate with 82% of input species detected, but metatranscriptomics produced a larger proportion of reads matching (Sanger) reference sequences. Metatranscriptomics with nuclear rRNA depletion may offer advantages over metabarcoding through reducing the number of spurious operational taxonomic units while retaining high detection rates, and offers natural enrichment of mitochondrial sequences which may enable increased species detection rates compared with metagenomics.}, }
@article {pmid29590046, year = {2018}, author = {Zhao, L and Zhang, F and Ding, X and Wu, G and Lam, YY and Wang, X and Fu, H and Xue, X and Lu, C and Ma, J and Yu, L and Xu, C and Ren, Z and Xu, Y and Xu, S and Shen, H and Zhu, X and Shi, Y and Shen, Q and Dong, W and Liu, R and Ling, Y and Zeng, Y and Wang, X and Zhang, Q and Wang, J and Wang, L and Wu, Y and Zeng, B and Wei, H and Zhang, M and Peng, Y and Zhang, C}, title = {Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6380}, pages = {1151-1156}, doi = {10.1126/science.aao5774}, pmid = {29590046}, issn = {1095-9203}, mesh = {Adult ; Aged ; Bacteria/classification/genetics/metabolism ; China ; Diabetes Mellitus, Type 2/*therapy ; Diet ; Dietary Fiber/*metabolism ; Fatty Acids, Volatile/*metabolism ; Feces ; Female ; Fermentation ; *Gastrointestinal Microbiome ; Glucagon-Like Peptide 1/metabolism ; Glycated Hemoglobin A/analysis ; Humans ; Hydrogen Sulfide/metabolism ; Indoles/metabolism ; Male ; Metagenomics ; Middle Aged ; }, abstract = {The gut microbiota benefits humans via short-chain fatty acid (SCFA) production from carbohydrate fermentation, and deficiency in SCFA production is associated with type 2 diabetes mellitus (T2DM). We conducted a randomized clinical study of specifically designed isoenergetic diets, together with fecal shotgun metagenomics, to show that a select group of SCFA-producing strains was promoted by dietary fibers and that most other potential producers were either diminished or unchanged in patients with T2DM. When the fiber-promoted SCFA producers were present in greater diversity and abundance, participants had better improvement in hemoglobin A1c levels, partly via increased glucagon-like peptide-1 production. Promotion of these positive responders diminished producers of metabolically detrimental compounds such as indole and hydrogen sulfide. Targeted restoration of these SCFA producers may present a novel ecological approach for managing T2DM.}, }
@article {pmid29572583, year = {2018}, author = {Verma, D and Garg, PK and Dubey, AK}, title = {Insights into the human oral microbiome.}, journal = {Archives of microbiology}, volume = {200}, number = {4}, pages = {525-540}, doi = {10.1007/s00203-018-1505-3}, pmid = {29572583}, issn = {1432-072X}, support = {SERB/LS-824/2013//Science and Engineering recruitment Board, New Delhi, India/ ; }, mesh = {Bacteria/genetics ; Health ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host's metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.}, }
@article {pmid29566905, year = {2017}, author = {Jazayeri, O and Daghighi, SM and Rezaee, F}, title = {Lifestyle alters GUT-bacteria function: Linking immune response and host.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {31}, number = {6}, pages = {625-635}, doi = {10.1016/j.bpg.2017.09.009}, pmid = {29566905}, issn = {1532-1916}, mesh = {Bacteria/*pathogenicity ; Bacterial Physiological Phenomena/*immunology ; Gastrointestinal Microbiome/*immunology ; Humans ; *Life Style ; Microbiota/*immunology ; }, abstract = {Microbiota in human is a &quot;mixture society&quot; of different species (i.e. bacteria, viruses, funguses) populations with a different way of relationship classification to Human. Human GUT serves as the host of the majority of different bacterial populations (GUT flora, more than 500 species), which are with us (&quot;from the beginning&quot;) in an innate manner known as the commensal (no harm to each other) and symbiotic (mutual benefit) relationship. A homeostatic balance of host-bacteria relationship is very important and vital for a normal health process. However, this beneficial relationship and delicate homeostatic state can be disrupted by the imbalance of microbiome-composition of gut microbiota, expressing a pathogenic state. A strict homeostatic balance of microbiome-composition strongly depends on several factors; 1- lifestyle, 2- geography, 3- ethnicities, 4- &quot;mom&quot; as prime of the type of bacterial colonization in infant and 5- the disease. With such diversity in individuals combined with huge number of different bacterial species and their interactions, it is wise to perform an in-depth systems biology (e.g. genomics, proteomics, glycomics, and etcetera) analysis of personalized microbiome. Only in this way, we are able to generate a map of complete GUT microbiota and, in turn, to determine its interaction with host and intra-interaction with pathogenic bacteria. A specific microbiome analysis provides us the knowledge to decipher the nature of interactions between the GUT microbiota and the host and its response to the invading bacteria in a pathogenic state. The GUT-bacteria composition is independent of geography and ethnicity but lifestyle well affects GUT-bacteria composition and function. Microbiome knowledge obtained by systems biology also helps us to change the behavior of GUT microbiota in response to the pathogenic microbes as protection. Functional microbiome changes in response to environmental factors will be discussed in this review.}, }
@article {pmid29546438, year = {2018}, author = {Rua, CPJ and de Oliveira, LS and Froes, A and Tschoeke, DA and Soares, AC and Leomil, L and Gregoracci, GB and Coutinho, R and Hajdu, E and Thompson, CC and Berlinck, RGS and Thompson, FL}, title = {Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1172-6}, pmid = {29546438}, issn = {1432-184X}, support = {CNE E-26/110.735/2013//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; CIMAR 1986/2014//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; BIOTA/BIOprospecTA grant 2013/50228-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/17616- 7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.}, }
@article {pmid29544175, year = {2018}, author = {Wang, C and Jiang, K and Zhou, J and Wu, B}, title = {Solidago canadensis invasion affects soil N-fixing bacterial communities in heterogeneous landscapes in urban ecosystems in East China.}, journal = {The Science of the total environment}, volume = {631-632}, number = {}, pages = {702-713}, doi = {10.1016/j.scitotenv.2018.03.061}, pmid = {29544175}, issn = {1879-1026}, mesh = {Biodiversity ; China ; *Ecosystem ; Environmental Monitoring ; *Introduced Species ; Soil/chemistry ; *Soil Microbiology ; Solidago/*growth &amp; development ; }, abstract = {Soil nitrogen-fixing bacterial communities (SNB) can increase the level of available soil N via biological N-fixation to facilitate successful invasion of several invasive plant species (IPS). Meanwhile, landscape heterogeneity can greatly enhance regional invasibility and increase the chances of successful invasion of IPS. Thus, it is important to understand the soil micro-ecological mechanisms driving the successful invasion of IPS in heterogeneous landscapes. This study performed cross-site comparisons, via metagenomics, to comprehensively analyze the effects of Solidago canadensis invasion on SNB in heterogeneous landscapes in urban ecosystems. Rhizospheric soil samples of S. canadensis were obtained from nine urban ecosystems [Three replicate quadrats (including uninvaded sites and invaded sites) for each type of urban ecosystem]. S. canadensis invasion did not significantly affect soil physicochemical properties, the taxonomic diversity of plant communities, or the diversity and richness of SNB. However, some SNB taxa (i.e., f_Micromonosporaceae, f_Oscillatoriaceae, and f_Bacillaceae) changed significantly with S. canadensis invasion. Thus, S. canadensis invasion may alter the community structure, rather than the diversity and richness of SNB, to facilitate its invasion process. Of the nine urban ecosystems, the diversity and richness of SNB was highest in farmland wasteland. Accordingly, the community invasibility of farmland wasteland may be higher than that of the other types of urban ecosystem. In brief, landscape heterogeneity, rather than S. canadensis invasion, was the strongest controlling factor for the diversity and richness of SNB. One possible reason may be the differences in soil electrical conductivity and the taxonomic diversity of plant communities in the nine urban ecosystems, which can cause notable shifts in the diversity and richness of SNB.}, }
@article {pmid29540269, year = {2018}, author = {Villamil, SI and Huerlimann, R and Morianos, C and Sarnyai, Z and Maes, GE}, title = {Adverse effect of early-life high-fat/high-carbohydrate (&quot;Western&quot;) diet on bacterial community in the distal bowel of mice.}, journal = {Nutrition research (New York, N.Y.)}, volume = {50}, number = {}, pages = {25-36}, doi = {10.1016/j.nutres.2017.11.008}, pmid = {29540269}, issn = {1879-0739}, abstract = {Obesity and other lifestyle diseases in modern society can be related to historical dietary changes from diets balanced in omega-6 and omega-3 to the unbalanced &quot;Western-type&quot; diet. It is recognized that diet influences the murine and human gut microbiome, and most research indicates that microbial diversity and composition are altered by high-fat diets (HFDs). However, good knowledge about the effects of early exposure to HFD on the maturation and structure of the bacterial community is limited. Using mice as model, we hypothesized that an HFD alters the early dynamic of the gut bacterial community toward an unstable/unhealthy state. By sequencing the V3 and V4 regions of the 16S ribosomal ribonucleic acid gene, we investigated the bacterial community in fecal samples of mice fed a control diet and an HFD at weaning (sampling time 1) and after 8 weeks of dietary intervention (11weeks of age; sampling time 2). Natural temporal microbiome maturation was evidenced by a general increase in microbial diversity and shifts in microbial community between sampling times 1 and 2 toward a mature community. However, the HFD led to significant structural segregation of the microbiome compared with controls; the HFD diet repressed health-enhancing bacteria (eg, Bifidobacterium and Akkermansia) and promoted health-detracting bacteria (ie, those associated with gut disorders, eg, Dorea). We suggest that early-life consumption of HFD negatively impacts the natural gut bacterial community maturation leading toward a potentially persistent unhealthy stage.}, }
@article {pmid29526222, year = {2018}, author = {Andeta, AF and Vandeweyer, D and Woldesenbet, F and Eshetu, F and Hailemicael, A and Woldeyes, F and Crauwels, S and Lievens, B and Ceusters, J and Vancampenhout, K and Van Campenhout, L}, title = {Fermentation of enset (Ensete ventricosum) in the Gamo highlands of Ethiopia: Physicochemical and microbial community dynamics.}, journal = {Food microbiology}, volume = {73}, number = {}, pages = {342-350}, doi = {10.1016/j.fm.2018.02.011}, pmid = {29526222}, issn = {1095-9998}, mesh = {Biodiversity ; Clostridium/classification/genetics/isolation &amp; purification/metabolism ; Ethiopia ; Fermentation ; Hydrogen-Ion Concentration ; Lactobacillales/classification/*isolation &amp; purification/metabolism ; Musaceae/chemistry/metabolism/*microbiology ; Temperature ; }, abstract = {Enset (Ensete ventricosum) provides staple food for 15 million people in Ethiopia after fermentation into kocho. The fermentation process has hardly been investigated and is prone to optimization. The aim of this study was to investigate the physicochemical and microbial dynamics of fermentation practices in the Gamo highlands. These practices show local variation, but two steps were omnipresent: scraping of the pseudostem and fermenting it in a pit or a bamboo basket. Enset plants were fragmented and fermented for two months in order to investigate the physicochemical (temperature, moisture content, pH and titratable acidity) and microbial dynamics (total viable aerobic counts, counts of Enterobacteriaceae, lactic acid bacteria, yeasts and moulds and Clostridium spores counts, and Illumina Miseq sequencing). Samples were taken on days 1, 7, 15, 17, 31 and 60. The pH decreased, whereas the titratable acidity increased during fermentation. Of all counts those of lactic acid bacteria and Clostridium spores increased during fermentation. Leuconostoc mesenteroides initiated the fermentation. Later on, Prevotella paludivivens, Lactobacillus sp. and Bifidobacterium minimum dominated. These three species are potential candidates for the development of a starter culture.}, }
@article {pmid29523545, year = {2018}, author = {Patin, NV and Pratte, ZA and Regensburger, M and Hall, E and Gilde, K and Dove, ADM and Stewart, FJ}, title = {Microbiome Dynamics in a Large Artificial Seawater Aquarium.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {10}, pages = {}, doi = {10.1128/AEM.00179-18}, pmid = {29523545}, issn = {1098-5336}, abstract = {Artificial habitats for animals have high commercial and societal value. Microbial communities (microbiomes) in such habitats may play ecological roles similar to those in nature. However, this hypothesis remains largely untested. Georgia Aquarium's Ocean Voyager (OV) exhibit is a closed-system aquatic habitat that mimics the oligotrophic open ocean and houses thousands of large marine animals, including fish, sea turtles, and whale sharks. We present a 14-month time series characterizing the OV water column microbiome. The composition and stability of the microbiome differed from those of natural marine environments with similar chemical features. The composition shifted dramatically over the span of 2 weeks and was characterized by bloom events featuring members of two heterotrophic bacterial lineages with cosmopolitan distributions in the oceans. The relative abundances of these lineages were inversely correlated, suggesting an overlap in ecological niches. Transcript mapping to metagenome-assembled genomes (MAGs) of these taxa identified unique characteristics, including the presence and activity of genes for the synthesis and degradation of cyanophycin, an amino acid polymer linked to environmental stress and found frequently in cyanobacteria but rarely in heterotrophic bacteria. The dominant MAGs also contained and transcribed plasmid-associated sequences, suggesting a role for conjugation in adaptation to the OV environment. These findings indicate a highly dynamic microbiome despite the stability of the physical and chemical parameters of the water column. Characterizing how such fluctuations affect microbial function may inform our understanding of animal health in closed aquaculture systems.IMPORTANCE Public aquariums play important societal roles, for example, by promoting science education and helping conserve biodiversity. The health of aquarium animals depends on interactions with the surrounding microbiome. However, the extent to which aquariums recreate a stable and natural microbial ecosystem is uncertain. This study describes the taxonomic composition of the water column microbiome over 14 months in a large indoor aquatic habitat, the Ocean Voyager exhibit at the Georgia Aquarium. Despite stable water column conditions, the exhibit experienced blooms in which the abundance of a single bacterial strain increased to over 65% of the community. Genome analysis indicated that the OV's dominant strains share unique adaptations, notably genes for storage polymers associated with environmental stress. These results, interpreted alongside data from natural ocean systems and another artificial seawater aquarium, suggest a highly dynamic aquarium microbiome and raise questions of how microbiome stability may affect the ecological health of the habitat.}, }
@article {pmid29522953, year = {2018}, author = {Cai, L and Chen, TB and Zheng, SW and Liu, HT and Zheng, GD}, title = {Decomposition of lignocellulose and readily degradable carbohydrates during sewage sludge biodrying, insights of the potential role of microorganisms from a metagenomic analysis.}, journal = {Chemosphere}, volume = {201}, number = {}, pages = {127-136}, doi = {10.1016/j.chemosphere.2018.02.177}, pmid = {29522953}, issn = {1879-1298}, mesh = {Carbohydrate Metabolism ; Carbohydrates/*analysis ; Hot Temperature ; Lignin/*analysis ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Sewage/*chemistry/microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Sewage sludge biodrying is a waste treatment method that uses bio-heat generated from organic degradation to remove moisture from sewage sludge. Lignocellulose and carbohydrate decomposition is important when assessing biodrying performance. This study investigated lignocellulose and carbohydrate decomposition, and the potential microbial functions during biodrying. We determined the lignocellulose and carbohydrate contents, assayed related enzyme activity, performed a complete metagenomic study on sewage sludge biodrying material during the thermophilic phase, annotated potential genetic function involved in the decomposition, and summarized the key metabolic pathways. The results indicated that lignocellulose, readily degradable carbohydrates, and starch, significantly decomposed after biodrying. During the thermophilic phase, the majority of lignocellulose and carbohydrate-related enzymes showed significantly higher activity, and glycoside hydrolases and glycosyl transferases showed higher gene counts and reads. Moreover, the top five microorganisms enriched with carbohydrate-active enzyme genes, i.e., Bacillus, Intrasporangium, Tetrasphaera, Rhodobacter, and Streptomyces, were also among the top ten ecologically dominant genera. These findings highlight the crucial phases for biodrying process, reveal the ecologically functional diversity of biodrying-originated microbial consortia, and suggest potential candidates for optimizing biodrying decomposition.}, }
@article {pmid29515540, year = {2018}, author = {Cuadrat, RRC and Ionescu, D and Dávila, AMR and Grossart, HP}, title = {Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {251}, doi = {10.3389/fmicb.2018.00251}, pmid = {29515540}, issn = {1664-302X}, abstract = {Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.}, }
@article {pmid29511180, year = {2018}, author = {Hu, Y and Sanders, JG and Łukasik, P and D'Amelio, CL and Millar, JS and Vann, DR and Lan, Y and Newton, JA and Schotanus, M and Kronauer, DJC and Pierce, NE and Moreau, CS and Wertz, JT and Engel, P and Russell, JA}, title = {Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {964}, doi = {10.1038/s41467-018-03357-y}, pmid = {29511180}, issn = {2041-1723}, mesh = {Amino Acids/metabolism ; Ammonia/metabolism ; Animals ; Ants/*microbiology/*physiology ; Diet ; *Gastrointestinal Microbiome/genetics ; Geography ; Herbivory/*physiology ; Metagenome ; Metagenomics ; Nitrogen/*metabolism ; Nitrogen Fixation/genetics ; Nitrogen Isotopes ; Symbiosis ; Urea/metabolism ; Urease/metabolism ; Uric Acid/metabolism ; }, abstract = {Nitrogen acquisition is a major challenge for herbivorous animals, and the repeated origins of herbivory across the ants have raised expectations that nutritional symbionts have shaped their diversification. Direct evidence for N provisioning by internally housed symbionts is rare in animals; among the ants, it has been documented for just one lineage. In this study we dissect functional contributions by bacteria from a conserved, multi-partite gut symbiosis in herbivorous Cephalotes ants through in vivo experiments, metagenomics, and in vitro assays. Gut bacteria recycle urea, and likely uric acid, using recycled N to synthesize essential amino acids that are acquired by hosts in substantial quantities. Specialized core symbionts of 17 studied Cephalotes species encode the pathways directing these activities, and several recycle N in vitro. These findings point to a highly efficient N economy, and a nutritional mutualism preserved for millions of years through the derived behaviors and gut anatomy of Cephalotes ants.}, }
@article {pmid29498741, year = {2018}, author = {Valeriani, F and Crognale, S and Protano, C and Gianfranceschi, G and Orsini, M and Vitali, M and Spica, VR}, title = {Metagenomic analysis of bacterial community in a travertine depositing hot spring.}, journal = {The new microbiologica}, volume = {41}, number = {2}, pages = {126-135}, pmid = {29498741}, issn = {1121-7138}, mesh = {Bacteria/*genetics/isolation &amp; purification ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Hot Springs/*microbiology ; Metagenomics/*methods ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Several factors influence bacteria biodiversity in hot springs. The impact of biotic and abiotic pathways on travertine deposition plays a key role in microbial ecology and in the final composition of the waterborne microbiota. The metabolism of some bacterial groups such as photoautotrophs or lithoautotrophs influences water chemistry, favoring carbonate precipitation processes. The role of microbial mats in mineral precipitation processes is not fully clarified. For the first time, a comprehensive metagenomic analysis has been undertaken in the historical Bullicame hot spring. Bacterial biodiversity was characterized and biomineralization activities were assigned to different genera. A higher biodiversity in mat samples compared to water samples was observed: Shannon index of 3.34 and 0.86, respectively. Based on the functional assignment of each Operational Taxonomic Unit, the bacteria involved in biologically- induced mineralization are prevalent in mat and released in the water. According to the principle that each geothermal water specimen has distinctive physic-chemical characteristics, our results suggest new interacting bio-actions within these ecosystems. The saturation index and the chemical composition, as the high concentration of sulfur species and HCO3, can be linked to create a selective environment where pioneer communities are able to live and shape the ecosystem.}, }
@article {pmid29497412, year = {2018}, author = {Garrido-Sanz, D and Manzano, J and Martín, M and Redondo-Nieto, M and Rivilla, R}, title = {Metagenomic Analysis of a Biphenyl-Degrading Soil Bacterial Consortium Reveals the Metabolic Roles of Specific Populations.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {232}, doi = {10.3389/fmicb.2018.00232}, pmid = {29497412}, issn = {1664-302X}, abstract = {Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source. This consortium is able to grow on biphenyl, benzoate, and protocatechuate. Whole-community DNA extracted from the consortium was used to analyze biodiversity by Illumina sequencing of a 16S rRNA gene amplicon library and to determine the metagenome by whole-genome shotgun Illumina sequencing. Biodiversity analysis shows that the consortium consists of 24 operational taxonomic units (≥97% identity). The consortium is dominated by strains belonging to the genus Pseudomonas, but also contains betaproteobacteria and Rhodococcus strains. whole-genome shotgun (WGS) analysis resulted in contigs containing 78.3 Mbp of sequenced DNA, representing around 65% of the expected DNA in the consortium. Bioinformatic analysis of this metagenome has identified the genes encoding the enzymes implicated in three pathways for the conversion of biphenyl to benzoate and five pathways from benzoate to tricarboxylic acid (TCA) cycle intermediates, allowing us to model the whole biodegradation network. By genus assignment of coding sequences, we have also been able to determine that the three biphenyl to benzoate pathways are carried out by Rhodococcus strains. In turn, strains belonging to Pseudomonas and Bordetella are the main responsible of three of the benzoate to TCA pathways while the benzoate conversion into TCA cycle intermediates via benzoyl-CoA and the catechol meta-cleavage pathways are carried out by beta proteobacteria belonging to genera such as Achromobacter and Variovorax. We have isolated a Rhodococcus strain WAY2 from the consortium which contains the genes encoding the three biphenyl to benzoate pathways indicating that this strain is responsible for all the biphenyl to benzoate transformations. The presented results show that metagenomic analysis of consortia allows the identification of bacteria active in biodegradation processes and the assignment of specific reactions and pathways to specific bacterial groups.}, }
@article {pmid29494648, year = {2018}, author = {Bhogoju, S and Nahashon, S and Wang, X and Darris, C and Kilonzo-Nthenge, A}, title = {A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0191029}, doi = {10.1371/journal.pone.0191029}, pmid = {29494648}, issn = {1932-6203}, mesh = {Animal Feed ; Animals ; Galliformes/genetics/*microbiology ; Gastrointestinal Microbiome/*genetics ; *Metagenome ; Metagenomics ; Phylogeny ; Poultry/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Probiotics are live microbial feed supplements that promote growth and health to the host by minimizing non-essential and pathogenic microorganisms in the host's gastrointestinal tract (GIT). The campaign to minimize excessive use of antibiotics in poultry production has necessitated development of probiotics with broad application in multiple poultry species. Design of such probiotics requires understanding of the diversity or similarity in microbial profiles among avian species of economic importance. Therefore, the objective of this research was to establish and compare the microbial profiles of the GIT of Guinea fowl and chicken and to establish the microbial diversity or similarity between the two avian species. A metagenomic approach consisting of the amplification and sequence analysis of the hypervariable regions V1-V9 of the 16S rRNA gene was used to identify the GIT microbes. Collectively, we detected more than 150 microbial families. The total number of microbial species detected in the chicken GIT was higher than that found in the Guinea Fowl GIT. Our studies also revealed phylogenetic diversity among the microbial species found in chicken and guinea fowl. The phylum Firmicutes was most abundant in both avian species whereas Phylum Actinobacteria was most abundant in chickens than Guinea fowls. The diversity of the microbial profiles found in broiler chickens and Guinea fowls suggest that the design of effective avian probiotics would require species specificity.}, }
@article {pmid29486880, year = {2018}, author = {Bodewes, R}, title = {Novel viruses in birds: Flying through the roof or is a cage needed?.}, journal = {Veterinary journal (London, England : 1997)}, volume = {233}, number = {}, pages = {55-62}, doi = {10.1016/j.tvjl.2017.12.023}, pmid = {29486880}, issn = {1532-2971}, mesh = {Animals ; Animals, Domestic/virology ; Animals, Wild/virology ; Bird Diseases/virology ; Birds/*virology ; Chickens/virology ; Columbidae/virology ; Ducks/virology ; Endangered Species ; Virus Diseases/veterinary ; Viruses/isolation &amp; purification/pathogenicity ; }, abstract = {Emerging viral diseases continue to have a major global impact on human beings and animals. To be able to take adequate measures in case of an outbreak of an emerging disease, rapid detection of the causative agent is a crucial first step. In this review, various aspects of virus discovery are discussed, with a special focus on recently discovered viruses in birds. Novel viruses with a potential major impact have been discovered in domestic and wild bird species in recent years using various virus discovery methods. Only a few studies report the detection of novel viruses in endangered bird species, although increased knowledge about viruses circulating in these species is important. Additional studies focusing on the exact role of a novel virus in disease and on the impact of a novel virus on bird populations are often lacking. Intensive collaboration between different disciplines is needed to obtain useful information about the role of these novel viruses.}, }
@article {pmid29474068, year = {2018}, author = {Lu, T and Ke, M and Peijnenburg, WJGM and Zhu, Y and Zhang, M and Sun, L and Fu, Z and Qian, H}, title = {Investigation of Rhizospheric Microbial Communities in Wheat, Barley, and Two Rice Varieties at the Seedling Stage.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {11}, pages = {2645-2653}, doi = {10.1021/acs.jafc.7b06155}, pmid = {29474068}, issn = {1520-5118}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Hordeum/*growth &amp; development/microbiology ; Oryza/*growth &amp; development/microbiology ; Rhizosphere ; Seedlings/growth &amp; development/microbiology ; *Soil Microbiology ; Triticum/*growth &amp; development/microbiology ; }, abstract = {The plant rhizosphere microbiota plays multiple roles in plant growth. We investigated the taxonomic and functional variations in the rhizosphere microbial community, examining both prokaryotes and eukaryotes, of four crops at the seedling stage: wheat, barley, and two rice varieties (indica and japonica) seeded in paddy soil. The diversity of rhizosphere communities in these four species was determined. Results showed that wheat and barley had much stronger selection effects than rice for the rhizosphere microbial community. Functional metagenomic profiling indicated that a series of sequences related to glycan, limonene, and pinene degradation pathways as well as some relatively rare functions related to N or S metabolism were enriched in the rhizosphere soil. We conclude that the four tested crops induced the formation of the microbial community with specific features that may influence the plant growth but stochastic processes also appreciably influenced the functional selection.}, }
@article {pmid29472560, year = {2018}, author = {Taş, N and Prestat, E and Wang, S and Wu, Y and Ulrich, C and Kneafsey, T and Tringe, SG and Torn, MS and Hubbard, SS and Jansson, JK}, title = {Landscape topography structures the soil microbiome in arctic polygonal tundra.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {777}, doi = {10.1038/s41467-018-03089-z}, pmid = {29472560}, issn = {2041-1723}, mesh = {Arctic Regions ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Carbon/metabolism ; Climate Change ; Methane/metabolism ; *Microbiota ; Permafrost/*microbiology ; Soil/chemistry ; Soil Microbiology ; Tundra ; }, abstract = {In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH4 oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N2O, reflecting low N2O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions.}, }
@article {pmid29463661, year = {2018}, author = {He, Z and Zhang, P and Wu, L and Rocha, AM and Tu, Q and Shi, Z and Wu, B and Qin, Y and Wang, J and Yan, Q and Curtis, D and Ning, D and Van Nostrand, JD and Wu, L and Yang, Y and Elias, DA and Watson, DB and Adams, MWW and Fields, MW and Alm, EJ and Hazen, TC and Adams, PD and Arkin, AP and Zhou, J}, title = {Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, doi = {10.1128/mBio.02435-17}, pmid = {29463661}, issn = {2150-7511}, abstract = {Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology.}, }
@article {pmid29454999, year = {2018}, author = {Wang, J and Tang, L and Zhou, H and Zhou, J and Glenn, TC and Shen, CL and Wang, JS}, title = {Long-term treatment with green tea polyphenols modifies the gut microbiome of female sprague-dawley rats.}, journal = {The Journal of nutritional biochemistry}, volume = {56}, number = {}, pages = {55-64}, doi = {10.1016/j.jnutbio.2018.01.005}, pmid = {29454999}, issn = {1873-4847}, support = {R24 TW009489/TW/FIC NIH HHS/United States ; U01 AT006691/AT/NCCIH NIH HHS/United States ; }, abstract = {Green tea polyphenols (GTP) have been shown to exert a spectrum of health benefits to animals and humans. It is plausible that the beneficial effects of GTP are a result of its interaction with the gut microbiota. This study evaluated the effect of long-term treatment with GTP on the gut microbiota of experimental rats and the potential linkage between changes of the gut microbiota with the beneficial effects of GTP. Six-month-old Sprague-Dawley rats were randomly allocated into three dosing regimens (0, 0.5%, and 1.5% of GTP) and followed for 6 months. At the end of month 3 or month 6, half of the animals from each group were sacrificed and their colon contents were collected for microbiome analysis using 16S ribosomal RNA and shotgun metagenomic community sequencing. GTP treatment significantly decreased the biodiversity and modified the microbial community in a dose-dependent manner; similar patterns were observed at both sampling times. Multiple operational taxonomic units and phylotypes were modified: the phylotypes Bacteroidetes and Oscillospira, previously linked to the lean phenotype in human and animal studies, were enriched; and Peptostreptococcaceae previously linked to colorectal cancer phenotype was depleted in GTP treated groups in a dose-dependent manner. Several microbial gene orthologs were modified, among which genes related to energy production and conversion were consistently enriched in samples from month 6 in a dose-dependent manner. This study showed that long-term treatment with GTP induced a dose-dependent modification of the gut microbiome in experimental rats, which might be linked to beneficial effects of GTP.}, }
@article {pmid29444186, year = {2018}, author = {Donovan, PD and Gonzalez, G and Higgins, DG and Butler, G and Ito, K}, title = {Identification of fungi in shotgun metagenomics datasets.}, journal = {PloS one}, volume = {13}, number = {2}, pages = {e0192898}, doi = {10.1371/journal.pone.0192898}, pmid = {29444186}, issn = {1932-6203}, mesh = {Animals ; Antarctic Regions ; Ascomycota/classification/genetics/isolation &amp; purification ; Candida tropicalis/genetics/pathogenicity ; Databases, Genetic ; Fungi/classification/*genetics/pathogenicity ; Humans ; Metagenome ; *Metagenomics ; Mice ; Microbiota/genetics ; Phylogeny ; Soil Microbiology ; Swine ; Zoonoses/microbiology ; }, abstract = {Metagenomics uses nucleic acid sequencing to characterize species diversity in different niches such as environmental biomes or the human microbiome. Most studies have used 16S rRNA amplicon sequencing to identify bacteria. However, the decreasing cost of sequencing has resulted in a gradual shift away from amplicon analyses and towards shotgun metagenomic sequencing. Shotgun metagenomic data can be used to identify a wide range of species, but have rarely been applied to fungal identification. Here, we develop a sequence classification pipeline, FindFungi, and use it to identify fungal sequences in public metagenome datasets. We focus primarily on animal metagenomes, especially those from pig and mouse microbiomes. We identified fungi in 39 of 70 datasets comprising 71 fungal species. At least 11 pathogenic species with zoonotic potential were identified, including Candida tropicalis. We identified Pseudogymnoascus species from 13 Antarctic soil samples initially analyzed for the presence of bacteria capable of degrading diesel oil. We also show that Candida tropicalis and Candida loboi are likely the same species. In addition, we identify several examples where contaminating DNA was erroneously included in fungal genome assemblies.}, }
@article {pmid29428461, year = {2018}, author = {Perfumo, A and Banat, IM and Marchant, R}, title = {Going Green and Cold: Biosurfactants from Low-Temperature Environments to Biotechnology Applications.}, journal = {Trends in biotechnology}, volume = {36}, number = {3}, pages = {277-289}, doi = {10.1016/j.tibtech.2017.10.016}, pmid = {29428461}, issn = {1879-3096}, abstract = {Approximately 80% of the Earth's biosphere is cold, at an average temperature of 5°C, and is populated by a diversity of microorganisms that are a precious source of molecules with high biotechnological potential. Biosurfactants from cold-adapted organisms can interact with multiple physical phases - water, ice, hydrophobic compounds, and gases - at low and freezing temperatures and be used in sustainable (green) and low-energy-impact (cold) products and processes. We review the biodiversity of microbial biosurfactants produced in cold habitats and provide a perspective on the most promising future applications in environmental and industrial technologies. Finally, we encourage exploring the cryosphere for novel types of biosurfactants via both culture screening and functional metagenomics.}, }
@article {pmid29427960, year = {2018}, author = {Fontana, A and Campanaro, S and Treu, L and Kougias, PG and Cappa, F and Morelli, L and Angelidaki, I}, title = {Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes.}, journal = {Water research}, volume = {134}, number = {}, pages = {181-191}, doi = {10.1016/j.watres.2018.02.001}, pmid = {29427960}, issn = {1879-2448}, abstract = {The present research is the first comprehensive study regarding the thermophilic anaerobic degradation of cheese wastewater, which combines the evaluation of different reactor configurations (i.e. single and two-stage continuous stirred tank reactors) on the process efficiency and the in-depth characterization of the microbial community structure using genome-centric metagenomics. Both reactor configurations showed acidification problems under the tested organic loading rates (OLRs) of 3.6 and 2.4 g COD/L-reactor day and the hydraulic retention time (HRT) of 15 days. However, the two-stage design reached a methane yield equal to 95% of the theoretical value, in contrast with the single stage configuration, which reached a maximum of 33% of the theoretical methane yield. The metagenomic analysis identified 22 new population genomes and revealed that the microbial compositions between the two configurations were remarkably different, demonstrating a higher methanogenic biodiversity in the two-stage configuration. In fact, the acidogenic reactor of the serial configuration was almost solely composed by the lactose degrader Bifidobacterium crudilactis UC0001. The predictive functional analyses of the main population genomes highlighted specific metabolic pathways responsible for the AD process and the mechanisms of main intermediates production. Particularly, the acetate accumulation experienced by the single stage configuration was mainly correlated to the low abundant syntrophic acetate oxidizer Tepidanaerobacter acetatoxydans UC0018 and to the absence of aceticlastic methanogens.}, }
@article {pmid29427518, year = {2018}, author = {Guirro, M and Costa, A and Gual-Grau, A and Mayneris-Perxachs, J and Torrell, H and Herrero, P and Canela, N and Arola, L}, title = {Multi-omics approach to elucidate the gut microbiota activity: Metaproteomics and metagenomics connection.}, journal = {Electrophoresis}, volume = {39}, number = {13}, pages = {1692-1701}, doi = {10.1002/elps.201700476}, pmid = {29427518}, issn = {1522-2683}, abstract = {Over the last few years, the application of high-throughput meta-omics methods has provided great progress in improving the knowledge of the gut ecosystem and linking its biodiversity to host health conditions, offering complementary support to classical microbiology. Gut microbiota plays a crucial role in relevant diseases such as obesity or cardiovascular disease (CVD), and its regulation is closely influenced by several factors, such as dietary composition. In fact, polyphenol-rich diets are the most palatable treatment to prevent hypertension associated with CVD, although the polyphenol-microbiota interactions have not been completely elucidated. For this reason, the aim of this study was to evaluate microbiota effect in obese rats supplemented by hesperidin, after being fed with cafeteria or standard diet, using a multi meta-omics approaches combining strategy of metagenomics and metaproteomics analysis. We reported that cafeteria diet induces obesity, resulting in changes in the microbiota composition, which are related to functional alterations at proteome level. In addition, hesperidin supplementation alters microbiota diversity and also proteins involved in important metabolic pathways. Overall, going deeper into strategies to integrate omics sciences is necessary to understand the complex relationships between the host, gut microbiota, and diet.}, }
@article {pmid29404427, year = {2018}, author = {Hester, ER and Harpenslager, SF and van Diggelen, JMH and Lamers, LL and Jetten, MSM and Lüke, C and Lücker, S and Welte, CU}, title = {Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities.}, journal = {mSystems}, volume = {3}, number = {1}, pages = {}, doi = {10.1128/mSystems.00214-17}, pmid = {29404427}, issn = {2379-5077}, support = {339880//European Research Council/International ; }, abstract = {Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O, and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acidobacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities. IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.}, }
@article {pmid29396619, year = {2018}, author = {Mehetre, G and Shah, M and Dastager, SG and Dharne, MS}, title = {Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India.}, journal = {Archives of microbiology}, volume = {200}, number = {5}, pages = {753-770}, doi = {10.1007/s00203-018-1484-4}, pmid = {29396619}, issn = {1432-072X}, support = {EMR/2014/000483//Science and Engineering Research Board/ ; }, mesh = {Amylases/analysis ; Bacteria/enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/analysis ; Biodiversity ; Hot Springs/*microbiology ; India ; Peptide Hydrolases/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Xylosidases/analysis ; }, abstract = {Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India. Molecular, phylogenetic and predictive functional characterization of the isolated bacterial population was done using 16S rRNA sequencing coupled with Tax4Fun tools. Furthermore, representative isolates were screened for important enzymes (cellulase, xylanase, amylase, and protease) and heavy metal tolerance (chromium, arsenic) properties. A total of 454 bacterial isolates obtained were mapped into 57 unique bacterial genera and 4 different bacterial phyla. Interestingly, 37 genera not previously isolated from Indian hot springs, were isolated for the first time in the present study. However, most of these genera (23 out of 37) were reported only in metagenomics studies from Indian and global hot springs. Furthermore, around 14 genera not previously cultivated and not detected in metagenomics studies of hot springs are documented here. The metabolic potential was ascertained by determining the abundance of specific genes using in silico based Tax4Fun tool, which identified around 315 metabolic pathways for metabolism of carbohydrates, synthesis of secondary metabolites and degradation of xenobiotic compounds. Bioprospection study revealed that 33 and 25 bacterial genera were positive for enzyme production and resistance to the heavy metals, respectively. The present study revealed the advantages of cultivation methods using a comprehensive multiple isolation approach for exploring untapped and unique bacterial diversity, and also utilities for various biotechnological and environmental applications.}, }
@article {pmid29371626, year = {2018}, author = {Carradec, Q and Pelletier, E and Da Silva, C and Alberti, A and Seeleuthner, Y and Blanc-Mathieu, R and Lima-Mendez, G and Rocha, F and Tirichine, L and Labadie, K and Kirilovsky, A and Bertrand, A and Engelen, S and Madoui, MA and Méheust, R and Poulain, J and Romac, S and Richter, DJ and Yoshikawa, G and Dimier, C and Kandels-Lewis, S and Picheral, M and Searson, S and ,  and Jaillon, O and Aury, JM and Karsenti, E and Sullivan, MB and Sunagawa, S and Bork, P and Not, F and Hingamp, P and Raes, J and Guidi, L and Ogata, H and de Vargas, C and Iudicone, D and Bowler, C and Wincker, P}, title = {A global ocean atlas of eukaryotic genes.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {373}, doi = {10.1038/s41467-017-02342-1}, pmid = {29371626}, issn = {2041-1723}, support = {294823//European Research Council/International ; }, mesh = {Amino Acid Sequence ; Animals ; *Aquatic Organisms ; Atlases as Topic ; Bacteria/classification/genetics ; Biodiversity ; Ecosystem ; Eukaryota/classification/*genetics ; Eukaryotic Cells/cytology/*metabolism ; *Metagenome ; Metagenomics/methods ; Oceans and Seas ; *Phylogeny ; Phytoplankton/classification/genetics ; Seawater ; Viruses/classification/genetics ; Zooplankton/classification/*genetics ; }, abstract = {While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.}, }
@article {pmid29361802, year = {2018}, author = {D'Auria, G and Artacho, A and Rojas, RA and Bautista, JS and Méndez, R and Gamboa, MT and Gamboa, JR and Gómez-Cruz, R}, title = {Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs.}, journal = {Genes}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/genes9010055}, pmid = {29361802}, issn = {2073-4425}, abstract = {New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300-500 mg L-1 H2S and <0.1 mg L-1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample.}, }
@article {pmid29355278, year = {2018}, author = {Cheng, M and Zhang, X and Zhu, J and Cheng, L and Cao, J and Wu, Z and Weng, P and Zheng, X}, title = {A metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity mice fed with oolong tea polyphenols.}, journal = {Food &amp; function}, volume = {9}, number = {2}, pages = {1079-1087}, doi = {10.1039/c7fo01570d}, pmid = {29355278}, issn = {2042-650X}, mesh = {Animals ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Camellia sinensis/*chemistry ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestines/metabolism/*microbiology ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/metabolism/microbiology ; Plant Extracts/*administration &amp; dosage ; Polyphenols/*administration &amp; dosage ; Tea/chemistry/metabolism ; }, abstract = {To investigate the modulatory effect of oolong tea polyphenols (OTP) on intestinal microbiota, OTP was prepared by column chromatography and its influence on the gut flora structure was analyzed by high-throughput sequencing with a human flora-associated high fat diet (HFD) induced obesity mouse model. We observed a robust increase in bacterial biodiversity and the abundance of genera known to be butyrate- and acetate-producing bacteria. A large increase in Bacteroidetes with a decrease in Firmicutes was observed after the administration of OTP for 4 weeks, and the corresponding decrease in the Firmicutes/Bacteroidetes ratio reflected the positive modulatory effect of OTP on the intestinal microbiota. In addition, KEGG pathways for the biosynthesis of amino acids, carbon metabolism, and the ribosome were among the most differentially expressed genes after OTP intervention. The current study revealed that OTP rich in tea catechins, especially O-methylated derivatives, may have prebiotic-like activity and can be used as a functional food component with potential therapeutic utility to prevent obesity-related metabolic disorders by manipulating the intestinal microbiota.}, }
@article {pmid29351302, year = {2018}, author = {Bzhalava, Z and Hultin, E and Dillner, J}, title = {Extension of the viral ecology in humans using viral profile hidden Markov models.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190938}, doi = {10.1371/journal.pone.0190938}, pmid = {29351302}, issn = {1932-6203}, mesh = {Algorithms ; Computational Biology ; Contig Mapping/statistics &amp; numerical data ; Databases, Protein/statistics &amp; numerical data ; Humans ; Markov Chains ; Metagenomics/statistics &amp; numerical data ; *Microbiota ; Phylogeny ; Viral Proteins/genetics ; Viruses/classification/*genetics/*isolation &amp; purification ; }, abstract = {When human samples are sequenced, many assembled contigs are &quot;unknown&quot;, as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, &quot;vFam&quot;. We used HMMER3 analysis of &quot;unknown&quot; human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family). In summary, we find that analysis using the HMMER3 algorithm and the &quot;vFam&quot; database greatly extended the detection of viruses in biospecimens from humans.}, }
@article {pmid29334812, year = {2018}, author = {Ding, W and Ma, C and Zhang, W and Chiang, H and Tam, C and Xu, Y and Zhang, G and Qian, PY}, title = {Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses.}, journal = {Biofouling}, volume = {34}, number = {1}, pages = {111-122}, doi = {10.1080/08927014.2017.1409891}, pmid = {29334812}, issn = {1029-2454}, mesh = {4-Butyrolactone/*analogs &amp; derivatives/pharmacology ; Biofilms/*drug effects ; Biofouling/*prevention &amp; control ; Cell Adhesion ; Metagenomics ; Microbial Consortia/*genetics ; Polyesters/*pharmacology ; Polyurethanes/*pharmacology ; Seawater ; Surface Properties ; Transcriptome ; }, abstract = {Butenolide is an environmentally friendly antifouling natural product, but its efficiency and mechanism in preventing biofilm formation have not been examined. Furthermore, controlling the release of butenolide from paints into seawater is technically challenging. A coating was developed by mixing butenolide with a biodegradable polymer, poly (ε-caprolactone)-based polyurethane, and a one-month in situ anti-biofilm test was conducted in a subtidal area. The constant release of butenolide from the surface suggested that its release was well controlled. Direct observation and confocal microscope investigation indicated that the coating was effective against both biofilm formation and attachment of large fouling organisms. Metatranscriptomic analysis of biofilm samples implied that the coating selectively inhibited the adhesion of microbes from a variety of phyla and targeted particular functional pathways including energy metabolism, drug transport and toxin release. These integrated analyses demonstrated the potential application of this butenolide/polymer coating as an anti-biofilm material.}, }
@article {pmid29330574, year = {2018}, author = {Koizumi, T and Hattori, M and Nara, K}, title = {Ectomycorrhizal fungal communities in alpine relict forests of Pinus pumila on Mt. Norikura, Japan.}, journal = {Mycorrhiza}, volume = {28}, number = {2}, pages = {129-145}, doi = {10.1007/s00572-017-0817-5}, pmid = {29330574}, issn = {1432-1890}, support = {25660115//Japan Society for the Promotion of Science/ ; 16J07343//Japan Society for the Promotion of Science/ ; }, mesh = {Altitude ; *Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; *Forests ; Japan ; Mycorrhizae/genetics/*physiology ; Pinus/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Ectomycorrhizal (ECM) symbioses are indispensable for the establishment of host trees, yet available information of ECM symbiosis in alpine forests is scarce. Pinus pumila is a typical ice age relict tree species in Japan and often forms monodominant dwarf vegetation above the tree line in mountains. We studied ECM fungi colonizing P. pumila on Mt. Norikura, Japan, with reference to host developmental stages, i.e., from current-year seedlings to mature trees. ECM fungal species were identified based on rDNA ITS sequences. Ninety-two ECM fungal species were confirmed from a total of 2480 root tips examined. Species in /suillus-rhizopogon and /wilcoxina were dominant in seedling roots. ECM fungal diversity increased with host development, due to the addition of species-rich fungal lineages (/cenococcum, /cortinarius, and /russula-lactarius) in late-successional stages. Such successional pattern of ECM fungi is similar to those in temperate pine systems, suggesting the predominant role of /suillus-rhizopogon in seedling establishment, even in relict alpine habitats fragmented and isolated for a geological time period. Most of the ECM fungi detected were also recorded in Europe or North America, indicating their potential Holarctic distribution and the possibility of their comigration with P. pumila through land bridges during ice ages. In addition, we found significant effects of soil properties on ECM fungal communities, which explained 34.1% of the total variation of the fungal communities. While alpine vegetation is regarded as vulnerable to the ongoing global warming, ECM fungal communities associated with P. pumila could be altered by the edaphic change induced by the warming.}, }
@article {pmid29321767, year = {2017}, author = {Soliman, T and Reimer, JD and Yang, SY and Villar-Briones, A and Roy, MC and Jenke-Kodama, H}, title = {Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2451}, doi = {10.3389/fmicb.2017.02451}, pmid = {29321767}, issn = {1664-302X}, abstract = {Microbial community diversity and chemodiversity were investigated in marine sediments adjacent to the Okinawan &quot;Kaichu-Doro&quot; Causeway, which was constructed 46 years ago to connect a group of four islands (Henza-jima, Miyagi-jima, Ikei-jima, Hamahiga-jima) to the Okinawan main island. This causeway was not built on pilings, but by land reclamation; hence, it now acts as a long, thin peninsula. The construction of this causeway was previously shown to have influenced the surrounding marine ecosystem, causing ecosystem fragmentation and loss of water circulation. In this study, we collected sediment cores (n = 10) from five paired sites in 1 m water depths. Each pair of sites consisted of one site each on the immediate north and south sides of the causeway. Originally the members of each pair were much closer to each other (<150 m) than to other pairs, but now the members of each pair are isolated by the causeway. Each core was 60-80 cm long and was divided into 15-cm layers. We examined the vertical diversity of microbial communities and chemical compounds to determine the correlation between chemodiversity and microbial communities among marine sediment cores and layers. Principal coordinate analyses (PCoA) of detected compounds and of bacterial and archaeal operational taxonomic units (OTUs) revealed that the north and south sides of the causeway are relatively isolated, with each side having unique microbial OTUs. Additionally, some bacterial families (e.g., Acidaminobacteraceae, Rhizobiaceae, and Xanthomonadaceae) were found only on the south side of Kaichu-Doro. Interestingly, we found that the relative abundance of OTUs for some microbial families increased from top to bottom, but this was reversed in some other families. We conclude that the causeway has altered microbial community composition and metabolite profiles in marine sediments.}, }
@article {pmid29312205, year = {2017}, author = {Karimi, E and Ramos, M and Gonçalves, JMS and Xavier, JR and Reis, MP and Costa, R}, title = {Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2499}, doi = {10.3389/fmicb.2017.02499}, pmid = {29312205}, issn = {1664-302X}, abstract = {Current knowledge of sponge microbiome functioning derives mostly from comparative analyses with bacterioplankton communities. We employed a metagenomics-centered approach to unveil the distinct features of the Spongia officinalis endosymbiotic consortium in the context of its two primary environmental vicinities. Microbial metagenomic DNA samples (n = 10) from sponges, seawater, and sediments were subjected to Hiseq Illumina sequencing (c. 15 million 100 bp reads per sample). Totals of 10,272 InterPro (IPR) predicted protein entries and 784 rRNA gene operational taxonomic units (OTUs, 97% cut-off) were uncovered from all metagenomes. Despite the large divergence in microbial community assembly between the surveyed biotopes, the S. officinalis symbiotic community shared slightly greater similarity (p < 0.05), in terms of both taxonomy and function, to sediment than to seawater communities. The vast majority of the dominant S. officinalis symbionts (i.e., OTUs), representing several, so-far uncultivable lineages in diverse bacterial phyla, displayed higher residual abundances in sediments than in seawater. CRISPR-Cas proteins and restriction endonucleases presented much higher frequencies (accompanied by lower viral abundances) in sponges than in the environment. However, several genomic features sharply enriched in the sponge specimens, including eukaryotic-like repeat motifs (ankyrins, tetratricopeptides, WD-40, and leucine-rich repeats), and genes encoding for plasmids, sulfatases, polyketide synthases, type IV secretion proteins, and terpene/terpenoid synthases presented, to varying degrees, higher frequencies in sediments than in seawater. In contrast, much higher abundances of motility and chemotaxis genes were found in sediments and seawater than in sponges. Higher cell and surface densities, sponge cell shedding and particle uptake, and putative chemical signaling processes favoring symbiont persistence in particulate matrices all may act as mechanisms underlying the observed degrees of taxonomic connectivity and functional convergence between sponges and sediments. The reduced frequency of motility and chemotaxis genes in the sponge microbiome reinforces the notion of a prevalent mutualistic mode of living inside the host. This study highlights the S. officinalis &quot;endosymbiome&quot; as a distinct consortium of uncultured prokaryotes displaying a likely &quot;sit-and-wait&quot; strategy to nutrient foraging coupled to sophisticated anti-viral defenses, unique natural product biosynthesis, nutrient utilization and detoxification capacities, and both microbe-microbe and host-microbe gene transfer amenability.}, }
@article {pmid29304124, year = {2018}, author = {Krehenwinkel, H and Fong, M and Kennedy, S and Huang, EG and Noriyuki, S and Cayetano, L and Gillespie, R}, title = {The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0189188}, doi = {10.1371/journal.pone.0189188}, pmid = {29304124}, issn = {1932-6203}, mesh = {Animals ; Arthropods/classification/*genetics/*microbiology ; Biodiversity ; DNA/*analysis/*genetics ; DNA Barcoding, Taxonomic/*methods/statistics &amp; numerical data ; DNA Primers ; Ecosystem ; Hawaii ; Metagenome ; Metagenomics/methods/statistics &amp; numerical data ; Microbiota/*genetics ; Polymerase Chain Reaction/methods ; Selection Bias ; }, abstract = {PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer choice, annealing temperature and cycle number. Our results show that DNA degradation does indeed bias community analyses. However, the effect of this bias is of minor importance compared to that induced by changes in PCR conditions. Analyses of the macro and microbiome from passively collected arthropod samples are thus well worth pursuing.}, }
@article {pmid29297295, year = {2017}, author = {Herath, D and Tang, SL and Tandon, K and Ackland, D and Halgamuge, SK}, title = {CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.}, journal = {BMC bioinformatics}, volume = {18}, number = {Suppl 16}, pages = {571}, doi = {10.1186/s12859-017-1967-3}, pmid = {29297295}, issn = {1471-2105}, abstract = {BACKGROUND: In metagenomics, the separation of nucleotide sequences belonging to an individual or closely matched populations is termed binning. Binning helps the evaluation of underlying microbial population structure as well as the recovery of individual genomes from a sample of uncultivable microbial organisms. Both supervised and unsupervised learning methods have been employed in binning; however, characterizing a metagenomic sample containing multiple strains remains a significant challenge. In this study, we designed and implemented a new workflow, Coverage and composition based binning of Metagenomes (CoMet), for binning contigs in a single metagenomic sample. CoMet utilizes coverage values and the compositional features of metagenomic contigs. The binning strategy in CoMet includes the initial grouping of contigs in guanine-cytosine (GC) content-coverage space and refinement of bins in tetranucleotide frequencies space in a purely unsupervised manner. With CoMet, the clustering algorithm DBSCAN is employed for binning contigs. The performances of CoMet were compared against four existing approaches for binning a single metagenomic sample, including MaxBin, Metawatt, MyCC (default) and MyCC (coverage) using multiple datasets including a sample comprised of multiple strains.<br><br>RESULTS: Binning methods based on both compositional features and coverages of contigs had higher performances than the method which is based only on compositional features of contigs. CoMet yielded higher or comparable precision in comparison to the existing binning methods on benchmark datasets of varying complexities. MyCC (coverage) had the highest ranking score in F1-score. However, the performances of CoMet were higher than MyCC (coverage) on the dataset containing multiple strains. Furthermore, CoMet recovered contigs of more species and was 18 - 39% higher in precision than the compared existing methods in discriminating species from the sample of multiple strains. CoMet resulted in higher precision than MyCC (default) and MyCC (coverage) on a real metagenome.<br><br>CONCLUSIONS: The approach proposed with CoMet for binning contigs, improves the precision of binning while characterizing more species in a single metagenomic sample and in a sample containing multiple strains. The F1-scores obtained from different binning strategies vary with different datasets; however, CoMet yields the highest F1-score with a sample comprised of multiple strains.}, }
@article {pmid29293631, year = {2018}, author = {Villegas, LEM and Campolina, TB and Barnabe, NR and Orfano, AS and Chaves, BA and Norris, DE and Pimenta, PFP and Secundino, NFC}, title = {Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190352}, doi = {10.1371/journal.pone.0190352}, pmid = {29293631}, issn = {1932-6203}, mesh = {Aedes/*microbiology/virology ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mosquito Vectors ; RNA, Ribosomal, 16S/genetics ; Zika Virus Infection/*microbiology ; }, abstract = {Zika is a re-emerging infection that has been considered a major threat to global public health. Currently at least 100 countries are at risk of Zika virus (ZIKV) transmission. Aedes aegypti is the main mosquito vector in the Americas. This vector is exposed to, and interacts symbiotically with a variety of microorganisms in its environment, which may result in the formation of a lifetime association. Here, the unknown effect that ZIKV exerts on the dynamic bacterial community harbored by this mosquito vector was investigated using a metagenomic analysis of its microbiota. Groups of Ae. aegypti were experimentally fed on sugar, blood and blood mixed with ZIKV, and held for 3 to 7 days after blood meal and eggs development respectively. The infected groups were processed by qPCR to confirm the presence of ZIKV. All groups were analyzed by metagenomics (Illumina Hiseq Sequencing) and 16S rRNA amplicon sequences were obtained to create bacterial taxonomic profiles. A core microbiota and exclusive bacterial taxa were identified that incorporate 50.5% of the predicted reads from the dataset, with 40 Gram-negative and 9 Gram-positive families. To address how ZIKV invasion may disturb the ecological balance of the Ae. aegypti microbiota, a CCA analysis coupled with an explanatory matrix was performed to support the biological interpretation of shifts in bacterial signatures. Two f-OTUs appeared as potential biomarkers of ZIKV infection: Rhodobacteraceae and Desulfuromonadaceae. Coincidentally, both f-OTUs were exclusively present in the ZIKV- infected blood-fed and ZIKV- infected gravid groups. In conclusion, this study shows that bacterial symbionts act as biomarkers of the insect physiological states and how they respond as a community when ZIKV invades Ae. aegypti. Basic knowledge of local haematophagous vectors and their associated microbiota is relevant when addressing transmission of vector-borne infectious diseases in their regional surroundings.}, }
@article {pmid29292539, year = {2018}, author = {Porter, TM and Hajibabaei, M}, title = {Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis.}, journal = {Molecular ecology}, volume = {27}, number = {2}, pages = {313-338}, doi = {10.1111/mec.14478}, pmid = {29292539}, issn = {1365-294X}, abstract = {The purpose of this review is to present the most common and emerging DNA-based methods used to generate data for biodiversity and biomonitoring studies. As environmental assessment and monitoring programmes may require biodiversity information at multiple levels, we pay particular attention to the DNA metabarcoding method and discuss a number of bioinformatic tools and considerations for producing DNA-based indicators using operational taxonomic units (OTUs), taxa at a variety of ranks and community composition. By developing the capacity to harness the advantages provided by the newest technologies, investigators can &quot;scale up&quot; by increasing the number of samples and replicates processed, the frequency of sampling over time and space, and even the depth of sampling such as by sequencing more reads per sample or more markers per sample. The ability to scale up is made possible by the reduced hands-on time and cost per sample provided by the newest kits, platforms and software tools. Results gleaned from broad-scale monitoring will provide opportunities to address key scientific questions linked to biodiversity and its dynamics across time and space as well as being more relevant for policymakers, enabling science-based decision-making, and provide a greater socio-economic impact. As genomic approaches are continually evolving, we provide this guide to methods used in biodiversity genomics.}, }
@article {pmid29272370, year = {2018}, author = {Laenen, L and Vergote, V and Kafetzopoulou, LE and Wawina, TB and Vassou, D and Cook, JA and Hugot, JP and Deboutte, W and Kang, HJ and Witkowski, PT and Köppen-Rung, P and Krüger, DH and Licková, M and Stang, A and Striešková, L and Szemeš, T and Markowski, J and Hejduk, J and Kafetzopoulos, D and Van Ranst, M and Yanagihara, R and Klempa, B and Maes, P}, title = {A Novel Hantavirus of the European Mole, Bruges Virus, Is Involved in Frequent Nova Virus Coinfections.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {45-55}, doi = {10.1093/gbe/evx268}, pmid = {29272370}, issn = {1759-6653}, support = {P20 GM103516/GM/NIGMS NIH HHS/United States ; R01 AI075057/AI/NIAID NIH HHS/United States ; U54 MD007601/MD/NIMHD NIH HHS/United States ; }, abstract = {Hantaviruses are zoonotic viruses with a complex evolutionary history of virus-host coevolution and cross-species transmission. Although hantaviruses have a broad reservoir host range, virus-host relationships were previously thought to be strict, with a single virus species infecting a single host species. Here, we describe Bruges virus, a novel hantavirus harbored by the European mole (Talpa europaea), which is the well-known host of Nova virus. Phylogenetic analyses of all three genomic segments showed tree topology inconsistencies, suggesting that Bruges virus has emerged from cross-species transmission and ancient reassortment events. A high number of coinfections with Bruges and Nova viruses was detected, but no evidence was found for reassortment between these two hantaviruses. These findings highlight the complexity of hantavirus evolution and the importance of further investigation of hantavirus-reservoir relationships.}, }
@article {pmid29261736, year = {2017}, author = {Camacho-Ortiz, A and Gutiérrez-Delgado, EM and Garcia-Mazcorro, JF and Mendoza-Olazarán, S and Martínez-Meléndez, A and Palau-Davila, L and Baines, SD and Maldonado-Garza, H and Garza-González, E}, title = {Randomized clinical trial to evaluate the effect of fecal microbiota transplant for initial Clostridium difficile infection in intestinal microbiome.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0189768}, doi = {10.1371/journal.pone.0189768}, pmid = {29261736}, issn = {1932-6203}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/genetics ; Biodiversity ; Clostridium Infections/drug therapy/*therapy ; Demography ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Genotype ; Humans ; Male ; Metagenomics ; Microbial Sensitivity Tests ; Middle Aged ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Tissue Donors ; Vancomycin/therapeutic use ; Young Adult ; }, abstract = {OBJECTIVE: The aim of this study was to evaluate the impact of fecal donor-unrelated donor mix (FMT-FURM) transplantation as first-line therapy for C. difficile infection (CDI) in intestinal microbiome.<br><br>METHODS: We designed an open, two-arm pilot study with oral vancomycin (250mg every 6 h for 10-14 days) or FMT-FURM as treatments for the first CDI episode in hospitalized adult patients in Hospital Universitario &quot;Dr. Jose Eleuterio Gonzalez&quot;. Patients were randomized by a closed envelope method in a 1: 1 ratio to either oral vancomycin or FMT-FURM. CDI resolution was considered when there was a reduction on the Bristol scale of at least 2 points, a reduction of at least 50% in the number of bowel movements, absence of fever, and resolution of abdominal pain (at least two criteria). From each patient, a fecal sample was obtained at days 0, 3, and 7 after treatment. Specimens were cultured to isolate C. difficile, and isolates were characterized by PCR. Susceptibility testing of isolates was performed using the agar dilution method. Fecal samples and FMT-FURM were analyzed by 16S rRNA sequencing.<br><br>RESULTS: We included 19 patients; 10 in the vancomycin arm and 9 in the FMT-FURM arm. However, one of the patients in the vancomycin arm and two patients in the FMT-FURM arm were eliminated. Symptoms resolved in 8/9 patients (88.9%) in the vancomycin group, while symptoms resolved in 4/7 patients (57.1%) after the first FMT-FURM dose (P = 0.26) and in 5/7 patients (71.4%) after the second dose (P = 0.55). During the study, no adverse effects attributable to FMT-FURM were observed in patients. Twelve isolates were recovered, most isolates carried tcdB, tcdA, cdtA, and cdtB, with an 18-bp deletion in tcdC. All isolates were resistant to ciprofloxacin and moxifloxacin but susceptible to metronidazole, linezolid, fidaxomicin, and tetracycline. In the FMT-FURM group, the bacterial composition was dominated by Firmicutes, Bacteroidetes, and Proteobacteria at all-time points and the microbiota were remarkably stable over time. The vancomycin group showed a very different pattern of the microbial composition when comparing to the FMT-FURM group over time.<br><br>CONCLUSION: The results of this preliminary study showed that FMT-FURM for initial CDI is associated with specific bacterial communities that do not resemble the donors' sample.}, }
@article {pmid29255014, year = {2018}, author = {Bergauer, K and Fernandez-Guerra, A and Garcia, JAL and Sprenger, RR and Stepanauskas, R and Pachiadaki, MG and Jensen, ON and Herndl, GJ}, title = {Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {3}, pages = {E400-E408}, doi = {10.1073/pnas.1708779115}, pmid = {29255014}, issn = {1091-6490}, support = {268595//European Research Council/International ; }, mesh = {Archaea/genetics/*metabolism ; Archaeal Proteins/*metabolism ; Atlantic Ocean ; Bacteria/genetics/*metabolism ; Bacterial Proteins/*metabolism ; Biodiversity ; Genome, Archaeal ; Genome, Bacterial ; Metagenomics ; Proteomics/*methods ; Seawater ; *Water Microbiology ; }, abstract = {The phylogenetic composition of the heterotrophic microbial community is depth stratified in the oceanic water column down to abyssopelagic layers. In the layers below the euphotic zone, it has been suggested that heterotrophic microbes rely largely on solubilized particulate organic matter as a carbon and energy source rather than on dissolved organic matter. To decipher whether changes in the phylogenetic composition with depth are reflected in changes in the bacterial and archaeal transporter proteins, we generated an extensive metaproteomic and metagenomic dataset of microbial communities collected from 100- to 5,000-m depth in the Atlantic Ocean. By identifying which compounds of the organic matter pool are absorbed, transported, and incorporated into microbial cells, intriguing insights into organic matter transformation in the deep ocean emerged. On average, solute transporters accounted for 23% of identified protein sequences in the lower euphotic and ∼39% in the bathypelagic layer, indicating the central role of heterotrophy in the dark ocean. In the bathypelagic layer, substrate affinities of expressed transporters suggest that, in addition to amino acids, peptides and carbohydrates, carboxylic acids and compatible solutes may be essential substrates for the microbial community. Key players with highest expression of solute transporters were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria, accounting for 40%, 11%, and 10%, respectively, of relative protein abundances. The in situ expression of solute transporters indicates that the heterotrophic prokaryotic community is geared toward the utilization of similar organic compounds throughout the water column, with yet higher abundances of transporters targeting aromatic compounds in the bathypelagic realm.}, }
@article {pmid29228901, year = {2017}, author = {Forsell, J and Bengtsson-Palme, J and Angelin, M and Johansson, A and Evengård, B and Granlund, M}, title = {The relation between Blastocystis and the intestinal microbiota in Swedish travellers.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {231}, doi = {10.1186/s12866-017-1139-7}, pmid = {29228901}, issn = {1471-2180}, mesh = {Adult ; Biodiversity ; Blastocystis/*classification/physiology ; Blastocystis Infections/epidemiology/*microbiology/*parasitology/transmission ; Feces/microbiology/parasitology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Prevalence ; Sweden/epidemiology ; *Travel ; Young Adult ; }, abstract = {BACKGROUND: Blastocystis sp. is a unicellular eukaryote that is commonly found in the human intestine. Its ability to cause disease is debated and a subject for ongoing research. In this study, faecal samples from 35 Swedish university students were examined through shotgun metagenomics before and after travel to the Indian peninsula or Central Africa. We aimed at assessing the impact of travel on Blastocystis carriage and seek associations between Blastocystis and the bacterial microbiota.<br><br>RESULTS: We found a prevalence of Blastocystis of 16/35 (46%) before travel and 15/35 (43%) after travel. The two most commonly Blastocystis subtypes (STs) found were ST3 and ST4, accounting for 20 of the 31 samples positive for Blastocystis. No mixed subtype carriage was detected. All ten individuals with a typable ST before and after travel maintained their initial ST. The composition of the gut bacterial community was not significantly different between Blastocystis-carriers and non-carriers. Interestingly, the presence of Blastocystis was accompanied with higher abundances of the bacterial genera Sporolactobacillus and Candidatus Carsonella. Blastocystis carriage was positively associated with high bacterial genus richness, and negatively correlated to the Bacteroides-driven enterotype. These associations were both largely dependent on ST4 - a subtype commonly described from Europe - while the globally prevalent ST3 did not show such significant relationships.<br><br>CONCLUSIONS: The high rate of Blastocystis subtype persistence found during travel indicates that long-term carriage of Blastocystis is common. The associations between Blastocystis and the bacterial microbiota found in this study could imply a link between Blastocystis and a healthy microbiota as well as with diets high in vegetables. Whether the associations between Blastocystis and the microbiota are resulting from the presence of Blastocystis, or are a prerequisite for colonization with Blastocystis, are interesting questions for further studies.}, }
@article {pmid29223543, year = {2018}, author = {Cowart, DA and Murphy, KR and Cheng, CC}, title = {Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula.}, journal = {Marine genomics}, volume = {37}, number = {}, pages = {148-160}, doi = {10.1016/j.margen.2017.11.003}, pmid = {29223543}, issn = {1876-7478}, abstract = {The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods. We collected water samples from four WAP shallow (≤300m) shelf regions, recovered the eDNA therein, and performed metagenomic shotgun sequencing and analyses to determine the effectiveness of this method to assess marine benthic faunal diversity; this includes the detection of deep-water predatory king crabs whose potential shoreward expansion to warming shelves has sparked much concern. Using a customized bioinformatics pipeline, we identified abundant signatures of common benthic invertebrate fauna, endemic notothenioid fishes, as well as lithodid king crabs. We also uncovered species richness and diversity comparable to biological inventories compiled by the use of traditional survey methods, supporting the efficacy of the eDNA shotgun sequencing approach. As the rate of eDNA degradation affects faunal detection sensitivity, we also quantified mitochondrial ND2 gene copies in eDNA derived from a WAP icefish and found ND2 copies persisted to at least 20days in the cold WAP water, much longer than values reported for temperate environments. We propose that eDNA metagenomic sequencing complements traditional sampling, and combining both will enable more inclusive biodiversity detection and faunal change monitoring in the vast Southern Ocean.}, }
@article {pmid29222756, year = {2018}, author = {Ye, C and Xu, N and Chen, X and Liu, L}, title = {Metabolic Model Reconstruction and Analysis of an Artificial Microbial Ecosystem.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1716}, number = {}, pages = {219-238}, doi = {10.1007/978-1-4939-7528-0_10}, pmid = {29222756}, issn = {1940-6029}, mesh = {Algorithms ; Metabolomics/*methods ; Metagenomics ; Microbial Consortia ; *Models, Biological ; Phylogeny ; }, abstract = {Microbial communities are widespread in the environment, and to isolate and identify species or to determine relations among microorganisms, some 'omics methods like metagenomics, proteomics, and metabolomics have been used. When combined with various 'omics data, models known as artificial microbial ecosystems (AME) are powerful methods that can make functional predictions about microbial communities. Reconstruction of an AME model is the first step for model analysis. Many techniques have been applied to the construction of AME models, e.g., the compartmentalization approach, community objectives method, and dynamic analysis approach. Of these approaches, species compartmentalization is the most relevant to genetics. Besides, some algorithms have been developed for the analysis of AME models. In this chapter, we present a general protocol for the use of the species compartmentalization method to reconstruct a model of microbial communities. Then, the analysis of an AME is discussed.}, }
@article {pmid29211769, year = {2017}, author = {Dong, X and Shulzhenko, N and Lemaitre, J and Greer, RL and Peremyslova, K and Quamruzzaman, Q and Rahman, M and Hasan, OS and Joya, SA and Golam, M and Christiani, DC and Morgun, A and Kile, ML}, title = {Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0188487}, doi = {10.1371/journal.pone.0188487}, pmid = {29211769}, issn = {1932-6203}, mesh = {Arsenic/*toxicity ; Bangladesh ; Child, Preschool ; Drinking Water/*chemistry ; Drug Resistance, Microbial ; *Environmental Exposure ; Female ; Humans ; Intestines/*microbiology ; Male ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*toxicity ; }, abstract = {BACKGROUND: Arsenic has antimicrobial properties at high doses yet few studies have examined its effect on gut microbiota. This warrants investigation since arsenic exposure increases the risk of many diseases in which gut microbiota have been shown to play a role. We examined the association between arsenic exposure from drinking water and the composition of intestinal microbiota in children exposed to low and high arsenic levels during prenatal development and early life.<br><br>RESULTS: 16S rRNA gene sequencing revealed that children with high arsenic exposure had a higher abundance of Proteobacteria in their stool compared to matched controls with low arsenic exposure. Furthermore, whole metagenome shotgun sequencing identified 332 bacterial SEED functions that were enriched in the high exposure group. A separate model showed that these genes, which included genes involved in virulence and multidrug resistance, were positively correlated with arsenic concentration within the group of children in the high arsenic group. We performed reference free genome assembly, and identified strains of E.coli as contributors to the arsenic enriched SEED functions. Further genome annotation of the E.coli genome revealed two strains containing two different arsenic resistance operons that are not present in the gut microbiome of a recently described European human cohort (Metagenomics of the Human Intestinal Tract, MetaHIT). We then performed quantification by qPCR of two arsenic resistant genes (ArsB, ArsC). We observed that the expression of these two operons was higher among the children with high arsenic exposure compared to matched controls.<br><br>CONCLUSIONS: This preliminary study indicates that arsenic exposure early in life was associated with altered gut microbiota in Bangladeshi children. The enrichment of E.coli arsenic resistance genes in the high exposure group provides an insight into the possible mechanisms of how this toxic compound could affect gut microbiota.}, }
@article {pmid29192628, year = {2017}, author = {Anukam, KC and Agbakoba, NR}, title = {A comparative study of the oral microbiome compositions of healthy postmenopausal, premenopausal, and prepubertal Nigerian females, using 16s rrna metagenomics methods.}, journal = {Nigerian journal of clinical practice}, volume = {20}, number = {10}, pages = {1250-1258}, doi = {10.4103/njcp.njcp_32_17}, pmid = {29192628}, issn = {1119-3077}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/*genetics ; Child ; Female ; Humans ; Metagenomics/*methods ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Pilot Projects ; *Postmenopause ; *Premenopause ; RNA, Ribosomal, 16S/*genetics ; Young Adult ; }, abstract = {INTRODUCTION: There is a paucity of information on the oral microbiome compositions of Nigerians, mostly due to lack of appropriate molecular techniques. In this pilot study, we sought to determine and characterize the oral bacterial compositions of &quot;healthy&quot; females.<br><br>MATERIALS AND METHODS: Oral samples were collected from three randomly selected females aged 56, 28, and 8 years. DNA was extracted and 16S rRNA V4 region was amplified using custom-barcoded primers before sequencing with Illumina MiSeq platform. Quantitative Insights into Microbial Ecology pipeline was used for 16S rRNA recognition. Distribution of taxonomic categories at different levels of resolution was done using the ribosomal RNA similarities to entries in the REFseq protein database. Diversity score was calculated based on the inverse Simpson's index.<br><br>RESULTS: The inverse Simpson's diversity index for the postmenopausal, premenopausal, and prepubertal was 7.74, 6.95, and 7.42 respectively. A total of 12 phyla, 70 genera, and 85 species were detected. Firmicutes followed by Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria dominated the oral microbiome of the subjects. Streptococcus thermophilus (33.19%) was the most abundance species in subject 1, while subject 2 was highly predominated by Haemophilus parainfluenzae (80.65%), and subject 3 was predominated by Haemophilus influenzae (23.05%).<br><br>CONCLUSION: The study has revealed that bacteria with varying diversities colonized the subjects and it highlighted the importance of metagenomics in deciphering the oral bacterial compositions from females of different age groups. More studies are needed using metagenomics approach, to appreciate these bacterial organisms that are associated with health and disease in our environment.}, }
@article {pmid29191900, year = {2017}, author = {Coles, VJ and Stukel, MR and Brooks, MT and Burd, A and Crump, BC and Moran, MA and Paul, JH and Satinsky, BM and Yager, PL and Zielinski, BL and Hood, RR}, title = {Ocean biogeochemistry modeled with emergent trait-based genomics.}, journal = {Science (New York, N.Y.)}, volume = {358}, number = {6367}, pages = {1149-1154}, doi = {10.1126/science.aan5712}, pmid = {29191900}, issn = {1095-9203}, mesh = {Atlantic Ocean ; Biochemical Phenomena/genetics ; Metabolic Networks and Pathways/*genetics ; Metagenome ; *Metagenomics ; Microbial Consortia/*genetics ; Models, Biological ; Seawater/*microbiology ; Transcriptome ; }, abstract = {Marine ecosystem models have advanced to incorporate metabolic pathways discovered with genomic sequencing, but direct comparisons between models and &quot;omics&quot; data are lacking. We developed a model that directly simulates metagenomes and metatranscriptomes for comparison with observations. Model microbes were randomly assigned genes for specialized functions, and communities of 68 species were simulated in the Atlantic Ocean. Unfit organisms were replaced, and the model self-organized to develop community genomes and transcriptomes. Emergent communities from simulations that were initialized with different cohorts of randomly generated microbes all produced realistic vertical and horizontal ocean nutrient, genome, and transcriptome gradients. Thus, the library of gene functions available to the community, rather than the distribution of functions among specific organisms, drove community assembly and biogeochemical gradients in the model ocean.}, }
@article {pmid29187204, year = {2017}, author = {Mallick, H and Ma, S and Franzosa, EA and Vatanen, T and Morgan, XC and Huttenhower, C}, title = {Experimental design and quantitative analysis of microbial community multiomics.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {228}, doi = {10.1186/s13059-017-1359-z}, pmid = {29187204}, issn = {1474-760X}, support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; Gene Expression Profiling/methods ; Humans ; *Metabolomics/methods ; *Metagenomics/methods ; *Microbiota ; *Proteomics/methods ; *Research Design ; }, abstract = {Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.}, }
@article {pmid29186720, year = {2017}, author = {Pampillón-González, L and Ortiz-Cornejo, NL and Luna-Guido, M and Dendooven, L and Navarro-Noya, YE}, title = {Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {27}, number = {5}, pages = {306-317}, doi = {10.1159/000479108}, pmid = {29186720}, issn = {1660-2412}, mesh = {Anaerobiosis ; Animals ; Animals, Domestic ; Archaea/*classification/genetics/*metabolism ; Bacteria, Anaerobic/*classification/genetics/*metabolism ; *Biofuels ; *Bioreactors ; Chemical Phenomena ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Farms ; Feces/*microbiology ; *Fermentation ; Metagenome/genetics ; Metagenomics/methods ; Methane/biosynthesis ; Mexico ; Microbial Consortia/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine ; Waste Disposal, Fluid ; Waste Water/microbiology ; }, abstract = {Biogas production from animal waste is an economically viable way to reduce environmental pollution and produce valuable products, i.e., methane and a nutrient-rich organic waste product. An anaerobic digestion reactor for biogas production from pig waste was sampled at the entrance, middle (digestion chamber), and exit of a digester, while the bacterial and archaeal community structure was studied by 16S rRNA gene metagenomics. The number of bacterial operational taxonomic units (OTU)-97% was 3-7 times larger than that of archaeal ones. Bacteria and Archaea found in feces of animals (e.g., Clostridiaceae, Lachnospiraceae, Ruminococcaceae, Methanosarcina, Methanolobus, Methanosaeta, and Methanospirillum) dominated the entrance of the digester. The digestion chamber was dominated by anaerobic sugar-fermenting OP9 bacteria and the syntrophic bacteria Candidatus Cloacamonas (Waste Water of Evry 1; WWE1). The methanogens dominant in the digestion chamber were the acetoclastic Methanosaeta and the hydrogenothrophic Methanoculleus and Methanospirillum. Similar bacterial and archaeal groups that dominated in the middle of the digestion chamber were found in the waste that left the digester. Predicted functions associated with degradation of xenobiotic compounds were significantly different between the sampling locations. The microbial community found in an anaerobic digestion reactor loaded with pig manure contained microorganisms with biochemical capacities related to the 4 phases of methane production.}, }
@article {pmid29186317, year = {2017}, author = {Dovrolis, N and Kolios, G and Spyrou, GM and Maroulakou, I}, title = {Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbx154}, pmid = {29186317}, issn = {1477-4054}, abstract = {Almost 2500 years after Hippocrates' observations on health and its direct association to the gastrointestinal tract, a paradigm shift has recently occurred, making the gut and its symbionts (bacteria, fungi, archaea and viruses) a point of convergence for studies. It is nowadays well established that the gut microflora's compositional diversity regulates via its genes (the microbiome) the host's health and provides preliminary insights into disease progression and regulation. The microbiome's involvement is evident in immunological and physiological studies that link changes in its biodiversity to its contributions to the host's phenotype but also in neurological investigations, substantiating the aptly named gut-brain axis. The definitive mechanisms of this last bidirectional interaction will be our main focus because it presents researchers with a new conundrum. In this review, we prospect current literature for computational analysis methodologies that accommodate the need for better understanding of the microbiome-gut-brain interactions and neurological disorder onset and progression, through cross-disciplinary systems biology applications. We will present bioinformatics tools used in exploring these synergies that help build and interpret microbial 16S ribosomal RNA data sets, produced by shotgun and high-throughput sequencing of healthy and neurological disorder samples stored in biological databases. These approaches provide alternative means for researchers to form hypotheses to their inquests faster, cheaper and swith precision. The goal of these studies relies on the integration of combined metagenomics and metabolomics assessments. An accurate characterization of the microbiome and its functionality can support new diagnostic, prognostic and therapeutic strategies for neurological disorders, customized for each individual host.}, }
@article {pmid29184025, year = {2017}, author = {Gnanaprakasam, ET and Lloyd, JR and Boothman, C and Ahmed, KM and Choudhury, I and Bostick, BC and van Geen, A and Mailloux, BJ}, title = {Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, doi = {10.1128/mBio.01326-17}, pmid = {29184025}, issn = {2150-7511}, support = {P42 ES010349/ES/NIEHS NIH HHS/United States ; }, mesh = {Arsenates/analysis ; Arsenic/*metabolism ; Arsenites/analysis ; Bacteria/*classification/*genetics ; Bangladesh ; *Biota ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/chemistry ; Groundwater/*microbiology ; Iron/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Long-term exposure to trace levels of arsenic (As) in shallow groundwater used for drinking and irrigation puts millions of people at risk of chronic disease. Although microbial processes are implicated in mobilizing arsenic from aquifer sediments into groundwater, the precise mechanism remains ambiguous. The goal of this work was to target, for the first time, a comprehensive suite of state-of-the-art molecular techniques in order to better constrain the relationship between indigenous microbial communities and the iron and arsenic mineral phases present in sediments at two well-characterized arsenic-impacted aquifers in Bangladesh. At both sites, arsenate [As(V)] was the major species of As present in sediments at depths with low aqueous As concentrations, while most sediment As was arsenite [As(III)] at depths with elevated aqueous As concentrations. This is consistent with a role for the microbial As(V) reduction in mobilizing arsenic. 16S rRNA gene analysis indicates that the arsenic-rich sediments were colonized by diverse bacterial communities implicated in both dissimilatory Fe(III) and As(V) reduction, while the correlation analyses involved phylogenetic groups not normally associated with As mobilization. Findings suggest that direct As redox transformations are central to arsenic fate and transport and that there is a residual reactive pool of both As(V) and Fe(III) in deeper sediments that could be released by microbial respiration in response to hydrologic perturbation, such as increased groundwater pumping that introduces reactive organic carbon to depth.IMPORTANCE The consumption of arsenic in waters collected from tube wells threatens the lives of millions worldwide and is particularly acute in the floodplains and deltas of southern Asia. The cause of arsenic mobilization from natural sediments within these aquifers to groundwater is complex, with recent studies suggesting that sediment-dwelling microorganisms may be the cause. In the absence of oxygen at depth, specialist bacteria are thought able to use metals within the sediments to support their metabolism. Via these processes, arsenic-contaminated iron minerals are transformed, resulting in the release of arsenic into the aquifer waters. Focusing on a field site in Bangladesh, a comprehensive, multidisciplinary study using state-of-the-art geological and microbiological techniques has helped better understand the microbes that are present naturally in a high-arsenic aquifer and how they may transform the chemistry of the sediment to potentially lethal effect.}, }
@article {pmid29184020, year = {2017}, author = {Luo, E and Aylward, FO and Mende, DR and DeLong, EF}, title = {Bacteriophage Distributions and Temporal Variability in the Ocean's Interior.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, doi = {10.1128/mBio.01903-17}, pmid = {29184020}, issn = {2150-7511}, mesh = {Bacteriophages/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Viral/analysis/genetics ; Genotype ; Lysogeny ; Metagenomics ; *Oceans and Seas ; Seawater/*virology ; Spatio-Temporal Analysis ; }, abstract = {Bacteriophages are numerically the most abundant DNA-containing entities in the oligotrophic ocean, yet how specific phage populations vary over time and space remains to be fully explored. Here, we conducted a metagenomic time-series survey of double-stranded DNA phages throughout the water column in the North Pacific Subtropical Gyre, encompassing 1.5 years from depths of 25 to 1,000 m. Viral gene sequences were identified in assembled metagenomic samples, yielding an estimated 172,385 different viral gene families. Viral marker gene distributions suggested that lysogeny was more prevalent at mesopelagic depths than in surface waters, consistent with prior prophage induction studies using mitomycin C. A total of 129 ALOHA viral genomes and genome fragments from 20 to 108 kbp were selected for further study, which represented the most abundant phages in the water column. Phage genotypes displayed discrete population structures. Most phages persisted throughout the time-series and displayed a strong depth structure that mirrored the stratified depth distributions of co-occurring bacterial taxa in the water column. Mesopelagic phages were distinct from surface water phages with respect to diversity, gene content, putative life histories, and temporal persistence, reflecting depth-dependent differences in host genomic architectures and phage reproductive strategies. The spatiotemporal distributions of the most abundant open-ocean bacteriophages that we report here provide new insight into viral temporal persistence, life history, and virus-host-environment interactions throughout the open-ocean water column.IMPORTANCE The North Pacific Subtropical Gyre represents one of the largest biomes on the planet, where microbial communities are central mediators of ecosystem dynamics and global biogeochemical cycles. Critical members of these communities are the viruses of marine bacteria, which can alter microbial metabolism and significantly influence their survival and productivity. To better understand these viral assemblages, we conducted genomic analyses of planktonic viruses over a seasonal cycle to ocean depths of 1,000 m. We identified 172,385 different viral gene families and 129 unique virus genotypes in this open-ocean setting. The spatiotemporal distributions of the most abundant open-ocean viruses that we report here provide new insights into viral temporal variability, life history, and virus-host-environment interactions throughout the water column.}, }
@article {pmid29184019, year = {2017}, author = {Chatzidaki-Livanis, M and Coyne, MJ and Roelofs, KG and Gentyala, RR and Caldwell, JM and Comstock, LE}, title = {Gut Symbiont Bacteroides fragilis Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, doi = {10.1128/mBio.01902-17}, pmid = {29184019}, issn = {2150-7511}, support = {R01 AI093771/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*metabolism ; *Antibiosis ; Bacterial Proteins/genetics/*secretion ; Bacteroides fragilis/growth &amp; development/metabolism/*physiology ; DNA Transposable Elements ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Gene Deletion ; Humans ; Metagenomics ; Microbiota ; Mutagenesis, Insertional ; Ubiquitin/genetics/*secretion ; }, abstract = {Human gut Bacteroides species produce different types of toxins that antagonize closely related members of the gut microbiota. Some are toxic effectors delivered by type VI secretion systems, and others are non-contact-dependent secreted antimicrobial proteins. Many strains of Bacteroides fragilis secrete antimicrobial molecules, but only one of these toxins has been described to date (Bacteroidales secreted antimicrobial protein 1 [BSAP-1]). In this study, we describe a novel secreted protein produced by B. fragilis strain 638R that mediated intraspecies antagonism. Using transposon mutagenesis and deletion mutation, we identified a gene encoding a eukaryotic-like ubiquitin protein (BfUbb) necessary for toxin activity against a subset of B. fragilis strains. The addition of ubb into a heterologous background strain conferred toxic activity on that strain. We found this gene to be one of the most highly expressed in the B. fragilis genome. The mature protein is 84% similar to human ubiquitin but has an N-terminal signal peptidase I (SpI) signal sequence and is secreted extracellularly. We found that the mature 76-amino-acid synthetic protein has very potent activity, confirming that BfUbb mediates the activity. Analyses of human gut metagenomic data sets revealed that ubb is present in 12% of the metagenomes that have evidence of B. fragilis As 638R produces both BSAP-1 and BfUbb, we performed a comprehensive analysis of the toxin activity of BSAP-1 and BfUbb against a set of 40 B. fragilis strains, revealing that 75% of B. fragilis strains are targeted by one or the other of these two secreted proteins of strain 638R.IMPORTANCE We are just beginning to understand some of the important interactions that occur between microbes of the human gut microbiota that dictate the composition and abundance of its constituent members. The ability of one member to produce molecules that directly kill a coresident member has been shown among minor gut species and is just starting to be studied in the abundant Bacteroides species. Here, we show that some strains of Bacteroides fragilis have acquired a gene encoding a secreted eukaryotic-like ubiquitin protein with potent inhibitory activity against other B. fragilis stains. This is the first bacterially encoded ubiquitin-like molecule shown to function like a bacterial toxin. This molecule is an example of a gut symbiont acquiring and adapting a eukaryotic molecule likely to increase its competitiveness in the mammalian gut. Understanding antagonistic factors produced by abundant gut symbionts is an important prerequisite to properly engineer strains to colonize the gut for health benefits.}, }
@article {pmid29173869, year = {2018}, author = {Heintz-Buschart, A and Wilmes, P}, title = {Human Gut Microbiome: Function Matters.}, journal = {Trends in microbiology}, volume = {26}, number = {7}, pages = {563-574}, doi = {10.1016/j.tim.2017.11.002}, pmid = {29173869}, issn = {1878-4380}, abstract = {The human gut microbiome represents a complex ecosystem contributing essential functions to its host. Recent large-scale metagenomic studies have provided insights into its structure and functional potential. However, the functional repertoire which is actually contributed to human physiology remains largely unexplored. Here, by leveraging recent omics datasets, we challenge current assumptions regarding key attributes of the functional gut microbiome, in particular with respect to its variability. We further argue that the closing of existing gaps in functional knowledge should be addressed by a most-wanted gene list, the development and application of molecular and cellular high-throughput measurements, the development and sensible use of experimental models, as well as the direct study of observable molecular effects in the human host.}, }
@article {pmid29169786, year = {2018}, author = {Kanokratana, P and Wongwilaiwalin, S and Mhuantong, W and Tangphatsornruang, S and Eurwilaichitr, L and Champreda, V}, title = {Characterization of cellulolytic microbial consortium enriched on Napier grass using metagenomic approaches.}, journal = {Journal of bioscience and bioengineering}, volume = {125}, number = {4}, pages = {439-447}, doi = {10.1016/j.jbiosc.2017.10.014}, pmid = {29169786}, issn = {1347-4421}, mesh = {Anaerobiosis ; Bacteroidetes/genetics/isolation &amp; purification/metabolism ; Biofuels/microbiology ; Cellulose/*metabolism ; Firmicutes/genetics/isolation &amp; purification/metabolism ; Lignin/metabolism ; *Metagenome ; *Metagenomics ; Microbial Consortia/*genetics ; Pennisetum/*metabolism/*microbiology ; Proteobacteria/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Energy grass is a promising substrate for production of biogas by anaerobic digestion. However, the conversion efficiency is limited by the enzymatically recalcitrant nature of cellulosic wastes. In this study, an active, structurally stable mesophilic lignocellulolytic degrading microbial consortium (Np-LMC) was constructed from forest compost soil microbiota by successive subcultivation on Napier grass under facultative anoxic conditions. According to tagged 16S rRNA gene amplicon sequencing, increasing abundance of facultative Proteobacteria was found in the middle of batch cycle which was then subsequently replaced by the cellulose degraders Firmicutes and Bacteroidetes along with decreasing CMCase, xylanase, and β-glucanase activity profiles in the supernatant after 5 days of incubation. Anaerobic/facultative bacteria Dysgonomonas and Sedimentibacter and aerobic bacteria Comamonas were the major genera found in Np-LMC. The consortium was active on degradation of the native and delignified grass. Direct shotgun sequencing of the consortium metagenome revealed relatively high abundance of genes encoding for various lignocellulose degrading enzymes in 23 glycosyl hydrolase (GH) families compared to previously reported cellulolytic microbial communities in mammalian digestive tracts. Enzymes attacking cellulose and hemicellulose were dominated by GH2, 3, 5, 9, 10, 26, 28 and 43 in addition to a variety of carbohydrate esterases (CE) and auxiliary activities (AA), reflecting adaptation of the enzyme systems to the native herbaceous substrate. The consortium identified here represents the microcosm specifically bred on energy grass, with potential for enhancing degradation of fibrous substrates in bioenergy industry.}, }
@article {pmid29169088, year = {2017}, author = {Maier, L and Typas, A}, title = {Systematically investigating the impact of medication on the gut microbiome.}, journal = {Current opinion in microbiology}, volume = {39}, number = {}, pages = {128-135}, doi = {10.1016/j.mib.2017.11.001}, pmid = {29169088}, issn = {1879-0364}, mesh = {Animals ; Gastrointestinal Microbiome/*drug effects ; Humans ; Models, Biological ; Prescription Drugs/*pharmacology ; }, abstract = {In the recent years, there is accumulating evidence for a strong impact of medication on the gut microbiota composition. This evidence comes from metagenomics-based associations and extends beyond classical antibacterials to a handful of human-targeted drugs. To answer whether such effects are direct and explore their consequences in human health, we need to develop experimental platforms that will allow for systematic profiling of drug-microbiota interactions. Here, we discuss approaches, considerations, experimental setups and strategies that can be used to tackle this need, but can be also readily transmitted to related questions in the microbiome field. A comprehensive understanding of how therapeutics interact with gut microbes will open up the path for further mechanistic dissection of such interactions, and ultimately improve not only our understanding of the gut microbiome, but also drug safety and efficacy.}, }
@article {pmid29163419, year = {2017}, author = {Cabello-Yeves, PJ and Ghai, R and Mehrshad, M and Picazo, A and Camacho, A and Rodriguez-Valera, F}, title = {Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2131}, doi = {10.3389/fmicb.2017.02131}, pmid = {29163419}, issn = {1664-302X}, abstract = {The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two freshwater reservoirs located close to each other (Tous and Amadorio, Spain). These metagenome-assembled genomes (MAGs) display a remarkable taxonomic diversity inside the phylum and comprise wide ranges of estimated genome sizes (from 1.8 to 6 Mb). Among all Verrucomicrobia studied we found some of the smallest genomes of the Spartobacteria and Opitutae classes described so far. Some of the Opitutae family MAGs were small, cosmopolitan, with a general heterotrophic metabolism with preference for carbohydrates, and capable of xylan, chitin, or cellulose degradation. Besides, we assembled large copiotroph genomes, which contain a higher number of transporters, polysaccharide degrading pathways and in general more strategies for the uptake of nutrients and carbohydrate-based metabolic pathways in comparison with the representatives with the smaller genomes. The diverse genomes revealed interesting features like green-light absorbing rhodopsins and a complete set of genes involved in nitrogen fixation. The large diversity in genome sizes and physiological properties emphasize the diversity of this clade in freshwaters enlarging even further the already broad eco-physiological range of these microbes.}, }
@article {pmid29161643, year = {2018}, author = {Silbande, A and Adenet, S and Chopin, C and Cornet, J and Smith-Ravin, J and Rochefort, K and Leroi, F}, title = {Effect of vacuum and modified atmosphere packaging on the microbiological, chemical and sensory properties of tropical red drum (Sciaenops ocellatus) fillets stored at 4°C.}, journal = {International journal of food microbiology}, volume = {266}, number = {}, pages = {31-41}, doi = {10.1016/j.ijfoodmicro.2017.10.015}, pmid = {29161643}, issn = {1879-3460}, mesh = {Animals ; Bacteria/isolation &amp; purification ; Biogenic Amines/analysis ; Colony Count, Microbial ; Fishes/*microbiology ; *Food Microbiology ; Food Packaging/*standards ; Metagenomics ; Microbiota ; Nitrogen/analysis ; *Vacuum ; }, abstract = {AIMS: The effect of vacuum (VP - 4°C) and CO2/N2-atmosphere (MAP - 4°C) packaging on the quality of red drum fillets compared with whole gutted iced fish was investigated.<br><br>METHODS AND RESULTS: A metagenomic approach, bacterial enumeration and isolation, biochemical and sensory analyses were carried out. The organoleptic rejection of whole fish was observed at day 15 whereas VP and MAP fillets appeared unacceptable only after 29days. At these dates, total mesophilic counts reached 107-108CFU g-1. According to Illumina MiSeq sequencing, Arthrobacter, Chryseobacterium, Brevibacterium, Staphylococcus and Kocuria were the main genera of the fresh red drum fillets. At the sensory rejection time, lactic acid bacteria (LAB), particularly Carnobacterium sp., dominated the microbiota of both types of packaging. The pH value of fresh samples was between 5.96 and 6.37 and did not vary greatly in all trials. Total volatile basic nitrogen (TVBN) and trimethylamine (TMA) concentrations were low and not represent reliable indicators of the spoilage, contrary to some biogenic amines (cadaverine, putrescine and tyramine).<br><br>CONCLUSION: Chilled packed fillets of red drum have an extended shelf-life compared to whole gutted iced fish. Overall, few differences in sensory and microbial quality were observed between the VP and MAP samples.<br><br>Next-Generation Sequencing (NGS) provided data on the microbiota of a tropical fish.}, }
@article {pmid29155257, year = {2018}, author = {Fonseca, JP and Hoffmann, L and Cabral, BCA and Dias, VHG and Miranda, MR and de Azevedo Martins, AC and Boschiero, C and Bastos, WR and Silva, R}, title = {Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve.}, journal = {Gene}, volume = {642}, number = {}, pages = {389-397}, doi = {10.1016/j.gene.2017.11.039}, pmid = {29155257}, issn = {1879-0038}, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Cluster Analysis ; Fungi/*classification/genetics/isolation &amp; purification ; Metagenomics/methods ; Microbiota ; Rainforest ; Rhizosphere ; Sequence Analysis, DNA/methods ; *Soil Microbiology ; }, abstract = {Pristine forest ecosystems provide a unique perspective for the study of plant-associated microbiota since they host a great microbial diversity. Although the Amazon forest is one of the hotspots of biodiversity around the world, few metagenomic studies described its microbial community diversity thus far. Understanding the environmental factors that can cause shifts in microbial profiles is key to improving soil health and biogeochemical cycles. Here we report a taxonomic and functional characterization of the microbiome from the rhizosphere of Brosimum guianense (Snakewood), a native tree, and bulk soil samples from a pristine Brazilian Amazon forest reserve (Cuniã), for the first time by the shotgun approach. We identified several fungi and bacteria taxon significantly enriched in forest rhizosphere compared to bulk soil samples. For archaea, the trend was the opposite, with many archaeal phylum and families being considerably more enriched in bulk soil compared to forest rhizosphere. Several fungal and bacterial decomposers like Postia placenta and Catenulispora acidiphila which help maintain healthy forest ecosystems were found enriched in our samples. Other bacterial species involved in nitrogen (Nitrobacter hamburgensis and Rhodopseudomonas palustris) and carbon cycling (Oligotropha carboxidovorans) were overrepresented in our samples indicating the importance of these metabolic pathways for the Amazon rainforest reserve soil health. Hierarchical clustering based on taxonomic similar microbial profiles grouped the forest rhizosphere samples in a distinct clade separated from bulk soil samples. Principal coordinate analysis of our samples with publicly available metagenomes from the Amazon region showed grouping into specific rhizosphere and bulk soil clusters, further indicating distinct microbial community profiles. In this work, we reported significant shifts in microbial community structure between forest rhizosphere and bulk soil samples from an Amazon forest reserve that are probably caused by more than one environmental factors such as rhizosphere and soil depth.}, }
@article {pmid29146247, year = {2018}, author = {Vepštaitė-Monstavičė, I and Lukša, J and Stanevičienė, R and Strazdaitė-Žielienė, Ž and Yurchenko, V and Serva, S and Servienė, E}, title = {Distribution of apple and blackcurrant microbiota in Lithuania and the Czech Republic.}, journal = {Microbiological research}, volume = {206}, number = {}, pages = {1-8}, doi = {10.1016/j.micres.2017.09.004}, pmid = {29146247}, issn = {1618-0623}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Czech Republic ; DNA, Bacterial/isolation &amp; purification ; DNA, Fungal/isolation &amp; purification ; Ecology ; Fruit/microbiology ; Fungi/classification/genetics/isolation &amp; purification ; Lithuania ; Malus/*microbiology ; Metagenomics/methods ; *Microbial Consortia ; *Microbiota/genetics ; Phylogeny ; Ribes/*microbiology ; }, abstract = {The microbial assemblies on the surface of plants correlate with specific climatic features, suggesting a direct link between environmental conditions and microbial inhabitation patterns. At the same time however, microbial communities demonstrate distinct profiles depending on the plant species and region of origin. In this study, we report Next Generation Sequencing-based metagenomic analysis of microbial communities associated with apple and blackcurrant fruits harvested from Lithuania and the Czech Republic. Differences in the taxonomic composition of eukaryotic and prokaryotic microorganisms were observed between plant types. Our results revealed limited geographic differentiation between the bacterial and fungal communities associated with apples. In contrast, blackcurrant berries harvested from different regions demonstrated high diversity in both bacterial and fungal microbiota structures. Among fungal and bacterial microorganisms, we identified both potentially beneficial (Cryptococcus, Hanseniaspora, Massilia, Rhodotorula, Sphingomonas) and phytopathogenic microorganisms (Cladosporium, Pantoea, Phoma, Pseudomonas, Septoria, Taphrina) indicating their important roles in ecological and evolutionary processes.}, }
@article {pmid29138298, year = {2017}, author = {Koskinen, K and Pausan, MR and Perras, AK and Beck, M and Bang, C and Mora, M and Schilhabel, A and Schmitz, R and Moissl-Eichinger, C}, title = {First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, doi = {10.1128/mBio.00824-17}, pmid = {29138298}, issn = {2150-7511}, mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; Gastrointestinal Tract/*microbiology ; Humans ; Lung/*microbiology ; Metagenomics/methods ; *Microbiota ; Nose/*microbiology ; Polymerase Chain Reaction/methods ; Skin/*microbiology ; }, abstract = {Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts.IMPORTANCE In summary, our study highlights the importance of the primers and data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract and on the skin and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.}, }
@article {pmid29128292, year = {2017}, author = {Herzog, B and Dötsch, A and Lemmer, H and Horn, H and Müller, E}, title = {Profiling 5-tolyltriazole biodegrading sludge communities using next-generation sequencing and denaturing gradient gel electrophoresis.}, journal = {Systematic and applied microbiology}, volume = {40}, number = {8}, pages = {508-515}, doi = {10.1016/j.syapm.2017.09.007}, pmid = {29128292}, issn = {1618-0984}, mesh = {Betaproteobacteria/classification/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Bioreactors/*microbiology ; Comamonadaceae/isolation &amp; purification/metabolism ; Denaturing Gradient Gel Electrophoresis/methods ; Flavobacterium/isolation &amp; purification/metabolism ; High-Throughput Nucleotide Sequencing ; Phyllobacteriaceae/classification/isolation &amp; purification/metabolism ; Pseudomonas/isolation &amp; purification/metabolism ; Sewage/*microbiology ; Triazoles/analysis/*metabolism ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {Efficient biodegradation of 5-tolyltriazole (5-TTri) in wastewater treatment would minimize its potential detrimental effects on aquatic systems. Therefore, in order to profile 5-TTri biodegrading activated sludge communities (ASC) by DGGE and NGS, acclimation experiments with (i) easily degradable substrates, and (ii) various complex substrates mimicking wastewater conditions were performed. DGGE revealed four genera: Aminobacter (family Phyllobacteriaceae), Flavobacterium (family Flavobacteriaceae), Pseudomonas (family Pseudomonaceae), and Hydrogenophaga (family Comamonadaceae). Metagenomics (DNA) revealed the dominant families Alcaligenaceae, Pseudomonadaceae and Comamonadaceae that also represented the most active families at the RNA level (metatranscriptomics), which might indicate their importance for 5-TTri biodegradation. ASC acclimation and the composition of the substrate significantly affected 5-TTri biodegradation and the development of biodegrading communities. Using acetate only, a moderate 5-TTri degrading community was detected with a very low biodiversity and Pseudomonas spp. as dominant organisms. In contrast, setups fed 'sludge supernatant' (a complex substrate) efficiently biodegraded 5-TTri and formed a more diverse microbial community but with Hydrogenophaga spp. as the dominant group. Finally, a hypothetical 5-TTri biodegradation pathway was constructed based exclusively on the detected, biodegradation-related, Hydrogenophaga spp. genes.}, }
@article {pmid29126267, year = {2017}, author = {Mancabelli, L and Milani, C and Lugli, GA and Turroni, F and Cocconi, D and van Sinderen, D and Ventura, M}, title = {Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {12}, pages = {}, doi = {10.1093/femsec/fix153}, pmid = {29126267}, issn = {1574-6941}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; Biomarkers ; Colitis, Ulcerative/*microbiology ; Crohn Disease/*microbiology ; Enterocolitis, Pseudomembranous/*microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Intestines/microbiology/pathology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Intestinal diseases, such as Crohn's disease (CD), ulcerative colitis (UC) and pseudomembranous colitis (CDI), are among the most common diseases in humans and may lead to more serious pathologies, e.g. colorectal cancer (CRC). Next generation sequencing has in recent years allowed the identification of correlations between intestinal bacteria and diseases, although the formulation of universal gut microbial biomarkers for such diseases is only in its infancy. In the current study, we selected and reanalyzed a total of 3048 public datasets obtained from 16S rRNA profiling of individuals affected by CD, UC, CDI and CRC. This meta-analysis revealed possible biases in the reconstruction of the gut microbiota composition due to the use of different primer pairs employed for PCR of 16S rRNA gene fragments. Notably, this approach also identified common features of individuals affected by gut diseases (DS), including lower biodiversity compared to control subjects. Moreover, potential universal intestinal disease microbial biomarkers were identified through cross-disease comparisons. In detail, CTRL showed high abundance of the genera Barnesiella, Ruminococcaceae UCG-005, Alistipes, Christensenellaceae R-7 group and unclassified member of Lachnospiraceae family, while DS exhibited high abundance of Lactobacillus, unclassified member of Erysipelotrichaceae family and Streptococcus genera.}, }
@article {pmid29126050, year = {2018}, author = {Abia, ALK and Alisoltani, A and Keshri, J and Ubomba-Jaswa, E}, title = {Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use.}, journal = {The Science of the total environment}, volume = {616-617}, number = {}, pages = {326-334}, doi = {10.1016/j.scitotenv.2017.10.322}, pmid = {29126050}, issn = {1879-1026}, mesh = {Bacteria/classification ; Biodiversity ; DNA, Bacterial/isolation &amp; purification ; Geologic Sediments/*microbiology ; *Metagenomics ; RNA, Ribosomal, 16S ; Rivers/*microbiology ; South Africa ; *Water Microbiology ; }, abstract = {Water quality is an important public health issue given that the presence of pathogenic organisms in such waters can adversely affect human and animal health. Despite the numerous studies conducted to assess the quality of environmental waters in many countries, limited efforts have been put on investigating the microbial quality of the sediments in developing countries and how this relates to different land uses. The present study evaluated the bacterial diversity in water and sediments in a highly used South African river to find out how the different land uses influenced the bacterial diversity, and to verify the human diseases functional classes of the bacterial populations. Samples were collected on river stretches influenced by an informal, a peri-urban and a rural settlement. Genomic DNA was extracted from water and sediment samples and sequenced on an Illumina® MiSeq platform targeting the 16S rRNA gene variable region V3-V4 from the genomic DNA. Metagenomic data analysis revealed that there was a great diversity in the microbial populations associated with the different land uses, with the informal settlement having the most considerable influence on the bacterial diversity in the water and sediments of the Apies River. The Proteobacteria (69.8%), Cyanobacteria (4.3%), Bacteroidetes (2.7%), and Actinobacteria (2.7%) were the most abundant phyla; the Alphaproteobacteria, Betaproteobacteria and Anaerolineae were the most recorded classes. Also, the sediments had a greater diversity and abundance in bacterial population than the water column. The functional profiles of the bacterial populations revealed an association with many human diseases including cancer pathways. Further studies that would isolate these potentially pathogenic organisms in the aquatic environment are therefore needed as this would help in protecting the lives of communities using such rivers, especially against emerging bacterial pathogens.}, }
@article {pmid29124770, year = {2018}, author = {Dulski, T and Zakęś, Z and Ciesielski, S}, title = {Characterization of the gut microbiota in early life stages of pikeperch Sander lucioperca.}, journal = {Journal of fish biology}, volume = {92}, number = {1}, pages = {94-104}, doi = {10.1111/jfb.13496}, pmid = {29124770}, issn = {1095-8649}, mesh = {Animals ; Aquaculture ; DNA, Bacterial/chemistry ; *Gastrointestinal Microbiome ; Metagenomics ; Perches/genetics/growth &amp; development/*microbiology ; Proteobacteria ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study characterized the gastrointestinal microbiome of nine juvenile farmed pikeperch Sander lucioperca using a metagenomics approach based on bacterial 16S rRNA gene sequencing. Potential changes in the gut microbiota during 2 months of S. lucioperca juvenile life were investigated. Results revealed that gut microbiota was dominated by Proteobacteria (95-92%), while other phyla Firmicutes (1-1·5%) and Actinobacteria (0·9-1·5%) were less abundant. At the family level, fish-gut microbiota were dominated by Enterobacteriaceae, which constituted c. 83% of all DNA sequence reads. Such a situation was present in all of the examined fish except one, which showed a different proportion of particular microbial taxa than the other fish. In this fish, a higher relative abundance (%) of Fusobacteria (21·0%), Bacteroidetes (9·5%) and Firmicutes (7·5%) was observed. There were no significant differences in the gut microbiome structure at different stages of development in the examined fish. This may indicate that Proteobacteria inhabiting the gut microbiota at an early stage of life are a necessary component of the pikeperch microbiome that may support proper nutrition of the fish. The information obtained on the gut microbiome could be useful in determining juvenile S. lucioperca health and improving rearing conditions by welfare monitoring in aquaculture.}, }
@article {pmid29120486, year = {2017}, author = {Miossec, MJ and Valenzuela, SL and Mendez, KN and Castro-Nallar, E}, title = {Computational Methods for Human Microbiome Analysis.}, journal = {Current protocols in microbiology}, volume = {47}, number = {}, pages = {1E.14.1-1E.14.17}, doi = {10.1002/cpmc.41}, pmid = {29120486}, issn = {1934-8533}, mesh = {Computational Biology/*methods ; Humans ; Metagenomics/*methods ; *Microbiota ; }, abstract = {As the field of microbiomics advances, the burden of computational work that scientists need to perform in order to extract biological insight has grown accordingly. Likewise, while human microbiome analyses are increasingly shifting toward a greater integration of various high-throughput data types, a core number of methods form the basis of nearly every study. In this unit, we present step-by-step protocols for five core stages of human microbiome research. The protocols presented in this unit provide a base case for human microbiome analysis, complete with sufficient detail for researchers to tailor certain aspects of the protocols to the specificities of their data. © 2017 by John Wiley &amp; Sons, Inc.}, }
@article {pmid29118049, year = {2017}, author = {Milani, C and Duranti, S and Bottacini, F and Casey, E and Turroni, F and Mahony, J and Belzer, C and Delgado Palacio, S and Arboleya Montes, S and Mancabelli, L and Lugli, GA and Rodriguez, JM and Bode, L and de Vos, W and Gueimonde, M and Margolles, A and van Sinderen, D and Ventura, M}, title = {The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {81}, number = {4}, pages = {}, doi = {10.1128/MMBR.00036-17}, pmid = {29118049}, issn = {1098-5557}, mesh = {Biomarkers/analysis ; Breast Feeding ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Immune System/*microbiology ; Infant ; *Infant Health ; Intestinal Diseases/microbiology ; *Maternal-Fetal Exchange ; Milk, Human/chemistry ; Pregnancy ; Probiotics/therapeutic use ; Symbiosis ; Whole Genome Sequencing ; }, abstract = {The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.}, }
@article {pmid29117585, year = {2018}, author = {Zainun, MY and Simarani, K}, title = {Metagenomics profiling for assessing microbial diversity in both active and closed landfills.}, journal = {The Science of the total environment}, volume = {616-617}, number = {}, pages = {269-278}, doi = {10.1016/j.scitotenv.2017.10.266}, pmid = {29117585}, issn = {1879-1026}, mesh = {Archaea/classification ; Bacteria/classification ; Biodiversity ; DNA, Archaeal/isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Malaysia ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/isolation &amp; purification ; *Soil Microbiology ; *Waste Disposal Facilities ; }, abstract = {The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS. The bacterial enumeration was examined on nutrient agar (NA) plates aerobically at 30°C. The soil DNA was extracted, purified and amplified prior to sequence the 16S rRNA gene for statistical and bioinformatics analyses. As a result, the average of bacteria for the closed landfill was higher compared to that for the active landfill at 9.16×107 and 1.50×107, respectively. The higher bacterial OTUs sequenced was also recorded in closed landfills compared to active landfill i.e. 6625 and 4552 OTUs respectively. The data from both landfills showed that the predominant phyla belonged to Proteobacteria (55.7%). On average, Bacteroidetes was the second highest phylum followed by Firmicutes for the active landfill. While the phyla for communities in closed landfill were dominated by phyla from Acidobacteria and Actinobacteria. There was also Euryarchaeota (Archaea) which became a minor phylum that was detected in active landfill, but almost completely absent in closed landfill. As such, the composition of bacterial communities suggests some variances between the bacterial communities found in active and closed landfills. Thus, this study offers new clues pertaining to bacterial diversity pattern between the varied types of landfills studied.}, }
@article {pmid29115413, year = {2018}, author = {Meng, F and Chen, T and Wang, X and Wang, X and Wei, H and Tian, P and Wang, H and Zhao, X and Shen, L and Xin, H}, title = {Evaluation of the accuracy and sensitivity of high‑throughput sequencing technology using known microbiota.}, journal = {Molecular medicine reports}, volume = {17}, number = {1}, pages = {408-413}, doi = {10.3892/mmr.2017.7849}, pmid = {29115413}, issn = {1791-3004}, mesh = {Biodiversity ; Computational Biology/methods ; Genome, Bacterial ; Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods/standards ; *Metagenome ; *Metagenomics/methods/standards ; *Microbiota ; }, abstract = {Next generation sequencing provides an excellent platform to explore microbiota in any given environment, and little work is required to evaluate the accuracy and sensitivity of high‑throughput sequencing technology. In the present study, a known microbiota containing Escherichia coli, Lactobacillus plantarum, Streptococcus thermophilus, Bifidobacterium bifidum, Bacillus subtilis, Enterococcus faecalis and Salmonella typhimurium was used to evaluate the high‑throughput sequencing technology. The results suggested that there were 122.7 operational taxonomic units (OTUs) in all groups, which is 17.5‑fold (the whole OTU number/the actual bacterial number) greater compared with the actual microbial number in each group, and the Venn method indicated that only 46.38% (64/138), 58.70% (81/138), 86.13% (118/137), 83.57% (117/140) and 89.29% (125/140) of the common OTUs were identified in groups A, B, C, D and E, of which the majority of OTUs did not belong to known bacteria. In addition, the DNA extraction and amplification efficiency failed to identify bacteria at the phylum, class, order, family, genus and species levels, which may further increase false information of microbial analysis. In conclusion, the present study provided basic datato investigate the potential drawbacks of high‑throughput sequencing technology, which will help researchers to avoid exaggerating the bacterial number when this technology is applied to study microbiota in particular environments.}, }
@article {pmid29113561, year = {2017}, author = {Rahman, MA and LaPierre, N and Rangwala, H and Barbara, D}, title = {Metagenome sequence clustering with hash-based canopies.}, journal = {Journal of bioinformatics and computational biology}, volume = {15}, number = {6}, pages = {1740006}, doi = {10.1142/S0219720017400066}, pmid = {29113561}, issn = {1757-6334}, abstract = {Metagenomics is the collective sequencing of co-existing microbial communities which are ubiquitous across various clinical and ecological environments. Due to the large volume and random short sequences (reads) obtained from community sequences, analysis of diversity, abundance and functions of different organisms within these communities are challenging tasks. We present a fast and scalable clustering algorithm for analyzing large-scale metagenome sequence data. Our approach achieves efficiency by partitioning the large number of sequence reads into groups (called canopies) using hashing. These canopies are then refined by using state-of-the-art sequence clustering algorithms. This canopy-clustering (CC) algorithm can be used as a pre-processing phase for computationally expensive clustering algorithms. We use and compare three hashing schemes for canopy construction with five popular and state-of-the-art sequence clustering methods. We evaluate our clustering algorithm on synthetic and real-world 16S and whole metagenome benchmarks. We demonstrate the ability of our proposed approach to determine meaningful Operational Taxonomic Units (OTU) and observe significant speedup with regards to run time when compared to different clustering algorithms. We also make our source code publicly available on Github. a.}, }
@article {pmid29107912, year = {2018}, author = {Oh, S and Hammes, F and Liu, WT}, title = {Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant.}, journal = {Water research}, volume = {128}, number = {}, pages = {278-285}, doi = {10.1016/j.watres.2017.10.054}, pmid = {29107912}, issn = {1879-2448}, mesh = {Bacteria/genetics ; Biofilms ; Charcoal ; Drinking Water ; Filtration ; *Metagenome ; Metagenomics ; *Microbial Consortia ; Phylogeny ; Silicon Dioxide ; *Water Microbiology ; *Water Purification ; }, abstract = {Microorganisms inhabiting filtration media of a drinking water treatment plant can be beneficial, because they metabolize biodegradable organic matter from source waters and those formed during disinfection processes, leading to the production of biologically stable drinking water. However, which microbial consortia colonize filters and what metabolic capacity they possess remain to be investigated. To gain insights into these issues, we performed metagenome sequencing and analysis of microbial communities in three different filters of a full-scale drinking water treatment plant (DWTP). Filter communities were sampled from a rapid sand filter (RSF), granular activated carbon filter (GAC), and slow sand filter (SSF), and from the Schmutzdecke (SCM, a biologically active scum layer accumulated on top of SSF), respectively. Analysis of community phylogenetic structure revealed that the filter bacterial communities significantly differed from those in the source water and final effluent communities, respectively. Network analysis identified a filter-specific colonization pattern of bacterial groups. Bradyrhizobiaceae were abundant in GAC, whereas Nitrospira were enriched in the sand-associated filters (RSF, SCM, and SSF). The GAC community was enriched with functions associated with aromatics degradation, many of which were encoded by Rhizobiales (∼30% of the total GAC community). Predicting minimum generation time (MGT) of prokaryotic communities suggested that the GAC community potentially select fast-growers (<15 h of MGT) among the four filter communities, consistent with the highest dissolved organic matter removal rate by GAC. Our findings provide new insights into the community phylogenetic structure, colonization pattern, and metabolic capacity that potentially contributes to organic matter removal achieved in the biofiltration stages of the full-scale DWTP.}, }
@article {pmid29101651, year = {2017}, author = {Quach, D and Britton, RA}, title = {Gut Microbiota and Bone Health.}, journal = {Advances in experimental medicine and biology}, volume = {1033}, number = {}, pages = {47-58}, doi = {10.1007/978-3-319-66653-2_4}, pmid = {29101651}, issn = {0065-2598}, mesh = {Animals ; Bone Remodeling/*physiology ; Bone and Bones/*physiology ; Brain/physiology ; Gastrointestinal Microbiome/drug effects/*physiology ; Gastrointestinal Tract/microbiology/*physiology ; Humans ; Prebiotics/administration &amp; dosage ; Probiotics/administration &amp; dosage ; Signal Transduction/drug effects ; }, abstract = {The past decade has seen an explosion of research in the area of how the bacteria that inhabit the human body impact health and disease. One of the more surprising concepts to emerge from this work is the ability of the intestinal microbiota to impact virtually all systems in the body. Recently, the role of gut bacteria in bone health and disease has received more significant attention. In this chapter, we review what has been learned about how the gut microbiome impacts bone health and discuss possible mechanisms of how the gut-bone axis may be connected. We also discuss the use of therapeutic microbes in the modulation of bone health. Finally, we propose an emerging field of the gut-brain-bone axis, in which the gut drives bone physiology via regulation of key hormones that are originally synthesized in the brain.}, }
@article {pmid29097494, year = {2018}, author = {Routy, B and Le Chatelier, E and Derosa, L and Duong, CPM and Alou, MT and Daillère, R and Fluckiger, A and Messaoudene, M and Rauber, C and Roberti, MP and Fidelle, M and Flament, C and Poirier-Colame, V and Opolon, P and Klein, C and Iribarren, K and Mondragón, L and Jacquelot, N and Qu, B and Ferrere, G and Clémenson, C and Mezquita, L and Masip, JR and Naltet, C and Brosseau, S and Kaderbhai, C and Richard, C and Rizvi, H and Levenez, F and Galleron, N and Quinquis, B and Pons, N and Ryffel, B and Minard-Colin, V and Gonin, P and Soria, JC and Deutsch, E and Loriot, Y and Ghiringhelli, F and Zalcman, G and Goldwasser, F and Escudier, B and Hellmann, MD and Eggermont, A and Raoult, D and Albiges, L and Kroemer, G and Zitvogel, L}, title = {Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6371}, pages = {91-97}, doi = {10.1126/science.aan3706}, pmid = {29097494}, issn = {1095-9203}, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Antibodies, Monoclonal/therapeutic use ; CD4 Antigens/immunology ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Immunotherapy/*methods ; Interleukin-12/immunology ; Metagenome/genetics ; Mice ; Neoplasms/*therapy ; Programmed Cell Death 1 Receptor/*antagonists &amp; inhibitors ; Receptors, CCR/immunology ; Receptors, CXCR3/immunology ; T-Lymphocytes/immunology ; Verrucomicrobia/genetics/immunology ; }, abstract = {Immune checkpoint inhibitors (ICIs) targeting the PD-1/PD-L1 axis induce sustained clinical responses in a sizable minority of cancer patients. We found that primary resistance to ICIs can be attributed to abnormal gut microbiome composition. Antibiotics inhibited the clinical benefit of ICIs in patients with advanced cancer. Fecal microbiota transplantation (FMT) from cancer patients who responded to ICIs into germ-free or antibiotic-treated mice ameliorated the antitumor effects of PD-1 blockade, whereas FMT from nonresponding patients failed to do so. Metagenomics of patient stool samples at diagnosis revealed correlations between clinical responses to ICIs and the relative abundance of Akkermansia muciniphila Oral supplementation with A. muciniphila after FMT with nonresponder feces restored the efficacy of PD-1 blockade in an interleukin-12-dependent manner by increasing the recruitment of CCR9+CXCR3+CD4+ T lymphocytes into mouse tumor beds.}, }
@article {pmid29096601, year = {2017}, author = {Alcon-Giner, C and Caim, S and Mitra, S and Ketskemety, J and Wegmann, U and Wain, J and Belteki, G and Clarke, P and Hall, LJ}, title = {Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {841}, doi = {10.1186/s12864-017-4229-x}, pmid = {29096601}, issn = {1471-2164}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Bifidobacterium/drug effects/genetics/isolation &amp; purification/physiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Genomics/*methods ; Humans ; Infant ; *Infant, Extremely Low Birth Weight ; Lactobacillus/drug effects/genetics/isolation &amp; purification/physiology ; Male ; Probiotics/pharmacology ; RNA, Ribosomal, 16S/*genetics ; Risk ; Sequence Analysis, RNA/*methods ; }, abstract = {BACKGROUND: Infants born prematurely, particularly extremely low birth weight infants (ELBW) have altered gut microbial communities. Factors such as maternal health, gut immaturity, delivery mode, and antibiotic treatments are associated with microbiota disturbances, and are linked to an increased risk of certain diseases such as necrotising enterocolitis. Therefore, there is a requirement to optimally characterise microbial profiles in this at-risk cohort, via standardisation of methods, particularly for studying the influence of microbiota therapies (e.g. probiotic supplementation) on community profiles and health outcomes. Profiling of faecal samples using the 16S rRNA gene is a cost-efficient method for large-scale clinical studies to gain insights into the gut microbiota and additionally allows characterisation of cohorts were sample quantities are compromised (e.g. ELBW infants). However, DNA extraction method, and the 16S rRNA region targeted can significantly change bacterial community profiles obtained, and so confound comparisons between studies. Thus, we sought to optimise a 16S rRNA profiling protocol to allow standardisation for studying ELBW infant faecal samples, with or without probiotic supplementation.<br><br>METHODS: Using ELBW faecal samples, we compared three different DNA extraction methods, and subsequently PCR amplified and sequenced three hypervariable regions of the 16S rRNA gene (V1 + V2 + V3), (V4 + V5) and (V6 + V7 + V8), and compared two bioinformatics approaches to analyse results (OTU and paired end). Paired shotgun metagenomics was used as a 'gold-standard'.<br><br>RESULTS: Results indicated a longer bead-beating step was required for optimal bacterial DNA extraction and that sequencing regions (V1 + V2 + V3) and (V6 + V7 + V8) provided the most representative taxonomic profiles, which was confirmed via shotgun analysis. Samples sequenced using the (V4 + V5) region were found to be underrepresented in specific taxa including Bifidobacterium, and had altered diversity profiles. Both bioinformatics 16S rRNA pipelines used in this study (OTU and paired end) presented similar taxonomic profiles at genus level.<br><br>CONCLUSIONS: We determined that DNA extraction from ELBW faecal samples, particularly those infants receiving probiotic supplementation, should include a prolonged beat-beating step. Furthermore, use of the 16S rRNA (V1 + V2 + V3) and (V6 + V7 + V8) regions provides reliable representation of ELBW microbiota profiles, while inclusion of the (V4 + V5) region may not be appropriate for studies where Bifidobacterium constitutes a resident microbiota member.}, }
@article {pmid29091761, year = {2017}, author = {Nakamoto, N and Amiya, T and Aoki, R and Taniki, N and Koda, Y and Miyamoto, K and Teratani, T and Suzuki, T and Chiba, S and Chu, PS and Hayashi, A and Yamaguchi, A and Shiba, S and Miyake, R and Katayama, T and Suda, W and Mikami, Y and Kamada, N and Ebinuma, H and Saito, H and Hattori, M and Kanai, T}, title = {Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice.}, journal = {Cell reports}, volume = {21}, number = {5}, pages = {1215-1226}, doi = {10.1016/j.celrep.2017.10.022}, pmid = {29091761}, issn = {2211-1247}, mesh = {Alanine Transaminase/blood ; Animals ; Chemical and Drug Induced Liver Injury/*immunology/pathology ; Dendritic Cells/cytology/metabolism ; Gastrointestinal Microbiome ; Histocompatibility Antigens Class II/metabolism ; *Immune Tolerance ; Immunity, Innate ; Interferon-gamma/metabolism ; Interleukin-10/metabolism ; Interleukins/metabolism ; Intestines/immunology/metabolism/microbiology ; Lactobacillus/*immunology/physiology ; Liver/immunology/metabolism/pathology ; Male ; Mice ; Mice, Inbred C57BL ; T-Lymphocytes, Regulatory/cytology/immunology/metabolism ; Toll-Like Receptor 9/metabolism ; Transforming Growth Factor beta/metabolism ; }, abstract = {Gut-derived microbial antigens trigger the innate immune system during acute liver injury. During recovery, regulatory immunity plays a role in suppressing inflammation; however, the precise mechanism underlying this process remains obscure. Here, we find that recruitment of immune-regulatory classical dendritic cells (cDCs) is crucial for liver tolerance in concanavalin A-induced acute liver injury. Acute liver injury resulted in enrichment of commensal Lactobacillus in the gut. Notably, Lactobacillus activated IL-22 production by gut innate lymphoid cells and raised systemic IL-22 levels. Gut-derived IL-22 enhanced mucosal barrier function and promoted the recruitment of regulatory cDCs to the liver. These cDCs produced IL-10 and TGF-β through TLR9 activation, preventing further liver inflammation. Collectively, our results indicate that beneficial gut microbes influence tolerogenic immune responses in the liver. Therefore, modulation of the gut microbiota might be a potential option to regulate liver tolerance.}, }
@article {pmid29088131, year = {2017}, author = {Woyke, T and Doud, DFR and Schulz, F}, title = {The trajectory of microbial single-cell sequencing.}, journal = {Nature methods}, volume = {14}, number = {11}, pages = {1045-1054}, doi = {10.1038/nmeth.4469}, pmid = {29088131}, issn = {1548-7105}, mesh = {Metagenomics ; Microbiota/genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Single-Cell Analysis ; }, abstract = {Over the past decade, it has become nearly routine to sequence genomes of individual microbial cells directly isolated from environmental samples ranging from deep-sea hydrothermal vents to insect guts, providing a powerful complement to shotgun metagenomics in microbial community studies. In this review, we address the technical aspects and challenges of single-cell genome sequencing and discuss some of the scientific endeavors that it has enabled. Specifically, we highlight newly added leaves and branches in the genomic tree of bacterial and archaeal life and illustrate the unique and exciting advantages that single-cell genomics offers over metagenomics, both now and in the near future.}, }
@article {pmid29085573, year = {2017}, author = {Herath, D and Jayasundara, D and Ackland, D and Saeed, I and Tang, SL and Halgamuge, S}, title = {Assessing Species Diversity Using Metavirome Data: Methods and Challenges.}, journal = {Computational and structural biotechnology journal}, volume = {15}, number = {}, pages = {447-455}, doi = {10.1016/j.csbj.2017.09.001}, pmid = {29085573}, issn = {2001-0370}, abstract = {Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods. In this review, existing bioinformatics methods for measuring species diversity using metavirome data are categorised broadly as either sequence similarity-dependent methods or sequence similarity-independent methods. The former includes a comparison of DNA fragments or assemblies generated in the experiment against reference databases for quantifying species diversity, whereas estimates from the latter are independent of the knowledge of existing sequence data. Current methods and tools are discussed in detail, including their applications and limitations. Drawbacks of the state-of-the-art method are demonstrated through results from a simulation. In addition, alternative approaches are proposed to overcome the challenges in estimating species diversity measures using metavirome data.}, }
@article {pmid29069412, year = {2017}, author = {De Anda, V and Zapata-Peñasco, I and Poot-Hernandez, AC and Eguiarte, LE and Contreras-Moreira, B and Souza, V}, title = {MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle.}, journal = {GigaScience}, volume = {6}, number = {11}, pages = {1-17}, doi = {10.1093/gigascience/gix096}, pmid = {29069412}, issn = {2047-217X}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Sequence Analysis, DNA/*methods ; *Software ; Sulfur/*metabolism ; }, abstract = {The increasing number of metagenomic and genomic sequences has dramatically improved our understanding of microbial diversity, yet our ability to infer metabolic capabilities in such datasets remains challenging. We describe the Multigenomic Entropy Based Score pipeline (MEBS), a software platform designed to evaluate, compare, and infer complex metabolic pathways in large &quot;omic&quot; datasets, including entire biogeochemical cycles. MEBS is open source and available through https://github.com/eead-csic-compbio/metagenome_Pfam_score. To demonstrate its use, we modeled the sulfur cycle by exhaustively curating the molecular and ecological elements involved (compounds, genes, metabolic pathways, and microbial taxa). This information was reduced to a collection of 112 characteristic Pfam protein domains and a list of complete-sequenced sulfur genomes. Using the mathematical framework of relative entropy (H΄), we quantitatively measured the enrichment of these domains among sulfur genomes. The entropy of each domain was used both to build up a final score that indicates whether a (meta)genomic sample contains the metabolic machinery of interest and to propose marker domains in metagenomic sequences such as DsrC (PF04358). MEBS was benchmarked with a dataset of 2107 non-redundant microbial genomes from RefSeq and 935 metagenomes from MG-RAST. Its performance, reproducibility, and robustness were evaluated using several approaches, including random sampling, linear regression models, receiver operator characteristic plots, and the area under the curve metric (AUC). Our results support the broad applicability of this algorithm to accurately classify (AUC = 0.985) hard-to-culture genomes (e.g., Candidatus Desulforudis audaxviator), previously characterized ones, and metagenomic environments such as hydrothermal vents, or deep-sea sediment. Our benchmark indicates that an entropy-based score can capture the metabolic machinery of interest and can be used to efficiently classify large genomic and metagenomic datasets, including uncultivated/unexplored taxa.}, }
@article {pmid29065967, year = {2017}, author = {Park, SJ and Kim, JH and Song, MY and Sung, YC and Lee, SW and Park, Y}, title = {PD-1 deficiency protects experimental colitis via alteration of gut microbiota.}, journal = {BMB reports}, volume = {50}, number = {11}, pages = {578-583}, pmid = {29065967}, issn = {1976-670X}, mesh = {Animals ; Bacteria/genetics ; Colitis/chemically induced/*metabolism/pathology/*prevention &amp; control ; Colon/pathology ; Cytokines/metabolism ; Disease Models, Animal ; Gastrointestinal Microbiome/physiology ; Inflammatory Bowel Diseases/metabolism ; Metagenomics/methods ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Programmed Cell Death 1 Ligand 2 Protein/genetics/*metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Programmed cell death-1 (PD-1) is a coinhibitory molecule and plays a pivotal role in immune regulation. Here, we demonstrate a role for PD-1 in pathogenesis of inflammatory bowel disease (IBD). Wild-type (WT) mice had severe wasting disease during experimentally induced colitis, while mice deficient for PD-1 (PD-1-/-) did not develop colon inflammation. Interestingly, PD-1-/- mice cohoused with WT mice became susceptible to colitis, suggesting that resistance of PD-1-/- mice to colitis is dependent on their gut microbiota. 16S rRNA gene-pyrosequencing analysis showed that PD-1-/- mice had altered composition of gut microbiota with significant reduction in Rikenellaceae family. These altered colon bacteria of PD-1-/- mice induced less amount of inflammatory mediators from colon epithelial cells, including interleukin (IL)-6, and inflammatory chemokines. Taken together, our study indicates that PD-1 expression is involved in the resistance to experimental colitis through altered bacterial communities of colon. [BMB Reports 2017; 50(11): 578-583].}, }
@article {pmid29061202, year = {2017}, author = {Volokhov, DV and Becker, DJ and Bergner, LM and Camus, MS and Orton, RJ and Chizhikov, VE and Altizer, SM and Streicker, DG}, title = {Novel hemotropic mycoplasmas are widespread and genetically diverse in vampire bats.}, journal = {Epidemiology and infection}, volume = {145}, number = {15}, pages = {3154-3167}, doi = {10.1017/S095026881700231X}, pmid = {29061202}, issn = {1469-4409}, support = {G0801822//Medical Research Council/United Kingdom ; 102507/Z/13/Z//Wellcome Trust/United Kingdom ; MC_UU_12014/12//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Belize ; Chiroptera/*microbiology ; DNA, Bacterial/genetics ; Disease Reservoirs/microbiology ; Genetic Variation/genetics ; Mycoplasma/*genetics ; Mycoplasma Infections/microbiology/transmission/*veterinary ; Peru ; Phylogeny ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bats (Order: Chiroptera) have been widely studied as reservoir hosts for viruses of concern for human and animal health. However, whether bats are equally competent hosts of non-viral pathogens such as bacteria remains an important open question. Here, we surveyed blood and saliva samples of vampire bats from Peru and Belize for hemotropic Mycoplasma spp. (hemoplasmas), bacteria that can cause inapparent infection or anemia in hosts. 16S rRNA gene amplification of blood showed 67% (150/223) of common vampire bats (Desmodus rotundus) were infected by hemoplasmas. Sequencing of the 16S rRNA gene amplicons revealed three novel genotypes that were phylogenetically related but not identical to hemoplasmas described from other (non-vampire) bat species, rodents, humans, and non-human primates. Hemoplasma prevalence in vampire bats was highest in non-reproductive and young individuals, did not differ by country, and was relatively stable over time (i.e., endemic). Metagenomics from pooled D. rotundus saliva from Peru detected non-hemotropic Mycoplasma species and hemoplasma genotypes phylogenetically similar to those identified in blood, providing indirect evidence for potential direct transmission of hemoplasmas through biting or social contacts. This study demonstrates vampire bats host several novel hemoplasmas and sheds light on risk factors for infection and basic transmission routes. Given the high frequency of direct contacts that arise when vampire bats feed on humans, domestic animals, and wildlife, the potential of these bacteria to be transmitted between species should be investigated in future work.}, }
@article {pmid29056339, year = {2017}, author = {Rosshart, SP and Vassallo, BG and Angeletti, D and Hutchinson, DS and Morgan, AP and Takeda, K and Hickman, HD and McCulloch, JA and Badger, JH and Ajami, NJ and Trinchieri, G and Pardo-Manuel de Villena, F and Yewdell, JW and Rehermann, B}, title = {Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance.}, journal = {Cell}, volume = {171}, number = {5}, pages = {1015-1028.e13}, doi = {10.1016/j.cell.2017.09.016}, pmid = {29056339}, issn = {1097-4172}, mesh = {Animals ; Animals, Laboratory ; Animals, Wild ; Carcinogenesis/immunology ; Disease Resistance ; Female ; *Gastrointestinal Microbiome ; Male ; Maryland ; Mice/*classification/immunology/*microbiology ; Mice, Inbred C57BL ; Peromyscus ; Virus Diseases/immunology ; }, abstract = {Laboratory mice, while paramount for understanding basic biological phenomena, are limited in modeling complex diseases of humans and other free-living mammals. Because the microbiome is a major factor in mammalian physiology, we aimed to identify a naturally evolved reference microbiome to better recapitulate physiological phenomena relevant in the natural world outside the laboratory. Among 21 distinct mouse populations worldwide, we identified a closely related wild relative to standard laboratory mouse strains. Its bacterial gut microbiome differed significantly from its laboratory mouse counterpart and was transferred to and maintained in laboratory mice over several generations. Laboratory mice reconstituted with natural microbiota exhibited reduced inflammation and increased survival following influenza virus infection and improved resistance against mutagen/inflammation-induced colorectal tumorigenesis. By demonstrating the host fitness-promoting traits of natural microbiota, our findings should enable the discovery of protective mechanisms relevant in the natural world and improve the modeling of complex diseases of free-living mammals. VIDEO ABSTRACT.}, }
@article {pmid29053686, year = {2017}, author = {Steffan, SA and Dharampal, PS and Diaz-Garcia, L and Currie, CR and Zalapa, J and Hittinger, CT}, title = {Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {128}, pages = {}, doi = {10.3791/54631}, pmid = {29053686}, issn = {1940-087X}, mesh = {Animals ; Bees/*physiology ; Fungicides, Industrial/*adverse effects ; Metagenomics/*methods ; Microbiota ; Pollen ; Yeasts ; }, abstract = {Growers often use fungicide sprays during bloom to protect crops against disease, which exposes bees to fungicide residues. Although considered &quot;bee-safe,&quot; there is mounting evidence that fungicide residues in pollen are associated with bee declines (for both honey and bumble bee species). While the mechanisms remain relatively unknown, researchers have speculated that bee-microbe symbioses are involved. Microbes play a pivotal role in the preservation and/or processing of pollen, which serves as nutrition for larval bees. By altering the microbial community, it is likely that fungicides disrupt these microbe-mediated services, and thereby compromise bee health. This manuscript describes the protocols used to investigate the indirect mechanism(s) by which fungicides may be causing colony decline. Cage experiments exposing bees to fungicide-treated flowers have already provided the first evidence that fungicides cause profound colony losses in a native bumble bee (Bombus impatiens). Using field-relevant doses of fungicides, a series of experiments have been developed to provide a finer description of microbial community dynamics of fungicide-exposed pollen. Shifts in the structural composition of fungal and bacterial assemblages within the pollen microbiome are investigated by next-generation sequencing and metagenomic analysis. Experiments developed herein have been designed to provide a mechanistic understanding of how fungicides affect the microbiome of pollen-provisions. Ultimately, these findings should shed light on the indirect pathway through which fungicides may be causing colony declines.}, }
@article {pmid29053145, year = {2018}, author = {Bernardo, P and Charles-Dominique, T and Barakat, M and Ortet, P and Fernandez, E and Filloux, D and Hartnady, P and Rebelo, TA and Cousins, SR and Mesleard, F and Cohez, D and Yavercovski, N and Varsani, A and Harkins, GW and Peterschmitt, M and Malmstrom, CM and Martin, DP and Roumagnac, P}, title = {Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {173-184}, doi = {10.1038/ismej.2017.155}, pmid = {29053145}, issn = {1751-7370}, mesh = {*Agriculture ; Biodiversity ; Climate ; Ecosystem ; France ; Metagenomics ; Plant Viruses/classification/genetics/*isolation &amp; purification ; Plants/virology ; South Africa ; }, abstract = {Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8-35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.}, }
@article {pmid29050881, year = {2017}, author = {Kvas, S and Rahn, J and Engel, K and Neufeld, JD and Villeneuve, PJ and Trevors, JT and Lee, H and Scroggins, RP and Beaudette, LA}, title = {Development of a microbial test suite and data integration method for assessing microbial health of contaminated soil.}, journal = {Journal of microbiological methods}, volume = {143}, number = {}, pages = {66-77}, doi = {10.1016/j.mimet.2017.10.004}, pmid = {29050881}, issn = {1872-8359}, mesh = {Biota/*drug effects ; Canada ; *Data Interpretation, Statistical ; *Environmental Pollution ; Forests ; Metagenomics/methods ; Microbiological Techniques/*methods ; Petroleum/analysis ; *Soil Microbiology ; Soil Pollutants/analysis ; }, abstract = {There is no standard methodology or guideline for assessing soil microbial health for the purposes of contaminant risk assessments. Here we propose a laboratory-based test suite and novel data integration method for evaluating soil microbial health using site-specific contaminated and reference soil. The test suite encompasses experiments for evaluating microbial biomass, activity, and diversity. The results from the tests are then integrated so that a Soil Microbial Health Score (SMHS) may be assigned. This test suite and data integration method was tested on soils from 3 different contaminated sites in Canada. The soil microbial health of a petroleum hydrocarbon (PHC) contaminated site was found to be 'Mildly Impacted' and 'Moderately Impacted' for two soil horizons at a boreal forest site. The soil microbial health of the mixed metal/PHC and mixed metal sites were both found to be 'Not Impacted'. Continued use of this test suite and data integration method will help create guidelines for assessing soil microbial health in ecological risk assessments.}, }
@article {pmid29049378, year = {2017}, author = {Oh, S and Yap, GC and Hong, PY and Huang, CH and Aw, MM and Shek, LP and Liu, WT and Lee, BW}, title = {Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0184955}, doi = {10.1371/journal.pone.0184955}, pmid = {29049378}, issn = {1932-6203}, mesh = {Case-Control Studies ; Eczema/*genetics/*immunology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Phylogeny ; Placebos ; }, abstract = {Gut microbiota play an important role in human immunological processes, potentially affecting allergic diseases such as eczema. The diversity and structure of gut microbiota in infants with eczema have been previously documented. This study aims to evaluate by comparative metagenomics differences in genetic content in gut microbiota of infants with eczema and their matched controls. Stools were collected at the age of one month old from twelve infants from an at risk birth cohort in a case control manner. Clinical follow up for atopic outcomes were carried out at the age of 12 and 24 months. Microbial genomic DNA were extracted from stool samples and used for shotgun sequencing. Comparative metagenomic analysis showed that immune-regulatory TCAAGCTTGA motifs were significantly enriched in the six healthy controls (C) communities compared to the six eczema subjects (E), with many encoded by Bifidobacterium (38% of the total motifs in the C communities). Draft genomes of five Bifidobacterium species populations (B. longum, B. bifidum, B. breve, B. dentium, and B. pseudocatenulatum) were recovered from metagenomic datasets. The B. longum BFN-121-2 genome encoded more TCAAGCTTGA motifs (4.2 copies per one million genome sequence) than other Bifidobacterium genomes. Additionally, the communities in the stool of controls (C) were also significantly enriched in functions associated with tetrapyrrole biosynthesis compared to those of eczema (E). Our results show distinct immune-modulatory genomic properties of gut microbiota in infants associated with eczema and provide new insights into potential role of gut microbiota in affecting human immune homeostasis.}, }
@article {pmid29041989, year = {2017}, author = {Dubinkina, VB and Tyakht, AV and Odintsova, VY and Yarygin, KS and Kovarsky, BA and Pavlenko, AV and Ischenko, DS and Popenko, AS and Alexeev, DG and Taraskina, AY and Nasyrova, RF and Krupitsky, EM and Shalikiani, NV and Bakulin, IG and Shcherbakov, PL and Skorodumova, LO and Larin, AK and Kostryukova, ES and Abdulkhakov, RA and Abdulkhakov, SR and Malanin, SY and Ismagilova, RK and Grigoryeva, TV and Ilina, EN and Govorun, VM}, title = {Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {141}, doi = {10.1186/s40168-017-0359-2}, pmid = {29041989}, issn = {2049-2618}, mesh = {Adult ; Alcoholism/*microbiology/physiopathology ; Bifidobacterium/isolation &amp; purification/pathogenicity/physiology ; Dysbiosis ; Enterobacteriaceae/isolation &amp; purification/physiology ; Ethanol/adverse effects/metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/physiology ; Humans ; Inflammation ; Lactobacillus/isolation &amp; purification/pathogenicity/physiology ; Liver/physiopathology ; Liver Cirrhosis/*microbiology/physiopathology ; Liver Diseases, Alcoholic/*microbiology/physiopathology/therapy ; Male ; Metagenomics/methods ; Middle Aged ; Probiotics/therapeutic use ; Symbiosis ; Virulence Factors ; Young Adult ; }, abstract = {BACKGROUND: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction. In order to differentiate the effects of these two factors, we conducted a comparative &quot;shotgun&quot; metagenomic survey of 99 patients with the alcohol dependence syndrome represented by two cohorts-with and without liver cirrhosis. The taxonomic and functional composition of the gut microbiota was subjected to a multifactor analysis including comparison with the external control group.<br><br>RESULTS: Alcoholic dependence and liver cirrhosis were associated with profound shifts in gut community structures and metabolic potential across the patients. The specific effects on species-level community composition were remarkably different between cohorts with and without liver cirrhosis. In both cases, the commensal microbiota was found to be depleted. Alcoholic dependence was inversely associated with the levels of butyrate-producing species from the Clostridiales order, while the cirrhosis-with multiple members of the Bacteroidales order. The opportunist pathogens linked to alcoholic dependence included pro-inflammatory Enterobacteriaceae, while the hallmarks of cirrhosis included an increase of oral microbes in the gut and more frequent occurrence of abnormal community structures. Interestingly, each of the two factors was associated with the expressed enrichment in many Bifidobacterium and Lactobacillus-but the exact set of the species was different between alcoholic dependence and liver cirrhosis. At the level of functional potential, the patients showed different patterns of increase in functions related to alcohol metabolism and virulence factors, as well as pathways related to inflammation.<br><br>CONCLUSIONS: Multiple shifts in the community structure and metabolic potential suggest strong negative influence of alcohol dependence and associated liver dysfunction on gut microbiota. The identified differences in patterns of impact between these two factors are important for planning of personalized treatment and prevention of these pathologies via microbiota modulation. Particularly, the expansion of Bifidobacterium and Lactobacillus suggests that probiotic interventions for patients with alcohol-related disorders using representatives of the same taxa should be considered with caution. Taxonomic and functional analysis shows an increased propensity of the gut microbiota to synthesis of the toxic acetaldehyde, suggesting higher risk of colorectal cancer and other pathologies in alcoholics.}, }
@article {pmid29041965, year = {2017}, author = {Noyes, NR and Weinroth, ME and Parker, JK and Dean, CJ and Lakin, SM and Raymond, RA and Rovira, P and Doster, E and Abdo, Z and Martin, JN and Jones, KL and Ruiz, J and Boucher, CA and Belk, KE and Morley, PS}, title = {Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {142}, doi = {10.1186/s40168-017-0361-8}, pmid = {29041965}, issn = {2049-2618}, mesh = {Drug Resistance, Microbial/*genetics ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Virulence/genetics ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias.<br><br>RESULTS: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins.<br><br>CONCLUSIONS: These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.}, }
@article {pmid29037173, year = {2017}, author = {Beisser, D and Graupner, N and Grossmann, L and Timm, H and Boenigk, J and Rahmann, S}, title = {TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {787}, doi = {10.1186/s12864-017-4168-6}, pmid = {29037173}, issn = {1471-2164}, mesh = {*Databases, Genetic ; Eukaryota/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics/*standards ; Reference Standards ; Software ; }, abstract = {BACKGROUND: High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task.<br><br>RESULTS: From the databases of the National Center for Biotechnology Information and Marine Microbial Eukaryote Transcriptome Sequencing Project, 142 references were selected in such a way that the taxa represent the main lineages within each of the seven supergroups of eukaryotes and possess predominantly complete transcriptomes or genomes. From these references, we created an annotated microeukaryotic reference database. We developed a tool called TaxMapper for a reliably mapping of sequencing reads against this database and filtering of unreliable assignments. For filtering, a classifier was trained and tested on each of the following: sequences of taxa in the database, sequences of taxa related to those in the database, and random sequences. Additionally, TaxMapper is part of a metatranscriptomic Snakemake workflow developed to perform quality assessment, functional and taxonomic annotation and (multivariate) statistical analysis including environmental data. The workflow is provided and described in detail to empower researchers to apply it for metatranscriptome analysis of any environmental sample.<br><br>CONCLUSIONS: TaxMapper shows superior performance compared to standard approaches, resulting in a higher number of true positive taxonomic assignments. Both the TaxMapper tool and the workflow are available as open-source code at Bitbucket under the MIT license: https://bitbucket.org/dbeisser/taxmapper and as a Bioconda package: https://bioconda.github.io/recipes/taxmapper/README.html .}, }
@article {pmid29029060, year = {2017}, author = {Berini, F and Casciello, C and Marcone, GL and Marinelli, F}, title = {Metagenomics: novel enzymes from non-culturable microbes.}, journal = {FEMS microbiology letters}, volume = {364}, number = {21}, pages = {}, doi = {10.1093/femsle/fnx211}, pmid = {29029060}, issn = {1574-6968}, mesh = {Bacteria/*enzymology ; *Bacterial Proteins/chemistry/classification/genetics ; Biocatalysis ; Environmental Microbiology ; *Enzymes/chemistry/classification/genetics ; Industrial Microbiology ; Metagenomics/*methods ; *Microbiota ; }, abstract = {In the transition to the post-petroleum economy, there is a growing demand for novel enzymes with high process performances to replace traditional chemistry with a more 'green' approach. To date, microorganisms encompass the richest source of industrial biocatalysts, but the Earth-living microbiota remains largely untapped by using traditional isolation and cultivation methods. Metagenomics, which is culture independent, represents a powerful tool for discovering novel enzymes from unculturable microorganisms. Herein, we summarize the variety of approaches adopted for mining environmental DNA and, based on a systematic literature review, we provide a comprehensive list of 332 industrially relevant enzymes discovered from metagenomes within the last three years.}, }
@article {pmid29027998, year = {2018}, author = {Arkhipova, K and Skvortsov, T and Quinn, JP and McGrath, JW and Allen, CC and Dutilh, BE and McElarney, Y and Kulakov, LA}, title = {Temporal dynamics of uncultured viruses: a new dimension in viral diversity.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {199-211}, doi = {10.1038/ismej.2017.157}, pmid = {29027998}, issn = {1751-7370}, mesh = {Bacteria/isolation &amp; purification ; Bacteriophages/genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; *Genome, Viral ; Lakes/microbiology/virology ; Metagenomics ; Viruses/*genetics/isolation &amp; purification ; }, abstract = {Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host-pathogen dynamics, where the viruses may peak before, during or after the peak in their host's abundance, providing new possibilities for modelling of their interactions. Time series metagenomics opens up a new dimension in viral profiling, which is essential to understand the full scale of viral diversity and evolution, and the ecological roles of these important factors in the global ecosystem.}, }
@article {pmid29019934, year = {2017}, author = {Kakuta, M and Suzuki, S and Izawa, K and Ishida, T and Akiyama, Y}, title = {A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data.}, journal = {International journal of molecular sciences}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/ijms18102124}, pmid = {29019934}, issn = {1422-0067}, mesh = {Algorithms ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Mouth/*microbiology ; Sequence Analysis, DNA/*methods ; *Sequence Homology, Nucleic Acid ; *Software ; }, abstract = {Sequence similarity searches have been widely used in the analyses of metagenomic sequencing data. Finding homologous sequences in a reference database enables the estimation of taxonomic and functional characteristics of each query sequence. Because current metagenomic sequencing data consist of a large number of nucleotide sequences, the time required for sequence similarity searches account for a large proportion of the total time. This time-consuming step makes it difficult to perform large-scale analyses. To analyze large-scale metagenomic data, such as those found in the human oral microbiome, we developed GHOST-MP (Genome-wide HOmology Search Tool on Massively Parallel system), a parallel sequence similarity search tool for massively parallel computing systems. This tool uses a fast search algorithm based on suffix arrays of query and database sequences and a hierarchical parallel search to accelerate the large-scale sequence similarity search of metagenomic sequencing data. The parallel computing efficiency and the search speed of this tool were evaluated. GHOST-MP was shown to be scalable over 10,000 CPU (Central Processing Unit) cores, and achieved over 80-fold acceleration compared with mpiBLAST using the same computational resources. We applied this tool to human oral metagenomic data, and the results indicate that the oral cavity, the oral vestibule, and plaque have different characteristics based on the functional gene category.}, }
@article {pmid29018189, year = {2017}, author = {Jie, Z and Xia, H and Zhong, SL and Feng, Q and Li, S and Liang, S and Zhong, H and Liu, Z and Gao, Y and Zhao, H and Zhang, D and Su, Z and Fang, Z and Lan, Z and Li, J and Xiao, L and Li, J and Li, R and Li, X and Li, F and Ren, H and Huang, Y and Peng, Y and Li, G and Wen, B and Dong, B and Chen, JY and Geng, QS and Zhang, ZW and Yang, H and Wang, J and Wang, J and Zhang, X and Madsen, L and Brix, S and Ning, G and Xu, X and Liu, X and Hou, Y and Jia, H and He, K and Kristiansen, K}, title = {The gut microbiome in atherosclerotic cardiovascular disease.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {845}, doi = {10.1038/s41467-017-00900-1}, pmid = {29018189}, issn = {2041-1723}, mesh = {Atherosclerosis/*microbiology ; Case-Control Studies ; Fermentation ; *Gastrointestinal Microbiome/drug effects ; Genome-Wide Association Study ; Humans ; Inflammation/microbiology ; Liver Cirrhosis/microbiology ; *Metagenome ; Metagenomics ; }, abstract = {The gut microbiota has been linked to cardiovascular diseases. However, the composition and functional capacity of the gut microbiome in relation to cardiovascular diseases have not been systematically examined. Here, we perform a metagenome-wide association study on stools from 218 individuals with atherosclerotic cardiovascular disease (ACVD) and 187 healthy controls. The ACVD gut microbiome deviates from the healthy status by increased abundance of Enterobacteriaceae and Streptococcus spp. and, functionally, in the potential for metabolism or transport of several molecules important for cardiovascular health. Although drug treatment represents a confounding factor, ACVD status, and not current drug use, is the major distinguishing feature in this cohort. We identify common themes by comparison with gut microbiome data associated with other cardiometabolic diseases (obesity and type 2 diabetes), with liver cirrhosis, and rheumatoid arthritis. Our data represent a comprehensive resource for further investigations on the role of the gut microbiome in promoting or preventing ACVD as well as other related diseases.The gut microbiota may play a role in cardiovascular diseases. Here, the authors perform a metagenome-wide association study on stools from individuals with atherosclerotic cardiovascular disease and healthy controls, identifying microbial strains and functions associated with the disease.}, }
@article {pmid28978331, year = {2017}, author = {Shamarina, D and Stoyantcheva, I and Mason, CE and Bibby, K and Elhaik, E}, title = {Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {132}, doi = {10.1186/s40168-017-0349-4}, pmid = {28978331}, issn = {2049-2618}, support = {R25 EB020393/EB/NIBIB NIH HHS/United States ; R01 ES021006/ES/NIEHS NIH HHS/United States ; }, mesh = {Environment Design ; *Ethics, Research ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; Public Opinion ; *Public Relations ; *Research ; }, abstract = {The public commonly associates microorganisms with pathogens. This suspicion of microorganisms is understandable, as historically microorganisms have killed more humans than any other agent while remaining largely unknown until the late seventeenth century with the works of van Leeuwenhoek and Kircher. Despite our improved understanding regarding microorganisms, the general public are apt to think of diseases rather than of the majority of harmless or beneficial species that inhabit our bodies and the built and natural environment. As long as microbiome research was confined to labs, the public's exposure to microbiology was limited. The recent launch of global microbiome surveys, such as the Earth Microbiome Project and MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) project, has raised ethical, financial, feasibility, and sustainability concerns as to the public's level of understanding and potential reaction to the findings, which, done improperly, risk negative implications for ongoing and future investigations, but done correctly, can facilitate a new vision of &quot;smart cities.&quot; To facilitate improved future research, we describe here the major concerns that our discussions with ethics committees, community leaders, and government officials have raised, and we expound on how to address them. We further discuss ethical considerations of microbiome surveys and provide practical recommendations for public engagement.}, }
@article {pmid28976007, year = {2017}, author = {Rosen, CE and Palm, NW}, title = {Functional Classification of the Gut Microbiota: The Key to Cracking the Microbiota Composition Code: Functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {12}, pages = {}, doi = {10.1002/bies.201700032}, pmid = {28976007}, issn = {1521-1878}, mesh = {Dysbiosis/genetics/*immunology/microbiology ; Gastrointestinal Microbiome/*immunology ; Gastrointestinal Tract/immunology/*microbiology ; Humans ; *Immunity, Innate ; Immunoglobulin A/genetics ; Metabolome/immunology ; Metagenome/*immunology ; Microbial Consortia/immunology ; Terminology as Topic ; }, abstract = {The last decade has seen an explosion of research on the gut microbiota-the trillions of microorganisms that colonize the human gut. It is now clear that interindividual diversity in microbiota composition plays an important role in determining susceptibility to a wide variety of diseases. However, identifying the precise changes in microbiota composition that play causal roles has remained a largely unrealized goal. Here, we propose that functional classifications of microbes based on their interactions with and effects on the host-particularly the host immune system-will illuminate the role of the microbiota in shaping human physiology. We outline the benefits of &quot;functional&quot; classification compared to phylogenetic classifications, and review current efforts at functional classification of the microbiota. Finally, we outline a theoretical framework for classifying host-microbiota interactions. Future advances enabling broader functional classifications of the microbiota promise to revolutionize our understanding of the role of gut microbes in health and disease.}, }
@article {pmid28974215, year = {2017}, author = {Lalremruata, A and Jeyaraj, S and Engleitner, T and Joanny, F and Lang, A and Bélard, S and Mombo-Ngoma, G and Ramharter, M and Kremsner, PG and Mordmüller, B and Held, J}, title = {Species and genotype diversity of Plasmodium in malaria patients from Gabon analysed by next generation sequencing.}, journal = {Malaria journal}, volume = {16}, number = {1}, pages = {398}, doi = {10.1186/s12936-017-2044-0}, pmid = {28974215}, issn = {1475-2875}, mesh = {*Biodiversity ; Gabon ; Genetic Variation ; *Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Malaria/diagnosis/parasitology ; Plasmodium/genetics/*physiology ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {BACKGROUND: Six Plasmodium species are known to naturally infect humans. Mixed species infections occur regularly but morphological discrimination by microscopy is difficult and multiplicity of infection (MOI) can only be evaluated by molecular methods. This study investigated the complexity of Plasmodium infections in patients treated for microscopically detected non-falciparum or mixed species malaria in Gabon.<br><br>METHODS: Ultra-deep sequencing of nucleus (18S rRNA), mitochondrion, and apicoplast encoded genes was used to evaluate Plasmodium species diversity and MOI in 46 symptomatic Gabonese patients with microscopically diagnosed non-falciparum or mixed species malaria.<br><br>RESULTS: Deep sequencing revealed a large complexity of confections in patients with uncomplicated malaria, both on species and genotype levels. Mixed infections involved up to four parasite species (Plasmodium falciparum, Plasmodium malariae, Plasmodium ovale curtisi, and P. ovale wallikeri). Multiple genotypes from each species were determined from the asexual 18S rRNA gene. 17 of 46 samples (37%) harboured multiple genotypes of at least one Plasmodium species. The number of genotypes per sample (MOI) was highest in P. malariae (n = 4), followed by P. ovale curtisi (n = 3), P. ovale wallikeri (n = 3), and P. falciparum (n = 2). The highest combined genotype complexity in samples that contained mixed-species infections was seven.<br><br>CONCLUSIONS: Ultra-deep sequencing showed an unexpected breadth of Plasmodium species and within species diversity in clinical samples. MOI of P. ovale curtisi, P. ovale wallikeri and P. malariae infections were higher than anticipated and contribute significantly to the burden of malaria in Gabon.}, }
@article {pmid28973392, year = {2017}, author = {Chen, YC and Greenbaum, J and Shen, H and Deng, HW}, title = {Association Between Gut Microbiota and Bone Health: Potential Mechanisms and Prospective.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {102}, number = {10}, pages = {3635-3646}, doi = {10.1210/jc.2017-00513}, pmid = {28973392}, issn = {1945-7197}, support = {R01 AR059781/AR/NIAMS NIH HHS/United States ; R01 AR069055/AR/NIAMS NIH HHS/United States ; D43 TW009107/TW/FIC NIH HHS/United States ; R01 GM109068/GM/NIGMS NIH HHS/United States ; R01 AR057049/AR/NIAMS NIH HHS/United States ; U19 AG055373/AG/NIA NIH HHS/United States ; P50 AR055081/AR/NIAMS NIH HHS/United States ; P20 GM109036/GM/NIGMS NIH HHS/United States ; R01 MH104680/MH/NIMH NIH HHS/United States ; R01 MH107354/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Animals, Laboratory ; Anti-Bacterial Agents/pharmacology ; Bone Resorption/microbiology ; Bone and Bones/drug effects/*metabolism ; Gastrointestinal Microbiome/*physiology ; Germ-Free Life ; Health ; Humans ; Prebiotics ; Probiotics/pharmacology ; }, abstract = {Context: It has been well established that the human gut microbiome plays a critical role in the regulation of important biological processes and the mechanisms underlying numerous complex diseases. Although researchers have only recently begun to study the relationship between the gut microbiota and bone metabolism, early efforts have provided increased evidence to suggest an important association.<br><br>Evidence Acquisition: In this study, we attempt to comprehensively summarize the relationship between the gut microbiota and bone metabolism by detailing the regulatory effects of the microbiome on various biological processes, including nutrient absorption and the intestinal mucosal barrier, immune system functionality, the gut-brain axis, and excretion of functional byproducts. In this review, we incorporate evidence from various types of studies, including observational, in vitro and in vivo animal experiments, as well as small efficacy clinic trails.<br><br>Evidence Synthesis: We review the various potential mechanisms of influence for the gut microbiota on the regulation of bone metabolism and discuss the importance of further examining the potential effects of the gut microbiota on the risk of osteoporosis in humans. Furthermore, we outline some useful tools/approaches for metagenomics research and present some prominent examples of metagenomics association studies in humans.<br><br>Conclusion: Current research efforts, although limited, clearly indicate that the gut microbiota may be implicated in bone metabolism, and therefore, further exploration of this relationship is a promising area of focus in bone health and osteoporosis research. Although most existing studies investigate this relationship using animal models, human studies are both needed and on the horizon.}, }
@article {pmid28970223, year = {2017}, author = {Xiao, C and Lu, ZM and Zhang, XJ and Wang, ST and Ao, L and Shen, CH and Shi, JS and Xu, ZH}, title = {Bio-Heat Is a Key Environmental Driver Shaping the Microbial Community of Medium-Temperature Daqu.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {23}, pages = {}, doi = {10.1128/AEM.01550-17}, pmid = {28970223}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; China ; Edible Grain/microbiology ; *Microbiota ; Temperature ; Wine/analysis/*microbiology ; }, abstract = {&quot;Daqu&quot; is a saccharifying and fermenting agent commonly used in the traditional solid-state fermentation industry (e.g., baijiu and vinegar). The patterns of microbial community succession and flavor formation are highly similar among batches, yet the mechanisms promoting temporal succession in the Daqu microbial ecology remain unclear. Here, we first correlated temporal profiles of microbial community succession with environmental variables (temperature, moisture, and titratable acidity) in medium temperature Daqu (MT-Daqu) throughout fermentation. Temperature dynamics significantly correlated (P < 0.05) with the quick succession of MT-Daqu microbiota in the first 12 d of fermentation, while the community structure was relatively stable after 12 d. Then, we explored the effect of temperature on the MT-Daqu community assembly. In the first 4 d of fermentation, the rapid propagation of most bacterial taxa and several fungal taxa, including Candida, Wickerhamomyces, and unclassified Dipodascaceae and Saccharomycetales species, significantly increased MT-Daqu temperature to 55°C. Subsequently, sustained bio-heat generated by microbial metabolism (53 to 56°C) within MT-Daqu inhibited the growth of most microbes from day 4 to day 12, while thermotolerant taxa, including Bacillus, unclassified Streptophyta, Weissella, Thermoactinomyces, Thermoascus, and Thermomyces survived or kept on growing. Furthermore, temperature as a major driving force on the shaping of MT-Daqu microbiota was validated. Lowering the fermentation temperature by placing the MT-Daqu in a 37°C incubator resulted in decreased relative abundances of thermotolerant taxa, including Bacillus, Thermoactinomyces, and Thermoascus, in the MT-Daqu microbiota. This study revealed that bio-heat functioned as a primary endogenous driver promoting the formation of functional MT-Daqu microbiota.IMPORTANCE Humans have mastered the Daqu preparation technique of cultivating functional microbiota on starchy grains over thousands of years, and it is well known that the metabolic activity of these microbes is key to the flavor production of Chinese baijiu. The pattern of microbial community succession and flavor formation remains highly similar between batches, yet mechanistic insight into these patterns and into microbial population fidelity to specific environmental conditions remains unclear. Our study revealed that bio-heat was generated within Daqu bricks in the first 4 d of fermentation, concomitant with rapid microbial propagation and metabolism. The sustained bio-heat may then function as a major endogenous driving force promoting the formation of the MT-Daqu microbiota from day 4 to day 12. The bio-heat-driven growth of thermotolerant microorganisms might contribute to the formation of flavor metabolites. This study provides useful information for the temperature-based modulation of microbiota function during the fermentation of Daqu.}, }
@article {pmid28969605, year = {2017}, author = {Zhai, P and Yang, L and Guo, X and Wang, Z and Guo, J and Wang, X and Zhu, H}, title = {MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {434}, doi = {10.1186/s12859-017-1849-8}, pmid = {28969605}, issn = {1471-2105}, mesh = {Data Interpretation, Statistical ; Gene Expression Profiling/methods ; Genes, Microbial ; Humans ; Metabolomics/methods ; Metagenomics/*methods ; Microbiota/genetics ; Proteomics/methods ; *Software ; }, abstract = {BACKGROUND: During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community.<br><br>RESULTS: We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples.<br><br>CONCLUSION: MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis. Moreover, since the automatically chosen two-group sample test is verified to be outperformed, MetaComp is friendly to users without adequate statistical training. These improvements are aiming to overcome the new challenges under big data era for all meta-omics data. MetaComp is available at: http://cqb.pku.edu.cn/ZhuLab/MetaComp/ and https://github.com/pzhaipku/MetaComp/ .}, }
@article {pmid28967204, year = {2017}, author = {Ferrario, C and Alessandri, G and Mancabelli, L and Gering, E and Mangifesta, M and Milani, C and Lugli, GA and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and Hiyashi, R and Mackie, R and van Sinderen, D and Ventura, M}, title = {Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses.}, journal = {Environmental microbiology}, volume = {19}, number = {11}, pages = {4771-4783}, doi = {10.1111/1462-2920.13943}, pmid = {28967204}, issn = {1462-2920}, mesh = {Animals ; Bacteria/*classification/genetics/*isolation &amp; purification ; Cecum/*microbiology ; Chickens/*microbiology ; Diet ; Gastrointestinal Microbiome/*genetics ; Geography ; Humans ; Metagenomics ; }, abstract = {Different factors may modulate the gut microbiota of animals. In any particular environment, diet, genetic factors and human influences can shape the bacterial communities residing in the gastrointestinal tract. Metagenomic approaches have significantly expanded our knowledge on microbiota dynamics inside hosts, yet cultivation and isolation of bacterial members of these complex ecosystems may still be necessary to fully understand interactions between bacterial communities and their host. A dual approach, involving culture-independent and -dependent techniques, was used here to decipher the microbiota communities that inhabit the gastro intestinal tract of free-range, broiler and feral chickens. In silico analysis revealed the presence of a core microbiota that is typical of those animals that live in different geographical areas and that have limited contact with humans. Anthropic influences guide the metabolic potential and the presence of antibiotic resistance genes of these different bacterial communities. Culturomics attempts, based on different cultivation conditions, were applied to reconstruct in vitro the microbiota of feral chickens. A unique strain collection representing members of the four major phyla of the poultry microbiota was assembled, including bacterial strains that are not typically retrieved from the chicken gut.}, }
@article {pmid28961809, year = {2017}, author = {Goss-Souza, D and Mendes, LW and Borges, CD and Baretta, D and Tsai, SM and Rodrigues, JLM}, title = {Soil microbial community dynamics and assembly under long-term land use change.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {10}, pages = {}, doi = {10.1093/femsec/fix109}, pmid = {28961809}, issn = {1574-6941}, mesh = {Archaea/classification/isolation &amp; purification ; Bacteria/classification/isolation &amp; purification ; Biodiversity ; Conservation of Natural Resources ; *Forests ; Grassland ; Metagenome ; *Soil Microbiology ; }, abstract = {We evaluated the bacterial and archaeal community dynamics and assembly in soils under forest, grassland and no-till cropping, using a high-throughput shotgun metagenomics approach. No significant alterations in alpha diversity were observed among different land uses, but beta diversity in grassland was lower than that observed in forest and no-till soils. Grassland communities showed assembly that predominantly followed the neutral model, i.e. high homogenizing selection with moderate dispersion, leading to biotic homogenization. Both no-till and forest soil communities were found to have assembly that predominantly followed a niche model, i.e. low rates of dispersal and weak homogenizing selection, resulting in maintenance of higher beta diversity relative to grasslands, indicating niche specialization or variable selection. Taken together, our results indicate that the patterns of assembly and their governing processes are dependent on the land use employed after deforestation, with consequences for taxa turnover and microbial functional potential.}, }
@article {pmid28961409, year = {2017}, author = {Williamson, KE and Fuhrmann, JJ and Wommack, KE and Radosevich, M}, title = {Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory.}, journal = {Annual review of virology}, volume = {4}, number = {1}, pages = {201-219}, doi = {10.1146/annurev-virology-101416-041639}, pmid = {28961409}, issn = {2327-0578}, mesh = {*Biodiversity ; DNA, Single-Stranded/isolation &amp; purification ; *Ecosystem ; Food Chain ; Gene Transfer, Horizontal ; Genome, Viral ; Humans ; Metagenomics ; *Soil Microbiology ; Virus Physiological Phenomena ; Viruses/*genetics ; }, abstract = {Viral abundance in soils can range from below detection limits in hot deserts to over 1 billion per gram in wetlands. Abundance appears to be strongly influenced by water availability and temperature, but a lack of informational standards creates difficulties for cross-study analysis. Soil viral diversity is severely underestimated and undersampled, although current measures of viral richness are higher for soils than for aquatic ecosystems. Both morphometric and metagenomic analyses have raised questions about the prevalence of nontailed, ssDNA viruses in soils. Soil is complex and critically important to terrestrial biodiversity and human civilization, but impacts of viral activities on soil ecosystem services are poorly understood. While information from aquatic systems and medical microbiology suggests the potential for viral influences on nutrient cycles, food web interactions, gene transfer, and other key processes in soils, very few empirical data are available. To understand the soil virome, much work remains.}, }
@article {pmid28955471, year = {2017}, author = {van Nieuwenhuijzen, EJ and Houbraken, JAMP and Punt, PJ and Roeselers, G and Adan, OCG and Samson, RA}, title = {The fungal composition of natural biofinishes on oil-treated wood.}, journal = {Fungal biology and biotechnology}, volume = {4}, number = {}, pages = {2}, doi = {10.1186/s40694-017-0030-5}, pmid = {28955471}, issn = {2054-3085}, abstract = {BACKGROUND: Biofinished wood is considered to be a decorative and protective material for outdoor constructions, showing advantages compared to traditional treated wood in terms of sustainability and self-repair. Natural dark wood staining fungi are essential to biofinish formation on wood. Although all sorts of outdoor situated timber are subjected to fungal staining, the homogenous dark staining called biofinish has only been detected on specific vegetable oil-treated substrates. Revealing the fungal composition of various natural biofinishes on wood is a first step to understand and control biofinish formation for industrial application.<br><br>RESULTS: A culture-based survey of fungi in natural biofinishes on oil-treated wood samples showed the common wood stain fungus Aureobasidium and the recently described genus Superstratomyces to be predominant constituents. A culture-independent approach, based on amplification of the internal transcribed spacer regions, cloning and Sanger sequencing, resulted in clone libraries of two types of biofinishes. Aureobasidium was present in both biofinish types, but was only predominant in biofinishes on pine sapwood treated with raw linseed oil. Most cloned sequences of the other biofinish type (pine sapwood treated with olive oil) could not be identified. In addition, a more in-depth overview of the fungal composition of biofinishes was obtained with Illumina amplicon sequencing that targeted the internal transcribed spacer region 1. All investigated samples, that varied in wood species, (oil) treatments and exposure times, contained Aureobasidium and this genus was predominant in the biofinishes on pine sapwood treated with raw linseed oil. Lapidomyces was the predominant genus in most of the other biofinishes and present in all other samples. Surprisingly, Superstratomyces, which was predominantly detected by the cultivation-based approach, could not be found with the Illumina sequencing approach, while Lapidomyces was not detected in the culture-based approach.<br><br>CONCLUSIONS: Overall, the culture-based approach and two culture-independent methods that were used in this study revealed that natural biofinishes were composed of multiple fungal genera always containing the common wood staining mould Aureobasidium. Besides Aureobasidium, the use of other fungal genera for the production of biofinished wood has to be considered.}, }
@article {pmid28955177, year = {2017}, author = {Ericsson, AC and Montonye, DR and Smith, CR and Franklin, CL}, title = {Modeling a Superorganism - Considerations Regarding the Use of &quot;Dirty&quot; Mice in Biomedical Research
.}, journal = {The Yale journal of biology and medicine}, volume = {90}, number = {3}, pages = {361-371}, pmid = {28955177}, issn = {1551-4056}, support = {U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Biomedical Research ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Microbiota/genetics/physiology ; T-Lymphocytes/metabolism/physiology ; }, abstract = {An ever-expanding body of evidence in both humans and animal models demonstrates the influence of the resident gut microbiota on host health and disease susceptibility. However, as unwanted bacterial, viral, protozoal, and parasitic agents have gradually been eliminated from colonies of purpose-bred laboratory mice, the resident microbiota has lost richness and complexity. Recent studies have shown that the ultra-hygienic environment of traditional laboratory mice and lack of antigenic exposure during development results in mice with an immune system more akin to that of a neonate than an adult human. In contrast, wild mice or mice purchased from pet stores are exposed to much greater antigen burdens and their immune system reflects this with significantly greater numbers of memory T cells and more robust vaccine responses. The current review explores the use of alternative sources for research rodents, with an emphasis on the differences in resident gut microbiota and pathogen burden between wild mice, pet store-origin mice, and traditional laboratory mice. Specifically, the literature is compared and contrasted to our own data reflecting the endogenous gut microbiota and pathogen load of wild and pet store mice, as well as the changes in both during and after procedures intended to eliminate certain zoonotic agents present in pet store mice. These data demonstrate that, while alternative sources of research rodents will likely provide models that are more translatable to the human condition, there are also several real-world considerations for scientists including contamination of research facilities and human health risks such as zoonotic diseases.}, }
@article {pmid28954247, year = {2018}, author = {Grohmann, A and Fehrmann, S and Vainshtein, Y and Haag, NL and Wiese, F and Stevens, P and Naegele, HJ and Oechsner, H and Hartsch, T and Sohn, K and Grumaz, C}, title = {Microbiome dynamics and adaptation of expression signatures during methane production failure and process recovery.}, journal = {Bioresource technology}, volume = {247}, number = {}, pages = {347-356}, doi = {10.1016/j.biortech.2017.08.214}, pmid = {28954247}, issn = {1873-2976}, mesh = {Acclimatization ; Anaerobiosis ; Archaea ; Biofuels ; *Bioreactors ; *Methane ; Microbiota ; }, abstract = {This study aimed to uncover microbial dynamics and transcriptional adaptations during mesophilic AD of maize silage and slurry. While one digester performed under optimal conditions, the investigations also evaluated the microbiome during a temperature drop mediated process failure accompanied by acidification and how it contributed to a process recovery. Composition and pathway activities were analyzed by whole genome shotgun (WGS) and metatranscriptome sequencing, respectively. A biodiversity of 112 species was observed with noticeable shifts over process time. Although four distinct groups of microbes could be identified with a correlating versatility according to substrate and to process disturbance, also tremendous effects on gene expression were monitored especially of the archaeal methane metabolism. Particularly, the expression of acetogenotrophic methanogenesis related genes was identified to be relevant for process regeneration.}, }
@article {pmid28950879, year = {2017}, author = {Valseth, K and Nesbø, CL and Easterday, WR and Turner, WC and Olsen, JS and Stenseth, NC and Haverkamp, THA}, title = {Temporal dynamics in microbial soil communities at anthrax carcass sites.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {206}, doi = {10.1186/s12866-017-1111-6}, pmid = {28950879}, issn = {1471-2180}, mesh = {Animals ; Anthrax/*microbiology/*veterinary ; Bacillus anthracis/classification/genetics/isolation &amp; purification/*physiology ; Biodiversity ; Cadaver ; DNA, Bacterial/analysis ; Ecology ; Equidae/microbiology ; Genes, rRNA ; Metagenomics ; Namibia ; Soil ; *Soil Microbiology ; Spores, Bacterial/genetics ; }, abstract = {BACKGROUND: Anthrax is a globally distributed disease affecting primarily herbivorous mammals. It is caused by the soil-dwelling and spore-forming bacterium Bacillus anthracis. The dormant B. anthracis spores become vegetative after ingestion by grazing mammals. After killing the host, B. anthracis cells return to the soil where they sporulate, completing the lifecycle of the bacterium. Here we present the first study describing temporal microbial soil community changes in Etosha National Park, Namibia, after decomposition of two plains zebra (Equus quagga) anthrax carcasses. To circumvent state-associated-challenges (i.e. vegetative cells/spores) we monitored B. anthracis throughout the period using cultivation, qPCR and shotgun metagenomic sequencing.<br><br>RESULTS: The combined results suggest that abundance estimation of spore-forming bacteria in their natural habitat by DNA-based approaches alone is insufficient due to poor recovery of DNA from spores. However, our combined approached allowed us to follow B. anthracis population dynamics (vegetative cells and spores) in the soil, along with closely related organisms from the B. cereus group, despite their high sequence similarity. Vegetative B. anthracis abundance peaked early in the time-series and then dropped when cells either sporulated or died. The time-series revealed that after carcass deposition, the typical semi-arid soil community (e.g. Frankiales and Rhizobiales species) becomes temporarily dominated by the orders Bacillales and Pseudomonadales, known to contain plant growth-promoting species.<br><br>CONCLUSION: Our work indicates that complementing DNA based approaches with cultivation may give a more complete picture of the ecology of spore forming pathogens. Furthermore, the results suggests that the increased vegetation biomass production found at carcass sites is due to both added nutrients and the proliferation of microbial taxa that can be beneficial for plant growth. Thus, future B. anthracis transmission events at carcass sites may be indirectly facilitated by the recruitment of plant-beneficial bacteria.}, }
@article {pmid28941534, year = {2017}, author = {Mourani, PM and Sontag, MK}, title = {Ventilator-Associated Pneumonia in Critically Ill Children: A New Paradigm.}, journal = {Pediatric clinics of North America}, volume = {64}, number = {5}, pages = {1039-1056}, doi = {10.1016/j.pcl.2017.06.005}, pmid = {28941534}, issn = {1557-8240}, mesh = {Child ; Critical Care/methods ; Critical Illness ; Humans ; Lung/microbiology ; Metagenomics ; Microbiota ; *Pneumonia, Ventilator-Associated/diagnosis/etiology/therapy ; Proteomics ; Risk Factors ; }, abstract = {Ventilator-associated pneumonia (VAP) is a serious complication of critical illness. Surveillance definitions have undergone revisions for more objective and consistent reporting. The 1 organism-1 disease paradigm for microbial involvement may not adequately apply to many cases of VAP, in which pathogens are introduced to a pre-existing and often complex microbial community that facilitates or hinders the potential pathogen, consequently determining whether progression to VAP occurs. As omics technology is applied to VAP, a paradigm is emerging incorporating simultaneous assessments of microbial populations and their activity, as well as the host response, to personalize prevention and treatment.}, }
@article {pmid28938903, year = {2017}, author = {O'Hara, NB and Reed, HJ and Afshinnekoo, E and Harvin, D and Caplan, N and Rosen, G and Frye, B and Woloszynek, S and Ounit, R and Levy, S and Butler, E and Mason, CE}, title = {Metagenomic characterization of ambulances across the USA.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {125}, doi = {10.1186/s40168-017-0339-6}, pmid = {28938903}, issn = {2049-2618}, support = {R01 AI125416/AI/NIAID NIH HHS/United States ; }, mesh = {*Ambulances ; Bacteria/classification/genetics/*isolation &amp; purification/pathogenicity ; Cross Infection/microbiology ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Hospitals ; Humans ; *Metagenome ; *Metagenomics ; *Microbial Consortia/genetics ; *Microbiota/genetics ; United States ; }, abstract = {BACKGROUND: Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some healthcare settings. However, there has been no study to date that has used this approach in pre-hospital settings, such as ambulances, an important first point-of-contact between patients and hospitals.<br><br>RESULTS: We sequenced 398 samples from 137 ambulances across the USA using shotgun sequencing. We analyzed these data to explore the microbial ecology of ambulances including characterizing microbial community composition, nosocomial pathogens, patterns of diversity, presence of functional pathways and antimicrobial resistance, and potential spatial and environmental factors that may contribute to community composition. We found that the top 10 most abundant species are either common built environment microbes, microbes associated with the human microbiome (e.g., skin), or are species associated with nosocomial infections. We also found widespread evidence of antimicrobial resistance markers (hits ~ 90% samples). We identified six factors that may influence the microbial ecology of ambulances including ambulance surfaces, geographical-related factors (including region, longitude, and latitude), and weather-related factors (including temperature and precipitation).<br><br>CONCLUSIONS: While the vast majority of microbial species classified were beneficial, we also found widespread evidence of species associated with nosocomial infections and antimicrobial resistance markers. This study indicates that metagenomics may be useful to characterize the microbial ecology of pre-hospital ambulance settings and that more rigorous testing and cleaning of ambulances may be warranted.}, }
@article {pmid28936948, year = {2017}, author = {Collins, J and Auchtung, JM}, title = {Control of Clostridium difficile Infection by Defined Microbial Communities.}, journal = {Microbiology spectrum}, volume = {5}, number = {5}, pages = {}, doi = {10.1128/microbiolspec.BAD-0009-2016}, pmid = {28936948}, issn = {2165-0497}, support = {R21 AI121522/AI/NIAID NIH HHS/United States ; R33 AI121522/AI/NIAID NIH HHS/United States ; U01 AI124290/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Clostridium Infections/*microbiology/*therapy ; Clostridium difficile/genetics/isolation &amp; purification/*physiology ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome ; Humans ; }, abstract = {Each year in the United States, billions of dollars are spent combating almost half a million Clostridium difficile infections (CDIs) and trying to reduce the ∼29,000 patient deaths in which C. difficile has an attributed role. In Europe, disease prevalence varies by country and level of surveillance, though yearly costs are estimated at €3 billion. One factor contributing to the significant health care burden of C. difficile is the relatively high frequency of recurrent CDIs. Recurrent CDI, i.e., a second episode of symptomatic CDI occurring within 8 weeks of successful initial CDI treatment, occurs in ∼25% of patients, with 35 to 65% of these patients experiencing multiple episodes of recurrent disease. Using microbial communities to treat recurrent CDI, either as whole fecal transplants or as defined consortia of bacterial isolates, has shown great success (in the case of fecal transplants) or potential promise (in the case of defined consortia of isolates). This review will briefly summarize the epidemiology and physiology of C. difficile infection, describe our current understanding of how fecal microbiota transplants treat recurrent CDI, and outline potential ways that knowledge can be used to rationally design and test alternative microbe-based therapeutics.}, }
@article {pmid28934964, year = {2017}, author = {McIntyre, ABR and Ounit, R and Afshinnekoo, E and Prill, RJ and Hénaff, E and Alexander, N and Minot, SS and Danko, D and Foox, J and Ahsanuddin, S and Tighe, S and Hasan, NA and Subramanian, P and Moffat, K and Levy, S and Lonardi, S and Greenfield, N and Colwell, RR and Rosen, GL and Mason, CE}, title = {Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {182}, doi = {10.1186/s13059-017-1299-7}, pmid = {28934964}, issn = {1474-760X}, support = {R01 AI125416/AI/NIAID NIH HHS/United States ; R01 ES021006/ES/NIEHS NIH HHS/United States ; R25 EB020393/EB/NIBIB NIH HHS/United States ; }, mesh = {Benchmarking/*methods/standards ; Contig Mapping/*methods/standards ; DNA Barcoding, Taxonomic/*methods/standards ; Humans ; *Metagenome ; Microbiota ; Phylogeny ; Sequence Analysis, DNA/*methods/standards ; *Software ; }, abstract = {BACKGROUND: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited.<br><br>RESULTS: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages.<br><br>CONCLUSIONS: This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.}, }
@article {pmid28934322, year = {2017}, author = {Moussa, TAA and Al-Zahrani, HS and Almaghrabi, OA and Abdelmoneim, TS and Fuller, MP}, title = {Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0185096}, doi = {10.1371/journal.pone.0185096}, pmid = {28934322}, issn = {1932-6203}, mesh = {Biodiversity ; Classification ; Fungi/*genetics ; *Metagenomics ; Oceans and Seas ; Phylogeny ; Polymerase Chain Reaction ; Saudi Arabia ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; }, abstract = {A total of 145007 reads were obtained from pyrosequencing for all the 4 samples. The total count ranged from 11,301,014 (Mecca old road) to 23,503,512 bp (Thuwal). A total of 460 fungal species belonging to 133 genera, 58 families, 33 orders, 13 classes and 4 phyla was identified across the four sites. The most abundant phylum at all four sites was Ascomycota followed by Basidiomycota. Four phyla (Ascomycota-99.31%, Basidiomycota-0.59%, Chytridiomycota-0.04%, Glomeromycota-0.03%) were detected in Khulais. Except for Glomeromycota, all phyla were detected at Mecca old road (Ascomycota-74.26%, Basidiomycota-25.71%, Chytridiomycota-0.01%) and Thuwal (Ascomycota-99.59%, Basidiomycota-0.40%, Chytridiomycota-0.002%); while only Ascomycota-90.98% and Basidiomycota-9.01% were detected in Asfan road. At the class level, Sordariomycetes was predominantly observed at Asfan road-59.88%, Khulais-68.26% and Thuwal-94.84%; while Pezizomycetes was dominant at Mecca old road-56.01%, was absent at Asfan road. Agaricomycetes was present only at Mecca old road-25.73%; while Tremellomycetes-5.77%, Malasseizomycetes-2.13% and Microbotryomycetes-1.10% were found only at Asfan road. The phylogenetic trees revealed that clear genus level differences are visible across all the four sites, with an overall predominance of Thielavia followed by Madurella, Aspergillus, and Gelasinospora. Chaetomium sp., Aspergillus caespitosus and Aspergillus sp. were found in moderate (Mecca old road and Thuwal) to abundant (Asfan road and Khulais) quantities. Thielavia sp., Thielavia hyalocarpa and Madurella sp. are found in moderate quantities at Khulais and Mecca old road, while in abundant levels at Asfan road and Thuwal. Fusarium equisati and F. oxysporum were detected at Thuwal and Khulais. Sordaria araneosa was present at Khulais, while Malasseiza globosa species was detected in moderate quantities across all sites except Khulais.}, }
@article {pmid28927227, year = {2017}, author = {Cannon, K and Byrne, B and Happe, J and Wu, K and Ward, L and Chesnel, L and Louie, T}, title = {Enteric microbiome profiles during a randomized Phase 2 clinical trial of surotomycin versus vancomycin for the treatment of Clostridium difficile infection.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {12}, pages = {3453-3461}, doi = {10.1093/jac/dkx318}, pmid = {28927227}, issn = {1460-2091}, mesh = {Administration, Oral ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/administration &amp; dosage/*adverse effects ; Bacteria/classification/*isolation &amp; purification ; Bacterial Load ; Bacteriological Techniques ; Clostridium Infections/*drug therapy ; Double-Blind Method ; Dysbiosis/*chemically induced ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Lipopeptides/administration &amp; dosage/*adverse effects ; Male ; Metagenomics ; Middle Aged ; Peptides, Cyclic/administration &amp; dosage/*adverse effects ; Real-Time Polymerase Chain Reaction ; Time Factors ; Vancomycin/administration &amp; dosage/*adverse effects ; Young Adult ; }, abstract = {Objectives: The effects of surotomycin (CB-183,315, MK-4261), a bactericidal cyclic lipopeptide, and vancomycin, the current standard-of-care for Clostridium difficile infection (CDI), on intestinal pathogens and microbiota were evaluated parallel to a Phase 2 randomized, double-blind clinical trial.<br><br>Methods: The single-centre cohort included 26 patients receiving surotomycin [125 or 250 mg twice daily (n = 9 each)] or oral vancomycin [125 mg four times daily (n = 8)] for 10 days. Faecal samples were collected at days 0-42 to quantify both C. difficile by conventional culture and the major components of the microbiome by quantitative PCR.<br><br>Results: Surotomycin 250 mg twice daily or vancomycin 125 mg four times daily reduced faecal C. difficile counts from ∼105-107 log10 cfu/g at baseline to ≤ 102 cfu/g by days 4-10 of treatment. Day 10 counts of C. difficile in 3/9 patients receiving surotomycin 125 mg twice daily remained detectable, including one patient who failed to achieve clinical cure. Bacteroidetes and Prevotella mean counts increased 0.7 log10 or remained unchanged with surotomycin 125 and 250 mg twice daily, respectively, whereas vancomycin reduced counts by 2.5-3.2 log10 (P < 0.02). Vancomycin reduced Firmicutes counts by 2.5-2.8 log10; surotomycin moderately suppressed these microbes in a dose-dependent manner.<br><br>Conclusions: In this Phase 2 trial substudy, compared with vancomycin 125 mg four times daily, surotomycin 250 mg twice daily is as active in vivo against C. difficile, but was more sparing of microbiota. Surotomycin is no longer in development due to failed Phase 3 efficacy results.}, }
@article {pmid28923537, year = {2017}, author = {Frankel, AE and Coughlin, LA and Kim, J and Froehlich, TW and Xie, Y and Frenkel, EP and Koh, AY}, title = {Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients.}, journal = {Neoplasia (New York, N.Y.)}, volume = {19}, number = {10}, pages = {848-855}, doi = {10.1016/j.neo.2017.08.004}, pmid = {28923537}, issn = {1476-5586}, support = {P30 CA142543/CA/NCI NIH HHS/United States ; R01 CA152301/CA/NCI NIH HHS/United States ; R01 CA172211/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Antineoplastic Agents, Immunological/pharmacology/therapeutic use ; Biomarkers, Tumor ; Chromatography, High Pressure Liquid ; Cluster Analysis ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Melanoma/drug therapy/*etiology/*metabolism/pathology ; *Metabolomics/methods ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; Molecular Targeted Therapy ; Neoplasm Metastasis ; Neoplasm Staging ; Prognosis ; Tandem Mass Spectrometry ; Treatment Outcome ; }, abstract = {This is the first prospective study of the effects of human gut microbiota and metabolites on immune checkpoint inhibitor (ICT) response in metastatic melanoma patients. Whereas many melanoma patients exhibit profound response to ICT, there are fewer options for patients failing ICT-particularly with BRAF-wild-type disease. In preclinical studies, specific gut microbiota promotes regression of melanoma in mice. We therefore conducted a study of the effects of pretreatment gut microbiota and metabolites on ICT Response Evaluation Criteria in Solid Tumors response in 39 metastatic melanoma patients treated with ipilimumab, nivolumab, ipilimumab plus nivolumab (IN), or pembrolizumab (P). IN yielded 67% responses and 8% stable disease; P achieved 23% responses and 23% stable disease. ICT responders for all types of therapies were enriched for Bacteroides caccae. Among IN responders, the gut microbiome was enriched for Faecalibacterium prausnitzii, Bacteroides thetaiotamicron, and Holdemania filiformis. Among P responders, the microbiome was enriched for Dorea formicogenerans. Unbiased shotgun metabolomics revealed high levels of anacardic acid in ICT responders. Based on these pilot studies, both additional confirmatory clinical studies and preclinical testing of these bacterial species and metabolites are warranted to confirm their ICT enhancing activity.}, }
@article {pmid28915922, year = {2017}, author = {Winglee, K and Howard, AG and Sha, W and Gharaibeh, RZ and Liu, J and Jin, D and Fodor, AA and Gordon-Larsen, P}, title = {Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {121}, doi = {10.1186/s40168-017-0338-7}, pmid = {28915922}, issn = {2049-2618}, support = {UL1 TR001111/TR/NCATS NIH HHS/United States ; P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 DK104371/DK/NIDDK NIH HHS/United States ; R01 HL108427/HL/NHLBI NIH HHS/United States ; R24 HD050924/HD/NICHD NIH HHS/United States ; }, mesh = {Aged ; Bacteria/*genetics/pathogenicity ; China ; *Diet, Western ; Drug Resistance, Microbial/*genetics ; Escherichia coli/genetics/pathogenicity ; Feeding Behavior ; Female ; *Gastrointestinal Microbiome/genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metabolome ; Metagenomics ; Middle Aged ; Shigella/genetics/pathogenicity ; *Urbanization ; Virulence/genetics ; }, abstract = {BACKGROUND: Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition has been shown to vary across continents and in traditional versus Westernized societies, few studies have examined urban-rural differences in neighboring communities within a single country undergoing rapid urbanization. In this study, we compared the gut microbiome, plasma metabolome, dietary habits, and health biomarkers of rural and urban people from a single Chinese province.<br><br>RESULTS: We identified significant differences in the microbiota and microbiota-related plasma metabolites in rural versus recently urban subjects from the Hunan province of China. Microbes with higher relative abundance in Chinese urban samples have been associated with disease in other studies and were substantially more prevalent in the Human Microbiome Project cohort of American subjects. Furthermore, using whole metagenome sequencing, we found that urbanization was associated with a loss of microbial diversity and changes in the relative abundances of Viruses, Archaea, and Bacteria. Gene diversity, however, increased with urbanization, along with the proportion of reads associated with antibiotic resistance and virulence, which were strongly correlated with the presence of Escherichia and Shigella.<br><br>CONCLUSIONS: Our data suggest that urbanization has produced convergent evolution of the gut microbial composition in American and urban Chinese populations, resulting in similar compositional patterns of abundant microbes through similar lifestyles on different continents, including a loss of potentially beneficial bacteria and an increase in potentially harmful genes via increased relative abundance of Escherichia and Shigella.}, }
@article {pmid28904137, year = {2017}, author = {Wu, Q and Wang, X and Ding, Y and Hu, Y and Nie, Y and Wei, W and Ma, S and Yan, L and Zhu, L and Wei, F}, title = {Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1862}, pages = {}, doi = {10.1098/rspb.2017.0955}, pmid = {28904137}, issn = {1471-2954}, mesh = {Animals ; Diet/*veterinary ; Food ; *Gastrointestinal Microbiome ; Metagenomics ; Plant Leaves ; Plant Shoots ; *Seasons ; Ursidae/*microbiology ; }, abstract = {Wild giant pandas use different parts of bamboo (shoots, leaves and stems) and different bamboo species at different times of the year. Their usage of bamboo can be classified temporally into a distinct leaf stage, shoot stage and transition stage. An association between this usage pattern and variation in the giant panda gut microbiome remains unknown. Here, we found associations using a gut metagenomic approach and nutritional analyses whereby diversity of the gut microbial community in the leaf and shoot stages was significantly different. Functional metagenomic analysis showed that in the leaf stage, bacteria species over-represented genes involved in raw fibre utilization and cell cycle control. Thus, raw fibre utilization by the gut microbiome was guaranteed during the nutrient-deficient leaf stage by reinforcing gut microbiome robustness. During the protein-abundant shoot stage, the functional capacity of the gut microbiome expanded to include prokaryotic secretion and signal transduction activity, suggesting active interactions between the gut microbiome and host. These results illustrate that seasonal nutrient variation in wild giant pandas substantially influences gut microbiome composition and function. Nutritional interactions between gut microbiomes and hosts appear to be complex and further work is needed.}, }
@article {pmid28899105, year = {2017}, author = {Williams, B and Ghosh, M and Boucher, CAB and Bushman, F and Carrington-Lawrence, S and Collman, RG and Dandekar, S and Dang, Q and Malaspina, A and Paredes, R and Wilson, CC and Nowak, P and Klatt, NR and Lagenaur, L and Landay, AL}, title = {A Summary of the Second Annual HIV Microbiome Workshop.}, journal = {AIDS research and human retroviruses}, volume = {33}, number = {12}, pages = {1258-1264}, doi = {10.1089/aid.2017.0137}, pmid = {28899105}, issn = {1931-8405}, support = {P51 OD010425/OD/NIH HHS/United States ; }, mesh = {Bacteria/classification/*isolation &amp; purification ; Fungi/classification/*isolation &amp; purification ; HIV Infections/*pathology/*transmission/virology ; Humans ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Symbiosis/physiology ; }, abstract = {Commensal organisms appear to play significant roles in normal homeostasis as well as in the pathogenesis of HIV infection in a number of different organ systems. On November 17th and 18th, 2016, leading researchers from around the world met to discuss their insights on advances in our understanding of HIV and the microbiome at the National Institutes of Health (NIH) in Bethesda. Dr. Elhanan Borenstein of the University of Washington gave a keynote address where he discussed new developments in systems biology which hold the promise of illuminating the pathways by which these organisms interact with human physiology. He suggested that we need to get past correlations in microbiome research by using models and informatics which incorporate metagenomics to predict functional changes in the microbiome.}, }
@article {pmid28898777, year = {2017}, author = {Liu, P and Jia, S and He, X and Zhang, X and Ye, L}, title = {Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils.}, journal = {Chemosphere}, volume = {188}, number = {}, pages = {455-464}, doi = {10.1016/j.chemosphere.2017.08.162}, pmid = {28898777}, issn = {1879-1298}, mesh = {Agriculture/methods ; China ; Drug Resistance, Microbial/*genetics ; *Fertilizers ; Genes, Bacterial ; High-Throughput Screening Assays ; *Manure ; Metagenomics ; Microbiota/*drug effects/genetics ; Soil/*chemistry ; Soil Microbiology/*standards ; }, abstract = {Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and