@article {pmid31207407, year = {2019}, author = {Parente, E and De Filippis, F and Ercolini, D and Ricciardi, A and Zotta, T}, title = {Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database.}, journal = {International journal of food microbiology}, volume = {305}, number = {}, pages = {108249}, doi = {10.1016/j.ijfoodmicro.2019.108249}, pmid = {31207407}, issn = {1879-3460}, mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Databases, Factual ; *Food Microbiology ; Meat/microbiology ; *Microbiota ; Software ; }, abstract = {We present a new version of FoodMicrobionet, a database for the exploration of food bacterial communities. The database, available as an app built with the Shiny package of R, includes data from 44 studies and 2234 samples (food or food environment), covering dairy, meat, fruit and vegetables, cereal based and ready-to-eat foods. The interactive interface allows exploration of data, access to external resources (on line versions of the studies, sequence data on SRA, taxonomic databases), filtering samples on the basis of a number of criteria, aggregation of samples and bacterial taxa and export of data in a variety of formats. FoodMicrobionet is the largest collection of data on food bacterial communities and, due to the structure of sample metadata, largely derived from the European Food Safety Agency FoodEx2 classification, makes comparison and re-analysis of data from published and unpublished studies easy. Data exported from FoodMicrobionet can be readily used for graphical and statistical meta-analyses using open-source software (Gephi, Cytoscape, CoNet, and R packages and apps, such as phyloseq and Shiny-Phyloseq) thus providing scientists, risk assessors and industry with a wealth of information on the structure of food biomes.}, }
@article {pmid30666248, year = {2018}, author = {Malla, MA and Dubey, A and Kumar, A and Yadav, S and Hashem, A and Abd Allah, EF}, title = {Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {2868}, doi = {10.3389/fimmu.2018.02868}, pmid = {30666248}, issn = {1664-3224}, mesh = {Communicable Diseases/etiology/*microbiology ; Computational Biology/trends ; Dysbiosis/complications ; Forecasting ; High-Throughput Nucleotide Sequencing/instrumentation/*trends ; Host Microbial Interactions/*genetics ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenomics/*trends ; Microbiota/*physiology ; Nanotechnology/methods ; }, abstract = {The interaction between the human microbiome and immune system has an effect on several human metabolic functions and impacts our well-being. Additionally, the interaction between humans and microbes can also play a key role in determining the wellness or disease status of the human body. Dysbiosis is related to a plethora of diseases, including skin, inflammatory, metabolic, and neurological disorders. A better understanding of the host-microbe interaction is essential for determining the diagnosis and appropriate treatment of these ailments. The significance of the microbiome on host health has led to the emergence of new therapeutic approaches focused on the prescribed manipulation of the host microbiome, either by removing harmful taxa or reinstating missing beneficial taxa and the functional roles they perform. Culturing large numbers of microbial taxa in the laboratory is problematic at best, if not impossible. Consequently, this makes it very difficult to comprehensively catalog the individual members comprising a specific microbiome, as well as understanding how microbial communities function and influence host-pathogen interactions. Recent advances in sequencing technologies and computational tools have allowed an increasing number of metagenomic studies to be performed. These studies have provided key insights into the human microbiome and a host of other microbial communities in other environments. In the present review, the role of the microbiome as a therapeutic agent and its significance in human health and disease is discussed. Advances in high-throughput sequencing technologies for surveying host-microbe interactions are also discussed. Additionally, the correlation between the composition of the microbiome and infectious diseases as described in previously reported studies is covered as well. Lastly, recent advances in state-of-the-art bioinformatics software, workflows, and applications for analysing metagenomic data are summarized.}, }
@article {pmid30498254, year = {2018}, author = {Dutta, A and Dutta Gupta, S and Gupta, A and Sarkar, J and Roy, S and Mukherjee, A and Sar, P}, title = {Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17459}, pmid = {30498254}, issn = {2045-2322}, support = {MoES/P.O.(Seismo)/1(181)/2013//Ministry of Earth Sciences (MoES)/International ; }, mesh = {Biodiversity ; Computational Biology/methods ; *Environmental Microbiology ; Geologic Sediments/*microbiology ; India ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsrB and mcrA genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha-, Beta-, Gammaproteobacteria, Actinobacteria and Firmicutes, whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.}, }
@article {pmid30120375, year = {2018}, author = {Goldsmith, DB and Kellogg, CA and Morrison, CL and Gray, MA and Stone, RP and Waller, RG and Brooke, SD and Ross, SW}, title = {Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12383}, pmid = {30120375}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics/*microbiology ; Bacteria/classification/genetics ; *Biodiversity ; Computational Biology/methods ; *Genotype ; Metagenome ; Metagenomics/methods ; *Microbiota ; Microsatellite Repeats ; }, abstract = {Cold-water corals provide critical habitats for a multitude of marine species, but are understudied relative to tropical corals. Primnoa pacifica is a cold-water coral prevalent throughout Alaskan waters, while another species in the genus, Primnoa resedaeformis, is widely distributed in the Atlantic Ocean. This study examined the V4-V5 region of the 16S rRNA gene after amplifying and pyrosequencing bacterial DNA from samples of these species. Key differences between the two species' microbiomes included a robust presence of bacteria belonging to the Chlamydiales order in most of the P. pacifica samples, whereas no more than 2% of any microbial community from P. resedaeformis comprised these bacteria. Microbiomes of P. resedaeformis exhibited higher diversity than those of P. pacifica, and the two species largely clustered separately in a principal coordinate analysis. Comparison of P. resedaeformis microbiomes from samples collected in two submarine canyons revealed a significant difference between locations. This finding mirrored significant genetic differences among the P. resedaeformis from the two canyons based upon population genetic analysis of microsatellite loci. This study presents the first report of microbiomes associated with these two coral species.}, }
@article {pmid30046123, year = {2018}, author = {Imchen, M and Kumavath, R and Barh, D and Vaz, A and Góes-Neto, A and Tiwari, S and Ghosh, P and Wattam, AR and Azevedo, V}, title = {Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11187}, pmid = {30046123}, issn = {2045-2322}, support = {SB-EMEQ-051/2014//DST | Science and Engineering Research Board (SERB)/International ; }, mesh = {Bacteroidetes/genetics ; *Ecosystem ; Firmicutes/genetics ; Geologic Sediments/microbiology ; India ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Proteobacteria/genetics ; Wetlands ; }, abstract = {The mangrove ecosystem harbors a complex microbial community that plays crucial role in biogeochemical cycles. In this study, we analyzed mangrove sediments from India using de novo whole metagenome next generation sequencing (NGS) and compared their taxonomic and functional community structures to mangrove metagenomics samples from Brazil and Saudi Arabia. The most abundant phyla in the mangroves of all three countries was Proteobacteria, followed by Firmicutes and Bacteroidetes. A total of 1,942 genes were found to be common across all the mangrove sediments from each of the three countries. The mangrove resistome consistently showed high resistance to fluoroquinolone and acriflavine. A comparative study of the mangrove resistome with other ecosystems shows a higher frequency of heavy metal resistance in mangrove and terrestrial samples. Ocean samples had a higher abundance of drug resistance genes with fluoroquinolone and methicillin resistance genes being as high as 28.178% ± 3.619 and 10.776% ± 1.823. Genes involved in cobalt-zinc-cadmium resistance were higher in the mangrove (23.495% ± 4.701) and terrestrial (27.479% ± 4.605) ecosystems. Our comparative analysis of samples collected from a variety of habitats shows that genes involved in resistance to both heavy metals and antibiotics are ubiquitous, irrespective of the ecosystem examined.}, }
@article {pmid29941875, year = {2018}, author = {Buendía, E and Zakzuk, J and San-Juan-Vergara, H and Zurek, E and Ajami, NJ and Caraballo, L}, title = {Gut microbiota components are associated with fixed airway obstruction in asthmatic patients living in the tropics.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9582}, pmid = {29941875}, issn = {2045-2322}, mesh = {Adult ; Asthma/*microbiology/*physiopathology ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; Humans ; Lung/*physiopathology ; Male ; Phenotype ; *Tropical Climate ; }, abstract = {Microbiome composition has been associated to several inflammatory diseases, including asthma. There are few studies exploring the relationships of gut microbiota with airway obstruction pheonotypes in adult asthma, especially those living in the tropics. We sought to evaluate the relationships of gut microbiota with the airway obstruction and other variables of interest in asthmatic patients living in the tropics according to three phenotypes: No Airway Obstruction (NAO), Reversible Airway Obstruction (RAO) or Fixed Airway Obstruction (FAO). We found that Streptococcaceae:Streptococcus and Enterobacteriaceae:Escherichia-Shigella consistently discriminated asthmatic individuals suffering FAO from NAO or RAO, plus Veillonellaceae:Megasphaera when comparing FAO and RAO (p < 0.05; FDR < 0.05). In the FAO, the network showing the genus relations was less complex and interconnected. Several Rumminococcaceae, Lachnospiraceae and Clostridiales were enriched in patients with low specific IgE levels to mites and Ascaris. All patients shared a common exposure framework; control medication usage and smoking habit were uncommon and equally distributed between them. In conclusion, in this tropical asthmatic population, components of human gut microbiota are associated with the presence of a FAO phenotype and lower specific IgE response to mites and Ascaris.}, }
@article {pmid29937540, year = {2018}, author = {Lagier, JC and Dubourg, G and Million, M and Cadoret, F and Bilen, M and Fenollar, F and Levasseur, A and Rolain, JM and Fournier, PE and Raoult, D}, title = {Culturing the human microbiota and culturomics.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {}, pages = {540-550}, doi = {10.1038/s41579-018-0041-0}, pmid = {29937540}, issn = {1740-1534}, mesh = {Bacteria/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacteriological Techniques/*methods/trends ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; *Microbiota ; }, abstract = {The gut microbiota has an important role in the maintenance of human health and in disease pathogenesis. This importance was realized through the advent of omics technologies and their application to improve our knowledge of the gut microbial ecosystem. In particular, the use of metagenomics has revealed the diversity of the gut microbiota, but it has also highlighted that the majority of bacteria in the gut remain uncultured. Culturomics was developed to culture and identify unknown bacteria that inhabit the human gut as a part of the rebirth of culture techniques in microbiology. Consisting of multiple culture conditions combined with the rapid identification of bacteria, the culturomic approach has enabled the culture of hundreds of new microorganisms that are associated with humans, providing exciting new perspectives on host-bacteria relationships. In this Review, we discuss why and how culturomics was developed. We describe how culturomics has extended our understanding of bacterial diversity and then explore how culturomics can be applied to the study of the human microbiota and the potential implications for human health.}, }
@article {pmid29912385, year = {2018}, author = {Bengtsson-Palme, J and Richardson, RT and Meola, M and Wurzbacher, C and Tremblay, ÉD and Thorell, K and Kanger, K and Eriksson, KM and Bilodeau, GJ and Johnson, RM and Hartmann, M and Nilsson, RH}, title = {Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {23}, pages = {4027-4033}, pmid = {29912385}, issn = {1367-4811}, mesh = {Computational Biology ; *DNA Barcoding, Taxonomic ; *Genetic Markers ; *Metagenomics ; *Phylogeny ; *Software ; }, abstract = {Motivation: Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.<br><br>Results: We evaluated the Metaxa2 Database Builder on 11 commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.<br><br>Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid29531234, year = {2018}, author = {Penington, JS and Penno, MAS and Ngui, KM and Ajami, NJ and Roth-Schulze, AJ and Wilcox, SA and Bandala-Sanchez, E and Wentworth, JM and Barry, SC and Brown, CY and Couper, JJ and Petrosino, JF and Papenfuss, AT and Harrison, LC and , }, title = {Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4386}, pmid = {29531234}, issn = {2045-2322}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Australia ; Cryopreservation/methods ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Individuality ; RNA, Ribosomal, 16S/*genetics/standards ; Sequence Analysis, DNA ; Specimen Handling/*methods ; United States ; }, abstract = {To optimise fecal sampling for reproducible analysis of the gut microbiome, we compared different methods of sample collection and sequencing of 16S rRNA genes at two centers. Samples collected from six individuals on three consecutive days were placed in commercial collection tubes (OMNIgeneGut OMR-200) or in sterile screw-top tubes in a home fridge or home freezer for 6-24 h, before transfer and storage at -80 °C. Replicate samples were shipped to centers in Australia and the USA for DNA extraction and sequencing by their respective PCR protocols, and analysed with the same bioinformatic pipeline. Variation in gut microbiome was dominated by differences between individuals. Minor differences in the abundance of taxa were found between collection-processing methods and day of collection, and between the two centers. We conclude that collection with storage and transport at 4 °C within 24 h is adequate for 16S rRNA analysis of the gut microbiome. Other factors including differences in PCR and sequencing methods account for relatively minor variation compared to differences between individuals.}, }
@article {pmid29020222, year = {2018}, author = {Leung, V and Vincent, C and Edens, TJ and Miller, M and Manges, AR}, title = {Antimicrobial Resistance Gene Acquisition and Depletion Following Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {66}, number = {3}, pages = {456-457}, pmid = {29020222}, issn = {1537-6591}, mesh = {Anti-Bacterial Agents/pharmacology ; Clostridium Infections/*therapy ; Drug Resistance, Multiple, Bacterial/*genetics ; Fecal Microbiota Transplantation/*adverse effects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genes, Bacterial ; *Genes, MDR ; High-Throughput Nucleotide Sequencing ; Humans ; Recurrence ; }, abstract = {Fecal microbiota transplantation (FMT) may be a novel approach to eliminate multidrug-resistant bacteria from the gut and to prevent future infections. Using whole metagenome sequencing data from 8 FMT donor-recipient pairs, we identified 37 and 95 antimicrobial resistance genes that were acquired by or removed from FMT recipients, respectively.}, }
@article {pmid31627274, year = {2019}, author = {Maia, LMS and Pinto, AZL and Carvalho, MS and Melo, FL and Ribeiro, BM and Slhessarenko, RD}, title = {Novel Viruses in Mosquitoes from Brazilian Pantanal.}, journal = {Viruses}, volume = {11}, number = {10}, pages = {}, doi = {10.3390/v11100957}, pmid = {31627274}, issn = {1999-4915}, support = {407817/2013-1//Rede Pro-Centro-Oeste of viral biodiversity/ ; }, abstract = {Viruses are ubiquitous and diverse microorganisms arising as a result of interactions within their vertebrate and invertebrate hosts. Here we report the presence of different viruses in the salivary glands of 1657 mosquitoes classified over 28 culicinae species from the North region of the Brazilian Pantanal wetland through metagenomics, viral isolation, and RT-PCR. In total, 12 viruses were found, eight putative novel viruses with relatively low similarity with pre-existing species of viruses within their families, named Pirizal iflavirus, Furrundu phlebovirus, Pixé phlebovirus, Guampa vesiculovirus, Chacororé flavivirus, Rasqueado orbivirus, Uru chuvirus, and Bororo circovirus. We also found the already described Lobeira dielmorhabdovirus, Sabethes flavivirus, Araticum partitivirus, and Murici totivirus. Therefore, these findings underscore the vast diversity of culicinae and novel viruses yet to be explored in Pantanal, the largest wetland on the planet.}, }
@article {pmid30658995, year = {2019}, author = {Hildebrand, F and Moitinho-Silva, L and Blasche, S and Jahn, MT and Gossmann, TI and Huerta-Cepas, J and Hercog, R and Luetge, M and Bahram, M and Pryszlak, A and Alves, RJ and Waszak, SM and Zhu, A and Ye, L and Costea, PI and Aalvink, S and Belzer, C and Forslund, SK and Sunagawa, S and Hentschel, U and Merten, C and Patil, KR and Benes, V and Bork, P}, title = {Antibiotics-induced monodominance of a novel gut bacterial order.}, journal = {Gut}, volume = {68}, number = {10}, pages = {1781-1790}, doi = {10.1136/gutjnl-2018-317715}, pmid = {30658995}, issn = {1468-3288}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metagenomics/*methods ; Microbiota/drug effects/*genetics ; }, abstract = {OBJECTIVE: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species.<br><br>DESIGN: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria.<br><br>RESULTS: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, UBorkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals.<br><br>CONCLUSION: The bloom of UB. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.}, }
@article {pmid29624892, year = {2018}, author = {Kaur, K and Saxena, A and Debnath, I and O'Brien, JL and Ajami, NJ and Auchtung, TA and Petrosino, JF and Sougiannis, AJ and Depaep, S and Chumanevich, A and Gummadidala, PM and Omebeyinje, MH and Banerjee, S and Chatzistamou, I and Chakraborty, P and Fayad, R and Berger, FG and Carson, JA and Chanda, A}, title = {Antibiotic-mediated bacteriome depletion in ApcMin/+ mice is associated with reduction in mucus-producing goblet cells and increased colorectal cancer progression.}, journal = {Cancer medicine}, volume = {7}, number = {5}, pages = {2003-2012}, pmid = {29624892}, issn = {2045-7634}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 GM103336/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenomatous Polyposis Coli/*microbiology/*pathology ; Adenomatous Polyposis Coli Protein/genetics ; Animals ; Anti-Bacterial Agents/*adverse effects/*pharmacology ; Colon/pathology ; Disease Models, Animal ; Disease Progression ; Gastrointestinal Microbiome/*drug effects ; Goblet Cells/*cytology ; Intestinal Mucosa/microbiology/*pathology ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Neomycin/adverse effects/pharmacology ; Streptomycin/adverse effects/pharmacology ; Vancomycin/adverse effects/pharmacology ; }, abstract = {Recent epidemiological evidence suggests that exposure to antibiotics in early-to-middle adulthood is associated with an increased risk of colorectal adenoma. However, mechanistic studies in established preclinical cancer to examine these claims are extremely limited. Therefore, we investigated the effect of long-term exposure of an antibiotic cocktail composed of Vancomycin, Neomycin, and Streptomycin, on tumor development and progression in the ApcMin/+ mouse, an established genetic model for familial adenomatous polyposis. Clinical pathologies related to tumor development as well as intestinal and colon tissue histopathology were studied at ages 8, 12, and 16 weeks of age, which correspond to the approximate ages of development of neoplasia, gut inflammation with polyposis, and cancer progression, respectively, in this animal model. We show that the antibiotics significantly increase the severity of clinical symptoms, including effects on intestinal histology and goblet cell numbers. In addition, they promote small intestinal polyposis. Finally, metagenomic analysis of fecal samples demonstrated that antibiotic exposure is associated with a significant but nonuniform depletion of the animal's natural gut flora. Overall, these findings support the premise that long-term antibiotic exposure mediates the selected depletion of gut microbial communities and the concomitant thinning of the protective mucus layer, resulting in an increase in tumor development.}, }
@article {pmid30065291, year = {2018}, author = {Meier-Kolthoff, JP and Uchiyama, J and Yahara, H and Paez-Espino, D and Yahara, K}, title = {Investigation of recombination-intense viral groups and their genes in the Earth's virome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11496}, pmid = {30065291}, issn = {2045-2322}, support = {16H06429//Ministry of Education, Culture, Sports, Science, and Technology (MEXT)/International ; 16K21723//Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan/International ; 17H05826//Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan/International ; }, mesh = {Bacteria/virology ; Bacteriophages/genetics ; Biodiversity ; DNA, Viral/genetics ; Earth (Planet) ; Ecosystem ; Genome, Viral/*genetics ; Host Specificity/genetics ; Humans ; Metagenome/genetics ; Metagenomics/methods ; Mouth/virology ; Recombination, Genetic/*genetics ; Viruses/*genetics ; }, abstract = {Bacteriophages (phages), or bacterial viruses, are the most abundant and diverse biological entities that impact the global ecosystem. Recent advances in metagenomics have revealed their rampant abundance in the biosphere. A fundamental aspect of bacteriophages that remains unexplored in metagenomic data is the process of recombination as a driving force in evolution that occurs among different viruses within the same bacterial host. Here, we systematically examined signatures of recombination in every gene from 211 species-level viral groups in a recently obtained dataset of the Earth's virome that contain corresponding information on the host bacterial species. Our study revealed that signatures of recombination are widespread (84%) among the diverse viral groups. We identified 25 recombination-intense viral groups, widely distributed across the viral taxonomy, and present in bacterial species living in the human oral cavity. We also revealed a significant inverse association between the recombination-intense viral groups and Type II restriction endonucleases, that could be effective in reducing recombination among phages in a cell. Furthermore, we identified recombination-intense genes that are significantly enriched for encoding phage morphogenesis proteins. Changes in the viral genomic sequence by recombination may be important to escape cleavage by the host bacterial immune systems.}, }
@article {pmid29973630, year = {2018}, author = {Hart, ML and Ericsson, AC and Lloyd, KCK and Grimsrud, KN and Rogala, AR and Godfrey, VL and Nielsen, JN and Franklin, CL}, title = {Development of outbred CD1 mouse colonies with distinct standardized gut microbiota profiles for use in complex microbiota targeted studies.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10107}, pmid = {29973630}, issn = {2045-2322}, support = {T32 OD0112639//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; U42 OD010924/OD/NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; K01 OD019924/OD/NIH HHS/United States ; U42 OD012210/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; U2C DK092993/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Breeding/*methods ; Embryo Transfer/methods ; Fecal Microbiota Transplantation/*methods ; Female ; *Gastrointestinal Microbiome ; Housing, Animal ; Male ; Mice ; Mice, Inbred C57BL ; Models, Animal ; }, abstract = {Studies indicate that the gut microbiota (GM) can significantly influence both local and systemic host physiologic processes. With rising concern for optimization of experimental reproducibility and translatability, it is essential to consider the GM in study design. However, GM profiles can vary between rodent producers making consistency between models challenging. To circumvent this, we developed outbred CD1 mouse colonies with stable, complex GM profiles that can be used as donors for a variety of GM transfer techniques including rederivation, co-housing, cross-foster, and fecal microbiota transfer (FMT). CD1 embryos were surgically transferred into CD1 or C57BL/6 surrogate dams that varied by GM composition and complexity to establish four separate mouse colonies harboring GM profiles representative of contemporary mouse producers. Using targeted 16S rRNA amplicon sequencing, subsequent female offspring were found to have similar GM profiles to surrogate dams. Furthermore, breeding colonies of CD1 mice with distinct GM profiles were maintained for nine generations, demonstrating GM stability within these colonies. To confirm GM stability, we shipped cohorts of these four colonies to collaborating institutions and found no significant variation in GM composition. These mice are an invaluable experimental resource that can be used to investigate GM effects on mouse model phenotype.}, }
@article {pmid29930350, year = {2018}, author = {Dini-Andreote, F and van Elsas, JD and Olff, H and Salles, JF}, title = {Dispersal-competition tradeoff in microbiomes in the quest for land colonization.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9451}, pmid = {29930350}, issn = {2045-2322}, mesh = {*Biological Evolution ; *Metagenome ; *Microbiota ; Seawater/microbiology ; *Soil Microbiology ; }, abstract = {Ancestor microbes started colonizing inland habitats approximately 2.7 to 3.5 billion years ago. With some exceptions, the key physiological adaptations of microbiomes associated with marine-to-land transitions have remained elusive. This is essentially caused by the lack of suitable systems that depict changes in microbiomes across sufficiently large time scales. Here, we investigate the adaptive routes taken by microbiomes along a contemporary gradient of land formation. Using functional trait-based metagenomics, we show that a switch from a microbial 'dispersal' to a 'competition' response modus best characterizes the microbial trait changes during this eco-evolutionary trajectory. The 'dispersal' modus prevails in microbiomes at the boundary sites between land and sea. It encompasses traits conferring cell chemosensory and motile behaviors, thus allowing the local microbes to exploit short-lived nutritional patches in high-diffusion microhabitats. A systematic transition towards the 'competition' modus occurs progressively as the soil matures, which is likely due to forces of viscosity or strain that favor traits for competition and chemical defense. Concomitantly, progressive increases in the abundances of genes encoding antibiotic resistance and complex organic substrate degradation were found. Our findings constitute a novel perspective on the ecology and evolution of microbiome traits, tracking back one of the most seminal transitions in the evolutionary history of life.}, }
@article {pmid29700420, year = {2018}, author = {Richardson, JB and Dancy, BCR and Horton, CL and Lee, YS and Madejczyk, MS and Xu, ZZ and Ackermann, G and Humphrey, G and Palacios, G and Knight, R and Lewis, JA}, title = {Exposure to toxic metals triggers unique responses from the rat gut microbiota.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6578}, pmid = {29700420}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; *Heavy Metal Poisoning ; Metagenome ; Metagenomics/methods ; Metals, Heavy/*toxicity ; Rats ; }, abstract = {Our understanding of the interaction between the gut microbiota and host health has recently improved dramatically. However, the effects of toxic metal exposure on the gut microbiota remain poorly characterized. As this microbiota creates a critical interface between the external environment and the host's cells, it may play an important role in host outcomes during exposure. We therefore used 16S ribosomal RNA (rRNA) gene sequencing to track changes in the gut microbiota composition of rats exposed to heavy metals. Rats were exposed daily for five days to arsenic, cadmium, cobalt, chromium, nickel, or a vehicle control. Significant changes to microbiota composition were observed in response to high doses of chromium and cobalt, and significant dose-dependent changes were observed in response to arsenic, cadmium and nickel. Many of these perturbations were not uniform across metals. However, bacteria with higher numbers of iron-importing gene orthologs were overly represented after exposure to arsenic and nickel, suggesting some possibility of a shared response. These findings support the utility of the microbiota as a pre-clinical tool for identifying exposures to specific heavy metals. It is also clear that characterizing changes to the functional capabilities of microbiota is critical to understanding responses to metal exposure.}, }
@article {pmid29891968, year = {2018}, author = {Grey, EK and Bernatchez, L and Cassey, P and Deiner, K and Deveney, M and Howland, KL and Lacoursière-Roussel, A and Leong, SCY and Li, Y and Olds, B and Pfrender, ME and Prowse, TAA and Renshaw, MA and Lodge, DM}, title = {Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8843}, pmid = {29891968}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; DNA/*genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; *Environment ; Metagenomics/*methods ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer sets. While community dissimilarity patterns were consistent across primers and sampling effort, richness patterns were not, suggesting that richness estimates are extremely sensitive to primer choice and sampling effort. The survey detected 64 potential NIS, with COI identifying more known NIS from port checklists but 18 S identifying more operational taxonomic units shared between three or more ports that represent un-recorded potential NIS. Overall, we conclude that eDNA metabarcoding surveys can reveal global similarity patterns among ports across a broad array of taxa and can also detect potential NIS in these key habitats. However, richness estimates and species assignments require caution. Based on results of this study, we make several recommendations for port eDNA sampling design and suggest several areas for future research.}, }
@article {pmid29872163, year = {2018}, author = {Zhu, Y and Zhang, F and Zhang, C and Yang, L and Fan, G and Xu, Y and Sun, B and Li, X}, title = {Dynamic microbial succession of Shanxi aged vinegar and its correlation with flavor metabolites during different stages of acetic acid fermentation.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8612}, pmid = {29872163}, issn = {2045-2322}, mesh = {Acetic Acid/*metabolism ; Bacteria/*classification/*metabolism ; *Biota ; Fermentation ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Metabolomics ; Metagenomics ; Volatile Organic Compounds/metabolism ; }, abstract = {Shanxi aged vinegar (SAV), one of the famous Chinese vinegars, is produced by multispecies solid-state fermentation in which the acetic acid fermentation stage (AAF) is especially important. However, how bacterial succession and their metabolites change along with the different stages of AAF is still poorly understood. In this study, we investigated the dynamic bacterial succession and flavor formation in three batches of SAV using high-throughput sequencing and metabolomics approaches. It is interesting to find that AAF can be divided into three stages based on its bacterial community succession (early stage, days 0-4; medium stage, days 5-21; and later stage, days 22-26). Pantoea, Pediococcus, Lactococcus and Rhizobium played an important role in the early stage; Lactobacillus was dominant in the medium stage (67.72%); and Acetobacter, Komagataeibacter and Kroppenstedtia were the key bacteria in the later stage. A total of seven organic acids and 42 volatile constituents (esters, alcohol, ketones and aldehydes) were detected during the AAF. Spearman correlation analysis showed a significant correlation between the bacterial community and these flavor metabolites during the AAF of the SAV. This is the first report to explore the relationships between volatile flavor metabolites and bacterial community succession by a three-staged method and provide theoretical support for a flavor formation mechanism in traditional SAV.}, }
@article {pmid29802288, year = {2018}, author = {Waite, DW and Dsouza, M and Sekiguchi, Y and Hugenholtz, P and Taylor, MW}, title = {Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8128}, pmid = {29802288}, issn = {2045-2322}, mesh = {Animals ; *Endangered Species ; Feces/*microbiology ; Metagenomics/*methods ; *Microbiota ; Parrots/*genetics/*microbiology ; }, abstract = {The kakapo is a critically endangered, herbivorous parrot endemic to New Zealand. The kakapo hindgut hosts a dense microbial community of low taxonomic diversity, typically dominated by Escherichia fergusonii, and has proven to be a remarkably stable ecosystem, displaying little variation in core membership over years of study. To elucidate mechanisms underlying this robustness, we performed 16S rRNA gene-based co-occurrence network analysis to identify potential interactions between E. fergusonii and the wider bacterial community. Genomic and metagenomic sequencing were employed to facilitate interpretation of potential interactions observed in the network. E. fergusonii maintained very few correlations with other members of the microbiota, and isolates possessed genes for the generation of energy from a wide range of carbohydrate sources, including plant fibres such as cellulose. We surmise that this dominant microorganism is abundant not due to ecological interaction with other members of the microbiota, but its ability to metabolise a wide range of nutrients in the gut. This research represents the first concerted effort to understand the functional roles of the kakapo microbiota, and leverages metagenomic data to contextualise co-occurrence patterns. By combining these two techniques we provide a means for studying the diversity-stability hypothesis in the context of bacterial ecosystems.}, }
@article {pmid29670218, year = {2018}, author = {Jehrke, L and Stewart, FA and Droste, A and Beller, M}, title = {The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6215}, pmid = {29670218}, issn = {2045-2322}, mesh = {Animals ; Drosophila melanogaster/*genetics/*metabolism/*microbiology ; *Energy Metabolism ; Female ; Genetic Association Studies ; *Genetic Variation ; *Genome ; Genome-Wide Association Study ; Male ; Metabolome ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phenotype ; }, abstract = {The metabolic phenotype of an organism depends on a complex regulatory network, which integrates the plethora of intrinsic and external information and prioritizes the flow of nutrients accordingly. Given the rise of metabolic disorders including obesity, a detailed understanding of this regulatory network is in urgent need. Yet, our level of understanding is far from completeness and complicated by the discovery of additional layers in metabolic regulation, such as the impact of the microbial community present in the gut on the hosts' energy storage levels. Here, we investigate the interplay between genome variation, diet and the gut microbiome in the shaping of a metabolic phenotype. For this purpose, we reared a set of fully sequenced wild type Drosophila melanogaster flies under basal and nutritionally challenged conditions and performed metabolic and microbiome profiling experiments. Our results introduce the fly as a model system to investigate the impact of genome variation on the metabolic response to diet alterations and reveal candidate single nucleotide polymorphisms associated with different metabolic traits, as well as metabolite-metabolite and metabolite-microbe correlations. Intriguingly, the dietary changes affected the microbiome composition less than anticipated. These results challenge the current view of a rapidly changing microbiome in response to environmental fluctuations.}, }
@article {pmid29670191, year = {2018}, author = {Le Bastard, Q and Ward, T and Sidiropoulos, D and Hillmann, BM and Chun, CL and Sadowsky, MJ and Knights, D and Montassier, E}, title = {Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6219}, pmid = {29670191}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects/pharmacology ; Antineoplastic Agents/*adverse effects/pharmacology ; Biodiversity ; Disease Models, Animal ; Dysbiosis/*etiology/*microbiology/therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Mice ; }, abstract = {Fecal microbiota transplantation (FMT) is now widely used to treat recurrent Clostridium difficile infection, but has been less studied as a means to restore microbiome diversity and composition following antibiotic or chemotherapy treatments. The purpose of our study was to assess the efficacy of FMT to reverse antibiotic- and chemotherapy-induced gut dysbiosis in a mouse model. C57BL/6J mice were treated with ampicillin for 1 week and/or received a single intraperitoneal injection of 5-Fluorouracil. Fresh stool was collected and analyzed using shotgun metagenomics and the Illumina sequencing platform. Ampicillin caused a significant and immediate decrease in bacterial species richness and diversity that persisted for one week. In mice that received FMT, disruption of the intestinal microbiota was reversed immediately. Antibiotic and chemotherapy administration caused significant alteration in species distribution, including a decrease in the relative proportions of Clostridium scindens and Faecalibacterium prausnitzii, and an increase in known pathogenic species. In mice receiving FMT, we observed a significant increase in species known to exhibit anti-inflammatory properties. Moreover, chemotherapy led to a critical decrease in key 'health-promoting' species and to an altered functional profile, especially when chemotherapy was administered in tandem with antibiotics, and that FMT can ameliorate these effects.}, }
@article {pmid29700349, year = {2018}, author = {Lin, Z and Ye, W and Zu, X and Xie, H and Li, H and Li, Y and Zhang, W}, title = {Integrative metabolic and microbial profiling on patients with Spleen-yang-deficiency syndrome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6619}, pmid = {29700349}, issn = {2045-2322}, mesh = {Adult ; Aged ; Case-Control Studies ; Computational Biology/methods ; Female ; Gastrointestinal Microbiome ; Humans ; Male ; *Metabolome ; Metabolomics/methods ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Spleen/*immunology/*metabolism ; Syndrome ; Yang Deficiency/diagnosis/*immunology/*metabolism ; Young Adult ; }, abstract = {Gut microbiota is recognized as an indispensable &quot;metabolic organ&quot; that plays crucial roles in maintaining human health or initiating diseases. Spleen-yang-deficiency syndrome (SYDS) is a common syndrome of Traditional Chinese Medicine (TCM) clinic. It is a complex phenotype reflecting the overall changes of metabolism which are mainly caused by digestive disorders. However, little is known about the changes of gut microbiota and metabolism in patients with SYDS, as well as the crosstalk between gut microbiota and host metabolism. In the current study, an integrative metabolic and microbial profiling was performed on plasma, urine and feces from recruited SYDS and healthy individuals by using a LC-QTOFMS-based metabolomic and 16 s rRNA sequencing approaches. Our results showed a potentially significant contribution of gut dysbiosis to the metabolic disorders in SYDS. By integrating the differential gut bacteria with the metabolites, the results revealed some active bacterium of norank_f_CFT112H7, f_lachnospiraceae and bacteroides were closely involved in host mucosal integrity, bile acid metabolism and polysaccharides decomposition. Therefore, our results indicated the probable involvement of gut microbiota in mediating the metabolic changes, which warrants a further investigation on the role of gut microbiota in modulating the pathogenesis of SYDS.}, }
@article {pmid29674332, year = {2018}, author = {Du, F and Hinke, SA and Cavanaugh, C and Polidori, D and Wallace, N and Kirchner, T and Jennis, M and Lang, W and Kuo, GH and Gaul, MD and Lenhard, J and Demarest, K and Ajami, NJ and Liang, Y and Hornby, PJ}, title = {Potent Sodium/Glucose Cotransporter SGLT1/2 Dual Inhibition Improves Glycemic Control Without Marked Gastrointestinal Adaptation or Colonic Microbiota Changes in Rodents.}, journal = {The Journal of pharmacology and experimental therapeutics}, volume = {365}, number = {3}, pages = {676-687}, doi = {10.1124/jpet.118.248575}, pmid = {29674332}, issn = {1521-0103}, mesh = {Animals ; Biodiversity ; Blood Glucose/*metabolism ; Colon/*drug effects/metabolism/*microbiology ; Male ; Mice ; Microbiota/*drug effects ; Rats ; Sodium-Glucose Transporter 1/*antagonists &amp; inhibitors ; Sodium-Glucose Transporter 2/*metabolism ; Sodium-Glucose Transporter 2 Inhibitors/metabolism/*pharmacology ; }, abstract = {The sodium/glucose cotransporters (SGLT1 and SGLT2) transport glucose across the intestinal brush border and kidney tubule. Dual SGLT1/2 inhibition could reduce hyperglycemia more than SGLT2-selective inhibition in patients with type 2 diabetes. However, questions remain about altered gastrointestinal (GI) luminal glucose and tolerability, and this was evaluated in slc5a1-/- mice or with a potent dual inhibitor (compound 8; SGLT1 Ki = 1.5 ± 0.5 nM 100-fold greater potency than phlorizin; SGLT2 Ki = 0.4 ± 0.2 nM). 13C6-glucose uptake was quantified in slc5a1-/- mice and in isolated rat jejunum. Urinary glucose excretion (UGE), blood glucose (Sprague-Dawley rats), glucagon-like peptide 1 (GLP-1), and hemoglobin A1c (HbA1c) levels (Zucker diabetic fatty rats) were measured. Intestinal adaptation and rRNA gene sequencing was analyzed in C57Bl/6 mice. The blood 13C6-glucose area under the curve (AUC) was reduced in the absence of SGLT1 by 75% (245 ± 6 vs. 64 ± 6 mg/dl⋅h in wild-type vs. slc5a1-/- mice) and compound 8 inhibited its transport up to 50% in isolated rat jejunum. Compound 8 reduced glucose excursion more than SGLT2-selective inhibition (e.g., AUC = 129 ± 3 vs. 249 ± 5 mg/dl⋅h for 1 mg/kg compound 8 vs. dapagliflozin) with similar UGE but a lower renal glucose excretion threshold. In Zucker diabetic fatty rats, compound 8 decreased HbA1c and increased total GLP-1 without changes in jejunum SGLT1 expression, mucosal weight, or villus length. Overall, compound 8 (1 mg/kg for 6 days) did not increase cecal glucose concentrations or bacterial diversity in C57BL/6 mice. In conclusion, potent dual SGLT1/2 inhibition lowers blood glucose by reducing intestinal glucose absorption and the renal glucose threshold but minimally impacts the intestinal mucosa or luminal microbiota in chow-fed rodents.}, }
@article {pmid30657979, year = {2019}, author = {Liu, J and Lian, Q and Chen, Y and Qi, J}, title = {Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads.}, journal = {Nucleic acids research}, volume = {47}, number = {5}, pages = {e30}, doi = {10.1093/nar/gkz017}, pmid = {30657979}, issn = {1362-4962}, mesh = {*Algorithms ; Amino Acids/*genetics ; Datasets as Topic ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Genes/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Transcriptome/*genetics ; }, abstract = {Metagenomic studies, greatly promoted by the fast development of next-generation sequencing (NGS) technologies, uncover complex structures of microbial communities and their interactions with environment. As the majority of microbes lack information of genome sequences, it is essential to assemble prokaryotic genomes ab initio aiming to retrieve complete coding genes from various metabolic pathways. The complex nature of microbial composition and the burden of handling a vast amount of metagenomic data, bring great challenges to the development of effective and efficient bioinformatic tools. Here we present a protein assembler (MetaPA), based on de Bruijn graph searching on oligopeptide spaces and can be applied on both metagenomic and metatranscriptomic sequencing data. When public homologous protein sequences are involved to guide the assembling procedures, MetaPA assembles 85% of total proteins in complete sequences with high precision of 83% on real high-throughput sequencing datasets. Application of MetaPA on metatranscriptomic data successfully identifies the majority of actively transcribed genes validated in related studies. The results suggest that MetaPA has a good potential in both metagenomic and metatranscriptomic studies to characterize the composition and abundance of microbiota.}, }
@article {pmid30315079, year = {2018}, author = {Xia, F and Wang, JG and Zhu, T and Zou, B and Rhee, SK and Quan, ZX}, title = {Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox).}, journal = {Applied and environmental microbiology}, volume = {84}, number = {24}, pages = {}, pmid = {30315079}, issn = {1098-5336}, mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Geologic Sediments/chemistry ; Metagenomics ; Nitrates/metabolism ; Nitrification ; Nitrites/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Sewage/chemistry ; Soil/chemistry ; Soil Microbiology ; Water/chemistry ; }, abstract = {The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In addition, a relatively high proportion of comammox in tap and coastal water samples was confirmed via analysis of metagenomic data sets in public databases. The diversity of comammox was estimated by comammox-specific partial nested PCR amplification of the ammonia monooxygenase subunit A (amoA) gene, and phylogenetic analysis of comammox AmoA clearly showed a split of clade A into clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing among the various environmental samples. Moreover, compared to the amoA genes of AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher diversity indices. The ubiquitous distribution and high diversity of comammox indicate that they are likely overlooked contributors to nitrification in various ecosystems.IMPORTANCE The discovery of complete ammonia oxidizers (comammox), which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm that nitrification requires the activity of two types of microbes and redefines a key process in the biogeochemical nitrogen cycle. Understanding the functional relationships between comammox and other nitrifiers is important for ecological studies on the nitrogen cycle. Therefore, the diversity and contribution of comammox should be considered during ecological analyses of nitrifying microorganisms. In this study, a ubiquitous and highly diverse distribution of comammox was observed in various environmental samples, similar to the distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox was relatively high in coastal water and sediment samples, whereas it was nearly undetectable in open-ocean samples. The ubiquitous distribution and high diversity of comammox indicate that these microorganisms might be important contributors to nitrification.}, }
@article {pmid30054365, year = {2018}, author = {Esteban-Torres, M and Santamaría, L and Cabrera-Rubio, R and Plaza-Vinuesa, L and Crispie, F and de Las Rivas, B and Cotter, P and Muñoz, R}, title = {A Diverse Range of Human Gut Bacteria Have the Potential To Metabolize the Dietary Component Gallic Acid.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {19}, pages = {}, pmid = {30054365}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; DNA, Bacterial/genetics ; Feces/microbiology ; Gallic Acid/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human gut microbiota contains a broad variety of bacteria that possess functional genes, with resultant metabolites that affect human physiology and therefore health. Dietary gallates are phenolic components that are present in many foods and beverages and are regarded as having health-promoting attributes. However, the potential for metabolism of these phenolic compounds by the human microbiota remains largely unknown. The emergence of high-throughput sequencing (HTS) technologies allows this issue to be addressed. In this study, HTS was used to assess the incidence of gallate-decarboxylating bacteria within the gut microbiota of healthy individuals for whom bacterial diversity was previously determined to be high. This process was facilitated by the design and application of degenerate PCR primers to amplify a region encoding the catalytic C subunit of gallate decarboxylase (LpdC) from total metagenomic DNA extracted from human fecal samples. HTS resulted in the generation of a total of 3,261,967 sequence reads and revealed that the primary gallate-decarboxylating microbial phyla in the intestinal microbiota were Firmicutes (74.6%), Proteobacteria (17.6%), and Actinobacteria (7.8%). These reads corresponded to 53 genera, i.e., 47% of the bacterial genera detected previously in these samples. Among these genera, Anaerostipes and Klebsiella accounted for the majority of reads (40%). The usefulness of the HTS-lpdC method was demonstrated by the production of pyrogallol from gallic acid, as expected for functional gallate decarboxylases, among representative strains belonging to species identified in the human gut microbiota by this method.IMPORTANCE Despite the increasing wealth of sequencing data, the health contributions of many bacteria found in the human gut microbiota have yet to be elucidated. This study applies a novel experimental approach to predict the ability of gut microbes to carry out a specific metabolic activity, i.e., gallate metabolism. The study showed that, while gallate-decarboxylating bacteria represented 47% of the bacterial genera detected previously in the same human fecal samples, no gallate decarboxylase homologs were identified from representatives of Bacteroidetes The presence of functional gallate decarboxylases was demonstrated in representative Proteobacteria and Firmicutes strains from the human microbiota, an observation that could be of considerable relevance to the in vivo production of pyrogallol, a physiologically important bioactive compound.}, }
@article {pmid29898804, year = {2018}, author = {Misic, AM and Miedel, EL and Brice, AK and Cole, S and Zhang, GF and Dyer, CD and Secreto, A and Smith, AL and Danet-Desnoyers, G and Beiting, DP}, title = {Culture-independent Profiling of the Fecal Microbiome to Identify Microbial Species Associated with a Diarrheal Outbreak in Immunocompromised Mice.}, journal = {Comparative medicine}, volume = {68}, number = {4}, pages = {261-268}, pmid = {29898804}, issn = {1532-0820}, mesh = {Animals ; Diarrhea/epidemiology/*microbiology ; Disease Outbreaks ; Feces/*microbiology ; Genetic Variation ; Immunocompromised Host ; Metagenomics ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Microbiota/*genetics ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, RNA ; Whole Genome Sequencing ; }, abstract = {Immunocompromised mice are used frequently in biomedical research, in part because they accommodate the engraftment and study of primary human cells within a mouse model; however, these animals are susceptible to opportunistic infections and require special husbandry considerations. In 2015, an outbreak marked by high morbidity but low mortality swept through a colony of immunocompromised mice; this outbreak rapidly affected 75% of the colony and ultimately required complete depopulation of the barrier suite. Conventional microbiologic and molecular diagnostics were unsuccessful in determining the cause; therefore, we explored culture-independent methods to broadly profile the microbial community in the feces of affected animals. This approach identified 4 bacterial taxa- Candidatus Arthromitus, Clostridium celatum, Clostridiales bacterium VE202-01, and Bifidobacterium pseudolongum strain PV8-2- that were significantly enriched in the affected mice. Based on these results, specific changes were made to the animal husbandry procedures for immunocompromised mice. This case report highlights the utility of culture-independent methods in laboratory animal diagnostics.}, }
@article {pmid29872090, year = {2018}, author = {Paul, F and Otte, J and Schmitt, I and Dal Grande, F}, title = {Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8624}, pmid = {29872090}, issn = {2045-2322}, mesh = {Ascomycota/growth &amp; development ; Chlorophyta/*classification/*genetics/growth &amp; development ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Lichens/*growth &amp; development ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; Symbiosis ; }, abstract = {The implementation of HTS (high-throughput sequencing) approaches is rapidly changing our understanding of the lichen symbiosis, by uncovering high bacterial and fungal diversity, which is often host-specific. Recently, HTS methods revealed the presence of multiple photobionts inside a single thallus in several lichen species. This differs from Sanger technology, which typically yields a single, unambiguous algal sequence per individual. Here we compared HTS and Sanger methods for estimating the diversity of green algal symbionts within lichen thalli using 240 lichen individuals belonging to two species of lichen-forming fungi. According to HTS data, Sanger technology consistently yielded the most abundant photobiont sequence in the sample. However, if the second most abundant photobiont exceeded 30% of the total HTS reads in a sample, Sanger sequencing generally failed. Our results suggest that most lichen individuals in the two analyzed species, Lasallia hispanica and L. pustulata, indeed contain a single, predominant green algal photobiont. We conclude that Sanger sequencing is a valid approach to detect the dominant photobionts in lichen individuals and populations. We discuss which research areas in lichen ecology and evolution will continue to benefit from Sanger sequencing, and which areas will profit from HTS approaches to assessing symbiont diversity.}, }
@article {pmid29725134, year = {2018}, author = {ElNaker, NA and Elektorowicz, M and Naddeo, V and Hasan, SW and Yousef, AF}, title = {Assessment of Microbial Community Structure and Function in Serially Passaged Wastewater Electro-Bioreactor Sludge: An Approach to Enhance Sludge Settleability.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7013}, pmid = {29725134}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; Phosphorus/analysis ; Phylogeny ; Serial Passage ; Sewage/*microbiology ; Water Purification/*methods ; }, abstract = {Several studies have been carried out to understand bulking phenomena and the importance of environmental factors on sludge settling characteristics. The main objective of this study was to carry out functional characterization of microbial community structure of wastewater electro-bioreactor sludge as it undergoes serial passaging in the presence or absence of a current density over 15 days. Illumina MiSeq sequencing and QIIME were used to assess sludge microbial community shifts over time. (α) and (β) diversity analysis were conducted to assess the microbial diversity in electro-bioreactors. A phylogeny-based weighted UniFrac distance analysis was used to compare between bacterial communities while BIO-ENV trend and Spearman's rank correlation analysis were performed to investigate how reactor operational parameters correlated with bacterial community diversity. Results showed that the removal efficiency of soluble chemical oxygen demand (sCOD) ranged from 91-97%, while phosphorous (PO43--P) removal was approximately 99%. Phylogenetic analysis revealed stark differences in the development of sludge microbial communities in the control and treatment reactor. There was no mention of any studies aimed at characterizing functional microbial communities under electric field and the results communicated here are the first, to our knowledge, that address this gap in the literature.}, }
@article {pmid29725059, year = {2018}, author = {Dittmer, J and Bouchon, D}, title = {Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6998}, pmid = {29725059}, issn = {2045-2322}, mesh = {Animal Structures/*microbiology ; Animals ; Bacteria/classification/genetics ; Isopoda/*microbiology ; Metagenomics ; Microbial Interactions ; *Microbiota ; Wolbachia/*growth &amp; development ; }, abstract = {Wolbachia are widespread heritable endosymbionts of arthropods notorious for their profound effects on host fitness as well as for providing protection against viruses and eukaryotic parasites, indicating that they can interact with other microorganisms sharing the same host environment. Using the terrestrial isopod crustacean Armadillidium vulgare, its highly diverse microbiota (>200 bacterial genera) and its three feminizing Wolbachia strains (wVulC, wVulM, wVulP) as a model system, the present study demonstrates that Wolbachia can even influence the composition of a diverse bacterial community under both laboratory and natural conditions. While host origin is the major determinant of the taxonomic composition of the microbiota in A. vulgare, Wolbachia infection affected both the presence and, more importantly, the abundance of many bacterial taxa within each host population, possibly due to competitive interactions. Moreover, different Wolbachia strains had different impacts on microbiota composition. As such, infection with wVulC affected a higher number of taxa than infection with wVulM, possibly due to intrinsic differences in virulence and titer between these two strains. In conclusion, this study shows that heritable endosymbionts such as Wolbachia can act as biotic factors shaping the microbiota of arthropods, with as yet unknown consequences on host fitness.}, }
@article {pmid31595646, year = {2019}, author = {Strazzulli, A and Cobucci-Ponzano, B and Iacono, R and Giglio, R and Maurelli, L and Curci, N and Schiano-di-Cola, C and Santangelo, A and Contursi, P and Lombard, V and Henrissat, B and Lauro, FM and Fontes, CMGA and Moracci, M}, title = {Discovery of hyperstable carbohydrate-active enzymes through metagenomics of extreme environments.}, journal = {The FEBS journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/febs.15080}, pmid = {31595646}, issn = {1742-4658}, abstract = {The enzymes from hyperthermophilic microorganisms populating volcanic sites represent interesting cases of protein adaptation and biotransformations under conditions where conventional enzymes quickly denature. The difficulties in cultivating extremophiles severely limit access to this class of biocatalysts. To circumvent this problem, we embarked on the exploration of the biodiversity of the solfatara Pisciarelli, Agnano (Naples, Italy) to discover hyperthermophilic carbohydrate-active enzymes (CAZymes) and to characterize the entire set of such enzymes in this environment (CAZome). Here we report the results of the metagenomic analysis of two mud/water pools that greatly differ in both temperature and pH (T=85°C and pH 5.5; T=92°C and pH 1.5, for Pool1 and Pool2, respectively). DNA deep sequencing and following in-silico analysis led to 14,934 and 17,652 complete ORFs in Pool1 and Pool2, respectively. They exclusively belonged to archaeal cells and viruses with great genera variance within the phylum Crenarcheaota, which reflected the difference in temperature and pH of the two Pools. Surprisingly, 30% and 62% of all of the reads obtained from Pool1 and 2, respectively, had no match in nucleotide databanks. Genes associated with carbohydrate metabolism were 15% and 16% of the total in the two Pools, with 278 and 308 putative CAZymes in Pool1 and 2, corresponding to ~2.0% of all ORFs. Biochemical characterization of two CAZymes of a previously unknown archaeon revealed a novel subfamily GH5_19 β-mannanase/β-1,3-glucanase whose hemicellulose specificity correlates with the vegetation surrounding the sampling site, and a novel NAD+ dependent GH109 with a previously unreported β-N-acetylglucosaminide/β-glucoside specificity.}, }
@article {pmid29658784, year = {2018}, author = {Popic, V and Kuleshov, V and Snyder, M and Batzoglou, S}, title = {Fast Metagenomic Binning via Hashing and Bayesian Clustering.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {25}, number = {7}, pages = {677-688}, doi = {10.1089/cmb.2017.0250}, pmid = {29658784}, issn = {1557-8666}, mesh = {*Bayes Theorem ; Cluster Analysis ; Computational Biology/*statistics &amp; numerical data ; Humans ; Metagenome/genetics ; Metagenomics/*statistics &amp; numerical data ; Microbiota/*genetics ; }, abstract = {We introduce GATTACA, a framework for fast unsupervised binning of metagenomic contigs. Similar to recent approaches, GATTACA clusters contigs based on their coverage profiles across a large cohort of metagenomic samples; however, unlike previous methods that rely on read mapping, GATTACA quickly estimates these profiles from kmer counts stored in a compact index. This approach can result in over an order of magnitude speedup, while matching the accuracy of earlier methods on synthetic and real data benchmarks. It also provides a way to index metagenomic samples (e.g., from public repositories such as the Human Microbiome Project) offline once and reuse them across experiments; furthermore, the small size of the sample indices allows them to be easily transferred and stored. Leveraging the MinHash technique, GATTACA also provides an efficient way to identify publicly available metagenomic data that can be incorporated into the set of reference metagenomes to further improve binning accuracy. Thus, enabling easy indexing and reuse of publicly available metagenomic data sets, GATTACA makes accurate metagenomic analyses accessible to a much wider range of researchers.}, }
@article {pmid31564708, year = {2019}, author = {Zheng, A and Yi, H and Li, F and Han, L and Yu, J and Cheng, X and Su, H and Hong, K and Li, J}, title = {Changes in Gut Microbiome Structure and Function of Rats with Isoproterenol-Induced Heart Failure.}, journal = {International heart journal}, volume = {60}, number = {5}, pages = {1176-1183}, doi = {10.1536/ihj.18-194}, pmid = {31564708}, issn = {1349-3299}, mesh = {Animals ; Bacteria/*classification/genetics ; Disease Models, Animal ; Echocardiography ; Gastrointestinal Microbiome/*drug effects ; Heart Failure/chemically induced/diagnostic imaging/*microbiology ; High-Throughput Nucleotide Sequencing ; Injections, Intraperitoneal ; Isoproterenol/*adverse effects/pharmacology ; Male ; Metagenomics/*methods ; Phylogeny ; Rats ; Sequence Analysis, DNA ; }, abstract = {Recently, the potential role of gut microbiome (GM) in cardiovascular diseases has been revealed. Heart failure (HF) is one of the most prevalent cardiovascular diseases worldwide; however, whether GM dysbiosis participates in the development of HF remains largely unknown. This study aimed to investigate the specific changes in GM composition and function in isoproterenol (ISO)-induced HF in rats.The rats were divided into C (control), 4w-HF (ISO, 2.5 mg/kg/day for 4 weeks, intraperitoneally), and 2w-HF (ISO, 2.5 mg/kg/day for 2 weeks, intraperitoneally) groups. The cardiac structure and function in rats were assessed, and metagenomic analyses were then performed. Compared with the healthy control group, we found that the Shannon diversity index and microbial gene count in the 4w-HF and 2w-HF groups was drastically decreased. High-throughput sequencing showed that the three groups differed in intestinal bacterial community composition. Overgrowth of bacteria, such as Prevotella, was observed in the 4w-HF group, with reduced growth of bacteria, such as Roseburia, Lactobacillus, and Butyrivibrio, associated with healthy status compared with the C group on the genus level. Concomitant with the alteration of GM composition, underrepresentation of health-linked microbial function was observed in both the 4w-HF and 2w-HF groups compared with the C group.Iso-induced HF rats showed a significant decrease in the diversity and richness of the intestinal microbiome, with a downregulation of the key intestinal bacterial groups and overgrowth of bacteria considered to be involved in inflammatory responses as well as a decrease in health-linked microbial function. Our data indicated that altered GM may be a potential player in the pathogenesis and progression of HF.}, }
@article {pmid30097447, year = {2018}, author = {Burns, AS and Padilla, CC and Pratte, ZA and Gilde, K and Regensburger, M and Hall, E and Dove, ADM and Stewart, FJ}, title = {Broad Phylogenetic Diversity Associated with Nitrogen Loss through Sulfur Oxidation in a Large Public Marine Aquarium.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {20}, pages = {}, pmid = {30097447}, issn = {1098-5336}, mesh = {Bacteria/*classification/metabolism ; Biodiversity ; Bioreactors/microbiology ; *Denitrification ; *Genetic Variation ; Georgia ; Metagenomics ; Microbiota ; Nitrogen/*metabolism ; Oxidation-Reduction ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfur/*metabolism ; Waste Water ; }, abstract = {Denitrification by sulfur-oxidizing bacteria is an effective nitrate removal strategy in engineered aquatic systems. However, the community taxonomic and metabolic diversity of sulfur-driven denitrification (SDN) systems, as well as the relationship between nitrate removal and SDN community structure, remains underexplored. This is particularly true for SDN reactors applied to marine aquaria, despite the increasing use of this technology to supplement filtration. We applied 16S rRNA gene, metagenomic, and metatranscriptomic analyses to explore the microbial basis of SDN reactors operating on Georgia Aquarium's Ocean Voyager, the largest indoor closed-system seawater exhibit in the United States. The exhibit's two SDN systems vary in water retention time and nitrate removal efficiency. The systems also support significantly different microbial communities. These communities contain canonical SDN bacteria, including a strain related to Thiobacillus thioparus that dominates the system with the higher water retention time and nitrate removal but is effectively absent from the other system. Both systems contain a wide diversity of other microbes whose metagenome-assembled genomes contain genes of SDN metabolism. These include hundreds of strains of the epsilonproteobacterium Sulfurimonas, as well as gammaproteobacterial sulfur oxidizers of the Thiotrichales and Chromatiales, and a relative of Sedimenticolathiotaurini with complete denitrification potential. The SDN genes are transcribed and the taxonomic richness of the transcript pool varies markedly among the enzymatic steps, with some steps dominated by transcripts from noncanonical SDN taxa. These results indicate complex and variable SDN communities that may involve chemical dependencies among taxa as well as the potential for altering community structure to optimize nitrate removal.IMPORTANCE Engineered aquatic systems such as aquaria and aquaculture facilities have large societal value. Ensuring the health of animals in these systems requires understanding how microorganisms contribute to chemical cycling and waste removal. Focusing on the largest seawater aquarium in the United States, we explore the microbial communities in specialized reactors designed to remove excess nitrogen through the metabolic activity of sulfur-consuming microbes. We show that the diversity of microbes in these reactors is both high and highly variable, with distinct community types associated with significant differences in nitrogen removal rate. We also show that the genes encoding the metabolic steps of nitrogen removal are distributed broadly throughout community members, suggesting that the chemical transformations in this system are likely a result of microbes relying on other microbes. These results provide a framework for future studies exploring the contributions of different community members, both in waste removal and in structuring microbial biodiversity.}, }
@article {pmid30056005, year = {2018}, author = {Bankevich, A and Pevzner, PA}, title = {Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity.}, journal = {Cell systems}, volume = {7}, number = {2}, pages = {192-200.e3}, doi = {10.1016/j.cels.2018.06.009}, pmid = {30056005}, issn = {2405-4712}, mesh = {Algorithms ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Genetic Variation ; *Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA ; }, abstract = {Reduced microbiome diversity has been linked to several diseases. However, estimating the diversity of bacterial communities-the number and the total length of distinct genomes within a metagenome-remains an open problem in microbial ecology. Here, we describe an algorithm for estimating the microbial diversity in a metagenomic sample based on a joint analysis of short and long reads. Unlike previous approaches, the algorithm does not make any assumptions on the distribution of the frequencies of genomes within a metagenome (as in parametric methods) and does not require a large database that covers the total diversity (as in non-parametric methods). We estimate that genomes comprising a human gut metagenome have total length varying from 1.3 to 3.5 billion nucleotides, with genomes responsible for 50% of total abundance having total length varying from only 25 to 61 million nucleotides. In contrast, genomes comprising an aquifer sediment metagenome have more than two orders of magnitude larger total length (≈840 billion nucleotides).}, }
@article {pmid29884754, year = {2018}, author = {Lugli, GA and Mancino, W and Milani, C and Duranti, S and Turroni, F and van Sinderen, D and Ventura, M}, title = {Reconstruction of the Bifidobacterial Pan-Secretome Reveals the Network of Extracellular Interactions between Bifidobacteria and the Infant Gut.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {16}, pages = {}, pmid = {29884754}, issn = {1098-5336}, mesh = {Bifidobacterium/*genetics/*metabolism ; Bifidobacterium longum/genetics/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Glycomics ; Humans ; Infant ; Intestines/*microbiology ; *Metabolome ; Metagenome ; Milk, Human/metabolism ; Oligosaccharides/metabolism ; Proteome ; Symbiosis ; }, abstract = {The repertoire of secreted proteins decoded by a microorganism represents proteins released from or associated with the cell surface. In gut commensals, such as bifidobacteria, these proteins are perceived to be functionally relevant, as they regulate the interaction with the gut environment. In the current study, we screened the predicted proteome of over 300 bifidobacterial strains among the currently recognized bifidobacterial species to generate a comprehensive database encompassing bifidobacterial extracellular proteins. A glycobiome analysis of this predicted bifidobacterial secretome revealed that a correlation exists between particular bifidobacterial species and their capability to hydrolyze human milk oligosaccharides (HMOs) and intestinal glycoconjugates, such as mucin. Furthermore, an exploration of metatranscriptomic data sets of the infant gut microbiota allowed the evaluation of the expression of bifidobacterial genes encoding extracellular proteins, represented by ABC transporter substrate-binding proteins and glycoside hydrolases enzymes involved in the degradation of human milk oligosaccharides and mucin. Overall, this study provides insights into how bifidobacteria interact with their natural yet highly complex environment, the infant gut.IMPORTANCE The ecological success of bifidobacteria relies on the activity of extracellular proteins that are involved in the metabolism of nutrients and the interaction with the environment. To date, information on secreted proteins encoded by bifidobacteria is incomplete and just related to few species. In this study, we reconstructed the bifidobacterial pan-secretome, revealing extracellular proteins that modulate the interaction of bifidobacteria with their natural environment. Furthermore, a survey of the secretion systems between bifidobacterial genomes allowed the identification of a conserved Sec-dependent secretion machinery in all the analyzed genomes and the Tat protein translocation system in the chromosomes of 23 strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium aesculapii.}, }
@article {pmid29803476, year = {2018}, author = {González-Escobar, JL and Grajales-Lagunes, A and Smoliński, A and Chagolla-López, A and De Léon-Rodríguez, A and Barba de la Rosa, AP}, title = {Microbiota of edible Liometopum apiculatum ant larvae reveals potential functions related to their nutritional value.}, journal = {Food research international (Ottawa, Ont.)}, volume = {109}, number = {}, pages = {497-505}, doi = {10.1016/j.foodres.2018.04.049}, pmid = {29803476}, issn = {1873-7145}, mesh = {Animals ; Ants/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Female ; Food Analysis/methods ; Host-Pathogen Interactions ; Larva/microbiology ; Male ; Metagenomics ; *Microbiota ; *Nutritive Value ; Ribotyping ; Symbiosis ; }, abstract = {Edible insects, due to their high nutritive value, are currently considered as a potential renewable source for food and feed production. Liometopum apiculatum ants are widely distributed in arid and semi-arid ecosystems and their larvae (escamoles) are considered as a delicacy, however the microbial importance in L. apiculatum nutritional ecology is unknown. The aim of this research was to characterize the microorganisms associated with both L. apiculatum larvae and the reproductive adult ants using the 16S rRNA gene sequencing and culturomics approaches. The obligate endosymbionts were also investigated through microscopic analysis. The most abundant Phylum identified by sequencing in the larvae was Firmicutes while in adult ants was Proteobacteria. Interestingly, the culturomics results showed 15 genera corresponding to the bacteria identified by sequencing analysis. Particularly, it was observed a large population of nitrogen-fixing bacteria, which could be linked with the high protein content in escamoles. Endosymbionts were detected in bacteoriocytes, these bacteria are related with vitamins and essential amino acids biosynthesis, and both compounds contributing to the high nutritional value of escamoles. This is the first report of the microorganisms present in the escamolera ant ensuring their safety as food and opening new areas of nutritional ecological and food processing.}, }
@article {pmid29728382, year = {2018}, author = {Milani, C and Duranti, S and Mangifesta, M and Lugli, GA and Turroni, F and Mancabelli, L and Viappiani, A and Anzalone, R and Alessandri, G and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Phylotype-Level Profiling of Lactobacilli in Highly Complex Environments by Means of an Internal Transcribed Spacer-Based Metagenomic Approach.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {14}, pages = {}, pmid = {29728382}, issn = {1098-5336}, mesh = {Animals ; Cheese/microbiology ; Chickens ; DNA, Bacterial/genetics ; Female ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Host Microbial Interactions ; Humans ; Lactobacillus/classification/*genetics/*metabolism ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Vagina/microbiology ; }, abstract = {The genus Lactobacillus is a widespread taxon, members of which are highly relevant to functional and fermented foods, while they are also commonly present in host-associated gut and vaginal microbiota. Substantial efforts have been undertaken to disclose the genetic repertoire of all members of the genus Lactobacillus, and yet their species-level profiling in complex matrices is still undeveloped due to the poor phylotype resolution of profiling approaches based on the 16S rRNA gene. To overcome this limitation, an internal transcribed spacer (ITS)-based profiling method was developed to accurately profile lactobacilli at the species level. This approach encompasses a genus-specific primer pair combined with a database of ITS sequences retrieved from all available Lactobacillus genomes and a script for the QIIME software suite that performs all required steps to reconstruct a species-level profile. This methodology was applied to several environments, i.e., human gut and vagina and the ceca of free-range chickens, as well as whey and fresh cheese. Interestingly, the data collected confirmed a relevant role of lactobacilli present in functional and fermented foods in defining the population harbored by the human gut, while, unsurprisingly perhaps, the ceca of free-range chickens were observed to be dominated by lactobacilli characterized in birds living in natural environments. Moreover, vaginal swabs confirmed the existence of previously hypothesized community state types, while analysis of whey and fresh cheese revealed a dominant presence of single Lactobacillus species used as starters for cheese production. Furthermore, application of this ITS profiling method to a mock Lactobacillus community allowed a minimal resolution level of <0.006 ng/μl.IMPORTANCE The genus Lactobacillus is a large and ubiquitous taxon of high scientific and commercial relevance. Despite the fact that the genetic repertoire of Lactobacillus species has been extensively characterized, the ecology of this genus has been explored by metataxonomic techniques that are accurate down to the genus or phylogenetic group level only. Thus, the distribution of lactobacilli in environmental or processed food samples is relatively unexplored. The profiling protocol described here relies on the use of the internal transcribed spacer to perform an accurate classification in a target population of lactobacilli with a <0.006-ng/μl sensitivity. This approach was used to analyze five sample types collected from both human and animal host-associated microbiota, as well as from the cheese production chain. The availability of a tool for species-level profiling of lactobacilli may be highly useful for both academic research and a wide range of industrial applications.}, }
@article {pmid29651035, year = {2018}, author = {Zaheer, R and Noyes, N and Ortega Polo, R and Cook, SR and Marinier, E and Van Domselaar, G and Belk, KE and Morley, PS and McAllister, TA}, title = {Impact of sequencing depth on the characterization of the microbiome and resistome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5890}, pmid = {29651035}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Archaea/classification/drug effects/*genetics/isolation &amp; purification ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Cattle ; Drug Resistance/*genetics ; Feces/microbiology ; Fungal Proteins/genetics/metabolism ; Fungi/classification/drug effects/*genetics/isolation &amp; purification ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Expression ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Phylogeny ; Viral Proteins/genetics/metabolism ; Viruses/classification/drug effects/*genetics/isolation &amp; purification ; }, abstract = {Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.}, }
@article {pmid29593315, year = {2018}, author = {Sun, T and Wang, XQ and Zhao, ZL and Yu, SH and Yang, P and Chen, XM}, title = {A Lethal Fungus Infects the Chinese White Wax Scale Insect and Causes Dramatic Changes in the Host Microbiota.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5324}, pmid = {29593315}, issn = {2045-2322}, mesh = {Animals ; DNA, Ribosomal Spacer ; Female ; *Fungi/classification/genetics ; Hemiptera/*microbiology ; *Host-Pathogen Interactions ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {The Chinese white wax scale insect (Ericerus pela) is an economically valuable species with an important role in wax production. Recently, in a greenhouse in Kunming, we identified a genus of fungus that infects and kills E. pela females. This study sought to perform the molecular detection of entomopathogens and analyze the changes in the host microbiota after entomopathogen infection. We used library construction, high-throughput sequencing and real-time quantitative polymerase chain reaction (RT-qPCR) to identify the fungi infecting adult E. pela, to understand the changes in the host organism, and to determine the distribution of the entomopathogens. Cladosporium langeronii and C. sphaerospermum were the main pathogenic species that infected the E. pela females, and they were most prevalent in the dorsal cuticle. In vivo, after infection, the proportion of Cladosporium clearly increased. The infection had little influence on the fungal community but had a strong influence on the bacterial community. After infection, Arsenophonus was dominant, and numerous bacterial genera disappeared. However, Rickettsia, instead of Arsenophonus, became dominant in the Cladosporium-infected individuals that had also been infected with Rickettsia. We identified the species that infected E. pela females and determined the influence of infection on the host microorganisms.}, }
@article {pmid29593299, year = {2018}, author = {Wang, X and Wang, Z and Jiang, P and He, Y and Mu, Y and Lv, X and Zhuang, L}, title = {Bacterial diversity and community structure in the rhizosphere of four Ferula species.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5345}, pmid = {29593299}, issn = {2045-2322}, mesh = {*Bacteria/classification ; *Biodiversity ; Ferula/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The medicinal value of the Ferula L. has been recognized for more than a thousand years. Wild stocks of Ferula have declined dramatically because high economic value has led to overharvesting. The objective of this study was to compare the rhizosphere microbial community of four Ferula species [F. syreitschikowii K.-Pol., F. gracilis (Ledeb.) Ledeb., F. ferulaeoides (Steud.) Korov., and F. lehmannii Boiss.] in the northern part of Xinjiang, China. The 16S rRNA sequences of rhizosphere bacteria were obtained with an Illumina paired-end sequence platform. Analysis was conducted to determine the richness and diversity of the rhizosphere bacterial communities. Two-way ANOVA indicated that plant species and soil depth had no significant effect on the alpha diversity of rhizobacteria. Linear discriminant analysis effect size showed that F. lehmannii followed by F. ferulaeoides had the most biomarkers and the highest taxon level, F. syreitschikowii and F. gracilis the least, while F. syreitschikowii and F. gracilis had the least property. This trend is consistent with reports that the medicinal value of F. lehmannii and F. ferulaeoides is greater than that of F. gracilis and F. syreitschikowii. The results of this study provide information that could be used for the commercial cultivation of Ferula spp.}, }
@article {pmid29293174, year = {2018}, author = {Ikeda, M and Shimizu, K and Ogura, H and Kurakawa, T and Umemoto, E and Motooka, D and Nakamura, S and Ichimaru, N and Takeda, K and Takahara, S and Hirano, SI and Shimazu, T}, title = {Hydrogen-Rich Saline Regulates Intestinal Barrier Dysfunction, Dysbiosis, and Bacterial Translocation in a Murine Model of Sepsis.}, journal = {Shock (Augusta, Ga.)}, volume = {50}, number = {6}, pages = {640-647}, doi = {10.1097/SHK.0000000000001098}, pmid = {29293174}, issn = {1540-0514}, mesh = {Animals ; Bacterial Translocation/drug effects ; Disease Models, Animal ; Dysbiosis/*metabolism ; Enterobacteriaceae/genetics ; Hydrogen/pharmacology ; Intestinal Mucosa/*metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota/drug effects/genetics ; Oxidative Stress/drug effects/genetics ; RNA, Messenger/genetics ; RNA, Ribosomal, 16S/genetics ; Sepsis ; Tight Junction Proteins/genetics/metabolism ; }, abstract = {Bacterial translocation is a major cause of multiple organ dysfunction syndrome in critical illness, and its management is an important therapeutic strategy. In this study, we focused on the key factors responsible for bacterial translocation including the intestinal microbiome and investigated the impact of molecular hydrogen therapy as a countermeasure against bacterial translocation in a murine model of sepsis. The experimental protocols were divided into the sham, saline treatment (control), and hydrogen treatment (H2) groups. In the H2 group, 15 mL/kg of hydrogen-rich saline (7 ppm) was gavaged daily for 7 days following cecal ligation and puncture (CLP). In the control group, normal saline was gavaged in the same way. In the results, the 7-day survival rate was significantly improved in the H2 group versus the control group (69% vs. 31%, P < 0.05). The incidence of bacterial translocation at 24 h after CLP as assessed by cultivation of mesenteric lymph nodes and blood was significantly decreased in the H2 group versus the control group. Administration of hydrogen-rich saline also prevented the expansion of facultative anaerobic Enterobacteriaceae and ameliorated intestinal hyperpermeability at 24 h after CLP. Intestinal tissue levels of inflammatory mediators such as inducible nitric oxide synthases, tumor necrosis factor α, interleukin (IL)-1β, IL-6, and oxidative stress marker malondialdehyde at 6 h after CLP were down-regulated in the H2 group. These results suggest luminal administration of hydrogen-rich saline, which prevents intestinal dysbiosis, hyperpermeability, and bacterial translocation, could potentially be a new therapeutic strategy in critical illness.}, }
@article {pmid29192012, year = {2018}, author = {Zalewski, S and Stewart, CJ and Embleton, ND and Berrington, JE}, title = {Brief guide to the analysis, interpretation and presentation of microbiota data.}, journal = {Archives of disease in childhood. Education and practice edition}, volume = {103}, number = {6}, pages = {327-330}, doi = {10.1136/archdischild-2017-313838}, pmid = {29192012}, issn = {1743-0593}, mesh = {Computational Biology/*methods ; Humans ; *Microbiota ; }, }
@article {pmid31576426, year = {2019}, author = {Long, Y and Jiang, J and Hu, X and Zhou, J and Hu, J and Zhou, S}, title = {Actinobacterial community in Shuanghe Cave using culture-dependent and -independent approaches.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {10}, pages = {153}, doi = {10.1007/s11274-019-2713-y}, pmid = {31576426}, issn = {1573-0972}, support = {2016YFC0400702//National Key R&amp;D Program of China/ ; }, abstract = {Karst caves, considering to be the &quot;arks&quot; of biodiversity, often contain high levels of endemism. In the present study, the actinobacterial community in Shuanghe Cave, the longest cave in Asia, was analyzed for the first-time using culture-dependent and -independent (16S rRNA amplicon sequencing) approaches. The amplicon sequencing analysis revealed a broad taxonomic diversity in Shuanghe Cave, including 19 phyla (predominantly Actinobacteria) and 264 different genera. While the culture-dependent method got the unrepresentative but supplemental result, a total of 239 actinomycetes were isolated and were identified to seven genera based on culture features and 16S rRNA tests. Among the three habitats (soil, rock soil, and bat guano), the dominant phyla did not differ significantly, while the dominant genus community varied among different habitats, and the richness in soil and rock soil samples was higher than that in bat guano. Furthermore, 16 isolate strains showed antimicrobial activity, especially, the strain S142 (Streptomyces badius) and S761 (Actinoplanes friuliensis) exhibited the most promising activity against various pathogens. Overall, this work showed the abundant bacterial diversity and the antimicrobial potential of the isolates from the Shuanghe Cave.}, }
@article {pmid31561274, year = {2019}, author = {Bergner, LM and Orton, RJ and Benavides, JA and Becker, DJ and Tello, C and Biek, R and Streicker, DG}, title = {Demographic and environmental drivers of metagenomic viral diversity in vampire bats.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15250}, pmid = {31561274}, issn = {1365-294X}, abstract = {Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. We test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities which was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile-biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities.}, }
@article {pmid31546776, year = {2019}, author = {Hickl, O and Heintz-Buschart, A and Trautwein-Schult, A and Hercog, R and Bork, P and Wilmes, P and Becher, D}, title = {Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome.}, journal = {Microorganisms}, volume = {7}, number = {9}, pages = {}, doi = {10.3390/microorganisms7090367}, pmid = {31546776}, issn = {2076-2607}, support = {C15/BN/10404093//Fonds National de la Recherche Luxembourg/ ; FZT118//Deutsche Forschungsgemeinschaft/ ; }, abstract = {With the technological advances of the last decade, it is now feasible to analyze microbiome samples, such as human stool specimens, using multi-omic techniques. Given the inherent sample complexity, there exists a need for sample methods which preserve as much information as possible about the biological system at the time of sampling. Here, we analyzed human stool samples preserved and stored using different methods, applying metagenomics as well as metaproteomics. Our results demonstrate that sample preservation and storage have a significant effect on the taxonomic composition of identified proteins. The overall identification rates, as well as the proportion of proteins from Actinobacteria were much higher when samples were flash frozen. Preservation in RNAlater overall led to fewer protein identifications and a considerable increase in the share of Bacteroidetes, as well as Proteobacteria. Additionally, a decrease in the share of metabolism-related proteins and an increase of the relative amount of proteins involved in the processing of genetic information was observed for RNAlater-stored samples. This suggests that great care should be taken in choosing methods for the preservation and storage of microbiome samples, as well as in comparing the results of analyses using different sampling and storage methods. Flash freezing and subsequent storage at -80 °C should be chosen wherever possible.}, }
@article {pmid31545802, year = {2019}, author = {Guirro, M and Costa, A and Gual-Grau, A and Herrero, P and Torrell, H and Canela, N and Arola, L}, title = {Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: A multiomics approach.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0218143}, doi = {10.1371/journal.pone.0218143}, pmid = {31545802}, issn = {1932-6203}, abstract = {Obesity and its comorbidities are currently considered an epidemic, and the involved pathophysiology is well studied. Hypercaloric diets are tightly related to the obesity etiology and also cause alterations in gut microbiota functionality. Diet and antibiotics are known to play crucial roles in changes in the microbiota ecosystem and the disruption of its balance; therefore, the manipulation of gut microbiota may represent an accurate strategy to understand its relationship with obesity caused by diet. Fecal microbiota transplantation, during which fecal microbiota from a healthy donor is transplanted to an obese subject, has aroused interest as an effective approach for the treatment of obesity. To determine its success, a multiomics approach was used that combined metagenomics and metaproteomics to study microbiota composition and function. To do this, a study was performed in rats that evaluated the effect of a hypercaloric diet on the gut microbiota, and this was combined with antibiotic treatment to deplete the microbiota before fecal microbiota transplantation to verify its effects on gut microbiota-host homeostasis. Our results showed that a high-fat diet induces changes in microbiota biodiversity and alters its function in the host. Moreover, we found that antibiotics depleted the microbiota enough to reduce its bacterial content. Finally, we assessed the use of fecal microbiota transplantation as a complementary obesity therapy, and we found that it reversed the effects of antibiotics and reestablished the microbiota balance, which restored normal functioning and alleviated microbiota disruption. This new approach could be implemented to support the dietary and healthy habits recommended as a first option to maintain the homeostasis of the microbiota.}, }
@article {pmid31539947, year = {2019}, author = {Yadav, S and Kapley, A}, title = {Exploration of activated sludge resistome using metagenomics.}, journal = {The Science of the total environment}, volume = {692}, number = {}, pages = {1155-1164}, doi = {10.1016/j.scitotenv.2019.07.267}, pmid = {31539947}, issn = {1879-1026}, abstract = {Antibiotic resistance is a global problem. In India poor waste management and inadequate sanitary are key factors which encourage the dissemination of antimicrobial resistance. Microbial biodiversity serves as an invaluable source for diverse types of bioactive compounds that encompass most of the pharmaceuticals to date. Therefore, in this study, we used the metagenomic approach for the surveillance of antibiotic resistance genes, drug resistant microbes and mobile-genetic elements in two activated sludge metagenome samples collected from Ankleshwar, Gujarat, India. Proteobacteria were found to be the most abundant bacteria among the metagenome analyzed. Twenty-four genes conferring resistance to antibiotics and heavy metals were found. Multidrug resistant &quot;ESKAPE pathogens&quot; were also abundant in the sludge metagenome. Mobile genetic elements like IncP-1 plasmid pKJK5, IncP-1beta multi resistance plasmid and pB8 were also noticed in the higher abundance. These plasmids play an important role in the spread of antibiotic resistance by the horizontal gene transfer. Statistical analysis of both metagenome using STAMP software confirmed presence of mobile genetic elements such as gene transfer agents, phages, Prophages etc. which also play important role in the dissemination of antibiotic resistant genes.}, }
@article {pmid31507563, year = {2019}, author = {Liang, Y and Wang, L and Wang, Z and Zhao, J and Yang, Q and Wang, M and Yang, K and Zhang, L and Jiao, N and Zhang, Y}, title = {Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1951}, doi = {10.3389/fmicb.2019.01951}, pmid = {31507563}, issn = {1664-302X}, abstract = {A metagenomic analysis of the viral community from five surface and five deep sea water (>2000 m below the surface, mbs) samples collected from the central basin of the South China Sea and adjacent Northwest Pacific Ocean during July-August 2017 was conducted herein. We builded up a South China Sea DNA virome (SCSV) dataset of 29,967 viral Operational Taxonomic Units (vOTUs), which is comparable to the viral populations from the original Tara Ocean and Malaspina expeditions. The most abundant and widespread viral populations were from the uncultivated viruses annotated from the viral metagenomics. Only 74 and 37 vOTUs have similarity with the reported genomes from the cultivated viruses and the single-virus genomics, respectively. The community structures of deep sea viromes in the SCSV were generally different from the surface viromes. The carbon flux and nutrients (PO4 and NOx) were related to the surface and deep sea viromes in the SCSV, respectively. In the SCSV, the annotated vOTUs could be affiliated to the cultivated viruses mainly including Pelagibacter (SAR11) phage HTVC010P, Prochlorococcus phages (P-GSP1, P-SSM4, and P-TIM68), Cyanophages (MED4-184 and MED4-117) and Mycobacterium phages (Sparky and Squirty). It indicated that phage infection to the SAR11 cluster may occur ubiquitously and has significant impacts on bathypelagic SAR11 communities in the deep sea. Meanwhile, as Prochlorococcus is prominently distributed in the euphotic ocean, the existence of their potential phages in the deep sea suggested the sedimentation mechanism might contribute to the formation of the deep sea viromes. Intriguingly, the presence of Mycobacterium phages only in the deep sea viromes, suggests inhabitance of endemic viral populations in the deep sea viromes in the SCSV. This study provided an insight of the viral community in the South China Sea and for the first time uncovered the deep sea viral diversity in the central basin of the South China Sea.}, }
@article {pmid31465735, year = {2019}, author = {Guadagnini, D and Rocha, GZ and Santos, A and Assalin, HB and Hirabara, SM and Curi, R and Oliveira, AG and Prada, PO and Saad, MJA}, title = {Microbiota determines insulin sensitivity in TLR2-KO mice.}, journal = {Life sciences}, volume = {234}, number = {}, pages = {116793}, doi = {10.1016/j.lfs.2019.116793}, pmid = {31465735}, issn = {1879-0631}, mesh = {Animals ; Endoplasmic Reticulum Stress ; *Gastrointestinal Microbiome ; Gene Deletion ; Glucose Intolerance/genetics/metabolism/microbiology ; Housing, Animal ; Insulin/*metabolism ; *Insulin Resistance/genetics ; Male ; Mice, Inbred C57BL ; Mice, Knockout ; Toll-Like Receptor 2/*genetics/metabolism ; }, abstract = {INTRODUCTION: Environmental factors have a key role in the control of gut microbiota and obesity. TLR2 knockout (TLR2-/-) mice in some housing conditions are protected from diet-induced insulin resistance. However, in our housing conditions these animals are not protected from diet-induced insulin-resistance.<br><br>AIM: The aim of the present study was to investigate the influence of our animal housing conditions on the gut microbiota, glucose tolerance and insulin sensitivity in TLR2-/- mice.<br><br>MATERIAL AND METHODS: The microbiota was investigated by metagenomics, associated with hyperinsulinemic euglycemic clamp and GTT associated with insulin signaling through immunoblotting.<br><br>RESULTS: The results showed that TLR2-/- mice in our housing conditions presented a phenotype of metabolic syndrome characterized by insulin resistance, glucose intolerance and increase in body weight. This phenotype was associated with differences in microbiota in TLR2-/- mice that showed a decrease in the Proteobacteria and Bacteroidetes phyla and an increase in the Firmicutesphylum, associated with and in increase in the Oscillospira and Ruminococcus genera. Furthermore there is also an increase in circulating LPS and subclinical inflammation in TLR2-/-. The molecular mechanism that account for insulin resistance was an activation of TLR4, associated with ER stress and JNK activation. The phenotype and metabolic behavior was reversed by antibiotic treatment and reproduced in WT mice by microbiota transplantation.<br><br>CONCLUSIONS: Our data show, for the first time, that the intestinal microbiota can induce insulin resistance and obesity in an animal model that is genetically protected from these processes.}, }
@article {pmid31464899, year = {2019}, author = {Liang, W and Yang, Y and Wang, H and Wang, H and Yu, X and Lu, Y and Shen, S and Teng, L}, title = {Gut microbiota shifts in patients with gastric cancer in perioperative period.}, journal = {Medicine}, volume = {98}, number = {35}, pages = {e16626}, doi = {10.1097/MD.0000000000016626}, pmid = {31464899}, issn = {1536-5964}, mesh = {Adult ; Bacteria/*classification/genetics/isolation &amp; purification ; China ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Gastrectomy ; Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Perioperative Period ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Stomach Neoplasms/microbiology/*surgery ; }, abstract = {Gastric cancer (GC) is one of the common malignant tumors in China, with a high morbidity and mortality. With the development and application of high-throughput sequencing technologies and metagenomics, a great quantity of studies have shown that gastrointestinal microbiota is closely related to digestive system diseases. Although some studies have reported the effect of long-term follow-up after subtotal gastrectomy on intestinal flora changes in patients with GC. However, the features of gut microbiota and their shifts in patients with GC in perioperative period remain unclear.This study was designed to characterize fecal microbiota shifts of the patients with GC before and after the radical distal gastrectomy (RDG) during their hospital staying periods. Furthermore, fecal microbiota was also compared between the GC patients and healthy individuals.Patients who were diagnosed with advanced gastric adenocarcinoma at distal stomach were enrolled in the study. The bacterial burden within fecal samples was determined using quantitative polymerase chain reaction. To analyze the diversity and composition of gut microbiota from fecal DNA of 20 GC patients and 22 healthy controls, amplicons of the 16S rRNA gene from all subjects were pyrosequenced. To study gut microbiota shifts, the fecal microbiota from 6 GC patients before and after RDG was detected and subsequently analyzed. Short-chain fatty acids were also detected by chromatography spectrometer in these 6 GC patients.RDG had a moderate effect on bacterial richness and evenness, but had pronounced effects on the composition of postoperative gut microbiota compared with preoperative group. The relative abundances of genera Akkermansia, Esherichia/Shigella, Lactobacillus, and Dialister were significant changed in perioperative period. Remarkably, higher abundances of Escherichia/Shigella, Veillonella, and Clostridium XVIII and lower abundances of Bacteroides were observed in gut microbiota of overall GC patients compared to healthy controls.This study is the first study to characterize the altered gut microbiota within fecal samples from GC patients during perioperative period, and provide a new insights on such microbial perturbations as a potential effector of perioperative period phenotype. Further research must validate these discoveries and may evaluate targeted microbiota shifts to improve outcomes in GC patients.}, }
@article {pmid31448249, year = {2019}, author = {Pini Prato, A and Bartow-McKenney, C and Hudspeth, K and Mosconi, M and Rossi, V and Avanzini, S and Faticato, MG and Ceccherini, I and Lantieri, F and Mattioli, G and Larson, D and Pavan, W and De Filippo, C and Di Paola, M and Mavilio, D and Cavalieri, D}, title = {A Metagenomics Study on Hirschsprung's Disease Associated Enterocolitis: Biodiversity and Gut Microbial Homeostasis Depend on Resection Length and Patient's Clinical History.}, journal = {Frontiers in pediatrics}, volume = {7}, number = {}, pages = {326}, doi = {10.3389/fped.2019.00326}, pmid = {31448249}, issn = {2296-2360}, abstract = {Objectives: Since 2010, several researches demonstrated that microbiota dynamics correlate and can even predispose to Hirschsprung (HSCR) associated enterocolitis (HAEC). This study aims at assessing the structure of the microbiota of HSCR patients in relation to extent of aganglionosis and HAEC status. Methods: All consecutive HSCR patients admitted to Gaslini Institute (Genova, Italy) between May 2012 and November 2014 were enrolled. Institutional review board (IRB) approval was obtained. Stools were sampled and 16S rDNA V3-V4 regions were sequenced using the Illumina-MiSeq. Taxonomy assignments were performed using QIIME RDP. Alpha diversity indexes were analyzed by Shannon and Simpson Indexes, and Phylogenetic Diversity. Results: We enrolled 20 patients. Male to female ratio was 4:1. Six patients suffered from Total Colonic Aganglionosis (TCSA). Considering sample site (i.e., extent of aganglionosis), we confirmed the known relationship between sample site and both biodiversity and composition of intestinal microbiota. Patients with TCSA showed lower biodiversity and increased Proteobacteria/Bacteroidetes relative abundance ratio. When addressing biodiversity, composition and dynamics of TCSA patients we could not find any significant relationship with regard to HAEC occurrences. Conclusions: The composition of HAEC predisposing microbiota is specific to each patient. We could confirm that total colon resections can change the composition of intestinal microbiota and to dramatically reduce microbial diversity. The subsequent reduction of system robustness could expose TCSA patients to environmental microbes that might not be part of the normal microbiota. Future long-term studies should investigate both patients and their family environment, as well as their disease history.}, }
@article {pmid31448147, year = {2019}, author = {Wu, B and Hussain, M and Zhang, W and Stadler, M and Liu, X and Xiang, M}, title = {Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi.}, journal = {Mycology}, volume = {10}, number = {3}, pages = {127-140}, doi = {10.1080/21501203.2019.1614106}, pmid = {31448147}, issn = {2150-1203}, abstract = {The global bio-diversity of fungi has been extensively investigated and their species number has been estimated. Notably, the development of molecular phylogeny has revealed an unexpected fungal diversity and utilisation of culture-independent approaches including high-throughput amplicon sequencing has dramatically increased number of fungal operational taxonomic units. A number of novel taxa including new divisions, classes, orders and new families have been established in last decade. Many cryptic species were identified by molecular phylogeny. Based on recently generated data from culture-dependent and -independent survey on same samples, the fungal species on the earth were estimated to be 12 (11.7-13.2) million compared to 2.2-3.8 million species recently estimated by a variety of the estimation techniques. Moreover, it has been speculated that the current use of high-throughput sequencing techniques would reveal an even higher diversity than our current estimation. Recently, the formal classification of environmental sequences and permission of DNA sequence data as fungal names' type were proposed but strongly objected by the mycologist community. Surveys on fungi in unusual niches have indicated that many previously regarded &quot;unculturable fungi&quot; could be cultured on certain substrates under specific conditions. Moreover, the high-throughput amplicon sequencing, shotgun metagenomics and a single-cell genomics could be a powerful means to detect novel taxa. Here, we propose to separate the fungal types into physical type based on specimen, genome DNA (gDNA) type based on complete genome sequence of culturable and uncluturable fungal specimen and digital type based on environmental DNA sequence data. The physical and gDNA type should have priority, while the digital type can be temporal supplementary before the physical type and gDNA type being available. The fungal name based on the &quot;digital type&quot; could be assigned as the &quot;clade&quot; name + species name. The &quot;clade&quot; name could be the name of genus, family or order, etc. which the sequence of digital type affiliates to. Facilitating future cultivation efforts should be encouraged. Also, with the advancement in knowledge of fungi inhabiting various environments mostly because of rapid development of new detection technologies, more information should be expected for fungal diversity on our planet.}, }
@article {pmid31444199, year = {2019}, author = {Loit, K and Adamson, K and Bahram, M and Puusepp, R and Anslan, S and Kiiker, R and Drenkhan, R and Tedersoo, L}, title = {Relative Performance of MinION (Oxford Nanopore Technologies) vs. Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01368-19}, pmid = {31444199}, issn = {1098-5336}, abstract = {Culture-based molecular identification methods have revolutionized detection of pathogens, yet these methods are slow and may yield inconclusive results from environmental materials. The second-generation sequencing tools have much improved precision and sensitivity of detection, but these analyses are costly and may take several days to months. Of the third-generation sequencing techniques, the portable MinION device (Oxford Nanopore Technologies) has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performance of two third-generation sequencing instruments, MinION and Sequel (Pacific Biosciences) in identification and diagnostics of fungal and oomycete pathogens from conifer (Pinaceae spp.) needles and potato (Solanum tuberosum) leaves and tubers. We demonstrate that Sequel instrument is efficient for metabarcoding of complex samples, whereas MinION is not suited for this purpose due to the high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms and other associated organisms from plant tissues following both amplicon-based and PCR-free metagenomics approaches. Using the metagenomics approach with shortened DNA extraction and incubation times, we performed the entire MinION workflow from sample preparation through DNA extraction, sequencing, bioinformatics and interpretation in two and half hours. We advocate the use of MinION for rapid diagnostics of pathogens and potentially other organisms, but care needs to be taken to control or account for multiple potential technical biases.IMPORTANCE Microbial pathogens cause enormous losses to agriculture and forestry, but current combined culturing- and molecular identification-based detection methods are too slow for rapid identification and application of countermeasures. Here we develop new and rapid protocols for Oxford Nanopore MinION-based third-generation diagnostics of plant pathogens that greatly improves the speed of diagnostics. However, due to high error rate and technical biases in MinION, the Pacific BioSciences Sequel platform is more useful for in-depth amplicon-based biodiversity monitoring (metabarcoding) from complex environmental samples.}, }
@article {pmid31438955, year = {2019}, author = {Vavourakis, CD and Mehrshad, M and Balkema, C and van Hall, R and Andrei, AŞ and Ghai, R and Sorokin, DY and Muyzer, G}, title = {Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {69}, doi = {10.1186/s12915-019-0688-7}, pmid = {31438955}, issn = {1741-7007}, support = {322551/ERC_/European Research Council/International ; 322551/ERC_/European Research Council/International ; 322551/ERC_/European Research Council/International ; L200961651//Czech Academy of Sciences/ ; MSM200961801//Czech Academy of Sciences/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 24002002//SYAM-Gravitation Program/ ; RFBR 19-04-00401//Russian Foundation for Basic Research/ ; }, abstract = {BACKGROUND: The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions.<br><br>RESULTS: Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the &quot;Candidatus Woesearchaeota.&quot; Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes.<br><br>CONCLUSIONS: The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.}, }
@article {pmid31376000, year = {2019}, author = {Cowan, DA and Hopkins, DW and Jones, BE and Maggs-Kölling, G and Majewska, R and Ramond, JB}, title = {Microbiomics of Namib Desert habitats.}, journal = {Extremophiles : life under extreme conditions}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00792-019-01122-7}, pmid = {31376000}, issn = {1433-4909}, abstract = {The Namib Desert is one of the world's only truly coastal desert ecosystem. Until the end of the 1st decade of the twenty-first century, very little was known of the microbiology of this southwestern African desert, with the few reported studies being based solely on culture-dependent approaches. However, from 2010, an intense research program was undertaken by researchers from the University of the Western Cape Institute for Microbial Biotechnology and Metagenomics, and subsequently the University of Pretoria Centre for Microbial Ecology and Genomics, and their collaborators, led to a more detailed understanding of the ecology of the indigenous microbial communities in many Namib Desert biotopes. Namib Desert soils and the associated specialized niche communities are inhabited by a wide array of prokaryotic, lower eukaryotic and virus/phage taxa. These communities are highly heterogeneous on both small and large spatial scales, with community composition impacted by a range of macro- and micro-environmental factors, from water regime to soil particle size. Community functionality is also surprisingly non-homogeneous, with some taxa retaining functionality even under hyper-arid soil conditions, and with subtle changes in gene expression and phylotype abundances even on diel timescales. Despite the growing understanding of the structure and function of Namib Desert microbiomes, there remain enormous gaps in our knowledge. We have yet to quantify many of the processes in these soil communities, from regional nutrient cycling to community growth rates. Despite the progress that has been made, we still have little knowledge of either the role of phages in microbial community dynamics or inter-species interactions. Furthermore, the intense research efforts of the past decade have highlighted the immense scope for future microbiological research in this dynamic, enigmatic and charismatic region of Africa.}, }
@article {pmid31365065, year = {2019}, author = {Sutela, S and Poimala, A and Vainio, EJ}, title = {Viruses of fungi and oomycetes in the soil environment.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {9}, pages = {}, doi = {10.1093/femsec/fiz119}, pmid = {31365065}, issn = {1574-6941}, abstract = {Soils support a myriad of organisms hosting highly diverse viromes. In this minireview, we focus on viruses hosted by true fungi and oomycetes (members of Stamenopila, Chromalveolata) inhabiting bulk soil, rhizosphere and litter layer, and representing different ecological guilds, including fungal saprotrophs, mycorrhizal fungi, mutualistic endophytes and pathogens. Viruses infecting fungi and oomycetes are characterized by persistent intracellular nonlytic lifestyles and transmission via spores and/or hyphal contacts. Almost all fungal and oomycete viruses have genomes composed of single-stranded or double-stranded RNA, and recent studies have revealed numerous novel viruses representing yet unclassified family-level groups. Depending on the virus-host combination, infections can be asymptomatic, beneficial or detrimental to the host. Thus, mycovirus infections may contribute to the multiplex interactions of hosts, therefore likely affecting the dynamics of fungal communities required for the functioning of soil ecosystems. However, the effects of fungal and oomycete viruses on soil ecological processes are still mostly unknown. Interestingly, new metagenomics data suggest an extensive level of horizontal virus transfer between plants, fungi and insects.}, }
@article {pmid31354669, year = {2019}, author = {Raimondi, S and Amaretti, A and Gozzoli, C and Simone, M and Righini, L and Candeliere, F and Brun, P and Ardizzoni, A and Colombari, B and Paulone, S and Castagliuolo, I and Cavalieri, D and Blasi, E and Rossi, M and Peppoloni, S}, title = {Longitudinal Survey of Fungi in the Human Gut: ITS Profiling, Phenotyping, and Colonization.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1575}, doi = {10.3389/fmicb.2019.01575}, pmid = {31354669}, issn = {1664-302X}, abstract = {The fungal component of the intestinal microbiota of eight healthy subjects was studied over 12 months using metagenome survey and culture-based approaches. Aspergillus, Candida, Debaryomyces, Malassezia, Penicillium, Pichia, and Saccharomyces were the most recurrent and/or dominant fungal genera, according to metagenomic analysis. The biodiversity of fungal communities was lower and characterized by greater unevenness, when compared to bacterial microbiome. The dissimilarities both among subjects and over the time within the same subject suggested that most of the fungi passed through the gastro-intestinal tract (GIT) without becoming stable colonizers. Certain genera, such as Aspergillus and Penicillium, were isolated in a minority of cases, although they recurred abundantly and frequently in the metagenomics survey, likely being environmental or food-borne fungi that do not inhabit the GIT. Candida genus was recurrently detected. Candida albicans isolates dominated among the cultivable mycobiota and longitudinally persisted, likely as commensals inhabiting the intestine or regularly reaching it from Candida-colonized districts, such as the oral cavity. Other putative colonizers belonged to Candida zeylanoides, Geotrichum candidum, and Rhodotorula mucilaginosa, with persisting biotypes being identified. Phenotyping of fungal isolates indicated that C. albicans adhered to human epithelial cells more efficiently and produced greater amounts of biofilm in vitro than non-albicans Candida (NAC) and non-Candida fungi (NCF). The C. albicans isolates also induced the highest release of HBD-2 by human epithelial cells, further differing from NAC and NCF. Nine representative isolates were administered to mice to evaluate the ability to colonize the intestine. Only two out of three C. albicans strains persisted in stools of animals 2 weeks after the end of the oral administration, whereas NAC and NCF did not. These results confirm the allochthonous nature of most the intestinal fungi, while C. albicans appears to be commonly involved in stable colonization. A combination of specific genetic features in the microbe and in the host likely allow colonization from fungi normally present solely as passengers. It remains to be established if other species identified as potential colonizers, in addition to Candida, are true inhabitants of the GIT or rather reach the intestine spreading from other body districts.}, }
@article {pmid31338073, year = {2019}, author = {Praeg, N and Pauli, H and Illmer, P}, title = {Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1429}, doi = {10.3389/fmicb.2019.01429}, pmid = {31338073}, issn = {1664-302X}, abstract = {Serving as &quot;natural laboratories&quot;, altitudinal gradients can be used to study changes in the distribution of microorganisms in response to changing environmental conditions that typically occur over short geographical distances. Besides, rhizosphere zones of plants are known to be hot-spots for microbial diversity and to contain different microbial communities when compared with surrounding bulk soil. To discriminate the effects of altitude and plants, we investigated the microbial communities in the rhizosphere of Ranunculus glacialis and bulk soil along a high-alpine altitudinal gradient (2,600-3,400 m a.s.l.). The research area of this study was Mount (Mt.) &quot;Schrankogel&quot; in the Central Alps of Tyrol (Austria). Our results point to significantly different microbial diversities and community compositions in the different altitudinal belts. In the case of prokaryotes, environmental parameters could explain 41% of the total variation of soil communities, with pH and temperature being the strongest influencing factors. Comparing the effects derived from fraction (bulk vs. rhizosphere soil) and environmental factors, the effects of the roots of R. glacialis accounted for about one third of the explained variation. Fungal communities on the other hand were nearly exclusively influenced by environmental parameters accounting for 37.4% of the total variation. Both, for altitudinal zones as well as for bulk and rhizosphere fractions a couple of very specific biomarker taxa could be identified. Generally, the patterns of abundance of several taxa did not follow a steady increased or decreased trend along the altitudinal gradient but in many cases a maximal or minimal occurrence was established at mid-altitudes (3,000-3,100 m). This mid-altitudinal zone is a transition zone (the so-called alpine-nival ecotone) between the (lower) alpine grassland/tundra zone and the (upper) sparsely vegetated nival zone and was shown to correspond with the summer snow line. Climate change and the associated increase in temperature will shift this transition zone and thus, might also shift the described microbial patterns and biomarkers.}, }
@article {pmid31333598, year = {2019}, author = {Thomas, SC and Tamadonfar, KO and Seymour, CO and Lai, D and Dodsworth, JA and Murugapiran, SK and Eloe-Fadrosh, EA and Dijkstra, P and Hedlund, BP}, title = {Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1427}, doi = {10.3389/fmicb.2019.01427}, pmid = {31333598}, issn = {1664-302X}, abstract = {Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with 13C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60-95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across the temperature gradient and many individual metagenome-assembled genomes had complete pathways. In contrast, genes encoding cellulosomes and many genes involved in plant matter degradation and photosynthesis were absent at higher temperatures. In situ13C-CO2 production from labeled isotopomer pairs of glucose, pyruvate, and acetate suggested lower relative oxidative pentose phosphate pathway activity and/or fermentation at 60°C, and a stable or decreased maintenance energy demand at higher temperatures. Catabolism of 13C-labeled citrate, succinate, L-alanine, L-serine, and L-cysteine was observed at 85°C, demonstrating broad heterotrophic activity and confirming functioning of the TCA cycle. Together, these results suggest that temperature-driven losses in biodiversity and gene content in geothermal systems may not alter CCMP function or maintenance energy demands at a community level.}, }
@article {pmid31307536, year = {2019}, author = {Chen, J and McIlroy, SE and Archana, A and Baker, DM and Panagiotou, G}, title = {A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {104}, doi = {10.1186/s40168-019-0714-6}, pmid = {31307536}, issn = {2049-2618}, support = {2016-67//Environment and Conservation Fund/ ; }, abstract = {BACKGROUND: Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere.<br><br>RESULTS: Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants.<br><br>CONCLUSIONS: Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.}, }
@article {pmid31301473, year = {2019}, author = {Bengtsson-Palme, J and Milakovic, M and Švecová, H and Ganjto, M and Jonsson, V and Grabic, R and Udikovic-Kolic, N}, title = {Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.}, journal = {Water research}, volume = {162}, number = {}, pages = {437-445}, doi = {10.1016/j.watres.2019.06.073}, pmid = {31301473}, issn = {1879-2448}, abstract = {Antibiotic resistance is an emerging global health crisis, driven largely by overuse and misuse of antibiotics. However, there are examples in which the production of these antimicrobial agents has polluted the environment with active antibiotic residues, selecting for antibiotic resistant bacteria and the genes they carry. In this work, we have used shotgun metagenomics to investigate the taxonomic structure and resistance gene composition of sludge communities in a treatment plant in Croatia receiving wastewater from production of the macrolide antibiotic azithromycin. We found that the total abundance of antibiotic resistance genes was three times higher in sludge from the treatment plant receiving wastewater from pharmaceutical production than in municipal sludge from a sewage treatment plant in Zagreb. Surprisingly, macrolide resistance genes did not have higher abundances in the industrial sludge, but genes associated with mobile genetic elements such as integrons had. We conclude that at high concentrations of antibiotics, selection may favor taxonomic shifts towards intrinsically resistant species or strains harboring chromosomal resistance mutations rather than acquisition of mobile resistance determinants. Our results underscore the need for regulatory action also within Europe to avoid release of antibiotics into the environment.}, }
@article {pmid31293086, year = {2019}, author = {Ji, Y and Huotari, T and Roslin, T and Schmidt, NM and Wang, J and Yu, DW and Ovaskainen, O}, title = {SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13057}, pmid = {31293086}, issn = {1755-0998}, support = {31400470//National Natural Science Foundation of China/ ; 31500305//National Natural Science Foundation of China/ ; 31670536//National Natural Science Foundation of China/ ; 41661144002//National Natural Science Foundation of China/ ; 276909//Suomen Akatemia/ ; 284601//Suomen Akatemia/ ; 285803//Suomen Akatemia/ ; 309571//Suomen Akatemia/ ; //Jane and Aatos Erkko Foundation Grant/ ; 223257//Research Council of Norway through its Centres of Excellence Funding Scheme/ ; //Danish Environmental Protection Agency/ ; QYZDY-SSW-SMC024//Key Research Program of Frontier Sciences, CAS/ ; GJHZ1754//Bureau of International Cooperation/ ; XDA20050202//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2012FY110800//Ministry of Science and Technology of China/ ; GREKF18-04//State Key Laboratory of Genetic Resources and Evolution/ ; //Kunming Institute of Zoology/ ; //University of East Anglia/ ; //University of Chinese Academy of Sciences/ ; }, abstract = {The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 = .93, mitogenomes R2 = .95) and a high repeatability across environmental-sample replicates (barcodes R2 = .94, mitogenomes R2 = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities.}, }
@article {pmid31267680, year = {2019}, author = {Taubert, M and Grob, C and Crombie, A and Howat, AM and Burns, OJ and Weber, M and Lott, C and Kaster, AK and Vollmers, J and Jehmlich, N and von Bergen, M and Chen, Y and Murrell, JC}, title = {Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy.}, journal = {Environmental microbiology}, volume = {21}, number = {10}, pages = {3780-3795}, doi = {10.1111/1462-2920.14728}, pmid = {31267680}, issn = {1462-2920}, support = {GBMF3303//Gordon and Betty Moore Foundation/ ; ECF2016-626//Leverhulme Trust/ ; }, abstract = {The release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the sediment-water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined with 13 C-methane stable isotope probing, demonstrated that various members of the gammaproteobacterial family Methylococcaceae were the key players for methane oxidation, catalysing the first reaction step to methanol. We observed a transfer of carbon to methanol-oxidizing methylotrophs of the betaproteobacterial family Methylophilaceae, suggesting an interaction between methanotrophic and methylotrophic microorganisms that allowed for rapid methane oxidation. From our microcosms, we estimated methane oxidation rates of up to 871 nmol of methane per gram sediment per day. This implies that more than 50% of methane at the seep is removed by microbial oxidation at the sediment-water interface, based on previously reported in situ methane fluxes. The organic carbon produced was further assimilated by different heterotrophic microbes, demonstrating that the methane-oxidizing community supported a complex trophic network. Our results provide valuable eco-physiological insights into this specialized microbial community performing an ecosystem function of global relevance.}, }
@article {pmid31266971, year = {2019}, author = {Fernández-Correa, I and Truchado, DA and Gomez-Lucia, E and Doménech, A and Pérez-Tris, J and Schmidt-Chanasit, J and Cadar, D and Benítez, L}, title = {A novel group of avian astroviruses from Neotropical passerine birds broaden the diversity and host range of Astroviridae.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9513}, doi = {10.1038/s41598-019-45889-3}, pmid = {31266971}, issn = {2045-2322}, support = {CGL2017-82117-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&amp;#x00F3;n (Spanish Agencia Estatal de Investigaci&amp;#x00F3;n)/ ; CGL2017-82117-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&amp;#x00F3;n (Spanish Agencia Estatal de Investigaci&amp;#x00F3;n)/ ; CT27/16-CT28/16//Universidad Complutense de Madrid (Complutense University of Madrid)/ ; }, abstract = {Metagenomics is helping to expand the known diversity of viruses, especially of those with poorly studied hosts in remote areas. The Neotropical region harbors a considerable diversity of avian species that may play a role as both host and short-distance vectors of unknown viruses. Viral metagenomics of cloacal swabs from 50 Neotropical birds collected in French Guiana revealed the presence of four complete astrovirus genomes. They constitute an early diverging novel monophyletic clade within the Avastrovirus phylogeny, representing a putative new astrovirus species (provisionally designated as Avastrovirus 5) according to the International Committee on Taxonomy of Viruses (ICTV) classification criteria. Their genomic organization shares some characteristics with Avastrovirus but also with Mamastrovirus. The pan-astrovirus RT-PCR analysis of the cloacal samples of 406 wild Neotropical birds showed a community-level prevalence of 4.9% (5.1% in passerines, the highest described so far in this order of birds). By screening birds of a remote region, we expanded the known host range of astroviruses to the avian families Cardinalidae, Conopophagidae, Furnariidae, Thamnophilidae, Turdidae and Tyrannidae. Our results provide important first insights into the unexplored viral communities, the ecology, epidemiology and features of host-pathogen interactions that shape the evolution of avastroviruses in a remote Neotropical rainforest.}, }
@article {pmid31264806, year = {2019}, author = {Pereira, O and Hochart, C and Auguet, JC and Debroas, D and Galand, PE}, title = {Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean.}, journal = {MicrobiologyOpen}, volume = {8}, number = {9}, pages = {e00852}, doi = {10.1002/mbo3.852}, pmid = {31264806}, issn = {2045-8827}, support = {ANR-14-CE02-0004-01//Agence Nationale de la Recherche/ ; }, abstract = {Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re-analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co-occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene-coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.}, }
@article {pmid31250597, year = {2019}, author = {Wang, L and Li, Z and Liu, R and Li, L and Wang, W}, title = {Bacterial Diversity in Soybean Rhizosphere Soil at Seedling and Mature Stages.}, journal = {Polish journal of microbiology}, volume = {68}, number = {2}, pages = {281-284}, doi = {10.33073/pjm-2019-023}, pmid = {31250597}, issn = {2544-4646}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biota ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Rhizosphere ; Seedlings/growth &amp; development/*microbiology ; *Soil Microbiology ; Soybeans/growth &amp; development/*microbiology ; }, abstract = {Changes in the structural diversity of bacterial communities in soybean rhizospheres play important roles in plant growth and crop productivity. However, there are only a few studies on different soybean growth stages. Here, we investigated the changes in the bacterial community of soybean rhizosphere soil at two stages using Illumina high-throughput sequencing. The results showed that the bacterial abundance and diversity in the seeding stage were higher than those in the mature stage and that the diversity changed significantly. Actinobacteria, Acidobacteria, and Proteobacteria were the dominant bacteria in the soybean rhizosphere soil. Additionally, changes in Actinobacteria and Proteobacteria abundances showed opposite trends.<br><br>Changes in the structural diversity of bacterial communities in soybean rhizospheres play important roles in plant growth and crop productivity. However, there are only a few studies on different soybean growth stages. Here, we investigated the changes in the bacterial community of soybean rhizosphere soil at two stages using Illumina high-throughput sequencing. The results showed that the bacterial abundance and diversity in the seeding stage were higher than those in the mature stage and that the diversity changed significantly. Actinobacteria, Acidobacteria, and Proteobacteria were the dominant bacteria in the soybean rhizosphere soil. Additionally, changes in Actinobacteria and Proteobacteria abundances showed opposite trends.}, }
@article {pmid31250077, year = {2019}, author = {Goss-Souza, D and Mendes, LW and Rodrigues, JLM and Tsai, SM}, title = {Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01401-y}, pmid = {31250077}, issn = {1432-184X}, support = {2008/58114-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 140317/2014-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.}, }
@article {pmid31243255, year = {2019}, author = {Tamaki, H}, title = {Cultivation Renaissance in the Post-Metagenomics Era: Combining the New and Old.}, journal = {Microbes and environments}, volume = {34}, number = {2}, pages = {117-120}, doi = {10.1264/jsme2.ME3402rh}, pmid = {31243255}, issn = {1347-4405}, mesh = {*Archaea/classification/genetics/growth &amp; development ; *Bacteria/classification/genetics/growth &amp; development ; Biodiversity ; Drug Resistance, Microbial ; *Fungi/classification/genetics/growth &amp; development ; Host Microbial Interactions ; Humans ; *Metagenomics ; Microbiological Techniques/*trends ; Microbiota/genetics ; }, }
@article {pmid31239159, year = {2019}, author = {Costa, M and Weese, JS}, title = {Methods and basic concepts for microbiota assessment.}, journal = {Veterinary journal (London, England : 1997)}, volume = {249}, number = {}, pages = {10-15}, doi = {10.1016/j.tvjl.2019.05.005}, pmid = {31239159}, issn = {1532-2971}, mesh = {Animals ; Bacteria/genetics ; Bacteriological Techniques/*veterinary ; DNA, Bacterial ; Host Microbial Interactions ; *Microbiota ; Sequence Analysis, DNA/veterinary ; }, abstract = {There has been a marked increase in interest regarding complex microbial populations in recent years. The methodology used for microbial assessment has drastically changed over the last two decades and continues to advance at a rapid pace. Culture-based studies have been superseded by those based upon molecular methods, which have been largely used to discover new species and to better characterize complex communities, mainly driven by the advances in DNA sequencing, termed 'next generation sequencing'. These methodologies have allowed for a better understanding of the relationship between hosts and their microbiotas, which have important roles in health maintenance and in the pathophysiology of wide ranging conditions such as obesity, diabetes, allergic diseases and even behavioural changes. While most widely used in humans, these approaches are now commonly used in veterinary research, with increasing interest in direct clinical applications. As these methods provide novel insights that will constitute the basis for the development of new therapeutic and prevention strategies, and as commercial efforts to offer microbiota assessment as a clinical tool expand, it is essential for researchers and clinical veterinarians to understand and have the tools to be able to interpret research performed in this new fascinating field. The objective of this review is to describe some of the most common methods for characterization of microbial communities and to provide an overview of the basic concepts necessary for good interpretation of the research performed in this field.}, }
@article {pmid31236844, year = {2019}, author = {Kunath, BJ and Minniti, G and Skaugen, M and Hagen, LH and Vaaje-Kolstad, G and Eijsink, VGH and Pope, PB and Arntzen, MØ}, title = {Metaproteomics: Sample Preparation and Methodological Considerations.}, journal = {Advances in experimental medicine and biology}, volume = {1073}, number = {}, pages = {187-215}, doi = {10.1007/978-3-030-12298-0_8}, pmid = {31236844}, issn = {0065-2598}, mesh = {*Metagenomics ; *Microbial Consortia ; Proteins ; *Proteomics ; Specimen Handling/*methods ; }, abstract = {Meta-omic techniques have progressed rapidly in the past decade and are frequently used in microbial ecology to study microorganisms in their natural ecosystems independent from culture restrictions. Metaproteomics, in combination with metagenomics, enables quantitative assessment of expressed proteins and pathways from individual members of the consortium. Together, metaproteomics and metagenomics can provide a detailed understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize nutrients, and these insights can be obtained directly from environmental samples. Here, we outline key aspects of sample preparation, database generation, and other methodological considerations that are required for successful quantitative metaproteomic analyses and we describe case studies on the integration with metagenomics for enhanced functional output.}, }
@article {pmid31236715, year = {2019}, author = {Joishy, TK and Dehingia, M and Khan, MR}, title = {Bacterial diversity and metabolite profiles of curd prepared by natural fermentation of raw milk and back sloping of boiled milk.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {7}, pages = {102}, doi = {10.1007/s11274-019-2677-y}, pmid = {31236715}, issn = {1573-0972}, support = {BT/550/NE/U-Excel/2014//Department of Biotechnology , Ministry of Science and Technology/ ; DST/INSPIRE Fellowship/2015/IF150782//Department of Science and Technology, Ministry of Science and Technology/ ; }, mesh = {Animals ; Bacteria/*isolation &amp; purification/metabolism ; *Biodiversity ; DNA, Bacterial/genetics/isolation &amp; purification ; Enterococcus/isolation &amp; purification/metabolism ; *Fermentation ; Food Handling ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; Lactobacillales ; Lactobacillus/isolation &amp; purification/metabolism ; Lactococcus/isolation &amp; purification/metabolism ; Leuconostoc/isolation &amp; purification/metabolism ; Metagenomics ; Milk/*microbiology ; Multivariate Analysis ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; }, abstract = {Preparation of curd vary worldwide due to which its taste, texture and impact on human health also differ. In Assam, curd prepared from raw milk (RMC) is preferred over curd prepared from boiled milk (BMC), a tradition believed to have originated from the Mongoloid customs. Microbial diversity of raw milk (RM), boiled milk (BM), RMC and BMC collected from three farms were investigated by culture dependent and independent techniques. Additionally, metabolite profiles of RMC and BMC were studied by gas chromatography and mass spectroscopy. A total of 59 bacterial isolates were identified from the four different dairy products. In RM, lactic acid bacteria such as Lactococcus, Enterococcus, Lactobacillus and Leuconostoc were obtained along with the environmental bacteria like Bacillus, Staphylococcus, Acetobacter, Chryseobacterium, Streptococcus, Acinetobacter, Kocuria, Klebsiella and Macrococcus. Additionally, Prevotella, Oscillospira, Phascolarctobacterium and Akkermansia were also detected in BM by culture independent technique. In RMC and BMC, Lactococcus, Leuconostoc and Lactobacillus were prevalent. RM and RMC shared Enterococcus, Lactococcus, Streptococcus and Acinetobacter as common bacterial genera. However, no bacterial genus was common in BM and BMC. The correlation analysis revealed that Lactobacillus was negatively correlated to other bacterial genera. Oligotyping analysis revealed that Lactobacillus brevis and L.fermentum were abundant in RMC and BMC, respectively. In metabolomic study, ascorbic acid, dodecanoic acid and hexadecanoic acid were found to be significantly higher in RMC. Presence of different types of probiotics in these curds samples opens a new avenue to understand their effects on human health.}, }
@article {pmid31216991, year = {2019}, author = {Lo, C and Marculescu, R}, title = {MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 12}, pages = {314}, doi = {10.1186/s12859-019-2833-2}, pmid = {31216991}, issn = {1471-2105}, mesh = {*Algorithms ; Area Under Curve ; Databases, Genetic ; Humans ; Machine Learning ; Metagenomics/*methods ; Microbiota/genetics ; Models, Theoretical ; *Neural Networks (Computer) ; Phenotype ; ROC Curve ; Support Vector Machine ; }, abstract = {BACKGROUND: Microbiome profiles in the human body and environment niches have become publicly available due to recent advances in high-throughput sequencing technologies. Indeed, recent studies have already identified different microbiome profiles in healthy and sick individuals for a variety of diseases; this suggests that the microbiome profile can be used as a diagnostic tool in identifying the disease states of an individual. However, the high-dimensional nature of metagenomic data poses a significant challenge to existing machine learning models. Consequently, to enable personalized treatments, an efficient framework that can accurately and robustly differentiate between healthy and sick microbiome profiles is needed.<br><br>RESULTS: In this paper, we propose MetaNN (i.e., classification of host phenotypes from Metagenomic data using Neural Networks), a neural network framework which utilizes a new data augmentation technique to mitigate the effects of data over-fitting.<br><br>CONCLUSIONS: We show that MetaNN outperforms existing state-of-the-art models in terms of classification accuracy for both synthetic and real metagenomic data. These results pave the way towards developing personalized treatments for microbiome related diseases.}, }
@article {pmid31199220, year = {2019}, author = {Karabudak, S and Ari, O and Durmaz, B and Dal, T and Basyigit, T and Kalcioglu, MT and Durmaz, R}, title = {Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology.}, journal = {Journal of medical microbiology}, volume = {68}, number = {8}, pages = {1148-1158}, doi = {10.1099/jmm.0.001003}, pmid = {31199220}, issn = {1473-5644}, mesh = {Adult ; Bacteria/classification/genetics ; Female ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Microbiota/genetics ; Middle Aged ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Smoking ; Young Adult ; }, abstract = {PURPOSE: This study aimed to investigate the effect of smoking on the buccal microbiome and to analyse the descriptive ability of each of the seven hypervariable regions in their 16S rRNA genes.<br><br>METHODOLOGY: Microbiome compositions of 40 buccal swab samples collected from smokers (n =20) and non-smokers (n =20) were determined using 16S rRNA sequencing. Seven different 16S rRNA hypervariable regions (V2, V3, V4, V6-7, V8 and V9) in each sample were amplified using the Ion Torrent 16S Metagenomics kit and were sequenced on the Ion S5 instrument.<br><br>RESULTS: Seven hypervariable regions in the 16S rRNA gene were successfully sequenced for all samples tested. The data obtained with the V2 region was found to be informative but the consensus data generated according to a number of operational taxonomic unit reads gathered from all seven hypervariable regions gave the most accurate result. At the phylum level, no statistically significant difference was found between smokers and non-smokers whereas relative abundances of Veillonella atypica, Streptococcus australis, Prevotella melaninogenica, Prevotella salivae and Rothia mucilaginosa showed significant increases in the smoker group (P-adj=0.05). Alpha diversity results did not show a significant difference between the two groups; however, beta diversity analysis indicated that samples of smoker and non-smoker groups had a tendency to be clustered within themselves.<br><br>CONCLUSION: The results of the current study indicate that smoking is a factor influencing buccal microbiome composition. In addition, sequencing of all seven hypervariable regions yielded more accurate results than those with any of the single variable regions.}, }
@article {pmid31185897, year = {2019}, author = {Chen, CY and Tang, SL and Chou, ST}, title = {Taxonomy based performance metrics for evaluating taxonomic assignment methods.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {310}, doi = {10.1186/s12859-019-2896-0}, pmid = {31185897}, issn = {1471-2105}, support = {105-2410-H-002-101-MY3//The Ministry of Science and Technology of Taiwan/ ; }, mesh = {Bacteria/genetics ; Classification/*methods ; Databases, Genetic ; Metagenomics/*methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {BACKGROUND: Metagenomics experiments often make inferences about microbial communities by sequencing 16S and 18S rRNA, and taxonomic assignment is a fundamental step in such studies. This paper addresses the weaknesses in two types of metrics commonly used by previous studies for measuring the performance of existing taxonomic assignment methods: Sequence count based metrics and Binary error measurement. These metrics made performance evaluation results biased, less informative and mutually incomparable.<br><br>RESULTS: We investigated weaknesses in two types of metrics and proposed new performance metrics including Average Taxonomy Distance (ATD) and ATD_by_Taxa, together with the visualized ATD plot.<br><br>CONCLUSIONS: By comparing the evaluation results from four popular taxonomic assignment methods across three test data sets, we found the new metrics more robust, informative and comparable.}, }
@article {pmid31178526, year = {2019}, author = {Wang, N and Guo, Y and Li, G and Xia, Y and Ma, M and Zang, J and Ma, Y and Yin, X and Han, W and Lv, J and Cao, H}, title = {Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics.}, journal = {Microbes and environments}, volume = {34}, number = {2}, pages = {180-190}, doi = {10.1264/jsme2.ME18091}, pmid = {31178526}, issn = {1347-4405}, mesh = {Archaea/classification/genetics ; Archaeal Proteins/genetics/metabolism ; Arctic Regions ; Bacteria/classification/genetics ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Geologic Sediments/chemistry/*microbiology ; Lakes ; *Metagenomics ; Methane/metabolism ; *Microbiota/genetics ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3-V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.}, }
@article {pmid31171880, year = {2019}, author = {Yachida, S and Mizutani, S and Shiroma, H and Shiba, S and Nakajima, T and Sakamoto, T and Watanabe, H and Masuda, K and Nishimoto, Y and Kubo, M and Hosoda, F and Rokutan, H and Matsumoto, M and Takamaru, H and Yamada, M and Matsuda, T and Iwasaki, M and Yamaji, T and Yachida, T and Soga, T and Kurokawa, K and Toyoda, A and Ogura, Y and Hayashi, T and Hatakeyama, M and Nakagama, H and Saito, Y and Fukuda, S and Shibata, T and Yamada, T}, title = {Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer.}, journal = {Nature medicine}, volume = {25}, number = {6}, pages = {968-976}, doi = {10.1038/s41591-019-0458-7}, pmid = {31171880}, issn = {1546-170X}, mesh = {Adult ; Aged ; Case-Control Studies ; Colorectal Neoplasms/genetics/*metabolism/*microbiology ; Disease Progression ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Neoplasm Staging ; Young Adult ; }, abstract = {In most cases of sporadic colorectal cancers, tumorigenesis is a multistep process, involving genomic alterations in parallel with morphologic changes. In addition, accumulating evidence suggests that the human gut microbiome is linked to the development of colorectal cancer. Here we performed fecal metagenomic and metabolomic studies on samples from a large cohort of 616 participants who underwent colonoscopy to assess taxonomic and functional characteristics of gut microbiota and metabolites. Microbiome and metabolome shifts were apparent in cases of multiple polypoid adenomas and intramucosal carcinomas, in addition to more advanced lesions. We found two distinct patterns of microbiome elevations. First, the relative abundance of Fusobacterium nucleatum spp. was significantly (P < 0.005) elevated continuously from intramucosal carcinoma to more advanced stages. Second, Atopobium parvulum and Actinomyces odontolyticus, which co-occurred in intramucosal carcinomas, were significantly (P < 0.005) increased only in multiple polypoid adenomas and/or intramucosal carcinomas. Metabolome analyses showed that branched-chain amino acids and phenylalanine were significantly (P < 0.005) increased in intramucosal carcinomas and bile acids, including deoxycholate, were significantly (P < 0.005) elevated in multiple polypoid adenomas and/or intramucosal carcinomas. We identified metagenomic and metabolomic markers to discriminate cases of intramucosal carcinoma from the healthy controls. Our large-cohort multi-omics data indicate that shifts in the microbiome and metabolome occur from the very early stages of the development of colorectal cancer, which is of possible etiological and diagnostic importance.}, }
@article {pmid31167633, year = {2019}, author = {Zhong, C and Yang, Y and Yooseph, S}, title = {GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 11}, pages = {276}, doi = {10.1186/s12859-019-2818-1}, pmid = {31167633}, issn = {1471-2105}, mesh = {Algorithms ; Aquatic Organisms/genetics ; *Genes ; Metagenomics/*methods ; Microbiota/genetics ; ROC Curve ; Sequence Analysis, DNA/*methods ; *Sequence Homology, Nucleic Acid ; *Software ; Time Factors ; }, abstract = {BACKGROUND: A crucial task in metagenomic analysis is to annotate the function and taxonomy of the sequencing reads generated from a microbiome sample. In general, the reads can either be assembled into contigs and searched against reference databases, or individually searched without assembly. The first approach may suffer from fragmentary and incomplete assembly, while the second is hampered by the reduced functional signal contained in the short reads. To tackle these issues, we have previously developed GRASP (Guided Reference-based Assembly of Short Peptides), which accepts a reference protein sequence as input and aims to assemble its homologs from a database containing fragmentary protein sequences. In addition to a gene-centric assembly tool, GRASP also serves as a homolog search tool when using the assembled protein sequences as templates to recruit reads. GRASP has significantly improved recall rate (60-80% vs. 30-40%) compared to other homolog search tools such as BLAST. However, GRASP is both time- and space-consuming. Subsequently, we developed GRASPx, which is 30X faster than GRASP. Here, we present a completely redesigned algorithm, GRASP2, for this computational problem.<br><br>RESULTS: GRASP2 utilizes Burrows-Wheeler Transformation (BWT) and FM-index to perform assembly graph generation, and reduces the search space by employing a fast ungapped alignment strategy as a filter. GRASP2 also explicitly generates candidate paths prior to alignment, which effectively uncouples the iterative access of the assembly graph and alignment matrix. This strategy makes the execution of the program more efficient under current computer architecture, and contributes to GRASP2's speedup. GRASP2 is 8-fold faster than GRASPx (and 250-fold faster than GRASP) and uses 8-fold less memory while maintaining the original high recall rate of GRASP. GRASP2 reaches ~ 80% recall rate compared to that of ~ 40% generated by BLAST, both at a high precision level (> 95%). With such a high performance, GRASP2 is only ~3X slower than BLASTP.<br><br>CONCLUSION: GRASP2 is a high-performance gene-centric and homolog search tool with significant speedup compared to its predecessors, which makes GRASP2 a useful tool for metagenomics data analysis, GRASP2 is implemented in C++ and is freely available from http://www.sourceforge.net/projects/grasp2 .}, }
@article {pmid31142849, year = {2019}, author = {Fettweis, JM and Serrano, MG and Brooks, JP and Edwards, DJ and Girerd, PH and Parikh, HI and Huang, B and Arodz, TJ and Edupuganti, L and Glascock, AL and Xu, J and Jimenez, NR and Vivadelli, SC and Fong, SS and Sheth, NU and Jean, S and Lee, V and Bokhari, YA and Lara, AM and Mistry, SD and Duckworth, RA and Bradley, SP and Koparde, VN and Orenda, XV and Milton, SH and Rozycki, SK and Matveyev, AV and Wright, ML and Huzurbazar, SV and Jackson, EM and Smirnova, E and Korlach, J and Tsai, YC and Dickinson, MR and Brooks, JL and Drake, JI and Chaffin, DO and Sexton, AL and Gravett, MG and Rubens, CE and Wijesooriya, NR and Hendricks-Muñoz, KD and Jefferson, KK and Strauss, JF and Buck, GA}, title = {The vaginal microbiome and preterm birth.}, journal = {Nature medicine}, volume = {25}, number = {6}, pages = {1012-1021}, doi = {10.1038/s41591-019-0450-2}, pmid = {31142849}, issn = {1546-170X}, support = {R01 HD092415/HD/NICHD NIH HHS/United States ; UH3 AI083263/AI/NIAID NIH HHS/United States ; U54 DE023786/DE/NIDCR NIH HHS/United States ; R21 HD092965/HD/NICHD NIH HHS/United States ; UH2 AI083263/AI/NIAID NIH HHS/United States ; R25 GM090084/GM/NIGMS NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; }, mesh = {Adult ; African Americans ; Biodiversity ; Cohort Studies ; Cytokines/metabolism ; Female ; Host Microbial Interactions/immunology ; Humans ; Infant, Newborn ; Inflammation Mediators/metabolism ; Longitudinal Studies ; Metagenomics ; *Microbiota/genetics/immunology ; Premature Birth/etiology/immunology/*microbiology ; Risk Factors ; United States ; Vagina/immunology/*microbiology ; Young Adult ; }, abstract = {The incidence of preterm birth exceeds 10% worldwide. There are significant disparities in the frequency of preterm birth among populations within countries, and women of African ancestry disproportionately bear the burden of risk in the United States. In the present study, we report a community resource that includes 'omics' data from approximately 12,000 samples as part of the integrative Human Microbiome Project. Longitudinal analyses of 16S ribosomal RNA, metagenomic, metatranscriptomic and cytokine profiles from 45 preterm and 90 term birth controls identified harbingers of preterm birth in this cohort of women predominantly of African ancestry. Women who delivered preterm exhibited significantly lower vaginal levels of Lactobacillus crispatus and higher levels of BVAB1, Sneathia amnii, TM7-H1, a group of Prevotella species and nine additional taxa. The first representative genomes of BVAB1 and TM7-H1 are described. Preterm-birth-associated taxa were correlated with proinflammatory cytokines in vaginal fluid. These findings highlight new opportunities for assessment of the risk of preterm birth.}, }
@article {pmid31141902, year = {2019}, author = {Kallies, R and Hölzer, M and Brizola Toscan, R and Nunes da Rocha, U and Anders, J and Marz, M and Chatzinotas, A}, title = {Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters.}, journal = {Viruses}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/v11060484}, pmid = {31141902}, issn = {1999-4915}, support = {CRC 1076//Deutsche Forschungsgemeinschaft/ ; SPP-1596//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Viral ecology of terrestrial habitats is yet-to be extensively explored, in particular the terrestrial subsurface. One problem in obtaining viral sequences from groundwater aquifer samples is the relatively low amount of virus particles. As a result, the amount of extracted DNA may not be sufficient for direct sequencing of such samples. Here we compared three DNA amplification methods to enrich viral DNA from three pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory to evaluate potential bias created by the different amplification methods as determined by viral metagenomics. Linker amplification shotgun libraries resulted in lowest redundancy among the sequencing reads and showed the highest diversity, while multiple displacement amplification produced the highest number of contigs with the longest average contig size, suggesting a combination of these two methods is suitable for the successful enrichment of viral DNA from pristine groundwater samples. In total, we identified 27,173, 5,886 and 32,613 viral contigs from the three samples from which 11.92 to 18.65% could be assigned to taxonomy using blast. Among these, members of the Caudovirales order were the most abundant group (52.20 to 69.12%) dominated by Myoviridae and Siphoviridae. Those, and the high number of unknown viral sequences, substantially expand the known virosphere.}, }
@article {pmid31129398, year = {2019}, author = {Qi, M and Huang, H and Zhang, Y and Wang, H and Li, H and Lu, Z}, title = {Novel tetrahydrofuran (THF) degradation-associated genes and cooperation patterns of a THF-degrading microbial community as revealed by metagenomic.}, journal = {Chemosphere}, volume = {231}, number = {}, pages = {173-183}, doi = {10.1016/j.chemosphere.2019.05.137}, pmid = {31129398}, issn = {1879-1298}, mesh = {Actinomycetales ; Furans/analysis/*chemistry/metabolism ; Metagenome/*genetics ; Metagenomics ; Microbiota ; Mixed Function Oxygenases/genetics/metabolism ; Open Reading Frames ; }, abstract = {Our understanding of the tetrahydrofuran (THF) degradation in complex environment is limited. The majority of THF degrading genes reported are group V soluble diiron monooxygenases and share greater than 95% homology with one another. In this study, we used sole-carbon-source incubation combined with high-throughput metagenomic sequencing to investigate this contaminant's degradation in environmental samples. We identified as-yet-uncultivated microbe from the genera Pseudonocardia and fungi Scedosporium sp. (Scedosporium sp. was successfully isolated) as THF degraders as containing THF degradation genes, while microbes from the genera Bordetella, Pandoraea and Rhodanobacter functioned as main cooperators by utilizing acidic intermediates and providing anti-acid mechanisms. Furthermore, a 9387-bp THF degradation cluster designated thmX from the as-yet-uncultivated Pseudonocardia (with 6 main ORFs and with 79-93% amino acid sequence identity with previously reported clusters) was discovered. We also found a THF-degrading related cytochrome P450 monooxygenase from the genus Scedosporium and predicted its cognate reductase for the first time. All the genes and clusters mentioned above were successfully amplified from samples and cloned into the suitable expression vectors. This study will provide novel insights for understanding of THF degradation mechanisms under acid stress conditions and mining new THF degradation genes.}, }
@article {pmid31126262, year = {2019}, author = {Ke, S and Fang, S and He, M and Huang, X and Yang, H and Yang, B and Chen, C and Huang, L}, title = {Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition.}, journal = {BMC veterinary research}, volume = {15}, number = {1}, pages = {172}, doi = {10.1186/s12917-019-1918-5}, pmid = {31126262}, issn = {1746-6148}, support = {31772579//National Natural Science Foundation of China/ ; 31472071//National Natural Science Foundation of China/ ; }, mesh = {*Age Factors ; Animals ; Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Female ; Gastrointestinal Microbiome/*physiology ; Male ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sus scrofa/*microbiology ; }, abstract = {BACKGROUND: The gut microbiota impacts on a range of host biological processes, and the imbalances in its composition are associated with pathology. Though the understanding of contribution of the many factors, e.g. gender, diet and age, in the development of gut microbiota has been well established, the dynamic changes of the phylogenetic composition and the interaction networks along with the age remain unclear in pigs.<br><br>RESULTS: Here we applied 16S ribosomal RNA gene sequencing, enterotype-like clustering (Classification of the gut microbiome into distinct types) and phylogenetic co-occurrence network to explore the dynamic changes of pig gut microbiome following the ages with a successive investigation at four ages in a cohort of 953 pigs. We found that Firmicutes and Bacteroidetes are two predominant phyla throughout the experimental period. The richness of gut microbiota was significantly increased from 25 to 240 days of age. Principal coordinates analysis showed a clear difference in the gut microbial community compositions between pre-weaning piglets and the pigs at the other three age groups. The gut microbiota of pre-weaning piglets was clearly classified into two enterotypes, which were dominated by Fusobacterium and p-75-a5, respectively. However, Prevotella and Treponema were the main drivers of the enterotypes for pigs at the age of 80, 120 and 240 days. Besides the piglets, even some adult pigs switched putative enterotypes between ages. We confirmed that the topological features of phylogenetic co-occurrence networks, including scale, stability and complexity were increased along with the age. The biological significance for modules in the network of piglets were mainly associated with the utilization of simple carbohydrate and lactose, whereas the sub-networks identified at the ages of 80, 120 and 240 days may be involved in the digestion of complex dietary polysaccharide. The modules related to the metabolism of protein and amino acids could be identified in the networks at 120 and 240 days. This dynamic change of the functional capacities of gut microbiome was further supported by functional prediction analysis.<br><br>CONCLUSIONS: The present study provided meaningful biological insights into the age-based dynamic shifts of ecological community of porcine gut microbiota.}, }
@article {pmid31123265, year = {2019}, author = {Li, Y and Fu, X and Ma, J and Zhang, J and Hu, Y and Dong, W and Wan, Z and Li, Q and Kuang, YQ and Lan, K and Jin, X and Wang, JH and Zhang, C}, title = {Altered respiratory virome and serum cytokine profile associated with recurrent respiratory tract infections in children.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2288}, doi = {10.1038/s41467-019-10294-x}, pmid = {31123265}, issn = {2041-1723}, mesh = {Acute Disease ; Bacteriophages/genetics/*isolation &amp; purification ; Child ; Child, Preschool ; Cytokines/*blood/immunology ; Disease Susceptibility/blood/immunology/microbiology ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Infant ; Longitudinal Studies ; Male ; Metagenomics/methods ; Microbiota/genetics ; Propionibacterium/virology ; Proteomics/methods ; Recurrence ; Respiratory System/immunology/*virology ; Respiratory Tract Infections/*blood/immunology/microbiology ; Retrospective Studies ; }, abstract = {Recurrent acute respiratory tract infections (ARTIs) affect a large population, yet the specific decisive factors are largely unknown. Here we study a population of 4407 children diagnosed with ARTI, comparing respiratory virome and serum cytokine profiles associated with multiple ARTIs and single ARTI during a six-year period. The relative abundance of Propionibacterium phages is significantly elevated in multiple ARTIs compared to single ARTI group. Serum levels of TIMP-1 and PDGF-BB are markedly increased in multiple ARTIs compared to single-ARTI and non-ARTI controls, making these two cytokines potential predictors for multiple ARTIs. The presence of Propionibacterium phages is associated with higher levels of TIMP-1 and PDGF-BB. Receiver operating characteristic (ROC) curve analyses show that the combination of TIMP-1, PDGF-BB and Propionibacterium phages could be a strong predictor for multiple ARTIs. These findings indicate that respiratory microbe homeostasis and specific cytokines are associated with the onset of multiple ARTIs over time.}, }
@article {pmid31102963, year = {2019}, author = {Liu, S and Chen, Q and Zou, H and Yu, Y and Zhou, Z and Mao, J and Zhang, S}, title = {A metagenomic analysis of the relationship between microorganisms and flavor development in Shaoxing mechanized huangjiu fermentation mashes.}, journal = {International journal of food microbiology}, volume = {303}, number = {}, pages = {9-18}, doi = {10.1016/j.ijfoodmicro.2019.05.001}, pmid = {31102963}, issn = {1879-3460}, mesh = {Chromatography, High Pressure Liquid ; *Fermentation ; Fermented Foods/*microbiology ; Gas Chromatography-Mass Spectrometry ; *Metagenomics ; *Microbiota/genetics ; Taste ; }, abstract = {Complex microbial metabolism is responsible for the unique flavor of Shaoxing mechanized huangjiu. However, the relationship between the microorganisms present during fermentation and the formation of specific flavor components is difficult to understand. In this study, gas chromatography-mass spectrometry and high-performance liquid chromatography were used to identify flavor components, and a metagenomic sequencing approach was used to characterize the taxonomic and functional attributes of the Shaoxing mechanized huangjiu fermentation microbiota. The metagenomic sequencing data were used to predict the relationship between microorganisms and flavor formation. The chromatographic analysis identified amino acids, alcohols, acids, phenols and esters as major flavor components, and six microbial genera (Saccharomyces, Aspergillus, Saccharopolyspora, Staphylococcus, Lactobacillus, and Lactococcus) were most closely related to the production of these flavor components. This study helps clarify the different metabolic roles of microorganisms in flavor formation during Shaoxing huangjiu fermentation.}, }
@article {pmid31102141, year = {2019}, author = {Sahoo, K and Sahoo, RK and Gaur, M and Subudhi, E}, title = {Cellulolytic thermophilic microorganisms in white biotechnology: a review.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12223-019-00710-6}, pmid = {31102141}, issn = {1874-9356}, support = {YSS/2014/000413//Science and Engineering Research Board/ ; }, abstract = {Enzymes of microbial origin are of immense importance for organic material decomposition leading to bioremediation of organic waste, bioenergy generation, large-scale industrial bioprocesses, etc. The market demand for microbial cellulase enzyme is growing more rapidly which ultimately becomes the driving force towards research on this biocatalyst, widely used in various industrial activities. The use of novel cellulase genes obtained from various thermophiles through metagenomics and genetic engineering as well as following metabolic engineering pathways would be able to enhance the production of thermophilic cellulase at industrial scale. The present review is mainly focused on thermophilic cellulolytic bacteria, discoveries on cellulase gene, genetically modified cellulase, metabolic engineering, and their various industrial applications. A lot of lacunae are yet to overcome for thermophiles such as metagenome analysis, metabolic pathway modification study, search of heterologous hosts in gene expression system, and improved recombinant strain for better cellulase yield as well as value-added product formation.}, }
@article {pmid31101811, year = {2019}, author = {Sande, CJ and Njunge, JM and Mwongeli Ngoi, J and Mutunga, MN and Chege, T and Gicheru, ET and Gardiner, EM and Gwela, A and Green, CA and Drysdale, SB and Berkley, JA and Nokes, DJ and Pollard, AJ}, title = {Airway response to respiratory syncytial virus has incidental antibacterial effects.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2218}, doi = {10.1038/s41467-019-10222-z}, pmid = {31101811}, issn = {2041-1723}, support = {//Wellcome Trust/United Kingdom ; WT105882MA//Wellcome Trust (Wellcome)/International ; }, mesh = {Bacterial Infections/*immunology/microbiology ; Cell Degranulation/immunology ; Child, Preschool ; Humans ; Infant ; Infant, Newborn ; Kenya ; Metagenomics/methods ; Microbiota/immunology ; Neutrophils/*immunology ; Proteomics/methods ; Respiratory Mucosa/cytology/*immunology/microbiology ; Respiratory Syncytial Virus Infections/*immunology/virology ; Respiratory Syncytial Virus, Human/*immunology/isolation &amp; purification ; Streptococcus/immunology/isolation &amp; purification ; }, abstract = {RSV infection is typically associated with secondary bacterial infection. We hypothesise that the local airway immune response to RSV has incidental antibacterial effects. Using coordinated proteomics and metagenomics analysis we simultaneously analysed the microbiota and proteomes of the upper airway and determined direct antibacterial activity in airway secretions of RSV-infected children. Here, we report that the airway abundance of Streptococcus was higher in samples collected at the time of RSV infection compared with samples collected one month later. RSV infection is associated with neutrophil influx into the airway and degranulation and is marked by overexpression of proteins with known antibacterial activity including BPI, EPX, MPO and AZU1. Airway secretions of children infected with RSV, have significantly greater antibacterial activity compared to RSV-negative controls. This RSV-associated, neutrophil-mediated antibacterial response in the airway appears to act as a regulatory mechanism that modulates bacterial growth in the airways of RSV-infected children.}, }
@article {pmid31097033, year = {2019}, author = {Lugli, GA and Milani, C and Duranti, S and Alessandri, G and Turroni, F and Mancabelli, L and Tatoni, D and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {96}, doi = {10.1186/s13059-019-1711-6}, pmid = {31097033}, issn = {1474-760X}, mesh = {Animals ; Bifidobacterium/genetics/*isolation &amp; purification ; Callimico ; Callithrix ; Cattle ; Gastrointestinal Microbiome ; Metagenomics ; }, abstract = {Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method.}, }
@article {pmid31092601, year = {2019}, author = {Hu, H and da Costa, RR and Pilgaard, B and Schiøtt, M and Lange, L and Poulsen, M}, title = {Fungiculture in Termites Is Associated with a Mycolytic Gut Bacterial Community.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00165-19}, pmid = {31092601}, issn = {2379-5042}, mesh = {Animals ; Bacteria/enzymology/genetics ; *Diet ; Fungi/*growth &amp; development ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/enzymology/microbiology ; Isoptera/*enzymology/*microbiology ; Metagenome ; Phylogeny ; Plant Cells/metabolism ; Sequence Analysis, DNA ; Symbiosis ; Wood/metabolism ; }, abstract = {Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterize bacterial community compositions and use peptide-based functional annotation method to determine biomass-degrading enzymes and the bacterial taxa that encode them. We find that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, while wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Interestingly, wood-feeding termite gut bacterial genes code for abundant chitinolytic enzymes, suggesting that fungal biomass within the decaying wood likely contributes to gut bacterial or termite host nutrition. Across diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community composition, with the most marked difference being the communities coding for the mycolytic capacity of the fungus-growing termite gut.IMPORTANCE Understanding functional capacities of gut microbiomes is important to improve our understanding of symbiotic associations. Here, we use peptide-based functional annotation to show that the gut microbiomes of fungus-farming termites code for a wealth of enzymes that likely target the fungal diet the termites eat. Comparisons to other termites showed that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, whereas wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Across termites with different diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community compositions.}, }
@article {pmid31087993, year = {2019}, author = {Liu, ZQ and Zhang, Y and Ma, XS and Zhang, BK and Cao, MJ and Chen, CM}, title = {[Nitrogen Removal Characteristics and Analysis of Microbial Community Structure in an IEM-UF Simultaneous Separation and Denitrification System].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {40}, number = {3}, pages = {1419-1425}, doi = {10.13227/j.hjkx.201808051}, pmid = {31087993}, issn = {0250-3301}, mesh = {Bacteria/classification ; Bioreactors ; *Denitrification ; Ion Exchange ; *Microbiota ; Nitrogen/*isolation &amp; purification ; Ultrafiltration ; Waste Water ; }, abstract = {A system that combines an ion exchange membrane and ultrafiltration membrane (IEM-UF) to form a simultaneous separation and denitrification system was proposed for domestic sewage with a low carbon/nitrogen ratio. The removal of nitrogen and COD in the system was studied under a three phase operating condition. The characteristics of the microbial community in each reactor were analyzed using metagenomics. The results show that, the average rate of ammonia nitrogen enrichment in the separator reached above 116.1% when the current intensity was 0.2 A. When the system was at C/N 2.80 and operating well, the average removal rates of COD and TN reached above 90% and 50%, respectively. The maximum removal rate of TN was above 65.4%. The results of metagenomics showed a genus of phylum Nitrospirae (Nitrospira) and a genus of phylum Proteobacteria (Nitrosomonas), with the proportions of 12.23% and 2.31%, respectively. In the denitrifying reactor, Dechloromonas, Thauera, and Azospira were detected in the proportions 4.57%, 1.76%, and 1.03%, respectively. These proportions were far larger than those of other bacteria in this reactor. Meanwhile, the presence of iron autotrophic denitrifying bacteria increased the denitrification efficiency of the system.}, }
@article {pmid31086312, year = {2019}, author = {Wu, L and Ning, D and Zhang, B and Li, Y and Zhang, P and Shan, X and Zhang, Q and Brown, M and Li, Z and Van Nostrand, JD and Ling, F and Xiao, N and Zhang, Y and Vierheilig, J and Wells, GF and Yang, Y and Deng, Y and Tu, Q and Wang, A and ,  and Zhang, T and He, Z and Keller, J and Nielsen, PH and Alvarez, PJJ and Criddle, CS and Wagner, M and Tiedje, JM and He, Q and Curtis, TP and Stahl, DA and Alvarez-Cohen, L and Rittmann, BE and Wen, X and Zhou, J}, title = {Global diversity and biogeography of bacterial communities in wastewater treatment plants.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1183-1195}, doi = {10.1038/s41564-019-0426-5}, pmid = {31086312}, issn = {2058-5276}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; Geography ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Water Purification/statistics &amp; numerical data ; }, abstract = {Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.}, }
@article {pmid31073898, year = {2019}, author = {Zhao, H and Yan, B and Mo, S and Nie, S and Li, Q and Ou, Q and Wu, B and Jiang, G and Tang, J and Li, N and Jiang, C}, title = {Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {57}, number = {7}, pages = {575-586}, doi = {10.1007/s12275-019-8679-5}, pmid = {31073898}, issn = {1976-3794}, mesh = {*Archaea/classification/genetics/metabolism ; *Bacteria/classification/genetics/metabolism ; Carbohydrate Metabolism/genetics ; China ; Geologic Sediments/*microbiology ; Metagenomics/methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Wetlands ; }, abstract = {Mangrove sediment microorganisms play a vital role in the energy transformation and element cycling in marine wetland ecosystems. Using metagenomics analysis strategy, we compared the taxonomic structure and gene profile of the mangrove and non-mangrove sediment samples at the subtropical estuary in Beibu Gulf, South China Sea. Proteobacteria, Bacteroidetes, and Firmicutes were the most abundant bacterial phyla. Archaeal family Methanosarcinaceae and bacterial genera Vibrio and Dehalococcoides were significantly higher in the mangrove sediments than in the nonmangrove sediments. Functional analysis showed that &quot;Carbohydrate metabolism&quot; was the most abundant metabolic category. The feature of carbohydrate-active enzymes (CZs) was analyzed using the Carbohydrate-Active EnZymes Database. The significant differences of CZs between mangrove and non-mangrove sediments, were attributed to the amounts of polyphenol oxidase (EC 1.10.3.-), hexosyltransferase (EC 2.4.1.-), and β-N-acetylhexosaminidase (EC 3.2.1.52), which were higher in the mangrove sediment samples. Principal component analysis indicated that the microbial community and gene profile between mangrove and non-mangrove sediments were distinct. Redundancy analysis showed that total organic carbon is a significant factor that affects the microbial community and gene distribution. The results indicated that the mangrove ecosystem with massive amounts of organic carbon may promote the richness of carbohydrate metabolism genes and enhance the degradation and utilization of carbohydrates in the mangrove sediments.}, }
@article {pmid31064831, year = {2019}, author = {Haran, JP and Bhattarai, SK and Foley, SE and Dutta, P and Ward, DV and Bucci, V and McCormick, BA}, title = {Alzheimer's Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.00632-19}, pmid = {31064831}, issn = {2150-7511}, support = {R15 AI112985/AI/NIAID NIH HHS/United States ; R03 AG056356/AG/NIA NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; K23 AG057790/AG/NIA NIH HHS/United States ; R01 DK056754/DK/NIDDK NIH HHS/United States ; }, mesh = {ATP Binding Cassette Transporter, Subfamily B/*metabolism ; Aged ; Aged, 80 and over ; Alzheimer Disease/metabolism/*microbiology ; Bacteria/classification/isolation &amp; purification ; Dementia/microbiology ; *Dysbiosis ; Epithelial Cells/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Homeostasis ; Humans ; Inflammation/complications ; Intestines/microbiology ; Machine Learning ; Male ; Metabolic Networks and Pathways/immunology ; Metagenomics ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbiota-gut-brain axis is a bidirectional communication system that is poorly understood. Alzheimer's disease (AD), the most common cause of dementia, has long been associated with bacterial infections and inflammation-causing immunosenescence. Recent studies examining the intestinal microbiota of AD patients revealed that their microbiome differs from that of subjects without dementia. In this work, we prospectively enrolled 108 nursing home elders and followed each for up to 5 months, collecting longitudinal stool samples from which we performed metagenomic sequencing and in vitro T84 intestinal epithelial cell functional assays for P-glycoprotein (P-gp) expression, a critical mediator of intestinal homeostasis. Our analysis identified clinical parameters as well as numerous microbial taxa and functional genes that act as predictors of AD dementia in comparison to elders without dementia or with other dementia types. We further demonstrate that stool samples from elders with AD can induce lower P-gp expression levels in vitro those samples from elders without dementia or with other dementia types. We also paired functional studies with machine learning approaches to identify bacterial species differentiating the microbiome of AD elders from that of elders without dementia, which in turn are accurate predictors of the loss of dysregulation of the P-gp pathway. We observed that the microbiome of AD elders shows a lower proportion and prevalence of bacteria with the potential to synthesize butyrate, as well as higher abundances of taxa that are known to cause proinflammatory states. Therefore, a potential nexus between the intestinal microbiome and AD is the modulation of intestinal homeostasis by increases in inflammatory, and decreases in anti-inflammatory, microbial metabolism.IMPORTANCE Studies of the intestinal microbiome and AD have demonstrated associations with microbiome composition at the genus level among matched cohorts. We move this body of literature forward by more deeply investigating microbiome composition via metagenomics and by comparing AD patients against those without dementia and with other dementia types. We also exploit machine learning approaches that combine both metagenomic and clinical data. Finally, our functional studies using stool samples from elders demonstrate how the c microbiome of AD elders can affect intestinal health via dysregulation of the P-glycoprotein pathway. P-glycoprotein dysregulation contributes directly to inflammatory disorders of the intestine. Since AD has been long thought to be linked to chronic bacterial infections as a possible etiology, our findings therefore fill a gap in knowledge in the field of AD research by identifying a nexus between the microbiome, loss of intestinal homeostasis, and inflammation that may underlie this neurodegenerative disorder.}, }
@article {pmid31055095, year = {2019}, author = {Hassan, M and Essam, T and Mira, A and Megahed, S}, title = {Biomonitoring detoxification efficiency of an algal-bacterial microcosm system for treatment of coking wastewater: Harmonization between Chlorella vulgaris microalgae and wastewater microbiome.}, journal = {The Science of the total environment}, volume = {677}, number = {}, pages = {120-130}, doi = {10.1016/j.scitotenv.2019.04.304}, pmid = {31055095}, issn = {1879-1026}, mesh = {Bacteria/*metabolism ; Chlorella vulgaris/*metabolism ; Coke ; Egypt ; Environmental Monitoring/*methods ; Environmental Restoration and Remediation/*methods ; Microalgae/metabolism ; Microbiota ; Waste Water/*analysis/*microbiology ; Water Pollutants, Chemical/analysis ; Water Pollution, Chemical/prevention &amp; control ; }, abstract = {Nowadays, due to worldwide water shortage, water utilities are forced to re-evaluate treated wastewater. Consequently, wastewater treatment plants need to conduct biomonitoring. Coking wastewater (CWW) has toxic, mutative and carcinogenic components with threatening effect on the environment. CWW was selected as a model for complex highly toxic industrial wastewater that should be treated. CWW from Egypt was treated in a nine-liter photobioreactor using an algal-bacterial system. The photobioreactor was operated for 154 days changing different parameters (toxic load and light duration) for optimization. Optimized conditions achieved significant reduction (45%) in the operation cost. The algal-bacterial system was monitored using chemical assays (chemical oxygen demand and phenol analysis), bioassays (phytotoxicity, Artemia-toxicity, cytotoxicity, algal-bacterial ratio and settleability) and Illumina-MiSeq sequencing of 16S rRNA gene. The algal-bacterial system detoxified (in terms of phytotoxicity, cytotoxicity and Artemia-toxicity) CWW introduced as influent through all phases. A significant difference was recorded in the microbial diversity between influent and effluent samples. Four phyla dominated influent samples; Proteobacteria (77%), Firmicutes (11%), Bacteroidetes (5%) and Deferribacteres (3%) compared to only two in effluent samples; Proteobacteria (66%) and Bacteroidetes (26%). The significant relative-abundance of versatile aromatic degraders (Comamonadaceae and Pseudomonadaceae families) in influent samples conformed to the nature of CWW. Microbial community shifted and promoted the activity of catabolically versatile and xenobiotics degrading families (Chitinophagaceae and Xanthomonadaceae). Co-culture of microalgae had a positive effect on the biodegrading bacteria that was reflected by enhanced treatment efficiency, significant increase in relative abundance of bacterial genera with cyanide-decomposing potential and negative effect on waterborne pathogens.}, }
@article {pmid31055020, year = {2019}, author = {Xiao Joe, JT and Chiou, PP and Kuo, CY and Jia Lin, JH and Wu, JL and Lu, MW}, title = {The microbiota profile and transcriptome analysis of immune response during metamorphosis stages in orange spotted grouper (Epinephelus coioides).}, journal = {Fish &amp; shellfish immunology}, volume = {90}, number = {}, pages = {141-149}, doi = {10.1016/j.fsi.2019.03.063}, pmid = {31055020}, issn = {1095-9947}, mesh = {Animals ; Bass/*genetics/growth &amp; development/immunology/*microbiology ; Gastrointestinal Microbiome/*physiology ; Gene Expression Profiling ; Gene Expression Regulation/immunology ; Immunity, Innate/*genetics ; Metagenomics ; Metamorphosis, Biological/genetics/immunology ; Transcriptome/*immunology ; }, abstract = {Metamorphosis is a transformation process in larval development associated with changes in morphological and physiological features, including the immune system. The gastrointestinal tract harbors a plethora of bacteria, which might affect the digestion and absorption of nutrients, immunity, and gut-brain crosstalk in the host. In this study, we have performed metagenomic and transcriptomic analyses on the intestines of grouper at the pre-, mid- and post-metamorphosis stages. The sequencing data of 16S rRNA gene showed drastic changes in the microbial communities at different developmental stages. The transcriptomic data revealed that the leukocyte transendothelial migration and the phagosome pathways might play important roles in mediating immunity in grouper at the three developmental stages. This information will increase our understanding of the metamorphosis process in grouper larvae, and shed light on the development of antimicrobial strategy during larval development.}, }
@article {pmid31051396, year = {2019}, author = {Cabral, L and Noronha, MF and de Sousa, STP and Lacerda-Júnior, GV and Richter, L and Fostier, AH and Andreote, FD and Hess, M and Oliveira, VM}, title = {The metagenomic landscape of xenobiotics biodegradation in mangrove sediments.}, journal = {Ecotoxicology and environmental safety}, volume = {179}, number = {}, pages = {232-240}, doi = {10.1016/j.ecoenv.2019.04.044}, pmid = {31051396}, issn = {1090-2414}, mesh = {Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Gene Library ; *Geologic Sediments/chemistry/microbiology ; Hydrolases/genetics ; Metagenomics/*methods ; Metals, Heavy/*analysis/toxicity ; Microbiota/drug effects/*genetics ; Petroleum/analysis/toxicity ; *Wetlands ; Xenobiotics/*analysis/toxicity ; }, abstract = {Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.}, }
@article {pmid31043514, year = {2019}, author = {Escudeiro, P and Pothier, J and Dionisio, F and Nogueira, T}, title = {Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00135-19}, pmid = {31043514}, issn = {2379-5042}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Child ; Child, Preschool ; Drug Resistance, Microbial/*genetics ; *Environmental Microbiology ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/microbiology ; *Genetic Variation ; Humans ; Infant ; Metagenome ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Virulence ; Virulence Factors/genetics ; Young Adult ; }, abstract = {Human beings have used large amounts of antibiotics, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are affected as well. Therefore, both pathogenic and nonpathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still cooccurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes from different individuals and from distinct human populations across the world. We found a great diversity of antibiotic resistance determinants (AR diversity [ARd]) and virulence factors (VF diversity [VFd]) in metagenomes. Importantly there is a correlation between ARd and VFd, even after correcting for protein family richness. In the human gut, there are less ARd and VFd than in more diversified environments, and yet correlations between the ARd and VFd are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to nonexistent in the uncontacted Amerindian population. We conclude that there is cooccurrence of resistance and virulence determinants in human gut microbiomes, suggesting a possible coselective mechanism.IMPORTANCE Every year, thousands of tons of antibiotics are used, not only in human and animal health but also as growth promoters in livestock. Consequently, during the last 75 years, antibiotic-resistant bacterial strains have been selected in human and environmental microbial communities. This implies that, even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are also affected. Here, we performed a comparative study of environmental and human gut microbial communities issuing from different individuals and from distinct human populations across the world. We found that antibiotic resistance and pathogenicity are correlated and speculate that, by selecting for resistant bacteria, we may be selecting for more virulent strains as a side effect of antimicrobial therapy.}, }
@article {pmid31036930, year = {2019}, author = {Zhang, J and Liu, YX and Zhang, N and Hu, B and Jin, T and Xu, H and Qin, Y and Yan, P and Zhang, X and Guo, X and Hui, J and Cao, S and Wang, X and Wang, C and Wang, H and Qu, B and Fan, G and Yuan, L and Garrido-Oter, R and Chu, C and Bai, Y}, title = {NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice.}, journal = {Nature biotechnology}, volume = {37}, number = {6}, pages = {676-684}, doi = {10.1038/s41587-019-0104-4}, pmid = {31036930}, issn = {1546-1696}, mesh = {Alleles ; Anion Transport Proteins/chemistry/*genetics ; Bacteria/classification/*genetics ; Genotype ; Metagenomics ; Microbiota/*genetics ; Nitrogen/metabolism ; Oryza/*genetics/growth &amp; development/metabolism/microbiology ; Phylogeny ; Plant Breeding ; Plant Roots/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 japonica varieties grown in the field. We find that indica and japonica recruit distinct root microbiota. Notably, indica-enriched bacterial taxa are more diverse, and contain more genera with nitrogen metabolism functions, than japonica-enriched taxa. Using genetic approaches, we provide evidence that NRT1.1B, a rice nitrate transporter and sensor, is associated with the recruitment of a large proportion of indica-enriched bacteria. Metagenomic sequencing reveals that the ammonification process is less abundant in the root microbiome of the nrt1.1b mutant. We isolated 1,079 pure bacterial isolates from indica and japonica roots and derived synthetic communities (SynComs). Inoculation of IR24, an indica variety, with an indica-enriched SynCom improved rice growth in organic nitrogen conditions compared with a japonica-enriched SynCom. The links between plant genotype and root microbiota membership established in this study will inform breeding strategies to improve nitrogen use in crops.}, }
@article {pmid31036790, year = {2019}, author = {Ghani, MI and Ali, A and Atif, MJ and Ali, M and Amin, B and Anees, M and Khurshid, H and Cheng, Z}, title = {Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment.}, journal = {International journal of molecular sciences}, volume = {20}, number = {9}, pages = {}, doi = {10.3390/ijms20092125}, pmid = {31036790}, issn = {1422-0067}, support = {2016KTCL02-01//Shaanxi Provincial Sci Tech Innovation Plan/ ; 2016NY-048//Shaanxi provincial Agricultural Sci Tech Innovation and Development Plan/ ; NCI 1501//Xian City Agricultural Sci Tech Innovation Plan P.R China/ ; }, mesh = {Biodiversity ; *Garlic ; *High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; *Microbiota ; Soil/chemistry ; *Soil Microbiology ; *Solanum melongena ; }, abstract = {The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.}, }
@article {pmid31034867, year = {2019}, author = {Tsiaoussis, J and Antoniou, MN and Koliarakis, I and Mesnage, R and Vardavas, CI and Izotov, BN and Psaroulaki, A and Tsatsakis, A}, title = {Effects of single and combined toxic exposures on the gut microbiome: Current knowledge and future directions.}, journal = {Toxicology letters}, volume = {312}, number = {}, pages = {72-97}, doi = {10.1016/j.toxlet.2019.04.014}, pmid = {31034867}, issn = {1879-3169}, mesh = {Environmental Pollutants/*toxicity ; Gastrointestinal Microbiome/*drug effects ; Hazardous Substances/*toxicity ; Humans ; }, abstract = {Human populations are chronically exposed to mixtures of toxic chemicals. Predicting the health effects of these mixtures require a large amount of information on the mode of action of their components. Xenobiotic metabolism by bacteria inhabiting the gastrointestinal tract has a major influence on human health. Our review aims to explore the literature for studies looking to characterize the different modes of action and outcomes of major chemical pollutants, and some components of cosmetics and food additives, on gut microbial communities in order to facilitate an estimation of their potential mixture effects. We identified good evidence that exposure to heavy metals, pesticides, nanoparticles, polycyclic aromatic hydrocarbons, dioxins, furans, polychlorinated biphenyls, and non-caloric artificial sweeteners affect the gut microbiome and which is associated with the development of metabolic, malignant, inflammatory, or immune diseases. Answering the question 'Who is there?' is not sufficient to define the mode of action of a toxicant in predictive modeling of mixture effects. Therefore, we recommend that new studies focus to simulate real-life exposure to diverse chemicals (toxicants, cosmetic/food additives), including as mixtures, and which combine metagenomics, metatranscriptomics and metabolomic analytical methods achieving in that way a comprehensive evaluation of effects on human health.}, }
@article {pmid31031001, year = {2019}, author = {Gregory, AC and Zayed, AA and Conceição-Neto, N and Temperton, B and Bolduc, B and Alberti, A and Ardyna, M and Arkhipova, K and Carmichael, M and Cruaud, C and Dimier, C and Domínguez-Huerta, G and Ferland, J and Kandels, S and Liu, Y and Marec, C and Pesant, S and Picheral, M and Pisarev, S and Poulain, J and Tremblay, JÉ and Vik, D and ,  and Babin, M and Bowler, C and Culley, AI and de Vargas, C and Dutilh, BE and Iudicone, D and Karp-Boss, L and Roux, S and Sunagawa, S and Wincker, P and Sullivan, MB}, title = {Marine DNA Viral Macro- and Microdiversity from Pole to Pole.}, journal = {Cell}, volume = {177}, number = {5}, pages = {1109-1123.e14}, doi = {10.1016/j.cell.2019.03.040}, pmid = {31031001}, issn = {1097-4172}, support = {T32 AI112542/AI/NIAID NIH HHS/United States ; }, abstract = {Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.}, }
@article {pmid31030156, year = {2019}, author = {Darlison, J and Mogren, L and Rosberg, AK and Grudén, M and Minet, A and Liné, C and Mieli, M and Bengtsson, T and Håkansson, Å and Uhlig, E and Becher, PG and Karlsson, M and Alsanius, BW}, title = {Leaf mineral content govern microbial community structure in the phyllosphere of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia).}, journal = {The Science of the total environment}, volume = {675}, number = {}, pages = {501-512}, doi = {10.1016/j.scitotenv.2019.04.254}, pmid = {31030156}, issn = {1879-1026}, mesh = {Biodiversity ; Brassicaceae/chemistry/*microbiology ; *Environmental Monitoring ; Microbiota ; Minerals/*analysis ; Plant Leaves/chemistry/*microbiology ; Spinacia oleracea/chemistry/*microbiology ; }, abstract = {The plant microbiome is an important factor for plant health and productivity. While the impact of nitrogen (N) availability for plant growth and development is well established, its influence on the microbial phyllosphere community structure is unknown. We hypothesize that nitrogen impacts the growth and abundance of several microorganisms on the leaf surface. The bacterial and fungal communities of baby leaf spinach (Spinacia oleracea), and rocket (Diplotaxis tenuifolia) were investigated in a field trial for two years in a commercial setting. Nitrogen fertilizer was tested in four doses (basic nitrogen, basic + suboptimal, basic + commercial, basic + excess) with six replicates in each. Culture-independent (Illumina sequencing) and culture-dependent (viable count and identification of bacterial isolates) community studies were combined with monitoring of plant physiology and site weather conditions. This study found that alpha diversity of bacterial communities decreased in response to increasing nitrogen fertilizer dose, whereas viable counts showed no differences. Correspondingly, fungal communities of the spinach phyllosphere showed a decreasing pattern, whereas the decreasing diversity of fungal communities of rocket was not significant. Plant species and effects of annual variations on microbiome structure were observed for bacterial and fungal communities on both spinach and rocket. This study provides novel insights on the impact of nitrogen fertilizer regime on a nutrient scarce habitat, the phyllosphere.}, }
@article {pmid31027801, year = {2019}, author = {Pangallo, D and Kraková, L and Puškárová, A and Šoltys, K and Bučková, M and Koreňová, J and Budiš, J and Kuchta, T}, title = {Transcription activity of lactic acid bacterial proteolysis-related genes during cheese maturation.}, journal = {Food microbiology}, volume = {82}, number = {}, pages = {416-425}, doi = {10.1016/j.fm.2019.03.015}, pmid = {31027801}, issn = {1095-9998}, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; Cheese/*microbiology ; Female ; *Food Microbiology ; Gene Expression Profiling ; Lactobacillales/classification/genetics/isolation &amp; purification/*metabolism ; Metagenomics ; Microbiota/genetics ; Milk/microbiology ; Proteolysis ; RNA, Ribosomal, 16S/genetics ; Sheep ; Transcription, Genetic ; }, abstract = {The catabolism of milk protein in cheese is one way how the microorganisms influence the sensorial characteristics of the final product. In this investigation, we paid attention to four genes [prtP (cell-envelope proteinase gene), pepX (X-prolyl dipeptidyl aminopeptidase gene), pepN (aminopeptidase gene) and bcaT (branched chain aminotransferase gene)] responsible for the production of volatile aroma-active compounds from milk proteins by lactic acid bacteria (LAB). We studied the dynamics of these genes and their corresponding LAB host, during the maturation of a raw ewes' milk-based cheese, using metagenomics and metatranscriptomics approaches. The transcriptome-oriented experiments included the analysis of total RNA (at three stages of cheese maturation) and also the construction of specific cDNA sub-libraries of the abovementioned genes. The proteolytic transcriptome analysis was supported by following the transcription activity of 16S rRNA gene and by metagenomic investigation. The combination of the described methods permitted to screen the dynamics of targeted genes throughout the cheese production. Lactococci were the major players in the LAB group, but the analysis provided also information on the role and properties of members of the genus Lactobacillus, such as Lb. rhamnosus, Lb. helveticus, Lb. pentosus, Lb. curvatus, Lb. parabuchneri, Lb. plantarum, Lb. brevis, Lb. delbrueckii, Lb. paracasei, Lb. fermentum and Lb. heilongjiangensis, proteolysis-related genes of which were active during cheese ripening.}, }
@article {pmid31026582, year = {2019}, author = {Li, J and Rettedal, EA and van der Helm, E and Ellabaan, M and Panagiotou, G and Sommer, MOA}, title = {Antibiotic Treatment Drives the Diversification of the Human Gut Resistome.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {17}, number = {1}, pages = {39-51}, doi = {10.1016/j.gpb.2018.12.003}, pmid = {31026582}, issn = {2210-3244}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/isolation &amp; purification ; Drug Resistance, Bacterial/*genetics ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metagenomics ; Prospective Studies ; }, abstract = {Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.}, }
@article {pmid31026577, year = {2019}, author = {Jiang, X and Li, X and Yang, L and Liu, C and Wang, Q and Chi, W and Zhu, H}, title = {How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {17}, number = {1}, pages = {91-105}, doi = {10.1016/j.gpb.2018.09.003}, pmid = {31026577}, issn = {2210-3244}, mesh = {Gastrointestinal Microbiome/genetics ; *Genes, Microbial ; Humans ; Microbiota/*genetics ; Mining ; Models, Genetic ; Water Pollution ; }, abstract = {Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction (FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage (AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping (CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.}, }
@article {pmid31024486, year = {2019}, author = {Sirén, K and Mak, SST and Melkonian, C and Carøe, C and Swiegers, JH and Molenaar, D and Fischer, U and Gilbert, MTP}, title = {Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {697}, doi = {10.3389/fmicb.2019.00697}, pmid = {31024486}, issn = {1664-302X}, abstract = {Although there is an extensive tradition of research into the microbes that underlie the winemaking process, much remains to be learnt. We combined the high-throughput sequencing (HTS) tools of metabarcoding and metagenomics, to characterize how microbial communities of Riesling musts sampled at four different vineyards, and their subsequent spontaneously fermented derivatives, vary. We specifically explored community variation relating to three points: (i) how microbial communities vary by vineyard; (ii) how community biodiversity changes during alcoholic fermentation; and (iii) how microbial community varies between musts that successfully complete alcoholic fermentation and those that become 'stuck' in the process. Our metabarcoding data showed a general influence of microbial composition at the vineyard level. Two of the vineyards (4 and 5) had strikingly a change in the differential abundance of Metschnikowia. We therefore additionally performed shotgun metagenomic sequencing on a subset of the samples to provide preliminary insights into the potential relevance of this observation, and used the data to both investigate functional potential and reconstruct draft genomes (bins). At these two vineyards, we also observed an increase in non-Saccharomycetaceae fungal functions, and a decrease in bacterial functions during the early fermentation stage. The binning results yielded 11 coherent bins, with both vineyards sharing the yeast bins Hanseniaspora and Saccharomyces. Read recruitment and functional analysis of this data revealed that during fermentation, a high abundance of Metschnikowia might serve as a biocontrol agent against bacteria, via a putative iron depletion pathway, and this in turn could help Saccharomyces dominate the fermentation. During alcoholic fermentation, we observed a general decrease in biodiversity in both the metabarcoding and metagenomic data. Unexpected Micrococcus behavior was observed in vineyard 4 according to metagenomic analyses based on reference-based read mapping. Analysis of open reading frames using these data showed an increase of functions assigned to class Actinobacteria in the end of fermentation. Therefore, we hypothesize that bacteria might sit-and-wait until Saccharomyces activity slows down. Complementary approaches to annotation instead of relying a single database provide more coherent information true species. Lastly, our metabarcoding data enabled us to identify a relationship between stuck fermentations and Starmerella abundance. Given that robust chemical analysis indicated that although the stuck samples contained residual glucose, all fructose had been consumed, we hypothesize that this was because fructophilic Starmerella, rather than Saccharomyces, dominated these fermentations. Overall, our results showcase the different ways in which metagenomic analyses can improve our understanding of the wine alcoholic fermentation process.}, }
@article {pmid31023629, year = {2019}, author = {Tokarz, R and Tagliafierro, T and Sameroff, S and Cucura, DM and Oleynik, A and Che, X and Jain, K and Lipkin, WI}, title = {Microbiome analysis of Ixodes scapularis ticks from New York and Connecticut.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {4}, pages = {894-900}, doi = {10.1016/j.ttbdis.2019.04.011}, pmid = {31023629}, issn = {1877-9603}, mesh = {Anaplasma phagocytophilum/genetics/isolation &amp; purification ; Animals ; Babesia microti/genetics/isolation &amp; purification ; Bacteria/*genetics/isolation &amp; purification ; Borrelia/genetics/isolation &amp; purification ; Connecticut ; Encephalitis Viruses, Tick-Borne/genetics/isolation &amp; purification ; Female ; High-Throughput Nucleotide Sequencing ; Ixodes/*microbiology/parasitology/virology ; Male ; Metagenomics ; *Microbiota ; Nematoda/genetics/isolation &amp; purification ; New York ; Nymph/microbiology/parasitology/virology ; Rickettsia/genetics/isolation &amp; purification ; Viruses/*genetics/isolation &amp; purification ; }, abstract = {We employed high throughput sequencing to survey the microbiomes of Ixodes scapularis collected in New York and Connecticut. We examined 197 individual I. scapularis adults and pools from 132 adults and 197 nymphs. We detected Borrelia burgdorferi sensu stricto in 56.3% of individual ticks, Anaplasma phagocytophilum in 10.6%, Borrelia miyamotoi in 5%, Babesia microti in 7.6%, and Powassan virus in 3.6%. We did not detect Borrelia mayonii, Ehrlichia muris eauclairensis, Bartonella spp. or pathogenic Babesia species other than B. microti. The most abundant bacterium (65%), and only rickettsial species identified, was the endosymbiont Rickettsia buchneri. A filarial nematode was found in 13.7% of adult ticks. Fourteen viruses were detected including South Bay virus (22%) and blacklegged tick phlebovirus 1 and 2 (73%). This study provides insight into the microbial diversity of I. scapularis in New York State and Connecticut.}, }
@article {pmid31015324, year = {2019}, author = {Easton, AV and Quiñones, M and Vujkovic-Cvijin, I and Oliveira, RG and Kepha, S and Odiere, MR and Anderson, RM and Belkaid, Y and Nutman, TB}, title = {The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.00519-19}, pmid = {31015324}, issn = {2150-7511}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anthelmintics/*administration &amp; dosage ; Ascariasis/*drug therapy ; Bacteria/*classification/genetics ; Child ; Child, Preschool ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Kenya ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; Necatoriasis/*drug therapy ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rural Population ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Murine studies suggest that the presence of some species of intestinal helminths is associated with changes in host microbiota composition and diversity. However, studies in humans have produced varied conclusions, and the impact appears to vary widely depending on the helminth species present. To demonstrate how molecular approaches to the human gut microbiome can provide insights into the complex interplay among disparate organisms, DNA was extracted from cryopreserved stools collected from residents of 5 rural Kenyan villages prior to and 3 weeks and 3 months following albendazole (ALB) therapy. Samples were analyzed by quantitative PCR (qPCR) for the presence of 8 species of intestinal parasites and by MiSeq 16S rRNA gene sequencing. Based on pretreatment results, the presence of neither Ascaris lumbricoides nor Necator americanus infection significantly altered the overall diversity of the microbiota in comparison with age-matched controls. Following ALB therapy and clearance of soil-transmitted helminths (STH), there were significant increases in the proportion of the microbiota made up by Clostridiales (P = 0.0002; average fold change, 0.57) and reductions in the proportion made up by Enterobacteriales (P = 0.0004; average fold change, -0.58). There was a significant posttreatment decrease in Chao1 richness, even among individuals who were uninfected pretreatment, suggesting that antimicrobial effects must be considered in any posttreatment setting. Nevertheless, the helminth-associated changes in Clostridiales and Enterobacteriales suggest that clearance of STH, and of N. americanus in particular, alters the gut microbiota.IMPORTANCE The gut microbiome is an important factor in human health. It is affected by what we eat, what medicines we take, and what infections we acquire. In turn, it affects the way we absorb nutrients and whether we have excessive intestinal inflammation. Intestinal worms may have an important impact on the composition of the gut microbiome. Without a complete understanding of the impact of mass deworming programs on the microbiome, it is impossible to accurately calculate the cost-effectiveness of such public health interventions and to guard against any possible deleterious side effects. Our research examines this question in a &quot;real-world&quot; setting, using a longitudinal cohort, in which individuals with and without worm infections are treated with deworming medication and followed up at both three weeks and three months posttreatment. We quantify the impact of roundworms and hookworms on gut microbial composition, suggesting that the impact is small, but that treatment of hookworm infection results in significant changes. This work points to the need for follow-up studies to further examine the impact of hookworm on the gut microbiota and determine the health consequences of the observed changes.}, }
@article {pmid31013927, year = {2019}, author = {Laitinen, K and Mokkala, K}, title = {Overall Dietary Quality Relates to Gut Microbiota Diversity and Abundance.}, journal = {International journal of molecular sciences}, volume = {20}, number = {8}, pages = {}, doi = {10.3390/ijms20081835}, pmid = {31013927}, issn = {1422-0067}, support = {#258606//Academy of Finland/ ; -//State research funding for university level health research of the Turku University Hospital Expert Responsibility Area/ ; -//Diabetes Research Foundation/ ; -//Juho Vainio Foundation/ ; }, mesh = {Biodiversity ; *Diet ; Disease Susceptibility ; Female ; *Food Quality ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; Obesity ; Overweight ; Pregnancy ; Public Health Surveillance ; RNA, Ribosomal, 16S ; }, abstract = {Disturbances in gut microbiota homeostasis may have metabolic consequences with potentially serious clinical manifestations. Diet influences the host's metabolic health in several ways, either directly or indirectly by modulating the composition and function of gut microbiota. This study investigated the extent to which dietary quality is reflected in gut microbiota diversity in overweight and obese pregnant women at risk for metabolic complications. Dietary quality was measured by a validated index of diet quality (IDQ) and microbiota composition was analyzed using 16SrRNA gene sequencing from 84 women pregnant less than 18 weeks. The alpha diversity, measured as Chao1, observed operational taxonomic units (OTUs), phylogenetic diversity, and the Shannon index were calculated. The IDQ score correlated positively with the Shannon index (rho = 0.319, p = 0.003), but not with the other indexes. The women who had the highest dietary quality (highest IDQ quartile) had higher gut microbiota diversity in all the investigated indexes, when compared to the women with the lowest dietary quality (lowest IDQ quartile; p < 0.032). Consequently, a higher dietary quality was reflected in a higher gut microbiota diversity. The presented approach may aid in devising new tools for dietary counseling aiming at holistic health, as well as in microbiome studies, to control for dietary variance.}, }
@article {pmid31012060, year = {2019}, author = {Lorenzi, AS and Chia, MA and Lopes, FAC and Silva, GGZ and Edwards, RA and Bittencourt-Oliveira, MDC}, title = {Cyanobacterial biodiversity of semiarid public drinking water supply reservoirs assessed via next-generation DNA sequencing technology.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {57}, number = {6}, pages = {450-460}, doi = {10.1007/s12275-019-8349-7}, pmid = {31012060}, issn = {1976-3794}, mesh = {Bacterial Toxins/analysis/genetics/isolation &amp; purification ; *Biodiversity ; Brazil ; Cyanobacteria/*classification/genetics/*isolation &amp; purification ; DNA, Bacterial/analysis ; Drinking Water/*microbiology ; Environmental Monitoring/methods ; Genes, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Microcystis/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Saxitoxin/genetics ; Seasons ; Sequence Analysis, DNA/*methods ; Uracil/analogs &amp; derivatives ; *Water Microbiology ; *Water Supply ; }, abstract = {Next-generation DNA sequencing technology was applied to generate molecular data from semiarid reservoirs during well-defined seasons. Target sequences of 16S-23S rRNA ITS and cpcBA-IGS were used to reveal the taxonomic groups of cyanobacteria present in the samples, and genes coding for cyanotoxins such as microcystins (mcyE), saxitoxins (sxtA), and cylindrospermopsins (cyrJ) were investigated. The presence of saxitoxins in the environmental samples was evaluated using ELISA kit. Taxonomic analyses of high-throughput DNA sequencing data showed the dominance of the genus Microcystis in Mundaú reservoir. Furthermore, it was the most abundant genus in the dry season in Ingazeira reservoir. In the rainy season, 16S-23S rRNA ITS analysis revealed that Cylindrospermopsis raciborskii comprised 46.8% of the cyanobacterial community in Ingazeira reservoir, while the cpcBAIGS region revealed that C. raciborskii (31.8%) was the most abundant taxon followed by Sphaerospermopsis aphanizomenoides (17.3%) and Planktothrix zahidii (16.6%). Despite the presence of other potential toxin-producing genera, the detected sxtA gene belonged to C. raciborskii, while the mcyE gene belonged to Microcystis in both reservoirs. The detected mcyE gene had good correlation with MC content, while the amplification of the sxtA gene was related to the presence of STX. The cyrJ gene was not detected in these samples. Using DNA analyses, our results showed that the cyanobacterial composition of Mundaú reservoir was similar in successive dry seasons, and it varied between seasons in Ingazeira reservoir. In addition, our data suggest that some biases of analysis influenced the cyanobacterial communities seen in the NGS output of Ingazeira reservoir.}, }
@article {pmid31004827, year = {2019}, author = {Sung, CM and Lin, YF and Chen, KF and Ke, HM and Huang, HY and Gong, YN and Tsai, WS and You, JF and Lu, MJ and Cheng, HT and Lin, CY and Kuo, CJ and Tsai, IJ and Hsieh, SY}, title = {Predicting Clinical Outcomes of Cirrhosis Patients With Hepatic Encephalopathy From the Fecal Microbiome.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {8}, number = {2}, pages = {301-318.e2}, doi = {10.1016/j.jcmgh.2019.04.008}, pmid = {31004827}, issn = {2352-345X}, abstract = {BACKGROUND &amp; AIMS: Gut dysbiosis plays a role in hepatic encephalopathy (HE), while its relationship at the acute episode of overt HE (AHE), the disease progression and clinical outcomes remains unclear. We aimed to identify AHE-specific microbiome and its association to patients' outcomes.<br><br>METHODS: We profiled fecal microbiome changes for a cohort of 62 patients with cirrhosis and AHE i) before treatment, ii) 2-3 days after medication and iii) 2-3 months after recovery, and three control cohorts i) healthy individuals, patients with ii) compensated or iii) decompensated cirrhosis.<br><br>RESULTS: Comparison of the microbiome shift from compensated, decompensated cirrhosis, AHE to recovery revealed the AHE-specific gut-dysbiosis. The gut microbiome diversity was decreased during AHE, further reduced after medication, and only partially reversed during the recovery. The relative abundance of Bacteroidetes phylum in the microbiome decreased, whereas that of Firmicute, Proteobacteria and Actinobacteria increased in patients during AHE compared with those with compensated cirrhosis. A total of 70 operational taxonomic units (OTUs) were significantly different between AHE and decompensated cirrhosis abundances. Of them, the abundance of Veillonella parvula increased the most during AHE via a metagenomics recovery of the genomes. Moreover, the relative abundances of three (Alistipes, Bacteroides, Phascolarctobacterium) and five OTUs (Clostridium-XI, Bacteroides, Bacteroides, Lactobacillus, Clostridium-sedis) at AHE were respectively associated with HE recurrence and overall survival during the subsequent one-year follow-up.<br><br>CONCLUSIONS: AHE-specific gut OTUs were identified that may be involved in HE development and able to predict clinical outcomes, providing new strategies for the prevention and treatment of HE recurrence in patients with cirrhosis.}, }
@article {pmid31000700, year = {2019}, author = {Dong, X and Greening, C and Rattray, JE and Chakraborty, A and Chuvochina, M and Mayumi, D and Dolfing, J and Li, C and Brooks, JM and Bernard, BB and Groves, RA and Lewis, IA and Hubert, CRJ}, title = {Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1816}, doi = {10.1038/s41467-019-09747-0}, pmid = {31000700}, issn = {2041-1723}, mesh = {Acetates/metabolism ; Archaea/genetics/isolation &amp; purification/*metabolism ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; Metagenome ; Metagenomics/methods ; Mexico ; Microbial Interactions/physiology ; Microbiota/*physiology ; Petroleum/*metabolism ; }, abstract = {The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.}, }
@article {pmid30992350, year = {2019}, author = {Cobián Güemes, AG and Lim, YW and Quinn, RA and Conrad, DJ and Benler, S and Maughan, H and Edwards, R and Brettin, T and Cantú, VA and Cuevas, D and Hamidi, R and Dorrestein, P and Rohwer, F}, title = {Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.00431-19}, pmid = {30992350}, issn = {2150-7511}, mesh = {Adult ; Case-Control Studies ; Coinfection/complications ; Cystic Fibrosis/*complications/microbiology ; Disease Management ; *Disease Progression ; Escherichia coli Infections/*diagnosis ; Fatal Outcome ; Gene Expression Profiling ; *Genomics ; Humans ; Lung/*microbiology/physiopathology ; Male ; Metabolome ; *Metabolomics ; Metagenome ; Microbiota ; Shiga Toxin/genetics ; Shiga-Toxigenic Escherichia coli/genetics/pathogenicity ; }, abstract = {Pulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidly monitor active members of the viral and microbial community during acute CF exacerbations. To highlight CFRR, a case study of a CF patient is presented, in which an abrupt decline in lung function characterized a fatal exacerbation. The microbial community in the patient's lungs was closely monitored through the multi-omics strategy, which led to the identification of pathogenic shigatoxigenic Escherichia coli (STEC) expressing Shiga toxin. This case study illustrates the potential for the CFRR to deconstruct complicated disease dynamics and provide clinicians with alternative treatments to improve the outcomes of pulmonary exacerbations and expand the life spans of individuals with CF.IMPORTANCE Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient's microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenic Escherichia coli The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.}, }
@article {pmid30979963, year = {2019}, author = {Singer, GAC and Fahner, NA and Barnes, JG and McCarthy, A and Hajibabaei, M}, title = {Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5991}, doi = {10.1038/s41598-019-42455-9}, pmid = {30979963}, issn = {2045-2322}, abstract = {The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.}, }
@article {pmid30978480, year = {2019}, author = {Reddy, B and Pandey, J and Dubey, SK}, title = {Assessment of environmental gene tags linked with carbohydrate metabolism and chemolithotrophy associated microbial community in River Ganga.}, journal = {Gene}, volume = {704}, number = {}, pages = {31-41}, doi = {10.1016/j.gene.2019.04.004}, pmid = {30978480}, issn = {1879-0038}, mesh = {Animals ; Bacteria/classification/genetics/growth &amp; development ; Carbohydrate Metabolism/*genetics ; Chemoautotrophic Growth/*genetics ; DNA Barcoding, Taxonomic ; Environment ; Geologic Sediments/*microbiology ; Humans ; India ; Metabolic Networks and Pathways/genetics ; Metagenome ; *Metagenomics/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; }, abstract = {The microbial community mediated biogeochemical cycles play important role in global C-cycle and display a sensitive response to environmental changes. Limited information is available on microbial composition and functional diversity controlling biogeochemical cycles in the riverine environment. The Ganga River water and sediment samples were studied for environmental gene tags with reference to carbohydrate metabolism, photoheterotrophy and chemolithotrophy using high throughput shotgun metagenomic sequencing and functional annotation. The diversity of environmental gene tags specific microbial community was annotated against reference sequence database using Kaiju taxonomic classifier. The metagenomic analyses revealed that the river harbored a broad range of carbohydrate and energy metabolism genes. The in-depth investigation of metagenomic data revealed that the enzymes associated with reverse TCA cycle, Calvin-Benson cycle enzyme RuBisCO, starch and sucrose metabolism genes were highly abundant. The enzymes associated with sulfur metabolism such as EC:2.7.7.4 (sulfate to ammonium per sulfate), EC:1.8.1.2, EC:1.8.7.1 (sulfite to H2S) were prevalent in both the class of samples. The principal component analysis of the functional profiles revealed that the water and sediment samples were clustered distinctly suggesting that both the sites had variable abundance of functional genes and associated microbiota. The taxonomic classification showed abundance of Proteobacteria, Actinobacteria and Bacteroidetes phyla. Also, the metagenomic study showed the presence of purple sulfur bacteria viz. Thiodictyon, Nitrosococcus and purple non-sulfur bacteria viz. Bradyrhozobium and Rhodobacter. The study demonstrates that the Ganga River microbiome has prevalence of functional genes involved in carbohydrate anabolism and catabolism, and CO2 fixation with great prospects in cellulose and sulfide degrading enzyme production and characterization.}, }
@article {pmid30974142, year = {2019}, author = {Cheng, Y and Sibusiso, L and Hou, L and Jiang, H and Chen, P and Zhang, X and Wu, M and Tong, H}, title = {Sargassum fusiforme fucoidan modifies the gut microbiota during alleviation of streptozotocin-induced hyperglycemia in mice.}, journal = {International journal of biological macromolecules}, volume = {131}, number = {}, pages = {1162-1170}, doi = {10.1016/j.ijbiomac.2019.04.040}, pmid = {30974142}, issn = {1879-0003}, mesh = {Animals ; Blood Glucose/*drug effects ; Chemical Phenomena ; Diabetes Mellitus, Experimental ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Profiling ; Hyperglycemia/*blood/drug therapy/*etiology ; Liver/drug effects/metabolism/pathology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Oxidative Stress/drug effects ; Polysaccharides/*chemistry/*pharmacology ; Sargassum/*chemistry ; Spectrum Analysis ; Streptozocin/adverse effects ; Transcriptome ; }, abstract = {Diabetes is a complicated endocrine and metabolic disorder, which has become an epidemic health issue worldwide. Fucoidan is extensively distributed in the brown algae and several marine invertebrates exhibiting diverse biological activities. In the present study, the physicochemical property of Sargassum fusiforme fucoidan (SFF) and its effects on streptozotocin (STZ)-induced diabetic mice and gut microbiota were investigated. Diabetes mice not only showed abnormal blood glucose, but also accompanied by multiple symptoms, such as gradual emaciation, decreased body weight, increased food and water intake. Compared with diabetic mice after 6-week treatment, administration of SFF significantly decreased the fasting blood glucose, diet and water intake. Furthermore, SFF attenuated the pathological change in the heart and liver, improved the liver function, and suppressed oxidative stress in STZ-induced diabetic mice. Simultaneously, SFF significantly altered the gut microbiota in the faeces of diabetic mice, decreased the relative abundances of the diabetes-related intestinal bacteria, which is a potential mechanism for relieving the symptoms of diabetes. Therefore, SFF might be considered as one of the promising complementary and alternative medicines for the management of diabetes mellitus in future.}, }
@article {pmid30968165, year = {2019}, author = {Rossmassler, K and Snow, CD and Taggart, D and Brown, C and De Long, SK}, title = {Advancing biomarkers for anaerobic o-xylene biodegradation via metagenomic analysis of a methanogenic consortium.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {10}, pages = {4177-4192}, doi = {10.1007/s00253-019-09762-7}, pmid = {30968165}, issn = {1432-0614}, support = {CBET 1438660//National Science Foundation/ ; }, mesh = {Anaerobiosis ; *Biotransformation ; Enzymes/*genetics ; *Genetic Markers ; Metagenomics ; Microbial Consortia/*genetics ; Xylenes/*metabolism ; }, abstract = {Quantifying functional biomarker genes and their transcripts provides critical lines of evidence for contaminant biodegradation; however, accurate quantification depends on qPCR primers that contain no, or minimal, mismatches with the target gene. Developing accurate assays has been particularly challenging for genes encoding fumarate-adding enzymes (FAE) due to the high level of genetic diversity in this gene family. In this study, metagenomics applied to a field-derived, o-xylene-degrading methanogenic consortium revealed genes encoding FAE that would not be accurately quantifiable by any previously available PCR assays. Sequencing indicated that a gene similar to the napthylmethylsuccinate synthase gene (nmsA) was most abundant, although benzylsuccinate synthase genes (bssA) also were present along with genes encoding alkylsuccinate synthase (assA). Upregulation of the nmsA-like gene was observed during o-xylene degradation. Protein homology modeling indicated that mutations in the active site, relative to a BssA that acts on toluene, increase binding site volume and accessibility, potentially to accommodate the relatively larger o-xylene. The new nmsA-like gene was also detected at substantial concentrations at field sites with a history of xylene contamination.}, }
@article {pmid30967110, year = {2019}, author = {Hua, K and Zhang, X}, title = {Estimating the total genome length of a metagenomic sample using k-mers.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {183}, doi = {10.1186/s12864-019-5467-x}, pmid = {30967110}, issn = {1471-2164}, mesh = {Algorithms ; Datasets as Topic ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {BACKGROUND: Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition, limited availability of known reference genomes, and usually insufficient sequencing coverage.<br><br>RESULTS: As an initial step toward understanding the complete composition of a metagenomic sample, we studied the problem of estimating the total length of all distinct component genomes in a metagenomic sample. We showed that this problem can be solved by estimating the total number of distinct k-mers in all the metagenomic sequencing data. We proposed a method for this estimation based on the sequencing coverage distribution of observed k-mers, and introduced a k-mer redundancy index (KRI) to fill in the gap between the count of distinct k-mers and the total genome length. We showed the effectiveness of the proposed method on a set of carefully designed simulation data corresponding to multiple situations of true metagenomic data. Results on real data indicate that the uncaptured genomic information can vary dramatically across metagenomic samples, with the potential to mislead downstream analyses.<br><br>CONCLUSIONS: We proposed the question of how long the total genome length of all different species in a microbial community is and introduced a method to answer it.}, }
@article {pmid30967109, year = {2019}, author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T}, title = {ENIGMA: an enterotype-like unigram mixture model for microbial association analysis.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {191}, doi = {10.1186/s12864-019-5476-9}, pmid = {30967109}, issn = {1471-2164}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Case-Control Studies ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbial Interactions ; Microbiota ; *Models, Biological ; Parkinson Disease/genetics/*microbiology ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial communities form clusters called as &quot;enterotype&quot;, which are characterized by differences in specific bacterial taxa, making it difficult to analyze these data under health and disease conditions. Traditional probabilistic modeling cannot distinguish between the bacterial differences derived from enterotype and those related to a specific disease.<br><br>RESULTS: We propose a new probabilistic model, named as ENIGMA (Enterotype-like uNIGram mixture model for Microbial Association analysis), which can be used to address these problems. ENIGMA enabled simultaneous estimation of enterotype-like clusters characterized by the abundances of signature bacterial genera and the parameters of environmental effects associated with the disease.<br><br>CONCLUSION: In the simulation study, we evaluated the accuracy of parameter estimation. Furthermore, by analyzing the real-world data, we detected the bacteria related to Parkinson's disease. ENIGMA is implemented in R and is available from GitHub (https://github.com/abikoushi/enigma).}, }
@article {pmid30962514, year = {2019}, author = {Tan, S and Liu, J and Fang, Y and Hedlund, BP and Lian, ZH and Huang, LY and Li, JT and Huang, LN and Li, WJ and Jiang, HC and Dong, HL and Shu, WS}, title = {Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2044-2057}, doi = {10.1038/s41396-019-0415-y}, pmid = {30962514}, issn = {1751-7370}, support = {U1501232//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31570506//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41603074//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31600077//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41773132//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41622106//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31570500//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41630103//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2016A030312003//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; DEB-1557042//National Science Foundation (NSF)/ ; }, abstract = {Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.}, }
@article {pmid30962029, year = {2019}, author = {Brink, M and Rhode, C and Macey, BM and Christison, KW and Roodt-Wilding, R}, title = {Metagenomic assessment of body surface bacterial communities of the sea urchin, Tripneustes gratilla.}, journal = {Marine genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.margen.2019.03.010}, pmid = {30962029}, issn = {1876-7478}, abstract = {Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface bacterial communities associated with T. gratilla, using a 16S rDNA gene metagenomics approach, to provide insight into the bacterial agents associated with this aquaculture species, as well as with this balding disease. Bacterial samples were collected from non-lesioned healthy animals obtained from natural locations along the eastern coast of South Africa, as well as from different cultured cohorts: non-lesioned healthy-, lesioned diseased- and non-lesioned stressed animals. A total of 1,067,515 individual bacterial operational taxonomic units (OTUs) were identified, belonging to 133 family-, 123 genus- and 113 species level OTU groups. Alpha diversity analyses, based on Chao1, Shannon and Simpson indices, showed that there were no statistically significant differences (ANOVA; P > 0.05) between the respective cohorts, as all cohorts displayed a high degree of bacterial diversity. Similarly, beta diversity analyses (Non-metric multidimensional scaling) showed a large degree of overlapping OTUs across the four cohorts. Within each cohort, various OTUs commonly associated with marine environments were found, predominantly belonging to the families Vibrionaceae, Saprospiraceae, Flavobacteriaceae and Sphingomonadaceae. Differential abundance analysis (DESeq2) revealed that OTUs that are differentially abundant across cohorts were likely not responsible for this balding disease, suggesting that complex bacterial agents, rather than a specific pathogenic agent, are likely causing this disease. Furthermore, the putative metabolic functions assigned to the bacterial communities showed that heterotrophic bacteria appear to be responsible for tissue lysis of degrading animal matter. The results from this study, obtained through univariate and multivariate-based approaches, contributes to future management strategies of this emerging aquaculture species by providing insight into the bacterial communities associated with both natural and cultured environments.}, }
@article {pmid30958827, year = {2019}, author = {Martí, JM}, title = {Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.}, journal = {PLoS computational biology}, volume = {15}, number = {4}, pages = {e1006967}, doi = {10.1371/journal.pcbi.1006967}, pmid = {30958827}, issn = {1553-7358}, mesh = {Algorithms ; Big Data ; Computational Biology/methods ; DNA Contamination ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; Software ; Whole Genome Sequencing/methods ; }, abstract = {Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications. In addition to contamination-subtracted samples, Recentrifuge provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics. Regarding the first area, Recentrifuge's novel approach has already demonstrated its benefits showing that microbiomes of Arctic and Antarctic solar panels display similar taxonomic profiles. In the clinical field, to confirm Recentrifuge's ability to analyze complex metagenomes, we challenged it with data coming from a metagenomic investigation of RNA in plasma that suffered from critical contamination to the point of preventing any positive conclusion. Recentrifuge provided results that yielded new biological insight into the problem, supporting the growing evidence of a blood microbiota even in healthy individuals, mostly translocated from the gut, the oral cavity, and the genitourinary tract. We also developed a synthetic dataset carefully designed to rate the robust contamination removal algorithm, which demonstrated a significant improvement in specificity while retaining a high sensitivity even in the presence of cross-contaminants. Recentrifuge's official website is www.recentrifuge.org. The data and source code are anonymously and freely available on GitHub and PyPI. The computing code is licensed under the AGPLv3. The Recentrifuge Wiki is the most extensive and continually-updated source of documentation for Recentrifuge, covering installation, use cases, testing, and other useful topics.}, }
@article {pmid30955771, year = {2019}, author = {Cotta, SR and Cadete, LL and van Elsas, JD and Andreote, FD and Dias, ACF}, title = {Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {586-594}, doi = {10.1016/j.marpolbul.2019.03.001}, pmid = {30955771}, issn = {1879-3363}, mesh = {Bacteria/genetics/metabolism ; Biodiversity ; Brazil ; Carbon/metabolism ; Ecosystem ; Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota/genetics ; Sulfur/metabolism ; *Wetlands ; }, abstract = {Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks (&quot;blue carbon&quot;). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance.}, }
@article {pmid30955749, year = {2019}, author = {Fernandes, C and Kankonkar, H and Meena, RM and Menezes, G and Shenoy, BD and Khandeparker, R}, title = {Metagenomic analysis of tarball-associated bacteria from Goa, India.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {398-403}, doi = {10.1016/j.marpolbul.2019.02.040}, pmid = {30955749}, issn = {1879-3363}, mesh = {Biodegradation, Environmental ; Environmental Monitoring/*methods ; Humans ; India ; Marinobacter/genetics/isolation &amp; purification ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; Petroleum/*analysis ; Polycyclic Aromatic Hydrocarbons/*analysis ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*analysis ; }, abstract = {The beaches of Goa state in India are frequently polluted with tarballs, specifically during pre-monsoon and monsoon seasons. Tarballs contain hydrocarbons, including polycyclic aromatic hydrocarbons, which pose significant environmental risks. Microbes associated with tarballs reportedly possess capabilities to degrade toxic hydrocarbons present in tarballs. In this study, bacterial diversity associated with tarballs from Vagator and Morjim beaches of north Goa was analysed based on V3-V4 regions of 16S rRNA gene sequenced using Illumina Miseq Platform. The Proteobacterial members were dominant in both Vagator (≥85.5%) and Morjim (≥94.0%) samples. Many of the identified taxa have been previously reported as hydrocarbon degraders (e.g. Halomonas, Marinobacter) or possible human pathogens (e.g. Acinetobacter, Klebsiella, Rhodococcus, Staphylococcus, Vibrio). This is the first study reported on a metagenomic analysis of bacteria associated with tarballs from Goa.}, }
@article {pmid30953747, year = {2019}, author = {Wei, T and Bao, JY and Yang, HH and Lin, JF and Zheng, QW and Ye, ZW and Zou, Y and Li, X and Jiang, ZL and Guo, LQ}, title = {Musa basjoo regulates the gut microbiota in mice by rebalancing the abundance of probiotic and pathogen.}, journal = {Microbial pathogenesis}, volume = {131}, number = {}, pages = {205-211}, doi = {10.1016/j.micpath.2019.04.003}, pmid = {30953747}, issn = {1096-1208}, mesh = {Animal Feed ; Animals ; Bacteroides/physiology ; Cell Wall/metabolism ; China ; DNA, Ribosomal ; Disease Models, Animal ; Feces/microbiology ; Food Safety ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Lactobacillus casei/physiology ; Lactobacillus plantarum/physiology ; Metagenomics ; Mice/*microbiology ; Mice, Inbred BALB C ; Musa/*chemistry ; *Probiotics/classification/pharmacology ; Specific Pathogen-Free Organisms ; }, abstract = {Musa basjoo is a kind of popular slimming fruit in southern China. However, even though the trophic component and physiological effect are well studied, its internal mechanism in reconstructing gut microbiota remains unclear. In this study, maturity of M. basjoo were divided into four levels. Results indicated that M. basjoo in level Ⅱ (with 35% maturity) represented the greatest increase in the growth in vitro of probiotics, Lactobacillus plantarum FMNP01 and Lactobacillus casei FMNP02. After feeding M. basjoo with the middle dose (2.67 g/kg·BW) to mice for 21 days, gut microbiota from mice feces was isolated and sequenced. Results of 16SrDNA sequencing showed that the scattered genera of gut microbiota were significantly gathered. The amounts of different pathogens were decreased, while probiotics such as genera Bacteroides and Roseburia were significantly increased (p < 0.05). Results of function prediction indicated that the reconstruction of gut microbiota may due to the change in carbohydrate transportation, biosynthesis of cell wall, cell membrane, and cell envelope. This study has drawn a basic mechanism in reconstructing gut microbiota by feeding M. basjoo and lay out a foundation for further reach on the interaction between human as diner and M. basjoo as food.}, }
@article {pmid30953542, year = {2019}, author = {Raymond, F and Boissinot, M and Ouameur, AA and Déraspe, M and Plante, PL and Kpanou, SR and Bérubé, È and Huletsky, A and Roy, PH and Ouellette, M and Bergeron, MG and Corbeil, J}, title = {Culture-enriched human gut microbiomes reveal core and accessory resistance genes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {56}, doi = {10.1186/s40168-019-0669-7}, pmid = {30953542}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/drug effects/genetics/growth &amp; development ; Bacterial Proteins/genetics ; Bacteriological Techniques/*methods ; *Drug Resistance, Microbial ; Escherichia coli/genetics/growth &amp; development/isolation &amp; purification ; Feces/cytology/microbiology ; Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Humans ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer.<br><br>RESULTS: Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements.<br><br>CONCLUSION: Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.}, }
@article {pmid30953134, year = {2019}, author = {Grieco, MB and Lopes, FAC and Oliveira, LS and Tschoeke, DA and Popov, CC and Thompson, CC and Gonçalves, LC and Constantino, R and Martins, OB and Kruger, RH and de Souza, W and Thompson, FL}, title = {Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim.}, journal = {Current microbiology}, volume = {76}, number = {6}, pages = {687-697}, doi = {10.1007/s00284-019-01662-3}, pmid = {30953134}, issn = {1432-0991}, support = {563055/2010-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; E-26/ 110.634/2014//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, mesh = {Animals ; Bacteria/*classification/*genetics ; Biodiversity ; Brazil ; Feeding Behavior ; *Gastrointestinal Microbiome ; Isoptera/*microbiology/physiology ; Metagenomics ; }, abstract = {Although some previous studies have described the microbial diversity of termite in Brazil, the lack of studies about this subject is still evident. In the present study, we described by whole genome sequencing, the gut microbiota of seven species of termites (Termitidae) with different feeding habits from four Brazilian locations. For the litter species, the most abundant bacterial phylum was Firmicutes, where Cornitermes cumulans and Syntermes dirus (Syntermitinae) were identified. For the humus species, the most abundant bacterial phylum was Proteobacteria where three species were studied: Cyrilliotermes strictinasus (Syntermitinae), Grigiotermes bequaerti (Apicotermitinae), and Orthognathotermes mirim (Termitinae). For the wood termites, Firmicutes and Spirochaetes were the most abundant phyla, respectively, where two species were identified: Nasutitermes aquilinus and Nasutitermes jaraguae (Nasutitermitinae). The gut microbiota of all four examined subfamilies shared a conserved functional and carbohydrate-active enzyme profile and specialized in cellulose and chitin degradation. Taken together, these results provide insight into the partnerships between termite and microbes that permit the use of refractory energy sources.}, }
@article {pmid30953119, year = {2019}, author = {Deng, Y and Xu, X and Yin, X and Lu, H and Chen, G and Yu, J and Ruan, Y}, title = {Effect of stock density on the microbial community in biofloc water and Pacific white shrimp (Litopenaeus vannamei) gut microbiota.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {10}, pages = {4241-4252}, doi = {10.1007/s00253-019-09773-4}, pmid = {30953119}, issn = {1432-0614}, mesh = {Animals ; Aquaculture/*methods ; Bacteria/*classification/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; Penaeidae/*microbiology ; *Water Microbiology ; }, abstract = {Biofloc technology is an efficient approach for intensive shrimp culture. However, the extent to which this process can influence the composition of intestinal microbial community is still unknown. Here, we surveyed the shrimp intestinal bacteria as well as the floc water from three biofloc systems with different stock densities. Our study revealed a similar variation trend in phylum taxonomy level between floc bacteria and gut microbiota. Microbial community varied notably in floc water from different stock densities, while a core genus with dominating relative abundance was detected in gut samples. Extensive variation was discovered in gut microbiota, but still clustered into groups according to stock density. Our results indicated that shrimp intestinal microbiota as well as bacteria aggregated in flocs assembled into distinct communities from different stock densities, and the intestinal communities were more similar with the surrounding environment as the increase of stock density and resulting high floc biomass. The high stock density changed the core gut microbiota by reducing the relative abundance of Paracoccus and increasing that of Nocardioides, which may negatively influence shrimp performance. Therefore, this study helps us to understand further bacteria and host interactions in biofloc system.}, }
@article {pmid30947688, year = {2019}, author = {Sevigny, JL and Rothenheber, D and Diaz, KS and Zhang, Y and Agustsson, K and Bergeron, RD and Thomas, WK}, title = {Marker genes as predictors of shared genomic function.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {268}, doi = {10.1186/s12864-019-5641-1}, pmid = {30947688}, issn = {1471-2164}, support = {P20 GM103506/GM/NIGMS NIH HHS/United States ; 16-052: SA 16-18//Gulf of Mexico Research Initiative/ ; 5 P20 GM 10350605//National Institutes of Health: New Hampshire Idea Network of Biological Research Excellence/ ; }, mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genes, Bacterial/genetics/*physiology ; *Genetic Markers ; *Genome, Bacterial ; *Metagenome ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Although high-throughput marker gene studies provide valuable insight into the diversity and relative abundance of taxa in microbial communities, they do not provide direct measures of their functional capacity. Recently, scientists have shown a general desire to predict functional profiles of microbial communities based on phylogenetic identification inferred from marker genes, and recent tools have been developed to link the two. However, to date, no large-scale examination has quantified the correlation between the marker gene based taxonomic identity and protein coding gene conservation. Here we utilize 4872 representative prokaryotic genomes from NCBI to investigate the relationship between marker gene identity and shared protein coding gene content.<br><br>RESULTS: Even at 99-100% marker gene identity, genomes share on average less than 75% of their protein coding gene content. This occurs regardless of the marker gene(s) used: V4 region of the 16S rRNA, complete 16S rRNA, or single copy orthologs through a multi-locus sequence analysis. An important aspect related to this observation is the intra-organism variation of 16S copies from a single genome. Although the majority of 16S copies were found to have high sequence similarity (> 99%), several genomes contained copies that were highly diverged (< 97% identity).<br><br>CONCLUSIONS: This is the largest comparison between marker gene similarity and shared protein coding gene content to date. The study highlights the limitations of inferring a microbial community's functions based on marker gene phylogeny. The data presented expands upon the results of previous studies that examined one or few bacterial species and supports the hypothesis that 16S rRNA and other marker genes cannot be directly used to fully predict the functional potential of a bacterial community.}, }
@article {pmid30946154, 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 antiretroviral therapy-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.}, journal = {AIDS (London, England)}, volume = {33}, number = {6}, pages = {1001-1011}, doi = {10.1097/QAD.0000000000002131}, pmid = {30946154}, issn = {1473-5571}, abstract = {OBJECTIVE: Persistent inflammation and higher risk to develop cardiovascular diseases still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota 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 61 ART-treated PHIV (age range 3-30 years old) and 71 age-matched healthy controls. Blood and stool sample were collected at the same time and analyzed for gut microbiota composition and plasma biomarkers.<br><br>METHODS: Gut microbiota composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, inflammation and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4 and CD8T cells.<br><br>RESULTS: We identified two distinct gut microbiota profiles (groups 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, whereas gut microbiota of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of soluble E-selectine (P = 0.0296), intercellular adhesion molecule-1 (P = 0.0028), vascular adhesion molecule-1 (P = 0.0230), IL-6 (P = 0.0247) and soluble CD14 (P = 0.0142) in group A compared with group B.<br><br>CONCLUSION: Distinctive gut microbiota profiles are differently associated with inflammation, microbial translocation and VEA. Future studies are needed to understand the role of A. muciniphila and risk to develop cardiovascular diseases in PHIV.}, }
@article {pmid30942434, year = {2019}, author = {Liu, Z and Kong, Y and Gao, Y and Ren, Y and Zheng, C and Deng, X and Chen, T}, title = {Revealing the interaction between intrauterine adhesion and vaginal microbiota using high‑throughput sequencing.}, journal = {Molecular medicine reports}, volume = {19}, number = {5}, pages = {4167-4174}, doi = {10.3892/mmr.2019.10092}, pmid = {30942434}, issn = {1791-3004}, mesh = {Adolescent ; Adult ; Biodiversity ; Computational Biology/methods ; *Disease Susceptibility ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Public Health Surveillance ; Tissue Adhesions/diagnosis/epidemiology/*etiology ; Uterine Diseases/diagnosis/epidemiology/*etiology ; Vagina/*microbiology ; Young Adult ; }, abstract = {Intrauterine adhesion (IUA) is one of the most common diseases of the reproductive system. Due to the high postoperative recurrence rate of IUA, it is crucial to identify the possible causes of pathogenesis and recurrence of this disease. In the present study, a high‑throughput sequencing approach was applied to compare the vaginal microbiota between healthy women [healthy vaginal secretion (HVS) group] and patients with IUA [intrauterine adhesion patients' vaginal secretion (IAVS) group]. The results indicated that IUA had little effect on the number of vaginal bacterial species. However, at the phylum level, patients with IUA had a significantly lower percentage of Firmicutes and a higher percentage of Actinobacteria than the HVS group (P<0.05). At the genus level, ~50% of patients with IUA were found to have a marked reduction in probiotic Lactobacillus accompanied by an overgrowth of pathogenic Gardnerella and Prevotella (P<0.05), and the Principal Coordinates Analysis confirmed that 10/20 samples in the IAVS group were scattered far away from the HVS group. Therefore, it was concluded that the interaction between IUA and vaginal microbiota greatly influenced the vaginal diversity of patients with IUA. In order to increase the recovery rate and lower the recurrence rate of IUA, increasing the vaginal Lactobacillus population should be considered.}, }
@article {pmid30936548, year = {2019}, author = {Thomas, AM and Manghi, P and Asnicar, F and Pasolli, E and Armanini, F and Zolfo, M and Beghini, F and Manara, S and Karcher, N and Pozzi, C and Gandini, S and Serrano, D and Tarallo, S and Francavilla, A and Gallo, G and Trompetto, M and Ferrero, G and Mizutani, S and Shiroma, H and Shiba, S and Shibata, T and Yachida, S and Yamada, T and Wirbel, J and Schrotz-King, P and Ulrich, CM and Brenner, H and Arumugam, M and Bork, P and Zeller, G and Cordero, F and Dias-Neto, E and Setubal, JC and Tett, A and Pardini, B and Rescigno, M and Waldron, L and Naccarati, A and Segata, N}, title = {Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.}, journal = {Nature medicine}, volume = {25}, number = {4}, pages = {667-678}, doi = {10.1038/s41591-019-0405-7}, pmid = {30936548}, issn = {1546-170X}, support = {P30 CA042014/CA/NCI NIH HHS/United States ; R01 CA189184/CA/NCI NIH HHS/United States ; R01 CA207371/CA/NCI NIH HHS/United States ; }, mesh = {Biomarkers, Tumor/metabolism ; Choline/*metabolism ; Cohort Studies ; Colorectal Neoplasms/diagnosis/*metabolism/*microbiology ; Databases, Genetic ; Gastrointestinal Microbiome ; Humans ; Lyases/genetics/metabolism ; *Metagenomics ; Species Specificity ; }, abstract = {Several studies have investigated links between the gut microbiome and colorectal cancer (CRC), but questions remain about the replicability of biomarkers across cohorts and populations. We performed a meta-analysis of five publicly available datasets and two new cohorts and validated the findings on two additional cohorts, considering in total 969 fecal metagenomes. Unlike microbiome shifts associated with gastrointestinal syndromes, the gut microbiome in CRC showed reproducibly higher richness than controls (P < 0.01), partially due to expansions of species typically derived from the oral cavity. Meta-analysis of the microbiome functional potential identified gluconeogenesis and the putrefaction and fermentation pathways as being associated with CRC, whereas the stachyose and starch degradation pathways were associated with controls. Predictive microbiome signatures for CRC trained on multiple datasets showed consistently high accuracy in datasets not considered for model training and independent validation cohorts (average area under the curve, 0.84). Pooled analysis of raw metagenomes showed that the choline trimethylamine-lyase gene was overabundant in CRC (P = 0.001), identifying a relationship between microbiome choline metabolism and CRC. The combined analysis of heterogeneous CRC cohorts thus identified reproducible microbiome biomarkers and accurate disease-predictive models that can form the basis for clinical prognostic tests and hypothesis-driven mechanistic studies.}, }
@article {pmid30927638, year = {2019}, author = {Wei, Z and Yu, S and Huang, Z and Xiao, X and Tang, M and Li, B and Zhang, X}, title = {Simultaneous removal of elemental mercury and NO by mercury induced thermophilic community in membrane biofilm reactor.}, journal = {Ecotoxicology and environmental safety}, volume = {176}, number = {}, pages = {170-177}, doi = {10.1016/j.ecoenv.2019.03.082}, pmid = {30927638}, issn = {1090-2414}, mesh = {Biofilms/*growth &amp; development ; Bioreactors/*microbiology ; Denitrification ; Mercury/*analysis ; Metagenomics ; Microbiota/drug effects/genetics ; Nitric Oxide/*analysis ; Nitrification ; Oxidation-Reduction ; }, abstract = {Thermophilic membrane biofilm reactor (TMBR) for elemental mercury (Hg0) and NO removal in simulated flue gas was investigated at oxygen content of 6% and 60 °C. The performance, the microbial community structures, gene function and the mechanism for Hg0 and NO removal in the TMBR were evaluated. TMBR achieved effective simultaneous Hg0 and NO removal in 210 days of operation, Hg0 and NO removal efficiency were up to 88.9% and 85.3%, respectively. Mercury induced thermophilic community had been formed significantly. Comamonas, Pseudomonas, Desulfomicrobium, Burkholderia and Halomonas were thermophilic mercury resistant bacteria. Brucella, Paracoccus, Tepidiphilus, Proteobacteria, Pseudomonas and Symbiobacterium were nitrifying/denitrifying genera, and had functional genes of mercury and nitrogen metabolism, as shown by16S rDNA and metagenomic sequencing. The biofilm in TMBR was characterized by XPS, HPLC. XPS and HPLC spectra indicate the formation of a mercuric species (Hg2+) from mercury oxidation. TMBR used oxygen as electron acceptor, NO and Hg0 as electron donor in nitrification; O2, NO and NO3- could be used as electron acceptor and Hg0 as electron donor in denitrification.}, }
@article {pmid30927421, year = {2019}, author = {Ding, GC and Bai, M and Han, H and Li, H and Ding, X and Yang, H and Xu, T and Li, J}, title = {Microbial taxonomic, nitrogen cycling and phosphorus recycling community composition during long-term organic greenhouse farming.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, doi = {10.1093/femsec/fiz042}, pmid = {30927421}, issn = {1574-6941}, abstract = {Understanding the interplay between the farming system and soil microbiomes could aid the design of a sustainable and efficient farming system. A comparative greenhouse experiment consisting of organic (ORG), integrated (INT) and conventional (CON) farming systems was established in northern China in 2002. The effects of 12 years of organic farming on soil microbiomes were explored by metagenomic and 16S rRNA gene amplicon sequencing analyses. Long-term ORG shifted the community composition of dominant phyla, especially Acidobacteria, increased the relative abundance of Ignavibacteria and Acidobacteria Gp6 and decreased the relative abundance of Nitrosomonas, Bacillus and Paenibacillus. Metagenomic analysis further revealed that relative abundance of ammonia oxidizing microorganisms (Bacteria and Archaea) and anaerobic ammonium oxidation bacteria decreased during ORG. Conversely, the relative abundance of bacteria-carrying periplasmic nitrate reductases (napA) was slightly higher for ORG. Long-term organic farming also caused significant alterations to the community composition of functional groups associated with ammonia oxidation, denitrification and phosphorus recycling. In summary, this study provides key insights into the composition of soil microbiomes and long-term organic farming under greenhouse conditions.}, }
@article {pmid30926487, year = {2019}, author = {Ji, X and Hou, C and Zhang, X and Han, L and Yin, S and Peng, Q and Wang, M}, title = {Microbiome-metabolomic analysis of the impact of Zizyphus jujuba cv. Muzao polysaccharides consumption on colorectal cancer mice fecal microbiota and metabolites.}, journal = {International journal of biological macromolecules}, volume = {131}, number = {}, pages = {1067-1076}, doi = {10.1016/j.ijbiomac.2019.03.175}, pmid = {30926487}, issn = {1879-0003}, mesh = {Animal Feed ; Animals ; Biomarkers ; Colorectal Neoplasms/etiology/*metabolism/pathology ; Cytokines/metabolism ; Disease Models, Animal ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Inflammation Mediators/metabolism ; Male ; Metabolic Networks and Pathways ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Mice ; *Polysaccharides ; RNA, Ribosomal, 16S/genetics ; Ziziphus/*chemistry ; }, abstract = {It is still uncertain whether the consumption of Zizyphus jujuba cv. Muzao polysaccharides (ZMP) alleviates colorectal cancer (CRC) through the gut microbiota. In this study, we investigated the mortality, colon length, inflammatory factors and cecal microbiota, metabolites of healthy and azoxymethane (AOM) and dextran sodium sulfate (DSS) in induced CRC mice, consuming ZMP. Fecal-microbiota composition was examined using 16S rDNA sequencing and fecal-metabolome profiles were evaluated by ultra-high performance liquid chromatograph mass spectrometry (UHPLC-MS). The results showed ZMP consumption prevented CRC mouse colon shortening, decreased their mortality, reduced pro-inflammatory cytokines, increased the concentration of total short-chain fatty acids (SCFAs) and modulated gut microbiota in their feces. ZMP also increased the richness of Bifidobacterium, Bacteroides and Lactobacillus. In addition, among 39 perturbed metabolites, carbohydrate and amino acid production were noticeably altered. Moreover, higher correlations were found between fluctuant gut microbiota and metabolites. These findings provide mechanistic insights into the impact of dietary Zizyphus jujuba cv. Muzao polysaccharides on host health.}, }
@article {pmid30918994, year = {2019}, author = {Klima, CL and Holman, DB and Ralston, BJ and Stanford, K and Zaheer, R and Alexander, TW and McAllister, TA}, title = {Lower Respiratory Tract Microbiome and Resistome of Bovine Respiratory Disease Mortalities.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {446-456}, doi = {10.1007/s00248-019-01361-3}, pmid = {30918994}, issn = {1432-184X}, support = {2015R025R//Alberta Livestock and Meat Agency/ ; 001//Growing Forward II/ ; 001//Genomics Research Initiative/ ; }, mesh = {Alberta ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; Bacterial Infections/microbiology/mortality/*veterinary ; Cattle ; Cattle Diseases/*microbiology/mortality ; *Drug Resistance, Bacterial ; *Microbiota ; Respiratory System/*microbiology ; Respiratory Tract Diseases/microbiology/mortality/*veterinary ; }, abstract = {Bovine respiratory disease (BRD) continues to be a serious health problem in beef cattle production. A multifactorial condition, BRD encompasses several types of pneumonia that are associated with multiple viral and bacterial agents. Comprehensive identification of microbes associated with BRD fatalities could enhance our understanding of the range of pathogens that contribute to the disease and identify new therapeutic targets. This study used metagenomic analysis to describe the lower respiratory tract microbiome and resistome of 15 feedlot cattle BRD and 3 non-BRD mortalities along with any affiliated integrative and conjugative elements (ICEs). Known bacterial pathogens associated with BRD, including Histophilus somni, Mannheimia haemolytica, and Mycoplasma bovis, were relatively abundant (> 5%) in most, but not all samples. Other relatively abundant genera (> 1%) included Acinetobacter, Bacillus, Bacteroides, Clostridium, Enterococcus, and Pseudomonas. Antimicrobial resistance genes (ARGs) comprised up to 0.5% of sequences and many of these genes were associated with ICEs previously described within the Pasteurellaceae family. A total of 20 putative ICEs were detected among 16 samples. These results document the wide diversity of microorganisms in the lower respiratory tract of cattle that have succumbed to BRD. The data also strongly suggest that antimicrobial-resistant Pasteurellaceae strains are prevalent in BRD cases in Alberta and that the resistance observed is associated with ICEs. The presence of ICEs harboring a wide array of ARGs holds significant consequence for the effectiveness of drug therapies for the control of BRD in beef cattle.}, }
@article {pmid30918406, year = {2019}, author = {Zeevi, D and Korem, T and Godneva, A and Bar, N and Kurilshikov, A and Lotan-Pompan, M and Weinberger, A and Fu, J and Wijmenga, C and Zhernakova, A and Segal, E}, title = {Structural variation in the gut microbiome associates with host health.}, journal = {Nature}, volume = {568}, number = {7750}, pages = {43-48}, doi = {10.1038/s41586-019-1065-y}, pmid = {30918406}, issn = {1476-4687}, mesh = {Adaptation, Physiological/genetics ; Bacteria/classification/*genetics/growth &amp; development/metabolism ; Butyrates/metabolism ; Cohort Studies ; Disease Susceptibility/*microbiology ; Ecosystem ; Eubacterium/genetics/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics/physiology ; Genes, Bacterial/*genetics ; *Genetic Variation ; *Health ; Host Microbial Interactions/*genetics/physiology ; Humans ; Inositol/metabolism ; Metagenomics ; Microbial Viability/genetics ; Risk Factors ; }, abstract = {Differences in the presence of even a few genes between otherwise identical bacterial strains may result in critical phenotypic differences. Here we systematically identify microbial genomic structural variants (SVs) and find them to be prevalent in the human gut microbiome across phyla and to replicate in different cohorts. SVs are enriched for CRISPR-associated and antibiotic-producing functions and depleted from housekeeping genes, suggesting that they have a role in microbial adaptation. We find multiple associations between SVs and host disease risk factors, many of which replicate in an independent cohort. Exploring genes that are clustered in the same SV, we uncover several possible mechanistic links between the microbiome and its host, including a region in Anaerostipes hadrus that encodes a composite inositol catabolism-butyrate biosynthesis pathway, the presence of which is associated with lower host metabolic disease risk. Overall, our results uncover a nascent layer of variability in the microbiome that is associated with microbial adaptation and host health.}, }
@article {pmid30918057, year = {2019}, author = {Thomas, M and Wongkuna, S and Ghimire, S and Kumar, R and Antony, L and Doerner, KC and Singery, A and Nelson, E and Woyengo, T and Chankhamhaengdecha, S and Janvilisri, T and Scaria, J}, title = {Gut Microbial Dynamics during Conventionalization of Germfree Chicken.}, journal = {mSphere}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSphere.00035-19}, pmid = {30918057}, issn = {2379-5042}, mesh = {Animals ; Bacteria/*classification/isolation &amp; purification ; Bacteroidetes/classification/isolation &amp; purification ; Chickens/growth &amp; development ; DNA, Bacterial/genetics ; Firmicutes/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; *Germ-Free Life ; *Host Microbial Interactions ; Metagenomics ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A gnotobiotic Gallus gallus (chicken) model was developed to study the dynamics of intestinal microflora from hatching to 18 days of age employing metagenomics. Intestinal samples were collected from a local population of feral chickens and administered orally to germfree 3-day-old chicks. Animals were euthanized on days 9 and 18 postinoculation, and intestinal samples were collected and subjected to metagenomic analysis. On day 18, the five most prevalent phyla were Bacteroidetes (43.03 ± 3.19%), Firmicutes (38.51 ± 2.67%), Actinobacteria (6.77 ± 0.7%), Proteobacteria (6.38 ± 0.7%), and Spirochaetes (2.71 ± 0.55%). Principal-coordinate analysis showed that the day 18 variables clustered more closely than the day 9 variables, suggesting that the microbial communities had changed temporally. The Morista-Horn index values ranged from 0.7 to 1, indicating that the communities in the inoculum and in the day 9 and day 18 samples were more similar than dissimilar. The predicted functional profiles of the microbiomes of the inoculum and the day 9 and day 18 samples were also similar (values of 0.98 to 1). These results indicate that the gnotobiotic chicks stably maintained the phylogenetic diversity and predicted metabolic functionality of the inoculum community.IMPORTANCE The domestic chicken is the cornerstone of animal agriculture worldwide, with a flock population exceeding 40 billion birds/year. It serves as an economically valuable source of protein globally. The microbiome of poultry has important effects on chicken growth, feed conversion, immune status, and pathogen resistance. The aim of our research was to develop a gnotobiotic chicken model appropriate for the study chicken gut microbiota function. Our experimental model shows that young germfree chicks are able to colonize diverse sets of gut bacteria. Therefore, besides the use of this model to study mechanisms of gut microbiota interactions in the chicken gut, it could be also used for applied aspects such as determining the safety and efficacy of new probiotic strains derived from chicken gut microbiota.}, }
@article {pmid30915691, year = {2019}, author = {Akyol, Ç and Ozbayram, EG and Demirel, B and Onay, TT and Ince, O and Ince, B}, title = {Linking nano-ZnO contamination to microbial community profiling in sanitary landfill simulations.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {13}, pages = {13580-13591}, doi = {10.1007/s11356-019-04906-8}, pmid = {30915691}, issn = {1614-7499}, support = {112Y322//TUBITAK/ ; 13081//Boğaziçi University Research Fund Project/ ; }, mesh = {Archaea ; Bacteria ; Biofuels ; Bioreactors/*microbiology ; Microbiota ; RNA, Ribosomal, 16S/*chemistry ; Refuse Disposal/methods ; Solid Waste/*analysis ; Waste Disposal Facilities ; Zinc Oxide/*analysis/chemistry ; }, abstract = {Nanomaterials (NMs) commercially used for various activities mostly end up in landfills. Reduced biogas productions reported in landfill reactors create a need for more comprehensive research on these greatly-diverse microbial pools. In order to evaluate the impact of one of the most widely-used NMs, namely nano-zinc oxide (nano-ZnO), simulated bioreactor and conventional landfills were operated using real municipal solid waste (MSW) for 300 days with addition nano-ZnO. Leachate samples were taken at different phases and analyzed by 16S rRNA gene amplicon sequencing. The bacterial communities were distinctly characterized by Cloacamonaceae (phylum WWE1), Rhodocyclaceae (phylum Proteobacteria), Porphyromonadaceae (phylum Bacteroidetes), and Synergistaceae (phylum Synergistetes). The bacterial community in the bioreactors shifted at the end of the operation and was dominated by Rhodocyclaceae. There was not a major change in the bacterial community in the conventional reactors. The methanogenic archaeal diversity highly differed between the bioreactors and conventional reactors. The dominance of Methanomicrobiaceae was observed in the bioreactors during the peak methane-production period; however, their prominence shifted to WSA2 in the nano-ZnO-added bioreactor and to Methanocorpusculaceae in the control bioreactor towards the end. Methanocorpusculaceae was the most abundant family in both conventional control and nano-ZnO-containing reactors.}, }
@article {pmid30914068, year = {2019}, author = {Wang, W and Hu, H and Zijlstra, RT and Zheng, J and Gänzle, MG}, title = {Metagenomic reconstructions of gut microbial metabolism in weanling pigs.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {48}, doi = {10.1186/s40168-019-0662-1}, pmid = {30914068}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Bacteroidetes/genetics/isolation &amp; purification/metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dietary Carbohydrates/*metabolism ; Firmicutes/genetics/isolation &amp; purification/metabolism ; Gastrointestinal Microbiome ; Lactobacillus/genetics/isolation &amp; purification/metabolism ; Male ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Swine ; }, abstract = {BACKGROUND: The piglets' transition from milk to solid feed induces a succession of bacterial communities, enhancing the hosts' ability to harvest energy from dietary carbohydrates. To reconstruct microbial carbohydrate metabolism in weanling pigs, this study combined 16S rRNA gene sequencing (n = 191) and shotgun metagenomics (n = 72).<br><br>RESULTS: Time and wheat content in feed explained most of the variation of the microbiota as assessed by 16S rRNA gene sequencing in weanling pigs. De novo metagenomic binning reconstructed 360 high-quality genomes that represented 11 prokaryotic and 1 archaeal phylum. Analysis of carbohydrate metabolism in these genomes revealed that starch fermentation is carried out by a consortium of Firmicutes expressing extracellular α-(1 → 4)-glucan branching enzyme (GH13) and Bacteroidetes expressing periplasmic neopullulanase (GH13) and α-glucosidase (GH97). Fructans were degraded by extracellular GH32 enzymes from Bacteriodetes and Lactobacillus. Lactose fermentation by β-galactosidases (GH2 and GH42) was identified in Firmicutes. In conclusion, the assembly of 360 high-quality genomes as the first metagenomic reference for swine intestinal microbiota allowed identification of key microbial contributors to degradation of starch, fructans, and lactose.<br><br>CONCLUSIONS: Microbial consortia that are responsible for degradation of these glycans differ substantially from the microbial consortia that degrade the same glycans in humans. Our study thus enables improvement of feeding models with higher feed efficiency and better pathogen control for weanling pigs.}, }
@article {pmid30906284, year = {2019}, author = {Cycoń, M and Mrozik, A and Piotrowska-Seget, Z}, title = {Antibiotics in the Soil Environment-Degradation and Their Impact on Microbial Activity and Diversity.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {338}, doi = {10.3389/fmicb.2019.00338}, pmid = {30906284}, issn = {1664-302X}, abstract = {Antibiotics play a key role in the management of infectious diseases in humans, animals, livestock, and aquacultures all over the world. The release of increasing amount of antibiotics into waters and soils creates a potential threat to all microorganisms in these environments. This review addresses issues related to the fate and degradation of antibiotics in soils and the impact of antibiotics on the structural, genetic and functional diversity of microbial communities. Due to the emergence of bacterial resistance to antibiotics, which is considered a worldwide public health problem, the abundance and diversity of antibiotic resistance genes (ARGs) in soils are also discussed. When antibiotic residues enter the soil, the main processes determining their persistence are sorption to organic particles and degradation/transformation. The wide range of DT50 values for antibiotic residues in soils shows that the processes governing persistence depend on a number of different factors, e.g., physico-chemical properties of the residue, characteristics of the soil, and climatic factors (temperature, rainfall, and humidity). The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups (i.e., Gram-negative bacteria, Gram-positive bacteria, and fungi) in microbial communities. Studies using methods based on analyses of nucleic acids prove that antibiotics alter the biodiversity of microbial communities and the presence of many types of ARGs in soil are affected by agricultural and human activities. It is worth emphasizing that studies on ARGs in soil have resulted in the discovery of new genes and enzymes responsible for bacterial resistance to antibiotics. However, many ambiguous results indicate that precise estimation of the impact of antibiotics on the activity and diversity of soil microbial communities is a great challenge.}, }
@article {pmid30902785, year = {2019}, author = {Kumar, R and Mishra, A and Jha, B}, title = {Bacterial community structure and functional diversity in subsurface seawater from the western coastal ecosystem of the Arabian Sea, India.}, journal = {Gene}, volume = {701}, number = {}, pages = {55-64}, doi = {10.1016/j.gene.2019.02.099}, pmid = {30902785}, issn = {1879-0038}, mesh = {*Bacteria/classification/genetics/growth &amp; development ; *Biodiversity ; India ; Microbial Consortia/*physiology ; Oceans and Seas ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {The present study revealed the spatial variability of bacteria in relation to physicochemical variations at four different locations (Diu - DIU, Veraval - VER, Porbandar - POR and Okha - OKH) along the Gujarat coast (Arabian Sea, India). The natural habitat was analyzed for temperature, salinity, pH, total dissolved solids, total organic content, total inorganic content, biological oxygen demand, conductivity and total dissolved oxygen. The lowest salinity and conductivity were observed at the VER site, whereas the highest salinity and conductivity were measured with OKH samples. In contrast, the pH was slightly alkaline at all of the sites. The VER site contained the maximum total dissolved solids (TDS), total carbon (TC), total organic carbon (TOC), and total inorganic carbon (TIC), while OKH showed the maximum dissolve oxygen (DO), biological oxygen demand (BOD), pH, temperature, conductivity, and salinity. The physicochemical characteristics showed that the Gujarat coast is alkaline and has a nutrient heterogeneous nature. Average well color development (AWCD) values, calculated using Biolog EcoPlates, showed that the microbial community from VER contained the highest metabolic activities and could metabolize all 31 substrates, followed by DIU > OKH > POR samples. In contrast, the abundance of the bacterial community, determined by qRT-PCR, was maximum in VER samples, followed by OKH > POR > DIU samples. The Shannon and Simpson indices showed that DIU, POR and OKH seawater clone libraries were more diverse. Furthermore, Chao estimator revealed the high diversity of POR and DIU clone libraries. Interestingly, DIU and OKH did not share any common operational taxonomic units (OTUs), and overall, the maximum bacterial diversity was observed with the POR seawater sample. Moreover, these observations were supported by statistical analysis, such as canonical correspondence analysis (CCA) and principal component analysis (PCA). The molecular phylogeny revealed the dominance of Proteobacteria followed by Firmicutes. Within the Proteobacteria phylum, most of the sequences were affiliated with the Gammaproteobacteria class. In total, about 726 OTUs were observed from all four sites which covers 59.79% DIU, 87.5% VER, 50% POR and 98.83% OKH of samples. This study is the first report to describe physicochemical attributes and the bacterial diversity of the coastal area of Gujarat. The study will provide useful insights about bacterial diversity, distribution, and abundance, as well as their relationships with the habitat.}, }
@article {pmid30901843, year = {2019}, author = {Cortes, L and Wopereis, H and Tartiere, A and Piquenot, J and Gouw, JW and Tims, S and Knol, J and Chelsky, D}, title = {Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome.}, journal = {International journal of molecular sciences}, volume = {20}, number = {6}, pages = {}, doi = {10.3390/ijms20061430}, pmid = {30901843}, issn = {1422-0067}, mesh = {Anti-Bacterial Agents/pharmacology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/drug effects ; Humans ; Infant ; Informatics/methods ; Male ; Metagenome ; *Metagenomics/methods ; Proteome ; *Proteomics/methods ; *RNA, Ribosomal, 16S ; }, abstract = {A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.}, }
@article {pmid30901128, year = {2019}, author = {Martins, FMS and Galhardo, M and Filipe, AF and Teixeira, A and Pinheiro, P and Paupério, J and Alves, PC and Beja, P}, title = {Have the cake and eat it: Optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {863-876}, doi = {10.1111/1755-0998.13012}, pmid = {30901128}, issn = {1755-0998}, support = {PTDC/AAGMAA/2261/2014-POCI-1-145-FEDER-356016824//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/104703/2014//Fundação para a Ciência e a Tecnologia/ ; 668981//Horizon 2020 Framework Programme/ ; //EDP-Biodiversity Chair/ ; }, mesh = {Animals ; DNA/*genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Ecological Parameter Monitoring/*methods ; Fresh Water/*chemistry ; Invertebrates/classification/genetics ; Metagenomics/*methods ; }, abstract = {DNA metabarcoding can contribute to improving cost-effectiveness and accuracy of biological assessments of aquatic ecosystems, but significant optimization and standardization efforts are still required to mainstream its application into biomonitoring programmes. In assessments based on freshwater macroinvertebrates, a key challenge is that DNA is often extracted from cleaned, sorted and homogenized bulk samples, which is time-consuming and may be incompatible with sample preservation requirements of regulatory agencies. Here, we optimize and evaluate metabarcoding procedures based on DNA recovered from 96% ethanol used to preserve field samples and thus including potential PCR inhibitors and nontarget organisms. We sampled macroinvertebrates at five sites and subsampled the preservative ethanol at 1 to 14 days thereafter. DNA was extracted using column-based enzymatic (TISSUE) or mechanic (SOIL) protocols, or with a new magnetic-based enzymatic protocol (BEAD), and a 313-bp COI fragment was amplified. Metabarcoding detected at least 200 macroinvertebrate taxa, including most taxa detected through morphology and for which there was a reference barcode. Better results were obtained with BEAD than SOIL or TISSUE, and with subsamples taken 7-14 than 1-7 days after sampling, in terms of DNA concentration and integrity, taxa diversity and matching between metabarcoding and morphology. Most variation in community composition was explained by differences among sites, with small but significant contributions of subsampling day and extraction method, and negligible contributions of extraction and PCR replication. Our methods enhance reliability of preservative ethanol as a potential source of DNA for macroinvertebrate metabarcoding, with a strong potential application in freshwater biomonitoring.}, }
@article {pmid30894435, year = {2019}, author = {Majta, J and Odrzywolek, K and Milanovic, B and Hubar, V and Wrobel, S and Strycharz-Angrecka, E and Wojciechowski, S and Milanowska, K}, title = {Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population.}, journal = {mSphere}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSphereDirect.00152-19}, pmid = {30894435}, issn = {2379-5042}, mesh = {*Adaptation, Physiological ; Bacteroides/genetics/*metabolism ; Bifidobacterium/genetics/*metabolism ; Feces/microbiology ; Finland ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genome, Bacterial ; Humans ; Infant ; *Metabolic Networks and Pathways ; Metagenomics ; Milk, Human/*chemistry ; Oligosaccharides/metabolism ; }, abstract = {A variety of autoimmune and allergy events are becoming increasingly common, especially in Western countries. Some pieces of research link such conditions with the composition of microbiota during infancy. In this period, the predominant form of nutrition for gut microbiota is oligosaccharides from human milk (HMO). A number of gut-colonizing strains, such as Bifidobacterium and Bacteroides, are able to utilize HMO, but only some Bifidobacterium strains have evolved to digest the specific composition of human oligosaccharides. Differences in the proportions of the two genera that are able to utilize HMO have already been associated with the frequency of allergies and autoimmune diseases in the Finnish and the Russian populations. Our results show that differences in terms of the taxonomic annotation do not explain the reason for the differences in the Bifidobacterium/Bacteroides ratio between the Finnish and the Russian populations. In this paper, we present the results of function-level analysis. Unlike the typical workflow for gene abundance analysis, BiomeScout technology explains the differences in the Bifidobacterium/Bacteroides ratio. Our research shows the differences in the abundances of the two enzymes that are crucial for the utilization of short type 1 oligosaccharides.IMPORTANCE Knowing the limitations of taxonomy-based research, there is an emerging need for the development of higher-resolution techniques. The significance of this research is demonstrated by the novel method used for the analysis of function-level metagenomes. BiomeScout-the presented technology-utilizes proprietary algorithms for the detection of differences between functionalities present in metagenomic samples.}, }
@article {pmid30890181, year = {2019}, author = {Zheng, T and Li, J and Ni, Y and Kang, K and Misiakou, MA and Imamovic, L and Chow, BKC and Rode, AA and Bytzer, P and Sommer, M and Panagiotou, G}, title = {Mining, analyzing, and integrating viral signals from metagenomic data.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {42}, doi = {10.1186/s40168-019-0657-y}, pmid = {30890181}, issn = {2049-2618}, mesh = {Algorithms ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/*classification/isolation &amp; purification/virology ; Bacteriophages/*genetics ; CRISPR-Cas Systems ; Data Mining/*methods ; Feces/microbiology ; Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Metagenomics/*methods ; Random Allocation ; }, abstract = {BACKGROUND: Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagenomic sequencing data. Here we employed the random forest algorithm to develop VirMiner, a web-based phage contig prediction tool especially sensitive for high-abundances phage contigs, trained and validated by paired metagenomic and phagenomic sequencing data from the human gut flora.<br><br>RESULTS: VirMiner achieved 41.06% ± 17.51% sensitivity and 81.91% ± 4.04% specificity in the prediction of phage contigs. In particular, for the high-abundance phage contigs, VirMiner outperformed other tools (VirFinder and VirSorter) with much higher sensitivity (65.23% ± 16.94%) than VirFinder (34.63% ± 17.96%) and VirSorter (18.75% ± 15.23%) at almost the same specificity. Moreover, VirMiner provides the most comprehensive phage analysis pipeline which is comprised of metagenomic raw reads processing, functional annotation, phage contig identification, and phage-host relationship prediction (CRISPR-spacer recognition) and supports two-group comparison when the input (metagenomic sequence data) includes different conditions (e.g., case and control). Application of VirMiner to an independent cohort of human gut metagenomes obtained from individuals treated with antibiotics revealed that 122 KEGG orthology and 118 Pfam groups had significantly differential abundance in the pre-treatment samples compared to samples at the end of antibiotic administration, including clustered regularly interspaced short palindromic repeats (CRISPR), multidrug resistance, and protein transport. The VirMiner webserver is available at http://sbb.hku.hk/VirMiner/ .<br><br>CONCLUSIONS: We developed a comprehensive tool for phage prediction and analysis for metagenomic samples. Compared to VirSorter and VirFinder-the most widely used tools-VirMiner is able to capture more high-abundance phage contigs which could play key roles in infecting bacteria and modulating microbial community dynamics.<br><br>TRIAL REGISTRATION: The European Union Clinical Trials Register, EudraCT Number: 2013-003378-28 . Registered on 9 April 2014.}, }
@article {pmid30887686, year = {2019}, author = {Weyrich, LS and Farrer, AG and Eisenhofer, R and Arriola, LA and Young, J and Selway, CA and Handsley-Davis, M and Adler, CJ and Breen, J and Cooper, A}, title = {Laboratory contamination over time during low-biomass sample analysis.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {982-996}, doi = {10.1111/1755-0998.13011}, pmid = {30887686}, issn = {1755-0998}, support = {DECRA 150101574//Australian Research Council/ ; }, mesh = {*DNA Contamination ; *Diagnostic Errors ; Metagenomics/*methods ; Molecular Biology/*methods ; }, abstract = {Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a home-made silica-based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human-associated taxa in comparison to the home-made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.}, }
@article {pmid30886779, year = {2019}, author = {Eisenhofer, R and Weyrich, LS}, title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6594}, doi = {10.7717/peerj.6594}, pmid = {30886779}, issn = {2167-8359}, abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.}, }
@article {pmid30885807, year = {2019}, author = {Murray, AK and Zhang, L and Snape, J and Gaze, WH}, title = {Comparing the selective and co-selective effects of different antimicrobials in bacterial communities.}, journal = {International journal of antimicrobial agents}, volume = {53}, number = {6}, pages = {767-773}, doi = {10.1016/j.ijantimicag.2019.03.001}, pmid = {30885807}, issn = {1872-7913}, mesh = {Anti-Infective Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics ; Benzalkonium Compounds/pharmacology ; Biota/*drug effects ; Ciprofloxacin/pharmacology ; *Drug Resistance, Bacterial ; Evolution, Molecular ; Genes, Bacterial ; Metagenomics ; *Selection, Genetic ; Trimethoprim/pharmacology ; Waste Water/*microbiology ; }, abstract = {Bacterial communities are exposed to a cocktail of antimicrobial agents, including antibiotics, heavy metals and biocidal antimicrobials such as quaternary ammonium compounds (QACs). The extent to which these compounds may select or co-select for antimicrobial resistance (AMR) is not fully understood. In this study, human-associated, wastewater-derived bacterial communities were exposed to either benzalkonium chloride (BAC), ciprofloxacin or trimethoprim at sub-point-of-use concentrations for one week to determine selective and co-selective potential. Metagenome analyses were performed to determine effects on bacterial community structure and prevalence of antibiotic resistance genes (ARGs) and metal or biocide resistance genes (MBRGS). Ciprofloxacin had the greatest co-selective potential, significantly enriching for resistance mechanisms to multiple antibiotic classes. Conversely, BAC exposure significantly reduced relative abundance of ARGs and MBRGS, including the well characterised qac efflux genes. However, BAC exposure significantly impacted bacterial community structure. Therefore BAC, and potentially other QACs, did not play as significant a role in co-selection for AMR as antibiotics such as ciprofloxacin at sub-point-of-use concentrations in this study. This approach can be used to identify priority compounds for further study, to better understand evolution of AMR in bacterial communities exposed to sub-point-of-use concentrations of antimicrobials.}, }
@article {pmid30885780, year = {2019}, author = {Zuo, X and Deguchi, Y and Xu, W and Liu, Y and Li, HS and Wei, D and Tian, R and Chen, W and Xu, M and Yang, Y and Gao, S and Jaoude, JC and Liu, F and Chrieki, SP and Moussalli, MJ and Gagea, M and Sebastian, MM and Zheng, X and Tan, D and Broaddus, R and Wang, J and Ajami, NJ and Swennes, AG and Watowich, SS and Shureiqi, I}, title = {PPARD and Interferon Gamma Promote Transformation of Gastric Progenitor Cells and Tumorigenesis in Mice.}, journal = {Gastroenterology}, volume = {157}, number = {1}, pages = {163-178}, doi = {10.1053/j.gastro.2019.03.018}, pmid = {30885780}, issn = {1528-0012}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01 CA206539/CA/NCI NIH HHS/United States ; R01 CA195686/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 CA142969/CA/NCI NIH HHS/United States ; }, mesh = {Adenocarcinoma/genetics/immunology ; Animals ; Carcinogenesis/*genetics/immunology ; Cell Lineage ; Cell Transformation, Neoplastic/*genetics/immunology ; Chemokine CCL20/metabolism ; Chemokine CXCL1/metabolism ; Chemokines ; Cytokines/*immunology ; Feedback, Physiological ; Gastric Mucosa/*metabolism ; Gene Expression Profiling ; Inflammation ; Interferon-gamma/*immunology ; Mice ; Microbiota/immunology ; Microfilament Proteins/genetics ; Receptors, Cytoplasmic and Nuclear/*genetics ; Stem Cells/immunology/*metabolism ; Stomach/*immunology/microbiology ; Stomach Neoplasms/genetics/immunology ; }, abstract = {BACKGROUND &amp; AIMS: The peroxisome proliferator-activated receptor delta (PPARD) regulates cell metabolism, proliferation, and inflammation and has been associated with gastric and other cancers. Villin-positive epithelial cells are a small population of quiescent gastric progenitor cells. We expressed PPARD from a villin promoter to investigate the role of these cells and PPARD in development of gastric cancer.<br><br>METHODS: We analyzed gastric tissues from mice that express the Ppard (PPARD1 and PPARD2 mice) from a villin promoter, and mice that did not carry this transgene (controls), by histology and immunohistochemistry. We performed cell lineage-tracing experiments and analyzed the microbiomes, chemokine and cytokine production, and immune cells and transcriptomes of stomachs of these mice. We also performed immunohistochemical analysis of PPARD levels in 2 sets of human gastric tissue microarrays.<br><br>RESULTS: Thirty-eight percent of PPARD mice developed spontaneous, invasive gastric adenocarcinomas, with severe chronic inflammation. Levels of PPARD were increased in human gastric cancer tissues, compared with nontumor tissues, and associated with gastric cancer stage and grade. We found an inverse correlation between level of PPARD in tumor tissue and patient survival time. Gastric microbiomes from PPARD and control mice did not differ significantly. Lineage-tracing experiments identified villin-expressing gastric progenitor cells (VGPCs) as the origin of gastric tumors in PPARD mice. In these mice, PPARD up-regulated CCL20 and CXCL1, which increased infiltration of the gastric mucosa by immune cells. Immune cell production of inflammatory cytokines promoted chronic gastric inflammation and expansion and transformation of VGPCs, leading to tumorigenesis. We identified a positive-feedback loop between PPARD and interferon gamma signaling that sustained gastric inflammation to induce VGPC transformation and gastric carcinogenesis.<br><br>CONCLUSIONS: We found PPARD overexpression in VPGCs to result in inflammation, dysplasia, and tumor formation. PPARD and VGPCs might be therapeutic targets for stomach cancer.}, }
@article {pmid30885266, year = {2019}, author = {Westreich, ST and Ardeshir, A and Alkan, Z and Kable, ME and Korf, I and Lemay, DG}, title = {Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {41}, doi = {10.1186/s40168-019-0664-z}, pmid = {30885266}, issn = {2049-2618}, support = {P51 OD011107/OD/NIH HHS/United States ; S10 OD010786/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; Diarrhea/*genetics/metabolism/microbiology/parasitology ; Feces/microbiology ; Fucose/*metabolism ; Gastrointestinal Microbiome ; Gene Expression Profiling/*veterinary ; Gene Expression Regulation ; Macaca mulatta ; Metagenomics/*methods ; Mucins/*metabolism ; Proteolysis ; Sequence Analysis, RNA/veterinary ; Trichomonas/classification/genetics ; }, abstract = {BACKGROUND: Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease.<br><br>RESULTS: Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes.<br><br>CONCLUSIONS: The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites.}, }
@article {pmid30878035, year = {2019}, author = {Rowe, WP and Carrieri, AP and Alcon-Giner, C and Caim, S and Shaw, A and Sim, K and Kroll, JS and Hall, LJ and Pyzer-Knapp, EO and Winn, MD}, title = {Streaming histogram sketching for rapid microbiome analytics.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {40}, doi = {10.1186/s40168-019-0653-2}, pmid = {30878035}, issn = {2049-2618}, support = {BB/M011216/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; 100/974/C/13/Z//Wellcome Trust/United Kingdom ; BB/R012490/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004529/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteria/*classification ; Bacterial Infections/drug therapy ; Cohort Studies ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; Machine Learning ; Metagenomics/*methods ; Sequence Analysis, DNA ; Software ; }, abstract = {BACKGROUND: The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research, allowing for the design of new studies, augmentation of novel datasets and reanalysis of published works. This vast amount of microbiome data, as well as the widespread proliferation of microbiome research and the looming era of clinical metagenomics, means there is an urgent need to develop analytics that can process huge amounts of data in a short amount of time. To address this need, we propose a new method for tyrhe compact representation of microbiome sequencing data using similarity-preserving sketches of streaming k-mer spectra. These sketches allow for dissimilarity estimation, rapid microbiome catalogue searching and classification of microbiome samples in near real time.<br><br>RESULTS: We apply streaming histogram sketching to microbiome samples as a form of dimensionality reduction, creating a compressed 'histosketch' that can efficiently represent microbiome k-mer spectra. Using public microbiome datasets, we show that histosketches can be clustered by sample type using the pairwise Jaccard similarity estimation, consequently allowing for rapid microbiome similarity searches via a locality sensitive hashing indexing scheme. Furthermore, we use a 'real life' example to show that histosketches can train machine learning classifiers to accurately label microbiome samples. Specifically, using a collection of 108 novel microbiome samples from a cohort of premature neonates, we trained and tested a random forest classifier that could accurately predict whether the neonate had received antibiotic treatment (97% accuracy, 96% precision) and could subsequently be used to classify microbiome data streams in less than 3 s.<br><br>CONCLUSIONS: Our method offers a new approach to rapidly process microbiome data streams, allowing samples to be rapidly clustered, indexed and classified. We also provide our implementation, Histosketching Using Little K-mers (HULK), which can histosketch a typical 2 GB microbiome in 50 s on a standard laptop using four cores, with the sketch occupying 3000 bytes of disk space. (https://github.com/will-rowe/hulk).}, }
@article {pmid30876405, year = {2019}, author = {Doyle, SR and Illingworth, CJR and Laing, R and Bartley, DJ and Redman, E and Martinelli, A and Holroyd, N and Morrison, AA and Rezansoff, A and Tracey, A and Devaney, E and Berriman, M and Sargison, N and Cotton, JA and Gilleard, JS}, title = {Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {218}, doi = {10.1186/s12864-019-5592-6}, pmid = {30876405}, issn = {1471-2164}, support = {BB/M003949//Biotechnology and Biological Sciences Research Council/United Kingdom ; 098051 &amp; 206194//Wellcome Trust (GB)/ ; .//Rural and Environment Science and Analytical Services Division (GB)/ ; 101239/Z/13/Z//Wellcome and the Royal Society Sir Henry Dale Fellowship/ ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA, Helminth ; *Drug Resistance ; *Evolution, Molecular ; Genetic Variation ; Haemonchus/*drug effects/*genetics ; Insecticides/pharmacology ; Ivermectin/*pharmacology ; *Metagenomics ; *Quantitative Trait Loci ; }, abstract = {BACKGROUND: Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use of anthelmintics has driven the evolution of resistance in a number of species that infect livestock and companion animals, and there are growing concerns regarding the reduced efficacy in some human-infective helminths. Understanding the mechanisms by which resistance evolves is the focus of increasing interest; robust genetic analysis of helminths is challenging, and although many candidate genes have been proposed, the genetic basis of resistance remains poorly resolved.<br><br>RESULTS: Here, we present a genome-wide analysis of two genetic crosses between ivermectin resistant and sensitive isolates of the parasitic nematode Haemonchus contortus, an economically important gastrointestinal parasite of small ruminants and a model for anthelmintic research. Whole genome sequencing of parental populations, and key stages throughout the crosses, identified extensive genomic diversity that differentiates populations, but after backcrossing and selection, a single genomic quantitative trait locus (QTL) localised on chromosome V was revealed to be associated with ivermectin resistance. This QTL was common between the two geographically and genetically divergent resistant populations and did not include any leading candidate genes, suggestive of a previously uncharacterised mechanism and/or driver of resistance. Despite limited resolution due to low recombination in this region, population genetic analyses and novel evolutionary models supported strong selection at this QTL, driven by at least partial dominance of the resistant allele, and that large resistance-associated haplotype blocks were enriched in response to selection.<br><br>CONCLUSIONS: We have described the genetic architecture and mode of ivermectin selection, revealing a major genomic locus associated with ivermectin resistance, the most conclusive evidence to date in any parasitic nematode. This study highlights a novel genome-wide approach to the analysis of a genetic cross in non-model organisms with extreme genetic diversity, and the importance of a high-quality reference genome in interpreting the signals of selection so identified.}, }
@article {pmid30871469, year = {2019}, author = {Perz, AI and Giles, CB and Brown, CA and Porter, H and Roopnarinesingh, X and Wren, JD}, title = {MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {96}, doi = {10.1186/s12859-019-2623-x}, pmid = {30871469}, issn = {1471-2105}, support = {P20 GM103636/GM/NIGMS NIH HHS/United States ; P30 AG050911/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments. This could be a potentially powerful way to interpret new experiments, by identifying common themes and causes behind changes in species abundance.<br><br>RESULTS: We propose a novel framework for comparing microbial shifts between conditions. Using data from one of the largest human metagenome projects to date, the American Gut Project (AGP), we obtain differential abundance vectors for microbes using experimental condition information provided with the AGP metadata, such as patient age, dietary habits, or health status. We show it can be used to identify similar and opposing shifts in microbial species, and infer putative interactions between microbes. Our results show that groups of shifts with similar effects on microbiome can be identified and that similar dietary interventions display similar microbial abundance shifts.<br><br>CONCLUSIONS: Without comparison to prior data, it is difficult for experimentalists to know if their observed changes in species abundance have been observed by others, both in their conditions and in others they would never consider comparable. Yet, this can be a very important contextual factor in interpreting the significance of a shift. We've proposed and tested an algorithmic solution to this problem, which also allows for comparing the metagenomic signature shifts between conditions in the existing body of data.}, }
@article {pmid30871459, year = {2019}, author = {Thrash, A and Arick, M and Barbato, RA and Jones, RM and Douglas, TA and Esdale, J and Perkins, EJ and Garcia-Reyero, N}, title = {Keanu: a novel visualization tool to explore biodiversity in metagenomes.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {103}, doi = {10.1186/s12859-019-2629-4}, pmid = {30871459}, issn = {1471-2105}, mesh = {Biodiversity ; Metagenomics/*methods ; }, abstract = {BACKGROUND: One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, especially with metagenomics data or data suspected to be contaminated. Here, we describe the development and application of a command-line tool, Keanu, for visualizing and exploring sample content in metagenomics data. We developed Keanu as an interactive tool to make viewing complex data easier.<br><br>RESULTS: Keanu, a tool for exploring sequence content, helps a user to understand the presence and abundance of organisms in a sample by analyzing alignments against a database that contains taxonomy data and displaying them in an interactive web page. The content of a sample can be presented either as a collapsible tree, with node size indicating abundance, or as a bilevel partition graph, with arc size indicating abundance. Here, we illustrate how Keanu works by exploring shotgun metagenomics data from a sample collected from a bluff that contained paleosols and a krotovina in an alpine site in Ft. Greely, Alaska.<br><br>CONCLUSIONS: Keanu provides a simple means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu .}, }
@article {pmid30871224, year = {2019}, author = {Gurwara, S and Ajami, NJ and Jang, A and Hessel, FC and Chen, L and Plew, S and Wang, Z and Graham, DY and Hair, C and White, DL and Kramer, J and Kourkoumpetis, T and Hoffman, K and Cole, R and Hou, J and Husain, N and Jarbrink-Sehgal, M and Hernaez, R and Kanwal, F and Ketwaroo, G and Shah, R and Velez, M and Natarajan, Y and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon.}, journal = {Nutrients}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/nu11030613}, pmid = {30871224}, issn = {2072-6643}, support = {I01 CX001430/CX/CSRD VA/United States ; RP#140767//Cancer Prevention and Research Institute of Texas/ ; 1000//Gillson Longenbaugh Foundation/ ; 0000//Golfers Against Cancer/ ; }, mesh = {Aged ; Bacteria/*metabolism ; Colon/*microbiology ; Cross-Sectional Studies ; *Diet ; Food Analysis ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; Prospective Studies ; }, abstract = {One carbon (1C) metabolism nutrients influence epigenetic regulation and they are supplied by diet and synthesized by gut microbiota. We examined the association between dietary consumption of methyl donors (methionine, betaine and choline) and B vitamins (folate, B2, B6, and B12) and the community composition and structure of the colonic mucosa-associated gut microbiota determined by 16S rRNA gene sequencing in 97 colonic biopsies of 35 men. We used the food frequency questionnaire to assess daily consumption of nutrients, and the UPARSE and SILVA databases for operational taxonomic unit classification. The difference in bacterial diversity and taxonomic relative abundance were compared between low versus high consumption of these nutrients. False discover rate (FDR) adjusted p value < 0.05 indicated statistical significance. The bacterial richness and composition differed significantly by the consumption of folate and B vitamins (p < 0.001). Compared with higher consumption, a lower consumption of these nutrients was associated with a lower abundance of Akkermansia (folate), Roseburia (vitamin B2), and Faecalibacterium (vitamins B2, B6, and B12) but a higher abundance of Erysipelatoclostridium (vitamin B2) (FDR p values < 0.05). The community composition and structure of the colonic bacteria differed significantly by dietary consumption of folate and B vitamins.}, }
@article {pmid30868805, year = {2019}, author = {Liu, ZX and Xu, J and Sun, W and Shi, YH and Chen, SL}, title = {[Application of DNA metabarcoding in species identification of Chinese herbal medicines].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {44}, number = {1}, pages = {1-8}, doi = {10.19540/j.cnki.cjcmm.2019.0001}, pmid = {30868805}, issn = {1001-5302}, mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Drugs, Chinese Herbal/*analysis ; High-Throughput Nucleotide Sequencing ; Plants, Medicinal/*classification ; }, abstract = {DNA metabarcoding,one rapid and robust method using specific standard DNA fragments,has been widely used for rapid species identification of a bulk sample through high-throughput sequencing technologies.While it has been widely used in the studies of metagenomics,animal and plant biodiversity,it has gradually come to be used as a profitable method in species identification of mixed Chinese herbal medicines.In this paper,we mainly summarize the current studies of the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines.Moreover,high-throughput sequencing technologies adopted in those studies,such as Sanger,the next-generation,and third-generation sequencing technologies,are discussed.It is conducted to provide a theoretical guidance for the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines and in more other biodiversity studies.}, }
@article {pmid30866822, year = {2019}, author = {Lee, Y and Schmidt, H and Collier, TC and Conner, WR and Hanemaaijer, MJ and Slatkin, M and Marshall, JM and Chiu, JC and Smartt, CT and Lanzaro, GC and Mulligan, FS and Cornel, AJ}, title = {Genome-wide divergence among invasive populations of Aedes aegypti in California.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {204}, doi = {10.1186/s12864-019-5586-4}, pmid = {30866822}, issn = {1471-2164}, support = {U01CK000516//ACL HHS/United States ; HR0011-17-2-0047//Defense Sciences Office, DARPA/ ; 1U01CK000516//Centers for Disease Control and Prevention/ ; }, mesh = {Aedes/*classification/genetics ; Animals ; California ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Genome Size ; *Genome, Insect ; Introduced Species ; Metagenomics ; Mosquito Vectors/classification/genetics ; Phylogeny ; Phylogeography ; Whole Genome Sequencing/*veterinary ; }, abstract = {BACKGROUND: In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern CA as far south as San Diego and Imperial Counties. A number of published reports suggest that CA populations have been established from multiple independent introductions.<br><br>RESULTS: Here we report the first population genomics analyses of Ae. aegypti based on individual, field collected whole genome sequences. We analyzed 46 Ae. aegypti genomes to establish genetic relationships among populations from sites in California, Florida and South Africa. Based on 4.65 million high quality biallelic SNPs, we identified 3 major genetic clusters within California; one that includes all sample sites in the southern part of the state (South of Tehachapi mountain range) plus the town of Exeter in central California and two additional clusters in central California.<br><br>CONCLUSIONS: A lack of concordance between mitochondrial and nuclear genealogies suggests that the three founding populations were polymorphic for two main mitochondrial haplotypes prior to being introduced to California. One of these has been lost in the Clovis populations, possibly by a founder effect. Genome-wide comparisons indicate extensive differentiation between genetic clusters. Our observations support recent introductions of Ae. aegypti into California from multiple, genetically diverged source populations. Our data reveal signs of hybridization among diverged populations within CA. Genetic markers identified in this study will be of great value in pursuing classical population genetic studies which require larger sample sizes.}, }
@article {pmid30866812, year = {2019}, author = {Das, P and Babaei, P and Nielsen, J}, title = {Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {208}, doi = {10.1186/s12864-019-5591-7}, pmid = {30866812}, issn = {1471-2164}, support = {HEALTH-F4-2012-305312//METACARDIS/ ; }, mesh = {Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics ; China ; Feces/microbiology ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Metagenomics/*methods ; Phylogeny ; Phylogeography ; United States ; Vitamins/*metabolism ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Human gut microbial communities have been known to produce vitamins, which are subsequently absorbed by the host in the large intestine. However, the relationship between species with vitamin pathway associated functional features or their gene abundance in different states of health and disease is lacking. Here, we analyzed shotgun fecal metagenomes of individuals from four different countries for genes that are involved in vitamin biosynthetic pathways and transport mechanisms and corresponding species' abundance.<br><br>RESULTS: We found that the prevalence of these genes were found to be distributed across the dominant phyla of gut species. The number of positive correlations were high between species harboring genes related to vitamin biosynthetic pathways and transporter mechanisms than that with either alone. Although, the range of total gene abundances remained constant across healthy populations at the global level, species composition and their presence for metabolic pathway related genes determine the abundance and functional genetic content of vitamin metabolism. Based on metatranscriptomics data, the equation between abundance of vitamin-biosynthetic enzymes and vitamin-dependent enzymes suggests that the production and utilization potential of these enzymes seems way more complex usage allocations than just mere direct linear associations.<br><br>CONCLUSIONS: Our findings provide a rationale to examine and disentangle the interrelationship between B-vitamin dosage (dietary or microbe-mediated) on gut microbial members and the host, in the gut microbiota of individuals with under- or overnutrition.}, }
@article {pmid30866521, year = {2019}, author = {François, S and Mutuel, D and Duncan, AB and Rodrigues, LR and Danzelle, C and Lefevre, S and Santos, I and Frayssinet, M and Fernandez, E and Filloux, D and Roumagnac, P and Froissart, R and Ogliastro, M}, title = {A New Prevalent Densovirus Discovered in Acari. Insight from Metagenomics in Viral Communities Associated with Two-Spotted Mite (Tetranychus urticae) Populations.}, journal = {Viruses}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/v11030233}, pmid = {30866521}, issn = {1999-4915}, mesh = {Animals ; Capsid Proteins/genetics ; Densovirus/*genetics/*isolation &amp; purification ; Female ; *Genetic Variation ; Genome, Viral ; Metagenomics ; *Microbiota ; Phylogeny ; Plants/virology ; Prevalence ; Tetranychidae/*virology ; Viral Nonstructural Proteins/genetics ; }, abstract = {Viral metagenomics and high throughput sequence mining have revealed unexpected diversity, and the potential presence, of parvoviruses in animals from all phyla. Among arthropods, this diversity highlights the poor knowledge that we have regarding the evolutionary history of densoviruses. The aim of this study was to explore densovirus diversity in a small arthropod pest belonging to Acari, the two-spotted spider mite Tetranychus urticae, while using viral metagenomics based on virus-enrichment. Here, we present the viromes obtained from T. urticae laboratory populations made of contigs that are attributed to nine new potential viral species, including the complete sequence of a novel densovirus. The genome of this densovirus has an ambisens genomic organization and an unusually compact size with particularly small non-structural proteins and a predicted major capsid protein that lacks the typical PLA2 motif that is common to all ambidensoviruses described so far. In addition, we showed that this new densovirus had a wide prevalence across populations of mite species tested and a genomic diversity that likely correlates with the host phylogeny. In particular, we observed a low densovirus genomic diversity between the laboratory and natural populations, which suggests that virus within-species evolution is probably slower than initially thought. Lastly, we showed that this novel densovirus can be inoculated to the host plant following feeding by infected mites, and circulate through the plant vascular system. These findings offer new insights into densovirus prevalence, evolution, and ecology.}, }
@article {pmid30864326, year = {2019}, author = {Han, W and Ye, Y}, title = {A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {24}, number = {}, pages = {236-247}, pmid = {30864326}, issn = {2335-6936}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Carcinoma, Non-Small-Cell Lung/genetics/microbiology/therapy ; Carcinoma, Renal Cell/genetics/microbiology/therapy ; Computational Biology/methods ; Databases, Genetic ; Diabetes Mellitus, Type 2/genetics/microbiology ; *Genes, Microbial ; Genetic Markers ; Host Microbial Interactions/*genetics ; Humans ; Immunotherapy ; Kidney Neoplasms/genetics/microbiology/therapy ; Liver Cirrhosis/genetics/microbiology ; Lung Neoplasms/genetics/microbiology/therapy ; Machine Learning ; Metagenomics/methods/statistics &amp; numerical data ; Microbiota/*genetics ; Phenotype ; Translational Medical Research ; }, abstract = {The microbiome research is going through an evolutionary transition from focusing on the characterization of reference microbiomes associated with different environments/hosts to the translational applications, including using microbiome for disease diagnosis, improving the effcacy of cancer treatments, and prevention of diseases (e.g., using probiotics). Microbial markers have been identified from microbiome data derived from cohorts of patients with different diseases, treatment responsiveness, etc, and often predictors based on these markers were built for predicting host phenotype given a microbiome dataset (e.g., to predict if a person has type 2 diabetes given his or her microbiome data). Unfortunately, these microbial markers and predictors are often not published so are not reusable by others. In this paper, we report the curation of a repository of microbial marker genes and predictors built from these markers for microbiome-based prediction of host phenotype, and a computational pipeline called Mi2P (from Microbiome to Phenotype) for using the repository. As an initial effort, we focus on microbial marker genes related to two diseases, type 2 diabetes and liver cirrhosis, and immunotherapy efficacy for two types of cancer, non-small-cell lung cancer (NSCLC) and renal cell carcinoma (RCC). We characterized the marker genes from metagenomic data using our recently developed subtractive assembly approach. We showed that predictors built from these microbial marker genes can provide fast and reasonably accurate prediction of host phenotype given microbiome data. As understanding and making use of microbiome data (our second genome) is becoming vital as we move forward in this age of precision health and precision medicine, we believe that such a repository will be useful for enabling translational applications of microbiome data.}, }
@article {pmid30858573, year = {2019}, author = {Kessler, AJ and Chen, YJ and Waite, DW and Hutchinson, T and Koh, S and Popa, ME and Beardall, J and Hugenholtz, P and Cook, PLM and Greening, C}, title = {Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments.}, journal = {Nature microbiology}, volume = {4}, number = {6}, pages = {1014-1023}, doi = {10.1038/s41564-019-0391-z}, pmid = {30858573}, issn = {2058-5276}, mesh = {Bacteria/*genetics/*metabolism ; Bacteria, Anaerobic/metabolism ; Carbon Cycle ; *Fermentation ; Gammaproteobacteria/metabolism ; Geologic Sediments/*microbiology ; Hydrogen/metabolism ; Hydrogenase/classification/genetics ; *Hypoxia ; Metagenomics ; Microbiota ; Nitrates/metabolism ; Nitrites/metabolism ; Oceans and Seas ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Sulfates/metabolism ; }, abstract = {Permeable (sandy) sediments cover half of the continental margin and are major regulators of oceanic carbon cycling. The microbial communities within these highly dynamic sediments frequently shift between oxic and anoxic states, and hence are less stratified than those in cohesive (muddy) sediments. A major question is, therefore, how these communities maintain metabolism during oxic-anoxic transitions. Here, we show that molecular hydrogen (H2) accumulates in silicate sand sediments due to decoupling of bacterial fermentation and respiration processes following anoxia. In situ measurements show that H2 is 250-fold supersaturated in the water column overlying these sediments and has an isotopic composition consistent with fermentative production. Genome-resolved shotgun metagenomic profiling suggests that the sands harbour diverse and specialized microbial communities with a high abundance of [NiFe]-hydrogenase genes. Hydrogenase profiles predict that H2 is primarily produced by facultatively fermentative bacteria, including the dominant gammaproteobacterial family Woeseiaceae, and can be consumed by aerobic respiratory bacteria. Flow-through reactor and slurry experiments consistently demonstrate that H2 is rapidly produced by fermentation following anoxia, immediately consumed by aerobic respiration following reaeration and consumed by sulfate reduction only during prolonged anoxia. Hydrogenotrophic sulfur, nitrate and nitrite reducers were also detected, although contrary to previous hypotheses there was limited capacity for microalgal fermentation. In combination, these experiments confirm that fermentation dominates anoxic carbon mineralization in these permeable sediments and, in contrast to the case in cohesive sediments, is largely uncoupled from anaerobic respiration. Frequent changes in oxygen availability in these sediments may have selected for metabolically flexible bacteria while excluding strict anaerobes.}, }
@article {pmid30853028, year = {2019}, author = {Yason, JA and Liang, YR and Png, CW and Zhang, Y and Tan, KSW}, title = {Interactions between a pathogenic Blastocystis subtype and gut microbiota: in vitro and in vivo studies.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {30}, doi = {10.1186/s40168-019-0644-3}, pmid = {30853028}, issn = {2049-2618}, mesh = {Animals ; Bacterial Proteins/genetics ; Bifidobacterium longum/genetics/growth &amp; development ; Blastocystis/classification/*growth &amp; development/isolation &amp; purification/pathogenicity ; Blastocystis Infections/*microbiology ; Coculture Techniques ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Diseases/*microbiology ; *Gastrointestinal Microbiome ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; HT29 Cells ; Humans ; Lactobacillus/genetics/growth &amp; development ; Metagenomics ; Mice ; }, abstract = {BACKGROUND: Blastocystis is a common gut eukaryote detected in humans and animals. It has been associated with gastrointestinal disease in the past although recent metagenomic studies also suggest that it is a member of normal microbiota. This study investigates interactions between pathogenic human isolates belonging to Blastocystis subtype 7 (ST7) and bacterial representatives of the gut microbiota.<br><br>RESULTS: Generally, Blastocystis ST7 exerts a positive effect on the viability of representative gut bacteria except on Bifidobacterium longum. Gene expression analysis and flow cytometry indicate that the bacterium may be undergoing oxidative stress in the presence of Blastocystis. In vitro assays demonstrate that Blastocystis-induced host responses are able to decrease Bifidobacterium counts. Mice infected with Blastocystis also reveal a decrease in beneficial bacteria Bifidobacterium and Lactobacillus.<br><br>CONCLUSIONS: This study shows that particular isolates of Blastocystis ST7 cause changes in microbiota populations and potentially lead to an imbalance of the gut microbiota. This study suggests that certain isolates of Blastocystis exert their pathogenic effects through disruption of the gut microbiota and provides a counterpoint to the increasing reports indicating the commensal nature of this ubiquitous parasite.}, }
@article {pmid30850636, year = {2019}, author = {Hendriksen, RS and Munk, P and Njage, P and van Bunnik, B and McNally, L and Lukjancenko, O and Röder, T and Nieuwenhuijse, D and Pedersen, SK and Kjeldgaard, J and Kaas, RS and Clausen, PTLC and Vogt, JK and Leekitcharoenphon, P and van de Schans, MGM and Zuidema, T and de Roda Husman, AM and Rasmussen, S and Petersen, B and ,  and Amid, C and Cochrane, G and Sicheritz-Ponten, T and Schmitt, H and Alvarez, JRM and Aidara-Kane, A and Pamp, SJ and Lund, O and Hald, T and Woolhouse, M and Koopmans, MP and Vigre, H and Petersen, TN and Aarestrup, FM}, title = {Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1124}, doi = {10.1038/s41467-019-08853-3}, pmid = {30850636}, issn = {2041-1723}, support = {001//World Health Organization/International ; }, mesh = {Africa ; Asia ; Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Drug Resistance, Multiple, Bacterial/*genetics ; Epidemiological Monitoring ; Europe ; *Genes, Bacterial ; Humans ; *Metagenome ; Metagenomics/methods ; Microbial Consortia/drug effects/genetics ; North America ; Oceania ; Population Health ; Sewage/*microbiology ; Socioeconomic Factors ; South America ; }, abstract = {Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.}, }
@article {pmid30844070, year = {2019}, author = {Fritz, B and Stavnsbjerg, C and Markvart, M and Damgaard, PB and Nielsen, SH and Bjørndal, L and Qvortrup, K and Bjarnsholt, T}, title = {Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition.}, journal = {Pathogens and disease}, volume = {77}, number = {1}, pages = {}, doi = {10.1093/femspd/ftz013}, pmid = {30844070}, issn = {2049-632X}, mesh = {Bacteria/*classification/*genetics/ultrastructure ; Biodiversity ; *Biofilms ; Humans ; *Metagenome ; *Metagenomics ; }, abstract = {Bacterial biofilm infections often involve aggregates of bacteria heterogeneously distributed throughout a tissue or on a surface (such as an implanted medical device). Identification of a biofilm infection requires direct visualization via microscopy, followed by characterization of the microbial community by culturing or sequencing-based approaches. A sample, therefore, must be divided prior to analysis, often leading to inconsistent results. We demonstrate a combined approach, using scanning electron microscopy and next-generation shotgun sequencing, to visually identify a biofilm and characterize the microbial community, without dividing the sample. A clinical sample recovered from a patient following a dental root-filling procedure was prepared and visualized by scanning electron microscopy. DNA was then extracted from the sample several years later and analyzed by shotgun sequencing. The method was subsequently validated on in vitro cultures of Pseudomonas aeruginosa biofilm. Between 19 and 21 different genera and species were identified in the clinical sample with an estimated relative abundance greater than 1% by two different estimation approaches. Only eight genera identified were not associated with endodontic infections. This provides a proof-of-concept for a dual, microscopy and sequencing-based approach to identify and characterize bacterial biofilms, which could also easily be implemented in other scientific fields.}, }
@article {pmid30842211, year = {2019}, author = {Zuo, T and Lu, XJ and Zhang, Y and Cheung, CP and Lam, S and Zhang, F and Tang, W and Ching, JYL and Zhao, R and Chan, PKS and Sung, JJY and Yu, J and Chan, FKL and Cao, Q and Sheng, JQ and Ng, SC}, title = {Gut mucosal virome alterations in ulcerative colitis.}, journal = {Gut}, volume = {68}, number = {7}, pages = {1169-1179}, doi = {10.1136/gutjnl-2018-318131}, pmid = {30842211}, issn = {1468-3288}, mesh = {Adult ; Case-Control Studies ; China ; Colitis, Ulcerative/pathology/*virology ; Dysbiosis/pathology/*virology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*virology ; Male ; Rectum/pathology/*virology ; }, abstract = {OBJECTIVE: The pathogenesis of UC relates to gut microbiota dysbiosis. We postulate that alterations in the viral community populating the intestinal mucosa play an important role in UC pathogenesis. This study aims to characterise the mucosal virome and their functions in health and UC.<br><br>DESIGN: Deep metagenomics sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on the rectal mucosa of 167 subjects from three different geographical regions in China (UC=91; healthy controls=76). Virome and bacteriome alterations in UC mucosa were assessed and correlated with patient metadata. We applied partition around medoids clustering algorithm and classified mucosa viral communities into two clusters, referred to as mucosal virome metacommunities 1 and 2.<br><br>RESULTS: In UC, there was an expansion of mucosa viruses, particularly Caudovirales bacteriophages, and a decrease in mucosa Caudovirales diversity, richness and evenness compared with healthy controls. Altered mucosal virome correlated with intestinal inflammation. Interindividual dissimilarity between mucosal viromes was higher in UC than controls. Escherichia phage and Enterobacteria phage were more abundant in the mucosa of UC than controls. Compared with metacommunity 1, metacommunity 2 was predominated by UC subjects and displayed a significant loss of various viral species. Patients with UC showed substantial abrogation of diverse viral functions, whereas multiple viral functions, particularly functions of bacteriophages associated with host bacteria fitness and pathogenicity, were markedly enriched in UC mucosa. Intensive transkingdom correlations between mucosa viruses and bacteria were significantly depleted in UC.<br><br>CONCLUSION: We demonstrated for the first time that UC is characterised by substantial alterations of the mucosa virobiota with functional distortion. Enrichment of Caudovirales bacteriophages, increased phage/bacteria virulence functions and loss of viral-bacterial correlations in the UC mucosa highlight that mucosal virome may play an important role in UC pathogenesis.}, }
@article {pmid30841395, year = {2019}, author = {Cordeiro, MC and Garcia, GD and Rocha, AM and Tschoeke, DA and Campeão, ME and Appolinario, LR and Soares, AC and Leomil, L and Froes, A and Bahiense, L and Rezende, CE and de Almeida, MG and Rangel, TP and De Oliveira, BCV and de Almeida, DQR and Thompson, MC and Thompson, CC and Thompson, FL}, title = {Insights on the freshwater microbiomes metabolic changes associated with the world's largest mining disaster.}, journal = {The Science of the total environment}, volume = {654}, number = {}, pages = {1209-1217}, doi = {10.1016/j.scitotenv.2018.11.112}, pmid = {30841395}, issn = {1879-1026}, mesh = {*Chemical Hazard Release ; Disasters ; *Environmental Monitoring ; Fresh Water/*microbiology ; Microbiota ; Mining ; *Water Microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {To evaluate the impacts of the Fundão tailings dam failure (Minas Gerais, Brazil) on water quality of the Doce River, we analyzed metagenomics and physicochemical parameters during the month of the disaster and again 6 and 10 months after the disaster. To compare dam conditions before and after the failure, we performed a meta-analysis of physicochemical data from a public database. Immediately after the failure, suspended particulate matter (SPM) in the Doce River was 225-1877 mg L-1. Turbidity and dissolved aluminum and iron concentrations were extremely high, whereas dissolved oxygen was below Brazilian legislation norm (<5 mg L-1) in several locations. Six months later, physicochemical values were below thresholds set by Brazilian guidelines (e.g., SPM = 8-166 mg L-1). Short-term impacts on microbial communities included an increase in Actinobacteria and Bacteroidetes and gene sequences related to microbial virulence, motility, respiration, membrane transport, iron and nitrogen metabolism, suggesting changes in microbial metabolic profiles. The 11 recovered partial genomes from metagenomes (MAGs) had genes related to Fe cycle and metal resistance.}, }
@article {pmid30838598, year = {2019}, author = {Divaris, K and Shungin, D and Rodríguez-Cortés, A and Basta, PV and Roach, J and Cho, H and Wu, D and Ferreira Zandoná, AG and Ginnis, J and Ramamoorthy, S and Kinchen, JM and Kwintkiewicz, J and Butz, N and Ribeiro, AA and Azcarate-Peril, MA}, title = {The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1922}, number = {}, pages = {525-548}, doi = {10.1007/978-1-4939-9012-2_40}, pmid = {30838598}, issn = {1940-6029}, support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; U01 DE025046/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/*genetics/isolation &amp; purification/metabolism ; *Biofilms ; Child, Preschool ; DNA, Bacterial/genetics ; Dental Caries/etiology/*microbiology ; Gene Expression Profiling/methods ; Gingiva/microbiology ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Microbiota ; RNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods ; Software ; Specimen Handling/methods ; Tooth, Deciduous/*microbiology ; Transcriptome ; }, abstract = {Early childhood caries (ECC) is a biofilm-mediated disease. Social, environmental, and behavioral determinants as well as innate susceptibility are major influences on its incidence; however, from a pathogenetic standpoint, the disease is defined and driven by oral dysbiosis. In other words, the disease occurs when the natural equilibrium between the host and its oral microbiome shifts toward states that promote demineralization at the biofilm-tooth surface interface. Thus, a comprehensive understanding of dental caries as a disease requires the characterization of both the composition and the function or metabolic activity of the supragingival biofilm according to well-defined clinical statuses. However, taxonomic and functional information of the supragingival biofilm is rarely available in clinical cohorts, and its collection presents unique challenges among very young children. This paper presents a protocol and pipelines available for the conduct of supragingival biofilm microbiome studies among children in the primary dentition, that has been designed in the context of a large-scale population-based genetic epidemiologic study of ECC. The protocol is being developed for the collection of two supragingival biofilm samples from the maxillary primary dentition, enabling downstream taxonomic (e.g., metagenomics) and functional (e.g., transcriptomics and metabolomics) analyses. The protocol is being implemented in the assembly of a pediatric precision medicine cohort comprising over 6000 participants to date, contributing social, environmental, behavioral, clinical, and biological data informing ECC and other oral health outcomes.}, }
@article {pmid30834996, year = {2019}, author = {Boers, SA and Jansen, R and Hays, JP}, title = {Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {38}, number = {6}, pages = {1059-1070}, doi = {10.1007/s10096-019-03520-3}, pmid = {30834996}, issn = {1435-4373}, support = {602860//FP7 Health/ ; }, mesh = {DNA, Bacterial/genetics/standards ; Diagnostic Tests, Routine/*standards ; High-Throughput Nucleotide Sequencing/*standards ; Humans ; Infection/*diagnosis/epidemiology/microbiology ; Metagenomics/standards ; Microbiological Techniques/standards ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics/standards ; Sequence Analysis, DNA/standards ; }, abstract = {Recent advancements in next-generation sequencing (NGS) have provided the foundation for modern studies into the composition of microbial communities. The use of these NGS methods allows for the detection and identification of ('difficult-to-culture') microorganisms using a culture-independent strategy. In the field of routine clinical diagnostics however, the application of NGS is currently limited to microbial strain typing for epidemiological purposes only, even though the implementation of NGS for microbial community analysis may yield clinically important information. This lack of NGS implementation is due to many different factors, including issues relating to NGS method standardization and result reproducibility. In this review article, the authors provide a general introduction to the most widely used NGS methods currently available (i.e., targeted amplicon sequencing and shotgun metagenomics) and the strengths and weaknesses of each method is discussed. The focus of the publication then shifts toward 16S rRNA gene NGS methods, which are currently the most cost-effective and widely used NGS methods for research purposes, and are therefore more likely to be successfully implemented into routine clinical diagnostics in the short term. In this respect, the experimental pitfalls and biases created at each step of the 16S rRNA gene NGS workflow are explained, as well as their potential solutions. Finally, a novel diagnostic microbiota profiling platform ('MYcrobiota') is introduced, which was developed by the authors by taking into consideration the pitfalls, biases, and solutions explained in this article. The development of the MYcrobiota, and future NGS methodologies, will help pave the way toward the successful implementation of NGS methodologies into routine clinical diagnostics.}, }
@article {pmid30833550, year = {2019}, author = {Milanese, A and Mende, DR and Paoli, L and Salazar, G and Ruscheweyh, HJ and Cuenca, M and Hingamp, P and Alves, R and Costea, PI and Coelho, LP and Schmidt, TSB and Almeida, A and Mitchell, AL and Finn, RD and Huerta-Cepas, J and Bork, P and Zeller, G and Sunagawa, S}, title = {Microbial abundance, activity and population genomic profiling with mOTUs2.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1014}, doi = {10.1038/s41467-019-08844-4}, pmid = {30833550}, issn = {2041-1723}, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; Gene Expression Profiling ; Genes, Essential ; Genetic Markers ; Genome ; Host Microbial Interactions ; Humans ; *Metagenomics ; Microbiota/*genetics ; Molecular Sequence Annotation ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites).}, }
@article {pmid30826606, year = {2019}, author = {Bai, Y and Ruan, X and Xie, X and Yan, Z}, title = {Antibiotic resistome profile based on metagenomics in raw surface drinking water source and the influence of environmental factor: A case study in Huaihe River Basin, China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {248}, number = {}, pages = {438-447}, doi = {10.1016/j.envpol.2019.02.057}, pmid = {30826606}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacitracin/pharmacology ; Burkholderiaceae/drug effects/*genetics ; China ; Drinking Water/*microbiology ; Drug Resistance, Microbial/*genetics ; Flavobacterium/drug effects/*genetics ; Genes, Bacterial/genetics ; Humans ; Metagenomics ; Microbiota/drug effects ; Rivers/*microbiology ; Tetracyclines/pharmacology ; Verrucomicrobia/drug effects/*genetics ; beta-Lactams/pharmacology ; }, abstract = {The contamination with antibiotic resistance genes (ARGs) in raw drinking water source may pose a direct threat to human health. In this study, metagenomics sequencing and analysis were applied to investigate the ARG pattern in 12 drinking water sources in upper and middle reach of Huaihe River Basin, China. Based on the redundant analysis and multi-linear regression model, location, specific microbial taxa, number of livestock and health facilities significantly influenced the ARG profile in drinking water sources. Besides the cluster effect of ARG in samples from plain and bedrock mountain areas, the samples from fracture aquifer areas also showed a distinctive biogeographic pattern with that from porous aquifer areas. Putative ARGs host Opitutus and Flavobacterium were the enriched biomarkers in plain and fracture aquifer area respectively, which mainly carried bacitracin, multidrug, beta-lactam and tetracycline ARGs. This result illuminated that both natural background and anthropogenic activities in the watershed influenced the ARG profile in natural freshwater system significantly. The low MGEs abundance and absence of pathogen revealed a low ARG dissemination risk in sampled drinking water sources, while Polynucleobacter was an abundant ARGs host and was significantly related to the ARG profile, which indicated that specific bacteria was responsible for ARGs propagation and accumulation in surface freshwater system. Further researches are needed to assess human exposure to raw drinking water source and the potential risk, as well as the species interaction in microbial community and its impact on ARG propagation under oligotrophic condition.}, }
@article {pmid30814504, year = {2019}, author = {Mahnert, A and Moissl-Eichinger, C and Zojer, M and Bogumil, D and Mizrahi, I and Rattei, T and Martinez, JL and Berg, G}, title = {Man-made microbial resistances in built environments.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {968}, doi = {10.1038/s41467-019-08864-0}, pmid = {30814504}, issn = {2041-1723}, mesh = {Biodiversity ; *Built Environment ; *Drug Resistance, Microbial/genetics ; *Environmental Microbiology ; Gram-Negative Bacteria/drug effects/genetics/isolation &amp; purification ; Gram-Positive Bacteria/drug effects/genetics/isolation &amp; purification ; Humans ; Metagenome ; *Microbiota/drug effects/genetics ; }, abstract = {Antimicrobial resistance is a serious threat to global public health, but little is known about the effects of microbial control on the microbiota and its associated resistome. Here we compare the microbiota present on surfaces of clinical settings with other built environments. Using state-of-the-art metagenomics approaches and genome and plasmid reconstruction, we show that increased confinement and cleaning is associated with a loss of microbial diversity and a shift from Gram-positive bacteria, such as Actinobacteria and Firmicutes, to Gram-negative such as Proteobacteria. Moreover, the microbiome of highly maintained built environments has a different resistome when compared to other built environments, as well as a higher diversity in resistance genes. Our results highlight that the loss of microbial diversity correlates with an increase in resistance, and the need for implementing strategies to restore bacterial diversity in certain built environments.}, }
@article {pmid30808753, year = {2019}, author = {Ramírez-Flandes, S and González, B and Ulloa, O}, title = {Redox traits characterize the organization of global microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {9}, pages = {3630-3635}, doi = {10.1073/pnas.1817554116}, pmid = {30808753}, issn = {1091-6490}, mesh = {Ecology ; *Ecosystem ; Humans ; *Metagenomics ; Microbiota/*genetics ; *Oxidation-Reduction ; Soil Microbiology ; }, abstract = {The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a general ecological context. We used 247 microbial metagenomes from 18 biomes to determine which set of genes better characterizes the differences among biomes on the global scale. We show that profiles of oxidoreductase genes support the highest biome differentiation compared with profiles of other categories of enzymes, general protein-coding genes, transporter genes, and taxonomic gene markers. Based on oxidoreductases' description of microbial communities, the role of energetics in differentiation and particular ecosystem function of different biomes become readily apparent. We also show that taxonomic diversity is decoupled from functional diversity, e.g., grasslands and rhizospheres were the most diverse biomes in oxidoreductases but not in taxonomy. Considering that microbes underpin biogeochemical processes and nutrient recycling through oxidoreductases, this functional diversity should be relevant for a better understanding of the stability and conservation of biomes. Consequently, this approach might help to quantify the impact of environmental stressors on microbial ecosystems in the context of the global-scale biome crisis that our planet currently faces.}, }
@article {pmid30808694, year = {2019}, author = {Feng, J and Penton, CR and He, Z and Van Nostrand, JD and Yuan, MM and Wu, L and Wang, C and Qin, Y and Shi, ZJ and Guo, X and Schuur, EAG and Luo, Y and Bracho, R and Konstantinidis, KT and Cole, JR and Tiedje, JM and Yang, Y and Zhou, J}, title = {Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02521-18}, pmid = {30808694}, issn = {2150-7511}, mesh = {Alaska ; *Biota ; *Global Warming ; Metagenomics ; Microarray Analysis ; *Nitrogen Fixation ; Oxidoreductases/genetics ; Plant Development ; *Soil Microbiology ; Tundra ; }, abstract = {Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N2 fixation is the major source of biologically available N, the soil N2-fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene (nifH) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly (P < 0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore, more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem.IMPORTANCE With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N2 fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions.}, }
@article {pmid30808411, year = {2019}, author = {, }, title = {A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {31}, doi = {10.1186/s40168-019-0620-y}, pmid = {30808411}, issn = {2049-2618}, mesh = {Biomedical Research/*economics/*organization &amp; administration ; Humans ; Metagenomics/economics/organization &amp; administration ; Microbiota ; National Institutes of Health (U.S.) ; United States ; }, abstract = {The National Institutes of Health (NIH) is the primary federal government agency for biomedical research in the USA. NIH provides extensive support for human microbiome research with 21 of 27 NIH Institutes and Centers (ICs) currently funding this area through their extramural research programs. This analysis of the NIH extramural portfolio in human microbiome research briefly reviews the early history of this field at NIH, summarizes the program objectives and the resources developed in the recently completed 10-year (fiscal years 2007-2016) $215 M Human Microbiome Project (HMP) program, evaluates the scope and range of the $728 M NIH investment in extramural human microbiome research activities outside of the HMP over fiscal years 2012-2016, and highlights some specific areas of research which emerged from this investment. This analysis closes with a few comments on the technical needs and knowledge gaps which remain for this field to be able to advance over the next decade and for the outcomes of this research to be able to progress to microbiome-based interventions for treating disease and supporting health.}, }
@article {pmid30808380, year = {2019}, author = {DeMaere, MZ and Darling, AE}, title = {bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {46}, doi = {10.1186/s13059-019-1643-1}, pmid = {30808380}, issn = {1474-760X}, mesh = {Computer Simulation ; Feces/microbiology ; *Genome, Bacterial ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA ; *Software ; }, abstract = {Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth. We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs using a single time point. We validate the method and directly compare against a recently announced proprietary service, ProxiMeta. bin3C is an open-source pipeline and makes use of the Infomap clustering algorithm (https://github.com/cerebis/bin3C).}, }
@article {pmid30804518, year = {2019}, author = {Monnahan, P and Kolář, F and Baduel, P and Sailer, C and Koch, J and Horvath, R and Laenen, B and Schmickl, R and Paajanen, P and Šrámková, G and Bohutínská, M and Arnold, B and Weisman, CM and Marhold, K and Slotte, T and Bomblies, K and Yant, L}, title = {Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {3}, pages = {457-468}, doi = {10.1038/s41559-019-0807-4}, pmid = {30804518}, issn = {2397-334X}, mesh = {Arabidopsis/*genetics ; Evolution, Molecular ; *Gene Duplication ; *Gene Flow ; *Genome, Plant ; Metagenomics ; }, abstract = {Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced ~300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find that the impacts of polyploidy on population genomic processes are subtle yet pervasive, such as reduced efficiency of purifying selection, differences in linked selection and rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution and interploidy introgression likely conspire to shape the evolutionary potential of polyploids.}, }
@article {pmid30793504, year = {2019}, author = {Kwon, YM and Patra, AK and Chiura, HX and Kim, SJ}, title = {Production of extracellular vesicles with light-induced proton pump activity by proteorhodopsin-containing marine bacteria.}, journal = {MicrobiologyOpen}, volume = {8}, number = {8}, pages = {e00808}, doi = {10.1002/mbo3.808}, pmid = {30793504}, issn = {2045-8827}, support = {2019M00700//MABIK/ ; }, abstract = {The production and release of extracellular vesicles (EVs) is a common process occurring in various types of bacteria. However, little is known regarding the functions of EVs derived from marine bacteria. We observed that during cell growth, Sediminicola sp. YIK13, a proteorhodopsin (PR)-containing marine flavobacterium, produces EVs (S13EVs). Transmission electron microscopy showed that Sediminicola sp. YIK13 released two spherical vesicle types, with mono- and/or bi-layered membranes, in the culture. Interestingly, the S13EVs have an orange pigment, indicating the presence of putative carotenoid and PR pigments ascribed to the parental cells. The S13EVs demonstrated the same PR-derived absorption peak spectrum and light-induced proton pump activity as the parental cells. Western blot (immunoblot) analysis of the S13EVs revealed the presence of PR. We confirmed the 16S rRNA gene, pro gene, and genes required for chromophore retinal synthesis, namely blh and crtI, in the DNA packaged into these vesicles. In addition, by metagenomic sequencing, we found microbial rhodopsin-related genes in vesicles derived from natural aquatic environments. Our results suggest that EVs as well potentially pursue horizontal gene transfer of diverse microbial rhodopsin genes in marine ecosystems.}, }
@article {pmid30791436, year = {2019}, author = {Jaimes, JD and Jarosova, V and Vesely, O and Mekadim, C and Mrazek, J and Marsik, P and Killer, J and Smejkal, K and Kloucek, P and Havlik, J}, title = {Effect of Selected Stilbenoids on Human Fecal Microbiota.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {4}, pages = {}, doi = {10.3390/molecules24040744}, pmid = {30791436}, issn = {1420-3049}, support = {16-07193S//Grantová Agentura České Republiky/ ; CIGA 20172031//Česká Zemědělská Univerzita v Praze/ ; }, mesh = {Feces/*microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metagenome ; Metagenomics/methods ; Molecular Structure ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Stilbenes/*pharmacology ; }, abstract = {Dietary phenolics or polyphenols are mostly metabolized by the human gut microbiota. These metabolites appear to confer the beneficial health effects attributed to phenolics. Microbial composition affects the type of metabolites produced. Reciprocally, phenolics modulate microbial composition. Understanding this relationship could be used to positively impact health by phenolic supplementation and thus create favorable colonic conditions. This study explored the effect of six stilbenoids (batatasin III, oxyresveratrol, piceatannol, pinostilbene, resveratrol, thunalbene) on the gut microbiota composition. Stilbenoids were anaerobically fermented with fecal bacteria from four donors, samples were collected at 0 and 24 h, and effects on the microbiota were assessed by 16S rRNA gene sequencing. Statistical tests identified affected microbes at three taxonomic levels. Observed microbial composition modulation by stilbenoids included a decrease in the Firmicutes to Bacteroidetes ratio, a decrease in the relative abundance of strains from the genus Clostridium, and effects on the family Lachnospiraceae. A frequently observed effect was a further decrease of the relative abundance when compared to the control. An opposite effect to the control was observed for Faecalibacterium prausnitzii, whose relative abundance increased. Observed effects were more frequently attributed to resveratrol and piceatannol, followed by thunalbene and batatasin III.}, }
@article {pmid30782660, year = {2019}, author = {López-Pérez, M and Jayakumar, JM and Haro-Moreno, JM and Zaragoza-Solas, A and Reddi, G and Rodriguez-Valera, F and Shapiro, OH and Alam, M and Almagro-Moreno, S}, title = {Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02852-18}, pmid = {30782660}, issn = {2150-7511}, mesh = {Aquaculture ; Aquatic Organisms/microbiology ; Cluster Analysis ; Computational Biology ; *Ecotype ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; *Genotype ; Phenotype ; Recombination, Genetic ; Vibrio vulnificus/*classification/*genetics/isolation &amp; purification/physiology ; }, abstract = {Vibrio vulnificus, an opportunistic pathogen, is the causative agent of a life-threatening septicemia and a rising problem for aquaculture worldwide. The genetic factors that differentiate its clinical and environmental strains remain enigmatic. Furthermore, clinical strains have emerged from every clade of V. vulnificus In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species from an evolutionary and ecological point of view. Genome comparisons and bioinformatic analyses of 113 V. vulnificus isolates indicate that the population of V. vulnificus is made up of four different clusters. We found evidence that recombination and gene flow between the two largest clusters (cluster 1 [C1] and C2) have drastically decreased to the point where they are diverging independently. Pangenome and phenotypic analyses showed two markedly different lifestyles for these two clusters, indicating commensal (C2) and bloomer (C1) ecotypes, with differences in carbohydrate utilization, defense systems, and chemotaxis, among other characteristics. Nonetheless, we identified frequent intra- and interspecies exchange of mobile genetic elements (e.g., antibiotic resistance plasmids, novel &quot;chromids,&quot; or two different and concurrent type VI secretion systems) that provide high levels of genetic diversity in the population. Surprisingly, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together. We propose an evolutionary model of V. vulnificus that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections and emergence.IMPORTANCEVibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic. In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species to elucidate the traits that make these strains emerge as a human pathogen. The acquisition of different ecological determinants could have allowed the development of highly divergent clusters with different lifestyles within the same environment. However, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together, posing a potential risk of recombination and of emergence of novel variants. We propose a new evolutionary model that provides a perspective that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections.}, }
@article {pmid30782659, year = {2019}, author = {Klein, C and Gonzalez, D and Samwel, K and Kahesa, C and Mwaiselage, J and Aluthge, N and Fernando, S and West, JT and Wood, C and Angeletti, PC}, title = {Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02785-18}, pmid = {30782659}, issn = {2150-7511}, mesh = {Bacteria/*classification/genetics ; Cervix Uteri/*microbiology/*pathology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; HIV Infections/*complications ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; Precancerous Conditions/*epidemiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tanzania/epidemiology ; Uterine Cervical Neoplasms/*epidemiology ; }, abstract = {Nearly all cervical cancers are causally associated with human papillomavirus (HPV). The burden of HPV-associated dysplasias in sub-Saharan Africa is influenced by HIV. To investigate the role of the bacterial microbiome in cervical dysplasia, cytobrush samples were collected directly from cervical lesions of 144 Tanzanian women. The V4 hypervariable region of the 16S rRNA gene was amplified and deep sequenced. Alpha diversity metrics (Chao1, PD whole tree, and operational taxonomic unit [OTU] estimates) displayed significantly higher bacterial richness in HIV-positive patients (P = 0.01) than in HIV-negative patients. In HIV-positive patients, there was higher bacterial richness in patients with high-grade squamous intraepithelial lesions (HSIL) (P = 0.13) than those without lesions. The most abundant OTUs associated with high-grade squamous intraepithelial lesions were Mycoplasmatales, Pseudomonadales, and Staphylococcus We suggest that a chronic mycoplasma infection of the cervix may contribute to HPV-dependent dysplasia by sustained inflammatory signals.IMPORTANCE HPV is known to be the causal agent in the majority of cervical cancers. However, the role of the cervical bacterial microbiome in cervical cancer is not clear. To investigate that possibility, we collected cervical cytobrush samples from 144 Tanzanian women and performed deep sequencing of bacterial 16S rRNA genes. We found that HIV-positive patients had greater bacterial richness (P = 0.01) than HIV-negative patients. We also observed that women with high-grade squamous intraepithelial lesions (HSIL) had greater cervical bacterial diversity than women with cytologically normal cervices. Data from our precise sampling of cervical lesions leads us to propose that Mycoplasma contributes to a cervical microbiome status that promotes HPV-related cervical lesions. These results suggest a greater influence of the bacterial microbiota on the outcome of HPV infection than previously thought.}, }
@article {pmid30782206, year = {2019}, author = {Lagkouvardos, I and Lesker, TR and Hitch, TCA and Gálvez, EJC and Smit, N and Neuhaus, K and Wang, J and Baines, JF and Abt, B and Stecher, B and Overmann, J and Strowig, T and Clavel, T}, title = {Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {28}, doi = {10.1186/s40168-019-0637-2}, pmid = {30782206}, issn = {2049-2618}, mesh = {Animals ; Bacteriological Techniques/*methods ; Bacteroides/*classification/genetics/growth &amp; development ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gastrointestinal Microbiome ; Metagenomics/*methods ; Mice ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and detected in the intestine of other animals. Because they had not been cultured until recently and the family classification is still ambiguous, interaction with their host was difficult to study and confusion still exists regarding sequence data annotation.<br><br>METHODS: We investigated family S24-7 by combining data from large-scale 16S rRNA gene analysis and from functional and taxonomic studies of metagenomic and cultured species.<br><br>RESULTS: A total of 685 species was inferred by full-length 16S rRNA gene sequence clustering. While many species could not be assigned ecological habitats (93,045 samples analyzed), the mouse was the most commonly identified host (average of 20% relative abundance and nine co-occurring species). Shotgun metagenomics allowed reconstruction of 59 molecular species, of which 34 were representative of the 16S rRNA gene-derived species clusters. In addition, cultivation efforts allowed isolating five strains representing three species, including two novel taxa. Genome analysis revealed that S24-7 spp. are functionally distinct from neighboring families and versatile with respect to complex carbohydrate degradation.<br><br>CONCLUSIONS: We provide novel data on the diversity, ecology, and description of bacterial family S24-7, for which the name Muribaculaceae is proposed.}, }
@article {pmid30777011, year = {2019}, author = {Feng, Y and Ramnarine, VR and Bell, R and Volik, S and Davicioni, E and Hayes, VM and Ren, S and Collins, CC}, title = {Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {146}, doi = {10.1186/s12864-019-5457-z}, pmid = {30777011}, issn = {1471-2164}, support = {CSC201606325044//China Scholarship Council/ ; 201012TFF//Terry Fox Foundation/ ; T2013-01//Prostate Cancer Canada/ ; 81472397//National Natural Science Foundation of China/ ; }, mesh = {Aged ; Biodiversity ; Computational Biology/methods ; Humans ; Kaplan-Meier Estimate ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; Prostate/*microbiology/pathology ; Prostatic Neoplasms/*etiology/metabolism/mortality/pathology ; }, abstract = {BACKGROUND: Prostate cancer (PCa) is the most common malignant neoplasm among men in many countries. Since most precancerous and cancerous tissues show signs of inflammation, chronic bacterial prostatitis has been hypothesized to be a possible etiology. However, establishing a causal relationship between microbial inflammation and PCa requires a comprehensive analysis of the prostate microbiome. The aim of this study was to characterize the microbiome in prostate tissue of PCa patients and investigate its association with tumour clinical characteristics as well as host expression profiles.<br><br>RESULTS: The metagenome and metatranscriptome of tumour and the adjacent benign tissues were assessed in 65 Chinese radical prostatectomy specimens. Escherichia, Propionibacterium, Acinetobacter and Pseudomonas were abundant in both metagenome and metatranscriptome, thus constituting the core of the prostate microbiome. The biodiversity of the microbiomes could not be differentiated between the matched tumour/benign specimens or between the tumour specimens of low and high Gleason Scores. The expression profile of ten Pseudomonas genes was strongly correlated with that of eight host small RNA genes; three of the RNA genes may negatively associate with metastasis. Few viruses could be identified from the prostate microbiomes.<br><br>CONCLUSIONS: This is the first study of the human prostate microbiome employing an integrated metagenomics and metatranscriptomics approach. In this Chinese cohort, both metagenome and metatranscriptome analyses showed a non-sterile microenvironment in the prostate of PCa patients, but we did not find links between the microbiome and local progression of PCa. However, the correlated expression of Pseudomonas genes and human small RNA genes may provide tantalizing preliminary evidence that Pseudomonas infection may impede metastasis.}, }
@article {pmid30764497, year = {2019}, author = {Plaza-Díaz, J and Gómez-Fernández, A and Chueca, N and Torre-Aguilar, MJ and Gil, Á and Perez-Navero, JL and Flores-Rojas, K and Martín-Borreguero, P and Solis-Urra, P and Ruiz-Ojeda, FJ and Garcia, F and Gil-Campos, M}, title = {Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota.}, journal = {Nutrients}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/nu11020337}, pmid = {30764497}, issn = {2072-6643}, support = {404 Research Grant INVEST from the Spanish Society of Pediatrics and Red de Salud Materno Infantil (RED SAMID)//FUNDACIÓ AGRUPACIÓ Àmbit de la Infància/ ; }, mesh = {Autism Spectrum Disorder/*microbiology ; Bacteria/*classification/genetics ; Child, Preschool ; DNA, Bacterial/genetics ; Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; }, abstract = {New microbiome sequencing technologies provide novel information about the potential interactions among intestinal microorganisms and the host in some neuropathologies as autism spectrum disorders (ASD). The microbiota⁻gut⁻brain axis is an emerging aspect in the generation of autistic behaviors; evidence from animal models suggests that intestinal microbial shifts may produce changes fitting the clinical picture of autism. The aim of the present study was to evaluate the fecal metagenomic profiles in children with ASD and compare them with healthy participants. This comparison allows us to ascertain how mental regression (an important variable in ASD) could influence the intestinal microbiota profile. For this reason, a subclassification in children with ASD by mental regression (AMR) and no mental regression (ANMR) phenotype was performed. The present report was a descriptive observational study. Forty-eight children aged 2⁻6 years with ASD were included: 30 with ANMR and 18 with AMR. In addition, a control group of 57 normally developing children was selected and matched to the ASD group by sex and age. Fecal samples were analyzed with a metagenomic approach using a next-generation sequencing platform. Several differences between children with ASD, compared with the healthy group, were detected. Namely, Actinobacteria and Proteobacteria at phylum level, as well as, Actinobacteria, Bacilli, Erysipelotrichi, and Gammaproteobacteria at class level were found at higher proportions in children with ASD. Additionally, Proteobacteria levels showed to be augmented exclusively in AMR children. Preliminary results, using a principal component analysis, showed differential patterns in children with ASD, ANMR and AMR, compared to healthy group, both for intestinal microbiota and food patterns. In this study, we report, higher levels of Actinobacteria, Proteobacteria and Bacilli, aside from Erysipelotrichi, and Gammaproteobacteria in children with ASD compared to healthy group. Furthermore, AMR children exhibited higher levels of Proteobacteria. Further analysis using these preliminary results and mixing metagenomic and other &quot;omic&quot; technologies are needed in larger cohorts of children with ASD to confirm these intestinal microbiota changes.}, }
@article {pmid30763538, year = {2019}, author = {Gogokhia, L and Buhrke, K and Bell, R and Hoffman, B and Brown, DG and Hanke-Gogokhia, C and Ajami, NJ and Wong, MC and Ghazaryan, A and Valentine, JF and Porter, N and Martens, E and O'Connell, R and Jacob, V and Scherl, E and Crawford, C and Stephens, WZ and Casjens, SR and Longman, RS and Round, JL}, title = {Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {2}, pages = {285-299.e8}, doi = {10.1016/j.chom.2019.01.008}, pmid = {30763538}, issn = {1934-6069}, support = {//Wellcome Trust/United Kingdom ; DP2 GM111099/GM/NIGMS NIH HHS/United States ; R00 HL102228/HL/NHLBI NIH HHS/United States ; R01 GM114817/GM/NIGMS NIH HHS/United States ; R01 DK114252/DK/NIDDK NIH HHS/United States ; DP2 AT008746/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*virology ; *Bacteriophages ; CD4-Positive T-Lymphocytes/metabolism ; Colitis, Ulcerative/*immunology/*microbiology/pathology ; Colorectal Neoplasms/*immunology/*microbiology/pathology ; Disease Models, Animal ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; Interferon-gamma/metabolism ; Intestinal Mucosa/*immunology/*microbiology/pathology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Pilot Projects ; Prospective Studies ; Specific Pathogen-Free Organisms ; }, abstract = {Bacteriophages are the most abundant members of the microbiota and have the potential to shape gut bacterial communities. Changes to bacteriophage composition are associated with disease, but how phages impact mammalian health remains unclear. We noted an induction of host immunity when experimentally treating bacterially driven cancer, leading us to test whether bacteriophages alter immune responses. Treating germ-free mice with bacteriophages leads to immune cell expansion in the gut. Lactobacillus, Escherichia, and Bacteroides bacteriophages and phage DNA stimulated IFN-γ via the nucleotide-sensing receptor TLR9. The resultant immune responses were both phage and bacteria specific. Additionally, increasing bacteriophage levels exacerbated colitis via TLR9 and IFN-γ. Similarly, ulcerative colitis (UC) patients responsive to fecal microbiota transplantation (FMT) have reduced phages compared to non-responders, and mucosal IFN-γ positively correlates with bacteriophage levels. Bacteriophages from active UC patients induced more IFN-γ compared to healthy individuals. Collectively, these results indicate that bacteriophages can alter mucosal immunity to impact mammalian health.}, }
@article {pmid30761108, year = {2019}, author = {Ulloa, R and Moya-Beltrán, A and Rojas-Villalobos, C and Nuñez, H and Chiacchiarini, P and Donati, E and Giaveno, A and Quatrini, R}, title = {Domestication of Local Microbial Consortia for Efficient Recovery of Gold Through Top-Down Selection in Airlift Bioreactors.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {60}, doi = {10.3389/fmicb.2019.00060}, pmid = {30761108}, issn = {1664-302X}, abstract = {Extreme acidophiles play central roles in the geochemical cycling of diverse elements in low pH environments. This has been harnessed in biotechnologies such as biomining, where microorganisms facilitate the recovery of economically important metals such as gold. By generating both extreme acidity and a chemical oxidant (ferric iron) many species of prokaryotes that thrive in low pH environments not only catalyze mineral dissolution but also trigger both community and individual level adaptive changes. These changes vary in extent and direction depending on the ore mineralogy, water availability and local climate. The use of indigenous versus introduced microbial consortia in biomining practices is still a matter of debate. Yet, indigenous microbial consortia colonizing sulfidic ores that have been domesticated, i.e., selected for their ability to survive under specific polyextreme conditions, are claimed to outperform un-adapted foreign consortia. Despite this, little is known on the domestication of acidic microbial communities and the changes elicited in their members. In this study, high resolution targeted metagenomic techniques were used to analyze the changes occurring in the community structure of local microbial consortia acclimated to growing under extreme acidic conditions and adapted to endure the conditions imposed by the target mineral during biooxidation of a gold concentrate in an airlift reactor over a period of 2 years. The results indicated that operative conditions evolving through biooxidation of the mineral concentrate exerted strong selective pressures that, early on, purge biodiversity in favor of a few Acidithiobacillus spp. over other iron oxidizing acidophiles. Metagenomic analysis of the domesticated consortium present at the end of the adaptation experiment enabled reconstruction of the RVS1-MAG, a novel representative of Acidithiobacillus ferrooxidans from the Andacollo gold mineral district. Comparative genomic analysis performed with this genome draft revealed a net enrichment of gene functions related to heavy metal transport and stress management that are likely to play a significant role in adaptation and survival to adverse conditions experienced by these acidophiles during growth in presence of gold concentrates.}, }
@article {pmid30759800, year = {2019}, author = {Tremblay, ÉD and Kimoto, T and Bérubé, JA and Bilodeau, GJ}, title = {High-Throughput Sequencing to Investigate Phytopathogenic Fungal Propagules Caught in Baited Insect Traps.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {5}, number = {1}, pages = {}, doi = {10.3390/jof5010015}, pmid = {30759800}, issn = {2309-608X}, support = {OLF-P-1304, GRDI, QIS and CFIA OFL-P-1411, Genome Canada, and Genome BC (LSARP2112), CFIA-RPS and CFIA-TD and GRDI-CFIA mandated//Canadian Food Inspection Agency/ ; }, abstract = {Studying the means of dispersal of plant pathogens is crucial to better understand the dynamic interactions involved in plant infections. On one hand, entomologists rely mostly on both traditional molecular methods and morphological characteristics, to identify pests. On the other hand, high-throughput sequencing (HTS) is becoming the go-to avenue for scientists studying phytopathogens. These organisms sometimes infect plants, together with insects. Considering the growing number of exotic insect introductions in Canada, forest pest-management efforts would benefit from the development of a high-throughput strategy to investigate the phytopathogenic fungal and oomycete species interacting with wood-boring insects. We recycled formerly discarded preservative fluids from the Canadian Food Inspection Agency annual survey using insect traps and analysed more than one hundred samples originating from across Canada. Using the Ion Torrent Personal Genome Machine (PGM) HTS technology and fusion primers, we performed metabarcoding to screen unwanted fungi and oomycetes species, including Phytophthora spp. Community profiling was conducted on the four different wood-boring, insect-attracting semiochemicals; although the preservative (contained ethanol) also attracted other insects. Phytopathogenic fungi (e.g., Leptographium spp. and Merialaricis in the pine sawyer semiochemical) and oomycetes (mainly Peronospora spp. and Pythium aff. hypogynum in the General Longhorn semiochemical), solely associated with one of the four types of semiochemicals, were detected. This project demonstrated that the insect traps' semiochemical microbiome represents a new and powerful matrix for screening phytopathogens. Compared to traditional diagnostic techniques, the fluids allowed for a faster and higher throughput assessment of the biodiversity contained within. Additionally, minimal modifications to this approach would allow it to be used in other phytopathology fields.}, }
@article {pmid30759613, year = {2019}, author = {Wang, X and Li, X and Yu, L and Huang, L and Xiu, J and Lin, W and Zhang, Y}, title = {Characterizing the microbiome in petroleum reservoir flooded by different water sources.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {872-885}, doi = {10.1016/j.scitotenv.2018.10.410}, pmid = {30759613}, issn = {1879-1026}, mesh = {Betaproteobacteria/genetics/*metabolism ; China ; Environmental Monitoring ; Gammaproteobacteria/genetics/*metabolism ; Metagenomics ; *Microbiota/genetics ; Oil and Gas Fields/*microbiology ; Petroleum/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; Water Microbiology ; *Water Resources/supply &amp; distribution ; }, abstract = {Petroleum reservoir is an unusual subsurface biosphere, where indigenous microbes lived and evolved for million years. However, continual water injection changed the situation by introduction of new electron acceptors, donors and exogenous microbes. In this study, 16S-rRNA gene sequencing, comparative metagenomics and genomic bins reconstruction were employed to investigate the microbial community and metabolic potential in three typical water-flooded blocks of the Shen84 oil reservoir in Liaohe oil field, China. The results showed significant difference of microbial community compositions and metabolic characteristics existed between the injected water and the produced water/oil mixtures; however, there was considerable uniformity between the produced samples in different blocks. Microbial communities in the produced fluids were dominated by exogenous facultative microbes such as Pseudomonas and Thauera members from Proteobacteria phylum. Metabolic potentials for O2-dependent hydrocarbon degradation, dissimilarly nitrate reduction, and thiosulfate‑sulfur oxidation were much more abundant, whereas genes involved in dissimilatory sulfate reduction, anaerobic hydrocarbon degradation and methanogenesis were less abundant in the oil reservoir. Statistical analysis indicated the water composition had an obvious influence on microbial community composition and metabolic potential. The water-flooding process accompanied with introduction of nitrate or nitrite, and dissolved oxygen promoted the alteration of microbiome in oil reservoir from slow-growing anaerobic indigenous microbes (such as Thermotoga, Clostridia, and Syntrophobacter) to fast-growing opportunists as Beta- and Gama- Proteobacteria. The findings of this study shed light on the microbial ecology change in water flooded petroleum reservoir.}, }
@article {pmid30755506, year = {2019}, author = {Hausmann, B and Pelikan, C and Rattei, T and Loy, A and Pester, M}, title = {Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02189-18}, pmid = {30755506}, issn = {2150-7511}, mesh = {Bacterial Load ; Biomass ; Gene Expression Profiling ; Genome, Bacterial ; Metagenomics ; Peptococcaceae/*genetics/*growth &amp; development ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil Microbiology ; *Transcription, Genetic ; }, abstract = {Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize &quot;Candidatus Desulfosporosinus infrequens,&quot; a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 106 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of &quot;Ca. Desulfosporosinus infrequens&quot; increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days.IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.}, }
@article {pmid30747914, year = {2019}, author = {Gastauer, M and Vera, MPO and de Souza, KP and Pires, ES and Alves, R and Caldeira, CF and Ramos, SJ and Oliveira, G}, title = {A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining.}, journal = {Scientific data}, volume = {6}, number = {}, pages = {190008}, doi = {10.1038/sdata.2019.8}, pmid = {30747914}, issn = {2052-4463}, mesh = {Archaea/genetics ; Bacteria/genetics ; Brazil ; Environmental Monitoring/*methods ; High-Throughput Nucleotide Sequencing ; Iron ; Metagenomics/*methods ; *Microbiota/genetics ; Mining ; *Soil Microbiology ; Viruses/genetics ; }, abstract = {Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis. We used a paired-end library sequencing technology (NextSeq 500 Illumina); the reads were assembled using MEGAHIT. Coding DNA sequences (CDS) were identified using Kaiju in combination with non-redundant NCBI BLAST reference sequences containing archaea, bacteria, and viruses. Additionally, a functional classification was performed by EMG v2.3.2. Here, we provide the raw data and assembly (reads and contigs), followed by initial functional and taxonomic analysis, as a base-line for further studies of this kind. Further investigation is needed to fully understand the mechanisms of environmental rehabilitation in tropical regions, inspiring further researchers to explore this collection for hypothesis testing.}, }
@article {pmid30741334, year = {2019}, author = {Suleiman, M and Klippel, B and Busch, P and Schäfers, C and Moccand, C and Bel-Rhlid, R and Palzer, S and Antranikian, G}, title = {Enrichment of anaerobic heterotrophic thermophiles from four Azorean hot springs revealed different community composition and genera abundances using recalcitrant substrates.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {3}, pages = {277-281}, doi = {10.1007/s00792-019-01079-7}, pmid = {30741334}, issn = {1433-4909}, mesh = {*Archaea/classification/genetics/growth &amp; development/isolation &amp; purification ; *Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; *Biodiversity ; Hot Springs/*microbiology ; *Metagenome ; Metagenomics ; Portugal ; *Water Microbiology ; }, abstract = {DGGE analysis combined with a metagenomic approach was used to get insights into heterotrophic anoxic enrichment cultures of four hot springs of Vale das Furnas, Portugal, using the recalcitrant substrate spent coffee ground (SCG). Parallel enrichment cultures were performed using the major components of spent coffee ground, namely arabinogalactan, galactomannan, cellulose, and proteins. DGGE revealed that heterotrophic thermophilic bacteria are highly abundant in the hydrothermal springs and significant differences in community composition depending on the substrate were observed. DNA, isolated from enrichment cultures of different locations that were grown on the same substrate were pooled, and the respective metagenomes were analyzed. Results indicated that cultures grown on recalcitrant substrate SCG consists of a totally different thermophilic community, dominated by Dictyoglomus. Enrichments with galactomannan and arabinogalactan were dominated by Thermodesulfovibrio, while cultures with casein and cellulose were dominated by Thermus. This study indicates the high potential of thermophilic bacteria degrading recalcitrant substrate such as SCG and furthermore how the accessibility to complex polymers shapes the bacterial community.}, }
@article {pmid30740092, year = {2019}, author = {Grządziel, J and Gałązka, A}, title = {Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {6}, doi = {10.3389/fmicb.2019.00006}, pmid = {30740092}, issn = {1664-302X}, abstract = {The aim of the study was to investigate fungal genetic diversity in eight different types of soil in a long-term microplot experiment founded in 1881 in Puławy, Poland. The experiment consists of eight plots (14 m2), each 1 m deep with concrete walls, filled with profiles of different soils. The soils represent the most common Polish soil types (Cambic Leptosol, Fluvic Cambisol, Gleyic Chernozem, Cambisol and Haplic Cambisol, two Brunic Arenosols and Haplic Luvisol). Each soil was characterized by different pH (from 4.0 to 7.5) and organic carbon content (4.5-21.3 g kg-1). The soil structure was not destroyed by compaction because the soils had always been cultivated by hand. The same plant species were always grown in all plots at the same time and the soils received the same fertilization. Moreover, the soils were always under the same weather conditions. Ascomycota was the most abundant phylum in all samples, ranging from 70 to 90% of total fungi. Some genera (Mortierella, Solicoccozyma, and Mycosphaerella) were found to be adapted to a wide range of pH. Acidic soils were dominated by Talaromyces, Cladophialophora, Devriesia, and Saitozyma, while good quality soils primarily consisted of Plectosphaerella, Tetracladium, and Mortierella. The study confirmed previous reports that pH has a decisive influence on soil fungal diversity, but also indicated the strong impact of soil type itself. These studies have launched a new cycle of research in these historical soil profiles.}, }
@article {pmid30736849, year = {2019}, author = {Fritz, A and Hofmann, P and Majda, S and Dahms, E and Dröge, J and Fiedler, J and Lesker, TR and Belmann, P and DeMaere, MZ and Darling, AE and Sczyrba, A and Bremges, A and McHardy, AC}, title = {CAMISIM: simulating metagenomes and microbial communities.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {17}, doi = {10.1186/s40168-019-0633-6}, pmid = {30736849}, issn = {2049-2618}, mesh = {Algorithms ; Animals ; *Computer Simulation ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Mice ; Models, Biological ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {BACKGROUND: Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required.<br><br>RESULTS: We describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM.<br><br>CONCLUSIONS: CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation. All data sets and the software are freely available at https://github.com/CAMI-challenge/CAMISIM.}, }
@article {pmid30728080, year = {2019}, author = {Yu, K and Yi, S and Li, B and Guo, F and Peng, X and Wang, Z and Wu, Y and Alvarez-Cohen, L and Zhang, T}, title = {An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {16}, doi = {10.1186/s40168-019-0634-5}, pmid = {30728080}, issn = {2049-2618}, mesh = {Alcaligenaceae/genetics/isolation &amp; purification/*metabolism ; Benzhydryl Compounds/*metabolism ; *Biodegradation, Environmental ; Metagenomics ; Microbial Interactions/physiology ; Microbiota/physiology ; Phenols/*metabolism ; Pseudomonas/genetics/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sphingomonas/genetics/isolation &amp; purification/*metabolism ; }, abstract = {BACKGROUND: Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community-bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses.<br><br>RESULTS: The community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone.<br><br>CONCLUSION: The three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.}, }
@article {pmid30725462, year = {2019}, author = {Morales, E and Chen, J and Greathouse, KL}, title = {Compositional Analysis of the Human Microbiome in Cancer Research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1928}, number = {}, pages = {299-335}, doi = {10.1007/978-1-4939-9027-6_16}, pmid = {30725462}, issn = {1940-6029}, mesh = {Biological Evolution ; Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; *Research ; }, abstract = {Gut microbial composition has shown to be associated with obesity, diabetes mellitus, inflammatory bowel disease, colitis, autoimmune disorders, and cancer, among other diseases. Microbiome research has significantly evolved through the years and continues to advance as we develop new and better strategies to more accurately measure its composition and function. Careful selection of study design, inclusion and exclusion criteria of participants, and methodology are paramount to accurately analyze microbial structure. Here we present the most up-to-date available information on methods for gut microbial collection and analysis.}, }
@article {pmid30720800, year = {2019}, author = {Bukin, YS and Galachyants, YP and Morozov, IV and Bukin, SV and Zakharenko, AS and Zemskaya, TI}, title = {The effect of 16S rRNA region choice on bacterial community metabarcoding results.}, journal = {Scientific data}, volume = {6}, number = {}, pages = {190007}, doi = {10.1038/sdata.2019.7}, pmid = {30720800}, issn = {2052-4463}, mesh = {Bacteria/genetics ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing ; Lakes ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Russia ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {In this work, we compare the resolution of V2-V3 and V3-V4 16S rRNA regions for the purposes of estimating microbial community diversity using paired-end Illumina MiSeq reads, and show that the fragment, including V2 and V3 regions, has higher resolution for lower-rank taxa (genera and species). It allows for a more precise distance-based clustering of reads into species-level OTUs. Statistically convergent estimates of the diversity of major species (defined as those that together are covered by 95% of reads) can be achieved at the sample sizes of 10000 to 15000 reads. The relative error of the Shannon index estimate for this condition is lower than 4%.}, }
@article {pmid30719705, year = {2019}, author = {Cheng, L and Chen, Y and Zhang, X and Zheng, X and Cao, J and Wu, Z and Qin, W and Cheng, K}, title = {A metagenomic analysis of the modulatory effect of Cyclocarya paliurus flavonoids on the intestinal microbiome in a high-fat diet-induced obesity mouse model.}, journal = {Journal of the science of food and agriculture}, volume = {99}, number = {8}, pages = {3967-3975}, doi = {10.1002/jsfa.9622}, pmid = {30719705}, issn = {1097-0010}, support = {//K. C. Wong Magna Fund of Ningbo University/ ; 2017C02039//Key Research and Development Project of Zhejiang Province/ ; 2018C02047//Key Research and Development Project of Zhejiang Province/ ; LY19C200006//Zhejiang Provincial Natural Science Foundation of China/ ; }, mesh = {Adult ; Animals ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Dysbiosis/drug therapy/metabolism/microbiology ; Female ; Flavonoids/*administration &amp; dosage/analysis ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestines/*microbiology ; Juglandaceae/*chemistry ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/microbiology ; Plant Extracts/*administration &amp; dosage/analysis ; }, abstract = {BACKGROUND: As a result of a low bioavailability, the majority of Cyclocarya paliurus flavonoids (CPF) remain in the large intestine where they accumulate to exert a modulatory effect on the intestinal micro-ecology. Therefore, the present study investigated the modulatory effect of CPF on intestinal microbiota.<br><br>RESULTS: CPF dramatically ameliorated the obesity-induced gut dysbiosis. A significant decrease (P < 0.05) was observed in the ratio of Firmicutes/Bacteroidetes after CPF treatment for 8 weeks. Moreover, Kyoto Encyclopedia of Genes and Genomes pathways of biosynthesis of amino acids, the two-component system and ATP-binding cassette transporters enriched the most differentially expressed genes after CPF intervention.<br><br>CONCLUSION: The results of the present study indicate that CPF might have prebiotic-like activity and could be used as a functional food component with potential therapeutic utility to prevent obesity-related metabolic disorders by manipulating the gut flora and affecting certain metabolic pathways, thus contributing to the improvement of human health. © 2019 Society of Chemical Industry.}, }
@article {pmid30718869, year = {2019}, author = {Forster, SC and Kumar, N and Anonye, BO and Almeida, A and Viciani, E and Stares, MD and Dunn, M and Mkandawire, TT and Zhu, A and Shao, Y and Pike, LJ and Louie, T and Browne, HP and Mitchell, AL and Neville, BA and Finn, RD and Lawley, TD}, title = {A human gut bacterial genome and culture collection for improved metagenomic analyses.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {186-192}, doi = {10.1038/s41587-018-0009-7}, pmid = {30718869}, issn = {1546-1696}, mesh = {Bacteria/classification ; Computational Biology/methods ; Contig Mapping ; Gastrointestinal Microbiome ; *Genome, Bacterial ; Genome, Human ; Humans ; *Metagenome ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37%. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61% compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50% of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota.}, }
@article {pmid30718868, year = {2019}, author = {Zou, Y and Xue, W and Luo, G and Deng, Z and Qin, P and Guo, R and Sun, H and Xia, Y and Liang, S and Dai, Y and Wan, D and Jiang, R and Su, L and Feng, Q and Jie, Z and Guo, T and Xia, Z and Liu, C and Yu, J and Lin, Y and Tang, S and Huo, G and Xu, X and Hou, Y and Liu, X and Wang, J and Yang, H and Kristiansen, K and Li, J and Jia, H and Xiao, L}, title = {1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {179-185}, doi = {10.1038/s41587-018-0008-8}, pmid = {30718868}, issn = {1546-1696}, mesh = {Bacteria/classification ; Cluster Analysis ; Computational Biology/*methods ; Conserved Sequence ; Feces ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics ; Humans ; *Metagenome ; Metagenomics ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes.}, }
@article {pmid30718848, year = {2019}, author = {Valles-Colomer, M and Falony, G and Darzi, Y and Tigchelaar, EF and Wang, J and Tito, RY and Schiweck, C and Kurilshikov, A and Joossens, M and Wijmenga, C and Claes, S and Van Oudenhove, L and Zhernakova, A and Vieira-Silva, S and Raes, J}, title = {The neuroactive potential of the human gut microbiota in quality of life and depression.}, journal = {Nature microbiology}, volume = {4}, number = {4}, pages = {623-632}, doi = {10.1038/s41564-018-0337-x}, pmid = {30718848}, issn = {2058-5276}, mesh = {3,4-Dihydroxyphenylacetic Acid/metabolism ; Adult ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Cohort Studies ; Depression/metabolism/*microbiology/psychology ; Dopamine/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestines/microbiology ; Male ; Middle Aged ; Quality of Life ; }, abstract = {The relationship between gut microbial metabolism and mental health is one of the most intriguing and controversial topics in microbiome research. Bidirectional microbiota-gut-brain communication has mostly been explored in animal models, with human research lagging behind. Large-scale metagenomics studies could facilitate the translational process, but their interpretation is hampered by a lack of dedicated reference databases and tools to study the microbial neuroactive potential. Surveying a large microbiome population cohort (Flemish Gut Flora Project, n = 1,054) with validation in independent data sets (ntotal = 1,070), we studied how microbiome features correlate with host quality of life and depression. Butyrate-producing Faecalibacterium and Coprococcus bacteria were consistently associated with higher quality of life indicators. Together with Dialister, Coprococcus spp. were also depleted in depression, even after correcting for the confounding effects of antidepressants. Using a module-based analytical framework, we assembled a catalogue of neuroactive potential of sequenced gut prokaryotes. Gut-brain module analysis of faecal metagenomes identified the microbial synthesis potential of the dopamine metabolite 3,4-dihydroxyphenylacetic acid as correlating positively with mental quality of life and indicated a potential role of microbial γ-aminobutyric acid production in depression. Our results provide population-scale evidence for microbiome links to mental health, while emphasizing confounder importance.}, }
@article {pmid30717665, year = {2019}, author = {Jayasundara, D and Herath, D and Senanayake, D and Saeed, I and Yang, CY and Sun, Y and Chang, BC and Tang, SL and Halgamuge, SK}, title = {ENVirT: inference of ecological characteristics of viruses from metagenomic data.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 13}, pages = {377}, doi = {10.1186/s12859-018-2398-5}, pmid = {30717665}, issn = {1471-2105}, support = {LP140100670//Australian Research Council/ ; DP150103512//Australian Research Council/ ; }, mesh = {*Algorithms ; Computer Simulation ; *Ecological and Environmental Phenomena ; Fermented Foods ; Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Lakes/virology ; *Metagenomics ; Time Factors ; Viruses/genetics ; }, abstract = {BACKGROUND: Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databases to first estimate an average genome length of a viral community before being able to estimate other parameters, such as viral richness. Although this approach has been widely used, it can adversely skew results since the majority of viruses are yet to be catalogued in databases.<br><br>RESULTS: In this paper, we present ENVirT, a method for estimating the richness of novel viral mixtures, and for the first time we also show that it is possible to simultaneously estimate the average genome length without a priori information. This is shown to be a significant improvement over database-dependent methods, since we can now robustly analyze samples that may include novel viral types under-represented in current databases. We demonstrate that the viral richness estimates produced by ENVirT are several orders of magnitude higher in accuracy than the estimates produced by existing methods named PHACCS and CatchAll when benchmarked against simulated data. We repeated the analysis of 20 metavirome samples using ENVirT, which produced results in close agreement with complementary in virto analyses.<br><br>CONCLUSIONS: These insights were previously not captured by existing computational methods. As such, ENVirT is shown to be an essential tool for enhancing our understanding of novel viral populations.}, }
@article {pmid30715365, year = {2019}, author = {Goss-Souza, D and Mendes, LW and Borges, CD and Rodrigues, JLM and Tsai, SM}, title = {Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {3}, pages = {}, doi = {10.1093/femsec/fiz009}, pmid = {30715365}, issn = {1574-6941}, abstract = {The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due to liming and fertilization in long-term no-till cropping. Data revealed that long-term no-till cropping culminated in a decrease in Acidobacteria, Actinobacteria and Proteobacteria abundances. However, α- and β-Proteobacteria abundances were higher in the rhizosphere than in bulk soil, regardless of the time after forest-to-agriculture conversion. Changes in functional potential occurred predominantly in bulk soil, with decreases in functions related to potassium metabolism and virulence, disease and defense, while functions related to nucleic acids metabolism increased. Functions in the soybean rhizosphere remained stable, except for those related to potassium metabolism, which decreased after 20-year no-till cropping. Together, our results show that the soybean root system selects microbial taxa via trade-offs, to maintain functional resilience in the rhizosphere microbiome over time.}, }
@article {pmid30712189, year = {2019}, author = {Brito, EMS and Romero-Núñez, VM and Caretta, CA and Bertin, P and Valerdi-Negreros, JC and Guyoneaud, R and Goñi-Urriza, M}, title = {The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {2}, pages = {249-263}, doi = {10.1007/s00792-019-01078-8}, pmid = {30712189}, issn = {1433-4909}, support = {0627/15//Convocatoria de Apoyo a la Investigacion de la UG (DAIP)/ ; ANR-CONACyT-188775//Biometal Project/ ; }, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Hydrothermal Vents/*microbiology ; *Microbiota ; Phylogeny ; *Volcanic Eruptions ; }, abstract = {Vapor steam vents are prevailing structures on geothermal sites in which local geochemical conditions allow the development of extremophilic microorganisms. We describe the structure of the prokaryotic community able to grow on the walls and rocks of such microecosystems in two terrestrial Mexican volcanoes: Paricutín (PI and PII samples) and its satellite Sapichu (S sample). The investigated samples showed similar diversity indices, with few dominant OTUs (abundance > 1%): 21, 16 and 23, respectively for PI, PII and S. However, each steam vent showed a particular community profile: PI was dominated by photosynthetic bacteria (Cyanobacteria and Chloroflexia class), PII by Actinobacteria and Proteobacteria, and S by Ktedonobacteria class, Acidobacteria and Cyanobacteria phyla. Concerning the predicted metabolic potential, we found a dominance of cellular pathways, especially the ones for energy generation with metabolisms for sulfur respiration, nitrogen fixation, methanogenesis, carbon fixation, photosynthesis, and metals, among others. We suggest a different maturity stage for the three studied fumaroles, from the youngest (PI) to the oldest (S and PII), also influenced by the temperature and other geochemical parameters. Furthermore, four anaerobic strains were isolated, belonging to Clostridia class (Clostridium sphenoides, C. swellfunanium and Anaerocolumna cellulosilytica) and to Bacilli class (Paenibacillus azoreducens).}, }
@article {pmid30704595, year = {2019}, author = {Kamimura, BA and De Filippis, F and Sant'Ana, AS and Ercolini, D}, title = {Large-scale mapping of microbial diversity in artisanal Brazilian cheeses.}, journal = {Food microbiology}, volume = {80}, number = {}, pages = {40-49}, doi = {10.1016/j.fm.2018.12.014}, pmid = {30704595}, issn = {1095-9998}, mesh = {Animals ; *Biodiversity ; Brazil ; Cheese/*microbiology ; Cluster Analysis ; DNA, Bacterial/genetics ; *Food Microbiology ; Geography ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Brazilian artisanal cheeses are characterized by the use of raw milk and in some cases, natural starter cultures, known as &quot;pingo&quot;, as well as following simple and traditional manufacturing technology. In this study, a large-scale screening of the microbial ecology of 11 different types of artisanal cheeses produced in five geographical areas of Brazil was performed. Besides, the specific origin-related microbial signatures were identified. Clear geography- and technology-based differences in the microbiota were observed. Lactic acid bacteria dominated in all cheeses although Enterobacteriaceae and Staphylococcus also occurred in North, Northeast and Central cheeses. Differences in the lactic acid bacteria patterns were also highlighted: Streptococcus, Leuconostoc, Lactococcus and Lactobacillus were differently combined in terms of relative abundance according to product type and region of production. This study provides a comprehensive, unprecedented microbiological mapping of Brazilian cheeses, highlighting the impact of geographical origin and mode of production on microbial diversity. The results obtained will help to plan an evaluation of microbial contamination sources that will need to be studied for the improvement of cheese quality and safety.}, }
@article {pmid30701707, year = {2019}, author = {Jerde, CL and Wilson, EA and Dressler, TL}, title = {Measuring global fish species richness with eDNA metabarcoding.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {19-22}, doi = {10.1111/1755-0998.12929}, pmid = {30701707}, issn = {1755-0998}, support = {AID-OAA-A-16-00057//United States Agency for International Development/ ; }, mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA/chemistry/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification/*genetics ; French Guiana ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Water/chemistry ; }, abstract = {Despite mounting threats to global freshwater and marine biodiversity, including climate change, habitat alteration, overharvesting and pollution, we struggle to know which species are present below the water's surface that are suffering from these stressors. However, the idea that a water sample containing environmental DNA (eDNA) can be screened using high-throughput sequencing and bioinformatics to reveal the identity of aquatic species is a revolutionary advance for studying the patterns of species extirpation, invasive species establishment and the dynamics of species richness. To date, many of the critical tests of fisheries diversity using this metabarcoding approach have been conducted in lower diversity systems (<40 fish species), but in this issue of Molecular Ecology Resources, Cilleros et al. (2018) described their eDNA application in the species-rich French Guiana fishery (>200 fish species) and showed the greater potential and some limitations of using eDNA in species-rich environments.}, }
@article {pmid30698687, year = {2019}, author = {Dhakan, DB and Maji, A and Sharma, AK and Saxena, R and Pulikkan, J and Grace, T and Gomez, A and Scaria, J and Amato, KR and Sharma, VK}, title = {The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches.}, journal = {GigaScience}, volume = {8}, number = {3}, pages = {}, doi = {10.1093/gigascience/giz004}, pmid = {30698687}, issn = {2047-217X}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Cluster Analysis ; Discriminant Analysis ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; *Genes ; Humans ; India ; Infant ; Least-Squares Analysis ; Membrane Transport Proteins/metabolism ; *Metabolome ; Metabolomics/*methods ; Metagenome ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Statistics, Nonparametric ; Young Adult ; }, abstract = {BACKGROUND: Metagenomic studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health; however, the Indian gut microbiome has not been well explored. We analyzed the gut microbiome of 110 healthy individuals from two distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole-genome shotgun metagenomic sequencing, and metabolomic profiling of fecal and serum samples.<br><br>RESULTS: The gene catalogue established in this study emphasizes the uniqueness of the Indian gut microbiome in comparison to other populations. The gut microbiome of the cohort from North-Central India, which was primarily consuming a plant-based diet, was found to be associated with Prevotella and also showed an enrichment of branched chain amino acid (BCAA) and lipopolysaccharide biosynthesis pathways. In contrast, the gut microbiome of the cohort from Southern India, which was consuming an omnivorous diet, showed associations with Bacteroides, Ruminococcus, and Faecalibacterium and had an enrichment of short chain fatty acid biosynthesis pathway and BCAA transporters. This corroborated well with the metabolomics results, which showed higher concentration of BCAAs in the serum metabolome of the North-Central cohort and an association with Prevotella. In contrast, the concentration of BCAAs was found to be higher in the fecal metabolome of the Southern-India cohort and showed a positive correlation with the higher abundance of BCAA transporters.<br><br>CONCLUSIONS: The study reveals the unique composition of the Indian gut microbiome, establishes the Indian gut microbial gene catalogue, and compares it with the gut microbiome of other populations. The functional associations revealed using metagenomic and metabolomic approaches provide novel insights on the gut-microbe-metabolic axis, which will be useful for future epidemiological and translational researches.}, }
@article {pmid30696735, year = {2019}, author = {Baxter, NT and Schmidt, AW and Venkataraman, A and Kim, KS and Waldron, C and Schmidt, TM}, title = {Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, doi = {10.1128/mBio.02566-18}, pmid = {30696735}, issn = {2150-7511}, support = {52008119/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adolescent ; Adult ; Biostatistics ; Chemistry Techniques, Analytical ; Chicory ; Dietary Fiber/*administration &amp; dosage ; Fatty Acids, Volatile/*metabolism ; Feces/*chemistry/*microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inulin/administration &amp; dosage ; Metagenomics ; Solanum tuberosum ; Starch/administration &amp; dosage ; Young Adult ; Zea mays ; }, abstract = {Production of short-chain fatty acids (SCFAs), especially butyrate, in the gut microbiome is required for optimal health but is frequently limited by the lack of fermentable fiber in the diet. We attempted to increase butyrate production by supplementing the diets of 174 healthy young adults for 2 weeks with resistant starch from potatoes (RPS), resistant starch from maize (RMS), inulin from chicory root, or an accessible corn starch control. RPS resulted in the greatest increase in total SCFAs, including butyrate. Although the majority of microbiomes responded to RPS with increases in the relative abundance of bifidobacteria, those that responded with an increase in Ruminococcus bromii or Clostridium chartatabidum were more likely to yield higher butyrate concentrations, especially when their microbiota were replete with populations of the butyrate-producing species Eubacterium rectale RMS and inulin induced different changes in fecal communities, but they did not generate significant increases in fecal butyrate levels.IMPORTANCE These results reveal that not all fermentable fibers are equally capable of stimulating SCFA production, and they highlight the importance of the composition of an individual's microbiota in determining whether or not they respond to a specific dietary supplement. In particular, R. bromii or C. chartatabidum may be required for enhanced butyrate production in response to RS. Bifidobacteria, though proficient at degrading RS and inulin, may not contribute to the butyrogenic effect of those fermentable fibers in the short term.}, }
@article {pmid30696492, year = {2019}, author = {Cernava, T and Erlacher, A and Soh, J and Sensen, CW and Grube, M and Berg, G}, title = {Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.).}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {13}, doi = {10.1186/s40168-019-0624-7}, pmid = {30696492}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/pharmacology ; Base Sequence ; Brassicaceae/*microbiology ; Drug Resistance, Bacterial/genetics ; Enterobacteriaceae/*classification/genetics/*isolation &amp; purification ; Foodborne Diseases/microbiology ; Metagenome/*genetics ; Microbial Sensitivity Tests ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Arugula is a traditional medicinal plant and popular leafy green today. It is mainly consumed raw in the Western cuisine and known to contain various bioactive secondary metabolites. However, arugula has been also associated with high-profile outbreaks causing severe food-borne human diseases. A multiphasic approach integrating data from metagenomics, amplicon sequencing, and arugula-derived bacterial cultures was employed to understand the specificity of the indigenous microbiome and resistome of the edible plant parts.<br><br>RESULTS: Our results indicate that arugula is colonized by a diverse, plant habitat-specific microbiota. The indigenous phyllosphere bacterial community was shown to be dominated by Enterobacteriaceae, which are well-equipped with various antibiotic resistances. Unexpectedly, the prevalence of specific resistance mechanisms targeting therapeutic antibiotics (fluoroquinolone, chloramphenicol, phenicol, macrolide, aminocoumarin) was only surpassed by efflux pump assignments.<br><br>CONCLUSIONS: Enterobacteria, being core microbiome members of arugula, have a substantial implication in the overall resistome. Detailed insights into the natural occurrence of antibiotic resistances in arugula-associated microorganisms showed that the plant is a hotspot for distinctive defense mechanisms. The specific functioning of microorganisms in this unusual ecosystem provides a unique model to study antibiotic resistances in an ecological context.}, }
@article {pmid30694507, year = {2019}, author = {Delafont, V and Perrin, Y and Bouchon, D and Moulin, L and Héchard, Y}, title = {Targeted Metagenomics of Microbial Diversity in Free-Living Amoebae and Water Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1921}, number = {}, pages = {421-428}, doi = {10.1007/978-1-4939-9048-1_26}, pmid = {30694507}, issn = {1940-6029}, mesh = {Amoeba/*microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; *Water Microbiology ; }, abstract = {The presence of Legionella spp. in natural and man-made water systems is a great public health concern and heavily depends on the presence of free-living amoebae. Taking advantage of the development and affordability of next-generation sequencing technology, we present here a method to characterize the whole bacterial community directly from water samples, as well as from isolated free-living amoebae.}, }
@article {pmid30690359, year = {2019}, author = {Qiao, R and Sheng, C and Lu, Y and Zhang, Y and Ren, H and Lemos, B}, title = {Microplastics induce intestinal inflammation, oxidative stress, and disorders of metabolome and microbiome in zebrafish.}, journal = {The Science of the total environment}, volume = {662}, number = {}, pages = {246-253}, doi = {10.1016/j.scitotenv.2019.01.245}, pmid = {30690359}, issn = {1879-1026}, mesh = {Animals ; Dose-Response Relationship, Drug ; Dysbiosis/chemically induced/immunology/*physiopathology ; Fish Diseases/chemically induced/*immunology/physiopathology ; Gastrointestinal Microbiome/drug effects ; Inflammation/chemically induced/*immunology ; Intestines/immunology/physiology ; Metabolome/drug effects ; Metagenomics ; Oxidative Stress/drug effects ; Polystyrenes/*adverse effects/metabolism ; Random Allocation ; Toxicity Tests, Chronic ; Water Pollutants, Chemical/*adverse effects/metabolism ; *Zebrafish/metabolism/microbiology ; }, abstract = {Microplastics (MPs) can be ingested by a variety of species and mainly accumulate in the gut. However, the consequences of MPs exposure in the gut are largely unknown. Here we evaluated the impacts of MPs exposure in zebrafish gut. Animals were experimentally exposed to polystyrene MPs (5-μm beads; 50 μg/L and 500 μg/L) for 21 days and monitored for alterations in tissue histology, enzymatic biomarkers, gut microbiome and metabolomic responses. Inflammation and oxidative stress were observed in the zebrafish gut after exposed to MPs. Furthermore, significant alterations in the gut microbiome and tissue metabolic profiles were observed, with most of these were associated with oxidative stress, inflammation and lipid metabolism. This study provides evidence that MPs exposure causes gut damage as well as alterations in gut metabolome and microbiome, yielding novel insights into the consequences of MPs exposure.}, }
@article {pmid30685386, year = {2019}, author = {Liu, J and Johnson, R and Dillon, S and Kroehl, M and Frank, DN and Tuncil, YE and Zhang, X and Ir, D and Robertson, CE and Seifert, S and Higgins, J and Hamaker, B and Wilson, CC and Erlandson, KM}, title = {Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus.}, journal = {EBioMedicine}, volume = {40}, number = {}, pages = {583-594}, doi = {10.1016/j.ebiom.2019.01.033}, pmid = {30685386}, issn = {2352-3964}, support = {K23 AG050260/AG/NIA NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; T32 AG000279/AG/NIA NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; }, mesh = {Age Factors ; Aged ; Aged, 80 and over ; Biomarkers ; Case-Control Studies ; Computational Biology/methods ; Diet ; Dysbiosis ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; HIV Infections/*epidemiology/*virology ; HIV Seropositivity ; *HIV-1 ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; }, abstract = {BACKGROUND: HIV-1 infection and physiological aging are independently linked to elevated systemic inflammation and changes in enteric microbial communities (dysbiosis). However, knowledge of the direct effect of HIV infection on the aging microbiome and potential links to systemic inflammation is lacking.<br><br>METHODS: In a cross-sectional study of older people living with HIV (PLWH) (median age 61.5 years, N = 14) and uninfected controls (median 58 years, n = 22) we compared stool microbiota, levels of microbial metabolites (short-chain fatty acid levels, SCFA) and systemic inflammatory biomarkers by HIV serostatus and age.<br><br>FINDINGS: HIV and age were independently associated with distinct changes in the stool microbiome. For example, abundances of Enterobacter and Paraprevotella were higher and Eggerthella and Roseburia lower among PLWH compared to uninfected controls. Age-related microbiome changes also differed by HIV serostatus. Some bacteria with inflammatory potential (e.g. Escherichia) increased with age among PLWH, but not controls. Stool SCFA levels were similar between the two groups yet patterns of associations between individual microbial taxa and SCFA levels differed. Abundance of various genera including Escherichia and Bifidobacterium positively associated with inflammatory biomarkers (e.g. soluble Tumor Necrosis Factor Receptors) among PLWH, but not among controls.<br><br>INTERPRETATION: The age effect on the gut microbiome and associations between microbiota and microbial metabolites or systemic inflammation differed based on HIV serostatus, raising important implications for the impact of therapeutic interventions, dependent on HIV serostatus or age.}, }
@article {pmid30683956, year = {2019}, author = {Mahato, NK and Sharma, A and Singh, Y and Lal, R}, title = {Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics.}, journal = {Archives of microbiology}, volume = {201}, number = {3}, pages = {377-388}, doi = {10.1007/s00203-018-01616-6}, pmid = {30683956}, issn = {1432-072X}, support = {BT/PR15118/BCE/8/1141/2015//Department of Biotechnology, Ministry of Science and Technology/ ; }, mesh = {Altitude ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Flagella/genetics ; Geologic Sediments/*microbiology ; Hot Springs/*microbiology ; Hot Temperature ; India ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; Temperature ; Type IV Secretion Systems/genetics ; }, abstract = {Metagenomic surveys across microbial mat (~ 55 °C) samples of high-altitude (1760 m above sea level) Himalayan geothermal springs have revealed specialized community enriched with niche-specific functions. In this study, we have performed metagenomic sequence-based analyses to get insights into taxonomic composition and functional potential of hyperthermophiles in water (~ 95 °C) and sediment samples (78-98 °C). Community analyses revealed predominance of thermophilic bacterial and archeal genera dwelling in water in contrast to microbial mats (55 °C), namely Methylophilus, Methyloversatilis, Emticicia, Caulobacter, Thermus, Enhydrobacter and Pyrobaculum. Sediment samples having surface temperature (~ 78 °C) were colonized by Pyrobaculum and Chloroflexus while genus Massilia was found to be inhabited in high-temperature sediments (~ 98 °C). Functional analyses of metagenomic sequences revealed genetic enrichment of genes such as type IV secretion system, flagellar assembly and two-component system in contrast to mats. Furthermore, inter-sample comparison of enriched microbial diversity among water, sediment and microbial mats revealed habitat-specific clustering of the samples within same environment highlighting the role of temperature dynamics in modulating community structure across different habitats in same niche. However, function-based analysis demonstrated site-specific clustering among sediment, microbial mat and water samples. Furthermore, a novel thermophilic genotype of the genus Emticicia (designated as strain MM) was reconstructed from metagenome data. This is a correlative study between three major habitats present in geothermal spring environment, i.e., water, sediment and microbial mats revealing greater phylogenetic and functional dispersion emphasizing changing habitat-specific dynamics with temperature.}, }
@article {pmid30683856, year = {2019}, author = {Ellegaard, KM and Engel, P}, title = {Genomic diversity landscape of the honey bee gut microbiota.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {446}, doi = {10.1038/s41467-019-08303-0}, pmid = {30683856}, issn = {2041-1723}, mesh = {Age Factors ; Animals ; Bees/*microbiology ; Bifidobacterium/classification/*genetics/isolation &amp; purification ; *Biological Variation, Individual ; DNA, Bacterial/genetics ; Firmicutes/classification/*genetics/isolation &amp; purification ; Gammaproteobacteria/classification/*genetics/isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Metagenomics ; Microbial Consortia/genetics ; Phylogeny ; Symbiosis/physiology ; }, abstract = {The structure and distribution of genomic diversity in natural microbial communities is largely unexplored. Here, we used shotgun metagenomics to assess the diversity of the honey bee gut microbiota, a community consisting of few bacterial phylotypes. Our results show that most phylotypes are composed of sequence-discrete populations, which co-exist in individual bees and show age-specific abundance profiles. In contrast, strains present within these sequence-discrete populations were found to segregate into individual bees. Consequently, despite a conserved phylotype composition, each honey bee harbors a distinct community at the functional level. While ecological differentiation seems to facilitate coexistence at higher taxonomic levels, our findings suggest that, at the level of strains, priority effects during community assembly result in individualized profiles, despite the social lifestyle of the host. Our study underscores the need to move beyond phylotype-level characterizations to understand the function of this community, and illustrates its potential for strain-level analysis.}, }
@article {pmid30681281, year = {2019}, author = {Wang, J}, title = {A parsimony estimator of the number of populations from a STRUCTURE-like analysis.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {970-981}, doi = {10.1111/1755-0998.13000}, pmid = {30681281}, issn = {1755-0998}, mesh = {*Biodiversity ; Biostatistics/*methods ; Genetics, Population/*methods ; Metagenomics/*methods ; }, abstract = {Population genetics model based Bayesian methods have been proposed and widely applied to making unsupervised inference of population structure from a sample of multilocus genotypes. Usually they provide good estimates of the ancestry (or population membership) of sampled individuals by clustering them probabilistically or proportionally into (anonymous) populations. However, they have difficulties in accurately estimating the number of populations (K) represented by the sampled individuals. This study proposed a new ad hoc estimator of K, calculable from the output of a population clustering program such as STRUCTURE or ADMIXTURE. The new criterion, called parsimony index (PI), aims to identify the number of populations (K) which yields consistently the minimal admixture estimates of sampled individuals. Extensive simulated and empirical data were used to compare the accuracy of PI and two popular K estimators based on Pr[X|K] (i.e., the probability of genotype data X given K) and ΔK (i.e., the rate of change of the probability of data as a function of K) calculated from STRUCTURE outputs, and the accuracy of PI and the cross-validation method calculated from ADMIXTURE outputs. It was shown that PI was more accurate than the other methods consistently in various population structure (e.g., hierarchical island model, different extents of differentiation) and sampling (e.g., unbalanced sample sizes, different marker information contents) scenarios. The ΔK method was more accurate than the Pr[X|K] method only for hierarchically structured or highly inbred populations, and the opposite was true in the other scenarios. The PI method was implemented in a computer program, KFinder, which can be run on all major computer platforms.}, }
@article {pmid30680877, year = {2019}, author = {Alessandri, G and Milani, C and Mancabelli, L and Mangifesta, M and Lugli, GA and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M}, title = {Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features.}, journal = {Environmental microbiology}, volume = {21}, number = {4}, pages = {1331-1343}, doi = {10.1111/1462-2920.14540}, pmid = {30680877}, issn = {1462-2920}, support = {//EU Joint Programming Initiative - A Healthy Diet for a Healthy Life/ ; //Fondazione Cariparma/ ; //Ministero dell'Istruzione, dell'Università e della Ricerca/ ; 15/JP-HDHL/3280//Science Foundation Ireland/Ireland ; //JPI HDHL/ ; }, abstract = {Domestication of dogs from wolves is the oldest known example of ongoing animal selection, responsible for generating more than 300 dog breeds worldwide. In order to investigate the taxonomic and functional evolution of the canine gut microbiota, a multi-omics approach was applied to six wild wolves and 169 dog faecal samples, the latter encompassing 51 breeds, which fully covers currently known canine genetic biodiversity. Specifically, 16S rRNA gene and bifidobacterial Internally Transcribed Spacer (ITS) profiling were employed to reconstruct and then compare the canine core gut microbiota to those of wolves and humans, revealing that artificial selection and subsequent cohabitation of dogs with their owners influenced the microbial population of canine gut through loss and acquisition of specific bacterial taxa. Moreover, comparative analysis of the intestinal bacterial population of dogs fed on Bones and Raw Food (BARF) or commercial food (CF) diet, coupled with shotgun metagenomics, highlighted that both bacterial composition and metabolic repertoire of the canine gut microbiota have evolved to adapt to high-protein or high-carbohydrates intake. Altogether, these data indicate that artificial selection and domestication not only affected the canine genome, but also shaped extensively the bacterial population harboured by the canine gut.}, }
@article {pmid30680143, year = {2019}, author = {Rytkönen, S and Vesterinen, EJ and Westerduin, C and Leviäkangas, T and Vatka, E and Mutanen, M and Välimäki, P and Hukkanen, M and Suokas, M and Orell, M}, title = {From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web.}, journal = {Ecology and evolution}, volume = {9}, number = {1}, pages = {631-639}, doi = {10.1002/ece3.4787}, pmid = {30680143}, issn = {2045-7758}, abstract = {Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits Poecile montanus, Siberian tits Poecile cinctus, great tits Parus major and blue tits Cyanistes caeruleus) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (Betula spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.}, }
@article {pmid30678352, year = {2019}, author = {Yang, Q and Gao, C and Jiang, Y and Wang, M and Zhou, X and Shao, H and Gong, Z and McMinn, A}, title = {Metagenomic Characterization of the Viral Community of the South Scotia Ridge.}, journal = {Viruses}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/v11020095}, pmid = {30678352}, issn = {1999-4915}, mesh = {Antarctic Regions ; Bacteriophages/genetics ; *Genetic Variation ; *Genome, Viral ; *Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; Podoviridae/genetics/isolation &amp; purification ; Seawater/virology ; Viruses/*classification ; Water Microbiology ; }, abstract = {Viruses are the most abundant biological entities in aquatic ecosystems and harbor an enormous amount of genetic diversity. Whereas their influence on marine ecosystems is widely acknowledged, current information about their diversity remains limited. We conducted a viral metagenomic analysis of water samples collected during the austral summer of 2016 from the South Scotia Ridge (SSR), near the Antarctic Peninsula. The taxonomic composition and diversity of the viral communities were investigated, and a functional assessment of the sequences was performed. Phylotypic analysis showed that most viruses belonged to the order Caudovirales, especially the family Podoviridae (41.92⁻48.7%), which is similar to the situation in the Pacific Ocean. Functional analysis revealed a relatively high frequency of phage-associated and metabolism genes. Phylogenetic analyses of phage TerL and Capsid_NCLDV (nucleocytoplasmic large DNA viruses) marker genes indicated that many sequences associated with Caudovirales and NCLDV were novel and distinct from known phage genomes. High Phaeocystis globosa virus virophage (Pgvv) signatures were found and complete and partial Pgvv-like were obtained, which influence host⁻virus interactions. Our study expands existing knowledge of viral communities and their diversities from the Antarctic region and provides basic data for further exploring polar microbiomes.}, }
@article {pmid30669548, year = {2019}, author = {Chávez-Carbajal, A and Nirmalkar, K and Pérez-Lizaur, A and Hernández-Quiroz, F and Ramírez-Del-Alto, S and García-Mena, J and Hernández-Guerrero, C}, title = {Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome.}, journal = {International journal of molecular sciences}, volume = {20}, number = {2}, pages = {}, doi = {10.3390/ijms20020438}, pmid = {30669548}, issn = {1422-0067}, support = {11a Convocatoria Para Proyectos de Investigación Básica.//Universidad Iberoamericana Ciudad de México/ ; CONACyT-163235 INFR-2011-01//Consejo Nacional de Ciencia y Tecnología/ ; FONSEC SS/IMSS/ISSSTE-CONACYT-233361.//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Adult ; Biodiversity ; Female ; *Gastrointestinal Microbiome ; Humans ; *Metabolic Networks and Pathways ; Metabolic Syndrome/complications/*etiology/*metabolism ; Metagenome ; Metagenomics/methods ; Mexico ; Middle Aged ; Obesity/complications/*etiology/*metabolism ; RNA, Ribosomal, 16S ; Sex Factors ; Young Adult ; }, abstract = {Obesity is an excessive fat accumulation that could lead to complications like metabolic syndrome. There are reports on gut microbiota and metabolic syndrome in relation to dietary, host genetics, and other environmental factors; however, it is necessary to explore the role of the gut microbiota metabolic pathways in populations like Mexicans, where the prevalence of obesity and metabolic syndrome is high. This study identify alterations of the gut microbiota in a sample of healthy Mexican women (CO), women with obesity (OB), and women with obesity plus metabolic syndrome (OMS). We studied 67 women, characterizing their anthropometric and biochemical parameters along with their gut bacterial diversity by high-throughput DNA sequencing. Our results indicate that in OB or OMS women, Firmicutes was the most abundant bacterial phylum. We observed significant changes in abundances of bacteria belonging to the Ruminococcaceae, Lachnospiraceae, and Erysipelotrichaceae families and significant enrichment of gut bacteria from 16 different taxa that might explain the observed metabolic alterations between the groups. Finally, the predicted functional metagenome of the gut microbiota found in each category shows differences in metabolic pathways related to lipid metabolism. We demonstrate that Mexican women have a particular bacterial gut microbiota characteristic of each phenotype. There are bacteria that potentially explain the observed metabolic differences between the groups, and gut bacteria in OMS and OB conditions carry more genes of metabolic pathways implicated in lipid metabolism.}, }
@article {pmid30669029, year = {2019}, author = {Zeng, D and Yin, Q and Du, Q and Wu, G}, title = {System performance and microbial community in ethanol-fed anaerobic reactors acclimated with different organic carbon to sulfate ratios.}, journal = {Bioresource technology}, volume = {278}, number = {}, pages = {34-42}, doi = {10.1016/j.biortech.2019.01.047}, pmid = {30669029}, issn = {1873-2976}, mesh = {Bioreactors/microbiology ; Carbon/*metabolism ; Desulfovibrio/metabolism ; Ethanol/*metabolism ; *Microbiota ; Sulfates/*metabolism ; Sulfur Oxides/*metabolism ; Sulfur-Reducing Bacteria/metabolism ; }, abstract = {Sulfate influences the organics removal and methanogenic performance during anaerobic wastewater treatment. System performance, microbial community and metabolic pathways in ethanol-fed anaerobic reactors were investigated under different COD/SO42- ratios (2, 1 and 0.67) and control without sulfate addition. The sulfate removal percentages declined (99%, 60% and 49%) with decreasing COD/SO42- ratios, and methanogenesis was completely inhibited. Acetate accumulated to 903-734 mg/L, though propionate was constantly lower than 30 mg/L. Without sulfate, acetate and propionate did not accumulate, despite the extended time for propionate degradation. Incomplete oxidizing sulfate reducing bacteria (Desulfobulbus and Desulfomicrobium) and hydrolysis-acidification genera (Treponema and Bacteroidales) predominated but could not degrade acetate. Desulfobulbus was the key genus for propionate degradation through the pyruvate &amp; propanoate metabolism pathway. Pseudomonas and Desulfobulbus, possessing genes encoding Type IV pili and cytochrome c6 OmcF, respectively, potentially participated in the direct interspecies electron transfer in sulfate-rich conditions.}, }
@article {pmid30664775, year = {2019}, author = {Lin, M and Kussell, E}, title = {Inferring bacterial recombination rates from large-scale sequencing datasets.}, journal = {Nature methods}, volume = {16}, number = {2}, pages = {199-204}, doi = {10.1038/s41592-018-0293-7}, pmid = {30664775}, issn = {1548-7105}, mesh = {Computational Biology/*methods ; Computer Simulation ; *DNA, Ancient ; DNA, Bacterial ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; Gastrointestinal Microbiome ; Genetic Techniques ; Genetic Variation ; Helicobacter pylori/genetics ; History, Medieval ; Humans ; Metagenomics/*methods ; Models, Genetic ; Mutation ; Plague/history/microbiology ; *Recombination, Genetic ; *Sequence Analysis, DNA ; Yersinia pestis/genetics ; }, abstract = {We present a robust, computationally efficient method (https://github.com/kussell-lab/mcorr) for inferring the parameters of homologous recombination in bacteria, which can be applied in diverse datasets, from whole-genome sequencing to metagenomic shotgun sequencing data. Using correlation profiles of synonymous substitutions, we determine recombination rates and diversity levels of the shared gene pool that has contributed to a given sample. We validated the recombination parameters using data from laboratory experiments. We determined the recombination parameters for a wide range of bacterial species, and inferred the distribution of shared gene pools for global Helicobacter pylori isolates. Using metagenomics data of the infant gut microbiome, we measured the recombination parameters of multidrug-resistant Escherichia coli ST131. Lastly, we analyzed ancient samples of bacterial DNA from the Copper Age 'Iceman' mummy and from 14th century victims of the Black Death, obtaining measurements of bacterial recombination rates and gene pool diversity of earlier eras.}, }
@article {pmid30660184, year = {2019}, author = {Keijser, BJF and Agamennone, V and van den Broek, TJ and Caspers, M and van de Braak, A and Bomers, R and Havekes, M and Schoen, E and van Baak, M and Mioch, D and Bomers, L and Montijn, RC}, title = {Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {65}, doi = {10.1186/s12864-018-5419-x}, pmid = {30660184}, issn = {1471-2164}, support = {060.24960//Agentschap NL/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Dose-Response Relationship, Drug ; Drug Resistance, Microbial/*drug effects/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/genetics ; Genes, Bacterial/genetics ; Metagenomics/*methods ; Microbial Sensitivity Tests/methods ; Oxytetracycline/*pharmacology ; RNA, Ribosomal, 16S/chemistry/genetics ; Random Allocation ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Antibiotic therapy is commonly used in animal agriculture. Antibiotics excreted by the animals can contaminate farming environments, resulting in long term exposure of animals to sub-inhibitory levels of antibiotics. Little is known on the effect of this exposure on antibiotic resistance. In this study, we aimed to investigate the long term effects of sub-inhibitory levels of antibiotics on the gut microbiota composition and resistome of veal calves in vivo. Forty-two veal calves were randomly assigned to three groups. The first group (OTC-high) received therapeutic oral dosages of 1 g oxytetracycline (OTC), twice per day, during 5 days. The second group (OTC-low) received an oral dose of OTC of 100-200 μg per day during 7 weeks, mimicking animal exposure to environmental contamination. The third group (CTR) did not receive OTC, serving as unexposed control. Antibiotic residue levels were determined over time. The temporal effects on the gut microbiota and antibiotic resistance gene abundance was analysed by metagenomic sequencing.<br><br>RESULTS: In the therapeutic group, OTC levels exceeded MIC values. The low group remained at sub-inhibitory levels. The control group did not reach any significant OTC levels. 16S rRNA gene-based analysis revealed significant changes in the calf gut microbiota. Time-related changes accounted for most of the variation in the sequence data. Therapeutic application of OTC had transient effect, significantly impacting gut microbiota composition between day 0 and day 2. By metagenomic sequence analysis we identified six antibiotic resistance genes representing three gene classes (tetM, floR and mel) that differed in relative abundance between any of the intervention groups and the control. qPCR was used to validate observations made by metagenomic sequencing, revealing a peak of tetM abundance at day 28-35 in the OTC-high group. No increase in resistance genes abundance was seen in the OTC-low group.<br><br>CONCLUSIONS: Under the conditions tested, sub-therapeutic administration of OTC did not result in increased tetM resistance levels as observed in the therapeutic group.}, }
@article {pmid30659724, year = {2019}, author = {Turgay, E and Steinum, TM and Colquhoun, D and Karataş, S}, title = {Environmental biofilm communities associated with early-stage common dentex (Dentex dentex) culture.}, journal = {Journal of applied microbiology}, volume = {126}, number = {4}, pages = {1032-1043}, doi = {10.1111/jam.14205}, pmid = {30659724}, issn = {1365-2672}, support = {20950//Scientific Research Project Coordination Unit of Istanbul University/ ; }, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Biofilms/classification/*growth &amp; development ; *Life Cycle Stages ; Metagenomics ; Microbiota/*genetics ; Perciformes/*growth &amp; development/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {AIMS: To describe the biofilm microbiota associated with various feeding phases during larval common dentex (Dentex dentex) culture.<br><br>METHODS AND RESULTS: A targeted metagenomic (metagenetic) study was performed by means of 16S rRNA gene-based PCR and NextGen pyrosequencing. The resulting dataset was scrutinized with microbial community analysis software (r packages) using r/Rstudio. While median observed and estimated alpha-diversities were 171 ± 38 and 207 ± 27 taxa, respectively, 72·1-85·8% of individual biofilm communities comprised only 27-46 taxa. Members of the genus Methylobacterium and family Rhodobacteraceae dominated biofilms formed during all feeding phases while genera Nannochloropsis and Tetraselmis microalgae were major constituents of biofilms during rotifer live feeding. Both potential fish pathogenic genera, for example, Vibrio and putatively probiotic taxa, for example, Phaeobacter gallaeciensis were identified.<br><br>CONCLUSIONS: Relatively stable biofilm communities were identified during each feeding phase but varied significantly between feeding phases, most likely in response to the introduction of live feed/microalgae-associated bacteria into rearing tanks.<br><br>The structure of the bacterial communities identified represents a 'template' for successful larval dentex culture and provides a foundation for future investigations into failed production cycles.}, }
@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 {pmid30643240, year = {2019}, author = {Nakamoto, N and Sasaki, N and Aoki, R and Miyamoto, K and Suda, W and Teratani, T and Suzuki, T and Koda, Y and Chu, PS and Taniki, N and Yamaguchi, A and Kanamori, M and Kamada, N and Hattori, M and Ashida, H and Sakamoto, M and Atarashi, K and Narushima, S and Yoshimura, A and Honda, K and Sato, T and Kanai, T}, title = {Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis.}, journal = {Nature microbiology}, volume = {4}, number = {3}, pages = {492-503}, doi = {10.1038/s41564-018-0333-1}, pmid = {30643240}, issn = {2058-5276}, mesh = {Adult ; Aged ; Animals ; Bacterial Translocation ; Cholangitis, Sclerosing/*immunology/microbiology ; Colitis, Ulcerative/complications ; Enterococcus/isolation &amp; purification ; Epithelial Cells/microbiology/pathology ; Female ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; Intestines/immunology/*pathology ; Klebsiella pneumoniae/isolation &amp; purification/*pathogenicity ; Liver/*immunology/pathology ; Lymph Nodes/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Organoids/microbiology ; Proteus mirabilis/isolation &amp; purification ; Th17 Cells/*immunology ; }, abstract = {Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease and its frequent complication with ulcerative colitis highlights the pathogenic role of epithelial barrier dysfunction. Intestinal barrier dysfunction has been implicated in the pathogenesis of PSC, yet its underlying mechanism remains unknown. Here, we identify Klebsiella pneumonia in the microbiota of patients with PSC and demonstrate that K. pneumoniae disrupts the epithelial barrier to initiate bacterial translocation and liver inflammatory responses. Gnotobiotic mice inoculated with PSC-derived microbiota exhibited T helper 17 (TH17) cell responses in the liver and increased susceptibility to hepatobiliary injuries. Bacterial culture of mesenteric lymph nodes in these mice isolated K. pneumoniae, Proteus mirabilis and Enterococcus gallinarum, which were prevalently detected in patients with PSC. A bacterial-organoid co-culture system visualized the epithelial-damaging effect of PSC-derived K. pneumoniae that was associated with bacterial translocation and susceptibility to TH17-mediated hepatobiliary injuries. We also show that antibiotic treatment ameliorated the TH17 immune response induced by PSC-derived microbiota. These results highlight the role of pathobionts in intestinal barrier dysfunction and liver inflammation, providing insights into therapeutic strategies for PSC.}, }
@article {pmid30643213, year = {2019}, author = {Ronda, C and Chen, SP and Cabral, V and Yaung, SJ and Wang, HH}, title = {Metagenomic engineering of the mammalian gut microbiome in situ.}, journal = {Nature methods}, volume = {16}, number = {2}, pages = {167-170}, doi = {10.1038/s41592-018-0301-y}, pmid = {30643213}, issn = {1548-7105}, support = {DP5 OD009172/OD/NIH HHS/United States ; T32 GM007367/GM/NIGMS NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; F30 DK111145/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Cell Separation ; Escherichia coli/genetics ; Female ; Flow Cytometry ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/physiology ; Gene Transfer Techniques ; Genome ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; Microbiota/*genetics ; Plasmids/genetics ; Protein Engineering/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Engineering of microbial communities in open environments remains challenging. Here we describe a platform used to identify and modify genetically tractable mammalian microbiota by engineering community-wide horizontal gene transfer events in situ. With this approach, we demonstrate that diverse taxa in the mouse gut microbiome can be modified directly with a desired genetic payload. In situ microbiome engineering in living animals allows novel capabilities to be introduced into established communities in their native milieu.}, }
@article {pmid30642268, year = {2019}, author = {Aiemjoy, K and Altan, E and Aragie, S and Fry, DM and Phan, TG and Deng, X and Chanyalew, M and Tadesse, Z and Callahan, EK and Delwart, E and Keenan, JD}, title = {Viral species richness and composition in young children with loose or watery stool in Ethiopia.}, journal = {BMC infectious diseases}, volume = {19}, number = {1}, pages = {53}, doi = {10.1186/s12879-019-3674-3}, pmid = {30642268}, issn = {1471-2334}, support = {F31 HD088070-01A1//National Institute of Child Health and Human Development/ ; U10 EY016214//National Eye Institute/ ; R01 HL105770//National Heart, Lung, and Blood Institute/ ; }, mesh = {Biodiversity ; Caliciviridae Infections/virology ; Child, Preschool ; Diarrhea/epidemiology/*virology ; Ethiopia/epidemiology ; Feces/*virology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics ; Norovirus/genetics/isolation &amp; purification ; Picornaviridae/genetics/isolation &amp; purification ; Picornaviridae Infections/virology ; Prevalence ; Viruses/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: Stool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease.<br><br>METHODS: We examine the pediatric enteric virome across stool consistencies to evaluate differences in richness and community composition using fecal samples collected from children aged 0 to 5 years participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling.<br><br>RESULTS: Of 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The median age of children with stool samples was 36 months. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman's r = - 0.45, p = 0.013). The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95%CI 3.9, 7.7).<br><br>CONCLUSIONS: In conclusion, we documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition.}, }
@article {pmid30637962, year = {2019}, author = {Asante, J and Osei Sekyere, J}, title = {Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: advances and applications.}, journal = {Environmental microbiology reports}, volume = {11}, number = {2}, pages = {62-86}, doi = {10.1111/1758-2229.12735}, pmid = {30637962}, issn = {1758-2229}, mesh = {Animals ; Anti-Bacterial Agents/isolation &amp; purification/*pharmacology ; Bacteria/drug effects/genetics ; Bacterial Proteins/genetics/metabolism ; *Drug Discovery ; Drug Resistance, Bacterial/*genetics ; Environmental Microbiology ; Humans ; *Metagenomics ; Microbiota/*genetics ; }, abstract = {Our inability to cultivate most microorganisms, specifically bacteria, in the laboratory has for many years restricted our view and understanding of the bacterial meta-resistome in all living and nonliving environments. As a result, reservoirs, sources and distribution of antibiotic resistance genes (ARGS) and antibiotic-producers, as well as the effects of human activity and antibiotics on the selection and dissemination of ARGs were not well comprehended. With the advances made in the fields of metagenomics and metatranscriptomics, many of the hitherto little-understood concepts are becoming clearer. Further, the discovery of antibiotics such as lugdinin and lactocillin from the human microbiota, buttressed the importance of these new fields. Metagenomics and metatranscriptomics are becoming important clinical diagnostic tools for screening and detecting pathogens and ARGs, assessing the effects of antibiotics, other xenobiotics and human activity on the environment, characterizing the microbiome and the environmental resistome with lesser turnaround time and decreasing cost, as well as discovering antibiotic-producers. However, challenges with accurate binning, skewed ARGs databases, detection of less abundant and allelic variants of ARGs and efficient mobilome characterization remain. Ongoing efforts in long-read, phased- and single-cell sequencing, strain-resolved binning, chromosomal-conformation capture, DNA-methylation binning and deep-learning bioinformatic approaches offer promising prospects in reconstructing complete strain-level genomes and mobilomes from metagenomes.}, }
@article {pmid30635058, year = {2019}, author = {Simon, JC and Marchesi, JR and Mougel, C and Selosse, MA}, title = {Host-microbiota interactions: from holobiont theory to analysis.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {5}, doi = {10.1186/s40168-019-0619-4}, pmid = {30635058}, issn = {2049-2618}, mesh = {Animals ; Food Microbiology ; *Host Microbial Interactions ; Humans ; *Microbiota ; Plants/microbiology ; Symbiosis ; }, abstract = {In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series &quot;Host-microbiota interactions: from holobiont theory to analysis,&quot; we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.}, }
@article {pmid30628657, year = {2019}, author = {Chen, L and Li, H and Li, J and Chen, Y and Yang, Y}, title = {Lactobacillus rhamnosus GG treatment improves intestinal permeability and modulates microbiota dysbiosis in an experimental model of sepsis.}, journal = {International journal of molecular medicine}, volume = {43}, number = {3}, pages = {1139-1148}, doi = {10.3892/ijmm.2019.4050}, pmid = {30628657}, issn = {1791-244X}, mesh = {Animals ; Apoptosis ; Biomarkers ; Cell Proliferation ; Colon/metabolism/microbiology/pathology ; Disease Models, Animal ; *Dysbiosis ; *Gastrointestinal Microbiome ; Lactobacillus rhamnosus/*physiology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Mortality ; Permeability ; Phylogeny ; Probiotics/*administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Sepsis/diagnosis/*metabolism/*microbiology/therapy ; }, abstract = {Decrease of 'health‑benefiting' microbes and increase of pathogenic bacteria (a condition termed dysbiosis) in intensive care unit patients is considered to induce or aggravate sepsis (gut‑origin sepsis). Orally administered probiotics have been effective in the prevention of nosocomial infections. However, the mechanisms of probiotic‑induced anti‑infection and anti‑sepsis remain to be explored. In the present study, 4‑week‑old C57BL6 mice were orally administrated with Lactobacillus rhamnosus GG (LGG) or normal saline (control) 4 weeks prior to cecal ligation and puncture (CLP). A subset of the mice were sacrificed at 24 h post‑CLP, and the others were used for survival studies. Ileum tissues, blood and fecal samples were collected. The survival rate of septic mice pretreated with LGG was significantly improved compared with untreated mice. The levels of inflammatory cytokines were reduced in LGG‑pretreated septic mice. A decrease of colonic proliferation and epithelial tight junctions and an increase of colonic apoptosis were observed in control septic CLP+saline mice. LGG pretreatment reversed the colonic proliferation, apoptosis and expression of tight junction proteins to the levels of the sham group. LGG pretreatment improved the richness and diversity of intestinal microbiota in septic mice. The principal coordinates analysis clustering plots revealed a significant separate clustering in microbiota structure between three groups. Bacteria associated with energy consumption, including Bacteroidetes, with opportunistic infection, including Proteobacteria, Staphylococcaceae and Enterococcaceae, lipopolysaccharide producers, including Enterobacteriaceae, and facultative anaerobes, such as Bacteroidaceae and Erysipelotrichaceae, increased in septic mice. By contrast, bacteria associated with energy harvest, including Firmicutes, intestinal barrier function regulators, including Akkermansia, hepatic function regulators, including Coprococcus and Oscillospira, and obligate anaerobes, including Prevotellaceae, decreased in septic mice. With LGG pretreatment, the sepsis‑induced microbiota dysbiosis was reversed. The present results elucidated the potential mechanism of LGG treatment in sepsis, by improving intestinal permeability and modulating microbiota dysbiosis.}, }
@article {pmid30625669, year = {2019}, author = {Costeira, R and Doherty, R and Allen, CCR and Larkin, MJ and Kulakov, LA}, title = {Analysis of viral and bacterial communities in groundwater associated with contaminated land.}, journal = {The Science of the total environment}, volume = {656}, number = {}, pages = {1413-1426}, doi = {10.1016/j.scitotenv.2018.11.429}, pmid = {30625669}, issn = {1879-1026}, mesh = {Bacteria/classification/*genetics ; Groundwater/*microbiology/virology ; *Metagenome ; *Microbiota ; Northern Ireland ; Soil Pollutants/*analysis ; Viruses/classification/*genetics ; }, abstract = {This work aimed at the comprehensive analysis of total microbial communities inhabiting a typical hydrocarbon-polluted site, where chemical characteristics of the groundwater were readily available. To achieve this, a joint metagenomic characterization of bacteria and viruses surrounding a contaminant plume was performed over a one-year period. The results presented demonstrated that both potential hydrocarbon degraders and their bacteriophages were dominant around the plume, and that the viral and bacterial diversities found at the site were probably influenced by the pH of the groundwater. Niche-specific and dispersed associations between phages and bacteria were identified. The niche phage-host associations were found at the edge of the site and at the core of the plume where pH was the highest (9.52). The identified host populations included several classes of bacteria (e.g. Clostridia and Proteobacteria). Thirty-six viral generalists were also discovered, with BGW-G9 having the broadest host range across 23 taxa, including Pseudomonas, Polycyclovorans, Methylocaldum and Candidatus Magnetobacterium species. The phages with broad host ranges are presumed to have significant effects on prokaryotic production and horizontal gene transfer, and therefore impact the biodegradation processes conducted by various bacteria of the environment studied. This study for the first time characterized the phages and their bacterial hosts associated with a contaminant plume.}, }
@article {pmid30624596, year = {2019}, author = {Yadav, D and Dutta, A and Mande, SS}, title = {OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {26}, number = {2}, pages = {147-156}, doi = {10.1093/dnares/dsy045}, pmid = {30624596}, issn = {1756-1663}, mesh = {Bacteria/*classification/genetics ; Computational Biology/*methods ; *Databases, Genetic ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Bacterial ; *RNA, Ribosomal, 16S ; Sequence Analysis, DNA/methods ; }, abstract = {Many microbiome studies employ reference-based operational taxonomic unit (OTU)-picking methods, which in general, rely on databases cataloguing reference OTUs identified through clustering full-length 16S rRNA genes. Given that the rate of accumulation of mutations are not uniform throughout the length of a 16S rRNA gene across different taxonomic clades, results of OTU identification or taxonomic classification obtained using 'short-read' sequence queries (as generated by next-generation sequencing platforms) can be inconsistent and of suboptimal accuracy. De novo OTU clustering results too can significantly vary depending upon the hypervariable region (V-region) targeted for sequencing. As a consequence, comparison of microbiomes profiled in different scientific studies becomes difficult and often poses a challenge in analysing new findings in context of prior knowledge. The OTUX approach of reference-based OTU-picking proposes to overcome these limitations by using 'customized' OTU reference databases, which can cater to different sets of short-read sequences corresponding to different 16S V-regions. The results obtained with OTUX-approach (which are in terms of OTUX-OTU identifiers) can also be 'mapped back' or represented in terms of other OTU database identifiers/taxonomy, e.g. Greengenes, thus allowing for easy cross-study comparisons. Validation with simulated datasets indicates more efficient, accurate, and consistent taxonomic classifications obtained using OTUX-approach, as compared with conventional methods.}, }
@article {pmid30623233, year = {2019}, author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS}, title = {Chinese liver fluke Clonorchis sinensis infection changes the gut microbiome and increases probiotic Lactobacillus in mice.}, journal = {Parasitology research}, volume = {118}, number = {2}, pages = {693-699}, doi = {10.1007/s00436-018-6179-x}, pmid = {30623233}, issn = {1432-1955}, support = {NRF-2016R1A2B4016194//National Research Foundation of Korea/ ; 2011-0012166//National Research Foundation of Korea/ ; }, mesh = {Animals ; Clonorchiasis/*immunology/parasitology ; Clonorchis sinensis/growth &amp; development/*immunology ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing ; Lactobacillus/classification/cytology/*growth &amp; development ; Metacercariae/cytology ; Mice ; Mice, Inbred C57BL ; Probiotics/*analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Chinese liver fluke Clonorchis sinensis changes the host's immune system. Recently, it has been reported that helminths including C. sinensis can ameliorate immune-related diseases such as allergy. In addition, recent studies showed that helminth infection can alleviate immune-mediated disorders by altering the gut microbiome. However, changes in the gut microbiome due to C. sinensis have not been reported yet. In this study, changes in the gut microbiome of C57BL/6 mice infected with C. sinensis metacercariae were evaluated over time. Stool was analyzed by 16S rRNA amplicon analysis using high-throughput sequencing technology. There was no apparent difference in species richness and diversity between the infected and control groups. However, the composition of the microbiome was different between the infected and control groups at 20 days and 30 days post-infection, and the difference disappeared at 50 days post-infection. In particular, this microbiome alteration was associated with a change in the relative abundance of genus Lactobacillus and the probiotic Lactobacillus species that are known to have an immune-modulation role in immune-mediated diseases.}, }
@article {pmid30622080, year = {2019}, author = {Cota-Ruiz, K and López de Los Santos, Y and Hernández-Viezcas, JA and Delgado-Rios, M and Peralta-Videa, JR and Gardea-Torresdey, JL}, title = {A comparative metagenomic and spectroscopic analysis of soils from an international point of entry between the US and Mexico.}, journal = {Environment international}, volume = {123}, number = {}, pages = {558-566}, doi = {10.1016/j.envint.2018.12.055}, pmid = {30622080}, issn = {1873-6750}, support = {G12 MD007592/MD/NIMHD NIH HHS/United States ; }, mesh = {Agriculture ; Bacteria/classification ; Environmental Pollution ; Hydrocarbons/toxicity ; Metagenomics ; Metals, Heavy/toxicity ; Mexico ; *Microbiota ; Nitrogen/analysis ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*toxicity ; Spectrum Analysis ; }, abstract = {The Paso del Norte region is characterized by its dynamic industries and active agriculture. Throughout the years, urban and agricultural soils from this region have been exposed to xenobiotics, heavy metals, and excess of hydrocarbons. In this study, samples of urban [domestic workshops (DW)] and agricultural-intended (AI) soils from different sites of Ciudad Juárez, Mexico were evaluated for their fertility, element content, and microbial diversity. Chemical analyses showed that nitrites, nitrates, P, K, Mg, and Mn were predominantly higher in AI soils, compared to DW soils (p ≤ 0.05). The composition of soil microbial communities showed that Proteobacteria phylum was the most abundant in both soils (67%, p ≤ 0.05). In AI soils, Paracoccus denitrificans was reduced (p ≤ 0.05), concurring with an increment in nitrates, while the content of nitrogen was negatively correlated with the rhizobium group (r2 = -0.65, p ≤ 0.05). In DW soils, the Firmicutes phylum represented up to ~25%, and the relative abundance of Proteobacteria strongly correlated with a higher Cu content (r2 = 0.99, p ≤ 0.0001). The monotypic genus Sulfuricurvum was found only in oil-contaminated soil samples. Finally, all samples showed the presence of the recently created phylum Candidatus saccharibacteria. These results describe the productivity parameters of AI soils and its correlation to the microbial diversity, which are very important to understand and potentiate the productivity of soils. The data also suggest that soils impacted with hydrocarbons and metal(oid)s allow the reproduction of microorganisms with the potential to alleviate contaminated sites.}, }
@article {pmid30621868, year = {2019}, author = {Ottesen, A and Ramachandran, P and Reed, E and Gu, G and Gorham, S and Ducharme, D and Newell, M and Rideout, S and Turini, T and Hill, T and Strain, E and Brown, E}, title = {Metagenome tracking biogeographic agroecology: Phytobiota of tomatoes from Virginia, Maryland, North Carolina and California.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {132-136}, doi = {10.1016/j.fm.2018.12.001}, pmid = {30621868}, issn = {1095-9998}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; California ; *Food Microbiology ; Food Safety ; Lycopersicon esculentum/*microbiology ; Maryland ; Metagenomics ; Microbiota/*genetics ; North Carolina ; RNA, Ribosomal, 16S/genetics ; Salmonella/classification/genetics/isolation &amp; purification ; Virginia ; }, abstract = {Describing baseline microbiota associated with agricultural commodities in the field is an important step towards improving our understanding of a wide range of important objectives from plant pathology and horticultural sustainability, to food safety. Environmental pressures on plants (wind, dust, drought, water, temperature) vary by geography and characterizing the impact of these variable pressures on phyllosphere microbiota will contribute to improved stewardship of fresh produce for both plant and human health. A higher resolution understanding of the incidence of human pathogens on food plants and co-occurring phytobiota using metagenomic approaches (metagenome tracking) may contribute to improved source attribution and risk assessment in cases where human pathogens become introduced to agro-ecologies. Between 1990 and 2007, as many as 1990 culture-confirmed Salmonella illnesses were linked to tomatoes from as many as 12 multistate outbreaks (Bell et al., 2012; Bell et al., 2015; Bennett et al., 2014; CDC, 2004; CDC, 2007; Greene et al., 2005a; Gruszynski et al., 2014). When possible, source attribution for these incidents revealed a biogeographic trend, most events were associated with eastern growing regions. To improve our understanding of potential biogeographically linked trends in contamination of tomatoes by Salmonella, we profiled microbiota from the surfaces of tomatoes from Virginia, Maryland, North Carolina and California. Bacterial profiles from California tomatoes were completely different than those of Maryland, Virginia and North Carolina (which were highly similar to each other). A statistically significant enrichment of Firmicutes taxa was observed in California phytobiota compared to the three eastern states. Rhizobiaceae, Sphingobacteriaceae and Xanthobacteraceae were the most abundant bacterial families associated with tomatoes grown in eastern states. These baseline metagenomic profiles of phyllosphere microbiota may contribute to improved understanding of how certain ecologies provide supportive resources for human pathogens on plants and how components of certain agro-ecologies may play a role in the introduction of human pathogens to plants.}, }
@article {pmid30621867, year = {2019}, author = {Marino, M and Dubsky de Wittenau, G and Saccà, E and Cattonaro, F and Spadotto, A and Innocente, N and Radovic, S and Piasentier, E and Marroni, F}, title = {Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese.}, journal = {Food microbiology}, volume = {79}, number = {}, pages = {123-131}, doi = {10.1016/j.fm.2018.12.007}, pmid = {30621867}, issn = {1095-9998}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Buffaloes ; Cattle ; Cheese/analysis/*microbiology ; Cluster Analysis ; DNA, Bacterial/genetics ; *Food Microbiology ; Metagenomics ; Microbiota/*genetics ; Milk/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The microbiota of different types of Italian high-moisture Mozzarella cheese produced using cow or buffalo milk, acidified with natural or selected cultures, and sampled at the dairy or at the mass market, was evaluated using a Next Generation Sequencing approach, in order to identify possible drivers of the bacterial diversity. Cow Mozzarella and buffalo Mozzarella acidified with commercial cultures were dominated by Streptococcus thermophilus, while buffalo samples acidified with natural whey cultures showed similar prevalence of L. delbrueckii subsp. bulgaricus, L. helveticus and S. thermophilus. Moreover, several species of non-starter lactic acid bacteria were frequently detected. The diversity in cow Mozzarella microbiota was much higher than that of water buffalo samples. Cluster analysis clearly separated cow's cheeses from buffalo's ones, the former having a higher prevalence of psychrophilic taxa, and the latter of Lactobacillus and Streptococcus. A higher prevalence of psychrophilic species and potential spoilers was observed in samples collected at the mass retail, suggesting that longer exposures to cooling temperatures and longer production-to-consumption times could significantly affect microbiota diversity. Our results could help in detecting some kind of thermal abuse during the production or storage of mozzarella cheese.}, }
@article {pmid30619779, year = {2018}, author = {Hu, YL and Pang, W and Huang, Y and Zhang, Y and Zhang, CJ}, title = {The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {433}, doi = {10.3389/fcimb.2018.00433}, pmid = {30619779}, issn = {2235-2988}, mesh = {Adenocarcinoma/*complications/pathology ; Aged ; Bacteria/*classification/*genetics ; China ; Dysbiosis/*complications ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Middle Aged ; Stomach Neoplasms/*complications/pathology ; }, abstract = {Objective: Dysbiosis of gastric microbiota such as Helicobacter pylori plays a significant role in pathogenesis and progression of gastric cancer. Our aim was to evaluate the composition and functional effects of gastric microbiota in superficial gastritis (SG) and advanced gastric adenocarcinoma (GC). Methods: We carried out shotgun metagenomic sequencing on gastric wash samples from 6 patients with GC and 5 patients with SG. The taxonomic composition was profiled using MetaPhlAn2 and functional gene pathway was profiled using HUMAnN2. Differences in microbial composition and pathways between the two patient groups were assessed via LEfSe. Results: The gastric microbiota in GC patients was characterized by reduced species richness, enrichment of 13 bacterial taxa and depletion of 31 taxa (q < 0.05). The most representative taxa which were abundant in GC corresponded to the commensals or opportunistic pathogens that usually colonize the oral cavity, including genera Neisseria, Alloprevotella, and Aggregatibacter, species Streptococcus_mitis_oralis_pneumoniae and strain Porphyromonas_endodontalis.t_GCF_000174815. Each of the three GC-associated genera could separate GC from SG completely. In particular, Sphingobium yanoikuyae, a bacterium capable of degrading carcinogenic compounds, was depleted in GC. Functionally, pathways associated with the biosynthesis of lipopolysaccharide (LPS) and L-arginine were enriched in GC, whereas pathways involved in the fermentation of short chain fatty acids (SCFAs) and branched amino acid metabolism were more abundant in SG. Conclusions: Our results present new alterations in the gastric microbiome in patients with GC from a whole-genome perspective, suggesting that microbiome composition and function can be used for prognosis and diagnosis of GC.}, }
@article {pmid30619130, year = {2018}, author = {Timmers, PHA and Vavourakis, CD and Kleerebezem, R and Damsté, JSS and Muyzer, G and Stams, AJM and Sorokin, DY and Plugge, CM}, title = {Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3039}, doi = {10.3389/fmicb.2018.03039}, pmid = {30619130}, issn = {1664-302X}, support = {322551//European Research Council/International ; 323009//European Research Council/International ; }, abstract = {Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H2 and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was 'Candidatus Syntrophonatronum acetioxidans,' and a near-complete draft genome of this SAOB was reconstructed. 'Ca. S. acetioxidans' has all genes necessary for operating the Wood-Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na+-dependent ATP synthase and marker genes for 'salt-out' strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of 'Ca. S. acetioxidans' showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA gene amplicon datasets of the soda lake sediments showed a high similarity of reads to 'Ca. S. acetioxidans' with abundance as high as 1.3% of all reads, whereas aceticlastic methanogens and acetate oxidizing sulfate-reducers were not abundant (≤0.1%) or could not be detected. These combined results indicate that SAO is the primary anaerobic acetate oxidizing pathway at extreme haloalkaline conditions performed by haloalkaliphilic syntrophic consortia.}, }
@article {pmid30612183, year = {2019}, author = {Ding, W and Zhang, W and Alikunhi, NM and Batang, Z and Pei, B and Wang, R and Chen, L and Al-Suwailem, A and Qian, PY}, title = {Metagenomic Analysis of Zinc Surface-Associated Marine Biofilms.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {406-416}, doi = {10.1007/s00248-018-01313-3}, pmid = {30612183}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; *Biofilms ; Indian Ocean ; Metagenomics ; Phylogeny ; Seawater/analysis/*microbiology ; Zinc/analysis/*metabolism ; }, abstract = {Biofilms are a significant source of marine biofouling. Marine biofilm communities are established when microorganisms adhere to immersed surfaces. Despite the microbe-inhibiting effect of zinc surfaces, microbes can still attach to the surface and form biofilms. However, the diversity of biofilm-forming microbes that can attach to zinc surfaces and their common functional features remain elusive. Here, by analyzing 9,000,000 16S rRNA gene amplicon sequences and 270 Gb of metagenomic data, we comprehensively explored the taxa and functions related to biofilm formation in subtidal zones of the Red Sea. A clear difference was observed between the biofilm and adjacent seawater microbial communities in terms of the taxonomic structure at phylum and genus levels, and a huge number of genera were only present in the biofilms. Saturated alpha-diversity curves suggested the existence of more than 14,000 operational taxonomic units in one biofilm sample, which is much higher than previous estimates. Remarkably, the biofilms contained abundant and diverse transposase genes, which were localized along microbial chromosomal segments and co-existed with genes related to metal ion transport and resistance. Genomic analyses of two cyanobacterial strains that were abundant in the biofilms revealed a variety of metal ion transporters and transposases. Our analyses revealed the high diversity of biofilm-forming microbes that can attach to zinc surfaces and the ubiquitous role of transposase genes in microbial adaptation to toxic metal surfaces.}, }
@article {pmid30612083, year = {2019}, author = {Zhu, X and Campanaro, S and Treu, L and Kougias, PG and Angelidaki, I}, title = {Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics.}, journal = {Water research}, volume = {151}, number = {}, pages = {271-279}, doi = {10.1016/j.watres.2018.12.041}, pmid = {30612083}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Bioreactors ; Metagenome ; *Metagenomics ; Microbial Consortia ; }, abstract = {In typical anaerobic digestion (AD) systems, the microbial functional assertion is hampered by synchronised versatile metabolism required for heterogeneous substrates degradation. Thus, the intricate methanogenic process from organic compounds remains an enigma after decades of empirical operation. In this study, simplified AD microbial communities were obtained with substrate specifications and continuous reactor operation. Genome-centric metagenomic approach was followed to holistically investigate the metabolic pathways of the AD and the microbial synergistic networks. In total, 63 metagenome assembled genomes (MAGs) were assembled from 8 metagenomes acquired in specific methanogenic niches. The metabolic pathways were reconstructed from the annotated genes and their dynamicity under experimental conditions. The results show that the methanogenic niches nourish unique metabolism beyond current knowledge acquired from cultivation-based methods. A novel glucose mineralization model without acetate formation was proposed and asserted in a pair of syntrophs: Clostridiaceae sp. and Methanoculleus thermophilus. Moreover, the catabolic pathway was elucidated in uncharacterized syntrophic acetate oxidizers, Synergistaceae spp. A remarkable evolutionary insight is the discovery that electron transport and energy conservation mechanisms impose selective pressure on syntrophic partners. Overall, the functional roles of the individual microbes tightly rely on the catabolic pathways and cannot always be physiologically defined in accordance with conventional four-step AD concept. The substrate-specific systems provided a traceable microbial community to dissecting the AD process. The genome-centric metagenomics successfully constructed genomes of microbes that have not been previously isolated and illustrated metabolic pathways that beyond the current knowledge of AD process. This study provides new perspectives to unravel the AD microbial ecology and suggests more attention should be paid on uncharacterized metabolism specifically harboured by AD microbial communities.}, }
@article {pmid30609942, year = {2019}, author = {Yang, SH and Tandon, K and Lu, CY and Wada, N and Shih, CJ and Hsiao, SS and Jane, WN and Lee, TC and Yang, CM and Liu, CT and Denis, V and Wu, YT and Wang, LT and Huang, L and Lee, DC and Wu, YW and Yamashiro, H and Tang, SL}, title = {Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {3}, doi = {10.1186/s40168-018-0616-z}, pmid = {30609942}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/*microbiology ; Chlorobi/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a green layer beneath coral tissues, the anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris is dominant in the skeleton of Isopora palifera. However, due to inherent challenges in studying anaerobic microbes in coral skeleton, the reason for its niche preference and function are largely unknown.<br><br>RESULTS: This study characterized a diverse and dynamic community of endolithic microbes shaped by the availability of light and oxygen. In addition, anaerobic bacteria isolated from the coral skeleton were cultured for the first time to experimentally clarify the role of these GSB. This characterization includes GSB's abundance, genetic and genomic profiles, organelle structure, and specific metabolic functions and activity. Our results explain the advantages endolithic GSB receive from living in coral skeletons, the potential metabolic role of a clade of coral-associated Prosthecochloris (CAP) in the skeleton, and the nitrogen fixation ability of CAP.<br><br>CONCLUSION: We suggest that the endolithic microbial community in coral skeletons is diverse and dynamic and that light and oxygen are two crucial factors for shaping it. This study is the first to demonstrate the ability of nitrogen uptake by specific coral-associated endolithic bacteria and shed light on the role of endolithic bacteria in coral skeletons.}, }
@article {pmid30609875, year = {2019}, author = {Waseem, H and Jameel, S and Ali, J and Saleem Ur Rehman, H and Tauseef, I and Farooq, U and Jamal, A and Ali, MI}, title = {Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {1}, pages = {}, doi = {10.3390/molecules24010163}, pmid = {30609875}, issn = {1420-3049}, mesh = {Anti-Infective Agents/*pharmacology ; Computational Biology/methods ; Data Analysis ; *Drug Resistance, Microbial ; *Environmental Microbiology ; Gastrointestinal Microbiome ; Genes, Bacterial ; *High-Throughput Screening Assays ; Humans ; Metagenome ; Metagenomics/methods ; Quality Control ; *Real-Time Polymerase Chain Reaction ; }, abstract = {Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGenTM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.}, }
@article {pmid30606403, year = {2019}, author = {Gong, J and Noel, S and Pluznick, JL and Hamad, ARA and Rabb, H}, title = {Gut Microbiota-Kidney Cross-Talk in Acute Kidney Injury.}, journal = {Seminars in nephrology}, volume = {39}, number = {1}, pages = {107-116}, doi = {10.1016/j.semnephrol.2018.10.009}, pmid = {30606403}, issn = {1558-4488}, support = {R01 DK111209/DK/NIDDK NIH HHS/United States ; }, mesh = {Acute Kidney Injury/immunology/*microbiology ; Animals ; Blood Pressure ; Dysbiosis/*complications ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*immunology ; Humans ; Methylamines/metabolism ; Prebiotics ; Probiotics/therapeutic use ; Uremia/microbiology ; }, abstract = {The recent surge in research on the intestinal microbiota has greatly changed our understanding of human biology. Significant technical advances in DNA sequencing analysis and its application to metagenomics and metatranscriptomics has profoundly enhanced our ability to quantify and track complex microbial communities and to begin understanding their impact on human health and disease. This has led to a better understanding of the relationships between the intestinal microbiome and renal physiology/pathophysiology. In this review, we discuss the interactions between intestinal microbiota and kidney. We focus on select aspects including the intestinal barrier, immunologic and soluble mediators of microbiome effects, and effects of dysbiosis on acute kidney injury. Relevant studies on microbiome changes in other renal diseases are highlighted. We also introduce potential mechanisms of intervention with regard to gut microbiota in renal diseases.}, }
@article {pmid30606162, year = {2019}, author = {Xue, F and Nan, X and Li, Y and Pan, X and Guo, Y and Jiang, L and Xiong, B}, title = {Metagenomic insights into effects of thiamine supplementation on ruminal non-methanogen archaea in high-concentrate diets feeding dairy cows.}, journal = {BMC veterinary research}, volume = {15}, number = {1}, pages = {7}, doi = {10.1186/s12917-018-1745-0}, pmid = {30606162}, issn = {1746-6148}, support = {Grant No. 31572435//Project of National Nature Science Foundation of China/ ; 2016YFD0700205//National Key Research and Development Plan/ ; }, mesh = {Animal Feed ; Animals ; Archaea/*drug effects/genetics ; Cattle ; Diet/*veterinary ; *Dietary Supplements ; Eating/drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Hydrogen-Ion Concentration ; Lactation/drug effects ; Metagenomics ; Rumen/chemistry/*microbiology ; Thiamine/analysis/*pharmacology ; }, abstract = {BACKGROUND: Overfeeding of high-concentrate diet (HC) frequently leads to subacute ruminal acidosis (SARA) in modern dairy cows' production. Thiamine supplementation has been confirmed to attenuate HC induced SARA by increasing ruminal pH and ratio of acetate to propionate, and decreasing rumen lactate, biogenic amines and lipopolysaccharide (LPS). The effects of thiamine supplementation in HC on rumen bacteria and fungi profile had been detected in our previous studies, however, effects of thiamine supplementation in HC on rumen non-methanogen archaea is still unclear. The objective of the present study was therefore to investigate the effects of thiamine supplementation on ruminal archaea, especially non-methanogens in HC induced SARA cows.<br><br>RESULTS: HC feeding significantly decreased dry matter intake, milk production, milk fat content, ruminal pH and the concentrations of thiamine and acetate in rumen fluid compared with control diet (CON) (P < 0.05), while the concentrations of propionate and ammonia-nitrogen (NH3-N) were significantly increased compared with CON (P < 0.05). These changes caused by HC were inversed by thiamine supplementation (P < 0.05). The taxonomy results showed that ruminal archaea ranged from 0.37 to 0.47% of the whole microbiota. Four characterized phyla, a number of Candidatus archaea and almost 660 species were identified in the present study. In which Euryarchaeota occupied the largest proportion of the whole archaea. Furthermore, thiamine supplementation treatment significantly increased the relative abundance of non-methanogens compared with CON and HC treatments. Thaumarchaeota was increased in HC compared with CON. Thiamine supplementation significantly increased Crenarchaeota, Nanoarchaeota and the Candidatus phyla, however decreased Thaumarchaeota compared with HC treatment.<br><br>CONCLUSIONS: HC feeding significantly decreased ruminal pH and increased the content of NH3-N which led to N loss and the increase of the relative abundance of Thaumarchaeota. Thiamine supplementation increased ruminal pH, improved the activity of ammonia utilizing bacteria, and decreased Thaumarchaeota abundance to reduce the ruminal NH3 content and finally reduced N loss. Overall, these findings contributed to the understanding of thiamine's function in dairy cows and provided new strategies to improve dairy cows' health under high-concentrate feeding regime.}, }
@article {pmid30604012, year = {2019}, author = {Tyagi, A and Singh, B and Billekallu Thammegowda, NK and Singh, NK}, title = {Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome.}, journal = {Archives of microbiology}, volume = {201}, number = {3}, pages = {295-303}, doi = {10.1007/s00203-018-1615-y}, pmid = {30604012}, issn = {1432-072X}, support = {YSS/2014/000269//Science and Engineering Research Board/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Aquaculture ; *Bacteria/classification/drug effects/genetics ; Carps/*microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Fishes ; Gastrointestinal Microbiome/*genetics ; Gene Transfer, Horizontal ; Metabolic Networks and Pathways ; Metagenomics/methods ; Probiotics ; }, abstract = {Gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. With the presence of 36 phyla, 326 families and 985 genera, the fish gut microbiota was found to be quite diverse in nature. However, at the phylum level, more than three-fourths of gut microbes belonged to Proteobacteria. Very low prevalence of commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) in fish gut suggested the need to search for alternative probiotics for aquaculture use. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy metabolism (4%) and fermentation (2%). In conformity with herbivorous feeding habit of L. rohita, gut microbiome also had pathways for the degradation of cellulose, hemicellulose, chitin, pectin, starch, and other complex carbohydrates. High prevalence of Actinobacteria and antibiotic biosynthesis pathways in the fish gut microbiome indicated its potential for bioprospecting of potentially novel natural antibiotics. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment. The role of ARGs in fish gut microbiome needs further investigations.}, }
@article {pmid30601862, year = {2019}, author = {Thornbury, M and Sicheri, J and Slaine, P and Getz, LJ and Finlayson-Trick, E and Cook, J and Guinard, C and Boudreau, N and Jakeman, D and Rohde, J and McCormick, C}, title = {Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0209221}, doi = {10.1371/journal.pone.0209221}, pmid = {30601862}, issn = {1932-6203}, mesh = {Animals ; Endo-1,4-beta Xylanases/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Fermentation ; Glycoside Hydrolases/genetics/metabolism ; Kinetics ; Lignin/*metabolism ; Metagenomics ; Microbiota/*genetics/*physiology ; Phylogeny ; Porcupines/metabolism/*microbiology ; Recombinant Proteins/genetics/metabolism ; Synthetic Biology ; Xylosidases/genetics/metabolism ; beta-Glucosidase/genetics/metabolism ; }, abstract = {Plant cell walls are composed of cellulose, hemicellulose, and lignin, collectively known as lignocellulose. Microorganisms degrade lignocellulose to liberate sugars to meet metabolic demands. Using a metagenomic sequencing approach, we previously demonstrated that the microbiome of the North American porcupine (Erethizon dorsatum) is replete with genes that could encode lignocellulose-degrading enzymes. Here, we report the identification, synthesis and partial characterization of four novel genes from the porcupine microbiome encoding putative lignocellulose-degrading enzymes: β-glucosidase, α-L-arabinofuranosidase, β-xylosidase, and endo-1,4-β-xylanase. These genes were identified via conserved catalytic domains associated with cellulose- and hemicellulose-degradation. Phylogenetic trees were created for each of these putative enzymes to depict genetic relatedness to known enzymes. Candidate genes were synthesized and cloned into plasmid expression vectors for inducible protein expression and secretion. The putative β-glucosidase fusion protein was efficiently secreted but did not permit Escherichia coli (E. coli) to use cellobiose as a sole carbon source, nor did the affinity purified enzyme cleave p-Nitrophenyl β-D-glucopyranoside (p-NPG) substrate in vitro over a range of physiological pH levels (pH 5-7). The putative hemicellulose-degrading β-xylosidase and α-L-arabinofuranosidase enzymes also lacked in vitro enzyme activity, but the affinity purified endo-1,4-β-xylanase protein cleaved a 6-chloro-4-methylumbelliferyl xylobioside substrate in acidic and neutral conditions, with maximal activity at pH 7. At this optimal pH, KM, Vmax, and kcat were determined to be 32.005 ± 4.72 μM, 1.16x10-5 ± 3.55x10-7 M/s, and 94.72 s-1, respectively. Thus, our pipeline enabled successful identification and characterization of a novel hemicellulose-degrading enzyme from the porcupine microbiome. Progress towards the goal of introducing a complete lignocellulose-degradation pathway into E. coli will be accelerated by combining synthetic metagenomic approaches with functional metagenomic library screening, which can identify novel enzymes unrelated to those found in available databases.}, }
@article {pmid30598099, year = {2018}, author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T}, title = {A latent allocation model for the analysis of microbial composition and disease.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 19}, pages = {519}, doi = {10.1186/s12859-018-2530-6}, pmid = {30598099}, issn = {1471-2105}, mesh = {*Algorithms ; Bacteria/*classification ; Case-Control Studies ; Colorectal Neoplasms/*microbiology ; Computer Simulation ; Humans ; *Microbiota ; *Models, Statistical ; Parkinson Disease/*microbiology ; }, abstract = {BACKGROUND: Establishing the relationship between microbiota and specific diseases is important but requires appropriate statistical methodology. A specialized feature of microbiome count data is the presence of a large number of zeros, which makes it difficult to analyze in case-control studies. Most existing approaches either add a small number called a pseudo-count or use probability models such as the multinomial and Dirichlet-multinomial distributions to explain the excess zero counts, which may produce unnecessary biases and impose a correlation structure taht is unsuitable for microbiome data.<br><br>RESULTS: The purpose of this article is to develop a new probabilistic model, called BERnoulli and MUltinomial Distribution-based latent Allocation (BERMUDA), to address these problems. BERMUDA enables us to describe the differences in bacteria composition and a certain disease among samples. We also provide a simple and efficient learning procedure for the proposed model using an annealing EM algorithm.<br><br>CONCLUSION: We illustrate the performance of the proposed method both through both the simulation and real data analysis. BERMUDA is implemented with R and is available from GitHub (https://github.com/abikoushi/Bermuda).}, }
@article {pmid30598080, year = {2018}, author = {Chen, HM and Chang, TH and Lin, FM and Liang, C and Chiu, CM and Yang, TL and Yang, T and Huang, CY and Cheng, YN and Chang, YA and Chang, PY and Weng, SL}, title = {Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 10}, pages = {876}, doi = {10.1186/s12864-018-5284-7}, pmid = {30598080}, issn = {1471-2164}, mesh = {Adult ; DNA, Bacterial/genetics ; Female ; *Genetic Variation ; Humans ; Microbiota/*genetics ; Vagina/*microbiology ; Vaginosis, Bacterial/microbiology ; }, abstract = {BACKGROUND: One of the most common and recurrent vaginal infections is bacterial vaginosis (BV). The diagnosis is based on changes to the &quot;normal&quot; vaginal microbiome; however, the normal microbiome appears to differ according to reproductive status and ethnicity, and even among individuals within these groups. The Amsel criteria and Nugent score test are widely used for diagnosing BV; however, these tests are based on different criteria, and so may indicate distinct changes in the vaginal microbial community. Nevertheless, few studies have compared the results of these test against metagenomics analysis.<br><br>METHODS: Vaginal flora samples from 77 participants were classified according to the Amsel criteria and Nugent score test. The microbiota composition was analyzed using 16S ribosome RNA gene amplicon sequencing. Bioinformatics analysis and multivariate statistical analysis were used to evaluate the microbial diversity and function.<br><br>RESULTS: Only 3 % of the participants diagnosed BV negative using the Amsel criteria (A-) were BV-positive according to the Nugent score test (N+), while over half of the BV-positive patients using the Amsel criteria (A+) were BV-negative according to the Nugent score test (N-). Thirteen genera showed significant differences in distribution among BV status defined by BV tests (e.g., A - N-, A + N- and A + N+). Variations in the four most abundant taxa, Lactobacillus, Gardnerella, Prevotella, and Escherichia, were responsible for most of this dissimilarity. Furthermore, vaginal microbial diversity differed significantly among the three groups classified by the Nugent score test (N-, N+, and intermediate flora), but not between the Amsel criteria groups. Numerous predictive microbial functions, such as bacterial chemotaxis and bacterial invasion of epithelial cells, differed significantly among multiple BV test, but not between the A- and A+ groups.<br><br>CONCLUSIONS: Metagenomics analysis can greatly expand our current understanding of vaginal microbial diversity in health and disease. Metagenomics profiling may also provide more reliable diagnostic criteria for BV testing.}, }
@article {pmid30597002, year = {2019}, author = {Choi, I and Ponsero, AJ and Bomhoff, M and Youens-Clark, K and Hartman, JH and Hurwitz, BL}, title = {Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons.}, journal = {GigaScience}, volume = {8}, number = {2}, pages = {}, doi = {10.1093/gigascience/giy165}, pmid = {30597002}, issn = {2047-217X}, mesh = {Algorithms ; Cluster Analysis ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; *Software ; }, 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 {pmid30596703, year = {2018}, author = {Quinn, O and Gruber, MAM and Brown, RL and Baty, JW and Bulgarella, M and Lester, PJ}, title = {A metatranscriptomic analysis of diseased social wasps (Vespula vulgaris) for pathogens, with an experimental infection of larvae and nests.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209589}, doi = {10.1371/journal.pone.0209589}, pmid = {30596703}, issn = {1932-6203}, mesh = {Animals ; Gene Expression Profiling/methods ; *Host-Pathogen Interactions ; Larva/microbiology ; *Metagenome ; *Metagenomics ; *Microbiota ; Phylogeny ; Wasps/*microbiology/ultrastructure ; }, abstract = {Social wasps are a major pest in many countries around the world. Pathogens may influence wasp populations and could provide an option for population management via biological control. We investigated the pathology of nests of apparently healthy common wasps, Vespula vulgaris, with nests apparently suffering disease. First, next-generation sequencing and metatranscriptomic analysis were used to examine pathogen presence. The transcriptome of healthy and diseased V. vulgaris showed 27 known microbial phylotypes. Four of these were observed in diseased larvae alone (Aspergillus fumigatus, Moellerella wisconsensis, Moku virus, and the microsporidian Vavraia culicis). Kashmir Bee Virus (KBV) was found to be present in both healthy and diseased larvae. Moellerella wisconsensis is a human pathogen that was potentially misidentified in our wasps by the MEGAN analysis: it is more likely to be the related bacteria Hafnia alvei that is known to infect social insects. The closest identification to the putative pathogen identified as Vavraia culicis was likely to be another microsporidian Nosema vulgaris. PCR and subsequent Sanger sequencing using published or our own designed primers, confirmed the identity of Moellerella sp. (which may be Hafnia alvei), Aspergillus sp., KBV, Moku virus and Nosema. Secondly, we used an infection study by homogenising diseased wasp larvae and feeding them to entire nests of larvae in the laboratory. Three nests transinfected with diseased larvae all died within 19 days. No pathogen that we monitored, however, had a significantly higher prevalence in diseased than in healthy larvae. RT-qPCR analysis indicated that pathogen infections were significantly correlated, such as between KBV and Aspergillus sp. Social wasps clearly suffer from an array of pathogens, which may lead to the collapse of nests and larval death.}, }
@article {pmid30594064, year = {2019}, author = {Procopio, N and Ghignone, S and Williams, A and Chamberlain, A and Mello, A and Buckley, M}, title = {Metabarcoding to investigate changes in soil microbial communities within forensic burial contexts.}, journal = {Forensic science international. Genetics}, volume = {39}, number = {}, pages = {73-85}, doi = {10.1016/j.fsigen.2018.12.002}, pmid = {30594064}, issn = {1878-0326}, mesh = {Animals ; Burial ; DNA Barcoding, Taxonomic/*methods ; Forensic Sciences ; Metagenomics/methods ; Microbiota/*genetics ; Models, Animal ; Polymerase Chain Reaction ; *Postmortem Changes ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Swine ; }, abstract = {The estimation of the time elapsed since death (post-mortem interval, or PMI) is one of the key themes that forensic scientists have to address frequently. However, the estimation of PMI still suffers from poor accuracy and biases especially when decomposition stages are prolonged, so further improvements in methods for PMI estimation are desirable. Soil microbial communities associated with decomposing bodies have been shown to be good candidates for the estimation of the PMI of exposed bodies. Nevertheless, further research is required to better understand the bacterial succession associated with decomposition of buried carcasses in order to test its reliability and applicability for the estimation of PMI and to better understand the dynamics involved with decomposition within this particular scenario. Therefore we explored the succession of soil microbial communities associated with four decomposing pig carcasses (from one to six months PMI) using a metabarcoding approach. The sequencing of the bacterial 16S rRNA variable region 4 (V4) revealed trends linking particular microbial taxa with specific PMIs, and notably an increase in Proteobacteria, Firmicutes and Bacteroidetes at specific PMIs as well as a decrease in Acidobacteria. Our results, in accordance with previous studies conducted on exposed bodies of different mammalian species (including humans), also showed a general reduction of the taxonomic richness from two months PMI onwards, as well as an incomplete re-establishment of the starting soil microbial conditions after six months PMI. We also found specific mammal-derived taxa, such as Bacteroides spp., being still present in the soil after six months PMI. As such, this study serves as a baseline for additional research to allow the characterisation of biomarkers associated with specific PMIs. Due to the similarity between the results presented here and those reported in other types of decomposition studies we believe that the metabarcoding approach has considerable potential in the estimation of the PMI, particularly to clarify cases involving heavily skeletonised bodies or for the investigation of clandestine graves in which the carcass has been moved from its original place of deposition.}, }
@article {pmid30589606, year = {2019}, author = {Yasir, M and Qureshi, AK and Khan, I and Bibi, F and Rehan, M and Khan, SB and Azhar, EI}, title = {Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia.}, journal = {Omics : a journal of integrative biology}, volume = {23}, number = {1}, pages = {17-27}, doi = {10.1089/omi.2018.0176}, pmid = {30589606}, issn = {1557-8100}, mesh = {Bacteria/*genetics ; Biodiversity ; Hot Springs/*microbiology ; Hot Temperature ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Saudi Arabia ; Sequence Analysis, DNA/methods ; }, abstract = {Hot springs are natural habitats for thermophilic microorganisms and provide a significant opportunity for bioprospecting thermostable biomolecules. However, the scientific community has only a fragmented understanding of the microbial diversity and composition in these biotopes. In this study, bacterial diversity in sediment samples from six hot springs of Saudi Arabia was investigated using an improved culture-dependent approach. High-throughput MALDI-TOF MS (matrix assisted laser desorption/ionization mass spectrometry) and 16S rRNA genes sequencing were used for the identification of purified isolates. Most of the hot springs had a neutral pH and a temperature range of 45-89°C. Relatively higher colony-forming units (1.9 ± 0.45 × 104) were observed with 60°C incubation of an 89°C sediment sample from the hot spring at Ain al Harra1. Among the 536 purified isolates, 6 novel candidate species were found, and the remaining isolates represented 139 distinct species. Several species, such as Bacillus cereus, Bacillus subtilis, and Bacillus schlegelii, were ubiquitous in the hot springs sampled, but 102 of the identified species were uniquely distributed among the hot springs. Sixteen of the isolated thermophilic bacteria, including Geobacillus kaustophilus, Thermus oshimai, and Brevibacillus thermoruber, grew at ≥60°C. In addition, 21 species exhibited hydrolytic enzymatic activity. Most of these species belonged to Bacillus and Brevibacillus. Overall, this study contributes to global knowledgebase on bacterial communities by comprehensively profiling culture-based bacterial diversity in the hot springs of Saudi Arabia. Further studies are required for investigating bacteria from hot springs by a metagenomic approach.}, }
@article {pmid30588764, year = {2019}, author = {Woyke, T and Schulz, F}, title = {Entities inside one another - a matryoshka doll in biology?.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {26-28}, doi = {10.1111/1758-2229.12716}, pmid = {30588764}, issn = {1758-2229}, mesh = {*Biological Evolution ; Eukaryota/physiology ; Giant Viruses/physiology ; Metagenomics ; Microbial Consortia ; Organelles/physiology ; *Symbiosis ; Thiothrix/physiology ; }, }
@article {pmid30587114, year = {2018}, author = {Tyakht, AV and Manolov, AI and Kanygina, AV and Ischenko, DS and Kovarsky, BA and Popenko, AS and Pavlenko, AV and Elizarova, AV and Rakitina, DV and Baikova, JP and Ladygina, VG and Kostryukova, ES and Karpova, IY and Semashko, TA and Larin, AK and Grigoryeva, TV and Sinyagina, MN and Malanin, SY and Shcherbakov, PL and Kharitonova, AY and Khalif, IL and Shapina, MV and Maev, IV and Andreev, DN and Belousova, EA and Buzunova, YM and Alexeev, DG and Govorun, VM}, title = {Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {968}, doi = {10.1186/s12864-018-5306-5}, pmid = {30587114}, issn = {1471-2164}, support = {16-15-00258//Russian Science Foundation/ ; }, mesh = {Cluster Analysis ; Crohn Disease/microbiology/*pathology ; Escherichia coli/*genetics/isolation &amp; purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Genetic Variation ; Genome, Bacterial ; Humans ; Intestinal Mucosa/microbiology ; Metagenomics/*methods ; }, abstract = {BACKGROUND: Crohn's disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated.<br><br>METHODS: We performed a metagenomic study investigating the gut microbiota of patients with Crohn's disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability.<br><br>RESULTS: The abnormal shifts in the microbial community structures in Crohn's disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes.<br><br>CONCLUSIONS: The genomic diversity of Crohn's disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn's disease and the development of new strategies for the prevention and treatment of this disease.}, }
@article {pmid30584534, year = {2018}, author = {Ranjan, R and Rani, A and Finn, PW and Perkins, DL}, title = {Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {6074918}, doi = {10.1155/2018/6074918}, pmid = {30584534}, issn = {2314-6141}, support = {R01 AI053878/AI/NIAID NIH HHS/United States ; R01 HL081663/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Bacteria/genetics ; Biodiversity ; Dysbiosis/genetics/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Transcriptome/genetics ; }, abstract = {It is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of this study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced, and to determine if the data are comparable on different platforms. In this study, we perform ultradeep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We performed sequencing analysis using different Illumina platforms, with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others, and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.}, }
@article {pmid30584008, year = {2019}, author = {Liu, X and Shao, L and Liu, X and Ji, F and Mei, Y and Cheng, Y and Liu, F and Yan, C and Li, L and Ling, Z}, title = {Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer.}, journal = {EBioMedicine}, volume = {40}, number = {}, pages = {336-348}, doi = {10.1016/j.ebiom.2018.12.034}, pmid = {30584008}, issn = {2352-3964}, mesh = {Aged ; Biodiversity ; Cohort Studies ; Combined Modality Therapy ; Computational Biology/methods ; Dysbiosis ; Female ; Gastric Mucosa/*microbiology/pathology ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Neoplasm Grading ; Neoplasm Staging ; RNA, Ribosomal, 16S ; Stomach Neoplasms/*etiology/pathology/therapy ; }, abstract = {BACKGROUND: As part of the tumor microenvironment, the gastric microbiota play vital roles in tumor initiation, progression and metastasis, but stomach microhabitats are not always uniform. We aimed to characterize differences of gastric microbiota in stomach microhabitats associated with gastric cancer (GC) development.<br><br>METHODS: A cohort of 276 GC patients without preoperative chemotherapy was enrolled retrospectively, and 230 normal, 247 peritumoral and 229 tumoral tissues were obtained for gastric microbiota analysis targeting the 16S rRNA gene by MiSeq sequencing. The microbial diversity and composition, bacterial co-occurrence correlations and predictive functional profiles were compared across different microhabitats.<br><br>FINDINGS: GC-specific stomach microhabitats, not GC stages or types, determine the composition and diversity of the gastric microbiota. Most notably, bacterial richness was decreased in peritumoral and tumoral microhabitats, and the correlation network of abundant gastric bacteria was simplified in tumoral microhabitat. Helicobacter pylori (HP), Prevotella copri and Bacteroides uniformis were significantly decreased, whereas Prevotella melaninogenica, Streptococcus anginosus and Propionibacterium acnes were increased in tumoral microhabitat. Higher HP colonisation influenced the overall structure of the gastric microbiota in normal and peritumoral microhabitats. PiCRUSt analysis revealed that genes associated with nucleotide transport and metabolism and amino acid transport and metabolism were significantly enriched in tumoral microbiota, while gastric acid secretion was significantly higher in HP positive group of the tumoral microbiota.<br><br>INTERPRETATION: Our present study provided new insights into the roles of gastric microbiota in different stomach microhabitats in gastric carcinogenesis, especially the pathogenesis of HP. FUND: National Natural Science Foundation of China.}, }
@article {pmid30582999, year = {2019}, author = {Snowdon, RJ and Schiessl, S}, title = {Illuminating Crop Adaptation Using Population Genomics.}, journal = {Molecular plant}, volume = {12}, number = {1}, pages = {27-29}, doi = {10.1016/j.molp.2018.12.014}, pmid = {30582999}, issn = {1752-9867}, mesh = {Adaptation, Physiological/genetics ; Brassica rapa/*genetics ; Ecotype ; Genome ; Genomics ; Metagenomics ; }, }
@article {pmid30581850, year = {2018}, author = {Chen, WP and Chang, SH and Tang, CY and Liou, ML and Tsai, SJ and Lin, YL}, title = {Composition Analysis and Feature Selection of the Oral Microbiota Associated with Periodontal Disease.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {3130607}, doi = {10.1155/2018/3130607}, pmid = {30581850}, issn = {2314-6141}, mesh = {Bacteria/*genetics ; Chronic Periodontitis/*microbiology ; Gingiva/*microbiology ; Humans ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tooth/microbiology ; }, abstract = {Periodontitis is an inflammatory disease involving complex interactions between oral microorganisms and the host immune response. Understanding the structure of the microbiota community associated with periodontitis is essential for improving classifications and diagnoses of various types of periodontal diseases and will facilitate clinical decision-making. In this study, we used a 16S rRNA metagenomics approach to investigate and compare the compositions of the microbiota communities from 76 subgingival plagues samples, including 26 from healthy individuals and 50 from patients with periodontitis. Furthermore, we propose a novel feature selection algorithm for selecting features with more information from many variables with a combination of these features and machine learning methods were used to construct prediction models for predicting the health status of patients with periodontal disease. We identified a total of 12 phyla, 124 genera, and 355 species and observed differences between health- and periodontitis-associated bacterial communities at all phylogenetic levels. We discovered that the genera Porphyromonas, Treponema, Tannerella, Filifactor, and Aggregatibacter were more abundant in patients with periodontal disease, whereas Streptococcus, Haemophilus, Capnocytophaga, Gemella, Campylobacter, and Granulicatella were found at higher levels in healthy controls. Using our feature selection algorithm, random forests performed better in terms of predictive power than other methods and consumed the least amount of computational time.}, }
@article {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 {pmid30580413, year = {2019}, author = {Bridier, A}, title = {Exploring Foodborne Pathogen Ecology and Antimicrobial Resistance in the Light of Shotgun Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1918}, number = {}, pages = {229-245}, doi = {10.1007/978-1-4939-9000-9_19}, pmid = {30580413}, issn = {1940-6029}, mesh = {Anti-Infective Agents/pharmacology ; Bacteria/classification/genetics ; Biodiversity ; *Drug Resistance, Microbial ; Food Microbiology ; Food Safety ; Foodborne Diseases/diagnosis/*microbiology ; Genome ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; Whole Genome Sequencing ; }, abstract = {In this chapter, applications of shotgun metagenomics for taxonomic profiling and functional investigation of food microbial communities with a focus on antimicrobial resistance (AMR) were overviewed in the light of last data in the field. Potentialities of metagenomic approach, along with the challenges encountered for a wider and routinely use in food safety was discussed.}, }
@article {pmid30580412, year = {2019}, author = {Feye, KM and Ricke, SC}, title = {Establishment of a Standardized 16S rDNA Library Preparation to Enable Analysis of Microbiome in Poultry Processing Using Illumina MiSeq Platform.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1918}, number = {}, pages = {213-227}, doi = {10.1007/978-1-4939-9000-9_18}, pmid = {30580412}, issn = {1940-6029}, mesh = {Animals ; Data Analysis ; *Gene Library ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Metagenomics/methods ; *Microbiota ; Polymerase Chain Reaction ; Poultry/*microbiology ; Quality Control ; *RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety. This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.}, }
@article {pmid30579332, year = {2018}, author = {Getachew, B and Aubee, JI and Schottenfeld, RS and Csoka, AB and Thompson, KM and Tizabi, Y}, title = {Ketamine interactions with gut-microbiota in rats: relevance to its antidepressant and anti-inflammatory properties.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {222}, doi = {10.1186/s12866-018-1373-7}, pmid = {30579332}, issn = {1471-2180}, support = {R03 AA022479/AA/NIAAA NIH HHS/United States ; R21 AG047474/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Anti-Inflammatory Agents/*pharmacology ; Antidepressive Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestines/microbiology ; Ketamine/*pharmacology ; Male ; Rats ; Rats, Wistar ; }, abstract = {BACKGROUND: Appreciable evidence suggest that dysbiosis in microbiota, reflected in gut microbial imbalance plays a key role in the pathogenesis of neuropsychiatric disorders including depression and inflammatory diseases. Recently, the antidepressant properties of ketamine have gained prominence due to its fast and long lasting effects. Additional uses for ketamine in inflammatory disorders such as irritable bowel syndrome have been suggested. However, ketamine's exact mechanism of action and potential effects on microbiome is not known. Here, we examined the effects of low dose ketamine, known to induce antidepressant effects, on stool microbiome profile in adult male Wistar rats. Animals (5/group) were injected intraperitoneally with ketamine (2.5 mg/kg) or saline, daily for 7 days and sacrificed on day 8 when intestinal stools were collected and stored at - 80 °C. DNA was extracted from the samples and the 16 S rRNA gene-based microbiota analysis was performed using 16S Metagenomics application.<br><br>RESULTS: At genus-level, ketamine strikingly amplified Lactobacillus, Turicibacter and Sarcina by 3.3, 26 and 42 fold, respectively. Conversely, opportunistic pathogens Mucispirillum and Ruminococcus were reduced by approximately 2.6 and 26 fold, respectively, in ketamine group. Low levels of Lactobacillus and Turicibacter are associated with various disorders including depression and administration of certain species of Lactobacillus ameliorates depressive-like behavior in animal models. Hence, some of the antidepressant effects of ketamine might be mediated through its interaction with these gut bacteria. Additionally, high level of Ruminococcus is positively associated with the severity of irritable bowel syndrome (IBS), and some species of Mucispirillum have been associated with intestinal inflammation. Indirect evidence of anti-inflammatory role of Sarcina has been documented. Hence, some of the anti-inflammatory effects of ketamine and its usefulness in specific inflammatory diseases including IBS may be mediated through its interaction with these latter bacteria.<br><br>CONCLUSION: Our data suggest that at least some of the antidepressant and anti-inflammatory effects of daily ketamine treatment for 7 days may be mediated via its interaction with specific gut bacteria. These findings further validate the usefulness of microbiome as a target for therapeutic intervention and call for more detailed investigation of microbiome interaction with central mediators of mood and/or inflammatory disorders.}, }
@article {pmid30579193, year = {2019}, author = {Deng, Y and Wang, Y and Xia, Y and Zhang, AN and Zhao, Y and Zhang, T}, title = {Genomic resolution of bacterial populations in saccharin and cyclamate degradation.}, journal = {The Science of the total environment}, volume = {658}, number = {}, pages = {357-366}, doi = {10.1016/j.scitotenv.2018.12.162}, pmid = {30579193}, issn = {1879-1026}, mesh = {Alphaproteobacteria/genetics/isolation &amp; purification/metabolism ; *Biodegradation, Environmental ; Biodiversity ; Cyclamates/*metabolism ; *Genome, Bacterial ; Metagenomics/methods ; Methylobacteriaceae/genetics/isolation &amp; purification/metabolism ; Rhodocyclaceae/genetics/isolation &amp; purification/metabolism ; Saccharin/*metabolism ; Sphingomonadaceae/genetics/isolation &amp; purification/metabolism ; Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The benefits of extensive artificial sweeteners use come at a cost of their ubiquitous occurrence in the aquatic environment. Biodegradation is crucial for the removal of artificial sweeteners in the environment, yet comprehensive characterizations of the degradation consortia that degrade these compounds have not been initiated. Here, we performed metagenomic analysis of microbial communities fulfilling complete mineralization of two typical artificial sweeteners, i.e. saccharin and cyclamate. Genome-resolved metagenomics enabled the recovery and metabolic characterization of total 23 population genomes from 8 phyla in the two consortia, most of which represented novel species. The saccharin-degrading consortia was notably dominated by a betaproteobacterial genome from the family Rhodocyclaceae, accounting for 15.5% of total sequences. For the cyclamate enrichment, 28.1% of the total sequences were assigned to three similarly abundant Alphaproteobacteria population genomes belonging to the family Sphingomonadaceae and Methylobacteriaceae. The metabolic potential of these population genomes were examined to potentially identify the roles of these populations in biodegradation of artificial sweeteners, and focusing on the energy and nutrient metabolisms.}, }
@article {pmid30578963, year = {2019}, author = {Piewngam, P and Quiñones, M and Thirakittiwatthana, W and Yungyuen, T and Otto, M and Kiratisin, P}, title = {Composition of the intestinal microbiota in extended-spectrum β-lactamase-producing Enterobacteriaceae carriers and non-carriers in Thailand.}, journal = {International journal of antimicrobial agents}, volume = {53}, number = {4}, pages = {435-441}, doi = {10.1016/j.ijantimicag.2018.12.006}, pmid = {30578963}, issn = {1872-7913}, support = {Z01 AI000904-07/ImNIH/Intramural NIH HHS/United States ; ZIA AI000904/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Bacteroides/isolation &amp; purification ; Carrier State/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterobacteriaceae/*classification/genetics/metabolism ; Enterobacteriaceae Infections/*drug therapy/microbiology ; Farmers/statistics &amp; numerical data ; Gastrointestinal Microbiome/*genetics ; Healthy Volunteers/statistics &amp; numerical data ; Humans ; Intestines/*microbiology ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; Thailand ; beta-Lactamases/metabolism ; }, abstract = {There is increasing recognition that the intestinal microbiota govern human well-being and prevent diseases. Intestinal colonization by antibiotic-resistant pathogens, however, can lead to the spread of resistance as well as serious infections. Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) represent particularly dangerous pathogens, which are known to asymptomatically colonize the intestinal tract in the community. Here, we performed a 16S rRNA metagenomics sequence analysis to analyse differences in the microbiota composition between ESBL-E carriers and non-carriers in Thailand, where ESBL-E carriage rates are notoriously high. The most notable difference detected was that the phylum Bacteroidetes, and in particular, the species Bacteroides uniformis, were significantly more abundant in ESBL-E non-carriers than carriers. The Shannon diversity index in non-carriers (5.10 ± 0.69) was also lower than that in ESBL-E carriers (5.39 ± 0.48) without statistical significance (P=0.13). The overall beta diversity difference of the intestinal microbiota of ESBL-E carriers as compared to non-carriers was statistically significant (Adonis on weighted unifrac: R2=0.14, P=0.005). Furthermore, ESBL-E carriage was significantly lower in farmers than in those with other occupations. Our findings suggest that a dynamic interaction exists between microbiota diversity and ESBL-E carriage, which is possibly driven by dietary composition and may be exploited using probiotic approaches to control the spread of ESBL-E.}, }
@article {pmid30578263, year = {2019}, author = {Wegner, CE and Gaspar, M and Geesink, P and Herrmann, M and Marz, M and Küsel, K}, title = {Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {5}, pages = {}, doi = {10.1128/AEM.02346-18}, pmid = {30578263}, issn = {1098-5336}, abstract = {Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbor autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-omic profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes, and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, and ammonium oxidation [anammox]) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), depending on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Being dominated by a few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, and Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome depending on the availability of oxygen and inorganic electron donors, like ammonium.IMPORTANCE Groundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage, and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than does hydrochemistry.}, }
@article {pmid30577803, year = {2018}, author = {Chappell, T and Geva, S and Hogan, JM and Huygens, F and Rathnayake, IU and Rudd, S and Kelly, W and Perrin, D}, title = {Rapid analysis of metagenomic data using signature-based clustering.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 20}, pages = {509}, doi = {10.1186/s12859-018-2540-4}, pmid = {30577803}, issn = {1471-2105}, mesh = {Algorithms ; Cluster Analysis ; *Data Analysis ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; }, abstract = {BACKGROUND: Sequencing highly-variable 16S regions is a common and often effective approach to the study of microbial communities, and next-generation sequencing (NGS) technologies provide abundant quantities of data for analysis. However, the speed of existing analysis pipelines may limit our ability to work with these quantities of data. Furthermore, the limited coverage of existing 16S databases may hamper our ability to characterise these communities, particularly in the context of complex or poorly studied environments.<br><br>RESULTS: In this article we present the SigClust algorithm, a novel clustering method involving the transformation of sequence reads into binary signatures. When compared to other published methods, SigClust yields superior cluster coherence and separation of metagenomic read data, while operating within substantially reduced timeframes. We demonstrate its utility on published Illumina datasets and on a large collection of labelled wound reads sourced from patients in a wound clinic. The temporal analysis is based on tracking the dominant clusters of wound samples over time. The analysis can identify markers of both healing and non-healing wounds in response to treatment. Prominent clusters are found, corresponding to bacterial species known to be associated with unfavourable healing outcomes, including a number of strains of Staphylococcus aureus.<br><br>CONCLUSIONS: SigClust identifies clusters rapidly and supports an improved understanding of the wound microbiome without reliance on a reference database. The results indicate a promising use for a SigClust-based pipeline in wound analysis and prediction, and a possible novel method for wound management and treatment.}, }
@article {pmid30576077, year = {2019}, author = {Jeunen, GJ and Knapp, M and Spencer, HG and Lamare, MD and Taylor, HR and Stat, M and Bunce, M and Gemmell, NJ}, title = {Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {426-438}, doi = {10.1111/1755-0998.12982}, pmid = {30576077}, issn = {1755-0998}, mesh = {Aquatic Organisms/*classification/genetics/growth &amp; development ; *Biota ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Electron Transport Complex IV/genetics ; Eukaryota/*classification/genetics/growth &amp; development ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Movements ; }, abstract = {While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal of the eDNA signal. Currents and tidal influences could transport eDNA over great distances, inducing false-positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement of marine environments. In this study, we determined the ability of eDNA metabarcoding surveys to distinguish localized signals obtained from four marine habitats within a small spatial scale (<5 km) subject to significant tidal and along-shore water flow. Our eDNA metabarcoding survey detected 86 genera, within 77 families and across 11 phyla using three established metabarcoding assays targeting fish (16S rRNA gene), crustacean (16S rRNA gene) and eukaryotic (cytochrome oxidase subunit 1) diversity. Ordination and cluster analyses for both taxonomic and OTU data sets show distinct eDNA signals between the sampled habitats, suggesting dispersal of eDNA among habitats was limited. Individual taxa with strong habitat preferences displayed localized eDNA signals in accordance with their respective habitat, whereas taxa known to be less habitat-specific generated more ubiquitous signals. Our data add to evidence that eDNA metabarcoding surveys in marine environments detect a broad range of taxa that are spatially discrete. Our work also highlights that refinement of assay choice is essential to realize the full potential of eDNA metabarcoding surveys in marine biodiversity monitoring programs.}, }
@article {pmid30574802, year = {2019}, author = {Murphy, R and Morgan, XC and Wang, XY and Wickens, K and Purdie, G and Fitzharris, P and Otal, A and Lawley, B and Stanley, T and Barthow, C and Crane, J and Mitchell, EA and Tannock, GW}, title = {Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT.}, journal = {Beneficial microbes}, volume = {10}, number = {1}, pages = {5-17}, doi = {10.3920/BM2017.0191}, pmid = {30574802}, issn = {1876-2891}, mesh = {Adult ; Age Factors ; Biological Transport ; Breast Feeding ; Child, Preschool ; Dermatitis, Atopic/microbiology/*prevention &amp; control ; Dietary Supplements ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Glycerophosphates/metabolism ; Humans ; Infant ; Infant, Newborn ; Lactobacillus rhamnosus/*physiology ; Metagenomics ; Mothers ; Postpartum Period ; *Probiotics ; }, abstract = {Probiotic Lactobacillus rhamnosus HN001 given in early life has been shown to reduce infant eczema risk, but its effect on gut microbiota development has not been quantitatively and functionally examined. The aim of this study was to investigate the impact of early life probiotic exposure on the composition and functional capacity of infant gut microbiota from birth to 2 years considering the effects of age, delivery mode, antibiotics, pets and eczema. We performed shotgun metagenomic sequencing analysis of 650 infant faecal samples, collected at birth, 3, 12, and 24 months, as part of a randomised, controlled, 3-arm trial assessing the effect of L. rhamnosus HN001, Bifidobacterium animalis subsp. lactis HN019 supplementation on eczema development in 474 infants. There was a 50% reduced eczema risk in the HN001 probiotic group compared to placebo. Both mothers (from 35 weeks gestation until 6 months post-partum if breastfeeding) and infants (from birth to 2 years) received either a placebo or one of two probiotics, L. rhamnosus HN001 (6×109 cfu), or B. animalis subsp. lactis HN019 (9×109 cfu). L. rhamnosus HN001 probiotic supplementation was associated with increased overall glycerol-3 phosphate transport capacity and enrichment of L. rhamnosus. There were no other significant changes in infant gut microbiota composition or diversity. Increased capacity to transport glycerol-3-phosphate was positively correlated with relative abundance of L. rhamnosus. Children who developed eczema had gut microbiota with increased capacity for glycosaminoglycan degradation and flagellum assembly but had no significant differences in microbiota composition or diversity. Early life HN001 probiotic use is associated with both increased L. rhamnosus and increased infant gut microbiota functional capacity to transport glycerol-3 phosphate. The mechanistic relationship of such functional alteration in gut microbiota with reduced eczema risk and long-term health merits further investigation.}, }
@article {pmid30565880, year = {2019}, author = {Thorn, CE and Bergesch, C and Joyce, A and Sambrano, G and McDonnell, K and Brennan, F and Heyer, R and Benndorf, D and Abram, F}, title = {A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {439-455}, doi = {10.1111/1755-0998.12979}, pmid = {30565880}, issn = {1755-0998}, support = {//NUI Galway/ ; }, mesh = {Cost-Benefit Analysis ; DNA/genetics/*isolation &amp; purification ; Metagenomics/economics/*methods ; *Microbiota ; Proteins/analysis/*isolation &amp; purification ; Proteomics/economics/*methods ; RNA/genetics/*isolation &amp; purification ; *Soil Microbiology ; }, abstract = {The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform-based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5% to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures.}, }
@article {pmid30565165, year = {2019}, author = {Serena, G and Fasano, A}, title = {Use of Probiotics to Prevent Celiac Disease and IBD in Pediatrics.}, journal = {Advances in experimental medicine and biology}, volume = {1125}, number = {}, pages = {69-81}, doi = {10.1007/5584_2018_317}, pmid = {30565165}, issn = {0065-2598}, support = {R01 DK104344/DK/NIDDK NIH HHS/United States ; }, mesh = {Celiac Disease/*prevention &amp; control ; Child ; Dysbiosis/complications ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*prevention &amp; control ; Pediatrics ; Probiotics/*therapeutic use ; }, abstract = {The incidence of chronic inflammatory diseases (CIDs) is increasing worldwide. Their dramatic rise associated with limited effective strategies to slow down these epidemics calls for a better understanding of their pathophysiology in order to decrease the burdens on childhood. Several cross-sectional studies have demonstrated the association between intestinal dysbiosis and active diseases. Although informative, these studies do not mechanistically link alterations of the microflora with disease pathogenesis and, therefore, with potential therapeutic targets. More prospective studies are needed to determine whether intestinal dysbiosis plays a causative role in the onset and development of CIDs. Furthermore, given the complexity of the microflora interaction with the host, it is necessary to design a systems-level model of interactions between the host and the development of disease by integrating microbiome, metagenomics, metatranscriptomics, and metabolomics with either clinical either environmental data.In this chapter we will discuss the current knowledge regarding the microbiome's contribution to celiac disease and inflammatory bowel disease with a particular focus on how probiotics may be used as potential preventive therapy for CIDs.}, }
@article {pmid30562947, year = {2018}, author = {Ishii, C and Nakanishi, Y and Murakami, S and Nozu, R and Ueno, M and Hioki, K and Aw, W and Hirayama, A and Soga, T and Ito, M and Tomita, M and Fukuda, S}, title = {A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19124079}, pmid = {30562947}, issn = {1422-0067}, support = {15H01522//Japan Society for the Promotion of Science/ ; 16H04901//Japan Society for the Promotion of Science/ ; 17H05654//Japan Society for the Promotion of Science/ ; 18H04805//Japan Society for the Promotion of Science/ ; JPMJPR1537//Japan Science and Technology Agency/ ; }, mesh = {Animals ; *Diet ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metabolome ; *Metagenomics ; Mice ; *Ruminococcus/genetics/growth &amp; development ; }, abstract = {Intestinal microbiota and their metabolites are strongly associated with host physiology. Developments in DNA sequencing and mass spectrometry technologies have allowed us to obtain additional data that enhance our understanding of the interactions among microbiota, metabolites, and the host. However, the strategies used to analyze these datasets are not yet well developed. Here, we describe an original analytical strategy, metabologenomics, consisting of an integrated analysis of mass spectrometry-based metabolome data and high-throughput-sequencing-based microbiome data. Using this approach, we compared data obtained from C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber, to those from mice fed control rodent diet. The feces of the AD mice contained higher amounts of butyrate and propionate, and higher relative abundances of Oscillospira and Ruminococcus. The amount of butyrate positively correlated with the abundance of these bacterial genera. Furthermore, integrated analysis of the metabolome data and the predicted metagenomic data from Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) indicated that the abundance of genes associated with butyrate metabolism positively correlated with butyrate amounts. Thus, our metabologenomic approach is expected to provide new insights and understanding of intestinal metabolic dynamics in complex microbial ecosystems.}, }
@article {pmid30561093, year = {2019}, author = {Cherkasov, SV and Popova, LY and Vivtanenko, TV and Demina, RR and Khlopko, YA and Balkin, AS and Plotnikov, AO}, title = {Oral microbiomes in children with asthma and dental caries.}, journal = {Oral diseases}, volume = {25}, number = {3}, pages = {898-910}, doi = {10.1111/odi.13020}, pmid = {30561093}, issn = {1601-0825}, support = {18-7-8-26//Basic Research Program from the Ural Branch of the Russian Academy of Sciences/ ; }, mesh = {Asthma/*complications/microbiology ; Case-Control Studies ; Child, Preschool ; Computational Biology ; Dental Caries/*complications/microbiology ; Dental Plaque/*microbiology ; Female ; Humans ; Male ; *Microbiota ; Neisseria/isolation &amp; purification ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; Veillonella/isolation &amp; purification ; }, abstract = {OBJECTIVE: Recently, a significant association between dental caries and the severity of bronchial asthma in children has been revealed. This finding indicates a possible relationship between the oral microbiome and the pathogenesis of asthma. The purpose of our study was to estimate differences in the dental plaque microbiota of asthmatic children with and without dental caries by 16S rDNA sequencing.<br><br>MATERIAL AND METHODS: Dental plaque samples were obtained with a spoon excavator from the occlusal surface of one deciduous tooth (the second mandibular left molar in caries-free children and the most affected tooth in caries-affected children). Total DNA was extracted from dental plaque. DNA libraries were analysed by 16S rRNA gene sequencing on the MiSeq (Illumina) platform.<br><br>RESULTS: There were no significant differences in the composition of bacterial communities from both caries-affected and caries-free children with asthma. The &quot;caries-enriched&quot; genus was Veillonella (Veillonellaceae, Selenomonadales, Negativicutes). Relative abundance of Neisseria was significantly higher in caries-free children with asthma (p < 0.05).<br><br>CONCLUSIONS: The most significant difference in compared bacterial communities was a higher relative abundance of Veillonella in caries-affected plaques that suggests its involvement in pathogenesis of caries. Potential respiratory pathogens are present in oral cavity of both caries-affected and caries-free asthmatic children.}, }
@article {pmid30559737, year = {2018}, author = {Gong, Z and Liang, Y and Wang, M and Jiang, Y and Yang, Q and Xia, J and Zhou, X and You, S and Gao, C and Wang, J and He, J and Shao, H and McMinn, A}, title = {Viral Diversity and Its Relationship With Environmental Factors at the Surface and Deep Sea of Prydz Bay, Antarctica.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2981}, doi = {10.3389/fmicb.2018.02981}, pmid = {30559737}, issn = {1664-302X}, abstract = {A viral metagenomic analysis of five surface and two bottom water (878 meters below surface, mbs, and 3,357 mbs) samples from Prydz Bay, was conducted during February-March 2015. The results demonstrated that most of the DNA viruses were dsDNA viruses (79.73-94.06%, except at PBI1, 37.51%). Of these, Caudovirales (Siphoviridae, Myoviridae, and Podoviridae) phages were most abundant in surface seawater (67.67-71.99%), while nucleocytoplasmic large DNA viruses (NCLDVs) (Phycodnaviridae, Mimiviridae, and Pandoraviridae accounted for >30% of dsDNA viruses) were most abundant in the bottom water (3,357 mbs). Of the ssDNA viruses, Microviridae was the dominant family in PBI2, PBI3, PBOs, and PBI4b (57.09-87.55%), while Inoviridae (58.16%) was the dominant family in PBI1. Cellulophaga phages (phi38:1 and phi10:1) and Flavobacterium phage 11b, infecting the possible host strains affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, were abundant in surface water dsDNA viromes. The long contig (PBI2_1_C) from the viral metagenomes were most similar to the genome architectures of Cellulophaga phage phi10:1 and Flavobacterium phage 11b from the Arctic Ocean. Comparative analysis showed that the surface viral community of Prydz Bay could be clearly separated from other marine and freshwater environments. The deep sea viral community was similar to the deep sea viral metagenome at A Long-term Oligotrophic Habitat Assessment Station (ALOHA, at 22°45'N, 158°00'W). The multivariable analysis indicated that nutrients probably played an important role in shaping the local viral community structure. This study revealed the preliminary characteristics of the viral community in Prydz Bay, from both the surface and the deep sea. It provided evidence of the relationships between the virome and the environment in Prydz Bay and provided the first data from the deep sea viral community of the Southern Ocean.}, }
@article {pmid30559407, year = {2019}, author = {Vatanen, T and Plichta, DR and Somani, J and Münch, PC and Arthur, TD and Hall, AB and Rudolf, S and Oakeley, EJ and Ke, X and Young, RA and Haiser, HJ and Kolde, R and Yassour, M and Luopajärvi, K and Siljander, H and Virtanen, SM and Ilonen, J and Uibo, R and Tillmann, V and Mokurov, S and Dorshakova, N and Porter, JA and McHardy, AC and Lähdesmäki, H and Vlamakis, H and Huttenhower, C and Knip, M and Xavier, RJ}, title = {Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.}, journal = {Nature microbiology}, volume = {4}, number = {3}, pages = {470-479}, doi = {10.1038/s41564-018-0321-5}, pmid = {30559407}, issn = {2058-5276}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; UM1 AI110498/AI/NIAID NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Age Factors ; Bacteriophages/genetics ; Bacteroides/genetics/virology ; Bifidobacterium bifidum/genetics ; Bifidobacterium longum/genetics ; Child Development ; Child, Preschool ; Estonia ; Feces/microbiology ; Female ; Finland ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Infant ; Longitudinal Studies ; Male ; Metabolic Networks and Pathways ; Metagenomics ; Polymorphism, Single Nucleotide ; Probiotics ; Russia ; }, abstract = {The human gut microbiome matures towards the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood data sets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides, in which we identified evidence of variability deriving from Bacteroides-targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harboured Bifidobacterium longum subsp. infantis, a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.}, }
@article {pmid30559406, year = {2019}, author = {Kintses, B and Méhi, O and Ari, E and Számel, M and Györkei, Á and Jangir, PK and Nagy, I and Pál, F and Fekete, G and Tengölics, R and Nyerges, Á and Likó, I and Bálint, A and Molnár, T and Bálint, B and Vásárhelyi, BM and Bustamante, M and Papp, B and Pál, C}, title = {Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota.}, journal = {Nature microbiology}, volume = {4}, number = {3}, pages = {447-458}, doi = {10.1038/s41564-018-0313-5}, pmid = {30559406}, issn = {2058-5276}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Antimicrobial Cationic Peptides/*genetics ; Bacteria/*genetics ; Escherichia coli/genetics ; Gastrointestinal Microbiome/*genetics ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome, Bacterial ; Humans ; Metagenomics ; *Phylogeny ; }, abstract = {The human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs), which are ancient components of immune defence. Despite its medical importance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here, we show that AMP resistance and antibiotic resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics have revealed that AMP resistance genes originating from phylogenetically distant bacteria have only a limited potential to confer resistance in Escherichia coli, an intrinsically susceptible species. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota, with implications for disease risks.}, }
@article {pmid30559036, year = {2019}, author = {Freitas, RC and Marques, HIF and Silva, MACD and Cavalett, A and Odisi, EJ and Silva, BLD and Montemor, JE and Toyofuku, T and Kato, C and Fujikura, K and Kitazato, H and Lima, AOS}, title = {Evidence of selective pressure in whale fall microbiome proteins and its potential application to industry.}, journal = {Marine genomics}, volume = {45}, number = {}, pages = {21-27}, doi = {10.1016/j.margen.2018.11.004}, pmid = {30559036}, issn = {1876-7478}, mesh = {Animals ; Atlantic Ocean ; Bacterial Proteins/*genetics/metabolism ; *Metagenome ; *Microbiota ; *Selection, Genetic ; Whales/*microbiology ; }, abstract = {The present study addresses the microbiome of the first whale fall (YOKO 16) that has been described in the deep sea in the southern Atlantic Ocean (São Paulo Plateau; 4204 m depth), in terms of its metabolic uniqueness. Sets of ten thousand protein sequences from YOKO 16 and 29 public domain metagenomes (SRA and GenBank databases) that represent various marine, terrestrial and gut-associated microbial communities were analyzed. The determination of protein functionality, based on the KAAS server, indicated that the YOKO 16 microbiome has industrially-relevant proteins, such as proteases and lipases, that have low similarity (~50%) with previously-described enzymes. The amino acid usage in the YOKO 16 protein sequences (based on blastp and Clustal analysis) revealed a pattern of preference similar to that of extremophiles, with an increased usage of polar, charged and acidic amino acids and a decreased usage of nonpolar residues. We concluded that the targeted microbiome is of potential biotechnological use, which justifies the allocation of resources for the discovery of enzymes in deep-sea whale fall communities.}, }
@article {pmid30558682, year = {2018}, author = {Sirová, D and Bárta, J and Šimek, K and Posch, T and Pech, J and Stone, J and Borovec, J and Adamec, L and Vrba, J}, title = {Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {225}, doi = {10.1186/s40168-018-0600-7}, pmid = {30558682}, issn = {2049-2618}, mesh = {Aquatic Organisms/microbiology/physiology ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Algal/genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Fungi/*classification/genetics/isolation &amp; purification ; Gene Expression Profiling/methods ; Lamiales/*microbiology/physiology ; Metagenomics/*methods ; Microbial Consortia ; Phylogeny ; }, abstract = {BACKGROUND: Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricularia ecophysiology-the interactions with and within the complex communities of microorganisms colonizing their traps and external surfaces.<br><br>RESULTS: Bacteria, fungi, algae, and protozoa inhabit the miniature ecosystem of the Utricularia trap lumen and are involved in the regeneration of nutrients from complex organic matter. By combining molecular methods, microscopy, and other approaches to assess the trap-associated microbial community structure, diversity, function, as well as the nutrient turn-over potential of bacterivory, we gained insight into the nutrient acquisition strategies of the Utricularia hosts.<br><br>CONCLUSIONS: We conclude that Utricularia traps can, in terms of their ecophysiological function, be compared to microbial cultivators or farms, which center around complex microbial consortia acting synergistically to convert complex organic matter, often of algal origin, into a source of utilizable nutrients for the plants.}, }
@article {pmid30552020, year = {2018}, author = {Castellanos, JG and Woo, V and Viladomiu, M and Putzel, G and Lima, S and Diehl, GE and Marderstein, AR and Gandara, J and Perez, AR and Withers, DR and Targan, SR and Shih, DQ and Scherl, EJ and Longman, RS}, title = {Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis.}, journal = {Immunity}, volume = {49}, number = {6}, pages = {1077-1089.e5}, doi = {10.1016/j.immuni.2018.10.014}, pmid = {30552020}, issn = {1097-4180}, support = {R03 DK111852/DK/NIDDK NIH HHS/United States ; K08 DK099381/DK/NIDDK NIH HHS/United States ; UL1 TR002384/TR/NCATS NIH HHS/United States ; R01 AI125264/AI/NIAID NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; K08 DK093578/DK/NIDDK NIH HHS/United States ; R01 DK114252/DK/NIDDK NIH HHS/United States ; R01 DK056328/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Animals ; Colitis/genetics/*immunology/metabolism ; Female ; Humans ; Immunity, Innate/genetics/*immunology ; Interleukins/genetics/immunology/metabolism ; Intestinal Mucosa/immunology/metabolism/microbiology ; Lymphocyte Activation/genetics/immunology ; Lymphocytes/*immunology/metabolism ; Male ; Mice, Inbred C57BL ; Mice, Knockout ; Mice, Transgenic ; Microbiota/*immunology/physiology ; Middle Aged ; Phagocytes/cytology/immunology/metabolism ; T-Lymphocytes/immunology/metabolism ; Tumor Necrosis Factor Ligand Superfamily Member 15/genetics/*immunology/metabolism ; Young Adult ; }, abstract = {Inflammatory bowel disease (IBD) results from a dysregulated interaction between the microbiota and a genetically susceptible host. Genetic studies have linked TNFSF15 polymorphisms and its protein TNF-like ligand 1A (TL1A) with IBD, but the functional role of TL1A is not known. Here, we found that adherent IBD-associated microbiota induced TL1A release from CX3CR1+ mononuclear phagocytes (MNPs). Using cell-specific genetic deletion models, we identified an essential role for CX3CR1+MNP-derived TL1A in driving group 3 innate lymphoid cell (ILC3) production of interleukin-22 and mucosal healing during acute colitis. In contrast to this protective role in acute colitis, TL1A-dependent expression of co-stimulatory molecule OX40L in MHCII+ ILC3s during colitis led to co-stimulation of antigen-specific T cells that was required for chronic T cell colitis. These results identify a role for ILC3s in activating intestinal T cells and reveal a central role for TL1A in promoting ILC3 barrier immunity during colitis.}, }
@article {pmid30545401, year = {2018}, author = {Forbes, JD and Chen, CY and Knox, NC and Marrie, RA and El-Gabalawy, H and de Kievit, T and Alfa, M and Bernstein, CN and Van Domselaar, G}, title = {A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {221}, doi = {10.1186/s40168-018-0603-4}, pmid = {30545401}, issn = {2049-2618}, mesh = {Adult ; Arthritis, Rheumatoid/microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Case-Control Studies ; Colitis, Ulcerative/microbiology ; Crohn Disease/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dysbiosis/*diagnosis ; Female ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Machine Learning ; Male ; Metagenomics/*methods ; Middle Aged ; Multiple Sclerosis/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology is common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of the gut microbiome in IMIDs. This study used 16S rRNA gene amplicon sequencing to compare the gut microbiota of patients with Crohn's disease (CD; N = 20), ulcerative colitis (UC; N = 19), multiple sclerosis (MS; N = 19), and rheumatoid arthritis (RA; N = 21) versus healthy controls (HC; N = 23). Biological replicates were collected from participants within a 2-month interval. This study aimed to identify common (or unique) taxonomic biomarkers of IMIDs using both differential abundance testing and a machine learning approach.<br><br>RESULTS: Significant microbial community differences between cohorts were observed (pseudo F = 4.56; p = 0.01). Richness and diversity were significantly different between cohorts (pFDR < 0.001) and were lowest in CD while highest in HC. Abundances of Actinomyces, Eggerthella, Clostridium III, Faecalicoccus, and Streptococcus (pFDR < 0.001) were significantly higher in all disease cohorts relative to HC, whereas significantly lower abundances were observed for Gemmiger, Lachnospira, and Sporobacter (pFDR < 0.001). Several taxa were found to be differentially abundant in IMIDs versus HC including significantly higher abundances of Intestinibacter in CD, Bifidobacterium in UC, and unclassified Erysipelotrichaceae in MS and significantly lower abundances of Coprococcus in CD, Dialister in MS, and Roseburia in RA. A machine learning approach to classify disease versus HC was highest for CD (AUC = 0.93 and AUC = 0.95 for OTU and genus features, respectively) followed by MS, RA, and UC. Gemmiger and Faecalicoccus were identified as important features for classification of subjects to CD and HC. In general, features identified by differential abundance testing were consistent with machine learning feature importance.<br><br>CONCLUSIONS: This study identified several gut microbial taxa with differential abundance patterns common to IMIDs. We also found differentially abundant taxa between IMIDs. These taxa may serve as biomarkers for the detection and diagnosis of IMIDs and suggest there may be a common component to IMID etiology.}, }
@article {pmid30543873, year = {2019}, author = {Lima, DA and Cibulski, SP and Tochetto, C and Varela, APM and Finkler, F and Teixeira, TF and Loiko, MR and Cerva, C and Junqueira, DM and Mayer, FQ and Roehe, PM}, title = {The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics.}, journal = {Virus research}, volume = {261}, number = {}, pages = {9-20}, doi = {10.1016/j.virusres.2018.12.005}, pmid = {30543873}, issn = {1872-7492}, mesh = {Animals ; Chickens ; Feces/*virology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Malabsorption Syndromes/*veterinary/virology ; Metagenomics ; Poultry Diseases/*virology ; Viruses/*classification/*genetics ; }, abstract = {Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated. Through analysis of de novo assembled contigs, 144 contigs > 1000 nt were identified with hits to eukaryotic viral sequences, as determined by GenBank database. A number of known and unknown representatives of Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, as well as novel uncharacterized CRESS-DNA viruses, were identified. However, the distribution of sequence reads of viral genomes identified in diseased or healthy birds revealed no statistically significant differences. These findings indicate no association between the occurrence of MAS and enteric viruses. The viral genomes reported in the present study, including a variety of novel viruses, seem part of the normal intestinal microbiota of chickens.}, }
@article {pmid30522530, year = {2018}, author = {Edlund, A and Yang, Y and Yooseph, S and He, X and Shi, W and McLean, JS}, title = {Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {217}, pmid = {30522530}, issn = {2049-2618}, support = {R01 DE026186/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 GM095373/GM/NIGMS NIH HHS/United States ; K99 DE024543/DE/NIDCR NIH HHS/United States ; R00 DE024543/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Bacteria/*classification/genetics/growth &amp; development ; Bacterial Proteins/genetics ; Biofilms ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dental Plaque/*microbiology ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; Humans ; Hydrogen-Ion Concentration ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, 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 {pmid30537931, year = {2018}, author = {Benavides, A and Isaza, JP and Niño-García, JP and Alzate, JF and Cabarcas, F}, title = {CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes.}, journal = {BMC genomics}, volume = {19}, number = {Suppl 8}, pages = {858}, pmid = {30537931}, issn = {1471-2164}, mesh = {*Algorithms ; Colombia ; Genes, Bacterial ; Genetic Markers ; *Genome, Bacterial ; *Metagenomics ; Microbiota ; Phylogeny ; Sequence Analysis, DNA/*methods ; Xanthomonadaceae/*classification/*genetics ; }, abstract = {BACKGROUND: Hot spring bacteria have unique biological adaptations to survive the extreme conditions of these environments; these bacteria produce thermostable enzymes that can be used in biotechnological and industrial applications. However, sequencing these bacteria is complex, since it is not possible to culture them. As an alternative, genome shotgun sequencing of whole microbial communities can be used. The problem is that the classification of sequences within a metagenomic dataset is very challenging particularly when they include unknown microorganisms since they lack genomic reference. We failed to recover a bacterium genome from a hot spring metagenome using the available software tools, so we develop a new tool that allowed us to recover most of this genome.<br><br>RESULTS: We present a proteobacteria draft genome reconstructed from a Colombian's Andes hot spring metagenome. The genome seems to be from a new lineage within the family Rhodanobacteraceae of the class Gammaproteobacteria, closely related to the genus Dokdonella. We were able to generate this genome thanks to CLAME. CLAME, from Spanish &quot;CLAsificador MEtagenomico&quot;, is a tool to group reads in bins. We show that most reads from each bin belong to a single chromosome. CLAME is very effective recovering most of the reads belonging to the predominant species within a metagenome.<br><br>CONCLUSIONS: We developed a tool that can be used to extract genomes (or parts of them) from a complex metagenome.}, }
@article {pmid30535578, year = {2019}, author = {Zhang, F and Zheng, W and Xue, Y and Yao, W}, title = {Suhuai suckling piglet hindgut microbiome-metabolome responses to different dietary copper levels.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {2}, pages = {853-868}, doi = {10.1007/s00253-018-9533-0}, pmid = {30535578}, issn = {1432-0614}, support = {JATS[2018]287//The earmarked fund for Jiangsu Agricultural Industry Technology System/ ; 31372321//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Animals, Newborn ; Blood Chemical Analysis ; Copper/*administration &amp; dosage ; Diet/*methods ; Feces/chemistry ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Metabolome/*drug effects ; Metabolomics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Swine ; Trace Elements/*administration &amp; dosage ; }, abstract = {Unabsorbed copper accumulates in the hindgut of pigs that consume high levels of dietary copper, which enhances the coselection of antibiotic-resistant bacteria and is considered detrimental to the environment and to porcine health. In our study, a combination of 16S rRNA pyrosequencing and nontargeted metabolomics was used to investigate the microbiome-metabolome responses to dietary copper levels in the hindgut of suckling piglets. The results showed that the dietary copper level affected the abundance of several Clostridia genera and that the relative abundance of butyrate-producing bacteria, such as Coprococcus, Roseburia, and Acidaminococcus, was reduced in the 300 mg kg-1 (high) Cu group. Metabolomic analysis revealed that dietary copper levels affected protein and carbohydrate metabolites, protein biosynthesis, the urea cycle, galactose metabolism, gluconeogenesis, and amino acid metabolism (including the metabolism of arginine, proline, β-alanine, phenylalanine, tyrosine, and methionine). Furthermore, Pearson's correlation analysis showed that the abundance levels of Coprococcus (family Lachnospiraceae) and operational taxonomic unit (OTU) 18 (family Ruminococcaceae) were positively correlated with energy metabolism pathways (gluconeogenesis, glycolysis, and the pentose phosphate pathway). The abundance of Streptococcus was negatively correlated with amino acid metabolism pathways (protein biosynthesis, glycine, serine, threonine, methionine, phenylalanine, and tyrosine metabolism), and OTU583 and OTU1067 (family Rikenellaceae) were positively correlated with amino acid metabolism pathways. These results suggest that the copper levels consumed by LC (low-copper group) versus HC (high-copper group) animals alter the composition of the gut microbiota and modulate microbial metabolic pathways, which may further affect the health of suckling piglets.}, }
@article {pmid30532085, year = {2018}, author = {Chen, B and Yu, T and Xie, S and Du, K and Liang, X and Lan, Y and Sun, C and Lu, X and Shao, Y}, title = {Comparative shotgun metagenomic data of the silkworm Bombyx mori gut microbiome.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180285}, pmid = {30532085}, issn = {2052-4463}, mesh = {Acinetobacter/genetics ; Animals ; Bombyx/*microbiology ; Enterobacter/genetics ; Enterococcus/genetics ; *Gastrointestinal Microbiome ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; }, 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 {pmid30529583, year = {2019}, author = {Paramsothy, S and Nielsen, S and Kamm, MA and Deshpande, NP and Faith, JJ and Clemente, JC and Paramsothy, R and Walsh, AJ and van den Bogaerde, J and Samuel, D and Leong, RWL and Connor, S and Ng, W and Lin, E and Borody, TJ and Wilkins, MR and Colombel, JF and Mitchell, HM and Kaakoush, NO}, title = {Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis.}, journal = {Gastroenterology}, volume = {156}, number = {5}, pages = {1440-1454.e2}, doi = {10.1053/j.gastro.2018.12.001}, pmid = {30529583}, issn = {1528-0012}, mesh = {Bacteria/classification/genetics/growth &amp; development/*metabolism ; Biomarkers/metabolism ; Colitis, Ulcerative/diagnosis/microbiology/*therapy ; Double-Blind Method ; Fecal Microbiota Transplantation/adverse effects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metabolomics ; New South Wales ; Remission Induction ; Ribotyping ; Time Factors ; Treatment Outcome ; }, abstract = {BACKGROUND &amp; AIMS: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy.<br><br>METHODS: We performed a double-blind trial of 81 patients with active UC randomly assigned to groups that received an initial colonoscopic infusion and then intensive multidonor FMT or placebo enemas, 5 d/wk for 8 weeks. Patients in the FMT group received blended homogenized stool from 3-7 unrelated donors. Patients in the placebo group were eligible to receive open-label FMT after the double-blind study period. We collected 314 fecal samples from the patients at screening, every 4 weeks during treatment, and 8 weeks after the blinded or open-label FMT therapy. We also collected 160 large-bowel biopsy samples from the patients at study entry, at completion of 8 weeks of blinded therapy, and at the end of open-label FMT, if applicable. We analyzed 105 fecal samples from the 14 individual donors (n = 55), who in turn contributed to 21 multidonor batches (n = 50). Bacteria in colonic and fecal samples were analyzed by both 16S ribosomal RNA gene and transcript amplicon sequencing; 285 fecal samples were analyzed by shotgun metagenomics, and 60 fecal samples were analyzed for metabolome features.<br><br>RESULTS: FMT increased microbial diversity and altered composition, based on analyses of colon and fecal samples collected before vs after FMT. Diversity was greater in fecal and colon samples collected before and after FMT treatment from patients who achieved remission compared with patients who did not. Patients in remission after FMT had enrichment of Eubacterium hallii and Roseburia inulivorans compared with patients who did not achieve remission after FMT and had increased levels of short-chain fatty acid biosynthesis and secondary bile acids. Patients who did not achieve remission had enrichment of Fusobacterium gonidiaformans, Sutterella wadsworthensis, and Escherichia species and increased levels of heme and lipopolysaccharide biosynthesis. Bacteroides in donor stool were associated with remission in patients receiving FMT, and Streptococcus species in donor stool was associated with no response to FMT.<br><br>CONCLUSIONS: In an analysis of fecal and colonic mucosa samples from patients receiving FMT for active UC and stool samples from donors, we associated specific bacteria and metabolic pathways with induction of remission. These findings may be of value in the design of microbe-based therapies for UC. ClinicalTrials.gov, Number NCT01896635.}, }
@article {pmid30528276, year = {2019}, author = {Ramos-Barbero, MD and Martin-Cuadrado, AB and Viver, T and Santos, F and Martinez-Garcia, M and Antón, J}, title = {Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {1}, pages = {30-40}, doi = {10.1016/j.syapm.2018.11.001}, pmid = {30528276}, issn = {1618-0984}, mesh = {Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; *Genome, Microbial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; *Salinity ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next generation sequencing, are democratizing this powerful approach that is spreading from specialized research groups to the general public. Using metagenomes from hypersaline environments, as well as mock metagenomes composed of Archaea and Bacteria frequently found in these systems, we have analyzed the advantages and difficulties of the binning process in these extreme environments to tackle microbial population diversity. These extreme systems harbor relatively low species diversity but high intraspecific diversity, which can compromise metagenome assembly and therefore the whole binning process. The main goal is to compare the output of the binning process with what is previously known from the analyzed samples, based on years of study using different approaches. Several scenarios have been analyzed in detail: (i) a good quality bin from a species highly abundant in the environment; (ii) an intermediate quality bin with incongruences that can be solved by further analyses and manual curation, and (iii) a low-quality bin to investigate the failure to recover a very abundant microbial genome as well as some possible solutions. The latter can be considered the &quot;great metagenomics anomaly&quot; and is mainly due to assembly problems derived from the microdiversity of naturally co-existing populations in nature.}, }
@article {pmid30526624, year = {2018}, author = {Wu, G and Niu, M and Tang, W and Hu, J and Wei, G and He, Z and Chen, Y and Jiang, Y and Chen, P}, title = {L-Fucose ameliorates high-fat diet-induced obesity and hepatic steatosis in mice.}, journal = {Journal of translational medicine}, volume = {16}, number = {1}, pages = {344}, pmid = {30526624}, issn = {1479-5876}, support = {2016A030306043//Natural Science Foundation of Guangdong Province/International ; 2017B030314034//Natural Science Foundation of Guangdong Province/International ; 2016A020216015//China Association for Science and Technology/International ; }, mesh = {Adiposity/drug effects ; Animals ; Cecum/drug effects/microbiology ; *Diet, High-Fat ; Dysbiosis/complications/microbiology/pathology ; Feeding Behavior ; Fucose/pharmacology/*therapeutic use ; Gastrointestinal Microbiome/drug effects ; Glucose Tolerance Test ; Insulin ; Metagenomics ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*complications/*drug therapy/microbiology ; Obesity/*complications/*drug therapy/microbiology ; Weight Gain/drug effects ; }, abstract = {BACKGROUND: L-Fucose (Fuc), a six-deoxy hexose monosaccharide, is present endogenously in humans and animals and has a wide range of biological functions. In the present study, we aimed to examine the effect of Fuc on obesity and hepatic steatosis in mice fed a high-fat diet (HFD).<br><br>METHODS: C57BL/6 mice were fed a normal chow (NC) or HFD for 18 weeks to induce obesity and fatty liver. Fuc was administered intragastrically from the 8th week to the end of the experiment (18 weeks).<br><br>RESULTS: Metagenomic analysis showed that HFD altered the genomic profile of gut microbiota in the mice; specifically, expression of alpha-L-fucosidase, the gene responsible for Fuc generation, was markedly reduced in the HFD group compared with that in the NC group. Fuc treatment decreased body weight gain, fat accumulation, and hepatic triglyceride elevation in HFD-fed mice. In addition, Fuc decreased the levels of endotoxin-producing bacteria of the Desulfovibrionaceae family and restored HFD-induced enteric dysbiosis at both compositional and functional levels.<br><br>CONCLUSION: Our findings suggest that Fuc might be a novel strategy to treat HFD-induced obesity and fatty liver.}, }
@article {pmid30525950, year = {2019}, author = {Hibberd, AA and Yde, CC and Ziegler, ML and Honoré, AH and Saarinen, MT and Lahtinen, S and Stahl, B and Jensen, HM and Stenman, LK}, title = {Probiotic or synbiotic alters the gut microbiota and metabolism in a randomised controlled trial of weight management in overweight adults.}, journal = {Beneficial microbes}, volume = {10}, number = {2}, pages = {121-135}, doi = {10.3920/BM2018.0028}, pmid = {30525950}, issn = {1876-2891}, mesh = {Adult ; Aged ; Bacteria/classification/metabolism ; Body Fat Distribution ; Double-Blind Method ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; Metagenomics ; *Microbiota ; Middle Aged ; Obesity/*therapy ; Overweight/*therapy ; Placebos/administration &amp; dosage ; Probiotics/*administration &amp; dosage ; Synbiotics/*administration &amp; dosage ; Treatment Outcome ; }, abstract = {The gut microbiota contributes to host energy metabolism, and altered gut microbiota has been associated with obesity-related metabolic disorders. We previously reported that a probiotic alone or together with a prebiotic controls body fat mass in healthy overweight or obese individuals in a randomised, double-blind, placebo controlled clinical study (ClinicalTrials.gov NCT01978691). We now aimed to investigate whether changes in the gut microbiota may be associated with the observed clinical benefits. Faecal and plasma samples were obtained from a protocol compliant subset (n=134) of participants from a larger clinical study where participants were randomised (1:1:1:1) into four groups: (1) placebo, 12 g/d microcrystalline cellulose; (2) Litesse® Ultra™ polydextrose (LU), 12 g/day; (3) Bifidobacterium animalis subsp. lactis 420™ (B420), 1010 cfu/d in 12 g microcrystalline cellulose; (4) LU+B420, 1010 cfu/d of B420 in 12 g/d LU for 6 months of intervention. The faecal microbiota composition and metabolites were assessed as exploratory outcomes at baseline, 2, 4, 6 months, and +1 month post-intervention and correlated to obesity-related clinical outcomes. Lactobacillus and Akkermansia were more abundant with B420 at the end of the intervention. LU+B420 increased Akkermansia, Christensenellaceae and Methanobrevibacter, while Paraprevotella was reduced. Christensenellaceae was consistently increased in the LU and LU+B420 groups across the intervention time points, and correlated negatively to waist-hip ratio and energy intake at baseline, and waist-area body fat mass after 6 months treatment with LU+B420. Functional metagenome predictions indicated alterations in pathways related to cellular processes and metabolism. Plasma bile acids glycocholic acid, glycoursodeoxycholic acid, and taurohyodeoxycholic acid and tauroursodeoxycholic acid were reduced in LU+B420 compared to Placebo. Consumption of B420 and its combination with LU resulted in alterations of the gut microbiota and its metabolism, and may support improved gut barrier function and obesity-related markers.}, }
@article {pmid30521551, year = {2018}, author = {Vernocchi, P and Del Chierico, F and Russo, A and Majo, F and Rossitto, M and Valerio, M and Casadei, L and La Storia, A and De Filippis, F and Rizzo, C and Manetti, C and Paci, P and Ercolini, D and Marini, F and Fiscarelli, EV and Dallapiccola, B and Lucidi, V and Miccheli, A and Putignani, L}, title = {Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208171}, doi = {10.1371/journal.pone.0208171}, pmid = {30521551}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/adverse effects ; Bacteria/*isolation &amp; purification ; Child, Preschool ; Cohort Studies ; Cystic Fibrosis/drug therapy/genetics/*physiopathology ; Cystic Fibrosis Transmembrane Conductance Regulator/*genetics ; Dysbiosis/microbiology/physiopathology ; Exocrine Pancreatic Insufficiency/genetics/physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*physiology ; Host Microbial Interactions/physiology ; Humans ; Intestinal Mucosa/microbiology/*physiopathology ; Male ; Metabolomics ; Metagenomics ; Phenotype ; }, abstract = {BACKGROUND: Cystic fibrosis (CF) is a disorder affecting the respiratory, digestive, reproductive systems and sweat glands. This lethal hereditary disease has known or suspected links to the dysbiosis gut microbiota. High-throughput meta-omics-based approaches may assist in unveiling this complex network of symbiosis modifications.<br><br>OBJECTIVES: The aim of this study was to provide a predictive and functional model of the gut microbiota enterophenotype of pediatric patients affected by CF under clinical stability.<br><br>METHODS: Thirty-one fecal samples were collected from CF patients and healthy children (HC) (age range, 1-6 years) and analysed using targeted-metagenomics and metabolomics to characterize the ecology and metabolism of CF-linked gut microbiota. The multidimensional data were low fused and processed by chemometric classification analysis.<br><br>RESULTS: The fused metagenomics and metabolomics based gut microbiota profile was characterized by a high abundance of Propionibacterium, Staphylococcus and Clostridiaceae, including Clostridium difficile, and a low abundance of Eggerthella, Eubacterium, Ruminococcus, Dorea, Faecalibacterium prausnitzii, and Lachnospiraceae, associated with overexpression of 4-aminobutyrate (GABA), choline, ethanol, propylbutyrate, and pyridine and low levels of sarcosine, 4-methylphenol, uracil, glucose, acetate, phenol, benzaldehyde, and methylacetate. The CF gut microbiota pattern revealed an enterophenotype intrinsically linked to disease, regardless of age, and with dysbiosis uninduced by reduced pancreatic function and only partially related to oral antibiotic administration or lung colonization/infection.<br><br>CONCLUSIONS: All together, the results obtained suggest that the gut microbiota enterophenotypes of CF, together with endogenous and bacterial CF biomarkers, are direct expression of functional alterations at the intestinal level. Hence, it's possible to infer that CFTR impairment causes the gut ecosystem imbalance.This new understanding of CF host-gut microbiota interactions may be helpful to rationalize novel clinical interventions to improve the affected children's nutritional status and intestinal function.}, }
@article {pmid30518415, year = {2018}, author = {Alonso, L and Creuzé-des-Châtelliers, C and Trabac, T and Dubost, A and Moënne-Loccoz, Y and Pommier, T}, title = {Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {216}, pmid = {30518415}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Carbon Dioxide/analysis ; Caves/*microbiology ; DNA, Fungal/genetics ; France ; Fungi/*classification/genetics/isolation &amp; purification ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing ; Human Activities ; Humans ; Metagenomics ; Microbiota ; Phylogeny ; Seasons ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The World-famous UNESCO heritage from the Paleolithic human society, Lascaux Cave (France), has endeavored intense microclimatic perturbations, in part due to high touristic pressure. These perturbations have resulted in numerous disturbances of the cave ecosystem, including on its microbial compartment, which resulted in the formation of black stains especially on the rock faces of the passage. We investigated the cave microbiome in this part of Lascaux by sampling three mineral substrates (soil, banks, and inclined planes) on and outside stains to assess current cave microbial assemblage and explore the possibility that pigmented microorganisms involved in stain development occur as microbial consortia.<br><br>METHODS: Microbial abundance and diversity were assessed by means of quantitative PCR and high-throughput sequencing (Illumina MiSeq) of several DNA and cDNA taxonomic markers. Five sampling campaigns were carried out during winter and summer to embrace potential seasonal effect in this somewhat stable environment (based on measurements of temperature and CO2 concentration).<br><br>RESULTS: While the season or type of mineral substrate did not affect the abundances of bacteria and micro-eukaryotes on or outside stains, mineral substrate rather than stain presence appears to be the most significant factor determining microbial diversity and structuring microbial community, regardless of whether DNA or cDNA markers were considered. A phylogenetic signal was also detected in relation to substrate types, presence of stains but not with season among the OTUs common to the three substrates. Co-occurrence network analyses showed that most bacterial and fungal interactions were positive regardless of the factor tested (season, substrate, or stain), but these networks varied according to ecological conditions and time. Microorganisms known to harbor pigmentation ability were well established inside but also outside black stains, which may be prerequisite for subsequent stain formation.<br><br>CONCLUSIONS: This first high throughput sequencing performed in Lascaux Cave showed that black stains were secondary to mineral substrate in determining microbiome community structure, regardless of whether total or transcriptionally active bacterial and micro-eukaryotic communities were considered. These results revealed the potential for new stain formation and highlight the need for careful microbiome management to avoid further cave wall degradation.}, }
@article {pmid30518356, year = {2018}, author = {Bin, P and Tang, Z and Liu, S and Chen, S and Xia, Y and Liu, J and Wu, H and Zhu, G}, title = {Intestinal microbiota mediates Enterotoxigenic Escherichia coli-induced diarrhea in piglets.}, journal = {BMC veterinary research}, volume = {14}, number = {1}, pages = {385}, pmid = {30518356}, issn = {1746-6148}, mesh = {Animals ; Bacteria/classification/genetics ; Diarrhea/microbiology/*veterinary ; Dysbiosis/immunology/microbiology/*veterinary ; Enterotoxigenic Escherichia coli/immunology/physiology ; Escherichia coli Infections/veterinary ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*genetics/*immunology ; Intestinal Diseases/immunology/microbiology/*veterinary ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Swine ; Swine Diseases/immunology/*microbiology ; }, abstract = {BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) causes diarrhea in humans, cows, and pigs. The gut microbiota underlies pathology of several infectious diseases yet the role of the gut microbiota in the pathogenesis of ETEC-induced diarrhea is unknown.<br><br>RESULTS: By using an ETEC induced diarrheal model in piglet, we profiled the jejunal and fecal microbiota using metagenomics and 16S rRNA sequencing. A jejunal microbiota transplantation experiment was conducted to determine the role of the gut microbiota in ETEC-induced diarrhea. ETEC-induced diarrhea influenced the structure and function of gut microbiota. Diarrheal piglets had lower Bacteroidetes: Firmicutes ratio and microbiota diversity in the jejunum and feces, and lower percentage of Prevotella in the feces, but higher Lactococcus in the jejunum and higher Escherichia-Shigella in the feces. The transplantation of the jejunal microbiota from diarrheal piglets to uninfected piglets leaded to diarrhea after transplantation. Microbiota transplantation experiments also supported the notion that dysbiosis of gut microbiota is involved in the immune responses in ETEC-induced diarrhea.<br><br>CONCLUSION: We conclude that ETEC infection influences the gut microbiota and the dysbiosis of gut microbiota after ETEC infection mediates the immune responses in ETEC infection.}, }
@article {pmid30518125, year = {2018}, author = {Raimundo, I and Silva, SG and Costa, R and Keller-Costa, T}, title = {Bioactive Secondary Metabolites from Octocoral-Associated Microbes-New Chances for Blue Growth.}, journal = {Marine drugs}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/md16120485}, pmid = {30518125}, issn = {1660-3397}, support = {EXPL/MAR-EST/1664/2013//Fundação para a Ciência e a Tecnologia/ ; PTDC/MAR-BIO/1547/2014//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/genetics/*metabolism ; Biological Products/isolation &amp; purification/metabolism/*pharmacology ; Biosynthetic Pathways/*genetics ; Fungi/genetics/*metabolism ; Industrial Microbiology/methods ; Microbiota/physiology ; Multigene Family ; Symbiosis ; Technology, Pharmaceutical/methods ; }, abstract = {Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. However, mechanistic understanding of the contribution of microbial symbionts to the chemical diversity of octocorals is yet to be achieved. This review inventories the natural products so-far described for octocoral-derived bacteria and fungi, uncovering a true chemical arsenal of terpenes, steroids, alkaloids, and polyketides with antibacterial, antifungal, antiviral, antifouling, anticancer, anti-inflammatory, and antimalarial activities of enormous potential for blue growth. Genome mining of 15 bacterial associates (spanning 12 genera) cultivated from Eunicella spp. resulted in the identification of 440 putative and classifiable secondary metabolite biosynthetic gene clusters (BGCs), encompassing varied terpene-, polyketide-, bacteriocin-, and nonribosomal peptide-synthase BGCs. This points towards a widespread yet uncharted capacity of octocoral-associated bacteria to synthetize a broad range of natural products. However, to extend our knowledge and foster the near-future laboratory production of bioactive compounds from (cultivatable and currently uncultivatable) octocoral symbionts, optimal blending between targeted metagenomics, DNA recombinant technologies, improved symbiont cultivation, functional genomics, and analytical chemistry are required. Such a multidisciplinary undertaking is key to achieving a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties.}, }
@article {pmid30507071, year = {2019}, 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 = {11}, number = {2}, pages = {206-214}, doi = {10.1111/1758-2229.12724}, pmid = {30507071}, issn = {1758-2229}, support = {BB/L021471/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Genome, Fungal/genetics ; Italy ; Metagenomics/*methods ; Saccharomyces/classification/*genetics/isolation &amp; purification ; Saccharomyces cerevisiae/classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; *Soil Microbiology ; Trees ; }, abstract = {The species of the genus Saccharomyces are commonly inhabiting tree bark and the surrounding soil, but their abundance have likely been underestimated due to biases in culturing methods. Metagenomic studies have so far been unable to detect Saccharomyces species in wild environments. Here, we sequenced the mycobiome of soils surrounding different trees at various altitudes in the Italian Alps. To survey for yeasts species belonging to Saccharomyces genus rather than other fungal species, we performed a selectivity step involving the isolation of the internal transcribed spacer (ITS) region that is specific to this yeast group. Reads mapping to Saccharomyces species were detected in all soil samples, including reads for S. mikatae and for S. eubayanus. ITS1 alignment of the S. cerevisiae, S. paradoxus and S. kudriavzevii sequences showed up to three base pair polymorphisms with other known strains, indicating possible new lineages. Basidiomycetous fungi were still the dominant species, compared to the Ascomycota, but the selectivity step allowed for the first time the detection and study of the biodiversity of the Saccharomyces species in their natural environment.}, }
@article {pmid30504906, year = {2018}, author = {Wampach, L and Heintz-Buschart, A and Fritz, JV and Ramiro-Garcia, J and Habier, J and Herold, M and Narayanasamy, S and Kaysen, A and Hogan, AH and Bindl, L and Bottu, J and Halder, R and Sjöqvist, C and May, P and Andersson, AF and de Beaufort, C and Wilmes, P}, title = {Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5091}, doi = {10.1038/s41467-018-07631-x}, pmid = {30504906}, issn = {2041-1723}, mesh = {Cesarean Section ; Delivery, Obstetric ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; In Vitro Techniques ; Infant, Newborn ; Infectious Disease Transmission, Vertical ; Interleukin-18/metabolism ; Lipopolysaccharides/metabolism ; Metagenomics/methods ; Pregnancy ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {The rate of caesarean section delivery (CSD) is increasing worldwide. It remains unclear whether disruption of mother-to-neonate transmission of microbiota through CSD occurs and whether it affects human physiology. Here we perform metagenomic analysis of earliest gut microbial community structures and functions. We identify differences in encoded functions between microbiomes of vaginally delivered (VD) and CSD neonates. Several functional pathways are over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis. We link these enriched functions to individual-specific strains, which are transmitted from mothers to neonates in case of VD. The stimulation of primary human immune cells with LPS isolated from early stool samples of VD neonates results in higher levels of tumour necrosis factor (TNF-α) and interleukin 18 (IL-18). Accordingly, the observed levels of TNF-α and IL-18 in neonatal blood plasma are higher after VD. Taken together, our results support that CSD disrupts mother-to-neonate transmission of specific microbial strains, linked functional repertoires and immune-stimulatory potential during a critical window for neonatal immune system priming.}, }
@article {pmid30504642, year = {2019}, author = {Nakagawa, T and Tsuchiya, Y and Ueda, S and Fukui, M and Takahashi, R}, title = {Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan.}, journal = {Microbes and environments}, volume = {34}, number = {1}, pages = {13-22}, doi = {10.1264/jsme2.ME18103}, pmid = {30504642}, issn = {1347-4405}, mesh = {Ammonia/metabolism ; Archaea/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Geologic Sediments/*microbiology ; Japan ; Lakes/*microbiology ; Metagenomics ; *Microbiota/genetics ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics ; *Saline Waters ; *Water Microbiology ; Zosteraceae/*microbiology ; }, abstract = {Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.}, }
@article {pmid30504145, year = {2018}, author = {Tokuda, G and Mikaelyan, A and Fukui, C and Matsuura, Y and Watanabe, H and Fujishima, M and Brune, A}, title = {Fiber-associated spirochetes are major agents of hemicellulose degradation in the hindgut of wood-feeding higher termites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {51}, pages = {E11996-E12004}, doi = {10.1073/pnas.1810550115}, pmid = {30504145}, issn = {1091-6490}, mesh = {Animals ; Cellulases/genetics/metabolism ; Cellulose/metabolism ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Gene Expression Regulation, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Glycoside Hydrolases/genetics/metabolism ; Isoptera/*microbiology ; Metagenome/genetics ; Metagenomics ; Phylogeny ; Polysaccharides/*metabolism ; Sequence Analysis, DNA ; Spirochaetales/*enzymology/*genetics/*metabolism ; Symbiosis ; Wood/*metabolism ; Xylans/metabolism ; Xylosidases/classification/genetics/metabolism ; }, abstract = {Symbiotic digestion of lignocellulose in wood-feeding higher termites (family Termitidae) is a two-step process that involves endogenous host cellulases secreted in the midgut and a dense bacterial community in the hindgut compartment. The genomes of the bacterial gut microbiota encode diverse cellulolytic and hemicellulolytic enzymes, but the contributions of host and bacterial symbionts to lignocellulose degradation remain ambiguous. Our previous studies of Nasutitermes spp. documented that the wood fibers in the hindgut paunch are consistently colonized not only by uncultured members of Fibrobacteres, which have been implicated in cellulose degradation, but also by unique lineages of Spirochaetes. Here, we demonstrate that the degradation of xylan, the major component of hemicellulose, is restricted to the hindgut compartment, where it is preferentially hydrolyzed over cellulose. Metatranscriptomic analysis documented that the majority of glycoside hydrolase (GH) transcripts expressed by the fiber-associated bacterial community belong to family GH11, which consists exclusively of xylanases. The substrate specificity was further confirmed by heterologous expression of the gene encoding the predominant homolog. Although the most abundant transcripts of GH11 in Nasutitermes takasagoensis were phylogenetically placed among their homologs of Firmicutes, immunofluorescence microscopy, compositional binning of metagenomics contigs, and the genomic context of the homologs indicated that they are encoded by Spirochaetes and were most likely obtained by horizontal gene transfer among the intestinal microbiota. The major role of spirochetes in xylan degradation is unprecedented and assigns the fiber-associated Treponema clades in the hindgut of wood-feeding higher termites a prominent part in the breakdown of hemicelluloses.}, }
@article {pmid30503454, year = {2018}, author = {Hwang, J and Park, SY and Lee, S and Lee, TK}, title = {High diversity and potential translocation of DNA viruses in ballast water.}, journal = {Marine pollution bulletin}, volume = {137}, number = {}, pages = {449-455}, doi = {10.1016/j.marpolbul.2018.10.053}, pmid = {30503454}, issn = {1879-3363}, mesh = {Animals ; DNA Viruses/*genetics/*isolation &amp; purification ; Introduced Species ; Metagenomics ; Mexico ; New York ; Panama ; Republic of Korea ; Saudi Arabia ; *Ships ; Water/*analysis/chemistry ; Water Microbiology ; }, abstract = {Ballast water is a common vector for the transport of invasive species to new marine and aquatic environments. We used a metagenomics approach to examine the composition and diversity of viral communities in ballast water from ships originating in Mexico, Saudi Arabia, New York, and Panama, and in water from the port of their destination in Busan, Korea. Myoviridae was the most abundant virus family in ballast water, followed Podoviridae and Siphoviridae. We also identified viruses that infect invertebrates, amoebas, and algae in ballast water and in the Busan port water. Interestingly, there were several viruses that infect humans or other animals (Swinepox virus, Raccoonpox virus, Suid herpesvirus, and Human endogenous retrovirus) in the samples from New York and Panama. In addition, there were giant viruses in all the ballast water samples, especially, identified Megavirus chilensis in New York and Panama, and Pandoravirus salinus in Mexico and Saudi Arabia. These results provide detailed descriptions of the characteristics of the viruses present in ballast water, document significant viral diversity, and indicate the potential translocation of viruses via ballast water.}, }
@article {pmid30502941, year = {2018}, author = {Foutel-Rodier, T and Thierry, A and Koszul, R and Marbouty, M}, title = {Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut Microbiota.}, journal = {Methods in enzymology}, volume = {612}, number = {}, pages = {183-195}, doi = {10.1016/bs.mie.2018.08.001}, pmid = {30502941}, issn = {1557-7988}, mesh = {Animals ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/*genetics ; Metagenomics/*methods ; Sequence Analysis, DNA/methods ; }, abstract = {Microbial species thrive in very diverse environments and play fundamental roles in their equilibrium and dynamics. Metagenomics consists in extracting, sequencing, and studying the DNA present in ecosystems to better understand their regulation. Ideally, the maximal amount of information would be gathered from the full sequences of the genomes, episomes, and phages present in the microbial communities. Current high-throughput DNA sequencing produces reads ranging in size from a few dozen base pairs for the most commonly used technologies to several kb for emerging single-molecule real-time sequencing techniques. Although valuable information can be extracted from processing these DNA sequences into contigs, reconstructing full genomes remains a difficult task. Clustering contigs according to their similarities or read coverage covariations gives some insights on these genomes, but remains limited as viral sequences, or recent horizontal gene transfers, often differ from their host genomes. We recently developed meta3C, a proximity ligation approach that bins contigs in a sequence-independent way by quantifying and exploiting their tridimensional collisions frequencies in vivo. This technique has demonstrated a great potential to reconstruct genomes as well as to assign plasmids and phages to their hosts. It nevertheless requires a specific processing of the microbial samples before sequencing, which has to be carefully planned.}, }
@article {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 {pmid30509871, year = {2019}, author = {Kozyrskyj, AL and Bourque, SL and Ospina, MB}, title = {Microbiota be nimble.}, journal = {EBioMedicine}, volume = {39}, number = {}, pages = {21-22}, doi = {10.1016/j.ebiom.2018.11.058}, pmid = {30509871}, issn = {2352-3964}, mesh = {Dietary Carbohydrates/metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Metagenome ; Metagenomics/methods ; Pregnancy ; }, }
@article {pmid30509257, year = {2018}, author = {He, F and Liu, D and Zhang, L and Zhai, J and Ma, Y and Xu, Y and Jiang, G and Rong, K and Ma, J}, title = {Metagenomic analysis of captive Amur tiger faecal microbiome.}, journal = {BMC veterinary research}, volume = {14}, number = {1}, pages = {379}, pmid = {30509257}, issn = {1746-6148}, support = {31372209//National Natural Science Foundation of China/ ; 2572017AA20//The Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Animals, Zoo/*microbiology ; Bacteria/*classification/genetics/metabolism ; Endangered Species ; Feces/*microbiology ; *Gastrointestinal Microbiome ; *Metagenome ; Tigers/*microbiology ; }, abstract = {BACKGROUND: The gastrointestinal tracts of animals are home to large, complex communities of microbes. The compositions of these communities ultimately reflect the coevolution of microorganisms with their animal host and are influenced by the living environment, diet and immune status of the host. Gut microbes have been shown to be important for human disease and health, but little research exists in the gut microbiome of the Amur tiger, which is one of the most endangered species in the world.<br><br>RESULTS: In this study, we present the use of whole-metagenome shotgun sequencing to analyze the composition and functional structures of the gut microbiota in captive Amur tigers. Our results showed a high abundance of four major phyla in captive Amur tigers, including Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. Moreover, at the genus level, Escherichia, Collinsella and Fusobacterium were most abundant in the captive Amur tiger fecal metagenome. At the species level, Escherichia coli, Fusobacterium ulcerans and Fusobacterium varium were the species with highest abundances in the captive Amur tiger gut microbiota. The primary functional categories of the Amur tiger faecal metagenome were associated mainly with Carbohydrate metabolism, Membrane transport and Amino acid metabolism based on the KEGG pathway database. The comparative metagenomic analyses showed that the captive Amur tiger fecal metagenome had a lower abundance of Spirochaetes, Cyanobacteria and Ascomycota than other animals, and the primary functional categories were primarily associated with carbohydrate metabolism subsystems, clustering-based subsystems and protein metabolism.<br><br>CONCLUSIONS: We presented here for the first time the use of the shotgun metagenomic sequencing approach to study the composition and functional structures of the gut microbiota in captive Amur tiger.}, }
@article {pmid30502597, year = {2019}, author = {Yang, Y and Liu, G and Song, W and Ye, C and Lin, H and Li, Z and Liu, W}, title = {Plastics in the marine environment are reservoirs for antibiotic and metal resistance genes.}, journal = {Environment international}, volume = {123}, number = {}, pages = {79-86}, doi = {10.1016/j.envint.2018.11.061}, pmid = {30502597}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Microbial ; *Genes, Bacterial ; Metagenomics ; Metals ; *Microbiota ; Pacific Ocean ; *Plastics ; RNA, Ribosomal, 16S ; Seawater/microbiology ; Water Pollution/*analysis ; }, abstract = {Plastics have been accumulated offshore and in the deep oceans at an unprecedented scale. Microbial communities have colonized the plastisphere, which has become a reservoir for both antibiotic and metal resistance genes (ARGs and MRGs). This is the first analysis of the diversity, abundance, and co-occurrence of ARGs and MRGs, and their relationships within the microbial community, using metagenomic data of plastic particles observed in the North Pacific Gyre obtained from the National Centre for Biotechnology Information Sequence Read Archive database. The abundance of ARGs and MRGs in microbial communities on the plastics were in the ranges 7.07 × 10-4-1.21 × 10-2 and 5.51 × 10-3-4.82 × 10-2 copies per 16S rRNA, respectively. Both the Shannon-Wiener indices and richness of ARGs and MRGs in plastics microbiota were significantly greater than those of ARGs and MRGs in seawater microbiota in the North Pacific Gyre via one-way analysis of variance. Multidrug resistance genes and multi-metal resistance genes were the main classes of genes detected in plastic microbiota. There were no significant differences in the abundance or diversity of ARGs and MRGs between macroplastics biota and microplastics biota, indicating that particle size had no effect on resistance genes. Procrustes analysis suggested that microbial community composition was the determining factor of the ARG profile but not for MRG. Some ARGs and MRGs had a higher incidence of non-random co-occurrence, suggesting that the co-effects of selection for antibiotic or metal resistance are important factors influencing the resistome of the microbiota on the plastic particles.}, }
@article {pmid30489678, year = {2019}, author = {Vieira, FR and Pecchia, JA and Segato, F and Polikarpov, I}, title = {Exploring oyster mushroom (Pleurotus ostreatus) substrate preparation by varying phase I composting time: changes in bacterial communities and physicochemical composition of biomass impacting mushroom yields.}, journal = {Journal of applied microbiology}, volume = {126}, number = {3}, pages = {931-944}, doi = {10.1111/jam.14168}, pmid = {30489678}, issn = {1365-2672}, support = {005707/2012-05//Coordination for the Improvement of Higher Education Personnel/ ; 403090/2012-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 490022/2009-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 443916/2014-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; //University of São Paulo (USP) via NAP/ ; 2009/52840-7//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2013/21545-5//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2014/18714-2//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2015/13684-0//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; }, mesh = {*Bacteria/chemistry/metabolism ; Biodegradation, Environmental ; *Biomass ; *Composting ; *Microbial Consortia ; *Pleurotus/chemistry/metabolism ; }, abstract = {AIMS: To investigate characterization of the bacterial community composition and functionality and their impact on substrate biodegradation as well as mushroom yield.<br><br>METHODS AND RESULTS: Bacterial diversity, composition and functionality were accessed by DNA-derived analysis for a sugarcane straw-based substrate composted for either 5, 10 or 15 days. In addition, carbon and nitrogen losses, carbohydrate conversion and mushroom yields were measured for the different treatments. Changes were observed in the bacterial community diversity and composition after the process started, but not during the composting process itself. Following phase I, Acinetobacter sequences were recovered in high numbers, and selected genes associated with nitrogen metabolism and lignocellulose deconstruction were mapped. Substrate physicochemical composition showed elevated carbon and nitrogen losses after 10 and 15 days of phase I with reductions in mushroom yield.<br><br>CONCLUSIONS: Acinetobacter species appear to play an important role in substrate degradation processes, and a 5-day phase I period showed a significant higher mushroom yield compared to composting for either 10 or 15 days.<br><br>This study confers a better understanding of the bacterial community manipulation during the substrate preparation and their influence in substrate selectivity for the Pleurotus ostreatus cultivation.}, }
@article {pmid30489677, year = {2019}, author = {Sánchez-González, M and Álvarez-Uribe, H and Rivera-Solís, R and González-Burgos, A and Escalante-Réndiz, D and Rojas-Herrera, R}, title = {Analysis of a phenol-adapted microbial community: degradation capacity, taxonomy and metabolic description.}, journal = {Journal of applied microbiology}, volume = {126}, number = {3}, pages = {771-779}, doi = {10.1111/jam.14166}, pmid = {30489677}, issn = {1365-2672}, mesh = {Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Metagenomics ; *Microbiota ; Mixed Function Oxygenases/genetics/metabolism ; Phenol/*metabolism ; Phylogeny ; }, abstract = {AIMS: In this study, the ability of the consortium MR-01 to degrade phenol was determined. The effects of this chemical on the taxonomy and the metabolic behaviour were analysed through metagenomics.<br><br>METHODS AND RESULTS: Consortium MR-01 was acclimated in a sublethal concentration of phenol. After this process, the capacity to degrade this molecule was analysed. Results showed that degradation increased with the increment of the initial phenol concentration. Metagenomic analysis indicates that the consortium metabolized phenol under aerobic conditions using phenol 2-monooxygenase and the meta-cleavage pathway. Sequence of the enzymes involved in the phenol degradation was ascribed to the Actinomycetales and Chloroflexales orders, with relative abundances <1%. The most abundant genera were part of the Sphingomonadales order; however, the role of these species in the consortium is not clear.<br><br>CONCLUSIONS: Consortium MR-01 degrades efficiently high concentrations of phenol. The participation of extremophiles in the degradation process and the emergence of beneficial metabolic dependencies between the community members are some of the strategies used by the consortium to survive and develop under harsh environmental conditions.<br><br>This is one of the few studies describing the taxonomy and metabolic profile of a phenol degrading consortium.}, }
@article {pmid30486439, year = {2018}, author = {Yi, X and Yuan, J and Zhu, Y and Yi, X and Zhao, Q and Fang, K and Cao, L}, title = {Comparison of the Abundance and Community Structure of N-Cycling Bacteria in Paddy Rhizosphere Soil under Different Rice Cultivation Patterns.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19123772}, pmid = {30486439}, issn = {1422-0067}, mesh = {Bacteria/*classification/genetics/metabolism ; *Biodiversity ; Enzymes/genetics/metabolism ; Metagenome ; Metagenomics/methods ; Nitrogen ; Oryza/*microbiology ; Phylogeny ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Eco-agricultural systems aim to reduce the use of chemical fertilizers in order to improve sustainable production and maintain a healthy ecosystem. The aim of this study was to explore the effects of rice-frog farming on the bacterial community and N-cycling microbes in paddy rhizosphere soil. This experiment involved three rice cultivation patterns: Conventionally cultivated rice (CR), green rice-frog farming (GR), and organic rice-frog farming (OR). The rice yield, paddy soil enzyme activities, physicochemical variables and bacterial and N-cycling bacterial abundances were quantitatively analyzed. Rice-frog cultivations significantly increased soil protease, nitrate and reductase activity. Additionally, the nirS gene copy number and the relative abundance of denitrifying bacteria also increased, however urease activity and the relative abundance of nitrifying bacteria significantly decreased. The bacterial community richness and diversity of OR soil was significantly higher than that of the GR or CR soil. Nitrogen use efficiency (NUE) of GR was highest. The N-cycling bacterial community was positively correlated with the total carbon (TC), total nitrogren (TN) and carbon to nitrogen (C:N) ratio. The present work strengthens our current understanding of the soil bacterial community structure and its functions under rice-frog farming. The present work also provides certain theoretical support for the selection of rational rice cultivation patterns.}, }
@article {pmid30486388, year = {2018}, author = {Labbé, M and Raymond, F and Lévesque, A and Thaler, M and Mohit, V and Audet, M and Corbeil, J and Culley, A}, title = {Communities of Phytoplankton Viruses across the Transition Zone of the St. Lawrence Estuary.}, journal = {Viruses}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/v10120672}, pmid = {30486388}, issn = {1999-4915}, mesh = {Biodiversity ; Ecosystem ; Environment ; *Estuaries ; Evolution, Molecular ; Geography ; Metagenome ; Metagenomics/methods ; Phycodnaviridae/classification/genetics ; Phylogeny ; Phytoplankton/*virology ; RNA, Ribosomal, 18S ; *Water Microbiology ; }, abstract = {The St. Lawrence hydrographic system includes freshwater, brackish, and marine habitats, and is the largest waterway in North America by volume. The food-webs in these habitats are ultimately dependent on phytoplankton. Viral lysis is believed to be responsible for a major part of phytoplankton mortality. To better understand their role, we characterized the diversity and distribution of two viral taxa infecting phytoplankton: the picornaviruses and phycodnaviruses. Our study focused on the estuary transition zone, which is an important nursery for invertebrates and fishes. Both viral taxa were investigated by PCR amplification of conserved molecular markers and next-generation sequencing at six sites, ranging from freshwater to marine. Our results revealed few shared viral phylotypes between saltwater and freshwater sites. Salinity appeared to be the primary determinant of viral community composition. Moreover, our analysis indicated that the viruses identified in this region of the St. Lawrence diverge from classified viruses and homologous published environmental virotypes. These results suggest that DNA and RNA viruses infecting phytoplankton are likely active in the estuary transition zone, and that this region harbors its own unique viral assemblages.}, }
@article {pmid30486338, year = {2018}, author = {Amedei, A and Boem, F}, title = {I've Gut A Feeling: Microbiota Impacting the Conceptual and Experimental Perspectives of Personalized Medicine.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19123756}, pmid = {30486338}, issn = {1422-0067}, support = {FAS SALUTE 2014//Regione Toscana/ ; P2016.0808//Ente Cassa di Risparmio di Firenze/ ; }, mesh = {Animals ; Biodiversity ; Biological Therapy ; Disease Susceptibility ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genomics/methods ; Humans ; Metagenomics/methods ; Microbiota ; Organ Specificity ; *Precision Medicine/methods ; Research ; Symbiosis ; }, abstract = {In recent years, the human microbiota has gained increasing relevance both in research and clinical fields. Increasing studies seem to suggest the centrality of the microbiota and its composition both in the development and maintenance of what we call &quot;health&quot; and in generating and/or favoring (those cases in which the microbiota's complex relational architecture is dysregulated) the onset of pathological conditions. The complex relationships between the microbiota and human beings, which invest core notions of biomedicine such as &quot;health&quot; and &quot;individual,&quot; do concern not only problems of an empirical nature but seem to require the need to adopt new concepts and new perspectives in order to be properly analysed and utilized, especially for their therapeutic implementation. In this contribution we report and discuss some of the theoretical proposals and innovations (from the ecological component to the notion of polygenomic organism) aimed at producing this change of perspective. In conclusion, we summarily analyze what impact and what new challenges these new approaches might have on personalized/person centred/precision medicine.}, }
@article {pmid30485662, year = {2019}, author = {Koziol, A and Stat, M and Simpson, T and Jarman, S and DiBattista, JD and Harvey, ES and Marnane, M and McDonald, J and Bunce, M}, title = {Environmental DNA metabarcoding studies are critically affected by substrate selection.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {366-376}, doi = {10.1111/1755-0998.12971}, pmid = {30485662}, issn = {1755-0998}, support = {LP160100839//Australian Research Council/ ; }, mesh = {Aquatic Organisms/*classification/*genetics ; Australia ; *Biodiversity ; DNA/chemistry/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Kazakhstan ; Metagenomics/*methods ; Seawater ; }, abstract = {Effective biomonitoring is critical for driving management outcomes that ensure long-term sustainability of the marine environment. In recent years, environmental DNA (eDNA), coupled with metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data are needed on how to best implement eDNA field sampling approaches to maximize their utility for each specific application. The effect of the substrate chosen for eDNA sampling on the diversity of marine taxa detected by DNA metabarcoding has not yet been systematically analysed, despite aquatic systems being those most commonly targeted for eDNA studies. We investigated the effect of four commonly used eDNA substrates to explore taxonomic diversity: (a) surface water, (b) marine sediment, (c) settlement plates and (d) planktonic tows. With a focus on coastal ports, 332 eDNA samples from Australia (Indian and Southern oceans) and Kazakhstan (Caspian Sea) were collected and analysed by multi-assay DNA metabarcoding. Across study locations, between 30% and 52% of eukaryotic families detected were unique to a particular substrate and <6% of families were found in all four substrates. Taxonomic composition varied significantly depending on the substrate sampled implying that the suitability (and bias) of an eDNA substrate will depend on the focal taxa. These findings demonstrate that single substrate eDNA metabarcoding likely underestimates the total eukaryotic diversity. Future eDNA experimental design should consider incorporating multiple substrates or select substrate(s) best suited to the specific detection of target taxa.}, }
@article {pmid30482830, year = {2018}, author = {Espinoza, JL and Harkins, DM and Torralba, M and Gomez, A and Highlander, SK and Jones, MB and Leong, P and Saffery, R and Bockmann, M and Kuelbs, C and Inman, JM and Hughes, T and Craig, JM and Nelson, KE and Dupont, CL}, title = {Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30482830}, issn = {2150-7511}, support = {R01 DE019665/DE/NIDCR NIH HHS/United States ; R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Australia ; Bacteria/*classification/*genetics ; Child ; Child, Preschool ; Dental Caries/*microbiology ; Dental Plaque/*microbiology ; Humans ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {To address the question of how microbial diversity and function in the oral cavities of children relates to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. Caries phenotypes contained statistically significant enrichments in specific genome abundances and distinct community composition profiles, including strain-level changes. Metabolic pathways that are statistically associated with caries include several sugar-associated phosphotransferase systems, antimicrobial resistance, and metal transport. Numerous closely related previously uncharacterized microbes had substantial variation in central metabolism, including the loss of biosynthetic pathways resulting in auxotrophy, changing the ecological role. We also describe the first complete Gracilibacteria genomes from the human microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.IMPORTANCE Oral health has substantial economic importance, with over $100 billion spent on dental care in the United States annually. The microbiome plays a critical role in oral health, yet remains poorly classified. To address the question of how microbial diversity and function in the oral cavities of children relate to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. This unveiled several new previously uncharacterized but ubiquitous microbial lineages in the oral microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.}, }
@article {pmid30482513, year = {2019}, author = {Díaz-Sánchez, S and Hernández-Jarguín, A and Torina, A and de Mera, IGF and Blanda, V and Caracappa, S and Gortazar, C and de la Fuente, J}, title = {Characterization of the bacterial microbiota in wild-caught Ixodes ventalloi.}, journal = {Ticks and tick-borne diseases}, volume = {10}, number = {2}, pages = {336-343}, doi = {10.1016/j.ttbdis.2018.11.014}, pmid = {30482513}, issn = {1877-9603}, mesh = {Anaplasma/genetics ; Animals ; Borrelia/genetics ; DNA, Bacterial/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Ixodes/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sicily ; Symbiosis ; }, abstract = {Exploring the microbial diversity of ticks is crucial to understand geographical dispersion and pathogen transmission. Tick microbes participate in many biological processes implicated in the acquisition, maintenance, and transmission of pathogens, and actively promote host phenotypic changes, and adaptation to new environments. The microbial community of Ixodes ventalloi still remains unexplored. In this study, the bacterial microbiota of wild-caught I. ventalloi was characterized using shotgun-metagenomic sequencing in samples from unfed adults collected during December 2013-January 2014 in two locations from Sicily, Italy. The microbiota identified in I. ventalloi was mainly composed of symbiotic, commensal, and environmental bacteria. Interestingly, we identified the genera Anaplasma and Borrelia as members of the microbiota of I. ventalloi. These results advance our information on I. ventalloi microbiota composition, with potential implications in tick-host adaptation, geographic expansion, and vector competence.}, }
@article {pmid30481710, year = {2019}, author = {Abia, ALK and Alisoltani, A and Ubomba-Jaswa, E and Dippenaar, MA}, title = {Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments.}, journal = {The Science of the total environment}, volume = {655}, number = {}, pages = {831-841}, doi = {10.1016/j.scitotenv.2018.11.302}, pmid = {30481710}, issn = {1879-1026}, mesh = {Biodiversity ; *Cemeteries ; Cities ; *Environmental Monitoring ; Humans ; *Metagenomics ; Microbiota/genetics ; Molecular Sequence Annotation ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; South Africa ; }, abstract = {Recent studies have identified cemeteries as potential environmental reservoirs of multi-drug resistant pathogenic bacteria that could contaminate groundwater sources posing public health threats. However, these findings were based on the identification of culturable bacteria and at times not below burial grounds. Investigation on the bacterial diversity and functional profiles of bacterial communities above and below burial grounds in human cemeteries are few. The current study used high-throughput sequencing techniques to determine the bacterial composition and their associated functional profiles in cemetery soil samples collected at the surface and below burial ground in two South African cemeteries (Maitland Cemetery in Cape Town and Fontein Street Cemetery in Middelburg) to evaluate the potential health threat to surrounding populations through contamination of groundwater. Significant differences were observed between sample depths with the clustering of the surface (0 m) and the 2 m samples into separate groups. Pseudomonas and Corynebacterium were the most abundant genera across all samples. Pseudomonas and Rhodococcus were the dominant genera in the 2 m samples while Prauserella and Staphylococcus were dominant in the surface samples. The 2 m samples showed a lower alpha diversity but recorded higher proportions of human diseases functional classes compared to the surface samples. Human disease functional profiles revealed involvement, in infectious (cholera), neurodegenerative (Alzheimer's disease) cardiovascular (hypertrophic cardiomyopathy) immune system (Systemic lupus erythematosus) metabolic (Type I &amp; II diabetes) diseases and cancer. Antibiotic resistance and antibiotics synthesis signatures were also identified. Thus, cemeteries could be potential sources of microbial and antibiotic pollution in groundwater, especially in areas with shallow water tables such as Maitland. Selection of sites for use as cemeteries should, therefore, require a proper understanding of the hydrogeological characteristics of the selected site. However, further studies are required to trace the actual movement of these pollutants into groundwater resources.}, }
@article {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 {pmid30479272, year = {2018}, author = {Glover, AG and Wiklund, H and Chen, C and Dahlgren, TG}, title = {Managing a sustainable deep-sea 'blue economy' requires knowledge of what actually lives there.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30479272}, issn = {2050-084X}, mesh = {*Biodiversity ; Conservation of Energy Resources/*methods ; *Ecosystem ; Metagenomics/*methods ; *Oceans and Seas ; }, abstract = {Ensuring that the wealth of resources contained in our oceans are managed and developed in a sustainable manner is a priority for the emerging 'blue economy'. However, modern ecosystem-based management approaches do not translate well to regions where we know almost nothing about the individual species found in the ecosystem. Here, we propose a new taxon-focused approach to deep-sea conservation that includes regulatory oversight to set targets for the delivery of taxonomic data. For example, a five-year plan to deliver taxonomic and genomic knowledge on a thousand species in regions of the ocean earmarked for industrial activity is an achievable target. High-throughput, integrative taxonomy can, therefore, provide the data that is needed to monitor various ecosystem services (such as the natural history, connectivity, value and function of species) and to help break the regulatory deadlock of high-seas conservation.}, }
@article {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}, support = {BB/I001107/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, 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 {pmid30478001, year = {2018}, author = {Wei, S and Mortensen, MS and Stokholm, J and Brejnrod, AD and Thorsen, J and Rasmussen, MA and Trivedi, U and Bisgaard, H and Sørensen, SJ}, title = {Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial.}, journal = {EBioMedicine}, volume = {38}, number = {}, pages = {265-272}, doi = {10.1016/j.ebiom.2018.11.035}, pmid = {30478001}, issn = {2352-3964}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; Azithromycin/*pharmacology/therapeutic use ; Biodiversity ; Child, Preschool ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Male ; Metagenome ; Metagenomics ; Time Factors ; }, abstract = {BACKGROUND: Macrolides are commonly prescribed for respiratory infections and asthma-like episodes in children. While their clinical benefits have been proved, concerns regarding the side-effects of their therapeutic use have been raised. Here we assess the short- and long-term impacts of azithromycin on the gut microbiota of young children.<br><br>METHODS: We performed a randomized, double-blind, placebo-controlled trial in a group of children aged 12-36 months, diagnosed with recurrent asthma-like symptoms from the COPSAC2010 cohort. Each acute asthma-like episode was randomized to a 3-day course of azithromycin oral solution of 10 mg/kg per day or placebo. Azithromycin reduced episode duration by half, which was the primary end-point and reported previously. The assessment of gut microbiota after treatment was the secondary end-point and reported in this study. Fecal samples were collected 14 days after randomization (N = 59, short-term) and again at age 4 years (N = 49, long-term, of whom N = 18 were placebo treated) and investigated by 16S rRNA gene amplicon sequencing.<br><br>FINDINGS: Short-term, azithromycin caused a 23% reduction in observed richness and 13% reduction in Shannon diversity. Microbiota composition was shifted primarily in the Actinobacteria phylum, especially a reduction of abundance in the genus Bifidobacterium. Long-term (13-39 months after treatment), we did not observe any differences between the azithromycin and placebo recipients in their gut microbiota composition.<br><br>INTERPRETATION: Azithromycin treatment induced a perturbation in the gut microbiota 14 days after randomization but did not have long-lasting effects on the gut microbiota composition. However, it should be noted that our analyses included a limited number of fecal samples for the placebo treated group at age 4 years. FUND: Lundbeck Foundation, Danish Ministry of Health, Danish Council for Strategic Research, Capital Region Research Foundation, China Scholarship Council.}, }
@article {pmid30477563, year = {2018}, author = {Sinha, R and Ahsan, H and Blaser, M and Caporaso, JG and Carmical, JR and Chan, AT and Fodor, A and Gail, MH and Harris, CC and Helzlsouer, K and Huttenhower, C and Knight, R and Kong, HH and Lai, GY and Hutchinson, DLS and Le Marchand, L and Li, H and Orlich, MJ and Shi, J and Truelove, A and Verma, M and Vogtmann, E and White, O and Willett, W and Zheng, W and Mahabir, S and Abnet, C}, title = {Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {210}, pmid = {30477563}, issn = {2049-2618}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Humans ; Microbiota/*physiology ; Neoplasms/*etiology ; Prospective Studies ; Reproducibility of Results ; *Research Design ; }, abstract = {The National Cancer Institute (NCI) sponsored a 2-day workshop, &quot;Next Steps in Studying the Human Microbiome and Health in Prospective Studies,&quot; in Bethesda, Maryland, May 16-17, 2017. The workshop brought together researchers in the field to discuss the challenges of conducting microbiome studies, including study design, collection and processing of samples, bioinformatics and statistical methods, publishing results, and ensuring reproducibility of published results. The presenters emphasized the great potential of microbiome research in understanding the etiology of cancer. This report summarizes the workshop and presents practical suggestions for conducting microbiome studies, from workshop presenters, moderators, and participants.}, }
@article {pmid30474920, year = {2019}, author = {Bell, T}, title = {Next-generation experiments linking community structure and ecosystem functioning.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {20-22}, doi = {10.1111/1758-2229.12711}, pmid = {30474920}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/metabolism ; Biodiversity ; *Ecosystem ; Metagenomics ; Microbiota ; Population Dynamics ; Reproducibility of Results ; }, }
@article {pmid30474727, year = {2019}, author = {Meng, H and Zhou, Z and Wu, R and Wang, Y and Gu, JD}, title = {Diazotrophic microbial community and abundance in acidic subtropical natural and re-vegetated forest soils revealed by high-throughput sequencing of nifH gene.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {2}, pages = {995-1005}, doi = {10.1007/s00253-018-9466-7}, pmid = {30474727}, issn = {1432-0614}, support = {31470562//National Natural Science Foundation of China/ ; 701913//Hong Kong RGC GRF grant/ ; }, mesh = {Acids/analysis ; Archaea/*classification/enzymology/genetics/metabolism ; Bacteria/*classification/enzymology/genetics/metabolism ; Chemical Phenomena ; Forests ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; *Nitrogen Fixation ; Oxidoreductases/*genetics ; Seasons ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Biological nitrogen fixation (BNF) is an important natural biochemical process converting the inert dinitrogen gas (N2) in the atmosphere to ammonia (NH3) in the N cycle. In this study, the nifH gene was chosen to detect the diazotrophic microorganisms with high-throughput sequencing from five acidic forest soils, including three natural forests and two re-vegetated forests. Soil samples were taken in two seasons (summer and winter) at two depth layers (surface and lower depths). A dataset of 179,600 reads obtained from 20 samples were analyzed to provide the microbial community structure, diversity, abundance, and relationship with physiochemical parameters. Both archaea and bacteria were detected in these samples and diazotrophic bacteria were the dominant members contributing to the biological dinitrogen fixation in the acidic forest soils. Cyanobacteria, Firmicutes, Proteobacteria, Spirocheates, and Verrucomicrobia were observed, especially the Proteobacteria as the most abundant phylum. The core genera were Bradyrhizobium and Methylobacterium from α-Proteobacteia, and Desulfovibrio from δ-Proteobacteia in the phylum of Proteobacteia of these samples. The diversity indices and the gene abundances of all samples were higher in the surface layer than the lower layer. Diversity was apparently higher in re-vegetated forests than the natural forests. Significant positive correlation to the organic matter and nitrogen-related parameters was observed, but there was no significant seasonal variation on the community structure and diversity in these samples between the summer and winter. The application of high-throughput sequencing method provides a better understanding and more comprehensive information of diazotrophs in acidic forest soils than conventional and PCR-based ones.}, }
@article {pmid30470178, year = {2018}, author = {Griffith, BC and Weiss, BL and Aksoy, E and Mireji, PO and Auma, JE and Wamwiri, FN and Echodu, R and Murilla, G and Aksoy, S}, title = {Analysis of the gut-specific microbiome from field-captured tsetse flies, and its potential relevance to host trypanosome vector competence.}, journal = {BMC microbiology}, volume = {18}, number = {Suppl 1}, pages = {146}, pmid = {30470178}, issn = {1471-2180}, support = {D43 TW007391/TW/FIC NIH HHS/United States ; R01 AI051584/AI/NIAID NIH HHS/United States ; R01 AI068932/AI/NIAID NIH HHS/United States ; U01 AI115648/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; *Gastrointestinal Microbiome ; Geography ; High-Throughput Nucleotide Sequencing ; Insect Vectors/*microbiology/parasitology ; Kenya ; Symbiosis ; Trypanosoma/*physiology ; Tsetse Flies/*microbiology/parasitology ; Uganda ; }, abstract = {BACKGROUND: The tsetse fly (Glossina sp.) midgut is colonized by maternally transmitted and environmentally acquired bacteria. Additionally, the midgut serves as a niche in which pathogenic African trypanosomes reside within infected flies. Tsetse's bacterial microbiota impacts many aspects of the fly's physiology. However, little is known about the structure of tsetse's midgut-associated bacterial communities as they relate to geographically distinct fly habitats in east Africa and their contributions to parasite infection outcomes. We utilized culture dependent and independent methods to characterize the taxonomic structure and density of bacterial communities that reside within the midgut of tsetse flies collected at geographically distinct locations in Kenya and Uganda.<br><br>RESULTS: Using culture dependent methods, we isolated 34 strains of bacteria from four different tsetse species (G. pallidipes, G. brevipalpis, G. fuscipes and G. fuscipleuris) captured at three distinct locations in Kenya. To increase the depth of this study, we deep sequenced midguts from individual uninfected and trypanosome infected G. pallidipes captured at two distinct locations in Kenya and one in Uganda. We found that tsetse's obligate endosymbiont, Wigglesworthia, was the most abundant bacterium present in the midgut of G. pallidipes, and the density of this bacterium remained largely consistent regardless of whether or not its tsetse host was infected with trypanosomes. These fly populations also housed the commensal symbiont Sodalis, which was found at significantly higher densities in trypanosome infected compared to uninfected flies. Finally, midguts of field-captured G. pallidipes were colonized with distinct, low density communities of environmentally acquired microbes that differed in taxonomic structure depending on parasite infection status and the geographic location from which the flies were collected.<br><br>CONCLUSIONS: The results of this study will enhance our understanding of the tripartite relationship between tsetse, its microbiota and trypanosome vector competence. This information may be useful for developing novel disease control strategies or enhancing the efficacy of those already in use.}, }
@article {pmid30463925, year = {2018}, author = {Bulow, C and Langdon, A and Hink, T and Wallace, M and Reske, KA and Patel, S and Sun, X and Seiler, S and Jones, S and Kwon, JH and Burnham, CA and Dantas, G and Dubberke, ER}, title = {Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential.}, journal = {mSphere}, volume = {3}, number = {6}, pages = {}, pmid = {30463925}, issn = {2379-5042}, support = {KL2 TR002346/TR/NCATS NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; TL1 TR000449/TR/NCATS NIH HHS/United States ; TL1 TR002344/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Amoxicillin-Potassium Clavulanate Combination/*administration &amp; dosage ; Anti-Bacterial Agents/*administration &amp; dosage ; Enema ; Fecal Microbiota Transplantation/*methods ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; *Metabolism ; *Microbiota ; Middle Aged ; Treatment Outcome ; Young Adult ; beta-Lactamase Inhibitors/*administration &amp; dosage ; }, abstract = {Strategies to prevent multidrug-resistant organism (MDRO) infections are scarce, but autologous fecal microbiota transplantation (autoFMT) may limit gastrointestinal MDRO expansion. AutoFMT involves banking one's feces during a healthy state for later use in restoring gut microbiota following perturbation. This pilot study evaluated the effect of autoFMT on gastrointestinal microbiome taxonomic composition, resistance gene content, and metabolic capacity after exposure to amoxicillin-clavulanic acid (Amox-Clav). Ten healthy participants were enrolled. All received 5 days of Amox-Clav. Half were randomized to autoFMT, derived from stool collected pre-antimicrobial exposure, by enema, and half to saline enema. Participants submitted stool samples pre- and post-Amox-Clav and enema and during a 90-day follow-up period. Shotgun metagenomic sequencing revealed taxonomic composition, resistance gene content, and metabolic capacity. Amox-Clav significantly altered gut taxonomic composition in all participants (n = 10, P < 0.01); however, only three participants exhibited major changes at the phylum level following exposure. In the cohort as a whole, beta-lactamase genes were enriched following Amox-Clav (P < 0.05), and predicted metabolic capacity was significantly altered (P < 0.01). Species composition, metabolic capacity, and beta-lactamase abundance returned to pre-antimicrobial exposure state 7 days after either autoFMT or saline enema (P > 0.05, compared to enrollment). Alterations to microbial metabolic capacity occurred following antimicrobial exposure even in participants without substantial taxonomic disruption, potentially creating open niches for pathogen colonization. Our findings suggest that metabolic potential is an important consideration for complete assessment of antimicrobial impact on the microbiome. AutoFMT was well tolerated and may have contributed to phylogenetic recovery. (This study has been registered at ClinicalTrials.gov under identifier NCT02046525.)IMPORTANCE The spread of multidrug resistance among pathogenic organisms threatens the efficacy of antimicrobial treatment options. The human gut serves as a reservoir for many drug-resistant organisms and their resistance genes, and perturbation of the gut microbiome by antimicrobial exposure can open metabolic niches to resistant pathogens. Once established in the gut, antimicrobial-resistant bacteria can persist even after antimicrobial exposure ceases. Strategies to prevent multidrug-resistant organism (MDRO) infections are scarce, but autologous fecal microbiota transplantation (autoFMT) may limit gastrointestinal MDRO expansion. AutoFMT involves banking one's feces during a healthy state for later use in restoring gut microbiota following perturbation. This pilot study evaluated the effect of amoxicillin-clavulanic acid (Amox-Clav) exposure and autoFMT on gastrointestinal microbiome taxonomic composition, resistance gene content, and metabolic capacity. Importantly, we found that metabolic capacity was perturbed even in cases where gross phylogeny remained unchanged and that autoFMT was safe and well tolerated.}, }
@article {pmid30459421, year = {2018}, author = {Xu, J and Zhang, Y and Zhang, P and Trivedi, P and Riera, N and Wang, Y and Liu, X and Fan, G and Tang, J and Coletta-Filho, HD and Cubero, J and Deng, X and Ancona, V and Lu, Z and Zhong, B and Roper, MC and Capote, N and Catara, V and Pietersen, G and Vernière, C and Al-Sadi, AM and Li, L and Yang, F and Xu, X and Wang, J and Yang, H and Jin, T and Wang, N}, title = {The structure and function of the global citrus rhizosphere microbiome.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4894}, pmid = {30459421}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics ; Citrus/*microbiology ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/genetics ; Metagenome/genetics ; Metagenomics/classification/methods ; Microbiota/*genetics ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.}, }
@article {pmid30459334, year = {2018}, author = {Jersie-Christensen, RR and Lanigan, LT and Lyon, D and Mackie, M and Belstrøm, D and Kelstrup, CD and Fotakis, AK and Willerslev, E and Lynnerup, N and Jensen, LJ and Cappellini, E and Olsen, JV}, title = {Quantitative metaproteomics of medieval dental calculus reveals individual oral health status.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4744}, pmid = {30459334}, issn = {2041-1723}, mesh = {Adult ; Archaeology/methods ; Bacteria/classification ; Bacterial Proteins/analysis ; DNA, Ancient/analysis ; DNA, Bacterial/analysis ; Denmark ; Dental Calculus/*microbiology ; Dental Plaque/microbiology ; Dietary Proteins ; Female ; *Health Status ; Humans ; Male ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; *Oral Health ; Proteomics/*methods ; }, abstract = {The composition of ancient oral microbiomes has recently become accessible owing to advanced biomolecular methods such as metagenomics and metaproteomics, but the utility of metaproteomics for such analyses is less explored. Here, we use quantitative metaproteomics to characterize the dental calculus associated with the remains of 21 humans retrieved during the archeological excavation of the medieval (ca. 1100-1450 CE) cemetery of Tjærby, Denmark. We identify 3671 protein groups, covering 220 bacterial species and 81 genera across all medieval samples. The metaproteome profiles of bacterial and human proteins suggest two distinct groups of archeological remains corresponding to health-predisposed and oral disease-susceptible individuals, which is supported by comparison to the calculus metaproteomes of healthy living individuals. Notably, the groupings identified by metaproteomics are not apparent from the bioarchaeological analysis, illustrating that quantitative metaproteomics has the potential to provide additional levels of molecular information about the oral health status of individuals from archeological contexts.}, }
@article {pmid30459201, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Ruffin, MT and Koumpouras, CC and Schloss, PD}, title = {Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30459201}, issn = {2150-7511}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; U01 CA086400/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/genetics/virology ; Bacteriophages/*genetics/isolation &amp; purification ; Cohort Studies ; Colorectal Neoplasms/*diagnosis/microbiology/*virology ; Feces/microbiology/virology ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Viruses/*genetics ; }, abstract = {Human viruses (those that infect human cells) have been associated with many cancers, largely due to their mutagenic and functionally manipulative abilities. Despite this, cancer microbiome studies have focused almost exclusively on bacteria instead of viruses. We began evaluating the cancer virome by focusing on colorectal cancer, a primary cause of morbidity and mortality throughout the world and a cancer linked to altered colonic bacterial community compositions but with an unknown association with the gut virome. We used 16S rRNA gene, whole shotgun metagenomic, and purified virus metagenomic sequencing of stool to evaluate the differences in human colorectal cancer virus and bacterial community composition. Through random forest modeling, we identified differences in the healthy and colorectal cancer viromes. The cancer-associated virome consisted primarily of temperate bacteriophages that were also predicted to be bacterium-virus community network hubs. These results provide foundational evidence that bacteriophage communities are associated with colorectal cancer and potentially impact cancer progression by altering the bacterial host communities.IMPORTANCE Colorectal cancer is a leading cause of cancer-related death in the United States and worldwide. Its risk and severity have been linked to colonic bacterial community composition. Although human-specific viruses have been linked to other cancers and diseases, little is known about colorectal cancer virus communities. We addressed this knowledge gap by identifying differences in colonic virus communities in the stool of colorectal cancer patients and how they compared to bacterial community differences. The results suggested an indirect role for the virome in impacting colorectal cancer by modulating the associated bacterial community. These findings both support the idea of a biological role for viruses in colorectal cancer and provide a new understanding of basic colorectal cancer etiology.}, }
@article {pmid30458701, year = {2018}, author = {Banos, S and Lentendu, G and Kopf, A and Wubet, T and Glöckner, FO and Reich, M}, title = {A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {190}, pmid = {30458701}, issn = {1471-2180}, mesh = {Biodiversity ; DNA Primers/*genetics ; DNA, Fungal/*genetics ; Fungi/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/*genetics ; Species Specificity ; }, 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 {pmid30452938, year = {2018}, author = {Bilal, T and Malik, B and Hakeem, KR}, title = {Metagenomic analysis of uncultured microorganisms and their enzymatic attributes.}, journal = {Journal of microbiological methods}, volume = {155}, number = {}, pages = {65-69}, doi = {10.1016/j.mimet.2018.11.014}, pmid = {30452938}, issn = {1872-8359}, mesh = {Bioengineering/methods ; Biofuels ; Biotechnology ; Enzyme Activation ; *Enzymes/genetics/metabolism ; Extremophiles/*enzymology/*genetics ; Genome, Microbial/*genetics ; Genomics ; Metagenomics/*methods ; Microbiological Techniques/methods ; Microbiota/genetics ; }, abstract = {Although second generation biofuel technology is a sustainable route for bioethanol production it is not currently a robust technology because of certain hindrances viz., unavailability of potential enzyme resources, low efficiency of enzymes and restricted availability of potent enzymes that work under harsh conditions in industrial processes. Therefore, bioprospecting of extremophilic microorganisms using metagenomics is a promising alternative to discover novel microbes and enzymes with efficient tolerance to unfavourable conditions and thus could revolutionize the energy sector. Metagenomics a recent field in &quot;omics&quot; technology enables the genomic study of uncultured microorganisms with the goal of better understanding microbial dynamics. Metagenomics in conjunction with NextGen Sequencing technology facilitates the sequencing of microbial DNA directly from environmental samples and has expanded, and transformed our knowledge of the microbial world. However, filtering the meaningful information from the millions of genomic sequences offers a serious challenge to bioinformaticians. The current review holds the opinion tool 'know- how' to unravel the secrets of nature while expediting the bio-industrial world. We also discuss the novel biocatalytic agents discovered through metagenomics and how bioengineering plays a pivotal role to enhance their efficiency.}, }
@article {pmid30449316, year = {2018}, author = {Guerin, E and Shkoporov, A and Stockdale, SR and Clooney, AG and Ryan, FJ and Sutton, TDS and Draper, LA and Gonzalez-Tortuero, E and Ross, RP and Hill, C}, title = {Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut.}, journal = {Cell host &amp; microbe}, volume = {24}, number = {5}, pages = {653-664.e6}, doi = {10.1016/j.chom.2018.10.002}, pmid = {30449316}, issn = {1934-6069}, mesh = {Bacteriophages/*classification/*genetics/*physiology/ultrastructure ; Base Sequence ; Capsid Proteins/genetics ; DNA Viruses ; Feces/virology ; Fermentation ; *Gastrointestinal Microbiome ; Genome, Viral/genetics ; Genomics ; Humans ; Metagenomics/methods ; *Phylogeny ; Sequence Analysis ; Viral Proteins/genetics ; }, abstract = {CrAssphages represent the most abundant virus in the human gut microbiota, but the lack of available genome sequences for comparison has kept them enigmatic. Recently, sequence-based classification of distantly related crAss-like phages from multiple environments was reported, leading to a proposed familial-level taxonomic group. Here, we assembled the metagenomic sequencing reads from 702 human fecal virome/phageome samples and analyzed 99 complete circular crAss-like phage genomes and 150 contigs ≥70 kb. In silico comparative genomics and taxonomic analysis enabled a classification scheme of crAss-like phages from human fecal microbiomes into four candidate subfamilies composed of ten candidate genera. Laboratory analysis was performed on fecal samples from an individual harboring seven distinct crAss-like phages. We achieved crAss-like phage propagation in ex vivo human fecal fermentations and visualized short-tailed podoviruses by electron microscopy. Mass spectrometry of a crAss-like phage capsid protein could be linked to metagenomic sequencing data, confirming crAss-like phage structural annotations.}, }
@article {pmid30448738, year = {2019}, author = {Rehman, ZU and Ali, M and Iftikhar, H and Leiknes, T}, title = {Genome-resolved metagenomic analysis reveals roles of microbial community members in full-scale seawater reverse osmosis plant.}, journal = {Water research}, volume = {149}, number = {}, pages = {263-271}, doi = {10.1016/j.watres.2018.11.012}, pmid = {30448738}, issn = {1879-2448}, mesh = {Biofilms ; *Biofouling ; Membranes, Artificial ; *Microbiota ; Osmosis ; Seawater ; *Water Purification ; }, abstract = {Biofouling of Reverse Osmosis (RO) membrane is a significant issue for the water treatment industry. In this study, we apply the metagenomic shot-gun sequencing technology to characterise the composition and functional potential of the microbial community in a full-scale RO plant, at different stages of seawater treatment. We find Proteobacteria, Bacteroidetes and Planctomycetes to be the most abundant bacterial phyla. The genetic potential of the RO membrane microbial community shows the enrichment of genes involved in biofilm formation, representing the selective pressure of the biofilm formation process. We recover 31 metagenome-assembled genomes (MAGs) from intake (raw seawater), fouled RO membranes (leading and middle RO module) and brine reject water. A total of 25 MAGs are recovered from the biofilm samples (leading and middle RO modules), with 9 of them (36%) belonging to Planctomycetes. We investigate all 25 MAGs for genes (pili, flagella, quorum sensing, quorum quenching and nitrate reduction) that play an important role in biofilm formation and sustenance of cells. We show that Planctomycetes contain genes for the formation of flagella and pili, and the reduction of nitrate. Although genes for quorum sensing are not detected, quorum quenching genes are identified in the biofilm MAGs. Our results show that Planctomycetes, along with other microbes, play an important role in the formation and sustenance of biofilms on seawater RO membranes.}, }
@article {pmid30447983, year = {2019}, author = {Vasquez, AK and Ganda, EK and Capel, MB and Eicker, S and Virkler, PD and Bicalho, RC and Nydam, DV}, title = {The microbiome of Escherichia coli and culture-negative nonsevere clinical mastitis: Characterization and associations with linear score and milk production.}, journal = {Journal of dairy science}, volume = {102}, number = {1}, pages = {578-594}, doi = {10.3168/jds.2018-15062}, pmid = {30447983}, issn = {1525-3198}, mesh = {Animals ; Anti-Infective Agents/therapeutic use ; Bacteria/classification/genetics ; Biodiversity ; Cattle ; Escherichia coli/*isolation &amp; purification ; Female ; Lactation/*physiology ; Mastitis, Bovine/*microbiology ; Metagenomics ; Microbiota/*physiology ; Milk/microbiology ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Culture-negative and Escherichia coli cases are uncommonly treated in pathogen-based protocols for nonsevere mastitis. High-throughput 16S rRNA sequencing might reveal the presence of other pathogens and can provide information on microbial diversity. The objective was to explore the milk microbiome at the time of the mastitis event (enrollment) and its association with survival in the herd, milk production, and postevent linear score (LS) for cows with clinical mastitis characterized as negative or E. coli by culture. Fifty E. coli-positive and 35 culture-negative samples from cases were enrolled. No cases were treated with antimicrobials. All E. coli-positive quarters were characterized as transient; microbiological culture of samples taken 15 d postmastitis were negative for this organism. However, a difference in α-diversity (Shannon index) was present between enrollment and follow-up samples (3.8 vs. 5.1). When α-diversity was explored for enrollment E. coli samples, no relationship was observed between the Shannon indices of these samples and postmastitis LS. Alpha-diversity of the enrollment samples was lower for E. coli-positive cows that subsequently had greater losses in milk production. This difference was explained by a greater relative abundance of the family Enterobacteriaceae (67.8 vs. 38.4%) for cows that dropped in production. Analysis of composition of the microbiome identified one phylum, Proteobacteria, that differed between E. coli-positive cows that dropped in production and those that did not. Evaluation of β -diversity found no statistical relationship between postmastitis LS and the microbiome. When evaluating α- and β-diversities and composition of the microbiomes for culture-negative quarters, no associations were found for milk production changes and postmastitis LS. Three cows did not remain in the herd, limiting the ability to analyze survival. The findings suggest that a contributing factor to negative outcomes in E. coli-positive cows is relative abundance of this pathogen, and that no single or collective group of bacterial families is associated with milk production changes or postmastitis LS in culture-negative quarters. Although additional studies should be performed, the absence of associations between outcomes explored and microbial profiles in this study suggests that we are not missing opportunities by not treating nonsevere E. coli or culture-negative mastitis cases.}, }
@article {pmid30446434, year = {2018}, author = {Lucking, EF and O'Connor, KM and Strain, CR and Fouhy, F and Bastiaanssen, TFS and Burns, DP and Golubeva, AV and Stanton, C and Clarke, G and Cryan, JF and O'Halloran, KD}, title = {Chronic intermittent hypoxia disrupts cardiorespiratory homeostasis and gut microbiota composition in adult male guinea-pigs.}, journal = {EBioMedicine}, volume = {38}, number = {}, pages = {191-205}, doi = {10.1016/j.ebiom.2018.11.010}, pmid = {30446434}, issn = {2352-3964}, mesh = {Age Factors ; Animals ; Apnea/metabolism/physiopathology ; Basal Metabolism ; Biomarkers ; Brain Stem/metabolism ; Carotid Body ; *Gastrointestinal Microbiome ; Guinea Pigs ; Heart/*physiology/*physiopathology ; Homeostasis ; Hypoxia/*metabolism ; Male ; Metagenome ; Metagenomics ; Models, Animal ; Morbidity ; *Respiratory Physiological Phenomena ; Respiratory System/*physiopathology ; Sex Factors ; }, abstract = {BACKGROUND: Carotid body (peripheral oxygen sensor) sensitisation is pivotal in the development of chronic intermittent hypoxia (CIH)-induced hypertension. We sought to determine if exposure to CIH, modelling human sleep apnoea, adversely affects cardiorespiratory control in guinea-pigs, a species with hypoxia-insensitive carotid bodies. We reasoned that CIH-induced disruption of gut microbiota would evoke cardiorespiratory morbidity.<br><br>METHODS: Adult male guinea-pigs were exposed to CIH (6.5% O2 at nadir, 6 cycles.hour-1) for 8 h.day-1 for 12 consecutive days.<br><br>FINDINGS: CIH-exposed animals established reduced faecal microbiota species richness, with increased relative abundance of Bacteroidetes and reduced relative abundance of Firmicutes bacteria. Urinary corticosterone and noradrenaline levels were unchanged in CIH-exposed animals, but brainstem noradrenaline concentrations were lower compared with sham. Baseline ventilation was equivalent in CIH-exposed and sham animals; however, respiratory timing variability, sigh frequency and ventilation during hypoxic breathing were all lower in CIH-exposed animals. Baseline arterial blood pressure was unaffected by exposure to CIH, but β-adrenoceptor-dependent tachycardia and blunted bradycardia during phenylephrine-induced pressor responses was evident compared with sham controls.<br><br>INTERPRETATION: Increased carotid body chemo-afferent signalling appears obligatory for the development of CIH-induced hypertension and elevated chemoreflex control of breathing commonly reported in mammals, with hypoxia-sensitive carotid bodies. However, we reveal that exposure to modest CIH alters gut microbiota richness and composition, brainstem neurochemistry, and autonomic control of heart rate, independent of carotid body sensitisation, suggesting modulation of breathing and autonomic homeostasis via the microbiota-gut-brainstem axis. The findings have relevance to human sleep-disordered breathing.<br><br>FUNDING: The Department of Physiology, and APC Microbiome Ireland, UCC.}, }
@article {pmid30446169, year = {2019}, author = {Kosek, K and Kozioł, K and Luczkiewicz, A and Jankowska, K and Chmiel, S and Polkowska, Ż}, title = {Environmental characteristics of a tundra river system in Svalbard. Part 2: Chemical stress factors.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {1585-1596}, doi = {10.1016/j.scitotenv.2018.11.012}, pmid = {30446169}, issn = {1879-1026}, mesh = {Bacteria/classification/*drug effects ; *Environmental Monitoring ; Formaldehyde/analysis ; Metagenomics ; Metals/analysis ; Microbiota/*drug effects ; Phenols/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; Rivers/*chemistry/*microbiology ; Svalbard ; Tundra ; Water Pollutants, Chemical/*analysis ; }, abstract = {Bacterial communities in the Arctic environment are subject to multiple stress factors, including contaminants, although typically their concentrations are small. The Arctic contamination research has focused on persistent organic pollutants (POPs) because they are bioaccumulative, resistant to degradation and toxic for all organisms. Pollutants have entered the Arctic predominantly by atmospheric and oceanic long-range transport, and this was facilitated by their volatile or semi-volatile properties, while their chemical stability extended their lifetimes following emission. Chemicals present in the Arctic at detectable and quantifiable concentrations testify to their global impact. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. In this study, the abundance and the types of bacteria in the Arctic freshwater were examined and the microbial characteristics were compared to the amount of potentially harmful chemical compounds in particular elements of the Arctic catchment. The highest concentrations of all determined PAHs were observed in two samples in the vicinity of the estuary both in June and September 2016 and were 1964 ng L-1 (R12) and 3901 ng L-1 (R13) in June, and 2179 ng L-1 (R12) and 1349 ng L-1 (R13) in September. Remarkable concentrations of the sum of phenols and formaldehyde were detected also at the outflow of the Revelva river into the sea (R12) and were 0.24 mg L-1 in June and 0.35 mg L-1 in September 2016. The elevated concentrations of chemical compounds near the estuary suggest a potential impact of the water from the lower tributaries (including the glacier-fed stream measured at R13) or the sea currents and the sea aerosol as pollutant sources. The POPs' degradation at low temperature is not well understood but bacteria capable to degrading such compounds were noted in each sampling point.}, }
@article {pmid30442907, year = {2019}, author = {Zhou, W and Chow, KH and Fleming, E and Oh, J}, title = {Selective colonization ability of human fecal microbes in different mouse gut environments.}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {805-823}, doi = {10.1038/s41396-018-0312-9}, pmid = {30442907}, issn = {1751-7370}, support = {1 DP2 GM126893-01//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteroides/growth &amp; development/*physiology ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Genotype ; Humans ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; }, abstract = {Mammalian hosts constantly interact with diverse exogenous microbes, but only a subset of the microbes manage to colonize due to selective colonization resistance exerted by host genetic factors as well as the native microbiota of the host. An important question in microbial ecology and medical science is if such colonization resistance can discriminate closely related microbial species, or even closely related strains of the same species. Using human-mouse fecal microbiota transplantation and metagenomic shotgun sequencing, we reconstructed colonization patterns of human fecal microbes in mice with different genotypes (C57BL6/J vs. NSG) and with or without an intact gut microbiota. We found that mouse genotypes and the native mouse gut microbiota both exerted different selective pressures on exogenous colonizers: human fecal Bacteroides successfully established in the mice gut, however, different species of Bacteroides selectively enriched under different gut conditions, potentially due to a multitude of functional differences, ranging from versatility in nutrient acquisition to stress responses. Additionally, different clades of Bacteroides cellulosilyticus strains were selectively enriched in different gut conditions, suggesting that the fitness of conspecific microbial strains in a novel host environment could differ.}, }
@article {pmid30440093, year = {2019}, author = {Park, CH and Lee, AR and Lee, YR and Eun, CS and Lee, SK and Han, DS}, title = {Evaluation of gastric microbiome and metagenomic function in patients with intestinal metaplasia using 16S rRNA gene sequencing.}, journal = {Helicobacter}, volume = {24}, number = {1}, pages = {e12547}, doi = {10.1111/hel.12547}, pmid = {30440093}, issn = {1523-5378}, support = {//National Research Foundation of Korea (NRF)/ ; NRF-2017R1C1B5015928//Korea government (MSIP; Ministry of Science, ICT &amp; Future Planning)/ ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/classification/genetics/isolation &amp; purification ; Disease Progression ; Female ; Gastritis/microbiology/pathology ; Gastritis, Atrophic/drug therapy/microbiology/pathology ; Gastrointestinal Microbiome/drug effects/*genetics ; Helicobacter Infections/drug therapy/*microbiology/*pathology ; Helicobacter pylori/drug effects/genetics/isolation &amp; purification ; Humans ; Intestines/*microbiology/*pathology ; Male ; Metagenomics ; Metaplasia/*microbiology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Stomach Neoplasms/microbiology/pathology ; Type IV Secretion Systems/genetics ; Young Adult ; }, abstract = {BACKGROUND: Despite recent advances in studies on the gastric microbiome, the role of the non-Helicobacter pylori gastric microbiome in gastric carcinogenesis remains unclear. We evaluated the characteristics of the gastric microbiome and metagenomic functions in patients with IM.<br><br>METHODS: Participants were classified into six groups according to disease status (chronic superficial gastritis [CSG], intestinal metaplasia [IM], and cancer) and H. pylori- infection status (H. pylori-positive and H. pylori-negative). The gastric microbiome was analyzed in mucosal tissues at the gastric antrum by 16S rRNA gene sequencing. Moreover, we assessed the metagenome including the type IV secretion system (T4SS) gene, as T4SS proteins are essential for transferring CagA from H. pylori- into the human gastric epithelium.<br><br>RESULTS: Among the 138 included patients, 48, 9, 23, 14, 12, and 32 were classified into the H. pylori-negative CSG, H. pylori-negative IM, H. pylori-negative cancer, H. pylori-positive CSG, H. pylori-positive IM, and H. pylori-positive cancer groups, respectively. Cyanobacteria were predominant in the H. pylori-negative CSG group compared to in the H. pylori-negative IM and H. pylori-negative cancer groups (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 14.0% vs 4.2% vs 0.04%, P < 0.001). In contrast, Rhizobiales were commonly observed in the H. pylori-negative IM group (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 1.9% vs 15.4% vs 2.8%, P < 0.001). The relative abundance of Rhizobiales increased as H. pylori-infected stomachs progressed from gastritis to IM. In the H. pylori-negative IM group, genes encoding T4SS were prevalent among the metagenome. Additionally, after H. pylori- eradication therapy, the gastric microbiome was similar to the microbiome observed after spontaneous clearance of H. pylori-.<br><br>CONCLUSIONS: The relative abundance of Rhizobiales was higher in patients with H. pylori-negative IM than in those with H. pylori-negative CSG or cancer. Additionally, T4SS genes were highly observed in the metagenome of patients with IM. Highly abundant T4SS proteins in these patients may promote gastric carcinogenesis.}, }
@article {pmid30431224, year = {2019}, author = {Koskella, B}, title = {New approaches to characterizing bacteria-phage interactions in microbial communities and microbiomes.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {15-16}, doi = {10.1111/1758-2229.12706}, pmid = {30431224}, issn = {1758-2229}, mesh = {Bacteria/classification/*virology ; Bacteriophages/classification/genetics/*physiology ; Biodiversity ; Genetic Variation ; Genome, Viral/genetics ; Metagenomics ; *Microbiota ; Single-Cell Analysis ; }, }
@article {pmid30427852, year = {2018}, author = {Brito, TL and Campos, AB and Bastiaan von Meijenfeldt, FA and Daniel, JP and Ribeiro, GB and Silva, GGZ and Wilke, DV and de Moraes, DT and Dutilh, BE and Meirelles, PM and Trindade-Silva, AE}, title = {The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0200437}, pmid = {30427852}, issn = {1932-6203}, mesh = {Animals ; Bivalvia/*microbiology/physiology ; Gammaproteobacteria/*enzymology/genetics/*physiology ; Genomics ; Gills/microbiology ; Glycoside Hydrolases/genetics/*metabolism ; Metagenome ; Microbiota ; Multigene Family ; Phylogeny ; Polysaccharides/*metabolism ; Secondary Metabolism ; *Symbiosis ; Wood/metabolism/parasitology ; }, abstract = {Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae &quot;clade I&quot; strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills' metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.}, }
@article {pmid30427574, year = {2019}, author = {Barnes, RC and Kim, H and Fang, C and Bennett, W and Nemec, M and Sirven, MA and Suchodolski, JS and Deutz, N and Britton, RA and Mertens-Talcott, SU and Talcott, ST}, title = {Body Mass Index as a Determinant of Systemic Exposure to Gallotannin Metabolites during 6-Week Consumption of Mango (Mangifera indica L.) and Modulation of Intestinal Microbiota in Lean and Obese Individuals.}, journal = {Molecular nutrition &amp; food research}, volume = {63}, number = {2}, pages = {e1800512}, doi = {10.1002/mnfr.201800512}, pmid = {30427574}, issn = {1613-4133}, mesh = {Adult ; *Body Mass Index ; Fatty Acids, Volatile/biosynthesis ; Feces/chemistry ; Female ; *Gastrointestinal Microbiome ; Humans ; Hydrolyzable Tannins/*metabolism ; Male ; *Mangifera/chemistry ; Obesity/*metabolism/microbiology ; Phenols/analysis ; Polymerase Chain Reaction ; }, abstract = {SCOPE: This human clinical pilot trial investigated pharmacokinetics of gallotannin-metabolites and modulation of intestinal microbiota in healthy lean and obese individuals after 6 weeks of daily mango consumption.<br><br>METHODS AND RESULTS: Participants are divided into three groups: Lean Mango (LM: n = 12; BMI = 22.9 kg m-2), Obese Mango (OM: n = 9; BMI = 34.6 kg m-2), and Lean Control (LC: n = 11; BMI = 22.1 kg m-2). LM and OM consumed 400 g of mango per day for 6 weeks. LC consumed mango only on Days 0 and 42. After 6 weeks, LM experienced increased systemic exposure (AUC0-8h) to gallotannin-metabolites, 1.4-fold (p = 0.043). The greatest increase is 4-O-methyl-gallic acid, 3.3-fold (p = 0.0026). Cumulative urinary excretion of gallotannin-metabolites significantly increased in LM and OM, but not LC. For OM, qPCR data show increased levels of tannase-producing Lactococcus lactis and decreased levels of Clostridium leptum and Bacteroides thetaiotaomicron, bacteria associated with obesity. LM experienced an increased trend of fecal levels of butyric (1.3-fold; p = 0.09) and valeric acids (1.5-fold; p = 0.056). Plasma endotoxins showed a decreased trend in LM and OM.<br><br>CONCLUSION: Continuous mango intake significantly increased systemic exposure to gallotannin- metabolites and induced an increased trend for fecal short-chain fatty acids in lean but not obese individuals. This pharmacokinetic discrepancy may result in BMI-associated reduced gallotannin-derived health benefits.}, }
@article {pmid30425247, year = {2018}, author = {Hansen, LBS and Roager, HM and Søndertoft, NB and Gøbel, RJ and Kristensen, M and Vallès-Colomer, M and Vieira-Silva, S and Ibrügger, S and Lind, MV and Mærkedahl, RB and Bahl, MI and Madsen, ML and Havelund, J and Falony, G and Tetens, I and Nielsen, T and Allin, KH and Frandsen, HL and Hartmann, B and Holst, JJ and Sparholt, MH and Holck, J and Blennow, A and Moll, JM and Meyer, AS and Hoppe, C and Poulsen, JH and Carvalho, V and Sagnelli, D and Dalgaard, MD and Christensen, AF and Lydolph, MC and Ross, AB and Villas-Bôas, S and Brix, S and Sicheritz-Pontén, T and Buschard, K and Linneberg, A and Rumessen, JJ and Ekstrøm, CT and Ritz, C and Kristiansen, K and Nielsen, HB and Vestergaard, H and Færgeman, NJ and Raes, J and Frøkiær, H and Hansen, T and Lauritzen, L and Gupta, R and Licht, TR and Pedersen, O}, title = {A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4630}, pmid = {30425247}, issn = {2041-1723}, mesh = {Adult ; Aged ; Body Mass Index ; Creatinine/urine ; Cross-Over Studies ; Cytokines/blood ; DNA, Bacterial/analysis ; Denmark ; *Diet ; Fasting ; Feces/microbiology ; Female ; Fermentation ; *Gastrointestinal Microbiome/genetics ; Glutens/*administration &amp; dosage/*adverse effects ; Humans ; Hydrogen ; Intestines/microbiology ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Postprandial Period ; Self Report ; Young Adult ; }, abstract = {Adherence to a low-gluten diet has become increasingly common in parts of the general population. However, the effects of reducing gluten-rich food items including wheat, barley and rye cereals in healthy adults are unclear. Here, we undertook a randomised, controlled, cross-over trial involving 60 middle-aged Danish adults without known disorders with two 8-week interventions comparing a low-gluten diet (2 g gluten per day) and a high-gluten diet (18 g gluten per day), separated by a washout period of at least six weeks with habitual diet (12 g gluten per day). We find that, in comparison with a high-gluten diet, a low-gluten diet induces moderate changes in the intestinal microbiome, reduces fasting and postprandial hydrogen exhalation, and leads to improvements in self-reported bloating. These observations suggest that most of the effects of a low-gluten diet in non-coeliac adults may be driven by qualitative changes in dietary fibres.}, }
@article {pmid30424821, year = {2018}, author = {Singh, NK and Wood, JM and Karouia, F and Venkateswaran, K}, title = {Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {204}, pmid = {30424821}, issn = {2049-2618}, mesh = {Archaea/drug effects/genetics/*isolation &amp; purification ; Azides/pharmacology ; Bacteria/drug effects/genetics/*isolation &amp; purification ; Drug Resistance, Bacterial/*genetics ; Fungi/drug effects/genetics/*isolation &amp; purification ; Humans ; Metagenome/genetics ; Microbiota/drug effects/genetics ; Propidium/analogs &amp; derivatives/pharmacology ; *Space Flight ; *Spacecraft ; Virulence/genetics ; }, abstract = {BACKGROUND: The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms.<br><br>RESULTS: The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii, and Aspergillus lentulus. Even though Rhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3. The AMR signatures associated with β-lactam, cationic antimicrobial peptide, and vancomycin were detected. Prominent virulence factors were cobalt-zinc-cadmium resistance and multidrug-resistance efflux pumps.<br><br>CONCLUSIONS: There was an increase in AMR and virulence gene factors detected over the period sampled, and metagenome sequences of human pathogens persisted over time. Comparative analysis of the microbial compositions of ISS with Earth analogs revealed that the ISS environmental surfaces were different in microbial composition. Metagenomics coupled with PMA treatment would help future space missions to estimate problematic risk group microbial pathogens. Cataloging AMR/virulence characteristics, succession, accumulation, and persistence of microorganisms would facilitate the development of suitable countermeasures to reduce their presence in the closed built environment.}, }
@article {pmid30423107, year = {2018}, author = {García-Jiménez, B and de la Rosa, T and Wilkinson, MD}, title = {MDPbiome: microbiome engineering through prescriptive perturbations.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {17}, pages = {i838-i847}, pmid = {30423107}, issn = {1367-4811}, mesh = {Algorithms ; Markov Chains ; Metagenomics ; *Microbiota ; Molecular Conformation ; Software ; }, abstract = {Motivation: Recent microbiome dynamics studies highlight the current inability to predict the effects of external perturbations on complex microbial populations. To do so would be particularly advantageous in fields such as medicine, bioremediation or industrial scenarios.<br><br>Results: MDPbiome statistically models longitudinal metagenomics samples undergoing perturbations as a Markov Decision Process (MDP). Given a starting microbial composition, our MDPbiome system suggests the sequence of external perturbation(s) that will engineer that microbiome to a goal state, for example, a healthier or more performant composition. It also estimates intermediate microbiome states along the path, thus making it possible to avoid particularly undesirable/unhealthy states. We demonstrate MDPbiome performance over three real and distinct datasets, proving its flexibility, and the reliability and universality of its output 'optimal perturbation policy'. For example, an MDP created using a vaginal microbiome time series, with a goal of recovering from bacterial vaginosis, suggested avoidance of perturbations such as lubricants or sex toys; while another MDP provided a quantitative explanation for why salmonella vaccine accelerates gut microbiome maturation in chicks. This novel analytical approach has clear applications in medicine, where it could suggest low-impact clinical interventions that will lead to achievement or maintenance of a healthy microbial population, or alternately, the sequence of interventions necessary to avoid strongly negative microbiome states.<br><br>Code (https://github.com/beatrizgj/MDPbiome) and result files (https://tomdelarosa.shinyapps.io/MDPbiome/) are available online.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30420843, year = {2018}, author = {Alves, LF and Meleiro, LP and Silva, RN and Westmann, CA and Guazzaroni, ME}, title = {Novel Ethanol- and 5-Hydroxymethyl Furfural-Stimulated β-Glucosidase Retrieved From a Brazilian Secondary Atlantic Forest Soil Metagenome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2556}, pmid = {30420843}, issn = {1664-302X}, abstract = {Beta-glucosidases are key enzymes involved in lignocellulosic biomass degradation for bioethanol production, which complete the final step during cellulose hydrolysis by converting cellobiose into glucose. Currently, industry requires enzymes with improved catalytic performance or tolerance to process-specific parameters. In this sense, metagenomics has become a powerful tool for accessing and exploring the biochemical biodiversity present in different natural environments. Here, we report the identification of a novel β-glucosidase from metagenomic DNA isolated from soil samples enriched with decaying plant matter from a Secondary Atlantic Forest region. For this, we employed a functional screening approach using an optimized and synthetic broad host-range vector for library production. The novel β-glucosidase - named Lfa2 - displays three GH3-family conserved domains and conserved catalytic amino acids D283 and E487. The purified enzyme was most active in pH 5.5 and at 50°C, and showed hydrolytic activity toward several pNP synthetic substrates containing β-glucose, β-galactose, β-xylose, β-fucose, and α-arabinopyranose, as well as toward cellobiose. Lfa2 showed considerable glucose tolerance, exhibiting an IC50 of 300 mM glucose and 30% of remaining activity in 600 mM glucose. In addition, Lfa2 retained full or slightly enhanced activity in the presence of several metal ions. Further, β-glucosidase activity was increased by 1.7-fold in the presence of 10% (v/v) ethanol, a concentration that can be reached in conventional fermentation processes. Similarly, Lfa2 showed 1.7-fold enhanced activity at high concentrations of 5-hydroxymethyl furfural, one of the most important cellulase inhibitors in pretreated sugarcane bagasse hydrolysates. Moreover, the synergistic effect of Lfa2 on Bacillus subtilis GH5-CBM3 endoglucanase activity was demonstrated by the increased production of glucose (1.6-fold). Together, these results indicate that β-glucosidase Lfa2 is a promissory enzyme candidate for utilization in diverse industrial applications, such as cellulosic biomass degradation or flavor enhancement in winemaking and grape processing.}, }
@article {pmid30419949, year = {2018}, author = {Silverman, JD and Durand, HK and Bloom, RJ and Mukherjee, S and David, LA}, title = {Dynamic linear models guide design and analysis of microbiota studies within artificial human guts.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {202}, pmid = {30419949}, issn = {2049-2618}, support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; }, mesh = {Artificial Organs/*microbiology ; Bacteroides/*growth &amp; development ; Enterobacteriaceae/*growth &amp; development ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Linear Models ; *Models, Anatomic ; }, abstract = {BACKGROUND: Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models' fundamental biology include the timescales on which microbiota vary and the factors that drive such change. Answering these questions though requires overcoming analytical obstacles like estimating the effects of technical variation on observed microbiota dynamics, as well as the lack of appropriate benchmark datasets.<br><br>RESULTS: To address these obstacles, we created a modeling framework based on multinomial logistic-normal dynamic linear models (MALLARDs) and performed dense longitudinal sampling of four replicate artificial human guts over the course of 1 month. The resulting analyses revealed how the ratio of biological variation to technical variation from sample processing depends on sampling frequency. In particular, we find that at hourly sampling frequencies, 76% of observed variation could be ascribed to technical sources, which could also skew the observed covariation between taxa. We also found that the artificial guts demonstrated replicable trajectories even after a recovery from a transient feed disruption. Additionally, we observed irregular sub-daily oscillatory dynamics associated with the bacterial family Enterobacteriaceae within all four replicate vessels.<br><br>CONCLUSIONS: Our analyses suggest that, beyond variation due to sequence counting, technical variation from sample processing can obscure temporal variation from biological sources in artificial gut studies. Our analyses also supported hypotheses that human gut microbiota fluctuates on sub-daily timescales in the absence of a host and that microbiota can follow replicable trajectories in the presence of environmental driving forces. Finally, multiple aspects of our approach are generalizable and could ultimately be used to facilitate the design and analysis of longitudinal microbiota studies in vivo.}, }
@article {pmid30418043, year = {2018}, author = {Muleviciene, A and D'Amico, F and Turroni, S and Candela, M and Jankauskiene, A}, title = {Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {65}, number = {4}, pages = {551-564}, doi = {10.1556/030.65.2018.045}, pmid = {30418043}, issn = {1217-8950}, mesh = {Anemia, Iron-Deficiency/*complications ; Bacteria/classification/genetics ; Child ; Child, Preschool ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; *Microbiota ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Nutritional iron deficiency (ID) causes not only anemia but also malfunction of the entire human organism. Recently, a role of the gut microbiota has been hypothesized, but limited data are available especially in infants. Here, we performed a pilot study to explore the gut microbiota in 10 patients with iron deficiency anemia (IDA) and 10 healthy controls aged 6-34 months. Fresh stool samples were collected from diapers, and the fecal microbiota was profiled by next-generation sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Except for diet diversity, the breastfeeding status at the enrollment, the exclusive breastfeeding duration, and the introduction of complementary foods did not differ between groups. Distinct microbial signatures were found in IDA patients, with increased relative abundance of Enterobacteriaceae (mean relative abundance, patients vs. controls, 4.4% vs. 3.0%) and Veillonellaceae (13.7% vs. 3.6%), and reduced abundance of Coriobacteriaceae (3.5% vs. 8.8%) compared to healthy controls. A decreased Bifidobacteriaceae/Enterobacteriaceae ratio was observed in IDA patients. Notwithstanding the low sample size, our data highlight microbiota dysbalance in IDA worth for further investigations, aimed at unraveling the ID impact on the microbiome trajectory in early life, and the possible long-term consequences.}, }
@article {pmid30417889, year = {2018}, author = {Hyeon, JY and Mann, DA and Townsend, AM and Deng, X}, title = {Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {140}, pages = {}, pmid = {30417889}, issn = {1940-087X}, mesh = {Animals ; Cattle ; Environmental Monitoring ; Food Microbiology/*methods ; High-Throughput Nucleotide Sequencing ; Immunomagnetic Separation/*methods ; Metagenomics/*methods ; Microbiota ; Polymerase Chain Reaction ; *Salmonella enterica ; }, abstract = {Quasi-metagenomics sequencing refers to the sequencing-based analysis of modified microbiomes of food and environmental samples. In this protocol, microbiome modification is designed to concentrate genomic DNA of a target foodborne pathogen contaminant to facilitate the detection and subtyping of the pathogen in a single workflow. Here, we explain and demonstrate the sample preparation steps for the quasi-metagenomics analysis of Salmonella enterica from representative food and environmental samples including alfalfa sprouts, ground black pepper, ground beef, chicken breast and environmental swabs. Samples are first subjected to the culture enrichment of Salmonella for a shortened and adjustable duration (4-24 h). Salmonella cells are then selectively captured from the enrichment culture by immunomagnetic separation (IMS). Finally, multiple displacement amplification (MDA) is performed to amplify DNA from IMS-captured cells. The DNA output of this protocol can be sequenced by high throughput sequencing platforms. An optional quantitative PCR analysis can be performed to replace sequencing for Salmonella detection or assess the concentration of Salmonella DNA before sequencing.}, }
@article {pmid30414158, year = {2019}, author = {Bosch, TCG}, title = {Hydra as Model to Determine the Role of FOXO in Longevity.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1890}, number = {}, pages = {231-238}, doi = {10.1007/978-1-4939-8900-3_19}, pmid = {30414158}, issn = {1940-6029}, mesh = {Aging/genetics/metabolism ; Animals ; Animals, Genetically Modified ; Forkhead Transcription Factors/*genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Genes, Reporter ; Genetic Vectors/genetics ; Hydra/classification/*genetics/metabolism ; Longevity/*genetics ; Metagenome ; Metagenomics/methods ; Microbiota ; Molecular Imaging ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Recombinant Fusion Proteins ; Stem Cells/metabolism ; }, abstract = {In non-senescent Hydra, continuously high activity of transcription factor FOXO contributes to continuous stem cell proliferation. Here, we describe how genetic manipulation of Hydra polyps using embryo-microinjection allows uncovering the role of FOXO in coordinating both stem cell proliferation and antimicrobial peptide0073 , effector molecules of the innate immune system, and regulators of the microbiome.}, }
@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 {pmid30412889, year = {2019}, author = {Nathani, NM and Mootapally, C and Dave, BP}, title = {Antibiotic resistance genes allied to the pelagic sediment microbiome in the Gulf of Khambhat and Arabian Sea.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {446-454}, doi = {10.1016/j.scitotenv.2018.10.409}, pmid = {30412889}, issn = {1879-1026}, mesh = {Bacteria/classification/drug effects/*genetics/*isolation &amp; purification ; *Drug Resistance, Microbial ; Genes, Bacterial/*drug effects ; Geologic Sediments/*microbiology ; Indian Ocean ; *Microbiota ; }, abstract = {Antibiotics have been widely spread in the environments, imposing profound stress on the resistome of the residing microbes. Marine microbiomes are well established large reservoirs of novel antibiotics and corresponding resistance genes. The Gulf of Khambhat is known for its extreme tides and complex sedimentation process. We performed high throughput sequencing and applied bioinformatics techniques on pelagic sediment microbiome across four coordinates of the Gulf of Khambhat to assess the marine resistome, its corresponding bacterial community and compared with the open Arabian Sea sample. We identified a total of 2354 unique types of resistance genes, with most abundant and diverse gene profile in the area that had anthropogenic activities being carried out on-shore. The genes with >1% abundance in all samples included carA, macB, sav1866, tlrC, srmB, taeA, tetA, oleC and bcrA which belonged to the macrolides, glycopeptides and peptide drug classes. ARG enriched phyla distribution was quite varying between all the sites, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes among the dominant phyla. Based on the outcomes, we also propose potential biomarker candidates Desulfovibrio, Thermotaga and Pelobacter for antibiotic monitoring in the two of the Gulf samples probable contamination prone environments, and genera Nitrosocccus, Marinobacter and Streptomyces in the rest of the three studied samples. Outcomes support the concept that ARGs naturally originate in environments and human activities contribute to the dissemination of antibiotic resistance.}, }
@article {pmid30412047, year = {2018}, author = {Charles, J and Tangudu, CS and Hurt, SL and Tumescheit, C and Firth, AE and Garcia-Rejon, JE and Machain-Williams, C and Blitvich, BJ}, title = {Detection of novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico using metagenomics and characterization of their in vitro host ranges.}, journal = {The Journal of general virology}, volume = {99}, number = {12}, pages = {1729-1738}, doi = {10.1099/jgv.0.001165}, pmid = {30412047}, issn = {1465-2099}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI114720/AI/NIAID NIH HHS/United States ; R21 AI067281/AI/NIAID NIH HHS/United States ; 106207/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Biodiversity ; Cell Line ; Culicidae/*virology ; *Host Specificity ; Humans ; Metagenomics ; Mexico ; Phylogeny ; RNA Viruses/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Virus Cultivation ; }, abstract = {A metagenomics approach was used to detect novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico. A total of 1359 mosquitoes of 7 species and 5 genera (Aedes, Anopheles, Culex, Mansonia and Psorophora) were sorted into 37 pools, homogenized and inoculated onto monolayers of Aedes albopictus (C6/36) cells. A second blind passage was performed and then total RNA was extracted and analysed by RNA-seq. Two novel viruses, designated Uxmal virus and Mayapan virus, were identified. Uxmal virus was isolated from three pools of Aedes (Ochlerotatus) taeniorhynchus and phylogenetic data indicate that it should be classified within the recently proposed taxon Negevirus. Mayapan virus was recovered from two pools of Psorophora ferox and is most closely related to unclassified Nodaviridae-like viruses. Two recognized viruses were also detected: Culex flavivirus (family Flaviviridae) and Houston virus (family Mesoniviridae), with one and two isolates being recovered, respectively. The in vitro host ranges of all four viruses were determined by assessing their replicative abilities in cell lines of avian, human, monkey, hamster, murine, lepidopteran and mosquito (Aedes, Anopheles and Culex) origin, revealing that all viruses possess vertebrate replication-incompetent phenotypes. In conclusion, we report the isolation of both novel and recognized RNA viruses from mosquitoes collected in Mexico, and add to the growing plethora of viruses discovered recently through the use of metagenomics.}, }
@article {pmid30411190, year = {2019}, author = {Rossi, A and Bellone, A and Fokin, SI and Boscaro, V and Vannini, C}, title = {Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {232-242}, doi = {10.1007/s00248-018-1279-9}, pmid = {30411190}, issn = {1432-184X}, support = {565-60%2016//University of Pisa/ ; 565-60%2017//University of Pisa/ ; 565-FFABR 2017//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Biological Evolution ; Ciliophora/genetics/isolation &amp; purification/*microbiology/physiology ; Ecosystem ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Pilot Projects ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.}, }
@article {pmid30406041, year = {2018}, author = {Xiao, P and Li, C and Zhang, Y and Han, J and Guo, X and Xie, L and Tian, M and Li, Y and Wang, M and Liu, H and Ren, J and Zhou, H and Lu, H and Jin, N}, title = {Metagenomic Sequencing From Mosquitoes in China Reveals a Variety of Insect and Human Viruses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {364}, pmid = {30406041}, issn = {2235-2988}, mesh = {Animals ; *Biodiversity ; Cercopithecus aethiops ; China ; Computational Biology ; *Metagenomics ; Mosquito Vectors/*virology ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Viruses/*classification/*genetics ; }, abstract = {We collected 8,700 mosquitoes in three sites in China, which belonged to seven species. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The abundant viral sequences were detected and annotated belonging to more than 50 viral taxonomic families. The results were verified by PCR, followed by phylogenetic analysis. In the present study, we identified partial viral genes of dengue virus (DENV), a novel circovirus (CCV), densovirus (DNV), Japanese encephalitis virus (JEV), and Wuhan mosquito virus (WMV) in mosquitoes. Metagenomic analysis and PCR amplification revealed three DENV sequences, which were as homologous to the NS3 gene of DENV from Singapore isolated in 2005, with at least 91% nucleotide (nt) identity. Seven fragments of JEV encoding structural proteins were identified belonging to genotype I. They all shared high homology with structural protein genes of JEV isolated from Laos in 2009. The production of infectious virus particles of the newly isolated virus YunnanJEV2017-4 increased after passage from the BHK-21 cell line to the Vero cell line. Novel circovirus-related genes were identified and as being related to an unnamed gene of a mosquito circovirus (MCCV) sequence from the USA isolated in 2011, with at least 41% nt identity: this distant relationship suggests that the parent virus might belong to a novel circovirus genus. Additionally, numerous known viruses and some unknown viruses were also detected in mosquitoes from Yunnan province, China, which will be tested for propagation.}, }
@article {pmid30405577, year = {2018}, author = {Bertelli, C and Courtois, S and Rosikiewicz, M and Piriou, P and Aeby, S and Robert, S and Loret, JF and Greub, G}, title = {Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2520}, pmid = {30405577}, issn = {1664-302X}, abstract = {In drinking water distribution systems (DWDS), a disinfectant residual is usually applied to limit bacterial regrowth. However, delivering water with no or reduced chlorine residual could potentially decrease the selection for antimicrobial resistant microorganisms, favor bacterial regrowth and result in changes in bacterial populations. To evaluate the feasibility of water reduction in local DWDS while ensuring water safety, water quality was measured over 2 months in two different networks, each of them harboring sub-areas with normal and reduced chlorine. Water quality remained good in chlorine reduced samples, with limited development of total flora and absence of coliforms. Furthermore, 16S rRNA amplicon-based metagenomics was used to investigate the diversity and the composition of microbial communities in the sub-networks. Taxonomic classification of sequence reads showed a reduced bacterial diversity in sampling points with higher chlorine residuals. Chlorine disinfection created more homogeneous bacterial population, dominated by Pseudomonas, a genus that contains some major opportunistic pathogens such as P. aeruginosa. In the absence of chlorine, a larger and unknown biodiversity was unveiled, also highlighted by a decreased rate of taxonomic classification to the genus and species level. Overall, this experiment in a functional DWDS will facilitate the move toward potable water delivery systems without residual disinfectants and will improve water taste for consumers.}, }
@article {pmid30401779, year = {2018}, author = {Bratburd, JR and Keller, C and Vivas, E and Gemperline, E and Li, L and Rey, FE and Currie, CR}, title = {Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30401779}, issn = {2150-7511}, support = {U19 AI109673/AI/NIAID NIH HHS/United States ; R56 DK071801/DK/NIDDK NIH HHS/United States ; R01 DK108259/DK/NIDDK NIH HHS/United States ; S10 RR029531/RR/NCRR NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; R01 DK071801/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biosynthetic Pathways ; Candida albicans/pathogenicity ; Candidiasis/*microbiology ; Cecum/microbiology ; Disease Models, Animal ; Enterobacteriaceae/isolation &amp; purification ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; Male ; Metabolomics ; Metagenomics ; Mice ; Mice, Inbred C57BL ; *Microbiota ; Oxidative Stress ; Salmonella Infections, Animal/*microbiology ; Salmonella typhimurium/pathogenicity ; }, abstract = {The gut microbiota confers resistance to pathogens of the intestinal ecosystem, yet the dynamics of pathogen-microbiome interactions and the metabolites involved in this process remain largely unknown. Here, we use gnotobiotic mice infected with the virulent pathogen Salmonella enterica serovar Typhimurium or the opportunistic pathogen Candida albicans in combination with metagenomics and discovery metabolomics to identify changes in the community and metabolome during infection. To isolate the role of the microbiota in response to pathogens, we compared mice monocolonized with the pathogen, uninfected mice &quot;humanized&quot; with a synthetic human microbiome, or infected humanized mice. In Salmonella-infected mice, by 3 days into infection, microbiome community structure and function changed substantially, with a rise in Enterobacteriaceae strains and a reduction in biosynthetic gene cluster potential. In contrast, Candida-infected mice had few microbiome changes. The LC-MS metabolomic fingerprint of the cecum differed between mice monocolonized with either pathogen and humanized infected mice. Specifically, we identified an increase in glutathione disulfide, glutathione cysteine disulfide, inosine 5'-monophosphate, and hydroxybutyrylcarnitine in mice infected with Salmonella in contrast to uninfected mice and mice monocolonized with Salmonella These metabolites potentially play a role in pathogen-induced oxidative stress. These results provide insight into how the microbiota community members interact with each other and with pathogens on a metabolic level.IMPORTANCE The gut microbiota is increasingly recognized for playing a critical role in human health and disease, especially in conferring resistance to both virulent pathogens such as Salmonella, which infects 1.2 million people in the United States every year (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, et al., Emerg Infect Dis 17:7-15, 2011, https://doi.org/10.3201/eid1701.P11101), and opportunistic pathogens like Candida, which causes an estimated 46,000 cases of invasive candidiasis each year in the United States (Centers for Disease Control and Prevention, Antibiotic Resistance Threats in the United States, 2013, 2013). Using a gnotobiotic mouse model, we investigate potential changes in gut microbial community structure and function during infection using metagenomics and metabolomics. We observe that changes in the community and in biosynthetic gene cluster potential occur within 3 days for the virulent Salmonella enterica serovar Typhimurium, but there are minimal changes with a poorly colonizing Candida albicans In addition, the metabolome shifts depending on infection status, including changes in glutathione metabolites in response to Salmonella infection, potentially in response to host oxidative stress.}, }
@article {pmid30400812, year = {2018}, author = {Kumar, MS and Slud, EV and Okrah, K and Hicks, SC and Hannenhalli, S and Corrada Bravo, H}, title = {Analysis and correction of compositional bias in sparse sequencing count data.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {799}, pmid = {30400812}, issn = {1471-2164}, support = {K99 HG009007/HG/NHGRI NIH HHS/United States ; R01 RR021967/RR/NCRR NIH HHS/United States ; GM114267//National Institutes of Health/ ; R01 GM083084/GM/NIGMS NIH HHS/United States ; HG005220//National Institutes of Health/ ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R21 GM107683/GM/NIGMS NIH HHS/United States ; 1564785//National Science Foundation (US)/ ; R01 GM114267/GM/NIGMS NIH HHS/United States ; GM083084//National Institutes of Health/ ; R01 GM103552/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Bayes Theorem ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count data is compositional, measuring relative and not absolute abundances of the assayed features. This compositional bias confounds inference of absolute abundances. Commonly used count data normalization approaches like library size scaling/rarefaction/subsampling cannot correct for compositional or any other relevant technical bias that is uncorrelated with library size.<br><br>RESULTS: We demonstrate that existing techniques for estimating compositional bias fail with sparse metagenomic 16S count data and propose an empirical Bayes normalization approach to overcome this problem. In addition, we clarify the assumptions underlying frequently used scaling normalization methods in light of compositional bias, including scaling methods that were not designed directly to address it.<br><br>CONCLUSIONS: Compositional bias, induced by the sequencing machine, confounds inferences of absolute abundances. We present a normalization technique for compositional bias correction in sparse sequencing count data, and demonstrate its improved performance in metagenomic 16s survey data. Based on the distribution of technical bias estimates arising from several publicly available large scale 16s count datasets, we argue that detailed experiments specifically addressing the influence of compositional bias in metagenomics are needed.}, }
@article {pmid30397794, year = {2019}, author = {Lau, NS and Zarkasi, KZ and Md Sah, ASR and Shu-Chien, AC}, title = {Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {20-32}, doi = {10.1007/s00248-018-1283-0}, pmid = {30397794}, issn = {1432-184X}, mesh = {Aquaculture ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Lakes/chemistry/*microbiology ; Malaysia ; Metagenomics ; *Microbiota ; Nitrogen/analysis/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/analysis/metabolism ; }, abstract = {Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.}, }
@article {pmid30397356, year = {2018}, author = {Sun, L and Xie, C and Wang, G and Wu, Y and Wu, Q and Wang, X and Liu, J and Deng, Y and Xia, J and Chen, B and Zhang, S and Yun, C and Lian, G and Zhang, X and Zhang, H and Bisson, WH and Shi, J and Gao, X and Ge, P and Liu, C and Krausz, KW and Nichols, RG and Cai, J and Rimal, B and Patterson, AD and Wang, X and Gonzalez, FJ and Jiang, C}, title = {Gut microbiota and intestinal FXR mediate the clinical benefits of metformin.}, journal = {Nature medicine}, volume = {24}, number = {12}, pages = {1919-1929}, doi = {10.1038/s41591-018-0222-4}, pmid = {30397356}, issn = {1546-170X}, support = {T32 LM012415/LM/NLM NIH HHS/United States ; Z01 BC005561-20//NULL/International ; Z01 BC005561-21//NULL/International ; }, mesh = {Bacteroides/drug effects/pathogenicity ; Bile Acids and Salts/metabolism ; Diabetes Mellitus, Type 2/*drug therapy/genetics/microbiology/pathology ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/*drug effects/genetics ; Gene Expression Regulation, Bacterial/drug effects ; Glucose Intolerance/drug therapy/genetics/microbiology ; Humans ; Hyperglycemia/drug therapy/genetics/microbiology/pathology ; Metabolome/drug effects/genetics ; Metagenomics/methods ; Metformin/*administration &amp; dosage ; Obesity/*drug therapy/genetics/microbiology/pathology ; Receptors, Cytoplasmic and Nuclear/*genetics ; Ursodeoxycholic Acid/analogs &amp; derivatives ; }, abstract = {The anti-hyperglycemic effect of metformin is believed to be caused by its direct action on signaling processes in hepatocytes, leading to lower hepatic gluconeogenesis. Recently, metformin was reported to alter the gut microbiota community in humans, suggesting that the hyperglycemia-lowering action of the drug could be the result of modulating the population of gut microbiota. However, the critical microbial signaling metabolites and the host targets associated with the metabolic benefits of metformin remained elusive. Here, we performed metagenomic and metabolomic analysis of samples from individuals with newly diagnosed type 2 diabetes (T2D) naively treated with metformin for 3 d, which revealed that Bacteroides fragilis was decreased and the bile acid glycoursodeoxycholic acid (GUDCA) was increased in the gut. These changes were accompanied by inhibition of intestinal farnesoid X receptor (FXR) signaling. We further found that high-fat-diet (HFD)-fed mice colonized with B. fragilis were predisposed to more severe glucose intolerance, and the metabolic benefits of metformin treatment on glucose intolerance were abrogated. GUDCA was further identified as an intestinal FXR antagonist that improved various metabolic endpoints in mice with established obesity. Thus, we conclude that metformin acts in part through a B. fragilis-GUDCA-intestinal FXR axis to improve metabolic dysfunction, including hyperglycemia.}, }
@article {pmid30396371, year = {2018}, author = {Meisel, JS and Nasko, DJ and Brubach, B and Cepeda-Espinoza, V and Chopyk, J and Corrada-Bravo, H and Fedarko, M and Ghurye, J and Javkar, K and Olson, ND and Shah, N and Allard, SM and Bazinet, AL and Bergman, NH and Brown, A and Caporaso, JG and Conlan, S and DiRuggiero, J and Forry, SP and Hasan, NA and Kralj, J and Luethy, PM and Milton, DK and Ondov, BD and Preheim, S and Ratnayake, S and Rogers, SM and Rosovitz, MJ and Sakowski, EG and Schliebs, NO and Sommer, DD and Ternus, KL and Uritskiy, G and Zhang, SX and Pop, M and Treangen, TJ}, title = {Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {197}, pmid = {30396371}, issn = {2049-2618}, support = {R01 AI100947/AI/NIAID NIH HHS/United States ; U54 CA143924/CA/NCI NIH HHS/United States ; U54 CA143925/CA/NCI NIH HHS/United States ; R01 GM114267/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Warfare Agents ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/physiology ; Sequence Analysis, DNA/methods ; }, abstract = {The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.}, }
@article {pmid30396006, year = {2019}, author = {Velikonja, A and Lipoglavšek, L and Zorec, M and Orel, R and Avguštin, G}, title = {Alterations in gut microbiota composition and metabolic parameters after dietary intervention with barley beta glucans in patients with high risk for metabolic syndrome development.}, journal = {Anaerobe}, volume = {55}, number = {}, pages = {67-77}, doi = {10.1016/j.anaerobe.2018.11.002}, pmid = {30396006}, issn = {1095-8274}, mesh = {Adult ; Aged ; Cholesterol/blood ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet Therapy/*methods ; Dietary Fiber/*administration &amp; dosage ; Double-Blind Method ; Fatty Acids, Volatile/analysis ; Feces/chemistry ; Female ; Gastrointestinal Microbiome/*drug effects ; Healthy Volunteers ; Hordeum/*chemistry ; Humans ; Male ; Metabolic Syndrome/*therapy ; Middle Aged ; Phylogeny ; Placebos/administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Treatment Outcome ; beta-Glucans/*administration &amp; dosage ; }, abstract = {Metabolic syndrome is a complex disease that is exponentially increasing in the western world, and diet is one of the possible ways to improve the metabolic status of patients. Barley beta glucans are dietary fibres that show promise for improvement cholesterol levels and postprandial glucose response, but they have been rarely investigated in human trials with concurrent focus on gut microbiota. A double-blind, placebo-controlled, randomised clinical trial was conducted with 43 volunteers with high risk for metabolic syndrome development or with diagnosed metabolic syndrome. During a four-week intervention study, participants consumed experimental bread containing 6 g of barley beta glucans or equal bread but without beta glucans. After dietary intervention, total plasma cholesterol decreased in the test group (-0.26 ± 0.54, p = 0.019), but not in the control group. Short chain fatty acids (SCFA) composition in faeces significantly changed with increase of propionic acid in test group (43.2%, p = 0.045) and with decrease of acetic acid in control group (41.8%, p = 0.011). The microbiome analysis based on Illumina paired end sequencing of 16S rRNA genes showed a decrease in microbial diversity and richness in the test group. The pre-intervention gut microbiota composition showed higher abundance of health associated Bifidobacterium spp. and Akkermansia municiphila within cholesterol-responsive group, showing that diet-induced metabolic response is possibly dependent on individual gut microbiota composition.}, }
@article {pmid30394664, year = {2019}, author = {Spang, A and Offre, P}, title = {Towards a systematic understanding of differences between archaeal and bacterial diversity.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {9-12}, doi = {10.1111/1758-2229.12701}, pmid = {30394664}, issn = {1758-2229}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biodiversity ; Biological Evolution ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Single-Cell Analysis ; }, abstract = {In this crystal ball, we discuss emerging methodologies that can help reaching a synthesis on the biodiversity of Archaea and Bacteria and thereby inform a central enigma in microbiology, i.e. the fundamental split between these primary domains of life and the apparent lower diversity of the Archaea.}, }
@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/International ; FE0024297//Department of Energy's National Energy Technology Laboratory/International ; //U.S. Department of Energy Joint Genome Institute/International ; DE-AC02-05CH11231//Office of Science of the U.S. Department of Energy/International ; }, mesh = {Ecosystem ; Genome, Bacterial ; *Hydraulic Fracking ; Metagenome ; Methanosarcinaceae/genetics/*physiology ; Natural Gas ; Oil and Gas Fields ; }, 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 {pmid30390805, year = {2018}, author = {Wang, Q and Yang, F and Jia, H}, title = {Mining the Microbiome for Drug Targets.}, journal = {Methods in enzymology}, volume = {610}, number = {}, pages = {59-72}, doi = {10.1016/bs.mie.2018.09.014}, pmid = {30390805}, issn = {1557-7988}, mesh = {Drug Discovery/*methods ; Humans ; Metagenome/drug effects ; Metagenomics/*methods ; Microbiota/*drug effects ; Molecular Targeted Therapy/methods ; }, abstract = {The human microbiome is our &quot;other genome.&quot; Implicated in a growing list of complex diseases, for which genomic studies typically explain a portion of the disease susceptibility, the human gut microbiome has been at the spotlight for our understanding of human diseases. As the microbiome is intrinsically more variable than the human genome, it is important to take careful considerations at each step of a study. Here, we put forward our recommendations, which we envision would facilitate identification of true drug targets in the human microbiome in the colon as well as at other body sites.}, }
@article {pmid30390509, year = {2019}, author = {Leng, L and Nobu, MK and Narihiro, T and Yang, P and Amy Tan, GY and Lee, PH}, title = {Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: Pathways and mechanisms.}, journal = {Water research}, volume = {148}, number = {}, pages = {281-291}, doi = {10.1016/j.watres.2018.10.063}, pmid = {30390509}, issn = {1879-2448}, mesh = {Caproates ; Fermentation ; *Glycerol ; *Microbial Consortia ; Propylene Glycols ; }, abstract = {Glycerol is presently being generated in surplus with the rapid growth of the biodiesel industry and seeks ways to be upcycled, rather than to be treated with costs. Glycerol for the co-production of 1,3-propanediol (1,3-PDO) and caproate has a great prospect. Yet, its technical difficulty lies in the enhancement of caproate productivity, which requires the presence of ethanol as a co-substrate and necessitates the co-existence of functional microbes for glycerol fermentation and chain elongation. This study successfully achieved 6.38 mM C 1,3-PDO d-1 and 2.95 mM C caproate d-1 in a 2-L mixed-cultured semi-continuous fermenter with a glycerol-ethanol-acetate stoichiometric ratio of 4:3:1. Such conversions were mainly facilitated by a microbial community of Eubacterium limosum, Clostridium kluyveri and Massilibacterium senegalense. With such a synergistic microbiome, the co-production of 1,3-PDO and caproate was achieved from glycerol without ethanol addition. Based on metagenomics, E. limosum is capable of converting glycerol to 1,3-PDO, ethanol and H2, and also redirecting the electron potential of H2 into acetate via the Wood-Ljungdahl pathway, which is then used for chain elongation. C. kluyveri worked synergistically with E. limosum by consuming ethanol and acetate for caproate production. M. senegalense encodes for ethanol oxidation to acetate and butyrate, facilitating the generation of these intermediates for C. kluyveri elongation to caproate. During the transition between fermentation and elongation, an unexpected observation of poly-β-hydroxybutyrate (PHB) formation and reutilization by M. senegalense may be associated with butyrate formation for further caproate generation. The knowledge gleaned from the substrate constitute, microbial consortium and their synergetic metabolism demonstrates a resource upgrade potential for crude glycerol or glycerol-containing wastewater generated from the biodiesel industry.}, }
@article {pmid30388453, year = {2018}, author = {Vangay, P and Johnson, AJ and Ward, TL and Al-Ghalith, GA and Shields-Cutler, RR and Hillmann, BM and Lucas, SK and Beura, LK and Thompson, EA and Till, LM and Batres, R and Paw, B and Pergament, SL and Saenyakul, P and Xiong, M and Kim, AD and Kim, G and Masopust, D and Martens, EC and Angkurawaranon, C and McGready, R and Kashyap, PC and Culhane-Pera, KA and Knights, D}, title = {US Immigration Westernizes the Human Gut Microbiome.}, journal = {Cell}, volume = {175}, number = {4}, pages = {962-972.e10}, doi = {10.1016/j.cell.2018.10.029}, pmid = {30388453}, issn = {1097-4172}, support = {R01 DK114007/DK/NIDDK NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; *Asian Continental Ancestry Group ; Bacteroides/isolation &amp; purification ; Dietary Fiber/metabolism ; Emigrants and Immigrants ; *Emigration and Immigration ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Obesity/epidemiology/microbiology ; Prevotella/isolation &amp; purification ; United States ; }, abstract = {Many US immigrant populations develop metabolic diseases post immigration, but the causes are not well understood. Although the microbiome plays a role in metabolic disease, there have been no studies measuring the effects of US immigration on the gut microbiome. We collected stool, dietary recalls, and anthropometrics from 514 Hmong and Karen individuals living in Thailand and the United States, including first- and second-generation immigrants and 19 Karen individuals sampled before and after immigration, as well as from 36 US-born European American individuals. Using 16S and deep shotgun metagenomic DNA sequencing, we found that migration from a non-Western country to the United States is associated with immediate loss of gut microbiome diversity and function in which US-associated strains and functions displace native strains and functions. These effects increase with duration of US residence and are compounded by obesity and across generations.}, }
@article {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 {pmid30384205, year = {2019}, author = {Duan, Y and Awasthi, SK and Chen, H and Liu, T and Zhang, Z and Zhang, L and Awasthi, MK and Taherzadeh, MJ}, title = {Evaluating the impact of bamboo biochar on the fungal community succession during chicken manure composting.}, journal = {Bioresource technology}, volume = {272}, number = {}, pages = {308-314}, doi = {10.1016/j.biortech.2018.10.045}, pmid = {30384205}, issn = {1873-2976}, mesh = {Animals ; Charcoal/*metabolism ; Chickens ; *Composting ; Manure/*microbiology ; *Mycobiome ; Sasa/*metabolism ; }, abstract = {The objective of this study was to investigate the fungal community succession and variations in chicken manure (CM) compost with different concentration of bamboo biochar (BB) as additive via the using of metagenomics method. The consequent obviously revealed that Chytridiomycota, Mucoromycota, Ascomycota and Basidiomycota were the dominant phylum, while Batrachochytrium, Funneliformis, Mucor, Phizophagus and Pyronema were the pre-dominant genera in each treatment. Redundancy analyses indicated that higher dosage of biochar applied treatments has significant correlation between fungal communities and environmental factors. The diversity of fungal community was analogous but the relative abundance (RA) was inconsistent among the all treatments. In addition, the principal component analysis was also confirmed that T5 and T6 treatments have considerably correlation than other treatments. However, the mean value of RA remained maximum in higher dosage of biochar blended treatments. Ultimately, the RA of different fungal genus and species were influenced in CM compost by the BB amendment.}, }
@article {pmid30382616, year = {2019}, author = {Ganuza, M and Pastor, N and Boccolini, M and Erazo, J and Palacios, S and Oddino, C and Reynoso, MM and Rovera, M and Torres, AM}, title = {Evaluating the impact of the biocontrol agent Trichoderma harzianum ITEM 3636 on indigenous microbial communities from field soils.}, journal = {Journal of applied microbiology}, volume = {126}, number = {2}, pages = {608-623}, doi = {10.1111/jam.14147}, pmid = {30382616}, issn = {1365-2672}, support = {//Agencia Nacional de Promoción Científica y Tecnológica (MINCyT)/ ; }, mesh = {Agriculture ; Arachis ; Argentina ; Bacteria/genetics/isolation &amp; purification ; *Biological Control Agents ; Denaturing Gradient Gel Electrophoresis ; Fungi/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Microbiota ; Polymerase Chain Reaction ; Seeds ; Soil/chemistry ; *Soil Microbiology ; *Trichoderma ; }, abstract = {AIM: To investigate the impact of inoculating peanut seeds with the biocontrol agent Trichoderma harzianum ITEM 3636 on the structure of bacterial and fungal communities from agricultural soils.<br><br>METHODS AND RESULTS: Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing (NGS) of amplicons (or marker gene amplification metagenomics) were performed to investigate potential changes in the structure of microbial communities from fields located in a peanut-producing area in the province of Córdoba, Argentina. Fields had history of peanut smut (caused by Thecaphora frezii) incidence. The Shannon indexes (H'), which estimate diversity, obtained from the PCR-DGGE assays did not show significant differences neither for bacterial nor for fungal communities between control and inoculation treatments. On the other hand, the number of operational taxonomic units obtained after NGS was similar between all the analysed samples. Moreover, results of alpha and beta diversity showed that there were no significant variations between the relative abundances of the most representative bacterial and fungal phyla and genera, in both fields.<br><br>CONCLUSIONS: Trichoderma harzianum ITEM 3636 decreases the incidence and severity of agriculturally relevant diseases without causing significant changes in the microbial communities of agricultural soils.<br><br>Our investigations provide information on the structure of bacterial and fungal communities in peanut-producing fields after inoculation of seeds with a biocontrol agent.}, }
@article {pmid30376898, year = {2018}, author = {Leiby, JS and McCormick, K and Sherrill-Mix, S and Clarke, EL and Kessler, LR and Taylor, LJ and Hofstaedter, CE and Roche, AM and Mattei, LM and Bittinger, K and Elovitz, MA and Leite, R and Parry, S and Bushman, FD}, title = {Lack of detection of a human placenta microbiome in samples from preterm and term deliveries.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {196}, pmid = {30376898}, issn = {2049-2618}, support = {T32 AI007324/AI/NIAID NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; T32 AI007632/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Bacteria/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Female ; Humans ; Microbiota/*genetics ; Placenta/*microbiology ; Pregnancy ; Premature Birth ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Term Birth ; Uterus/*microbiology ; }, abstract = {BACKGROUND: Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is colonized with bacteria. For example, analysis of DNA from placenta samples yielded small proportions of microbial sequences which were proposed to represent normal bacterial colonization. However, an analysis by our group showed no distinction between background negative controls and placenta samples. Also supporting the idea that the womb is sterile is the observation that germ-free mammals can be generated by sterile delivery of neonates into a sterile isolator, after which neonates remain germ-free, which would seem to provide strong data in support of sterility of the womb.<br><br>RESULTS: To probe this further and to investigate possible placental colonization associated with spontaneous preterm birth, we carried out another study comparing microbiota in placenta samples from 20 term and 20 spontaneous preterm deliveries. Both 16S rRNA marker gene sequencing and shotgun metagenomic sequencing were used to characterize placenta and control samples. We first quantified absolute amounts of bacterial 16S rRNA gene sequences using 16S rRNA gene quantitative PCR (qPCR). As in our previous study, levels were found to be low in the placenta samples and indistinguishable from negative controls. Analysis by DNA sequencing did not yield a placenta microbiome distinct from negative controls, either using marker gene sequencing as in our previous work, or with shotgun metagenomic sequencing. Several types of artifacts, including erroneous read classifications and barcode misattribution, needed to be identified and removed from the data to clarify this point.<br><br>CONCLUSIONS: Our findings do not support the existence of a consistent placental microbiome, in either placenta from term deliveries or spontaneous preterm births.}, }
@article {pmid30373533, year = {2018}, author = {Yao, Y and Jin, Z and Lee, JH}, title = {An improved statistical model for taxonomic assignment of metagenomics.}, journal = {BMC genetics}, volume = {19}, number = {1}, pages = {98}, pmid = {30373533}, issn = {1471-2156}, support = {R03 AG054186/AG/NIA NIH HHS/United States ; R56 AG051876/AG/NIA NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/genetics ; Gastrointestinal Microbiome ; Humans ; Likelihood Functions ; Logistic Models ; Metagenomics/*methods ; *Models, Statistical ; Mouth/microbiology ; }, abstract = {BACKGROUND: With the advances in the next-generation sequencing technologies, researchers can now rapidly examine the composition of samples from humans and their surroundings. To enhance the accuracy of taxonomy assignments in metagenomic samples, we developed a method that allows multiple mismatch probabilities from different genomes.<br><br>RESULTS: We extended the algorithm of taxonomic assignment of metagenomic sequence reads (TAMER) by developing an improved method that can set a different mismatch probability for each genome rather than imposing a single parameter for all genomes, thereby obtaining a greater degree of accuracy. This method, which we call TADIP (Taxonomic Assignment of metagenomics based on DIfferent Probabilities), was comprehensively tested in simulated and real datasets. The results support that TADIP improved the performance of TAMER especially in large sample size datasets with high complexity.<br><br>CONCLUSIONS: TADIP was developed as a statistical model to improve the estimate accuracy of taxonomy assignments. Based on its varying mismatch probability setting and correlated variance matrix setting, its performance was enhanced for high complexity samples when compared with TAMER.}, }
@article {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 {pmid30370682, year = {2019}, author = {Nogueira, T and David, PHC and Pothier, J}, title = {Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach.}, journal = {Drug development research}, volume = {80}, number = {1}, pages = {86-97}, doi = {10.1002/ddr.21466}, pmid = {30370682}, issn = {1098-2299}, mesh = {Animals ; Anti-Bacterial Agents/adverse effects/*therapeutic use ; Bacterial Infections/drug therapy/genetics/metabolism ; Databases, Genetic/trends ; Dysbiosis/drug therapy/genetics/metabolism ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Metagenomics/*methods/trends ; Microbiota/*drug effects ; }, abstract = {The exposure of the human gut to antibiotics can have a great impact on human health. Antibiotics pertain to the preservation of human health and are useful tools for fighting bacterial infections. They can be used for curing infections and can play a critical role in immunocompromised or chronic patients, or in fighting childhood severe malnutrition. Yet, the genomic and phylogenetic diversity of the human gut changes under antibiotic exposure. Antibiotics can also have severe side effects on human gut health, due to the spreading of potential antibiotic resistance genetic traits and to their correlation with virulence of some bacterial pathogens. They can shape, and even disrupt, the composition and functioning diversity of the human gut microbiome. Traditionally bacterial antibiotic resistances have been evaluated at clone or population level. However, the understanding of these two apparently disparate perspectives as both friends and foes may come from the study of microbiomes as a whole and from the evaluation of both positive and negative effects of antibiotics on microbial community dynamics and diversity. In this review we present some metagenomic tools and databases that enable the studying of antibiotic resistance in human gut metagenomes, promoting the development of personalized medicine strategies, new antimicrobial therapy protocols and patient follow-up.}, }
@article {pmid30369115, year = {2018}, author = {Sivakala, KK and Jose, PA and Anandham, R and Thinesh, T and Jebakumar, SRD and Samaddar, S and Chatterjee, P and Sivakumar, N and Sa, T}, title = {Spatial Physiochemical and Metagenomic Analysis of Desert Environment.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {9}, pages = {1517-1526}, doi = {10.4014/jmb.1804.04005}, pmid = {30369115}, issn = {1738-8872}, mesh = {Bacteria/*chemistry/classification/*genetics/metabolism ; Biodiversity ; *Desert Climate ; India ; Metabolic Networks and Pathways ; *Metagenomics ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Spatial Analysis ; }, abstract = {Investigating the bacterial diversity and their metabolic capabilities are crucial for interpreting ecological patterns in desert environment, and assessing the presence of exploitable microbial resources. In this study, we evaluated the spatial heterogeneity of physico-chemical parameters, soil bacterial diversity and metabolic adaptation at meter scale. Soil samples were collected from two quadrates a desert environment (Thar Desert, India) which face hot arid climate with very little rainfall and extreme temperatures. Analysis of physico-chemical parameters and subsequent variance analysis (p-values < 0.05) revealed that sulfate, potassium and magnesium ions were the most variable between the quadrates. Microbial diversity of the two quadrates was studied using Illumina bar coded sequencing by targeting V3-V4 regions of 16S rDNA. As the results, 702504 high-quality sequence reads, assigned to 173 operationaltaxonomic units (OTUs) at species level. The most abundant phyla in both quadrates were Actinobacteria (38.72%), Proteobacteria (32.94%), and Acidobacteria (9.24%). At genus level, Gaiellarepresented highest prevalence, followed by Streptomyces, Solirubrobacter, Aciditerrimonas, Geminicoccus, Geodermatophilus, Microvirga, and Rubrobacter. Between the quadrates, significant difference (p-values < 0.05) was found in the abundance of Aciditerrimonas, Geodermatophilus Geminicoccus, Ilumatobacter, Marmoricola, Nakamurella and Solirubrobacter. Metabolic functional mapping revealed diverse biological activities, and was significantly correlated with physico-chemical parameters. The results revealed spatial variation of ions, microbial abundance and functional attributes in the studied quadrates, and patchy nature in local scale. Interestingly, abundance ofthe biotechnologically important phylum Actinobacteria, with large proposition of unclassified speciesin the desert suggested that this arid environment is the promising site for bioprospection.}, }
@article {pmid30368579, year = {2019}, author = {Zhu, L and Liao, R and Wu, N and Zhu, G and Yang, C}, title = {Heat stress mediates changes in fecal microbiome and functional pathways of laying hens.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {1}, pages = {461-472}, doi = {10.1007/s00253-018-9465-8}, pmid = {30368579}, issn = {1432-0614}, support = {CARS-40-K03//Agriculture Research System of China/ ; }, mesh = {Animals ; Chickens/*microbiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Heat-Shock Response/*physiology ; Lipids/blood ; Metabolic Networks and Pathways ; }, abstract = {Chicken gastrointestinal microbiota plays important roles in health, productivity, and disease. However, knowledge of the relationship between heat stress and the gut microbial ecosystem of poultry, especially laying hens, is still limited. Here, we aimed to provide important knowledge for heat stress intervention in the egg industry. We performed high-throughput sequencing metagenomics on fecal contents to unravel the microbial taxa and functional capacity of the gut microbiome of caged laying hens under heat stress. Results showed that the fecal microbial communities of laying hens were dominated by Firmicutes, Bacteroidetes, and Proteobacteria phyla. The Firmicutes were significantly decreased, and Bacteroidetes were increased in the fecal microbiota under heat stress. Functional prediction of these changes in microbiota revealed that metabolism-related pathways, including cysteine and methionine metabolism and benzoate degradation, were more abundant. Conversely, retinol metabolism and phenylpropanoid biosynthesis were decreased by heat stress, suggesting differences in metabolism between layers in different temperature environments. Clear contributions were identified between active taxa (genus level) and metabolic pathways, which were associated with the liver and intestinal dysfunction in layers. These data revealed that heat stress induced a significant taxonomic perturbation in the gut microbiome of caged laying hens. This was related to the negative effects of heat stress in poultry and provided important basic knowledge for heat stress intervention.}, }
@article {pmid30362648, year = {2019}, author = {Larivière-Gauthier, G and Thibodeau, A and Letellier, A and Yergeau, É and Fravalo, P}, title = {Salmonella shedding status of the sow affects the microbiota of their piglets at weaning.}, journal = {Journal of applied microbiology}, volume = {126}, number = {2}, pages = {411-423}, doi = {10.1111/jam.14139}, pmid = {30362648}, issn = {1365-2672}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Bacterial Shedding ; Female ; *Microbiota ; Pregnancy ; Salmonella/*isolation &amp; purification ; Swine/growth &amp; development/*microbiology ; Weaning ; }, abstract = {AIM: To observe the transfer of the digestive microbiota from sow to piglet, describe the impact of the sow's Salmonella shedding on this transfer and identify transferred populations that could be associated with the future Salmonella status of the piglets.<br><br>METHODS AND RESULTS: Salmonella shedding status of 19 sows was determined at the beginning and end of gestation. Four piglets were randomly selected from each sow. Using MiSeq, the microbiotas of the sows at the end of gestation and of their piglets 1 day before weaning were described. Results showed that the Salmonella shedding of the sows, the birth mother, the lairage room, the parity and the contamination of the lairage environment were associated to the microbiota of the piglets (permanova P < 0·05). Several genera were associated with piglets born from negative or positive sows.<br><br>CONCLUSION: There is a link between the microbiota of the sows at the end of gestation and the microbiota of their piglets at weaning, and the Salmonella shedding of the sow is associated with the microbiota of the piglets.<br><br>Salmonella status of the sows affects the microbiota of their piglets and could affect the long-term Salmonella colonization resistance of these animals and their health.}, }
@article {pmid30362076, year = {2019}, author = {Almeida, OGG and De Martinis, ECP}, title = {Bioinformatics tools to assess metagenomic data for applied microbiology.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {1}, pages = {69-82}, doi = {10.1007/s00253-018-9464-9}, pmid = {30362076}, issn = {1432-0614}, support = {17/13759-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 6762/2006-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; }, mesh = {Biodiversity ; Computational Biology/*methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Industrial Microbiology/*methods ; Metagenomics/*methods/statistics &amp; numerical data ; Phylogeny ; Quality Control ; }, abstract = {The reduction of the price of DNA sequencing has resulted in the emergence of large data sets to handle and analyze, especially in microbial ecosystems, which are characterized by high taxonomic and functional diversities. To assess the properties of these complex ecosystems, a conceptual background of the application of NGS technology and bioinformatics analysis to metagenomics is required. Accordingly, this article presents an overview of the evolution of knowledge of microbial ecology from traditional culture-dependent methods to culture-independent methods and the last frontier in knowledge, metagenomics. Topics that will be covered include sample preparation for NGS, starting with total DNA extraction and library preparation, followed by a brief discussion of the chemistry of NGS to help provide an understanding of which bioinformatics pipeline approach may be helpful for achieving a researcher's goals. The importance of selecting appropriate sequencing coverage and depth parameters to obtain a suitable measure of microbial diversity is discussed. As all DNA sequencing processes produce base-calling errors that compromise data analysis, including genome assembly and microbial functional analysis, dedicated software is presented and conceptually discussed with regard to potential applications in the general microbial ecology field.}, }
@article {pmid30359379, year = {2018}, author = {Bidot, WA and Ericsson, AC and Franklin, CL}, title = {Effects of water decontamination methods and bedding material on the gut microbiota.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0198305}, pmid = {30359379}, issn = {1932-6203}, support = {K01 OD019924/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Cecum/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Housing, Animal ; Mice, Inbred ICR ; *Water Microbiology ; Water Purification/*methods ; }, abstract = {Rodent models are invaluable to understanding health and disease in many areas of biomedical research. Unfortunately, many models suffer from lack of phenotype reproducibility. Our laboratory has shown that differences in gut microbiota (GM) can modulate phenotypes of models of colon cancer and inflammatory bowel disease. We and others have also shown that a number of factors associated with rodent research, including vendor, cage system, and bedding can alter GM. The objective of this study was to expand these studies to examine the effect of additional bedding materials and methods of water decontamination on GM diversity and composition. To this end, Crl:CD1 (ICR) mice were housed on corn cob or compressed paper chip bedding and provided water that was decontaminated by four different methods: autoclaving with reverse osmosis, autoclaving with hydrochloric acid, autoclaving with sulfuric acid, and autoclaving alone. Feces was collected at day 0, and at day 28 (endpoint), fecal and cecal samples were collected. DNA was extracted from samples, amplified by PCR using conserved bacterial primer sets and subjected to next generation sequencing. Sequence data were analyzed using Qiime and groups were compared using principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA). Two factor PERMANOVA of cecal GM data revealed significant changes when comparing bedding and water decontamination methods, while no significant effects were noted in the fecal GM data. Subsequent PERMANOVA and PCoA of cecal data revealed that several combinations of bedding and water decontamination methods resulted in differing GM, highlighting the complexity by which environmental factors interact to modulate GM.}, }
@article {pmid30358106, year = {2019}, author = {Siegenthaler, A and Wangensteen, OS and Soto, AZ and Benvenuto, C and Corrigan, L and Mariani, S}, title = {Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {206-220}, doi = {10.1111/1755-0998.12956}, pmid = {30358106}, issn = {1755-0998}, support = {//Santander Advantage Fund/ ; //University of Salford Manchester/ ; NE/N005759/1//Natural Environment Research Council/ ; //Mersey Gateway Environmental Trust/ ; }, mesh = {Animals ; *Biodiversity ; Crangonidae/*physiology ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV ; Estuaries ; Europe ; Feeding Behavior ; Fishes/*classification/*genetics ; *Gastrointestinal Contents ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; RNA, Ribosomal/genetics ; }, abstract = {Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time is one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity. Here, we evaluate the application of a novel, high-throughput DNA-based monitoring tool to assess fish diversity, based on the analysis of the gut contents of a generalist predator/scavenger, the European brown shrimp, Crangon crangon. Sediment and shrimp samples were collected from eight European estuaries, and DNA metabarcoding (using both 12S and COI markers) was carried out to infer fish assemblage composition. We detected 32 teleost species (16 and 20, for 12S and COI, respectively). Twice as many species were recovered using metabarcoding than by traditional net surveys. By comparing and interweaving trophic, environmental DNA and traditional survey-based techniques, we show that the DNA-assisted gut content analysis of a ubiquitous, easily accessible, generalist species may serve as a powerful, rapid and cost-effective tool for large-scale, routine estuarine biodiversity monitoring.}, }
@article {pmid30356699, year = {2018}, author = {Weißbecker, C and Wubet, T and Lentendu, G and Kühn, P and Scholten, T and Bruelheide, H and Buscot, F}, title = {Experimental Evidence of Functional Group-Dependent Effects of Tree Diversity on Soil Fungi in Subtropical Forests.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2312}, pmid = {30356699}, issn = {1664-302X}, abstract = {Deconvoluting the relative contributions made by specific biotic and abiotic drivers to soil fungal community compositions facilitates predictions about the functional responses of ecosystems to environmental changes, such as losses of plant diversity, but it is hindered by the complex interactions involved. Experimental assembly of tree species allows separation of the respective effects of plant community composition (biotic components) and soil properties (abiotic components), enabling much greater statistical power than can be achieved in observational studies. We therefore analyzed these contributions by assessing, via pyrotag sequencing of the internal transcribed spacer (ITS2) rDNA region, fungal communities in young subtropical forest plots included in a large experiment on the effects of tree species richness. Spatial variables and soil properties were the main drivers of soil fungal alpha and beta-diversity, implying strong early-stage environmental filtering and dispersal limitation. Tree related variables, such as tree community composition, significantly affected arbuscular mycorrhizal and pathogen fungal community structure, while differences in tree host species and host abundance affected ectomycorrhizal fungal community composition. At this early stage of the experiment, only a limited amount of carbon inputs (rhizodeposits and leaf litter) was being provided to the ecosystem due to the size of the tree saplings, and persisting legacy effects were observed. We thus expect to find increasing tree related effects on fungal community composition as forest development proceeds.}, }
@article {pmid30356187, year = {2018}, author = {Stewart, CJ and Ajami, NJ and O'Brien, JL and Hutchinson, DS and Smith, DP and Wong, MC and Ross, MC and Lloyd, RE and Doddapaneni, H and Metcalf, GA and Muzny, D and Gibbs, RA and Vatanen, T and Huttenhower, C and Xavier, RJ and Rewers, M and Hagopian, W and Toppari, J and Ziegler, AG and She, JX and Akolkar, B and Lernmark, A and Hyoty, H and Vehik, K and Krischer, JP and Petrosino, JF}, title = {Temporal development of the gut microbiome in early childhood from the TEDDY study.}, journal = {Nature}, volume = {562}, number = {7728}, pages = {583-588}, doi = {10.1038/s41586-018-0617-x}, pmid = {30356187}, issn = {1476-4687}, support = {UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063821/DK/NIDDK NIH HHS/United States ; HHSN267200700014C/DK/NIDDK NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UL1 TR001427/TR/NCATS NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Animals ; Bifidobacterium/classification/genetics/isolation &amp; purification ; Breast Feeding/statistics &amp; numerical data ; Case-Control Studies ; Child ; Child, Preschool ; Cluster Analysis ; Datasets as Topic ; Diabetes Mellitus, Type 1/immunology/microbiology ; Female ; Firmicutes/classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome/genetics/*immunology/*physiology ; Humans ; Infant ; Male ; Milk, Human/immunology/microbiology ; Pets ; RNA, Ribosomal, 16S/genetics ; Siblings ; *Surveys and Questionnaires ; Time Factors ; }, abstract = {The development of the microbiome from infancy to childhood is dependent on a range of factors, with microbial-immune crosstalk during this time thought to be involved in the pathobiology of later life diseases1-9 such as persistent islet autoimmunity and type 1 diabetes10-12. However, to our knowledge, no studies have performed extensive characterization of the microbiome in early life in a large, multi-centre population. Here we analyse longitudinal stool samples from 903 children between 3 and 46 months of age by 16S rRNA gene sequencing (n = 12,005) and metagenomic sequencing (n = 10,867), as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We show that the developing gut microbiome undergoes three distinct phases of microbiome progression: a developmental phase (months 3-14), a transitional phase (months 15-30), and a stable phase (months 31-46). Receipt of breast milk, either exclusive or partial, was the most significant factor associated with the microbiome structure. Breastfeeding was associated with higher levels of Bifidobacterium species (B. breve and B. bifidum), and the cessation of breast milk resulted in faster maturation of the gut microbiome, as marked by the phylum Firmicutes. Birth mode was also significantly associated with the microbiome during the developmental phase, driven by higher levels of Bacteroides species (particularly B. fragilis) in infants delivered vaginally. Bacteroides was also associated with increased gut diversity and faster maturation, regardless of the birth mode. Environmental factors including geographical location and household exposures (such as siblings and furry pets) also represented important covariates. A nested case-control analysis revealed subtle associations between microbial taxonomy and the development of islet autoimmunity or type 1 diabetes. These data determine the structural and functional assembly of the microbiome in early life and provide a foundation for targeted mechanistic investigation into the consequences of microbial-immune crosstalk for long-term health.}, }
@article {pmid30356183, year = {2018}, author = {Vatanen, T and Franzosa, EA and Schwager, R and Tripathi, S and Arthur, TD and Vehik, K and Lernmark, Å and Hagopian, WA and Rewers, MJ and She, JX and Toppari, J and Ziegler, AG and Akolkar, B and Krischer, JP and Stewart, CJ and Ajami, NJ and Petrosino, JF and Gevers, D and Lähdesmäki, H and Vlamakis, H and Huttenhower, C and Xavier, RJ}, title = {The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.}, journal = {Nature}, volume = {562}, number = {7728}, pages = {589-594}, doi = {10.1038/s41586-018-0620-2}, pmid = {30356183}, issn = {1476-4687}, support = {UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063821/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; HHSN267200700014C/DK/NIDDK NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UL1 TR001427/TR/NCATS NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; }, mesh = {Age of Onset ; Animals ; Bifidobacterium/enzymology/genetics/isolation &amp; purification ; Breast Feeding ; Child, Preschool ; Diabetes Mellitus, Type 1/*epidemiology/genetics/*microbiology/prevention &amp; control ; Disease Models, Animal ; European Continental Ancestry Group ; Fatty Acids, Volatile/pharmacology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/immunology/*physiology ; *Health Surveys ; Humans ; Infant ; Islets of Langerhans/immunology ; Longitudinal Studies ; Male ; Mice ; Milk, Human/immunology/microbiology ; Proteobacteria/enzymology/genetics/isolation &amp; purification ; }, abstract = {Type 1 diabetes (T1D) is an autoimmune disease that targets pancreatic islet beta cells and incorporates genetic and environmental factors1, including complex genetic elements2, patient exposures3 and the gut microbiome4. Viral infections5 and broader gut dysbioses6 have been identified as potential causes or contributing factors; however, human studies have not yet identified microbial compositional or functional triggers that are predictive of islet autoimmunity or T1D. Here we analyse 10,913 metagenomes in stool samples from 783 mostly white, non-Hispanic children. The samples were collected monthly from three months of age until the clinical end point (islet autoimmunity or T1D) in the The Environmental Determinants of Diabetes in the Young (TEDDY) study, to characterize the natural history of the early gut microbiome in connection to islet autoimmunity, T1D diagnosis, and other common early life events such as antibiotic treatments and probiotics. The microbiomes of control children contained more genes that were related to fermentation and the biosynthesis of short-chain fatty acids, but these were not consistently associated with particular taxa across geographically diverse clinical centres, suggesting that microbial factors associated with T1D are taxonomically diffuse but functionally more coherent. When we investigated the broader establishment and development of the infant microbiome, both taxonomic and functional profiles were dynamic and highly individualized, and dominated in the first year of life by one of three largely exclusive Bifidobacterium species (B. bifidum, B. breve or B. longum) or by the phylum Proteobacteria. In particular, the strain-specific carriage of genes for the utilization of human milk oligosaccharide within a subset of B. longum was present specifically in breast-fed infants. These analyses of TEDDY gut metagenomes provide, to our knowledge, the largest and most detailed longitudinal functional profile of the developing gut microbiome in relation to islet autoimmunity, T1D and other early childhood events. Together with existing evidence from human cohorts7,8 and a T1D mouse model9, these data support the protective effects of short-chain fatty acids in early-onset human T1D.}, }
@article {pmid30356154, year = {2018}, author = {Solden, LM and Naas, AE and Roux, S and Daly, RA and Collins, WB and Nicora, CD and Purvine, SO and Hoyt, DW and Schückel, J and Jørgensen, B and Willats, W and Spalinger, DE and Firkins, JL and Lipton, MS and Sullivan, MB and Pope, PB and Wrighton, KC}, title = {Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem.}, journal = {Nature microbiology}, volume = {3}, number = {11}, pages = {1274-1284}, doi = {10.1038/s41564-018-0225-4}, pmid = {30356154}, issn = {2058-5276}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Carbon/*metabolism ; Host Microbial Interactions ; Metabolic Networks and Pathways ; Metagenomics ; *Microbial Consortia ; Phylogeny ; Proteomics ; *Rumen/metabolism/microbiology/virology ; Ruminants ; Viruses/classification/genetics/isolation &amp; purification/metabolism ; Wood/metabolism ; }, abstract = {Because of their agricultural value, there is a great body of research dedicated to understanding the microorganisms responsible for rumen carbon degradation. However, we lack a holistic view of the microbial food web responsible for carbon processing in this ecosystem. Here, we sampled rumen-fistulated moose, allowing access to rumen microbial communities actively degrading woody plant biomass in real time. We resolved 1,193 viral contigs and 77 unique, near-complete microbial metagenome-assembled genomes, many of which lacked previous metabolic insights. Plant-derived metabolites were measured with NMR and carbohydrate microarrays to quantify the carbon nutrient landscape. Network analyses directly linked measured metabolites to expressed proteins from these unique metagenome-assembled genomes, revealing a genome-resolved three-tiered carbohydrate-fuelled trophic system. This provided a glimpse into microbial specialization into functional guilds defined by specific metabolites. To validate our proteomic inferences, the catalytic activity of a polysaccharide utilization locus from a highly connected metabolic hub genome was confirmed using heterologous gene expression. Viral detected proteins and linkages to microbial hosts demonstrated that phage are active controllers of rumen ecosystem function. Our findings elucidate the microbial and viral members, as well as their metabolic interdependencies, that support in situ carbon degradation in the rumen ecosystem.}, }
@article {pmid30355340, year = {2018}, author = {Mailhe, M and Ricaboni, D and Vitton, V and Gonzalez, JM and Bachar, D and Dubourg, G and Cadoret, F and Robert, C and Delerce, J and Levasseur, A and Fournier, PE and Angelakis, E and Lagier, JC and Raoult, D}, title = {Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {157}, pmid = {30355340}, issn = {1471-2180}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/isolation &amp; purification ; Colon/*microbiology ; Colonoscopy ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Endoscopy, Digestive System ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Hydrogen-Ion Concentration ; Male ; *Metagenomics ; Middle Aged ; Proton Pump Inhibitors/administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Stomach/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: Most studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene.<br><br>RESULTS: Using culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p < 0.02). We isolated fewer aero-intolerant species in the upper gut: 37 from the stomach and 150 from the left colon (p < 0.004). Using metagenomics, 1,021 species were identified. The upper gut microbiota was revealed to be less rich than the lower gut microbiota, with 37,622 reads from the stomach, 28,390 from the duodenum, and 79,047 from the left colon (p < 0.009). There were fewer reads for aero-intolerant species in the upper gut (8,656 in the stomach, 5,188 in the duodenum and 72,262 in the left colon, p < 0.02). Patients taking proton pump inhibitors (PPI) were then revealed to have a higher stomach pH and a greater diversity of species in the upper digestive tract than patients not receiving treatment (p < 0.001).<br><br>CONCLUSION: Significant modifications in bacterial composition and diversity exist throughout the gastrointestinal tract. We suggest that the upper gut may be key to understanding the relationship between the gut microbiota and health.}, }
@article {pmid30354816, year = {2018}, author = {Ganesh, BP and Nelson, JW and Eskew, JR and Ganesan, A and Ajami, NJ and Petrosino, JF and Bryan, RM and Durgan, DJ}, title = {Prebiotics, Probiotics, and Acetate Supplementation Prevent Hypertension in a Model of Obstructive Sleep Apnea.}, journal = {Hypertension (Dallas, Tex. : 1979)}, volume = {72}, number = {5}, pages = {1141-1150}, pmid = {30354816}, issn = {1524-4563}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 HL134838/HL/NHLBI NIH HHS/United States ; R01 NS080531/NS/NINDS NIH HHS/United States ; }, mesh = {Acetates/*therapeutic use ; Animals ; Blood Pressure/physiology ; Disease Models, Animal ; Gastrointestinal Microbiome/physiology ; Hypertension/complications/*prevention &amp; control ; Male ; *Prebiotics ; *Probiotics ; Rats ; Rats, Long-Evans ; Sleep Apnea, Obstructive/*complications ; }, abstract = {Disruption of the gut microbiota, termed gut dysbiosis, has been described in animal models of hypertension and hypertensive patients. We have shown that gut dysbiosis plays a causal role in the development of hypertension in a rat model of obstructive sleep apnea (OSA). Functional analysis of the dysbiotic microbiota in OSA demonstrates a loss of short chain fatty acid-producing bacteria. However, measurements of short chain fatty acid concentrations and testing of their role in blood pressure regulation are lacking. We hypothesized that reduced short chain fatty acids in the gut are responsible for OSA-induced hypertension. OSA significantly increased systolic blood pressure at 7 and 14 days (P<0.05), an effect that was abolished by the probiotic Clostridium butyricum or the prebiotic Hylon VII. The 16S rRNA analysis identified several short chain fatty acid-producing bacteria that were significantly increased by Cbutyricum and Hylon treatment. Acetate concentration in the cecum was decreased by 48% after OSA (P<0.05), an effect that was prevented by Cbutyricum and Hylon. Cbutyricum and Hylon reduced OSA-induced dysbiosis, epithelial goblet cell loss, mucus barrier thinning, and activation of brain microglia (P<0.05 for each). To examine the role of acetate in OSA-induced hypertension, we chronically infused acetate into the cecum during 2 weeks of sham or OSA. Restoring cecal acetate concentration prevented OSA-induced gut inflammation and hypertension (P<0.05). These studies identify acetate as a key player in OSA-induced hypertension. We demonstrate that various methods to increase cecal acetate concentrations are protective from the adverse effects of OSA on the microbiota, gut, brain, and blood pressure.}, }
@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 {pmid30350766, year = {2018}, author = {Bassene, H and Niang, EHA and Fenollar, F and Dipankar, B and Doucouré, S and Ali, E and Michelle, C and Raoult, D and Sokhna, C and Mediannikov, O}, title = {16S Metagenomic Comparison of Plasmodium falciparum-Infected and Noninfected Anopheles gambiae and Anopheles funestus Microbiota from Senegal.}, journal = {The American journal of tropical medicine and hygiene}, volume = {99}, number = {6}, pages = {1489-1498}, pmid = {30350766}, issn = {1476-1645}, mesh = {Actinobacteria/classification/*genetics/isolation &amp; purification ; Animals ; Anopheles/*microbiology ; Disease Eradication/methods ; Firmicutes/classification/*genetics/isolation &amp; purification ; Humans ; Malaria, Falciparum/epidemiology/parasitology/prevention &amp; control/*transmission ; Metagenomics/methods ; Microbiota/genetics ; Mosquito Control/methods ; Mosquito Vectors/*microbiology ; Phylogeny ; Plasmodium falciparum/pathogenicity/physiology ; Principal Component Analysis ; Proteobacteria/classification/*genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; Senegal/epidemiology ; }, abstract = {In the context of the pre-elimination of malaria, biological control may provide an alternative or additional tool to current malaria control strategies. During their various stages of development, mosquitoes undergo subsequent changes in their associated microbiota, depending on their environment and nutritional status. Although Anopheles gambiae s.l. and Anopheles funestus are the two major malaria vectors in Senegal, the composition of their microbiota is not yet well known. In this study, we explored the microbiota of mosquitoes naturally infected or not by Plasmodium falciparum (Pf) using the 16S ribosomal RNA gene-based bacterial metagenomic approach. In both vector species, the microbiota was more diverse in Pf-infected samples than in the noninfected ones, although the total number of reads appeared to be higher in noninfected mosquitoes. Overall, the microbiota was different between the two vector species. Noteworthy, the bacterial microbiota was significantly different between Pf-positive and Pf-negative groups whatever the species, but was similar between individuals of the same infection status within a species. Overall, the phylum of Proteobacteria was the most predominant in both species, with bacteria of the genus Burkholderia outweighing the others in noninfected vectors. The presence of some specific bacterial species such as Asaia bogorensis, Enterobacter cloacae, Burkholderia fungorum, and Burkholderia cepacia was also observed in Pf-free samples only. These preliminary observations pave the way for further characterization of the mosquito microbiota to select promising bacterial candidates for potential use in an innovative approach to controlling malaria and overcoming the challenges to achieving a malaria-free world.}, }
@article {pmid30349083, year = {2018}, author = {Palleja, A and Mikkelsen, KH and Forslund, SK and Kashani, A and Allin, KH and Nielsen, T and Hansen, TH and Liang, S and Feng, Q and Zhang, C and Pyl, PT and Coelho, LP and Yang, H and Wang, J and Typas, A and Nielsen, MF and Nielsen, HB and Bork, P and Wang, J and Vilsbøll, T and Hansen, T and Knop, FK and Arumugam, M and Pedersen, O}, title = {Recovery of gut microbiota of healthy adults following antibiotic exposure.}, journal = {Nature microbiology}, volume = {3}, number = {11}, pages = {1255-1265}, doi = {10.1038/s41564-018-0257-9}, pmid = {30349083}, issn = {2058-5276}, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Biodiversity ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/*physiology ; Genes, Bacterial ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; Virulence Factors/genetics ; Young Adult ; }, abstract = {To minimize the impact of antibiotics, gut microorganisms harbour and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing-based metagenomics, we analysed the partial eradication and subsequent regrowth of the gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 last-resort antibiotics: meropenem, gentamicin and vancomycin. Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and the depletion of Bifidobacterium species and butyrate producers. The gut microbiota of the subjects recovered to near-baseline composition within 1.5 months, although 9 common species, which were present in all subjects before the treatment, remained undetectable in most of the subjects after 180 days. Species that harbour β-lactam resistance genes were positively selected for during and after the intervention. Harbouring glycopeptide or aminoglycoside resistance genes increased the odds of de novo colonization, however, the former also decreased the odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention and their antibiotics resistance gene carriage modulates their recovery processes.}, }
@article {pmid30346157, year = {2018}, author = {Sun, W and Xiao, E and Häggblom, M and Krumins, V and Dong, Y and Sun, X and Li, F and Wang, Q and Li, B and Yan, B}, title = {Bacterial Survival Strategies in an Alkaline Tailing Site and the Physiological Mechanisms of Dominant Phylotypes As Revealed by Metagenomic Analyses.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {22}, pages = {13370-13380}, doi = {10.1021/acs.est.8b03853}, pmid = {30346157}, issn = {1520-5851}, mesh = {*Bacteria ; Biodegradation, Environmental ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {Microorganisms inhabiting mine tailings require specific metabolic strategies to survive, which may hold potential for pollution clean up. Effective in situ bioremediation will rely on an in-depth understanding of the function of the bacterial communities, especially the abundant and metabolically active phylotypes. In this study, the bacterial communities collected from an alkaline tailing site were profiled by 16S rRNA gene amplicon sequencing as well as shotgun metagenomic analysis. Our results indicated that potentials for carbon and nitrogen fixation as well as metal resistance and transformation were widespread among the bacterial community members, especially in highly enriched phylotypes, such as members of Thiobacillus and Meiothermus. Important functional microbial guilds including carbon and nitrogen fixers may contribute to phytoremediation by providing nutrients for hyperaccumulator plants. In addition, metal-metabolizing bacteria may influence metal speciation and solubility. This discovery provides an understanding for microbial survival strategies in the tailings and lays the foundation for future potential manipulation of the tailing microbiome for in situ bioremediation.}, }
@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 {pmid30342721, year = {2018}, author = {Free, A and McDonald, MA and Pagaling, E}, title = {Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems.}, journal = {Advances in applied microbiology}, volume = {105}, number = {}, pages = {131-189}, doi = {10.1016/bs.aambs.2018.07.002}, pmid = {30342721}, issn = {0065-2164}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Ecosystem ; Industrial Microbiology/*methods/trends ; *Metabolism ; *Microbial Consortia ; }, abstract = {The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.}, }
@article {pmid30342083, year = {2018}, author = {De Mol, ML and Snoeck, N and De Maeseneire, SL and Soetaert, WK}, title = {Hidden antibiotics: Where to uncover?.}, journal = {Biotechnology advances}, volume = {36}, number = {8}, pages = {2201-2218}, doi = {10.1016/j.biotechadv.2018.10.008}, pmid = {30342083}, issn = {1873-1899}, mesh = {Animals ; *Anti-Bacterial Agents/isolation &amp; purification/pharmacology ; Bacteria/chemistry/drug effects/genetics ; *Drug Discovery ; Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics ; Mice ; *Synthetic Biology ; }, abstract = {The struggle of humans versus pathogens is a never ending battle. Since the discovery of antibiotics humans have tipped the scales in their favour, but today bacteria are nullifying this advantage by developing resistance mechanisms against these molecules. The plethora of different antibiotics active against pathogens is shrinking while the discovery of new molecules is arduous. Especially the development of drugs active against Gram- pathogens continues slowly. New strategies to discover novel, potent antibiotics are hence needed. Adopting the optimistic view of technological singularity, innovative and disruptive approaches are required and hence proposed to lift the current conundrum. In this review, questions are answered on where and how to look for new natural product hit molecules with antibacterial activity, on how the field of synthetic biology can aid the contemporary pharmaceutical challenge and whether we are ready to make the transition towards other approaches, such as narrow-spectrum antibiotics and phage therapy.}, }
@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 {pmid30338752, year = {2018}, author = {Abranches, J and Zeng, L and Kajfasz, JK and Palmer, SR and Chakraborty, B and Wen, ZT and Richards, VP and Brady, LJ and Lemos, JA}, title = {Biology of Oral Streptococci.}, journal = {Microbiology spectrum}, volume = {6}, number = {5}, pages = {}, pmid = {30338752}, issn = {2165-0497}, support = {R01 DE019452/DE/NIDCR NIH HHS/United States ; R21 DE025348/DE/NIDCR NIH HHS/United States ; R01 DE022559/DE/NIDCR NIH HHS/United States ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; R01 DE019783/DE/NIDCR NIH HHS/United States ; }, mesh = {Carbohydrate Metabolism ; Dental Caries/microbiology ; Endocarditis/microbiology ; Fermentation ; Humans ; Hydrogen Peroxide/metabolism ; Metagenomics ; Microbiota/physiology ; Mouth/*microbiology ; Phylogeny ; Streptococcus/classification/genetics/pathogenicity/*physiology ; Streptococcus gordonii/metabolism ; Streptococcus mutans ; Streptococcus salivarius/metabolism ; }, abstract = {Bacteria belonging to the genus Streptococcus are the first inhabitants of the oral cavity, which can be acquired right after birth and thus play an important role in the assembly of the oral microbiota. In this article, we discuss the different oral environments inhabited by streptococci and the species that occupy each niche. Special attention is given to the taxonomy of Streptococcus, because this genus is now divided into eight distinct groups, and oral species are found in six of them. Oral streptococci produce an arsenal of adhesive molecules that allow them to efficiently colonize different tissues in the mouth. Also, they have a remarkable ability to metabolize carbohydrates via fermentation, thereby generating acids as byproducts. Excessive acidification of the oral environment by aciduric species such as Streptococcus mutans is directly associated with the development of dental caries. However, less acid-tolerant species such as Streptococcus salivarius and Streptococcus gordonii produce large amounts of alkali, displaying an important role in the acid-base physiology of the oral cavity. Another important characteristic of certain oral streptococci is their ability to generate hydrogen peroxide that can inhibit the growth of S. mutans. Thus, oral streptococci can also be beneficial to the host by producing molecules that are inhibitory to pathogenic species. Lastly, commensal and pathogenic streptococci residing in the oral cavity can eventually gain access to the bloodstream and cause systemic infections such as infective endocarditis.}, }
@article {pmid30338244, year = {2018}, author = {Saxena, R and Mittal, P and Clavaud, C and Dhakan, DB and Hegde, P and Veeranagaiah, MM and Saha, S and Souverain, L and Roy, N and Breton, L and Misra, N and Sharma, VK}, title = {Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {346}, pmid = {30338244}, issn = {2235-2988}, mesh = {Adult ; Bacteria/classification/*isolation &amp; purification ; Dandruff/*microbiology ; Female ; Fungi/classification/*isolation &amp; purification ; Humans ; India ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Scalp/*microbiology ; *Symbiosis ; Young Adult ; }, abstract = {Several scalp microbiome studies from different populations have revealed the association of dandruff with bacterial and fungal dysbiosis. However, the functional role of scalp microbiota in scalp disorders and health remains scarcely explored. Here, we examined the bacterial and fungal diversity of the scalp microbiome and their potential functional role in the healthy and dandruff scalp of 140 Indian women. Propionibacterium acnes and Staphylococcus epidermidis emerged as the core bacterial species, where the former was associated with a healthy scalp and the latter with dandruff scalp. Along with the commonly occurring Malassezia species (M. restricta and M. globosa) on the scalp, a strikingly high association of dandruff with yet uncharacterized Malassezia species was observed in the core mycobiome. Functional analysis showed that the fungal microbiome was enriched in pathways majorly implicated in cell-host adhesion in the dandruff scalp, while the bacterial microbiome showed a conspicuous enrichment of pathways related to the synthesis and metabolism of amino acids, biotin, and other B-vitamins, which are reported as essential nutrients for hair growth. A systematic measurement of scalp clinical and physiological parameters was also carried out, which showed significant correlations with the microbiome and their associated functional pathways. The results point toward a new potential role of bacterial commensals in maintaining the scalp nutrient homoeostasis and highlights an important and yet unknown role of the scalp microbiome, similar to the gut microbiome. This study, therefore, provides new perspectives on the better understanding of the pathophysiology of dandruff.}, }
@article {pmid30336790, year = {2018}, author = {Liu, YR and Delgado-Baquerizo, M and Bi, L and Zhu, J and He, JZ}, title = {Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {183}, pmid = {30336790}, issn = {2049-2618}, mesh = {Bacteroidetes/classification/genetics/*growth &amp; development ; Biodiversity ; China ; Environmental Monitoring ; Environmental Pollution/*analysis ; Firmicutes/classification/genetics/*growth &amp; development ; Mercury/*analysis ; Metagenome/genetics ; Methylmercury Compounds/*analysis ; Microbiota/genetics ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {BACKGROUND: The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulating bacterial abundance, diversity, and co-occurrence network. We also investigated the associations between Hg contents and the relative abundance of microbial functional genes by analyzing the soil metagenomes from a subset of those sites.<br><br>RESULTS: We found that soil Hg largely influenced the taxonomic and functional attributes of microbial communities in the two studied regions. In general, Hg pollution was negatively related to bacterial abundance, but positively related to the diversity of bacteria in two separate regions. We also found some consistent associations between soil Hg contents and the community composition of bacteria. For example, soil total Hg content was positively related to the relative abundance of Firmicutes and Bacteroidetes in both paddy and upland soils. In contrast, the methylmercury (MeHg) concentration was negatively correlated to the relative abundance of Nitrospirae in the two types of soils. Increases in soil Hg pollution correlated with drastic changes in the relative abundance of ecological clusters within the co-occurrence network of bacterial communities for the two regions. Using metagenomic data, we were also able to detect the effect of Hg pollution on multiple functional genes relevant to key soil processes such as element cycles and Hg transformations (e.g., methylation and reduction).<br><br>CONCLUSIONS: Together, our study provides solid evidence that Hg pollution has predictable and significant effects on multiple taxonomic and functional attributes including bacterial abundance, diversity, and the relative abundance of ecological clusters and functional genes. Our results suggest an increase in soil Hg pollution linked to human activities will lead to predictable shifts in the taxonomic and functional attributes in the Hg-impacted areas, with potential implications for sustainable management of agricultural ecosystems and elsewhere.}, }
@article {pmid30332487, year = {2018}, author = {Wyman, SK and Avila-Herrera, A and Nayfach, S and Pollard, KS}, title = {A most wanted list of conserved microbial protein families with no known domains.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0205749}, pmid = {30332487}, issn = {1932-6203}, mesh = {Bacterial Proteins/*chemistry/genetics ; Computational Biology ; *Databases, Nucleic Acid ; Humans ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Protein Domains/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The number and proportion of genes with no known function are growing rapidly. To quantify this phenomenon and provide criteria for prioritizing genes for functional characterization, we developed a bioinformatics pipeline that identifies robustly defined protein families with no annotated domains, ranks these with respect to phylogenetic breadth, and identifies them in metagenomics data. We applied this approach to 271 965 protein families from the SFams database and discovered many with no functional annotation, including >118 000 families lacking any known protein domain. From these, we prioritized 6 668 conserved protein families with at least three sequences from organisms in at least two distinct classes. These Function Unknown Families (FUnkFams) are present in Tara Oceans Expedition and Human Microbiome Project metagenomes, with distributions associated with sampling environment. Our findings highlight the extent of functional novelty in sequence databases and establish an approach for creating a &quot;most wanted&quot; list of genes to prioritize for further characterization.}, }
@article {pmid30326954, year = {2018}, author = {Korpela, K and Salonen, A and Vepsäläinen, O and Suomalainen, M and Kolmeder, C and Varjosalo, M and Miettinen, S and Kukkonen, K and Savilahti, E and Kuitunen, M and de Vos, WM}, title = {Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {182}, pmid = {30326954}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage ; Bifidobacterium/*classification ; Breast Feeding ; Cesarean Section ; Clostridium/isolation &amp; purification ; Dietary Supplements ; Double-Blind Method ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Infant ; Lactobacillus rhamnosus/*classification ; Male ; Pregnancy ; Probiotics/*administration &amp; dosage ; Propionibacterium/*classification ; Proteobacteria/isolation &amp; purification ; }, abstract = {BACKGROUND: Infants born by caesarean section or receiving antibiotics are at increased risk of developing metabolic, inflammatory and immunological diseases, potentially due to disruption of normal gut microbiota at a critical developmental time window. We investigated whether probiotic supplementation could ameliorate the effects of antibiotic use or caesarean birth on infant microbiota in a double blind, placebo-controlled randomized clinical trial. Mothers were given a multispecies probiotic, consisting of Bifidobacterium breve Bb99 (Bp99 2 × 108 cfu) Propionibacterium freundenreichii subsp. shermanii JS (2 × 109cfu), Lactobacillus rhamnosus Lc705 (5 × 109 cfu) and Lactobacillus rhamnosus GG (5 × 109 cfu) (N = 168 breastfed and 31 formula-fed), or placebo supplement (N = 201 breastfed and 22 formula-fed) during pregnancy, and the infants were given the same supplement. Faecal samples of the infants were collected at 3 months and analyzed using taxonomic, metagenomic and metaproteomic approaches.<br><br>RESULTS: The probiotic supplement had a strong overall impact on the microbiota composition, but the effect depended on the infant's diet. Only breastfed infants showed the expected increase in bifidobacteria and reduction in Proteobacteria and Clostridia. In the placebo group, both birth mode and antibiotic use were significantly associated with altered microbiota composition and function, particularly reduced Bifidobacterium abundance. In the probiotic group, the effects of antibiotics and birth mode were either completely eliminated or reduced.<br><br>CONCLUSIONS: The results indicate that it is possible to correct undesired changes in microbiota composition and function caused by antibiotic treatments or caesarean birth by supplementing infants with a probiotic mixture together with at least partial breastfeeding.<br><br>TRIAL REGISTRATION: clinicaltrials.gov NCT00298337 . Registered March 2, 2006.}, }
@article {pmid30325092, year = {2019}, author = {Zhang, SY and Tsementzi, D and Hatt, JK and Bivins, A and Khelurkar, N and Brown, J and Tripathi, SN and Konstantinidis, KT}, title = {Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics.}, journal = {Environmental microbiology}, volume = {21}, number = {1}, pages = {182-196}, doi = {10.1111/1462-2920.14439}, pmid = {30325092}, issn = {1462-2920}, support = {//Georgia Institute of Technology/ ; DEB 1241046//National Science Foundation/ ; }, abstract = {Little is known about microbial communities in the Ganges River, India and how they respond to intensive anthropogenic inputs. Here we applied shotgun metagenomics sequencing to study microbial community dynamics and function in planktonic samples collected along an approximately 700 km river transect, including urban cities and rural settings in upstream waters, before and after the monsoon rainy season. Our results showed that 11%-32% of the microbes represented terrestrial, sewage and human inputs (allochthonous). Sewage inputs significantly contributed to the higher abundance, by 13-fold of human gut microbiome (HG) associated sequences and 2-fold of antibiotic resistance genes (ARGs) in the Ganges relative to other riverine ecosystems in Europe, North and South America. Metagenome-assembled genome sequences (MAGs) representing allochthonous populations were detectable and tractable across the river after 1-2 days of (downstream) transport (> 200 km apart). Only approximately 8% of these MAGs were abundant in U.S. freshwater ecosystems, revealing distinct biodiversity for the Ganges. Microbial communities in the rainy season exhibited increased alpha-diversity and spatial heterogeneity and showed significantly weaker distance-decay patterns compared with the dry season. These results advance our understanding of the Ganges microbial communities and how they respond to anthropogenic pollution.}, }
@article {pmid30311571, year = {2018}, author = {Shillitoe, EJ}, title = {The Microbiome of Oral Cancer.}, journal = {Critical reviews in oncogenesis}, volume = {23}, number = {3-4}, pages = {153-160}, doi = {10.1615/CritRevOncog.2018027422}, pmid = {30311571}, issn = {0893-9675}, mesh = {Animals ; Bacterial Infections/complications/microbiology ; Cell Transformation, Neoplastic ; Disease Susceptibility ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth Neoplasms/*etiology ; Mycoses/complications/microbiology ; Virus Diseases/complications/virology ; }, abstract = {The pathogenesis of oral cancer is complex, and not all relevant factors involved in it have been determined. In particular, the role of the microbiota is not well understood because of difficulties in isolating and culturing its organisms. However, the recent development of metagenomic sequencing allows the discovery of all the DNA sequences in a specimen, and thus, the microbiome is now under intensive investigation. Studies of the bacteriome, the mycobiome, and the virome have revealed new organisms and have uncovered various differences between healthy persons and patients with oral cancer. In addition, sequencing of human samples shows the existence of DNA sequences that may be from novel microbes but are actually of unknown origin and so are referred to as the dark matter. The large volumes of data that are being produced by sequencing projects must be studied further to reveal novel pathogens and new pathways in the development of oral cancer.}, }
@article {pmid30309375, year = {2018}, author = {Zepeda Mendoza, ML and Roggenbuck, M and Manzano Vargas, K and Hansen, LH and Brunak, S and Gilbert, MTP and Sicheritz-Pontén, T}, title = {Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.}, journal = {Acta veterinaria Scandinavica}, volume = {60}, number = {1}, pages = {61}, pmid = {30309375}, issn = {1751-0147}, support = {R52-A5062//Lundbeckfonden/ ; }, mesh = {Adaptation, Biological ; Animals ; Animals, Wild/microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Falconiformes/*microbiology/physiology ; *Feeding Behavior ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Skin/*microbiology ; }, abstract = {BACKGROUND: Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut.<br><br>RESULTS: We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut.<br><br>CONCLUSIONS: Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.}, }
@article {pmid30308944, year = {2018}, author = {Fehlbaum, S and Prudence, K and Kieboom, J and Heerikhuisen, M and van den Broek, T and Schuren, FHJ and Steinert, RE and Raederstorff, D}, title = {In Vitro Fermentation of Selected Prebiotics and Their Effects on the Composition and Activity of the Adult Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {19}, number = {10}, pages = {}, pmid = {30308944}, issn = {1422-0067}, mesh = {*Biodiversity ; Dietary Fiber ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; *Prebiotics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recently, the concept of prebiotics has been revisited to expand beyond non-digestible oligosaccharides, and the requirements for selective stimulation were extended to include microbial groups other than, and additional to, bifidobacteria and lactobacilli. Here, the gut microbiota-modulating effects of well-known and novel prebiotics were studied. An in vitro fermentation screening platform (i-screen) was inoculated with adult fecal microbiota, exposed to different dietary fibers that had a range of concentrations (inulin, alpha-linked galacto-oligosaccharides (alpha-GOS), beta-linked GOS, xylo-oligosaccharides (XOS) from corn cobs and high-fiber sugar cane, and beta-glucan from oats), and compared to a positive fructo-oligosaccharide (FOS) control and a negative control (no fiber addition). All dietary fibers displayed prebiotic activity, with beta-glucan showing more distinct effects on the microbial composition and metabolism compared to the other fibers. Beta-glucan induced the growth of Prevotella and Roseburia with a concomitant increase in propionate production. Inulin and both forms of GOS and XOS had a strong bifidogenic effect on the microbial composition. A dose-response effect was observed for butyrate when exposed to beta-glucan and inulin. The findings of this study support the potential for alpha-GOS, XOS, and oat beta-glucan to serve as novel prebiotics, due to their association with the positive shifts in microbiome composition and short-chain fatty acid production that point to potential health benefits.}, }
@article {pmid30308887, year = {2019}, author = {Coble, AA and Flinders, CA and Homyack, JA and Penaluna, BE and Cronn, RC and Weitemier, K}, title = {eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications.}, journal = {The Science of the total environment}, volume = {649}, number = {}, pages = {1157-1170}, doi = {10.1016/j.scitotenv.2018.08.370}, pmid = {30308887}, issn = {1879-1026}, mesh = {Aquatic Organisms/*chemistry ; DNA/*analysis ; *Environment ; Environmental Monitoring/*methods ; *Forestry ; Fresh Water ; Hydrobiology/*methods ; }, abstract = {Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our objectives are to describe potential applications of eDNA across the wood products supply chain extending from regenerating forests, harvesting, and wood transport, to manufacturing facilities, and to review the current state of the science in this context. To meet our second objective, we summarize the taxa examined with targeted (PCR, qPCR or ddPCR) or metagenomic eDNA methods (eDNA metabarcoding), evaluate how estimated species richness compares between traditional field sampling and eDNA metabarcoding approaches, and compare the geographical representation of prior eDNA studies in freshwater ecosystems to global wood baskets. Potential applications of eDNA include evaluating the effects of forestry and forest manufacturing activities on aquatic biota, delineating fish-bearing versus non fish-bearing reaches, evaluating effectiveness of constructed road crossings for freshwater organism passage, and determining the presence of at-risk species. Studies using targeted eDNA approaches focused on fish, amphibians, and invertebrates, while metagenomic studies focused on fish, invertebrates, and microorganisms. Rare, threatened, or endangered species received the least attention in targeted eDNA research, but are arguably of greatest interest to sustainable forestry and forest manufacturing that seek to preserve freshwater biodiversity. Ultimately, using eDNA methods will enable forestry and forest manufacturing managers to have data-driven prioritization for conservation actions for all freshwater species.}, }
@article {pmid30308248, year = {2018}, author = {Hessler, T and Harrison, STL and Huddy, RJ}, title = {Stratification of microbial communities throughout a biological sulphate reducing up-flow anaerobic packed bed reactor, revealed through 16S metagenomics.}, journal = {Research in microbiology}, volume = {169}, number = {10}, pages = {543-551}, doi = {10.1016/j.resmic.2018.09.003}, pmid = {30308248}, issn = {1769-7123}, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Bioreactors/*microbiology ; DNA, Bacterial/genetics ; Genome, Bacterial ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sulfur Compounds/*metabolism ; }, abstract = {Biological sulphate reduction (BSR) is a promising low-cost treatment of acid rock drainage effluents. In this paper, the system performance and microbial ecology of a lactate supplemented BSR up-flow anaerobic packed bed reactor (UAPBR) are evaluated across reactor height and compared to a continuous stirred tank reactor (CSTR). The biomass concentrations of planktonic and biofilm communities were quantified and subsequently characterised by 16S rRNA gene amplicon sequencing. The defined microbial communities were shown to correlate with differing availability of lactate, volatile fatty acids produced from lactate degradation and sulphate concentration. The UAPBR was able to achieve near complete sulphate conversion at a 4-day hydraulic residence time (HRT) at a sulphate feed concentration of 10.41 mM (1 g/L). The high volumetric sulphate reduction rate of 0.184 mM/L.h achieved in the first third of the reactor was attributed to OTUs present in the planktonic and biofilm communities. While the scavenging of sulphate within the final third of the UAPBR was attributed to an acetate oxidising genus of SRB which was not detected in the lactate-fed CSTR. The detailed analyses of the microbial communities throughout the UAPBR and CSTR contribute to the growing understanding of the impact of the microbial communities of BSR reactors on system performance.}, }
@article {pmid30305166, year = {2018}, author = {Guyomar, C and Legeai, F and Jousselin, E and Mougel, C and Lemaitre, C and Simon, JC}, title = {Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {181}, pmid = {30305166}, issn = {2049-2618}, mesh = {Animals ; Aphids/*microbiology ; Buchnera/classification/genetics/*isolation &amp; purification ; Genome, Bacterial/genetics ; Metagenome/genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rickettsia/classification/genetics/*isolation &amp; purification ; Symbiosis/*physiology ; }, abstract = {BACKGROUND: Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact.<br><br>RESULTS: We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host.<br><br>CONCLUSIONS: We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.}, }
@article {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 {pmid30298261, year = {2018}, author = {Adeolu, M and Parkinson, J and Xiong, X}, title = {Analyzing Metabolic Pathways in Microbiomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {291-307}, doi = {10.1007/978-1-4939-8728-3_18}, pmid = {30298261}, issn = {1940-6029}, mesh = {High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metabolic Networks and Pathways ; Metagenomics ; *Microbiota ; *Transcriptome ; }, abstract = {Understanding the metabolic activity of a microbial community, at both the level of the individual microbe and the whole microbiome, provides fundamental biological, biochemical, and clinical insights into the nature of the microbial community and interactions with their hosts in health and disease. Here, we discuss a method to examine the expression of metabolic pathways in microbial communities using data from metatranscriptomic next-generation sequencing data. The methodology described here encompasses enzyme function annotation, differential enzyme expression and pathway enrichment analyses, and visualization of metabolic networks with differential enzyme expression levels.}, }
@article {pmid30298260, year = {2018}, author = {Dunn, KA and Andrews, K and Bashwih, RO and Bielawski, JP}, title = {Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {267-289}, doi = {10.1007/978-1-4939-8728-3_17}, pmid = {30298260}, issn = {1940-6029}, mesh = {*Algorithms ; *Bayes Theorem ; Computational Biology/*methods ; Metagenomics/*methods ; *Microbiota ; }, abstract = {Microbial samples taken from an environment often represent mixtures of communities, where each community is composed of overlapping assemblages of species. Such data represent a serious analytical challenge, as the community structures will be present as complex mixtures, there will be very large numbers of component species, and the species abundance will often be sparse over samples. The structure and complexity of these samples will vary according to both biotic and abiotic factors, and classical methods of data analysis will have a limited value in this setting. A novel Bayesian modeling framework, called BioMiCo, was developed to meet this challenge. BioMiCo takes abundance data derived from environmental DNA, and models each sample by a two-level mixture, where environmental OTUs contribute community structures, and those structures are related to the known biotic and abiotic features of each sample. The model is constrained by Dirichlet priors, which induces compact structures, minimizes variance, and maximizes model interpretability. BioMiCo is trained on a portion of the data, and once trained a BioMiCo model can be employed to make predictions about the features of new samples. This chapter provides a set of protocols that illustrate the application of BioMiCo to real inference problems. Each protocol is designed around the analysis of a real dataset, which was carefully chosen to illustrate specific aspects of real data analysis. With these protocols, users of BioMiCo will be able to undertake basic research into the properties of complex microbial systems, as well as develop predictive models for applied microbiomics.}, }
@article {pmid30298257, year = {2018}, author = {Hug, LA}, title = {Subsampled Assemblies and Hybrid Nucleotide Composition/Differential Coverage Binning for Genome-Resolved Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {215-225}, doi = {10.1007/978-1-4939-8728-3_14}, pmid = {30298257}, issn = {1940-6029}, mesh = {Algorithms ; *Genome, Microbial ; Metagenomics/*methods ; *Microbiota ; Nucleotides/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Metagenomic analyses for reconstruction of genomes from mixed microbial community datasets now routinely allow rapid, accurate genome recovery for tens to hundreds of organisms from environmental samples. This chapter provides a step-by-step protocol for reconstructing genomes from metagenomic datasets, with a focus on the most abundant community members. Subsampling assembly approaches are implemented to improve assembly of abundant genome sequences, an iterative process that targets progressively less abundant populations and improves total community representation in the final merged assembly. A hybrid approach to genome binning is described, combining differential coverage information from a series of metagenomic samples with nucleotide composition information. This approach strengthens binning through application of multiple independent variables for contig clustering. Genome curation through error correction and gap closure leads to high-quality draft genomes, and, for some community members, closed and complete genome sequences reconstructed directly from environmental samples.}, }
@article {pmid30298255, year = {2018}, author = {Zhang, Q}, title = {Metagenome Assembly and Contig Assignment.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {179-192}, doi = {10.1007/978-1-4939-8728-3_12}, pmid = {30298255}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenome ; Microbiota ; Molecular Sequence Annotation ; *Software ; }, abstract = {The recent development of metagenomic assembly has revolutionized metagenomic data analysis, thanks to the improvement of sequencing techniques, more powerful computational infrastructure and the development of novel algorithms and methods. Using longer assembled contigs rather than raw reads improves the process of metagenomic binning and annotation significantly, ultimately resulting in a deeper understanding of the microbial dynamics of the metagenomic samples being analyzed. In this chapter, we demonstrate a typical metagenomic analysis pipeline including raw read quality evaluation and trimming, assembly and contig binning. Alternative tools that can be used for each step are also discussed.}, }
@article {pmid30298253, year = {2018}, author = {McMurdie, PJ}, title = {Normalization of Microbiome Profiling Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {143-168}, doi = {10.1007/978-1-4939-8728-3_10}, pmid = {30298253}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Computational Biology/*methods ; Data Analysis ; High-Throughput Nucleotide Sequencing/*methods ; *Metagenome ; *Microbiota ; Phylogeny ; *Software ; }, abstract = {Normalization is a term that is often used but rarely defined and poorly understood. The number of choices of normalization procedure is large-some are inappropriate or inadmissible-and all are narrowly relevant to a specific analysis that depends on both the nature of the data and the question being asked. This chapter describes key definitions of normalization as they apply in metagenomics, mainly for taxonomic profiling data; while also demonstrating specific, reproducible examples of normalization procedures in the context of analysis techniques for which they were intended. The analysis and graphics code is distributed as a supplemental companion to this chapter so that the motivated reader can re-use it on new data.}, }
@article {pmid30298244, year = {2018}, author = {Daly, RA and Wrighton, KC and Wilkins, MJ}, title = {Characterizing the Deep Terrestrial Subsurface Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {1-15}, doi = {10.1007/978-1-4939-8728-3_1}, pmid = {30298244}, issn = {1940-6029}, mesh = {Bacteria/*classification/*genetics ; Biomass ; DNA, Bacterial/*analysis ; Gene Library ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota ; Soil Microbiology ; Water Microbiology ; }, abstract = {A large portion of the earth's biomass resides in the subsurface and recent studies have expanded our knowledge of indigenous microbial life. Advances in the field of metagenomics now allow analysis of microbial communities from low-biomass samples such as deep (>2.5 km) shale core samples. Here we present protocols for the best practices in contamination control, handling core material, extraction of nucleic acids, and low-input library preparation for subsequent metagenomic sequencing.}, }
@article {pmid30291903, year = {2018}, author = {Matsumoto, A and Yamagishi, Y and Miyamoto, K and Oka, K and Takahashi, M and Mikamo, H}, title = {Characterization of the vaginal microbiota of Japanese women.}, journal = {Anaerobe}, volume = {54}, number = {}, pages = {172-177}, doi = {10.1016/j.anaerobe.2018.10.001}, pmid = {30291903}, issn = {1095-8274}, mesh = {Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; Female ; Humans ; Japan ; Lactobacillus/classification/genetics/isolation &amp; purification ; *Microbiota ; Phylogeny ; Pregnancy ; Sex Work/statistics &amp; numerical data ; Vagina/*microbiology ; Young Adult ; }, abstract = {The composition of vaginal microbiota changes throughout life in response to health status, sexual activity, and pregnancy. Here the constitution of the vaginal microbiota among non-pregnant women, pregnant woman, and commercial sex workers (CSWs) in Japan were compared. Vaginal samples were obtained from 54 women between January 2014 and February 2015 and the microbiota of each was analyzed by 16S metagenomics as well as cluster and diversity analyses to identify differences. In addition, vaginal Lactobacillus spp. were isolated for comparison. Furthermore, data regarding the use of ritodrine hydrochloride by pregnant women was collected from medical charts. The vaginal microbiota were clustered into three groups. Group 1 was most often dominated by Lactobacillus spp., whereas groups 2 and 3 included not only Lactobacillus spp. but also Bifidobacterium, Atopobium, Prevotella, and Gardnerella spp., in addition to a few other taxa. In non-pregnant women, the proportions of microbes in groups 1, 2, and 3 were 31.8%, 36.4%, and 31.8%, respectively. In pregnant women, the abundance of group 1 microbes was notably greater than that of groups 2 and 3 (66.7% vs. 12.5% and 20.8%, respectively). In CSWs, the prevalence of group 3 microbes was far greater than that of group 1 (87.5% vs. 12.5%, respectively). The alpha diversity of non-pregnant women was significantly greater than that of pregnant women. The detection rate of live Lactobacillus spp. in CSWs was lower than in pregnant and non-pregnant women (25% vs. 50% and 68.2%, respectively). The vaginal microbiota of most pregnant women (60%) who received ritodrine hydrochloride was not dominated by Lactobacillus spp. These results suggest that there were clear differences in the colonization rate of Lactobacillus spp. among non-pregnant, pregnant, and CSW women groups. In addition, the dominance of Lactobacillus may influence the risk of preterm birth among women who received ritodrine hydrochloride during pregnancy.}, }
@article {pmid30287886, year = {2019}, author = {Kuntal, BK and Chandrakar, P and Sadhu, S and Mande, SS}, title = {'NetShift': a methodology for understanding 'driver microbes' from healthy and disease microbiome datasets.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {442-454}, doi = {10.1038/s41396-018-0291-x}, pmid = {30287886}, issn = {1751-7370}, mesh = {Databases, Factual ; Humans ; Metagenomics/*methods ; *Microbial Consortia ; *Microbiota ; Models, Biological ; }, abstract = {The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called 'NetShift' to quantify rewiring and community changes in microbial association networks between healthy and disease. Additionally, we devise a score to identify important microbial taxa which serve as 'drivers' from the healthy to disease. We demonstrate the validity of our score on a number of scenarios and apply our methodology on two real world metagenomic datasets. The 'NetShift' methodology is also implemented as a web-based application available at https://web.rniapps.net/netshift.}, }
@article {pmid30287354, year = {2018}, author = {Staley, C and Sadowsky, MJ}, title = {Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies.}, journal = {Journal of microbiological methods}, volume = {154}, number = {}, pages = {14-18}, doi = {10.1016/j.mimet.2018.09.020}, pmid = {30287354}, issn = {1872-8359}, mesh = {Algorithms ; Biodiversity ; Biostatistics/methods ; Computational Biology/methods ; DNA/analysis/isolation &amp; purification ; *Data Analysis ; Ecology ; Ecosystem ; Environment ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeography ; Sequence Analysis, DNA/methods ; Specimen Handling/*methods ; }, abstract = {Recent advancements in metagenomic-based studies, especially analyses of amplicon-based DNA sequencing targeting taxonomic marker genes, has led to an unprecedented characterization of microbial communities from diverse ecosystems around the world. While originally constrained by a lack of appropriate analytical tools and sequencing depth, new technologies and computational and statistical algorithms have been developed to handle highly dimensional, next-generation sequencing datasets. Both these tools allow for the robust analysis of structural and distributional patterns of microbiota essential for the understanding of microbial ecology and biogeography. Furthermore, consortia of individual laboratories working on large interdisciplinary research programs, like the Human and Earth Microbiome Projects, have developed standardized protocols for DNA extraction, sequencing pipelines, and bioinformatics. These approaches provide large repositories of publicly available data to serve as references for on-going and future, hypothesis-driven studies to better characterize the roles of microbial communities in diverse ecosystems. In this review, we outline the currently available statistical approaches and tools to aid in statistically powered study designs and analyses. Given what is now known about the enormous diversity and variability of the microbial communities in aquatic and terrestrial habitats, we also discuss practical considerations for sample collection. Due to the extensive advances made in the field of metagenomics over the last decade, rigorous, well replicated, hypothesis-driven studies are: 1) needed, 2) now possible, and 3) essential to make best use of sequencing-based technologies to characterize the roles of microbial communities in the structure and function of diverse ecosystems.}, }
@article {pmid30286722, year = {2018}, author = {Mancini, MV and Damiani, C and Accoti, A and Tallarita, M and Nunzi, E and Cappelli, A and Bozic, J and Catanzani, R and Rossi, P and Valzano, M and Serrao, A and Ricci, I and Spaccapelo, R and Favia, G}, title = {Estimating bacteria diversity in different organs of nine species of mosquito by next generation sequencing.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {126}, pmid = {30286722}, issn = {1471-2180}, mesh = {Animal Structures/*microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Culicidae/classification/*microbiology ; DNA, Bacterial/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Male ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Symbiosis in insects is accumulating significant amount of studies: the description of a wide array of mutualistic associations across the evolutionary history of insects suggests that resident microbiota acts as a driving force by affecting several aspects of hosts biology. Among arthropods, mosquito midgut microbiota has been largely investigated, providing crucial insights on the role and implications of host-symbiont relationships. However, limited amount of studies addressed their efforts on the investigation of microbiota colonizing salivary glands and reproductive tracts, crucial organs for pathogen invasion and vertical transmission of symbiotic microorganisms. Using 16S rRNA gene sequencing-based approach, we analysed the microbiota of gut, salivary glands and reproductive tracts of several mosquito species, representing some of the main vectors of diseases, aiming at describing the dynamics of bacterial communities within the individual.<br><br>RESULTS: We identified a shared core microbiota between different mosquito species, although interesting inter- and intra-species differences were detected. Additionally, our results showed deep divergences between genera, underlining microbiota specificity and adaptation to their host.<br><br>CONCLUSIONS: The comprehensive landscape of the bacterial microbiota components may ultimately provide crucial insights and novel targets for possible application of symbionts in innovative strategies for the control of vector borne diseases, globally named Symbiotic Control (SC), and suggesting that the holobiont of different mosquito species may significantly vary. Moreover, mosquito species are characterized by distinctive microbiota in different organs, likely reflecting different functions and/or adaptation processes.}, }
@article {pmid30285861, year = {2018}, author = {O'Neill, AM and Gallo, RL}, title = {Host-microbiome interactions and recent progress into understanding the biology of acne vulgaris.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {177}, pmid = {30285861}, issn = {2049-2618}, support = {R01 AI116576/AI/NIAID NIH HHS/United States ; R01 AR064781/AR/NIAMS NIH HHS/United States ; R01 AR069653/AR/NIAMS NIH HHS/United States ; U19 AI117673/AI/NIAID NIH HHS/United States ; }, mesh = {Acne Vulgaris/drug therapy/*microbiology ; Dysbiosis/microbiology ; Hair Follicle/*microbiology ; Humans ; Metagenome/genetics ; Microbiota/genetics ; Propionibacterium acnes/*genetics/isolation &amp; purification ; Sebaceous Glands/*microbiology ; Staphylococcus epidermidis/*genetics/isolation &amp; purification ; }, abstract = {Acne is one of the most common skin diseases worldwide and results in major health care costs and significant morbidity to severely affected individuals. However, the pathophysiology of this disorder is not well understood. Host-microbiome interactions that affect both innate and adaptive immune homeostasis appear to be a central factor in this disease, with recent observations suggesting that the composition and activities of the microbiota in acne is perturbed. Staphylococcus epidermidis and Cutibacterium acnes (C. acnes; formerly Propionibacterium acnes) are two major inhabitants of the skin that are thought to contribute to the disease but are also known to promote health by inhibiting the growth and invasion of pathogens. Because C. acnes is ubiquitous in sebaceous-rich skin, it is typically labeled as the etiological agent of acne yet it fails to fulfill all of Koch's postulates. The outdated model of acne progression proposes that increased sebum production promotes over-proliferation of C. acnes in a plugged hair follicle, thereby driving inflammation. In contrast, growing evidence indicates that C. acnes is equally abundant in both unaffected and acne-affected follicles. Moreover, recent advances in metagenomic sequencing of the acne microbiome have revealed a diverse population structure distinct from healthy individuals, uncovering new lineage-specific virulence determinants. In this article, we review recent developments in the interactions of skin microbes with host immunity, discussing the contribution of dysbiosis to the immunobiology of acne and newly emerging skin microbiome-based therapeutics to treat acne.}, }
@article {pmid30285625, year = {2018}, author = {Pacchioni, F and Esposito, A and Giacobazzi, E and Bettua, C and Struffi, P and Jousson, O}, title = {Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {124}, pmid = {30285625}, issn = {1471-2180}, mesh = {Air Microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Fresh Water/*microbiology ; Groundwater/*microbiology ; *Microbiota ; Phylogeny ; Plants, Medicinal/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The presence of microrganisms in pharmaceutical production plant environments is typically monitored by cultural methods, however these cannot detect the unculturable fraction of the microbial community. To get more accurate information on the composition of these indoor microbial communities, both water and air microbiome from a pharmaceutical production plant were profiled by 16S amplicon sequencing.<br><br>RESULTS: In the water system, we found taxa which typically characterize surface freshwater, groundwater and oligotrophic environments. The airborne microbiome resulted dominated by taxa usually found in outdoor air in combination with human-associated taxa. The alpha- and beta- diversity values showed that the heat-based sanitization process of the water plant affects the composition of the water microbiome by transiently increasing both diversity and evenness. Taxonomic compositional shifts were also detected in response to sanitization, consisting in an increase of Firmicutes and α-Proteobacteria. On the other hand, seasonality seems to be the main driver of bacterial community composition in air of this work environment.<br><br>CONCLUSIONS: This approach resulted useful to describe the taxonomy of these indoor microbiomes and could be further applied to other built environments, in which the knowledge of the microbiome composition is of relevance. In addition, this study could assist in the design of new guidelines to improve microbiological quality control in indoor work environments.}, }
@article {pmid30281913, year = {2019}, author = {Jusino, MA and Banik, MT and Palmer, JM and Wray, AK and Xiao, L and Pelton, E and Barber, JR and Kawahara, AY and Gratton, C and Peery, MZ and Lindner, DL}, title = {An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {176-190}, doi = {10.1111/1755-0998.12951}, pmid = {30281913}, issn = {1755-0998}, support = {//United States Forest Service, Northern Research Station/ ; Hatch Formula Funds//University of Wisconsin-Madison, Wisconsin Agricultural Experiment Station/ ; IOS-1121739//National Science Foundation/ ; IOS-1121807//National Science Foundation/ ; }, mesh = {Animals ; *Chiroptera ; Computational Biology/*methods ; DNA/chemistry/genetics/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Feces/chemistry ; *Feeding Behavior ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; }, abstract = {DNA analysis of predator faeces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To better characterize insectivorous animal diets, we used DNA from a diverse set of arthropods to assess PCR biases of commonly used and novel primer pairs for the mitochondrial gene, cytochrome oxidase C subunit 1 (COI). We compared diversity recovered from HTS of bat guano samples using a commonly used primer pair &quot;ZBJ&quot; to results using the novel primer pair &quot;ANML.&quot; To parameterize our bioinformatics pipeline, we created an arthropod mock community consisting of single-copy (cloned) COI sequences. To examine biases associated with both PCR and HTS, mock community members were combined in equimolar amounts both pre- and post-PCR. We validated our system using guano from bats fed known diets and using composite samples of morphologically identified insects collected in pitfall traps. In PCR tests, the ANML primer pair amplified 58 of 59 arthropod taxa (98%), whereas ZBJ amplified 24-40 of 59 taxa (41%-68%). Furthermore, in an HTS comparison of field-collected samples, the ANML primers detected nearly fourfold more arthropod taxa than the ZBJ primers. The additional arthropods detected include medically and economically relevant insect groups such as mosquitoes. Results revealed biases at both the PCR and sequencing levels, demonstrating the pitfalls associated with using HTS read numbers as proxies for abundance. The use of an arthropod mock community allowed for improved bioinformatics pipeline parameterization.}, }
@article {pmid30275573, year = {2018}, author = {Gonzalez, A and Navas-Molina, JA and Kosciolek, T and McDonald, D and Vázquez-Baeza, Y and Ackermann, G and DeReus, J and Janssen, S and Swafford, AD and Orchanian, SB and Sanders, JG and Shorenstein, J and Holste, H and Petrus, S and Robbins-Pianka, A and Brislawn, CJ and Wang, M and Rideout, JR and Bolyen, E and Dillon, M and Caporaso, JG and Dorrestein, PC and Knight, R}, title = {Qiita: rapid, web-enabled microbiome meta-analysis.}, journal = {Nature methods}, volume = {15}, number = {10}, pages = {796-798}, pmid = {30275573}, issn = {1548-7105}, support = {R01 HG004872/HG/NHGRI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Humans ; *Internet ; *Metagenomics ; *Microbiota ; *Software ; User-Computer Interface ; }, abstract = {Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.}, }
@article {pmid30272305, year = {2018}, author = {Zhou, S and Cai, Y and Wang, M and Yang, WD and Duan, N}, title = {Oral microbial flora of patients with Sicca syndrome.}, journal = {Molecular medicine reports}, volume = {18}, number = {6}, pages = {4895-4903}, pmid = {30272305}, issn = {1791-3004}, mesh = {Biodiversity ; Case-Control Studies ; Computational Biology/methods ; Female ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Sjogren's Syndrome/*etiology ; }, abstract = {Primary sicca syndrome (pSS) is a systemic autoimmune disease. However, its exact etiology and pathogenesis remain elusive. Various infectious factors have been identified to be closely associated with the occurrence and development of PSS. The present study aimed to assess the composition of the oral microbial flora of patients with pSS in China in order to provide guidance for treatment. The microbial flora of nine patients with pSS and five healthy controls from East China was evaluated in saliva samples using high‑throughput sequencing. A high microbial diversity was detected in the pSS and control groups, with bacteroidetes, firmicutes and proteobacteria constituting the largest phyla in the two groups. Compared with the control group, bacteroidetes and actinobacteria were significantly more abundant in the pSS group, whereas proteobacteria were significantly less abundant. However, no significant differences in bacterial richness and diversity were observed between the two groups. According to a Kyoto Encyclopedia of Genes and Genomes linear discriminant analysis, genes regulating cell apoptosis and the immune and digestive systems were significantly upregulated in the pSS group compared with those in the control group. In conclusion, the present study provided basic data on the flora of the oral cavity in patients with pSS from East China and may serve as a reference for the treatment of this condition.}, }
@article {pmid30271256, year = {2018}, author = {Anslan, S and Nilsson, RH and Wurzbacher, C and Baldrian, P and Leho Tedersoo,  and Bahram, M}, title = {Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding.}, journal = {MycoKeys}, volume = {}, number = {39}, pages = {29-40}, pmid = {30271256}, issn = {1314-4049}, abstract = {Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.}, }
@article {pmid30270610, year = {2018}, author = {Fan, Y and Ya-E, Z and Ji-Dong, W and Yu-Fan, L and Ying, Z and Ya-Lun, S and Meng-Yu, M and Rui-Ling, Z}, title = {Comparison of Microbial Diversity and Composition in Jejunum and Colon of the Alcohol-dependent Rats.}, journal = {Journal of microbiology and biotechnology}, volume = {28}, number = {11}, pages = {1883-1895}, doi = {10.4014/jmb.1806.06050}, pmid = {30270610}, issn = {1738-8872}, mesh = {Alcoholism/*microbiology ; Animals ; Bacteria/classification/genetics ; *Biodiversity ; Colon/*microbiology ; Disease Models, Animal ; Dysbiosis/*microbiology ; Ethanol/adverse effects ; Gastrointestinal Microbiome/genetics ; Jejunum/*microbiology ; Male ; Metabolic Networks and Pathways/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Wistar ; }, abstract = {Alcohol dependence is a global public health problem, yet the mechanisms of alcohol dependence are incompletely understood. The traditional view has been that ethanol alters various neurotransmitters and their receptors in the brain and causes the addiction. However, an increasing amount of experimental evidence suggests that gut microbiota also influence brain functions via gut-to-brain interactions, and may therefore induce the development of alcohol use disorders. In this study, a rat model of alcohol dependence and withdrawal was employed, the gut microbiota composition was analyzed by high-throughput 16S rRNA gene sequencing, and the metagenome function was predicted by PICRUSt software. The results suggested that chronic alcohol consumption did not significantly alter the diversity and richness of gut microbiota in the jejunum and colon, but rather markedly changed the microbiota composition structure in the colon. The phyla Bacteroidetes and eight genera including Bacteroidales S24-7, Ruminococcaceae, Parabacteroides, Butyricimonas, et al were drastically increased, however the genus Lactobacillus and gauvreauii in the colon were significantly decreased in the alcohol dependence group compared with the withdrawal and control groups. The microbial functional prediction analysis revealed that the proportions of amino acid metabolism, polyketide sugar unit biosynthesis and peroxisome were significantly increased in the AD group. This study demonstrated that chronic alcohol consumption has a dramatic effect on the microbiota composition structure in the colon but few effects on the jejunum. Inducement of colonic microbiota dysbiosis due to alcohol abuse seems to be a factor of alcohol dependence, which suggests that modulating colonic microbiota composition might be a potentially new target for treating alcohol addiction.}, }
@article {pmid30269123, year = {2018}, author = {Hattori, M}, title = {[Ecology and function of human microbiomes.].}, journal = {Clinical calcium}, volume = {28}, number = {10}, pages = {1398-1405}, doi = {CliCa181013981405}, pmid = {30269123}, issn = {0917-5857}, mesh = {Bacteria ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; }, abstract = {Hundreds of trillions of bacteria consisting of ~1,000 species reside in various human body sites to form bacterial communities(microbiomes)specific for the sites. In the past decade, the human microbiome research in the world incredibly advanced by development of a culture-independent metagenomic analysis based on next-generation sequencing technologies. Particularly, current studies have revealed that the human gut microbiome is profoundly associated with the host's health and disease.}, }
@article {pmid30267472, year = {2019}, author = {Suchan, T and Talavera, G and Sáez, L and Ronikier, M and Vila, R}, title = {Pollen metabarcoding as a tool for tracking long-distance insect migrations.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {149-162}, doi = {10.1111/1755-0998.12948}, pmid = {30267472}, issn = {1755-0998}, support = {CGL2016-76322//AEI/FEDER, UE/ ; IJCI-2016-29083//MINECO programme Juan de la Cierva Incorporación/ ; LRB16/1015//British Ecological Society/ ; //Polish Academy of Sciences statutory fund/ ; 622716//FP7/ ; WW1-300R-18//National Geographic Society/ ; }, mesh = {Africa ; *Animal Migration ; Animals ; Arabia ; Butterflies/*physiology ; DNA Barcoding, Taxonomic/*methods ; Entomology/*methods ; Mediterranean Region ; Metagenomics/*methods ; Pollen/*genetics ; Spain ; }, abstract = {Insects account for a large portion of Earth's biodiversity and are key players for ecosystems, notably as pollinators. While insect migration is suspected to represent a natural phenomenon of major importance, remarkably little is known about it, except for a few flagship species. The reason for this situation is mainly due to technical limitations in the study of insect movement. Here, we propose using metabarcoding of pollen carried by insects as a method for tracking their migrations. We developed a flexible and simple protocol allowing efficient multiplexing and not requiring DNA extraction, one of the most time-consuming part of metabarcoding protocols, and apply this method to the study of the long-distance migration of the butterfly Vanessa cardui, an emerging model for insect migration. We collected 47 butterfly samples along the Mediterranean coast of Spain in spring and performed metabarcoding of pollen collected from their bodies to test for potential arrivals from the African continent. In total, we detected 157 plant species from 23 orders, most of which (82.8%) were insect-pollinated. Taxa present in Africa-Arabia represented 73.2% of our data set, and 19.1% were endemic to this region, strongly supporting the hypothesis that migratory butterflies colonize southern Europe from Africa in spring. Moreover, our data suggest that a northwards trans-Saharan migration in spring is plausible for early arrivals (February) into Europe, as shown by the presence of Saharan floristic elements. Our results demonstrate the possibility of regular insect-mediated transcontinental pollination, with potential implications for ecosystem functioning, agriculture and plant phylogeography.}, }
@article {pmid30267313, year = {2018}, author = {Song, EJ and Lee, ES and Nam, YD}, title = {Progress of analytical tools and techniques for human gut microbiome research.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {56}, number = {10}, pages = {693-705}, pmid = {30267313}, issn = {1976-3794}, mesh = {Computational Biology/*trends ; Data Analysis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/*trends ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Massive DNA sequencing studies have expanded our insights and understanding of the ecological and functional characteristics of the gut microbiome. Advanced sequencing technologies allow us to understand the close association of the gut microbiome with human health and critical illnesses. In the future, analyses of the gut microbiome will provide key information associating with human individual health, which will help provide personalized health care for diseases. Numerous molecular biological analysis tools have been rapidly developed and employed for the gut microbiome researches; however, methodological differences among researchers lead to inconsistent data, limiting extensive share of data. It is therefore very essential to standardize the current methodologies and establish appropriate pipelines for human gut microbiome research. Herein, we review the methods and procedures currently available for studying the human gut microbiome, including fecal sample collection, metagenomic DNA extraction, massive DNA sequencing, and data analyses with bioinformatics. We believe that this review will contribute to the progress of gut microbiome research in the clinical and practical aspects of human health.}, }
@article {pmid30266729, year = {2018}, author = {Vital, M and Howe, A and Bergeron, N and Krauss, RM and Jansson, JK and Tiedje, JM}, title = {Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {23}, pages = {}, pmid = {30266729}, issn = {1098-5336}, support = {RC1 DK086472/DK/NIDDK NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; UL1 TR000004/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Bacteria/classification/*genetics/*isolation &amp; purification/metabolism ; Diabetes Mellitus, Type 2/diet therapy/metabolism/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Phylogeny ; Starch/analysis/*metabolism ; }, abstract = {Several studies monitoring alterations in the community structure upon resistant starch (RS) interventions are available, although comprehensive function-based analyses are lacking. Recently, a multiomics approach based on 16S rRNA gene sequencing, metaproteomics, and metabolomics on fecal samples from individuals subjected to high and low doses of type 2 RS (RS2; 48 g and 3 g/2,500 kcal, respectively, daily for 2 weeks) in a crossover intervention experiment was performed. In the present study, we did pathway-based metagenomic analyses on samples from a subset of individuals (n = 12) from that study to obtain additional detailed insights into the functional structure at high resolution during RS2 intervention. A mechanistic framework based on obtained results is proposed where primary degradation was governed by Firmicutes, with Ruminococcus bromii as a major taxon involved, providing fermentation substrates and increased acetate concentrations for the growth of various major butyrate producers exhibiting the enzyme butyryl-coenzyme A (CoA):acetate CoA-transferase. H2-scavenging sulfite reducers and acetogens concurrently increased. Individual responses of gut microbiota were noted, where seven of the 12 participants displayed all features of the outlined pattern, whereas four individuals showed mixed behavior and one subject was unresponsive. Intervention order did not affect the outcome, emphasizing a constant substrate supply for maintaining specific functional communities.IMPORTANCE Manipulation of gut microbiota is increasingly recognized as a promising approach to reduce various noncommunicable diseases, such as obesity and type 2 diabetes. Specific dietary supplements, including resistant starches (RS), are often a focus, yet comprehensive insights into functional responses of microbiota are largely lacking. Furthermore, unresponsiveness in certain individuals is poorly understood. Our data indicate that distinct parts of microbiota work jointly to degrade RS and successively form health-promoting fermentation end products. It highlights the need to consider both primary degraders and specific more-downstream-acting bacterial groups in order to achieve desired intervention outcomes. The gained insights will assist the design of personalized treatment strategies based on an individual's microbiota.}, }
@article {pmid30266101, year = {2018}, author = {Alneberg, J and Karlsson, CMG and Divne, AM and Bergin, C and Homa, F and Lindh, MV and Hugerth, LW and Ettema, TJG and Bertilsson, S and Andersson, AF and Pinhassi, J}, title = {Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {173}, pmid = {30266101}, issn = {2049-2618}, support = {310039//European Research Council/International ; }, mesh = {Bacteria/classification/*genetics ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Microbiota/*genetics ; *Nucleic Acid Amplification Techniques ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sweden ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.<br><br>RESULTS: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.<br><br>CONCLUSIONS: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.}, }
@article {pmid30261940, year = {2018}, author = {Denman, SE and Morgavi, DP and McSweeney, CS}, title = {Review: The application of omics to rumen microbiota function.}, journal = {Animal : an international journal of animal bioscience}, volume = {12}, number = {s2}, pages = {s233-s245}, doi = {10.1017/S175173111800229X}, pmid = {30261940}, issn = {1751-732X}, mesh = {Animals ; Bacteria/*classification/genetics ; Gastrointestinal Microbiome/*genetics ; Gene Expression Profiling/veterinary ; *Genomics ; Livestock ; *Metagenome ; Metagenomics ; Methane/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/metabolism ; }, abstract = {Rumen microbiome profiling uses 16S rRNA (18S rRNA, internal transcribed spacer) gene sequencing, a method that usually sequences a small portion of a single gene and is often biased and varies between different laboratories. Functional information can be inferred from this data, but only for those that are closely related to known annotated species, and even then may not truly reflect the function performed within the environment being studied. Genome sequencing of isolates and metagenome-assembled genomes has now reached a stage where representation of the majority of rumen bacterial genera are covered, but this still only represents a portion of rumen microbial species. The creation of a microbial genome (bins) database with associated functional annotations will provide a consistent reference to allow mapping of RNA-Seq reads for functional gene analysis from within the rumen microbiome. The integration of multiple omic analytics is linking functional gene activity, metabolic pathways and rumen metabolites with the responsible microbiota, supporting our biological understanding of the rumen system. The application of these techniques has advanced our understanding of the major microbial populations and functional pathways that are used in relation to lower methane emissions, higher feed efficiencies and responses to different feeding regimes. Continued and more precise use of these tools will lead to a detailed and comprehensive understanding of compositional and functional capacity and design of techniques for the directed intervention and manipulation of the rumen microbiota towards a desired state.}, }
@article {pmid30260956, year = {2018}, author = {Hunt, KA and Jennings, RM and Inskeep, WP and Carlson, RP}, title = {Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community.}, journal = {PLoS computational biology}, volume = {14}, number = {9}, pages = {e1006431}, pmid = {30260956}, issn = {1553-7358}, support = {U01 EB019416/EB/NIBIB NIH HHS/United States ; }, mesh = {Autotrophic Processes ; Biomass ; Carbon/chemistry ; Computer Simulation ; Electron Transport ; Electrons ; Ferric Compounds/*chemistry ; Genome, Archaeal ; Heterotrophic Processes ; Hot Temperature ; Iron/chemistry ; Metagenomics ; *Microbiota ; Oxygen/chemistry ; Phylogeny ; Sulfides/chemistry ; Sulfolobaceae/*metabolism ; Transcriptome ; }, abstract = {Interactions among microbial community members can lead to emergent properties, such as enhanced productivity, stability, and robustness. Iron-oxide mats in acidic (pH 2-4), high-temperature (> 65 °C) springs of Yellowstone National Park contain relatively simple microbial communities and are well-characterized geochemically. Consequently, these communities are excellent model systems for studying the metabolic activity of individual populations and key microbial interactions. The primary goals of the current study were to integrate data collected in situ with in silico calculations across process-scales encompassing enzymatic activity, cellular metabolism, community interactions, and ecosystem biogeochemistry, as well as to predict and quantify the functional limits of autotroph-heterotroph interactions. Metagenomic and transcriptomic data were used to reconstruct carbon and energy metabolisms of an important autotroph (Metallosphaera yellowstonensis) and heterotroph (Geoarchaeum sp. OSPB) from the studied Fe(III)-oxide mat communities. Standard and hybrid elementary flux mode and flux balance analyses of metabolic models predicted cellular- and community-level metabolic acclimations to simulated environmental stresses, respectively. In situ geochemical analyses, including oxygen depth-profiles, Fe(III)-oxide deposition rates, stable carbon isotopes and mat biomass concentrations, were combined with cellular models to explore autotroph-heterotroph interactions important to community structure-function. Integration of metabolic modeling with in situ measurements, including the relative population abundance of autotrophs to heterotrophs, demonstrated that Fe(III)-oxide mat communities operate at their maximum total community growth rate (i.e. sum of autotroph and heterotroph growth rates), as opposed to net community growth rate (i.e. total community growth rate subtracting autotroph consumed by heterotroph), as predicted from the maximum power principle. Integration of multiscale data with ecological theory provides a basis for predicting autotroph-heterotroph interactions and community-level cellular organization.}, }
@article {pmid30258172, year = {2019}, author = {Wilhelm, RC and Singh, R and Eltis, LD and Mohn, WW}, title = {Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {413-429}, doi = {10.1038/s41396-018-0279-6}, pmid = {30258172}, issn = {1751-7370}, mesh = {Bacteria/genetics/*metabolism ; Biomass ; Forests ; Fungi/genetics/metabolism ; Isotopes ; Lignin/*metabolism ; *Metagenomics ; Microbiota ; North America ; Soil/*chemistry ; *Soil Microbiology ; Wood/metabolism ; }, abstract = {Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin, cellulose and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of 13C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated 13C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.}, }
@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 {pmid30257633, year = {2018}, author = {White, LS and Van den Bogaerde, J and Kamm, M}, title = {The gut microbiota: cause and cure of gut diseases.}, journal = {The Medical journal of Australia}, volume = {209}, number = {7}, pages = {312-317}, pmid = {30257633}, issn = {1326-5377}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Diseases/microbiology/physiopathology/therapy ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Humans ; Inflammatory Bowel Diseases/microbiology/physiopathology/therapy ; Liver Diseases/microbiology/physiopathology/therapy ; Metabolic Syndrome/microbiology/physiopathology/therapy ; Metagenomics ; Mice ; *Obesity/microbiology/physiopathology/therapy ; }, abstract = {The gastrointestinal microbiota is emerging as a central factor in the pathogenesis of a range of gastrointestinal and hepatic disorders. Epidemiological studies, and experimental studies in animals and humans, have highlighted a likely causative role of this microbial community in the modern global epidemics of inflammatory bowel disease, non-alcoholic fatty liver disease, non-alcoholic steato-hepatitis, obesity and metabolic syndrome. New techniques for microbial culture and gene sequencing are enabling the identification of specific pathogens and protective organisms in these conditions. Factors that change the microbiota are being defined: dietary pattern, specific foods, food additives in processed food and drinks, such as emulsifiers and non-sugar sweeteners, and antibiotics. Microbiota changes in early life appear critical to the later development of a range of inflammatory disorders. For many of these conditions, the treatment paradigm will change, at least in part, from immune suppression and drug therapy to treatments that reshape the microbiota or restore its integrity. These treatments include dietary changes, specific microbial manipulation and faecal microbiota transplantation. A dialogue is needed regarding population strategies that target disease prevention. This will include how food is produced, what additives it contains, and how it is processed. Widespread use of antibiotics, from agricultural and veterinary to medicinal settings, needs more attention. At the individual level, microbial profiles may be able to predict who is at risk of disease when subjected to particular environmental influences, and what microbial restoration is needed to minimise risk.}, }
@article {pmid30252582, year = {2019}, author = {Ungaro, F and Massimino, L and Furfaro, F and Rimoldi, V and Peyrin-Biroulet, L and D'Alessio, S and Danese, S}, title = {Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease.}, journal = {Gut microbes}, volume = {10}, number = {2}, pages = {149-158}, doi = {10.1080/19490976.2018.1511664}, pmid = {30252582}, issn = {1949-0984}, mesh = {Adolescent ; Child ; Colitis, Ulcerative/diagnosis/pathology/virology ; Crohn Disease/diagnosis/pathology/virology ; Databases, Factual ; Feces/virology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammation/pathology/virology ; Inflammatory Bowel Diseases/diagnosis/pathology/*virology ; Intestinal Mucosa/pathology/*virology ; Male ; Metagenomics ; Viruses/classification/genetics/isolation &amp; purification ; }, abstract = {Intestinal dysbiosis is one of the causes underlying the pathogenesis of inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn's disease (CD). Besides bacteria, microbiota comprises both prokaryotic and eukaryotic viruses, that together compose the gut virome. Few works have defined the viral composition of stools, while the virome populating intestinal mucosae from early-diagnosed IBD patients has never been studied. Here we show that, by in-depth metagenomic analysis of RNA-Seq data obtained from gut mucosae of young treatment-naïve patients, early-diagnosed for CD and UC, and from healthy subjects (Ctrl), UC patients display significantly higher levels of eukaryotic Hepadnaviridae transcripts by comparison with both Ctrl and CD patients, whereas CD patients show increased abundance of Hepeviridae versus Ctrl. Moreover, we found that UC gut mucosa is characterized by lower levels of Polydnaviridae and Tymoviridae, whereas the mucosa of patients with CD showed a reduced abundance of Virgaviridae. Our findings support the idea that certain eukaryotic viruses might trigger intestinal inflammation and contribute to IBD pathogenesis and pave the way not only for the discovery of novel diagnostic biomarkers but also for the development of anti-viral drugs for the treatment of IBD.}, }
@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 {pmid30250051, year = {2019}, author = {Ju, F and Beck, K and Yin, X and Maccagnan, A and McArdell, CS and Singer, HP and Johnson, DR and Zhang, T and Bürgmann, H}, title = {Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {346-360}, doi = {10.1038/s41396-018-0277-8}, pmid = {30250051}, issn = {1751-7370}, mesh = {Anti-Bacterial Agents/analysis ; Bacteria/drug effects/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Metagenome ; Metagenomics ; *Microbiota ; Transcriptome ; Up-Regulation ; Waste Disposal, Fluid ; Waste Water/chemistry/*microbiology ; }, abstract = {Wastewater treatment plants (WWTPs) are implicated as hotspots for the dissemination of antibacterial resistance into the environment. However, the in situ processes governing removal, persistence, and evolution of resistance genes during wastewater treatment remain poorly understood. Here, we used quantitative metagenomic and metatranscriptomic approaches to achieve a broad-spectrum view of the flow and expression of genes related to antibacterial resistance to over 20 classes of antibiotics, 65 biocides, and 22 metals. All compartments of 12 WWTPs share persistent resistance genes with detectable transcriptional activities that were comparatively higher in the secondary effluent, where mobility genes also show higher relative abundance and expression ratios. The richness and abundance of resistance genes vary greatly across metagenomes from different treatment compartments, and their relative and absolute abundances correlate with bacterial community composition and biomass concentration. No strong drivers of resistome composition could be identified among the chemical stressors analyzed, although the sub-inhibitory concentration (hundreds of ng/L) of macrolide antibiotics in wastewater correlates with macrolide and vancomycin resistance genes. Contig-based analysis shows considerable co-localization between resistance and mobility genes and implies a history of substantial horizontal resistance transfer involving human bacterial pathogens. Based on these findings, we propose future inclusion of mobility incidence (M%) and host pathogenicity of antibiotic resistance genes in their quantitative health risk ranking models with an ultimate goal to assess the biological significance of wastewater resistomes with regard to disease control in humans or domestic livestock.}, }
@article {pmid30249182, year = {2018}, author = {Cavalcanti, GS and Shukla, P and Morris, M and Ribeiro, B and Foley, M and Doane, MP and Thompson, CC and Edwards, MS and Dinsdale, EA and Thompson, FL}, title = {Rhodoliths holobionts in a changing ocean: host-microbes interactions mediate coralline algae resilience under ocean acidification.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {701}, pmid = {30249182}, issn = {1471-2164}, mesh = {Biodiversity ; Hydrogen-Ion Concentration ; Metagenome ; *Microbiota/genetics ; Oceans and Seas ; Photosynthesis ; Rhodophyta/metabolism/*microbiology/physiology ; Seawater/chemistry/microbiology ; Stress, Physiological ; }, abstract = {BACKGROUND: Life in the ocean will increasingly have to contend with a complex matrix of concurrent shifts in environmental properties that impact their physiology and control their life histories. Rhodoliths are coralline red algae (Corallinales, Rhodophyta) that are photosynthesizers, calcifiers, and ecosystem engineers and therefore represent important targets for ocean acidification (OA) research. Here, we exposed live rhodoliths to near-future OA conditions to investigate responses in their photosynthetic capacity, calcium carbonate production, and associated microbiome using carbon uptake, decalcification assays, and whole genome shotgun sequencing metagenomic analysis, respectively. The results from our live rhodolith assays were compared to similar manipulations on dead rhodolith (calcareous skeleton) biofilms and water column microbial communities, thereby enabling the assessment of host-microbiome interaction under climate-driven environmental perturbations.<br><br>RESULTS: Under high pCO2 conditions, live rhodoliths exhibited positive physiological responses, i.e. increased photosynthetic activity, and no calcium carbonate biomass loss over time. Further, whereas the microbiome associated with live rhodoliths remained stable and resembled a healthy holobiont, the microbial community associated with the water column changed after exposure to elevated pCO2.<br><br>CONCLUSIONS: Our results suggest that a tightly regulated microbial-host interaction, as evidenced by the stability of the rhodolith microbiome recorded here under OA-like conditions, is important for host resilience to environmental stress. This study extends the scarce comprehension of microbes associated with rhodolith beds and their reaction to increased pCO2, providing a more comprehensive approach to OA studies by assessing the host holobiont.}, }
@article {pmid30248115, year = {2018}, author = {Kurobe, T and Lehman, PW and Hammock, BG and Bolotaolo, MB and Lesmeister, S and Teh, SJ}, title = {Biodiversity of cyanobacteria and other aquatic microorganisms across a freshwater to brackish water gradient determined by shotgun metagenomic sequencing analysis in the San Francisco Estuary, USA.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0203953}, pmid = {30248115}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Chlorophyta/classification/genetics ; Cyanobacteria/classification/*genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Diatoms/classification/genetics/isolation &amp; purification ; Estuaries ; Fresh Water/microbiology ; Genotype ; Harmful Algal Bloom ; Metagenomics ; Microcystis/genetics/isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction ; Saline Waters ; Salinity ; San Francisco ; Spatio-Temporal Analysis ; *Water Microbiology ; }, abstract = {Blooms of Microcystis and other harmful cyanobacteria can degrade water quality by producing cyanotoxins or other toxic compounds. The goals of this study were (1) to facilitate understanding of community structure for various aquatic microorganisms in brackish water and freshwater regions with emphasis on cyanobacteria, and (2) to test a hypothesis that Microcystis genotypes that tolerate higher salinity were blooming in brackish water environments during the severe drought, 2014. Shotgun metagenomic analysis revealed that cyanobacteria dominated the brackish water region while bacteria dominated the freshwater region. A group of cyanobacteria (e.g., Aphanizomenon, Microcystis, Planktothrix, Pseudanabaena), bacteria (e.g., Bacillus, Porphyrobacter), and diatoms (Phaeodactylum and Thalassiosira) were abundant in the brackish water region. In contrast, Hassallia (cyanobacteria) and green algae (Nannochloropsis, Chlamydomonas, and Volvox) were abundant in the landward freshwater region. Station variation was also apparent. One landward sampling station located downstream of an urbanized area differed substantially from the other stations in terms of both water chemistry and community structure, with a higher percentage of arthropods, green algae, and eukaryotes. Screening of the Microcystis internal transcribed spacer region revealed six representative genotypes, and two of which were successfully quantified using qPCR (Genotypes I and VI). Both genotypes occurred predominantly in the freshwater region, so the data from this study did not support the hypothesis that salinity tolerant Microcystis genotypes bloomed in the brackish water region in 2014.}, }
@article {pmid30246365, year = {2018}, author = {Murakami, T and Segawa, T and Takeuchi, N and Barcaza Sepúlveda, G and Labarca, P and Kohshima, S and Hongoh, Y}, title = {Metagenomic analyses highlight the symbiotic association between the glacier stonefly Andiperla willinki and its bacterial gut community.}, journal = {Environmental microbiology}, volume = {20}, number = {11}, pages = {4170-4183}, doi = {10.1111/1462-2920.14420}, pmid = {30246365}, issn = {1462-2920}, support = {16H04840//Japan Society for the Promotion of Science/International ; 17K19423//Japan Society for the Promotion of Science/International ; 22241005//Japan Society for the Promotion of Science/International ; 23117003//Japan Society for the Promotion of Science/International ; 26241020//Japan Society for the Promotion of Science/International ; GS009//NEXT/International ; }, mesh = {Animals ; Bacteria/classification/*genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Ecosystem ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Ice Cover/*parasitology ; In Situ Hybridization, Fluorescence ; Insecta/*microbiology/physiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {The glacier stonefly Andiperla willinki is the largest metazoan inhabiting the Patagonian glaciers. In this study, we analysed the gut microbiome of the aquatic nymphs by 16S rRNA gene amplicon and metagenomic sequencing. The bacterial gut community was consistently dominated by taxa typical of animal digestive tracts, such as Dysgonomonadaceae and Lachnospiraceae, as well as those generally indigenous to glacier environments, such as Polaromonas. Interestingly, the dominant Polaromonas phylotypes detected in the stonefly gut were almost never detected in the glacier surface habitat. Fluorescence in situ hybridization analysis revealed that the bacterial lineages typical of animal guts colonized the gut wall in a co-aggregated form, while Polaromonas cells were not included in the aggregates. Draft genomes of several dominant bacterial lineages were reconstructed from metagenomic datasets and indicated that the predominant Dysgonomonadaceae bacterium is capable of degrading various polysaccharides derived from host-ingested food, such as algae, and that other dominant bacterial lineages ferment saccharides liberated by the polysaccharide degradation. Our results suggest that the gut bacteria-host association in the glacier stonefly contributes to host nutrition as well as material cycles in the glacier environment.}, }
@article {pmid30242595, year = {2018}, author = {Hemmat-Jou, MH and Safari-Sinegani, AA and Mirzaie-Asl, A and Tahmourespour, A}, title = {Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach.}, journal = {Ecotoxicology (London, England)}, volume = {27}, number = {9}, pages = {1281-1291}, pmid = {30242595}, issn = {1573-3017}, mesh = {Environmental Monitoring/*methods ; Metagenome ; *Metagenomics ; Metals, Heavy/*toxicity ; Soil ; *Soil Microbiology ; Soil Pollutants/*toxicity ; }, abstract = {Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.}, }
@article {pmid30240699, year = {2018}, author = {Harris, L and van Zyl, LJ and Kirby-McCullough, BM and Damelin, LH and Tiemessen, CT and Trindade, M}, title = {Identification and sequence analysis of two novel cryptic plasmids isolated from the vaginal mucosa of South African women.}, journal = {Plasmid}, volume = {98}, number = {}, pages = {56-62}, doi = {10.1016/j.plasmid.2018.09.008}, pmid = {30240699}, issn = {1095-9890}, mesh = {DNA, Bacterial/*genetics ; Female ; Humans ; Lactobacillus/classification/*genetics/*isolation &amp; purification/metabolism ; Microbiota ; Mucous Membrane/*microbiology ; Phylogeny ; Plasmids/chemistry/*genetics ; Sequence Analysis, DNA ; South Africa/epidemiology ; Vagina/*microbiology ; Vaginosis, Bacterial/epidemiology/*microbiology ; }, abstract = {The vaginal mucosa is dominated by Gram positive, rod shaped lactobacilli which serve as a natural barrier against infection. In both healthy- and bacterial vaginosis (BV)-infected women Lactobacillus crispatus and Lactobacillus jensenii have been found to be the predominant Lactobacillus species. Many studies have been conducted to assess factors influencing lactobacilli dominance in the vaginal microbiome. In the present study two plasmids, pLc4 and pLc17, isolated from vaginal Lactobacillus strains of both healthy and BV-infected women were characterized. The smaller plasmid, pLc4 (4224 bp), was detected in both L. crispatus and L. jensenii strains, while pLc17 was only detected in L. crispatus. Based on its nucleotide sequence pLc4 appears highly novel, with its replication protein having 44% identity to the replication initiation protein of pSMQ173b_03. Phylogenetic analysis with other Rolling Circle Replication plasmids confirmed that pLc4 shows a low degree of similarity to these plasmids. Plasmid pLc17 (16,663 bp) appears to carry both a RCR replicon and a theta replicon, which is rare in naturally occurring plasmids. pLc4 was maintained at a high copy number of 29, while pLc17 appears to be a medium copy number plasmid maintained at 11 copies per chromosome. While sequence analysis is a valuable tool to study cryptic plasmids, further function-based analysis will be required in order to fully elucidate the role of these plasmids within the vaginal milieu.}, }
@article {pmid30240114, year = {2019}, author = {Bergner, LM and Orton, RJ and da Silva Filipe, A and Shaw, AE and Becker, DJ and Tello, C and Biek, R and Streicker, DG}, title = {Using noninvasive metagenomics to characterize viral communities from wildlife.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {128-143}, doi = {10.1111/1755-0998.12946}, pmid = {30240114}, issn = {1755-0998}, support = {//Wellcome Trust/United Kingdom ; 102507/Z/13/Z//Sir Henry Dale Fellowship, jointly funded by the Wellcome Trust and Royal Society/ ; 102507/Z/13/A//Wellcome-Beit Prize/ ; MC_UU_12014/12//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Biodiversity ; Chiroptera/*virology ; Feces/virology ; Metagenomics/*methods ; Oropharynx/virology ; Peru ; Sequence Analysis, DNA/*methods ; Specimen Handling/*methods ; Virus Diseases/*veterinary/virology ; Viruses/*classification/*genetics ; }, abstract = {Microbial communities play an important role in organismal and ecosystem health. While high-throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time.}, }
@article {pmid30234027, year = {2018}, author = {Wang, Z and Zolnik, CP and Qiu, Y and Usyk, M and Wang, T and Strickler, HD and Isasi, CR and Kaplan, RC and Kurland, IJ and Qi, Q and Burk, RD}, title = {Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {301}, pmid = {30234027}, issn = {2235-2988}, support = {K01 HL129892/HL/NHLBI NIH HHS/United States ; K12 GM102779/GM/NIGMS NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R01 HL126543/HL/NHLBI NIH HHS/United States ; R01 HL132794/HL/NHLBI NIH HHS/United States ; R01 HL083760/HL/NHLBI NIH HHS/United States ; R01 HL095140/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; U01 AI035004/AI/NIAID NIH HHS/United States ; P30 CA013330/CA/NCI NIH HHS/United States ; P30 DK041296/DK/NIDDK NIH HHS/United States ; P30 AI124414/AI/NIAID NIH HHS/United States ; }, mesh = {Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids/analysis ; Feces/*chemistry/*microbiology ; Healthy Volunteers ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Specimen Handling/*methods ; Temperature ; }, abstract = {Background: Integrated microbiome and metabolomics analyses hold the potential to reveal interactions between host and microbiota in relation to disease risks. However, there are few studies evaluating how field methods influence fecal microbiome characterization and metabolomics profiling. Methods: Five fecal collection methods [immediate freezing at -20°C without preservative, OMNIgene GUT, 95% ethanol, RNAlater, and Flinders Technology Associates (FTA) cards] were used to collect 40 fecal samples from eight healthy volunteers. We performed gut microbiota 16S rRNA sequencing, untargeted metabolomics profiling, and targeted metabolomics focusing on short chained fatty acids (SCFAs). Metrics included α-diversity and β-diversity as well as distributions of predominant phyla. To evaluate the concordance with the &quot;gold standard&quot; immediate freezing, the intraclass correlation coefficients (ICCs) for alternate fecal collection systems were calculated. Correlations between SCFAs and gut microbiota were also examined. Results: The FTA cards had the highest ICCs compared to the immediate freezing method for α-diversity indices (ICCs = 0.96, 0.96, 0.76 for Shannon index, Simpson's Index, Chao-1 Index, respectively), followed by OMNIgene GUT, RNAlater, and 95% ethanol. High ICCs (all >0.88) were observed for all methods for the β-diversity metric. For untargeted metabolomics, in comparison to immediate freezing which detected 621 metabolites at ≥75% detectability level, 95% ethanol showed the largest overlapping set of metabolites (n = 430; 69.2%), followed by FTA cards (n = 330; 53.1%) and OMNIgene GUT (n = 213; 34.3%). Both OMNIgene GUT (ICCs = 0.82, 0.93, 0.64) and FTA cards (ICCs = 0.87, 0.85, 0.54) had acceptable ICCs for the top three predominant SCFAs (butyric acid, propionic acid and acetic acid). Nominally significant correlations between bacterial genera and SCFAs (P < 0.05) were observed in fecal samples collected by different methods. Of note, a high correlation between the genus Blautia (known butyrate producer) and butyric acid was observed for both immediate freezing (r = 0.83) and FTA cards (r = 0.74). Conclusions: Four alternative fecal collection methods are generally comparable with immediate freezing, but there are differences in certain measures of the gut microbiome and fecal metabolome across methods. Choice of method depends on the research interests, simplicity of fecal collection procedures and ease of transportation to the lab, especially for large epidemiological studies.}, }
@article {pmid30232678, year = {2019}, author = {Osman, JR and Regeard, C and Badel, C and Fernandes, G and DuBow, MS}, title = {Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France).}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {3}, pages = {351-365}, doi = {10.1007/s10482-018-1164-z}, pmid = {30232678}, issn = {1572-9699}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Estuaries ; France ; Geologic Sediments/*microbiology ; Mediterranean Sea ; Metagenomics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Salinity is an important environmental factor influencing microbial community composition. To better understand this influence, we determined the bacterial communities present in 17 different sites of brackish sediment (underwater) and soil (surface) samples from the Camargue region (Rhône river delta) in southern France during the fall of 2013 and 2014 using pyrosequencing of the V3-V4 regions of the 16S rRNA genes amplified by PCR. This region is known for abundant flora and fauna and, though saline, 30% of rice consumed in France is grown here. We found that bacterial abundance in 1 g of soil or sediment, calculated by qPCR, was higher in sediments than in surface soil samples. Members belonging to the Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes phyla dominated the bacterial communities of sediment samples, while members belonging to the Proteobacteria, Bacteroidetes, Gemmatimonadetes, Actinobacteria, Firmicutes and Acidobacteria phyla dominated the bacterial communities of the soil samples. The most abundant bacterial genera present in the saline sediments and soils from the Camargue belonged mostly to halophilic and sulphate reducing bacteria, suggesting that the Camargue may be a valuable system to investigate saline, yet agriculturally productive, sediment and soil microbial ecosystem.}, }
@article {pmid30232167, year = {2018}, author = {Ingala, MR and Simmons, NB and Perkins, SL}, title = {Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30232167}, issn = {2379-5042}, mesh = {Animals ; Chiroptera/*microbiology ; *Diet ; Ecology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; *Metagenomics ; Phylogeny ; }, abstract = {Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome.}, }
@article {pmid30231921, year = {2018}, author = {Vavourakis, CD and Andrei, AS and Mehrshad, M and Ghai, R and Sorokin, DY and Muyzer, G}, title = {A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {168}, pmid = {30231921}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; Carbon Cycle ; Genetic Variation ; Genome, Bacterial ; Geologic Sediments/analysis/*microbiology ; Lakes/analysis/*microbiology ; Metagenome ; Metagenomics ; Microbiota ; Nitrogen Cycle ; Phylogeny ; Sodium Chloride/analysis ; }, abstract = {BACKGROUND: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.<br><br>RESULTS: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.<br><br>CONCLUSIONS: Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.}, }
@article {pmid30227897, year = {2018}, author = {Arora-Williams, K and Olesen, SW and Scandella, BP and Delwiche, K and Spencer, SJ and Myers, EM and Abraham, S and Sooklal, A and Preheim, SP}, title = {Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {165}, pmid = {30227897}, issn = {2049-2618}, mesh = {Bacteria/classification/isolation &amp; purification/metabolism ; Carbon/chemistry/metabolism ; Ecosystem ; Lakes/*chemistry/*microbiology ; Metagenome ; Metagenomics ; Methane/chemistry/metabolism ; *Microbiota ; Oxidation-Reduction ; Oxygen/chemistry/metabolism ; }, abstract = {BACKGROUND: Microbial processes are intricately linked to the depletion of oxygen in in-land and coastal water bodies, with devastating economic and ecological consequences. Microorganisms deplete oxygen during biomass decomposition, degrading the habitat of many economically important aquatic animals. Microbes then turn to alternative electron acceptors, which alter nutrient cycling and generate potent greenhouse gases. As oxygen depletion is expected to worsen with altered land use and climate change, understanding how chemical and microbial dynamics impact dead zones will aid modeling efforts to guide remediation strategies. More work is needed to understand the complex interplay between microbial genes, populations, and biogeochemistry during oxygen depletion.<br><br>RESULTS: Here, we used 16S rRNA gene surveys, shotgun metagenomic sequencing, and a previously developed biogeochemical model to identify genes and microbial populations implicated in major biogeochemical transformations in a model lake ecosystem. Shotgun metagenomic sequencing was done for one time point in Aug., 2013, and 16S rRNA gene sequencing was done for a 5-month time series (Mar.-Aug., 2013) to capture the spatiotemporal dynamics of genes and microorganisms mediating the modeled processes. Metagenomic binning analysis resulted in many metagenome-assembled genomes (MAGs) that are implicated in the modeled processes through gene content similarity to cultured organism and the presence of key genes involved in these pathways. The MAGs suggested some populations are capable of methane and sulfide oxidation coupled to nitrate reduction. Using the model, we observe that modulating these processes has a substantial impact on overall lake biogeochemistry. Additionally, 16S rRNA gene sequences from the metagenomic and amplicon libraries were linked to processes through the MAGs. We compared the dynamics of microbial populations in the water column to the model predictions. Many microbial populations involved in primary carbon oxidation had dynamics similar to the model, while those associated with secondary oxidation processes deviated substantially.<br><br>CONCLUSIONS: This work demonstrates that the unique capabilities of resident microbial populations will substantially impact the concentration and speciation of chemicals in the water column, unless other microbial processes adjust to compensate for these differences. It further highlights the importance of the biological aspects of biogeochemical processes, such as fluctuations in microbial population dynamics. Integrating gene and population dynamics into biogeochemical models has the potential to improve predictions of the community response under altered scenarios to guide remediation efforts.}, }
@article {pmid30225935, year = {2019}, author = {Drinkwater, R and Schnell, IB and Bohmann, K and Bernard, H and Veron, G and Clare, E and Gilbert, MTP and Rossiter, SJ}, title = {Using metabarcoding to compare the suitability of two blood-feeding leech species for sampling mammalian diversity in North Borneo.}, journal = {Molecular ecology resources}, volume = {19}, number = {1}, pages = {105-117}, doi = {10.1111/1755-0998.12943}, pmid = {30225935}, issn = {1755-0998}, support = {SAS-2016-100//The Leverhulme Trust/ ; NE/K016148/1//Natural Environment Research Council/ ; DFF 5051-00140//The Danish Council for Independent Research/ ; }, mesh = {Animals ; Borneo ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/chemistry/genetics ; *Feeding Behavior ; High-Throughput Nucleotide Sequencing ; *Host Specificity ; Leeches/*physiology ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. To address these questions, we collected spatially matched samples of two congeneric leech species Haemadipsa picta and Haemadipsa sumatrana from lowland rainforest in Borneo. For each species, we pooled ~500 leeches into batches of 10 individuals, performed PCR to target a section of the mammalian 16S rRNA locus and undertook sequencing of amplicon libraries using an Illumina MiSeq. In total, we identified sequences from 14 mammalian genera, spanning nine families and five orders. We found greater numbers of detections, and higher diversity of OTUs, in H. picta compared with H. sumatrana, with rodents only present in the former leech species. However, comparison of samples from across the landscape revealed no significant difference in mammal community composition between the leech species. We therefore suggest that H. picta is the more suitable iDNA sampler in this degraded Bornean forest. We conclude that the choice of invertebrate sampler can influence the detectability of different mammal groups and that this should be accounted for when designing iDNA studies.}, }
@article {pmid30221538, year = {2018}, author = {Venkataraman, A and Parlov, M and Hu, P and Schnell, D and Wei, X and Tiesman, JP}, title = {Spike-in genomic DNA for validating performance of metagenomics workflows.}, journal = {BioTechniques}, volume = {65}, number = {6}, pages = {315-321}, doi = {10.2144/btn-2018-0089}, pmid = {30221538}, issn = {1940-9818}, mesh = {Bacteria/*genetics/isolation &amp; purification ; DNA, Bacterial/*genetics/isolation &amp; purification ; Gene Library ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; *Microbiota ; Rhodopseudomonas/genetics/isolation &amp; purification ; *Workflow ; }, abstract = {Shotgun metagenomics is a powerful platform to characterize human microbiomes. However, to translate such survey data into consumer-relevant products or services, it is critical to have a robust metagenomics workflow. We present a tool - spike-in DNA - to assess performance of metagenomics workflows. The spike-in is DNA from two organisms - Alivibrio fischeri and Rhodopseudomonas palustris, in a ratio of 4:1 added to samples before DNA extraction. With a valid workflow, the output ratio of relative abundances of these organisms should be close to 4. This expectation was tested in samples of varying diversities (n = 110), and the mean ratio was 4.73 (99% CI [4.0, 5.24]). We anticipate this tool to be a relevant community resource for assessing the quality of shotgun metagenomics workflows and thereby enable robust characterization of microbiomes.}, }
@article {pmid30219103, year = {2018}, author = {Uritskiy, GV and DiRuggiero, J and Taylor, J}, title = {MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {158}, pmid = {30219103}, issn = {2049-2618}, support = {R01 AI134384/AI/NIAID NIH HHS/United States ; T32 GM007231/GM/NIGMS NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/genetics/isolation &amp; purification ; Data Analysis ; Data Mining ; Gastrointestinal Microbiome ; *Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; *Software ; }, abstract = {BACKGROUND: The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization.<br><br>RESULTS: To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP's hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization.<br><br>CONCLUSIONS: MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP .}, }
@article {pmid30217078, year = {2018}, author = {Li, Y and Hingamp, P and Watai, H and Endo, H and Yoshida, T and Ogata, H}, title = {Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters.}, journal = {Viruses}, volume = {10}, number = {9}, pages = {}, pmid = {30217078}, issn = {1999-4915}, support = {203143100025//Canon Foundation for Scientific Research/International ; 16KT0020//Japan Society for the Promotion of Science/International ; 17H03850//Japan Society for the Promotion of Science/International ; 26430184//Japan Society for the Promotion of Science/International ; 2016-28//Institute for Chemical Research, Kyoto University/International ; 2017-25//Institute for Chemical Research, Kyoto University/International ; ANR-11-BTBR-0008//French Investments for the Future program/International ; }, mesh = {*Biodiversity ; Computational Biology/methods ; Genome, Viral ; Giant Viruses/*classification/*genetics ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Polymerase Chain Reaction/methods ; Seawater/*virology ; *Water Microbiology ; }, abstract = {&quot;Megaviridae&quot; is a proposed family of giant viruses infecting unicellular eukaryotes. These viruses are ubiquitous in the sea and have impact on marine microbial community structure and dynamics through their lytic infection cycle. However, their diversity and biogeography have been poorly characterized due to the scarce detection of Megaviridae sequences in metagenomes, as well as the limitation of reference sequences used to design specific primers for this viral group. Here, we propose a set of 82 degenerated primers (referred to as MEGAPRIMER), targeting DNA polymerase genes (polBs) of Megaviridae. MEGAPRIMER was designed based on 921 Megaviridae polBs from sequenced genomes and metagenomes. By applying this primer set to environmental DNA meta-barcoding of a coastal seawater sample, we report 5595 non-singleton operational taxonomic units (OTUs) of Megaviridae at 97% nucleotide sequence identity. The majority of the OTUs were found to form diverse clades, which were phylogenetically distantly phylogenetically related to known viruses such as Mimivirus. The Megaviridae OTUs detected in this study outnumber the giant virus OTUs identified in previous individual studies by more than an order of magnitude. Hence, MEGAPRIMER represents a useful tool to study the diversity of Megaviridae at the population level in natural environments.}, }
@article {pmid30213145, year = {2018}, author = {Gómez-Villegas, P and Vigara, J and León, R}, title = {Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain).}, journal = {Marine drugs}, volume = {16}, number = {9}, pages = {}, pmid = {30213145}, issn = {1660-3397}, support = {0055_ALGARED_PLUS_5_E//INTERREG VA España-Portugal (POCTEP) 2014-2020 Cooperation Program/ ; }, mesh = {Bacteroidetes/*genetics/isolation &amp; purification ; Biodiversity ; Biotechnology/methods ; DNA, Bacterial/isolation &amp; purification ; Genetic Variation ; Halobacteriales/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; Spain ; *Water Microbiology ; Wetlands ; }, abstract = {The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypers