@article {pmid30886779,
year = {2019},
author = {Eisenhofer, R and Weyrich, LS},
title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6594},
doi = {10.7717/peerj.6594},
pmid = {30886779},
issn = {2167-8359},
abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.},
}

@article {pmid30690359,
year = {2019},
author = {Qiao, R and Sheng, C and Lu, Y and Zhang, Y and Ren, H and Lemos, B},
title = {Microplastics induce intestinal inflammation, oxidative stress, and disorders of metabolome and microbiome in zebrafish.},
journal = {The Science of the total environment},
volume = {662},
number = {},
pages = {246-253},
doi = {10.1016/j.scitotenv.2019.01.245},
pmid = {30690359},
issn = {1879-1026},
mesh = {Animals ; Dose-Response Relationship, Drug ; Dysbiosis/chemically induced/immunology/*physiopathology ; Fish Diseases/chemically induced/*immunology/physiopathology ; Gastrointestinal Microbiome/drug effects ; Inflammation/chemically induced/*immunology ; Intestines/immunology/physiology ; Metabolome/drug effects ; Metagenomics ; Oxidative Stress/drug effects ; Polystyrenes/*adverse effects/metabolism ; Random Allocation ; Toxicity Tests, Chronic ; Water Pollutants, Chemical/*adverse effects/metabolism ; *Zebrafish/metabolism/microbiology ; },
abstract = {Microplastics (MPs) can be ingested by a variety of species and mainly accumulate in the gut. However, the consequences of MPs exposure in the gut are largely unknown. Here we evaluated the impacts of MPs exposure in zebrafish gut. Animals were experimentally exposed to polystyrene MPs (5-μm beads; 50 μg/L and 500 μg/L) for 21 days and monitored for alterations in tissue histology, enzymatic biomarkers, gut microbiome and metabolomic responses. Inflammation and oxidative stress were observed in the zebrafish gut after exposed to MPs. Furthermore, significant alterations in the gut microbiome and tissue metabolic profiles were observed, with most of these were associated with oxidative stress, inflammation and lipid metabolism. This study provides evidence that MPs exposure causes gut damage as well as alterations in gut metabolome and microbiome, yielding novel insights into the consequences of MPs exposure.},
}

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

@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.},
}

Australia
Bacteria/*classification/*genetics
Child
Child, Preschool
Dental Caries/*microbiology
Dental Plaque/*microbiology
Humans
Metabolic Networks and Pathways/genetics
Metagenomics
*Microbiota
Sequence Analysis, DNA

@article {pmid29695035,
year = {2018},
author = {Yuan, QS and Yang, P and Wu, AB and Zuo, DY and He, WJ and Guo, MW and Huang, T and Li, HP and Liao, YC},
title = {Variation in the Microbiome, Trichothecenes, and Aflatoxins in Stored Wheat Grains in Wuhan, China.},
journal = {Toxins},
volume = {10},
number = {5},
pages = {},
pmid = {29695035},
issn = {2072-6651},
mesh = {Aflatoxins/*analysis ; Agriculture/methods ; Bacteria/genetics/isolation & purification ; China ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; Edible Grain/*chemistry/*microbiology ; Environmental Monitoring ; Food Contamination/*analysis ; Fungi/genetics/isolation & purification ; Microbiota ; Trichothecenes/*analysis ; Triticum/*chemistry/*microbiology ; },
abstract = {Contamination by fungal and bacterial species and their metabolites can affect grain quality and health of wheat consumers. In this study, sequence analyses of conserved DNA regions of fungi and bacteria combined with determination of trichothecenes and aflatoxins revealed the microbiome and mycotoxins of wheat from different silo positions (top, middle, and bottom) and storage times (3, 6, 9, and 12 months). The fungal community in wheat on the first day of storage (T₀) included 105 classified species (81 genera) and 41 unclassified species. Four species had over 10% of the relative abundance: Alternaria alternata (12%), Filobasidium floriforme (27%), Fusarium graminearum (12%), and Wallemia sebi (12%). Fungal diversity and relative abundance of Fusarium in wheat from top silo positions were significantly lower than at other silo positions during storage. Nivalenol and deoxynivalenol in wheat were 13⁻34% higher in all positions at 3 months compared to T₀, and mycotoxins in wheat from middle and bottom positions at 6 to 12 months were 24⁻57% higher than at T₀. The relative abundance of toxigenic Aspergillus and aflatoxins were low at T₀ and during storage. This study provides information on implementation and design of fungus and mycotoxin management strategies as well as prediction models.},
}

Aflatoxins/*analysis
Agriculture/methods
Bacteria/genetics/isolation & purification
China
DNA, Bacterial/analysis
DNA, Fungal/analysis
Edible Grain/*chemistry/*microbiology
Environmental Monitoring
Food Contamination/*analysis
Fungi/genetics/isolation & purification
Microbiota
Trichothecenes/*analysis
Triticum/*chemistry/*microbiology

@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 & 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.},
}

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 & distribution

@article {pmid29274958,
year = {2018},
author = {Li, F and Neves, ALA and Ghoshal, B and Guan, LL},
title = {Symposium review: Mining metagenomic and metatranscriptomic data for clues about microbial metabolic functions in ruminants.},
journal = {Journal of dairy science},
volume = {101},
number = {6},
pages = {5605-5618},
doi = {10.3168/jds.2017-13356},
pmid = {29274958},
issn = {1525-3198},
mesh = {Animals ; Gene Expression Profiling ; *Metagenomics ; Methane/metabolism ; Microbiota ; Rumen/*microbiology ; *Ruminants ; Transcriptome ; },
abstract = {Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption. To date, hundreds to thousands of microbial phylotypes have been identified in the rumen using culture-independent molecular-based approaches, and genomic information of rumen microorganisms is rapidly accumulating through the single genome sequencing. However, functional characteristics of the rumen microbiome have not been well described because there are numerous uncultivable microorganisms in the rumen. The advent of metagenomics and metatranscriptomics along with advanced bioinformatics methods can help us better understand mechanisms of the rumen fermentation, which is vital for improving nutrient utilization and animal productivity. Therefore, in this review, we summarize a general workflow to conduct rumen metagenomics and metatranscriptomics and discuss how the data can be interpreted to be useful information. Moreover, we review recent literatures studying associations between the rumen microbiome and host phenotypes (e.g., feed efficiency and methane emissions) using these approaches, aiming to provide a useful guide to include studying the rumen microbiome as one of the research objectives using these 2 approaches.},
}

Animals
Gene Expression Profiling
*Metagenomics
Methane/metabolism
Microbiota
Rumen/*microbiology
*Ruminants
Transcriptome

@article {pmid30871459,
year = {2019},
author = {Thrash, A and Arick, M and Barbato, RA and Jones, RM and Douglas, TA and Esdale, J and Perkins, EJ and Garcia-Reyero, N},
title = {Keanu: a novel visualization tool to explore biodiversity in metagenomes.},
journal = {BMC bioinformatics},
volume = {20},
number = {Suppl 2},
pages = {103},
doi = {10.1186/s12859-019-2629-4},
pmid = {30871459},
issn = {1471-2105},
abstract = {BACKGROUND: One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, especially with metagenomics data or data suspected to be contaminated. Here, we describe the development and application of a command-line tool, Keanu, for visualizing and exploring sample content in metagenomics data. We developed Keanu as an interactive tool to make viewing complex data easier.

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.

CONCLUSIONS: Keanu provides a simple means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu .},
}

@article {pmid30623233,
year = {2019},
author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS},
title = {Chinese liver fluke Clonorchis sinensis infection changes the gut microbiome and increases probiotic Lactobacillus in mice.},
journal = {Parasitology research},
volume = {118},
number = {2},
pages = {693-699},
doi = {10.1007/s00436-018-6179-x},
pmid = {30623233},
issn = {1432-1955},
support = {NRF-2016R1A2B4016194//National Research Foundation of Korea/ ; 2011-0012166//National Research Foundation of Korea/ ; },
mesh = {Animals ; Clonorchiasis/*immunology/parasitology ; Clonorchis sinensis/growth & development/*immunology ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing ; Lactobacillus/classification/cytology/*growth & 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.},
}

Animals
Clonorchiasis/*immunology/parasitology
Clonorchis sinensis/growth & development/*immunology
Feces/microbiology
Gastrointestinal Microbiome/*physiology
High-Throughput Nucleotide Sequencing
Lactobacillus/classification/cytology/*growth & development
Metacercariae/cytology
Mice
Mice, Inbred C57BL
Probiotics/*analysis
RNA, Ribosomal, 16S/genetics

@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.},
}

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

@article {pmid29611114,
year = {2018},
author = {Wang, J and Chen, L and Zhao, N and Xu, X and Xu, Y and Zhu, B},
title = {Of genes and microbes: solving the intricacies in host genomes.},
journal = {Protein & cell},
volume = {9},
number = {5},
pages = {446-461},
pmid = {29611114},
issn = {1674-8018},
mesh = {Animals ; Biomedical Research ; *Genes ; *Genetic Variation ; *Genome ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenomics ; *Microbiota ; },
abstract = {Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.},
}

Animals
Biomedical Research
*Genes
*Genetic Variation
*Genome
Host-Pathogen Interactions/*genetics
Humans
Metagenomics
*Microbiota

@article {pmid29482661,
year = {2018},
author = {Han, M and Hao, L and Lin, Y and Li, F and Wang, J and Yang, H and Xiao, L and Kristiansen, K and Jia, H and Li, J},
title = {A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {43},
pmid = {29482661},
issn = {2049-2618},
support = {2017YFC0909700//National Key Research and Development Program of China/International ; 31601073//National Natural Science Foundation of China/International ; JSGG20160229172752028//Shenzhen Municipal Government of China/International ; JCYJ20160229172757249//Shenzhen Municipal Government of China/International ; },
mesh = {Bacteria/*genetics/metabolism ; Bromides/*chemistry ; DNA, Bacterial/*genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenomics ; Pyridinium Compounds/*chemistry ; Specimen Handling/*methods ; Temperature ; },
abstract = {BACKGROUND: The number of large-scale studies on the gut microbiota in human cohorts is rapidly increasing. However, the few and expensive options for storage of fecal samples at room temperature have been an obstacle for large-scale metagenomic studies and the development of clinical/commercial personal metagenomic sequencing.

RESULTS: In this study, we systematically tested a novel N-octylpyridinium bromide-based fecal sample preservation method and compared it with other currently used storage methods. We found that the N-octylpyridinium bromide-based method enabled preservation of the bacterial composition in fecal samples transported and stored at room temperature for up to at least 14 days.

CONCLUSIONS: We describe a novel chemical stabilizer that allows cost-effective transportation and storage at room temperature for several days with preservation of bacterial composition. This method will facilitate sample collection even in remote area and also enable transport via normal commercial transportation routes.},
}

Bacteria/*genetics/metabolism
Bromides/*chemistry
DNA, Bacterial/*genetics
Feces/*microbiology
Gastrointestinal Microbiome/*genetics
Humans
*Metagenomics
Pyridinium Compounds/*chemistry
Specimen Handling/*methods
Temperature

@article {pmid28827532,
year = {2017},
author = {Jiang, J and Song, Z and Yang, X and Mao, Z and Nie, X and Guo, H and Peng, X},
title = {Microbial community analysis of apple rhizosphere around Bohai Gulf.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8918},
pmid = {28827532},
issn = {2045-2322},
mesh = {Biodiversity ; Environment ; Malus/*microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Plant Roots/microbiology ; *Rhizosphere ; *Soil Microbiology ; },
abstract = {Bohai Gulf is the main area for apple tree cultivation in China. Consecutive replanting significantly affects the yield and quality of apple trees in this area. Microecological imbalance in apple trees' rhizospheres caused by variation in the soil microbial community is considered the primary cause of apple replant disease (ARD). This study analysed the microbial communities of the rhizospheres of perennial apple trees (PAT) and apple tree saplings under replanting (ATS) around Bohai Gulf using high-throughput sequencing. The results revealed increased populations of typical pathogenic fungi Verticillium and bacteria Xanthomonadaceae, and decreased populations of beneficial bacterial populations Pseudomonas and Bacillus with replanting, suggesting that competition between pathogens and beneficial microbes varies according to the ratio of pathogens to beneficial microbes in rhizosphere soil under the replanting system. Meanwhile, replanting was accompanied by an increase in the antagonistic bacteria Arthrobacter and fungus Chaetomium, suggesting that increased numbers of pathogens can lead to more instances of antagonism. Redundancy analysis (RDA) revealed site position and the main soil properties (pH, organic matter, available N, available K, available P, and moisture) affected the microbial community composition. It found clear differences in soil microbial communities and demonstrated a better understanding of the causes for ARD.},
}

Biodiversity
Environment
Malus/*microbiology
Metagenome
Metagenomics
*Microbiota
Plant Roots/microbiology
*Rhizosphere
*Soil Microbiology

@article {pmid28821872,
year = {2017},
author = {Nakagawa, S and Saito, H and Tame, A and Hirai, M and Yamaguchi, H and Sunata, T and Aida, M and Muto, H and Sawayama, S and Takaki, Y},
title = {Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8764},
pmid = {28821872},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; Fish Diseases/microbiology ; Helicobacter/*classification/*genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Starfish/*microbiology ; },
abstract = {Marine invertebrates associate with diverse microorganisms. Microorganisms even inhabit coelomic fluid (CF), namely, the fluid filling the main body cavity of echinoderms. The CF microbiota potentially impacts host health and disease. Here, we analysed the CF microbiota in two common coastal starfish species, Patiria pectinifera and Asterias amurensis. Although microbial community structures were highly variable among individual starfish, those of P. pectinifera were compositionally similar to those in the surrounding seawater. By contrast, many A. amurensis individuals harboured unique microbes in the CF, which was dominated by the unclassified Thiotrichales or previously unknown Helicobacter-related taxon. In some individuals, the Helicobacter-related taxon was the most abundant genus-level taxon, accounting for up to 97.3% of reads obtained from the CF microbial community. Fluorescence in situ hybridization using a Helicobacter-related-taxon-specific probe suggested that probe-reactive cells in A. amurensis were spiral-shaped, morphologically similar to known Helicobacter species. Electron microscopy revealed that the spiral cells had a prosthecate-like polar appendage that has never been reported in Helicobacter species. Although culture of Helicobacter-related taxon was unsuccessful, this is the first report of the dominance of a Helicobacter-related taxon in invertebrates and non-digestive organs, reshaping our knowledge of the phylogeography of Helicobacter-related taxa.},
}

Animals
*Biodiversity
Fish Diseases/microbiology
Helicobacter/*classification/*genetics
Metagenome
Metagenomics/methods
*Microbiota
Phylogeography
RNA, Ribosomal, 16S/genetics
Starfish/*microbiology

@article {pmid28821814,
year = {2017},
author = {Fang, D and Shi, D and Lv, L and Gu, S and Wu, W and Chen, Y and Guo, J and Li, A and Hu, X and Guo, F and Ye, J and Li, Y and Li, L},
title = {Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8770},
pmid = {28821814},
issn = {2045-2322},
mesh = {Animals ; Bifidobacterium/*physiology ; Bifidobacterium pseudocatenulatum/*physiology ; Cytokines/blood/metabolism ; Galactosamine/*adverse effects ; Gastrointestinal Microbiome/*drug effects ; Inflammation Mediators/blood/metabolism ; Intestinal Mucosa/drug effects/metabolism/pathology ; Liver Diseases/*etiology/metabolism/pathology ; Male ; Metagenome ; Metagenomics ; Models, Biological ; Rats ; },
abstract = {The gut microbiota is altered in liver diseases, and several probiotics have been shown to reduce the degree of liver damage. We hypothesized that oral administration of specific Bifidobacterium strains isolated from healthy guts could attenuate liver injury. Five strains were tested in this study. Acute liver injury was induced by D-galactosamine after pretreating Sprague-Dawley rats with the Bifidobacterium strains, and liver function, liver and ileum histology, plasma cytokines, bacterial translocation and the gut microbiome were assessed. Two strains, Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10, conferred liver protection, as well as alleviated the increase in plasma M-CSF, MIP-1α and MCP-1 and bacterial translocation. They also ameliorated ileal mucosal injury and gut flora dysbiosis, especially the enrichment of the opportunistic pathogen Parasutterella and the depletion of the SCFA-producing bacteria Anaerostipes, Coprococcus and Clostridium XI. Negative correlations were found between MIP-1α / MCP-1 and Odoribacter (LI09 group) and MIP-1α / M-CSF and Flavonifractor (LI10 group). Our results indicate that the liver protection effects might be mediated through gut microbiota modification, which thus affect the host immune profile. The desirable characteristics of these two strains may enable them to serve as potential probiotics for the prevention or adjuvant treatment of liver injury.},
}

Animals
Bifidobacterium/*physiology
Bifidobacterium pseudocatenulatum/*physiology
Cytokines/blood/metabolism
Galactosamine/*adverse effects
Gastrointestinal Microbiome/*drug effects
Inflammation Mediators/blood/metabolism
Intestinal Mucosa/drug effects/metabolism/pathology
Liver Diseases/*etiology/metabolism/pathology
Male
Metagenome
Metagenomics
Models, Biological
Rats

@article {pmid28821731,
year = {2017},
author = {Glymenaki, M and Barnes, A and O'Hagan, S and Warhurst, G and McBain, AJ and Wilson, ID and Kell, DB and Else, KJ and Cruickshank, SM},
title = {Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8836},
pmid = {28821731},
issn = {2045-2322},
support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Chromatography, High Pressure Liquid ; Colitis/*etiology/*metabolism ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; Genotype ; Inflammatory Bowel Diseases/etiology/metabolism ; Male ; Mass Spectrometry ; *Metabolome ; *Metabolomics/methods ; Metagenome ; Metagenomics ; Mice ; Mice, Knockout ; *Phenotype ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Inflammatory bowel disease (IBD) is associated with altered microbiota composition and metabolism, but it is unclear whether these changes precede inflammation or are the result of it since current studies have mainly focused on changes after the onset of disease. We previously showed differences in mucus gut microbiota composition preceded colitis-induced inflammation and stool microbial differences only became apparent at colitis onset. In the present study, we aimed to investigate whether microbial dysbiosis was associated with differences in both predicted microbial gene content and endogenous metabolite profiles. We examined the functional potential of mucus and stool microbial communities in the mdr1a -/- mouse model of colitis and littermate controls using PICRUSt on 16S rRNA sequencing data. Our findings indicate that despite changes in microbial composition, microbial functional pathways were stable before and during the development of mucosal inflammation. LC-MS-based metabolic phenotyping (metabotyping) in urine samples confirmed that metabolite profiles in mdr1a -/- mice were remarkably unaffected by development of intestinal inflammation and there were no differences in previously published metabolic markers of IBD. Metabolic profiles did, however, discriminate the colitis-prone mdr1a -/- genotype from controls. Our results indicate resilience of the metabolic network irrespective of inflammation. Importantly as metabolites differentiated genotype, genotype-differentiating metabolites could potentially predict IBD risk.},
}

Animals
Chromatography, High Pressure Liquid
Colitis/*etiology/*metabolism
Disease Models, Animal
Disease Susceptibility
*Gastrointestinal Microbiome
Genotype
Inflammatory Bowel Diseases/etiology/metabolism
Male
Mass Spectrometry
*Metabolome
*Metabolomics/methods
Metagenome
Metagenomics
Mice
Mice, Knockout
*Phenotype
RNA, Ribosomal, 16S/genetics

@article {pmid30868805,
year = {2019},
author = {Liu, ZX and Xu, J and Sun, W and Shi, YH and Chen, SL},
title = {[Application of DNA metabarcoding in species identification of Chinese herbal medicines].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {44},
number = {1},
pages = {1-8},
doi = {10.19540/j.cnki.cjcmm.2019.0001},
pmid = {30868805},
issn = {1001-5302},
abstract = {DNA metabarcoding,one rapid and robust method using specific standard DNA fragments,has been widely used for rapid species identification of a bulk sample through high-throughput sequencing technologies.While it has been widely used in the studies of metagenomics,animal and plant biodiversity,it has gradually come to be used as a profitable method in species identification of mixed Chinese herbal medicines.In this paper,we mainly summarize the current studies of the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines.Moreover,high-throughput sequencing technologies adopted in those studies,such as Sanger,the next-generation,and third-generation sequencing technologies,are discussed.It is conducted to provide a theoretical guidance for the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines and in more other biodiversity studies.},
}

@article {pmid30594064,
year = {2019},
author = {Procopio, N and Ghignone, S and Williams, A and Chamberlain, A and Mello, A and Buckley, M},
title = {Metabarcoding to investigate changes in soil microbial communities within forensic burial contexts.},
journal = {Forensic science international. Genetics},
volume = {39},
number = {},
pages = {73-85},
doi = {10.1016/j.fsigen.2018.12.002},
pmid = {30594064},
issn = {1878-0326},
mesh = {Animals ; Burial ; DNA Barcoding, Taxonomic/*methods ; Forensic Sciences ; Metagenomics/methods ; Microbiota/*genetics ; Models, Animal ; Polymerase Chain Reaction ; *Postmortem Changes ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Swine ; },
abstract = {The estimation of the time elapsed since death (post-mortem interval, or PMI) is one of the key themes that forensic scientists have to address frequently. However, the estimation of PMI still suffers from poor accuracy and biases especially when decomposition stages are prolonged, so further improvements in methods for PMI estimation are desirable. Soil microbial communities associated with decomposing bodies have been shown to be good candidates for the estimation of the PMI of exposed bodies. Nevertheless, further research is required to better understand the bacterial succession associated with decomposition of buried carcasses in order to test its reliability and applicability for the estimation of PMI and to better understand the dynamics involved with decomposition within this particular scenario. Therefore we explored the succession of soil microbial communities associated with four decomposing pig carcasses (from one to six months PMI) using a metabarcoding approach. The sequencing of the bacterial 16S rRNA variable region 4 (V4) revealed trends linking particular microbial taxa with specific PMIs, and notably an increase in Proteobacteria, Firmicutes and Bacteroidetes at specific PMIs as well as a decrease in Acidobacteria. Our results, in accordance with previous studies conducted on exposed bodies of different mammalian species (including humans), also showed a general reduction of the taxonomic richness from two months PMI onwards, as well as an incomplete re-establishment of the starting soil microbial conditions after six months PMI. We also found specific mammal-derived taxa, such as Bacteroides spp., being still present in the soil after six months PMI. As such, this study serves as a baseline for additional research to allow the characterisation of biomarkers associated with specific PMIs. Due to the similarity between the results presented here and those reported in other types of decomposition studies we believe that the metabarcoding approach has considerable potential in the estimation of the PMI, particularly to clarify cases involving heavily skeletonised bodies or for the investigation of clandestine graves in which the carcass has been moved from its original place of deposition.},
}

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

@article {pmid30010734,
year = {2018},
author = {Geng, S and Cheng, S and Li, Y and Wen, Z and Ma, X and Jiang, X and Wang, Y and Han, X},
title = {Faecal Microbiota Transplantation Reduces Susceptibility to Epithelial Injury and Modulates Tryptophan Metabolism of the Microbial Community in a Piglet Model.},
journal = {Journal of Crohn's & colitis},
volume = {12},
number = {11},
pages = {1359-1374},
doi = {10.1093/ecco-jcc/jjy103},
pmid = {30010734},
issn = {1876-4479},
mesh = {Animals ; Colitis/chemically induced/pathology/*prevention & control ; *Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*physiology ; Homeostasis ; Indoleacetic Acids/metabolism ; Interleukins/metabolism ; Intestinal Mucosa/metabolism/*pathology ; Lipopolysaccharides ; Mass Spectrometry ; Metabolome ; RNA, Ribosomal, 16S/analysis ; Receptors, Aryl Hydrocarbon/metabolism ; Swine ; Tryptophan/*metabolism ; },
abstract = {Background and Aims: Faecal microbiota transplantation [FMT] has shown promise as a treatment for inflammatory bowel disease [IBD]. Using a piglet model, our previous study indicated that exogenous faecal microbiota can increase the expressions of tight junction proteins, mucin and antimicrobial peptide in the intestinal mucosa, suggesting a beneficial effect of FMT on gut barrier and gastrointestinal health. However, specific connections between FMT-induced microbial changes and modulation of the intestinal barrier remain to be fully illustrated. Here, we aimed to determine the potential role of metabolic function of gut microbiota in the beneficial effects of FMT.

Methods: The influence of FMT on the maintenance of intestinal homeostasis was assessed by early-life gut microbiota intervention on newborn piglets and subsequent lipopolysaccharide [LPS] challenge. Analysis of the gut microbiome and metabolome was carried out by 16S rRNA gene sequencing and multiple mass spectrometry platforms.

Results: FMT modulated the diversity and composition of colonic microbiota and reduced the susceptibility to LPS-induced destruction of epithelial integrity and severe inflammatory response. Metabolomic analysis revealed functional changes of the gut metabolome along with a significant increase of the typical microbiota-derived tryptophan catabolite indole-3-acetic acid in the colonic lumen. In concordance with the metabolome data, metagenomics prediction analysis based on 16S rRNA gene sequencing also demonstrated that FMT modulated the metabolic functions of gut microbiota associated with indole alkaloid biosynthesis, cytochrome P450 and intestinal homeostasis, which coincided with up-regulation of cytokine interleukin-22 and enhanced activation of aryl hydrocarbon receptor in the recipient colon.

Conclusions: Our data reveal a regulatory effect of FMT on tryptophan metabolism of gut microbiota in the recipient colon, which may play a potential role in maintenance of the intestinal barrier.},
}

Animals
Colitis/chemically induced/pathology/*prevention & control
*Fecal Microbiota Transplantation
Gastrointestinal Microbiome/*physiology
Homeostasis
Indoleacetic Acids/metabolism
Interleukins/metabolism
Intestinal Mucosa/metabolism/*pathology
Lipopolysaccharides
Mass Spectrometry
Metabolome
RNA, Ribosomal, 16S/analysis
Receptors, Aryl Hydrocarbon/metabolism
Swine
Tryptophan/*metabolism

@article {pmid29786880,
year = {2018},
author = {Sánchez-Sanhueza, G and Bello-Toledo, H and González-Rocha, G and Gonçalves, AT and Valenzuela, V and Gallardo-Escárate, C},
title = {Metagenomic study of bacterial microbiota in persistent endodontic infections using Next-generation sequencing.},
journal = {International endodontic journal},
volume = {51},
number = {12},
pages = {1336-1348},
doi = {10.1111/iej.12953},
pmid = {29786880},
issn = {1365-2591},
support = {folio 21130022//CONICYT-PCHA/Doctorado Nacional/2013/ ; N°214.102.016-1 IN//VRID UDEC/ ; },
mesh = {Adult ; Bacteria/*classification/*genetics/*pathogenicity ; Biodiversity ; Chile ; DNA, Bacterial/analysis ; Dental Pulp Cavity/*microbiology ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; Periapical Periodontitis/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Canal Therapy ; },
abstract = {AIM: To determine the bacterial microbiota in root canals associated with persistent apical periodontitis and their relationship with the clinical characteristics of patients using next-generation sequencing (NGS).

METHODOLOGY: Bacterial samples from root canals associated with teeth having persistent apical periodontitis were taken from 24 patients undergoing root canal retreatment. Bacterial DNA was extracted, and V3-V4 variable regions of the 16S rRNA gene were amplified. The amplification was deep sequenced by Illumina technology to establish the metagenetic relationships among the bacterial species identified. The composition and diversity of microbial communities in the root canal and their relationships with clinical features were analysed. Parametric and nonparametric tests were used to analyse differences between patient characteristics and microbial data.

RESULTS: A total of 86 different operational taxonomic units (OTUs) were identified and Good's nonparametric coverage estimator method indicated that 99.9 ± 0.00001% diversity was recovered per sample. The largest number of bacteria belonged to the phylum Proteobacteria. According to the medical history from the American Society of Anesthesiologists (ASA) Classification System, ASA II-III had higher richness estimates and distinct phylogenetic relationships compared to ASA I individuals (P < 0.05). Periapical index (PAI) score 5 was associated with increased microbiota diversity in comparison to PAI score 4, and this index was reduced in symptomatic patients.

CONCLUSIONS: Based on the findings of this study, it is possible to suggest a close relationship between several clinical features and greater microbiota diversity with persistent endodontic infections. This work provides a better understanding on how microbial communities interact with their host and vice versa.},
}

Adult
Bacteria/*classification/*genetics/*pathogenicity
Biodiversity
Chile
DNA, Bacterial/analysis
Dental Pulp Cavity/*microbiology
Female
High-Throughput Nucleotide Sequencing/*methods
Humans
Male
Metagenomics/*methods
Microbiota/*genetics
Middle Aged
Periapical Periodontitis/*microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Root Canal Therapy

@article {pmid29524500,
year = {2018},
author = {Ruppé, E and Schrenzel, J},
title = {Messages from the second International Conference on Clinical Metagenomics (ICCMg2).},
journal = {Microbes and infection},
volume = {20},
number = {4},
pages = {222-227},
doi = {10.1016/j.micinf.2018.02.005},
pmid = {29524500},
issn = {1769-714X},
mesh = {Bacteria/genetics/isolation & purification/pathogenicity ; Clinical Laboratory Techniques/standards/trends ; Computational Biology ; Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/standards/trends ; Humans ; Metagenome/genetics ; *Metagenomics/standards/trends ; Microbiota/genetics ; },
abstract = {Clinical metagenomics (CMg) refers to as the application of metagenomic sequencing of clinical samples in order to recover clinically-relevant information. Due to the increasing access to next-generation sequencing (NGS) facilities, CMg is a gast-growing field. In this context, we held the second International Conference on Clinical Metagenomics (ICCMg2) in Geneva in October 2017. During the two days of the conference, several aspects of CMg were addressed, which we propose to summarize in the present manuscript. Besides, we also discuss the evolution of CMg from the last conference held in 2016. In brief, many technical issues related to CMg are expected to be successfully addressed in the coming years. Conversely, assessing the clinical value of CMg, implementing a quality process, storage of data and the ethics of CMg are emerging challenges.},
}

Bacteria/genetics/isolation & purification/pathogenicity
Clinical Laboratory Techniques/standards/trends
Computational Biology
Drug Resistance, Bacterial/genetics
High-Throughput Nucleotide Sequencing/standards/trends
Humans
Metagenome/genetics
*Metagenomics/standards/trends
Microbiota/genetics

@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 & 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.},
}

Animals
Bacteria/genetics/isolation & purification
Cecum/microbiology
Feces/microbiology
Female
*Gastrointestinal Microbiome
Housing, Animal
Mice, Inbred ICR
*Water Microbiology
Water Purification/*methods

@article {pmid29906449,
year = {2018},
author = {Tropini, C and Moss, EL and Merrill, BD and Ng, KM and Higginbottom, SK and Casavant, EP and Gonzalez, CG and Fremin, B and Bouley, DM and Elias, JE and Bhatt, AS and Huang, KC and Sonnenburg, JL},
title = {Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota.},
journal = {Cell},
volume = {173},
number = {7},
pages = {1742-1754.e17},
pmid = {29906449},
issn = {1097-4172},
support = {K08 CA184420/CA/NCI NIH HHS/United States ; P50 GM107615/GM/NIGMS NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bacteroidetes/drug effects/genetics/isolation & purification ; Cecum/chemistry/metabolism/microbiology/pathology ; Colon/chemistry/microbiology/pathology ; Cytokines/metabolism ; Diarrhea/immunology/microbiology/*pathology/veterinary ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Glycoside Hydrolases/metabolism ; Humans ; Immunity, Humoral/drug effects ; Immunoglobulin G/metabolism ; Intestinal Mucosa/microbiology/pathology ; Metagenomics ; Mice ; Osmolar Concentration ; Polyethylene Glycols/metabolism/*pharmacology ; Proteome/analysis ; RNA, Ribosomal, 16S/chemistry/genetics ; Verrucomicrobia/drug effects/genetics/isolation & purification ; },
abstract = {Osmotic diarrhea is a prevalent condition in humans caused by food intolerance, malabsorption, and widespread laxative use. Here, we assess the resilience of the gut ecosystem to osmotic perturbation at multiple length and timescales using mice as model hosts. Osmotic stress caused reproducible extinction of highly abundant taxa and expansion of less prevalent members in human and mouse microbiotas. Quantitative imaging revealed decimation of the mucus barrier during osmotic perturbation, followed by recovery. The immune system exhibited temporary changes in cytokine levels and a lasting IgG response against commensal bacteria. Increased osmolality prevented growth of commensal strains in vitro, revealing one mechanism contributing to extinction. Environmental availability of microbiota members mitigated extinction events, demonstrating how species reintroduction can affect community resilience. Our findings (1) demonstrate that even mild osmotic diarrhea can cause lasting changes to the microbiota and host and (2) lay the foundation for interventions that increase system-wide resilience.},
}

Animals
Bacteroidetes/drug effects/genetics/isolation & purification
Cecum/chemistry/metabolism/microbiology/pathology
Colon/chemistry/microbiology/pathology
Cytokines/metabolism
Diarrhea/immunology/microbiology/*pathology/veterinary
Feces/microbiology
Gastrointestinal Microbiome/*drug effects
Glycoside Hydrolases/metabolism
Humans
Immunity, Humoral/drug effects
Immunoglobulin G/metabolism
Intestinal Mucosa/microbiology/pathology
Metagenomics
Mice
Osmolar Concentration
Polyethylene Glycols/metabolism/*pharmacology
Proteome/analysis
RNA, Ribosomal, 16S/chemistry/genetics
Verrucomicrobia/drug effects/genetics/isolation & purification

@article {pmid28940049,
year = {2018},
author = {Tremlett, H and Waubant, E},
title = {The Gut Microbiota and Pediatric Multiple Sclerosis: Recent Findings.},
journal = {Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics},
volume = {15},
number = {1},
pages = {102-108},
pmid = {28940049},
issn = {1878-7479},
mesh = {Biomarkers ; Child ; *Gastrointestinal Microbiome ; Humans ; Multiple Sclerosis/immunology/*microbiology ; Recurrence ; },
abstract = {Pediatric multiple sclerosis (MS) is a chronic, life-long neurological condition associated with inflammation and degeneration in the brain and spinal cord. Fortunately, < 5% of people with MS have their onset in childhood years. However, studying these very-early-onset cases of MS offers key advantages. In particular, with fewer years lived, children have had a limited range of exposures, potentially enhancing our ability to identify what might cause MS. Further, as the actual timing of the biological MS onset is unknown, the possibility to study these children much closer to the real onset of disease is far greater than in the typical adult with MS. Whether MS (in children or adults) can be prevented is unknown and the available drugs are only modestly effective in modifying the disease course and are not without risk. Emerging evidence is providing insight into the gut microbiota's potential role in triggering and shaping neurological conditions such as MS. The limited number of studies in humans with MS and absence of prior work in pediatric MS motivated the following 3 fundamental questions, addressed in 2 cross-sectional and 1 longitudinal investigation in children with and without MS: 1) Does the gut microbiota composition differ between children with and without MS? 2) Is there an association between the gut microbiota and host immune markers in children with and without MS? 3) Is the gut microbiota associated with the future risk of a MS relapse?},
}

Biomarkers
Child
*Gastrointestinal Microbiome
Humans
Multiple Sclerosis/immunology/*microbiology
Recurrence

@article {pmid30075203,
year = {2018},
author = {Kumar, M and Ji, B and Babaei, P and Das, P and Lappa, D and Ramakrishnan, G and Fox, TE and Haque, R and Petri, WA and Bäckhed, F and Nielsen, J},
title = {Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling.},
journal = {Metabolic engineering},
volume = {49},
number = {},
pages = {128-142},
doi = {10.1016/j.ymben.2018.07.018},
pmid = {30075203},
issn = {1096-7184},
mesh = {Amino Acids/*blood ; Child ; *Child Nutrition Disorders/blood/genetics/microbiology ; Child, Preschool ; *Dysbiosis/blood/genetics/microbiology ; Female ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; Humans ; Male ; },
abstract = {Malnutrition is a severe non-communicable disease, which is prevalent in children from low-income countries. Recently, a number of metagenomics studies have illustrated associations between the altered gut microbiota and child malnutrition. However, these studies did not examine metabolic functions and interactions between individual species in the gut microbiota during health and malnutrition. Here, we applied genome-scale metabolic modeling to model the gut microbial species, which were selected from healthy and malnourished children from three countries. Our analysis showed reduced metabolite production capabilities in children from two low-income countries compared with a high-income country. Additionally, the models were also used to predict the community-level metabolic potentials of gut microbes and the patterns of pairwise interactions among species. Hereby we found that due to bacterial interactions there may be reduced production of certain amino acids in malnourished children compared with healthy children from the same communities. To gain insight into alterations in the metabolism of malnourished (stunted) children, we also performed targeted plasma metabolic profiling in the first 2 years of life of 25 healthy and 25 stunted children. Plasma metabolic profiling further revealed that stunted children had reduced plasma levels of essential amino acids compared to healthy controls. Our analyses provide a framework for future efforts towards further characterization of gut microbial metabolic capabilities and their contribution to malnutrition.},
}

Amino Acids/*blood
Child
*Child Nutrition Disorders/blood/genetics/microbiology
Child, Preschool
*Dysbiosis/blood/genetics/microbiology
Female
*Gastrointestinal Microbiome
*Genome, Bacterial
Humans
Male

@article {pmid30037148,
year = {2018},
author = {Cross, ST and Kapuscinski, ML and Perino, J and Maertens, BL and Weger-Lucarelli, J and Ebel, GD and Stenglein, MD},
title = {Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms.},
journal = {Viruses},
volume = {10},
number = {7},
pages = {},
pmid = {30037148},
issn = {1999-4915},
support = {UL1 TR002535/TR/NCATS NIH HHS/United States ; },
mesh = {Animals ; Bacteria/genetics/isolation & purification ; Borrelia burgdorferi/genetics/isolation & purification ; Coinfection/epidemiology/*microbiology/*virology ; Eukaryota/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Ixodes/genetics/*microbiology/*virology ; Lyme Disease ; Microbiota/genetics ; Orthobunyavirus/genetics/isolation & purification ; Phlebovirus/genetics/isolation & purification ; Prevalence ; Symbiosis ; Tick Infestations/epidemiology/microbiology/virology ; Tick-Borne Diseases/*epidemiology/microbiology/virology ; Viruses/genetics/isolation & purification ; Wisconsin/epidemiology ; },
abstract = {Ixodes scapularis ticks harbor a variety of microorganisms, including eukaryotes, bacteria and viruses. Some of these can be transmitted to and cause disease in humans and other vertebrates. Others are not pathogenic, but may impact the ability of the tick to harbor and transmit pathogens. A growing number of studies have examined the influence of bacteria on tick vector competence but the influence of the tick virome remains less clear, despite a surge in the discovery of tick-associated viruses. In this study, we performed shotgun RNA sequencing on 112 individual adult I. scapularis collected in Wisconsin, USA. We characterized the abundance, prevalence and co-infection rates of viruses, bacteria and eukaryotic microorganisms. We identified pairs of tick-infecting microorganisms whose observed co-infection rates were higher or lower than would be expected, or whose RNA levels were positively correlated in co-infected ticks. Many of these co-occurrence and correlation relationships involved two bunyaviruses, South Bay virus and blacklegged tick phlebovirus-1. These viruses were also the most prevalent microorganisms in the ticks we sampled, and had the highest average RNA levels. Evidence of associations between microbes included a positive correlation between RNA levels of South Bay virus and Borrelia burgdorferi, the Lyme disease agent. These findings contribute to the rationale for experimental studies on the impact of viruses on tick biology and vector competence.},
}

Animals
Bacteria/genetics/isolation & purification
Borrelia burgdorferi/genetics/isolation & purification
Coinfection/epidemiology/*microbiology/*virology
Eukaryota/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
Ixodes/genetics/*microbiology/*virology
Lyme Disease
Microbiota/genetics
Orthobunyavirus/genetics/isolation & purification
Phlebovirus/genetics/isolation & purification
Prevalence
Symbiosis
Tick Infestations/epidemiology/microbiology/virology
Tick-Borne Diseases/*epidemiology/microbiology/virology
Viruses/genetics/isolation & purification
Wisconsin/epidemiology

@article {pmid29600282,
year = {2018},
author = {Auchtung, TA and Fofanova, TY and Stewart, CJ and Nash, AK and Wong, MC and Gesell, JR and Auchtung, JM and Ajami, NJ and Petrosino, JF},
title = {Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi.},
journal = {mSphere},
volume = {3},
number = {2},
pages = {},
pmid = {29600282},
issn = {2379-5042},
support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; },
mesh = {Adult ; Candida albicans/genetics/isolation & purification ; DNA, Ribosomal Spacer/genetics ; Diet ; Feces/microbiology ; Food Microbiology ; Fungi/*classification/isolation & purification ; Gastrointestinal Tract/*microbiology/physiology ; Healthy Volunteers ; Humans ; Mouth/microbiology ; Mycobiome/*physiology ; RNA, Ribosomal, 18S/genetics ; Saccharomyces cerevisiae/genetics/isolation & purification ; Saliva/microbiology ; Sequence Analysis, DNA ; },
abstract = {A wide diversity of fungi have been detected in the human gastrointestinal (GI) tract with the potential to provide or influence important functions. However, many of the fungi most commonly detected in stool samples are also present in food or the oral cavity. Therefore, to recognize which gut fungi are likely to have a sustained influence on human health, there is a need to separate transient members of the GI tract from true colonizers. To identify colonizing fungi, the eukaryotic rRNA operon's second internal transcribed spacer (ITS2) was sequenced from the stool, saliva, and food of healthy adults following consumption of different controlled diets. Unlike most bacterial 16S rRNA genes, the only fungal ITS2 operational taxonomic units (OTUs) detected in stool DNA across multiple diets were also present in saliva and/or food. Additional analyses, including culture-based approaches and sequencing of the 18S rRNA gene, ITS2 cDNA, and DNA extracted using alternative methods, failed to detect additional fungi. Two abundant fungi, Saccharomyces cerevisiae and Candida albicans, were examined further in healthy volunteers. Saccharomyces became undetectable in stool when a S. cerevisiae-free diet was consumed, and the levels of C. albicans in stool were dramatically reduced by more frequent cleaning of teeth. Extremely low fungal abundance, the inability of fungi to grow under conditions mimicking the distal gut, and evidence from analysis of other public datasets further support the hypothesis that fungi do not routinely colonize the GI tracts of healthy adults. IMPORTANCE We sought to identify the fungi that colonize healthy GI tracts and that have a sustained influence on the diverse functions of the gut microbiome. Instead, we found that all fungi in the stool of healthy volunteers could be explained by their presence in oral and dietary sources and that our results, together with those from other analyses, support the model that there is little or no gastrointestinal colonization by fungi. This may be due to Westernization, primate evolution, fungal ecology, and/or the strong defenses of a healthy immune system. Importantly, fungal colonization of the GI tract may often be indicative of disease. As fungi can cause serious infections in immunocompromised individuals and are found at increased abundance in multiple disorders of the GI tract, understanding normal fungal colonization is essential for proper treatment and prevention of fungal pathogenesis.},
}

Adult
Candida albicans/genetics/isolation & purification
DNA, Ribosomal Spacer/genetics
Diet
Feces/microbiology
Food Microbiology
Fungi/*classification/isolation & purification
Gastrointestinal Tract/*microbiology/physiology
Healthy Volunteers
Humans
Mouth/microbiology
Mycobiome/*physiology
RNA, Ribosomal, 18S/genetics
Saccharomyces cerevisiae/genetics/isolation & purification
Saliva/microbiology
Sequence Analysis, DNA

@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 & 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.},
}

Animals
Anthozoa/*microbiology
Bacteria/genetics/*metabolism
Biological Products/isolation & purification/metabolism/*pharmacology
Biosynthetic Pathways/*genetics
Fungi/genetics/*metabolism
Industrial Microbiology/methods
Microbiota/physiology
Multigene Family
Symbiosis
Technology, Pharmaceutical/methods

@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.},
}

*Biodiversity
Conservation of Energy Resources/*methods
*Ecosystem
Metagenomics/*methods
*Oceans and Seas

@article {pmid30108167,
year = {2018},
author = {Peura, S and Buck, M and Aalto, SL and Morales, SE and Nykänen, H and Eiler, A},
title = {Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake.},
journal = {mBio},
volume = {9},
number = {4},
pages = {},
pmid = {30108167},
issn = {2150-7511},
mesh = {Anaerobiosis ; *Autotrophic Processes ; *Biota ; Carbon/*metabolism ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Finland ; Lakes/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Oxygen-stratified lakes are typical for the boreal zone and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study, we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome-assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in an oxygen-depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, potentially deriving their energy from reactions related to sulfur, iron, and nitrogen transformations. The community, as well as the functions, was stratified along the redox gradient. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing toward a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change-associated fluctuations in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole-lake metabolism even beyond the impact to the phototrophic community.IMPORTANCE Autotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into the organic form, facilitating the survival of all other organisms. In certain environments, the autotrophic production is limited by environmental conditions and the food web is supported by external carbon inputs. One such environment is stratified boreal lakes, which are one of the biggest natural sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of utmost importance for the future climate. Here, we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the anoxic, poorly illuminated layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics.},
}

Anaerobiosis
*Autotrophic Processes
*Biota
Carbon/*metabolism
Cluster Analysis
DNA, Ribosomal/chemistry/genetics
Finland
Lakes/*microbiology
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid30042197,
year = {2018},
author = {Murray, AK and Zhang, L and Yin, X and Zhang, T and Buckling, A and Snape, J and Gaze, WH},
title = {Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities.},
journal = {mBio},
volume = {9},
number = {4},
pages = {},
pmid = {30042197},
issn = {2150-7511},
support = {BB/L502509/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Anti-Bacterial Agents/*pharmacology ; Cefotaxime/*pharmacology ; *Cephalosporin Resistance ; Cephalosporinase/genetics/metabolism ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; Microbiota/*drug effects ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Selection, Genetic ; Sequence Analysis, DNA ; Sewage/*microbiology ; },
abstract = {Recent research has demonstrated that selection for antibiotic resistance occurs at very low antibiotic concentrations in single-species experiments, but the relevance of these findings when species are embedded in complex microbial communities is unclear. We show that the strength of selection for naturally occurring resistance alleles in a complex community remains constant from low subinhibitory to above clinically relevant concentrations. Selection increases with antibiotic concentration before reaching a plateau where selection remains constant over a 2-order-magnitude concentration range. This is likely to be due to cross protection of the susceptible bacteria in the community following rapid extracellular antibiotic degradation by the resistant population, shown experimentally through a combination of chemical quantification and bacterial growth experiments. Metagenome and 16S rRNA analyses of sewage-derived bacterial communities evolved under cefotaxime exposure show preferential enrichment for blaCTX-M genes over all other beta-lactamase genes, as well as positive selection and co-selection for antibiotic resistant, opportunistic pathogens. These findings have far-reaching implications for our understanding of the evolution of antibiotic resistance, by challenging the long-standing assumption that selection occurs in a dose-dependent manner.IMPORTANCE Antibiotic resistance is one of the greatest global issues facing society. Still, comparatively little is known about selection for resistance at very low antibiotic concentrations. We show that the strength of selection for clinically important resistance genes within a complex bacterial community can remain constant across a large antibiotic concentration range (wide selective space). Therefore, largely understudied ecological compartments could be just as important as clinical environments for selection of antibiotic resistance.},
}

Anti-Bacterial Agents/*pharmacology
Cefotaxime/*pharmacology
*Cephalosporin Resistance
Cephalosporinase/genetics/metabolism
Cluster Analysis
DNA, Ribosomal/chemistry/genetics
Metagenomics
Microbiota/*drug effects
Phylogeny
RNA, Ribosomal, 16S/genetics
*Selection, Genetic
Sequence Analysis, DNA
Sewage/*microbiology

@article {pmid29621980,
year = {2018},
author = {Pace, RM and Prince, AL and Ma, J and Belfort, BDW and Harvey, AS and Hu, M and Baquero, K and Blundell, P and Takahashi, D and Dean, T and Kievit, P and Sullivan, EL and Friedman, JE and Grove, K and Aagaard, KM},
title = {Modulations in the offspring gut microbiome are refractory to postnatal synbiotic supplementation among juvenile primates.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {28},
pmid = {29621980},
issn = {1471-2180},
support = {F32 HD082969/HD/NICHD NIH HHS/United States ; R01 MH107508/MH/NIMH NIH HHS/United States ; K12 GM084897/GM/NIGMS NIH HHS/United States ; R24DK090964//National Institute of Child Health and Human Development/International ; 1RO1DK089201//National Institute of Child Health and Human Development/International ; DP2 OD001500/OD/NIH HHS/United States ; F32HD082969//National Institute of Child Health and Human Development/International ; DP21DP2OD001500//NIH Director New Innovator Pioneer Award/International ; R01 DK089201/DK/NIDDK NIH HHS/United States ; K12GM084897/NH/NIH HHS/United States ; R24 DK090964/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bacteria/*classification/genetics/*metabolism ; *Diet, High-Fat ; Dysbiosis/microbiology ; Enterococcus/physiology ; Faecalibacterium ; Feces/microbiology ; Female ; Firmicutes ; Gastrointestinal Microbiome/genetics/*physiology ; Lactobacillus/physiology ; Lipids/blood ; Macaca/microbiology ; Male ; Metabolic Networks and Pathways ; Metagenomics ; Primates/*microbiology ; Probiotics ; Psyllium ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; *Synbiotics ; Triglycerides/blood ; },
abstract = {BACKGROUND: We and others have previously shown that alterations in the mammalian gut microbiome are associated with diet, notably early life exposure to a maternal high fat diet (HFD). Here, we aimed to further these studies by examining alterations in the gut microbiome of juvenile Japanese macaques (Macaca fuscata) that were exposed to a maternal HFD, weaned onto a control diet, and later supplemented with a synbiotic comprised of psyllium seed and Enterococcus and Lactobacillus species.

RESULTS: Eighteen month old offspring (n = 7) of 36% HFD fed dams were fed a control (14% fat) diet post weaning, then were synbiotic supplemented for 75 days and longitudinal stool and serum samples were obtained. All stool samples were subjected to 16S rRNA metagenomic sequencing, and microbiome profiles and serum lipids and triglycerides were compared to untreated, healthy age matched and diet matched controls (n = 7). Overall, 16S-based metagenomic analysis revealed that supplementation exerted minimal alterations to the gut microbiome including transient increased abundance of Lactobacillus species and decreased abundance of few bacterial genera, including Faecalibacterium and Anaerovibrio. However, serum lipid analysis revealed significant decreases in triglycerides, cholesterol, and LDL (p < 0.05). Nevertheless, supplemented juveniles challenged 4 months later were not protected from HFD-induced gut dysbiosis.

CONCLUSIONS: Synbiotic supplementation is temporally associated with alterations in the gut microbiome and host lipid profiles of juvenile Japanese macaques that were previously exposed to a maternal HFD. Despite these presumptive temporal benefits, a protective effect against later HFD-challenge gut dysbiosis was not observed.},
}

Animals
Bacteria/*classification/genetics/*metabolism
*Diet, High-Fat
Dysbiosis/microbiology
Enterococcus/physiology
Faecalibacterium
Feces/microbiology
Female
Firmicutes
Gastrointestinal Microbiome/genetics/*physiology
Lactobacillus/physiology
Lipids/blood
Macaca/microbiology
Male
Metabolic Networks and Pathways
Metagenomics
Primates/*microbiology
Probiotics
Psyllium
RNA, Ribosomal, 16S/genetics
Species Specificity
*Synbiotics
Triglycerides/blood

@article {pmid28819272,
year = {2017},
author = {Concheri, G and Stevanato, P and Zaccone, C and Shotyk, W and D'Orazio, V and Miano, T and Piffanelli, P and Rizzi, V and Ferrandi, C and Squartini, A},
title = {Rapid peat accumulation favours the occurrence of both fen and bog microbial communities within a Mediterranean, free-floating peat island.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8511},
pmid = {28819272},
issn = {2045-2322},
mesh = {Bacteria/*classification/genetics ; DNA, Bacterial/chemistry/genetics/isolation & purification ; DNA, Fungal/chemistry/genetics/isolation & purification ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/genetics ; *Islands ; Italy ; Metagenomics ; *Microbiota ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Wetlands ; },
abstract = {The unique environment of a 4m-thick, free-floating peat island within the Posta Fibreno lake (Central Italy) was analyzed using DNA-based techniques to assess bacterial and fungal community members identity and abundance. Two depths were sampled at 41 and 279 cm from the surface, the former corresponding to an emerged portion of Sphagnum residues accumulated less than 30 yrs ago, and the latter mainly consisting of silty peat belonging to the deeply submerged part of the island, dating back to 1520-1660 AD. The corresponding communities were very diverse, each of them dominated by a different member of the Delta-proteobacteria class for prokaryotes. Among Eukaryotes, Ascomycota prevailed in the shallow layer while Basidiomycota were abundant in the deep sample. The identity of taxa partitioning between acidic surface layer and neutral core is very reminiscent of the differences reported between bogs and fens respectively, supporting the view of Posta Fibreno as a relic transitional floating mire. Moreover, some microbial taxa show an unusual concurrent species convergence between this sub-Mediterranean site and far Nordic or circumpolar environments. This study represents the first report describing the biotic assemblages of such a peculiar environment, and provides some insights into the possible mechanisms of its evolution.},
}

Bacteria/*classification/genetics
DNA, Bacterial/chemistry/genetics/isolation & purification
DNA, Fungal/chemistry/genetics/isolation & purification
DNA, Ribosomal/chemistry/genetics
DNA, Ribosomal Spacer/chemistry/genetics
Fungi/*classification/genetics
*Islands
Italy
Metagenomics
*Microbiota
Phylogeny
Polymerase Chain Reaction
Sequence Analysis, DNA
*Soil Microbiology
Wetlands

@article {pmid28819242,
year = {2017},
author = {Lim, Y and Totsika, M and Morrison, M and Punyadeera, C},
title = {The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8523},
pmid = {28819242},
issn = {2045-2322},
mesh = {Adult ; Bacteria/classification/genetics ; Cluster Analysis ; DNA, Bacterial/analysis/genetics/*isolation & purification ; DNA, Ribosomal/chemistry/genetics ; Healthy Volunteers ; Humans ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Saliva/*microbiology ; Sequence Analysis, DNA ; Specimen Handling/*methods ; Young Adult ; beta-Globins/analysis/genetics ; },
abstract = {Saliva has attracted attention as a diagnostic fluid due to the association of oral microbiota with systemic diseases. However, the lack of standardised methods for saliva collection has led to the slow uptake of saliva in microbiome research. The aim of this study was to systematically evaluate the potential effects on salivary microbiome profiles using different methods of saliva collection, storage and gDNA extraction. Three types of saliva fractions were collected from healthy individuals with or without the gDNA stabilising buffer. Subsequently, three types of gDNA extraction methods were evaluated to determine the gDNA extraction efficiencies from saliva samples. The purity of total bacterial gDNA was evaluated using the ratio of human β-globin to bacterial 16S rRNA PCR while 16S rRNA gene amplicon sequencing was carried out to identify the bacterial profiles present in these samples. The quantity and quality of extracted gDNA were similar among all three gDNA extraction methods and there were no statistically significant differences in the bacterial profiles among different saliva fractions at the genus-level of taxonomic classification. In conclusion, saliva sampling, processing and gDNA preparation do not have major influence on microbiome profiles.},
}

Adult
Bacteria/classification/genetics
Cluster Analysis
DNA, Bacterial/analysis/genetics/*isolation & purification
DNA, Ribosomal/chemistry/genetics
Healthy Volunteers
Humans
Metagenomics/*methods
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics
Real-Time Polymerase Chain Reaction
Saliva/*microbiology
Sequence Analysis, DNA
Specimen Handling/*methods
Young Adult
beta-Globins/analysis/genetics

@article {pmid29543557,
year = {2018},
author = {Kiely, CJ and Pavli, P and O'Brien, CL},
title = {The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome.},
journal = {Gut microbes},
volume = {9},
number = {6},
pages = {477-485},
pmid = {29543557},
issn = {1949-0984},
mesh = {Adult ; Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; Colitis, Ulcerative/microbiology/pathology ; Crohn Disease/microbiology/pathology ; Endoscopy, Gastrointestinal ; *Gastrointestinal Microbiome ; Humans ; Inflammation/pathology ; Inflammatory Bowel Diseases/*microbiology/*pathology ; Intestinal Mucosa/*microbiology/*pathology ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Time Factors ; },
abstract = {Studies of the human intestinal microbiome in patients with inflammatory bowel disease (IBD) consistently show that there are differences (an abnormal or unbalanced microbiome, "dysbiosis") when compared to healthy subjects. We sought to describe changes in the microbiome in individual patients over time, and determine the clinical factors that are associated with significant alteration. Forty-two mucosal biopsies were collected from 20 patients that were spaced an average of 2.4 years apart. These were analysed using bacterial 16S rRNA gene high-throughput sequencing methods. Presence of active inflammation was determined endoscopically and histologically. Inferred metagenomics analysis was conducted using the PICRUSt package. We found that the differences in the microbiome over time in individual patients were greatest in the presence of ongoing intestinal inflammation, as determined by the Yue and Clayton theta distance between sample pairs (adjusted p = 0.00031). Samples from patients with previous abdominal surgery had lower alpha (within sample) diversity compared with those with no prior operations (mean Shannon index 2.083, 2.510 respectively, p = 0.017). There were no changes in the inferred bacterial metagenomic profile. The microbiome in IBD undergoes considerable fluctuation over time. These changes are greatest when there is histologically confirmed inflammation at both time-points.},
}

Adult
Bacteria/classification/genetics/isolation & purification
*Biodiversity
Colitis, Ulcerative/microbiology/pathology
Crohn Disease/microbiology/pathology
Endoscopy, Gastrointestinal
*Gastrointestinal Microbiome
Humans
Inflammation/pathology
Inflammatory Bowel Diseases/*microbiology/*pathology
Intestinal Mucosa/*microbiology/*pathology
Metagenomics
Middle Aged
RNA, Ribosomal, 16S/genetics
Risk Factors
Time Factors

@article {pmid29980437,
year = {2018},
author = {Kim, M and Galan, C and Hill, AA and Wu, WJ and Fehlner-Peach, H and Song, HW and Schady, D and Bettini, ML and Simpson, KW and Longman, RS and Littman, DR and Diehl, GE},
title = {Critical Role for the Microbiota in CX3CR1+ Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses.},
journal = {Immunity},
volume = {49},
number = {1},
pages = {151-163.e5},
pmid = {29980437},
issn = {1097-4180},
support = {R21 AI123945/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; T32 AI053831/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 AI036211/AI/NIAID NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 AI125264/AI/NIAID NIH HHS/United States ; R01 DK114252/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Antigen Presentation ; Bacterial Adhesion/immunology ; CX3C Chemokine Receptor 1/*metabolism ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*immunology ; Homeostasis ; Immune Tolerance ; Immunity, Mucosal ; Inflammation/immunology ; Inflammatory Bowel Diseases/immunology ; Interleukin-10/immunology/metabolism ; Intestinal Mucosa/*immunology/microbiology ; Male ; Mice ; Mononuclear Phagocyte System/*immunology ; RAW 264.7 Cells ; T-Lymphocytes, Regulatory/*immunology ; Th1 Cells/*immunology ; },
abstract = {The intestinal barrier is vulnerable to damage by microbiota-induced inflammation that is normally restrained through mechanisms promoting homeostasis. Such disruptions contribute to autoimmune and inflammatory diseases including inflammatory bowel disease. We identified a regulatory loop whereby, in the presence of the normal microbiota, intestinal antigen-presenting cells (APCs) expressing the chemokine receptor CX3CR1 reduced expansion of intestinal microbe-specific T helper 1 (Th1) cells and promoted generation of regulatory T cells responsive to food antigens and the microbiota itself. We identified that disruption of the microbiota resulted in CX3CR1+ APC-dependent inflammatory Th1 cell responses with increased pathology after pathogen infection. Colonization with microbes that can adhere to the epithelium was able to compensate for intestinal microbiota loss, indicating that although microbial interactions with the epithelium can be pathogenic, they can also activate homeostatic regulatory mechanisms. Our results identify a cellular mechanism by which the microbiota limits intestinal inflammation and promotes tissue homeostasis.},
}

Animals
Antigen Presentation
Bacterial Adhesion/immunology
CX3C Chemokine Receptor 1/*metabolism
Disease Models, Animal
Female
Gastrointestinal Microbiome/*immunology
Homeostasis
Immune Tolerance
Immunity, Mucosal
Inflammation/immunology
Inflammatory Bowel Diseases/immunology
Interleukin-10/immunology/metabolism
Intestinal Mucosa/*immunology/microbiology
Male
Mice
Mononuclear Phagocyte System/*immunology
RAW 264.7 Cells
T-Lymphocytes, Regulatory/*immunology
Th1 Cells/*immunology

@article {pmid28811583,
year = {2017},
author = {Chen, CH and Lin, YL and Chen, KH and Chen, WP and Chen, ZF and Kuo, HY and Hung, HF and Tang, CY and Liou, ML},
title = {Bacterial diversity among four healthcare-associated institutes in Taiwan.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8230},
pmid = {28811583},
issn = {2045-2322},
mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Cross Infection/epidemiology/microbiology ; *Environmental Microbiology ; *Health Facilities ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Taiwan/epidemiology ; },
abstract = {Indoor microbial communities have important implications for human health, especially in health-care institutes (HCIs). The factors that determine the diversity and composition of microbiomes in a built environment remain unclear. Herein, we used 16S rRNA amplicon sequencing to investigate the relationships between building attributes and surface bacterial communities among four HCIs located in three buildings. We examined the surface bacterial communities and environmental parameters in the buildings supplied with different ventilation types and compared the results using a Dirichlet multinomial mixture (DMM)-based approach. A total of 203 samples from the four HCIs were analyzed. Four bacterial communities were grouped using the DMM-based approach, which were highly similar to those in the 4 HCIs. The α-diversity and β-diversity in the naturally ventilated building were different from the conditioner-ventilated building. The bacterial source composition varied across each building. Nine genera were found as the core microbiota shared by all the areas, of which Acinetobacter, Enterobacter, Pseudomonas, and Staphylococcus are regarded as healthcare-associated pathogens (HAPs). The observed relationship between environmental parameters such as core microbiota and surface bacterial diversity suggests that we might manage indoor environments by creating new sanitation protocols, adjusting the ventilation design, and further understanding the transmission routes of HAPs.},
}

Bacteria/*classification/*genetics
*Biodiversity
Cross Infection/epidemiology/microbiology
*Environmental Microbiology
*Health Facilities
High-Throughput Nucleotide Sequencing
Humans
Metagenomics/methods
Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics
Taiwan/epidemiology

@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.},
}

Bacteria/*genetics
Biodiversity
Hot Springs/*microbiology
Hot Temperature
Metagenomics/methods
RNA, Ribosomal, 16S/genetics
Saudi Arabia
Sequence Analysis, DNA/methods

@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.},
}

Bacteria/*classification/genetics/metabolism
*Biodiversity
Enzymes/genetics/metabolism
Metagenome
Metagenomics/methods
Nitrogen
Oryza/*microbiology
Phylogeny
*Rhizosphere
Soil/chemistry
*Soil Microbiology

@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 "health" 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 "health" and "individual," 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.},
}

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

@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 & purification ; Biodiversity ; Chlorophyta/classification/genetics ; Cyanobacteria/classification/*genetics/*isolation & purification ; DNA, Bacterial/genetics ; Diatoms/classification/genetics/isolation & purification ; Estuaries ; Fresh Water/microbiology ; Genotype ; Harmful Algal Bloom ; Metagenomics ; Microcystis/genetics/isolation & 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.},
}

Bacteria/classification/genetics/isolation & purification
Biodiversity
Chlorophyta/classification/genetics
Cyanobacteria/classification/*genetics/*isolation & purification
DNA, Bacterial/genetics
Diatoms/classification/genetics/isolation & purification
Estuaries
Fresh Water/microbiology
Genotype
Harmful Algal Bloom
Metagenomics
Microcystis/genetics/isolation & purification
Phylogeny
Polymerase Chain Reaction
Saline Waters
Salinity
San Francisco
Spatio-Temporal Analysis
*Water Microbiology

@article {pmid29459499,
year = {2018},
author = {Kato, S and Sakai, S and Hirai, M and Tasumi, E and Nishizawa, M and Suzuki, K and Takai, K},
title = {Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle.},
journal = {Microbes and environments},
volume = {33},
number = {1},
pages = {107-110},
pmid = {29459499},
issn = {1347-4405},
mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics/metabolism ; *Bacterial Physiological Phenomena ; Biodiversity ; Denitrification ; Ecosystem ; Hot Springs/microbiology ; Metagenome ; *Metagenomics ; Nitrification ; Nitrogen/metabolism ; *Nitrogen Cycle ; Soil Microbiology ; },
abstract = {Many thermophiles thriving in a natural high-temperature environment remain uncultivated, and their ecophysiological functions in the biogeochemical cycle remain unclear. In the present study, we performed long-term continuous cultivation at 65°C and 70°C using a microbial mat sample, collected from a subsurface geothermal stream, as the inoculum, and reconstructed the whole genome of the maintained populations using metagenomics. Some metagenome-assembled genomes (MAGs), affiliated into phylum-level bacterial and archaeal clades without cultivated representatives, contained genes involved in nitrogen metabolism including nitrification and denitrification. Our results show genetic components and their potential interactions for the biogeochemical nitrogen cycle in a subsurface geothermal environment.},
}

Archaea/*genetics/physiology
Bacteria/*genetics/metabolism
*Bacterial Physiological Phenomena
Biodiversity
Denitrification
Ecosystem
Hot Springs/microbiology
Metagenome
*Metagenomics
Nitrification
Nitrogen/metabolism
*Nitrogen Cycle
Soil Microbiology

@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 & 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.},
}

Animals
*Biodiversity
Computational Biology
DNA/chemistry/genetics/isolation & purification
DNA Barcoding, Taxonomic/*methods
Fishes/*classification/*genetics
French Guiana
High-Throughput Nucleotide Sequencing
Metagenomics/*methods
Water/chemistry

@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 & purification ; Picornaviridae/genetics/isolation & purification ; Picornaviridae Infections/virology ; Prevalence ; Viruses/genetics/*isolation & purification ; },
abstract = {BACKGROUND: Stool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease.

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.

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).

CONCLUSIONS: In conclusion, we documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition.},
}

Biodiversity
Caliciviridae Infections/virology
Child, Preschool
Diarrhea/epidemiology/*virology
Ethiopia/epidemiology
Feces/*virology
Female
Humans
Infant
Infant, Newborn
Male
Metagenomics
Norovirus/genetics/isolation & purification
Picornaviridae/genetics/isolation & purification
Picornaviridae Infections/virology
Prevalence
Viruses/genetics/*isolation & purification

@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.},
}

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

@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 & development ; Biodiversity ; China ; Environmental Monitoring ; Environmental Pollution/*analysis ; Firmicutes/classification/genetics/*growth & 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.

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).

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.},
}

Bacteroidetes/classification/genetics/*growth & development
Biodiversity
China
Environmental Monitoring
Environmental Pollution/*analysis
Firmicutes/classification/genetics/*growth & development
Mercury/*analysis
Metagenome/genetics
Methylmercury Compounds/*analysis
Microbiota/genetics
Soil/chemistry
Soil Microbiology
Soil Pollutants/*analysis

@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 & dosage ; Bifidobacterium/*classification ; Breast Feeding ; Cesarean Section ; Clostridium/isolation & purification ; Dietary Supplements ; Double-Blind Method ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Infant ; Lactobacillus rhamnosus/*classification ; Male ; Pregnancy ; Probiotics/*administration & dosage ; Propionibacterium/*classification ; Proteobacteria/isolation & 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.

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.

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.

TRIAL REGISTRATION: clinicaltrials.gov NCT00298337 . Registered March 2, 2006.},
}

Anti-Bacterial Agents/*administration & dosage
Bifidobacterium/*classification
Breast Feeding
Cesarean Section
Clostridium/isolation & purification
Dietary Supplements
Double-Blind Method
Feces/microbiology
Female
Gastrointestinal Microbiome/*drug effects/physiology
Humans
Infant
Lactobacillus rhamnosus/*classification
Male
Pregnancy
Probiotics/*administration & dosage
Propionibacterium/*classification
Proteobacteria/isolation & purification

@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 & purification ; Genome, Bacterial/genetics ; Metagenome/genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rickettsia/classification/genetics/*isolation & 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.

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.

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.},
}

Animals
Aphids/*microbiology
Buchnera/classification/genetics/*isolation & purification
Genome, Bacterial/genetics
Metagenome/genetics
Metagenomics
Microbiota/*genetics
Phylogeny
RNA, Ribosomal, 16S/genetics
Rickettsia/classification/genetics/*isolation & purification
Symbiosis/*physiology

@article {pmid30285861,
year = {2018},
author = {O'Neill, AM and Gallo, RL},
title = {Host-microbiome interactions and recent progress into understanding the biology of acne vulgaris.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {177},
pmid = {30285861},
issn = {2049-2618},
support = {R01 AR069653/AR/NIAMS NIH HHS/United States ; U19 AI117673/AI/NIAID NIH HHS/United States ; R01 AR064781/AR/NIAMS NIH HHS/United States ; R01 AI116576/AI/NIAID NIH HHS/United States ; },
mesh = {Acne Vulgaris/drug therapy/*microbiology ; Dysbiosis/microbiology ; Hair Follicle/*microbiology ; Humans ; Metagenome/genetics ; Microbiota/genetics ; Propionibacterium acnes/*genetics/isolation & purification ; Sebaceous Glands/*microbiology ; Staphylococcus epidermidis/*genetics/isolation & 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.},
}

Acne Vulgaris/drug therapy/*microbiology
Dysbiosis/microbiology
Hair Follicle/*microbiology
Humans
Metagenome/genetics
Microbiota/genetics
Propionibacterium acnes/*genetics/isolation & purification
Sebaceous Glands/*microbiology
Staphylococcus epidermidis/*genetics/isolation & purification

@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 & 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 "ZBJ" to results using the novel primer pair "ANML." 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.},
}

Animals
*Chiroptera
Computational Biology/*methods
DNA/chemistry/genetics/isolation & purification
Electron Transport Complex IV/genetics
Feces/chemistry
*Feeding Behavior
High-Throughput Nucleotide Sequencing/*methods
Metagenomics/*methods

@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.},
}

Africa
*Animal Migration
Animals
Arabia
Butterflies/*physiology
DNA Barcoding, Taxonomic/*methods
Entomology/*methods
Mediterranean Region
Metagenomics/*methods
Pollen/*genetics
Spain

@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.

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.

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.},
}

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

@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.},
}

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

@article {pmid29768738,
year = {2019},
author = {Cilleros, K and Valentini, A and Allard, L and Dejean, T and Etienne, R and Grenouillet, G and Iribar, A and Taberlet, P and Vigouroux, R and Brosse, S},
title = {Unlocking biodiversity and conservation studies in high-diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes.},
journal = {Molecular ecology resources},
volume = {19},
number = {1},
pages = {27-46},
doi = {10.1111/1755-0998.12900},
pmid = {29768738},
issn = {1755-0998},
mesh = {Animals ; *Biodiversity ; DNA/chemistry/*genetics/*isolation & purification ; DNA Barcoding, Taxonomic/*methods ; Fishes/*classification/genetics ; Fresh Water/*chemistry ; Guyana ; Metagenomics/*methods ; },
abstract = {Determining the species compositions of local assemblages is a prerequisite to understanding how anthropogenic disturbances affect biodiversity. However, biodiversity measurements often remain incomplete due to the limited efficiency of sampling methods. This is particularly true in freshwater tropical environments that host rich fish assemblages, for which assessments are uncertain and often rely on destructive methods. Developing an efficient and nondestructive method to assess biodiversity in tropical freshwaters is highly important. In this study, we tested the efficiency of environmental DNA (eDNA) metabarcoding to assess the fish diversity of 39 Guianese sites. We compared the diversity and composition of assemblages obtained using traditional and metabarcoding methods. More than 7,000 individual fish belonging to 203 Guianese fish species were collected by traditional sampling methods, and ~17 million reads were produced by metabarcoding, among which ~8 million reads were assigned to 148 fish taxonomic units, including 132 fish species. The two methods detected a similar number of species at each site, but the species identities partially matched. The assemblage compositions from the different drainage basins were better discriminated using metabarcoding, revealing that while traditional methods provide a more complete but spatially limited inventory of fish assemblages, metabarcoding provides a more partial but spatially extensive inventory. eDNA metabarcoding can therefore be used for rapid and large-scale biodiversity assessments, while at a local scale, the two approaches are complementary and enable an understanding of realistic fish biodiversity.},
}

Animals
*Biodiversity
DNA/chemistry/*genetics/*isolation & purification
DNA Barcoding, Taxonomic/*methods
Fishes/*classification/genetics
Fresh Water/*chemistry
Guyana
Metagenomics/*methods

@article {pmid29253074,
year = {2018},
author = {Huang, L and Krüger, J and Sczyrba, A},
title = {Analyzing large scale genomic data on the cloud with Sparkhit.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {9},
pages = {1457-1465},
pmid = {29253074},
issn = {1367-4811},
mesh = {Algorithms ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; *Software ; },
abstract = {Motivation: The increasing amount of next-generation sequencing data poses a fundamental challenge on large scale genomic analytics. Existing tools use different distributed computational platforms to scale-out bioinformatics workloads. However, the scalability of these tools is not efficient. Moreover, they have heavy run time overheads when pre-processing large amounts of data. To address these limitations, we have developed Sparkhit: a distributed bioinformatics framework built on top of the Apache Spark platform.

Results: Sparkhit integrates a variety of analytical methods. It is implemented in the Spark extended MapReduce model. It runs 92-157 times faster than MetaSpark on metagenomic fragment recruitment and 18-32 times faster than Crossbow on data pre-processing. We analyzed 100 terabytes of data across four genomic projects in the cloud in 21 h, which includes the run times of cluster deployment and data downloading. Furthermore, our application on the entire Human Microbiome Project shotgun sequencing data was completed in 2 h, presenting an approach to easily associate large amounts of public datasets with reference data.

Sparkhit is freely available at: https://rhinempi.github.io/sparkhit/.

Contact: asczyrba@cebitec.uni-bielefeld.de.

Supplementary information: Supplementary data are available at Bioinformatics online.},
}

Algorithms
High-Throughput Nucleotide Sequencing/*methods
Humans
Metagenomics/*methods
Microbiota/genetics
Sequence Analysis, DNA/methods
*Software

@article {pmid29211828,
year = {2018},
author = {Orakov, AN and Sakenova, NK and Sorokin, A and Goryanin, II},
title = {ASAR: visual analysis of metagenomes in R.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {8},
pages = {1404-1405},
pmid = {29211828},
issn = {1367-4811},
mesh = {Metagenomics/*methods ; Microbiota/*genetics ; *Software ; },
abstract = {Motivation: Functional and taxonomic analyses are critical steps in understanding interspecific interactions within microbial communities. Currently, such analyses are run separately, which complicates interpretation of results. Here we present the ASAR interactive tool for simultaneous analysis of metagenomic data in three dimensions: taxonomy, function, metagenome.

Results: An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

Source code of the ASAR is accessible at GitHub (https://github.com/Askarbek-orakov/ASAR).

Contact: askarbek.orakov@nu.edu.kz or goryanin@gmail.com.},
}

Metagenomics/*methods
Microbiota/*genetics
*Software

@article {pmid29028892,
year = {2018},
author = {Weber, N and Liou, D and Dommer, J and MacMenamin, P and Quiñones, M and Misner, I and Oler, AJ and Wan, J and Kim, L and Coakley McCarthy, M and Ezeji, S and Noble, K and Hurt, DE},
title = {Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {8},
pages = {1411-1413},
pmid = {29028892},
issn = {1367-4811},
mesh = {*Cloud Computing ; Computational Biology/*methods ; Humans ; Metagenomics/methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA ; *Software ; },
abstract = {Motivation: Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools.

Results: The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights. Nephele integrates common microbiome analysis tools as well as valuable reference datasets like the healthy human subjects cohort of the Human Microbiome Project (HMP). Nephele is built on the Amazon Web Services cloud, which provides centralized and automated storage and compute capacity, thereby reducing the burden on researchers and their institutions.

https://nephele.niaid.nih.gov and https://github.com/niaid/Nephele.

Contact: darrell.hurt@nih.gov.},
}

*Cloud Computing
Computational Biology/*methods
Humans
Metagenomics/methods
Microbiota/*genetics
Sequence Analysis, DNA/methods
Sequence Analysis, RNA
*Software

@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.},
}

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

@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 & 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.},
}

Bacteria/classification/drug effects/*genetics/*isolation & purification
*Drug Resistance, Microbial
Genes, Bacterial/*drug effects
Geologic Sediments/*microbiology
Indian Ocean
*Microbiota

@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 & purification ; *Biological Control Agents ; Denaturing Gradient Gel Electrophoresis ; Fungi/genetics/isolation & 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.

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.

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.

Our investigations provide information on the structure of bacterial and fungal communities in peanut-producing fields after inoculation of seeds with a biocontrol agent.},
}

Agriculture
Arachis
Argentina
Bacteria/genetics/isolation & purification
*Biological Control Agents
Denaturing Gradient Gel Electrophoresis
Fungi/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
Microbiota
Polymerase Chain Reaction
Seeds
Soil/chemistry
*Soil Microbiology
*Trichoderma

@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 & purification ; Swine/growth & 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.

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.

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.

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.},
}

Animals
*Bacterial Shedding
Female
*Microbiota
Pregnancy
Salmonella/*isolation & purification
Swine/growth & development/*microbiology
Weaning

@article {pmid29920461,
year = {2018},
author = {Graham, EB and Crump, AR and Kennedy, DW and Arntzen, E and Fansler, S and Purvine, SO and Nicora, CD and Nelson, W and Tfaily, MM and Stegen, JC},
title = {Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone.},
journal = {The Science of the total environment},
volume = {642},
number = {},
pages = {742-753},
doi = {10.1016/j.scitotenv.2018.05.256},
pmid = {29920461},
issn = {1879-1026},
mesh = {Carbon ; Environmental Monitoring/*methods ; Groundwater ; Metabolome/*physiology ; Microbiota ; Rivers ; },
abstract = {Biogeochemical hotspots are pervasive at terrestrial-aquatic interfaces, particularly within groundwater-surface water mixing zones (hyporheic zones), and they are critical to understanding spatiotemporal variation in biogeochemical cycling. Here, we use multi 'omic comparisons of hotspots to low-activity sediments to gain mechanistic insight into hyporheic zone organic matter processing. We hypothesized that microbiome structure and function, as described by metagenomics and metaproteomics, would distinguish hotspots from low-activity sediments by shifting metabolism towards carbohydrate-utilizing pathways and elucidate discrete mechanisms governing organic matter processing in each location. We also expected these differences to be reflected in the metabolome, whereby hotspot carbon (C) pools and metabolite transformations therein would be enriched in sugar-associated compounds. In contrast to expectations, we found pronounced phenotypic plasticity in the hyporheic zone microbiome that was denoted by similar microbiome structure, functional potential, and expression across sediments with dissimilar metabolic rates. Instead, diverse nitrogenous metabolites and biochemical transformations characterized hotspots. Metabolomes also corresponded more strongly to aerobic metabolism than bulk C or N content only (explaining 67% vs. 42% and 37% of variation respectively), and bulk C and N did not improve statistical models based on metabolome composition alone. These results point to organic nitrogen as a significant regulatory factor influencing hyporheic zone organic matter processing. Based on our findings, we propose incorporating knowledge of metabolic pathways associated with different chemical fractions of C pools into ecosystem models will enhance prediction accuracy.},
}

Carbon
Environmental Monitoring/*methods
Groundwater
Metabolome/*physiology
Microbiota
Rivers

@article {pmid29667371,
year = {2019},
author = {Han, Z and Sun, J and Lv, A and Wang, A},
title = {Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi.},
journal = {MicrobiologyOpen},
volume = {8},
number = {1},
pages = {e00626},
doi = {10.1002/mbo3.626},
pmid = {29667371},
issn = {2045-8827},
mesh = {Animals ; Carps/microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics/*isolation & purification ; DNA, Ribosomal/chemistry/genetics/*isolation & purification ; *Gastrointestinal Microbiome ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {This study examined the technical bias associated with different DNA extraction methods used in microbiome research. Three methods were used to extract genomic DNA from the same intestinal microbiota sample that was taken from the koi carp Cyprinus carpio var. koi, after which their microbial diversity and community structure were investigated on the basis of a 16S rDNA high-throughput sequencing analysis. Biased results were observed in relation to the number of reads, alpha diversity indexes and taxonomic composition among the three DNA extraction protocols. A total of 1,381 OTUs from the intestinal bacteria were obtained, with 852, 759, and 698 OTUs acquired, using the Lysozyme and Ultrasonic Lysis method, Zirmil-beating Cell Disruption method, and a QIAamp Fast DNA Stool Mini Kit, respectively. Additionally, 336 OTUs were commonly acquired, using the three methods. The results showed that the alpha diversity indexes (Rarefaction, Shannon, and Chao1) of the community that were determined using the Lysozyme and Ultrasonic Lysis method were higher than those obtained with the Zirmil-beating Cell Disruption method, while the Zirmil method results were higher than those measured, using the QIAamp Fast DNA Stool Mini Kit. Moreover, all the major phyla (ratio>1%) could be identified with all three DNA extraction methods, but the phyla present at a lower abundance (ratio <1%) could not. Similar findings were observed at the genus level. Taken together, these findings indicated that the bias observed in the results about the community structure occurred primarily in OTUs with a lower abundance. The results of this study demonstrate that possible bias exists in community analyses, and researchers should therefore be conservative when drawing conclusions about community structures based on the currently available DNA extraction methods.},
}

Animals
Carps/microbiology
Cluster Analysis
DNA, Bacterial/chemistry/genetics/*isolation & purification
DNA, Ribosomal/chemistry/genetics/*isolation & purification
*Gastrointestinal Microbiome
Metagenomics/*methods
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid28798374,
year = {2017},
author = {Patel, SH and Vaidya, YH and Patel, RJ and Pandit, RJ and Joshi, CG and Kunjadiya, AP},
title = {Culture independent assessment of human milk microbial community in lactational mastitis.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {7804},
pmid = {28798374},
issn = {2045-2322},
mesh = {Bacteria/*classification/genetics ; Case-Control Studies ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Gene Regulatory Networks ; Humans ; Lactation ; Mastitis/*microbiology ; Metagenomics/*methods ; Microbiota ; Milk, Human/*microbiology ; Odds Ratio ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Breastfeeding undoubtedly provides important benefits to the mother-infant dyad and should be encouraged. Mastitis, one of the common but major cause of premature weaning among lactating women, is an inflammation of connective tissue within the mammary gland. This study reports the influence of mastitis on human milk microbiota by utilizing 16 S rRNA gene sequencing approach. We sampled and sequenced microbiome from 50 human milk samples, including 16 subacute mastitis (SAM), 16 acute mastitis (AM) and 18 healthy-controls. Compared to controls, SAM and AM microbiota were quite distinct and drastically reduced. Genera including, Aeromonas, Staphylococcus, Ralstonia, Klebsiella, Serratia, Enterococcus and Pseudomonas were significantly enriched in SAM and AM samples, while Acinetobacter, Ruminococcus, Clostridium, Faecalibacterium and Eubacterium were consistently depleted. Further analysis of our samples revealed positive aerotolerant odds ratio, indicating dramatic depletion of obligate anaerobes and enrichment of aerotolerant bacteria during the course of mastitis. In addition, predicted functional metagenomics identified several gene pathways related to bacterial proliferation and colonization (e.g. two-component system, bacterial secretion system and motility proteins) in SAM and AM samples. In conclusion, our study confirmed previous hypothesis that mastitis women have lower microbial diversity, increased abundance of opportunistic pathogens and depletion of commensal obligate anaerobes.},
}

Bacteria/*classification/genetics
Case-Control Studies
DNA, Bacterial/genetics
DNA, Ribosomal/genetics
Female
Gene Regulatory Networks
Humans
Lactation
Mastitis/*microbiology
Metagenomics/*methods
Microbiota
Milk, Human/*microbiology
Odds Ratio
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA/*methods

@article {pmid29931479,
year = {2018},
author = {Philips, CA and Phadke, N and Ganesan, K and Ranade, S and Augustine, P},
title = {Corticosteroids, nutrition, pentoxifylline, or fecal microbiota transplantation for severe alcoholic hepatitis.},
journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology},
volume = {37},
number = {3},
pages = {215-225},
pmid = {29931479},
issn = {0975-0711},
mesh = {Administration, Oral ; Adult ; Aged ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Hepatitis, Alcoholic/microbiology/*therapy ; Humans ; Male ; Middle Aged ; *Nutrition Therapy ; Pentoxifylline/*therapeutic use ; Prednisolone/*administration & dosage ; Severity of Illness Index ; Treatment Outcome ; },
abstract = {INTRODUCTION: Alcohol-induced intestinal dysbiosis is central to the development of the severe alcoholic liver disease. We present the first study to compare outcomes in patients of severe alcoholic hepatitis (SAH) on nutritional therapy, corticosteroids, pentoxifylline, and healthy donor fecal transplantation (FMT) and discuss distinct microbial community and microbiome metabolic functional changes after FMT.

METHODS: Out of 1271 liver disease patients, 809 (63.7%) were diagnosed to have the alcoholic liver disease, of which 51 patients (8 treated with corticosteroids, 17 with nutritional support only, 10 with pentoxifylline, 16 receiving FMT) were included. Clinical, biochemical parameters, liver disease, and alcoholic hepatitis severity scores at baseline and mortality at the end of 1 and 3 months were analyzed between groups. Stool microbiota (SM) analysis was performed for healthy controls (HC) and respective recipients after FMT.

RESULTS: All the patients were male. The proportions of patients surviving at the end of 1 and 3 months in the steroids, nutrition, pentoxifylline, and FMT group were 63%, 47%, 40% and 75% [p = 0.179] and 38%, 29%, 30%, and 75% [p = 0.036], respectively. When compared with FMT, relative risk and hazard ratios for death were higher in all the other groups. Following FMT, distinct and beneficial modulation of SM and pathways of dysregulated metabolism, infections, inflammation, and oxidative stress in SAH patients were noted in tandem with improved clinical outcomes.

CONCLUSIONS: Healthy donor FMT for SAH improves survival beyond what is offered by current therapies and can function as a cost-effective bridge to liver transplant (LT) or for improving transplant-free survival. Larger studies and randomized trials are unmet needs.},
}

Administration, Oral
Adult
Aged
*Fecal Microbiota Transplantation
Feces/microbiology
Female
Gastrointestinal Microbiome
Hepatitis, Alcoholic/microbiology/*therapy
Humans
Male
Middle Aged
*Nutrition Therapy
Pentoxifylline/*therapeutic use
Prednisolone/*administration & dosage
Severity of Illness Index
Treatment Outcome

@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 & 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.},
}

Bacteria/classification/*genetics/isolation & purification
Bacterial Physiological Phenomena
Biodiversity
*Biofilms
Indian Ocean
Metagenomics
Phylogeny
Seawater/analysis/*microbiology
Zinc/analysis/*metabolism

@article {pmid30177353,
year = {2018},
author = {Rhoads, JM and Collins, J and Fatheree, NY and Hashmi, SS and Taylor, CM and Luo, M and Hoang, TK and Gleason, WA and Van Arsdall, MR and Navarro, F and Liu, Y},
title = {Infant Colic Represents Gut Inflammation and Dysbiosis.},
journal = {The Journal of pediatrics},
volume = {203},
number = {},
pages = {55-61.e3},
doi = {10.1016/j.jpeds.2018.07.042},
pmid = {30177353},
issn = {1097-6833},
mesh = {Acinetobacter/isolation & purification ; Breast Feeding ; Case-Control Studies ; Colic/*complications ; Dysbiosis/*diagnosis ; Feces/*chemistry/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Infant Formula ; Infant, Newborn ; Inflammation/*diagnosis ; Lactobacillus/isolation & purification ; Leukocyte L1 Antigen Complex/*analysis ; Male ; },
abstract = {OBJECTIVE: To dissect potential confounding effects of breast milk and formula feeding on crying + fussing, fecal calprotectin, and gut microbiota in babies with colic. We hypothesized that infant colic is associated with gut inflammation linked to intestinal dysbiosis.

STUDY DESIGN: A nested case-control design of 3 of our studies was used to analyze clinical and laboratory data at presentation, comparing babies with colic with controls. All investigators other than the biostatistician were blinded during data analysis. Subjects were recruited based on their age and crying + fussy time. We screened 65 infants, 37 with colic, as defined by Barr diary (crying + fussing time >3 hours daily), who were compared with 28 noncolicky infants.

RESULTS: Fecal calprotectin was elevated in babies with colic. For each mode of infant feeding (breast milk, formula, or breast + formula), infants' fecal calprotectin was higher in babies with colic. Infants with colic had similar levels of fecal alpha diversity (richness) when compared with controls, and alpha diversity was lower in breast-fed babies. Beta diversity at the phylum level revealed significant differences in microbial population. A phylum difference resulted from reduced Actinobacteria (95% of which are Bifidobacilli) in babies with colic. Species significantly associated with colic were Acinetobacter and Lactobacillus iners.

CONCLUSIONS: Colic is linked with gut inflammation (as determined by fecal calprotectin) and dysbiosis, independent of mode of feeding, with fewer Bifidobacilli.

TRIAL REGISTRATION: Clinicaltrials.gov: NCT01279265 and NCT01849991.},
}

Acinetobacter/isolation & purification
Breast Feeding
Case-Control Studies
Colic/*complications
Dysbiosis/*diagnosis
Feces/*chemistry/microbiology
Female
Gastrointestinal Microbiome
Humans
Infant
Infant Formula
Infant, Newborn
Inflammation/*diagnosis
Lactobacillus/isolation & purification
Leukocyte L1 Antigen Complex/*analysis
Male

@article {pmid29956164,
year = {2018},
author = {Tang, MS and Bowcutt, R and Loke, P},
title = {Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1799},
number = {},
pages = {359-370},
doi = {10.1007/978-1-4939-7896-0_26},
pmid = {29956164},
issn = {1940-6029},
mesh = {Animals ; Gastrointestinal Microbiome/*immunology ; Helminthiasis/diagnosis/immunology/parasitology ; Helminths/immunology ; Host-Pathogen Interactions ; *Immunity ; Metagenome ; Metagenomics/methods ; Mice ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The microbial communities that reside within the mammalian host play important roles in the development of a robust host immune system. With the advent of sequencing technology and barcoding strategy of the bacterial 16S ribosomal RNA (rRNA) gene, microbiota studies are becoming more economical but also more important in many immunology studies. Here, we described a representative study protocol to characterize how the microbiota changes during an intestinal helminth infection, with emphasis on subtle aspects of the experimental design that are critical for data interpretation.},
}

Animals
Gastrointestinal Microbiome/*immunology
Helminthiasis/diagnosis/immunology/parasitology
Helminths/immunology
Host-Pathogen Interactions
*Immunity
Metagenome
Metagenomics/methods
Mice
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid29371652,
year = {2018},
author = {Fernández, L and Rodríguez, A and García, P},
title = {Phage or foe: an insight into the impact of viral predation on microbial communities.},
journal = {The ISME journal},
volume = {12},
number = {5},
pages = {1171-1179},
pmid = {29371652},
issn = {1751-7370},
mesh = {Bacteria/genetics/*metabolism/pathogenicity ; Bacteriophages/*physiology ; Biological Evolution ; Genomics ; Metagenomics ; *Microbial Interactions ; Microbiota ; Proteomics ; },
abstract = {Since their discovery, bacteriophages have been traditionally regarded as the natural enemies of bacteria. However, recent advances in molecular biology techniques, especially data from "omics" analyses, have revealed that the interplay between bacterial viruses and their hosts is far more intricate than initially thought. On the one hand, we have become more aware of the impact of viral predation on the composition and genetic makeup of microbial communities thanks to genomic and metagenomic approaches. Moreover, data obtained from transcriptomic, proteomic, and metabolomic studies have shown that responses to phage predation are complex and diverse, varying greatly depending on the bacterial host, phage, and multiplicity of infection. Interestingly, phage exposure may alter different phenotypes, including virulence and biofilm formation. The complexity of the interactions between microbes and their viral predators is also evidenced by the link between quorum-sensing signaling pathways and bacteriophage resistance. Overall, new data increasingly suggests that both temperate and virulent phages have a positive effect on the evolution and adaptation of microbial populations. From this perspective, further research is still necessary to fully understand the interactions between phage and host under conditions that allow co-existence of both populations, reflecting more accurately the dynamics in natural microbial communities.},
}

Bacteria/genetics/*metabolism/pathogenicity
Bacteriophages/*physiology
Biological Evolution
Genomics
Metagenomics
*Microbial Interactions
Microbiota
Proteomics

@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.},
}

Animals
Chickens
Feces/*virology
*Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing
Malabsorption Syndromes/*veterinary/virology
Metagenomics
Poultry Diseases/*virology
Viruses/*classification/*genetics

@article {pmid30152883,
year = {2018},
author = {Toivonen, L and Hasegawa, K and Ajami, NJ and Celedón, JC and Mansbach, JM and Petrosino, JF and Camargo, CA},
title = {Circulating 25-hydroxyvitamin D, nasopharyngeal microbiota, and bronchiolitis severity.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {29},
number = {8},
pages = {877-880},
pmid = {30152883},
issn = {1399-3038},
support = {//Päivikki ja Sakari Sohlbergin Säätiö/International ; R01 AI134940/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; R01 AI137091/AI/NIAID NIH HHS/United States ; //Suomen Lääketieteen Säätiö/International ; UG3 OD023253/OD/NIH HHS/United States ; },
mesh = {Bronchiolitis/*etiology ; Cohort Studies ; Female ; Humans ; Infant ; Male ; Microbiota/genetics/*immunology ; Nasopharynx/*microbiology ; Prospective Studies ; Risk Factors ; United States ; Vitamin D/*analogs & derivatives/blood ; },
}

Bronchiolitis/*etiology
Cohort Studies
Female
Humans
Infant
Male
Microbiota/genetics/*immunology
Nasopharynx/*microbiology
Prospective Studies
Risk Factors
United States
Vitamin D/*analogs & derivatives/blood

@article {pmid29729376,
year = {2018},
author = {Li, M and Zhou, M and Tian, X and Tan, C and McDaniel, CT and Hassett, DJ and Gu, T},
title = {Microbial fuel cell (MFC) power performance improvement through enhanced microbial electrogenicity.},
journal = {Biotechnology advances},
volume = {36},
number = {4},
pages = {1316-1327},
doi = {10.1016/j.biotechadv.2018.04.010},
pmid = {29729376},
issn = {1873-1899},
mesh = {*Bioelectric Energy Sources ; *Biofilms ; *Microbial Consortia ; Oxidation-Reduction ; Synthetic Biology ; },
abstract = {Within the past 5 years, tremendous advances have been made to maximize the performance of microbial fuel cells (MFCs) for both "clean" bioenergy production and bioremediation. Most research efforts have focused on parameters including (i) optimizing reactor configuration, (ii) electrode construction, (iii) addition of redox-active, electron donating mediators, (iv) biofilm acclimation and feed nutrient adjustment, as well as (v) other parameters that contribute to enhanced MFC performance. To date, tremendous advances have been made, but further improvements are needed for MFCs to be economically practical. In this review, the diversity of electrogenic microorganisms and microbial community changes in mixed cultures are discussed. More importantly, different approaches including chemical/genetic modifications and gene regulation of exoelectrogens, synthetic biology approaches and bacterial community cooperation are reviewed. Advances in recent years in metagenomics and microbiomes have allowed researchers to improve bacterial electrogenicity of robust biofilms in MFCs using novel, unconventional approaches. Taken together, this review provides some important and timely information to researchers who are examining additional means to enhance power production of MFCs.},
}

*Bioelectric Energy Sources
*Biofilms
*Microbial Consortia
Oxidation-Reduction
Synthetic Biology

@article {pmid29575679,
year = {2018},
author = {Zhou, Y and Zhu, H and Yao, Q},
title = {Contrasting P acquisition strategies of the bacterial communities associated with legume and grass in subtropical orchard soil.},
journal = {Environmental microbiology reports},
volume = {10},
number = {3},
pages = {310-319},
doi = {10.1111/1758-2229.12641},
pmid = {29575679},
issn = {1758-2229},
mesh = {Bacteria/*classification/isolation & purification/metabolism ; Metagenomics ; Microbiota ; Paspalum/metabolism/*microbiology ; Phosphorus/*metabolism ; Pterocarpus/metabolism/*microbiology ; *Soil Microbiology ; Turkey ; },
abstract = {Phosphorus (P) cycling is a fundamental process driven by microorganisms, and plants can regulate P cycling directly or via their influence on the soil microbial community. However, the differential P cycling patterns associated with legumes and grass are largely unknown. Therefore, we investigated the microbial community involved in P cycling in subtropical soil grown with stylo (Stylosanthes guianensis, legume) or bahiagrass (Paspalum notatum, grass) using metagenomic sequencing. P fractionation indicated that sparingly soluble inorganic P (Pi) accounted for approximately 75% of P pool. Bacteria involved in sparingly soluble Pi solubilization (pqq, gad, JEN) were more abundant in bahiagrass soil, with Candidatus Pelagibacter, Trichodesmium, Neorickettsia, Nitrobacter, Paraburkholderia, Candidatus Solibacter, Burkholderia as major contributors. In contrast, bacteria involved in organic P (Po) mineralization (php, glpQ, phn) were more abundant in stylo soil, consistent with phosphatase activity and Frankia, Kyrpidia, Thermobispora, Streptomyces, Rhodococcus were major contributors. Bacteria taking up low molecular-weight Po were more abundant in stylo soil than in bahiagrass soil, while those taking up Pi were less abundant. These data suggest that bacterial communities associated with legumes and grass develop contrasting P acquisition strategies, highlighting the possibility of intercropping with legumes and grass for better P cycling.},
}

Bacteria/*classification/isolation & purification/metabolism
Metagenomics
Microbiota
Paspalum/metabolism/*microbiology
Phosphorus/*metabolism
Pterocarpus/metabolism/*microbiology
*Soil Microbiology
Turkey

@article {pmid29515974,
year = {2018},
author = {Ewan, VC and Reid, WDK and Shirley, M and Simpson, AJ and Rushton, SP and Wade, WG},
title = {Oropharyngeal Microbiota in Frail Older Patients Unaffected by Time in Hospital.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {42},
pmid = {29515974},
issn = {2235-2988},
support = {G0800440//Medical Research Council/United Kingdom ; },
mesh = {Aged ; Aged, 80 and over ; Biodiversity ; Carrier State/*epidemiology ; Cross Infection/epidemiology/microbiology ; Female ; *Geriatric Assessment ; *Hospitalization ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Oropharynx/*microbiology ; Pharyngitis/epidemiology/microbiology ; Time Factors ; },
abstract = {Respiratory tract infections are the commonest nosocomial infections, and occur predominantly in frailer, older patients with multiple comorbidities. The oropharyngeal microbiota is the major reservoir of infection. This study explored the relative contributions of time in hospital and patient demographics to the community structure of the oropharyngeal microbiota in older patients with lower limb fracture. We collected 167 throat swabs from 53 patients (mean age 83) over 14 days after hospitalization, and analyzed these using 16S rRNA gene sequencing. We calculated frailty/comorbidity indices, undertook dental examinations and collected data on respiratory tract infections. We analyzed microbial community composition using correspondence (CA) and canonical correspondence analysis. Ten patients were treated for respiratory tract infection. Microbial community structure was related to frailty, number of teeth and comorbidity on admission, with comorbidity exerting the largest effect. Time in hospital neither significantly changed alpha (t = -0.910, p = 0.365) nor beta diversity (CA1 t = 0.022, p = 0.982; CA2 t = -0.513, p = 0.609) of microbial communities in patient samples. Incidence of respiratory pathogens were not associated with time in hospital (t = -0.207, p = 0.837), nor with alpha diversity of the oral microbiota (t = -1.599, p = 0.113). Patient characteristics at admission, rather than time in hospital, influenced the community structure of the oral microbiota.},
}

Aged
Aged, 80 and over
Biodiversity
Carrier State/*epidemiology
Cross Infection/epidemiology/microbiology
Female
*Geriatric Assessment
*Hospitalization
Humans
Male
Metagenome
Metagenomics/methods
*Microbiota
Oropharynx/*microbiology
Pharyngitis/epidemiology/microbiology
Time Factors

@article {pmid29488349,
year = {2018},
author = {Lang-Yona, N and Maier, S and Macholdt, DS and Müller-Germann, I and Yordanova, P and Rodriguez-Caballero, E and Jochum, KP and Al-Amri, A and Andreae, MO and Fröhlich-Nowoisky, J and Weber, B},
title = {Insights into microbial involvement in desert varnish formation retrieved from metagenomic analysis.},
journal = {Environmental microbiology reports},
volume = {10},
number = {3},
pages = {264-271},
doi = {10.1111/1758-2229.12634},
pmid = {29488349},
issn = {1758-2229},
mesh = {Actinobacteria/*classification/genetics/isolation & purification/metabolism ; Clay/*microbiology ; Cyanobacteria/*classification/genetics/isolation & purification/metabolism ; Ferric Compounds/*metabolism ; Manganese Compounds/*metabolism ; Metagenomics/methods ; Microbiota/genetics ; Oxides/*metabolism ; Proteobacteria/*classification/genetics/isolation & purification/metabolism ; Sequence Analysis, DNA/methods ; *Soil Microbiology ; },
abstract = {Desert varnishes are dark rock coatings observed in arid environments and might resemble Mn-rich coatings found on Martian rocks. Their formation mechanism is not fully understood and the possible microbial involvement is under debate. In this study, we applied DNA metagenomic Shotgun sequencing of varnish and surrounding soil to evaluate the composition of the microbial community and its potential metabolic function. We found that the α diversity was lower in varnish compared to soil samples (p value < 0.05), suggesting distinct populations with significantly higher abundance of Actinobacteria, Proteobacteria and Cyanobacteria within the varnish. Additionally, we observed increased levels of transition metal metabolic processes in varnish compared to soil samples. Nevertheless, potentially relevant enzymes for varnish formation were detected at low to insignificant levels in both niches, indicating no current direct microbial involvement in Mn oxidation. This finding is supported by quantitative genomic analysis, elemental analysis, fluorescence imaging and scanning transmission X-ray microscopy. We thus conclude that the distinct microbial communities detected in desert varnish originate from settled Aeolian microbes, which colonized this nutrient-enriched niche, and discuss possible indirect contributions of microorganisms to the formation of desert varnish.},
}

Actinobacteria/*classification/genetics/isolation & purification/metabolism
Clay/*microbiology
Cyanobacteria/*classification/genetics/isolation & purification/metabolism
Ferric Compounds/*metabolism
Manganese Compounds/*metabolism
Metagenomics/methods
Microbiota/genetics
Oxides/*metabolism
Proteobacteria/*classification/genetics/isolation & purification/metabolism
Sequence Analysis, DNA/methods
*Soil Microbiology

@article {pmid29368406,
year = {2018},
author = {Chai, ZY and He, ZL and Deng, YY and Yang, YF and Tang, YZ},
title = {Cultivation of seaweed Gracilaria lemaneiformis enhanced biodiversity in a eukaryotic plankton community as revealed via metagenomic analyses.},
journal = {Molecular ecology},
volume = {27},
number = {4},
pages = {1081-1093},
doi = {10.1111/mec.14496},
pmid = {29368406},
issn = {1365-294X},
mesh = {*Biodiversity ; Biomass ; China ; Geography ; Gracilaria/*growth & development ; *Metagenomics ; Phylogeny ; Plankton/*genetics ; Principal Component Analysis ; RNA, Ribosomal, 28S/genetics ; Seaweed/*growth & development ; },
abstract = {Plankton diversity reflects the quality and health of waters and should be monitored as a critical feature of marine ecosystems. This study applied a pair of 28S rRNA gene-specific primers and pyrosequencing to assess the effects of large-scale cultivation of the seaweed Gracilaria lemaneiformis on the biodiversity of eukaryotic plankton community in the coastal water of Guangdong, China. With 1 million sequences (2,221 operational taxonomic units [OTUs]) obtained from 51 samples, we found that the biodiversity of eukaryotic plankton community was significantly higher in the seaweed cultivation area than that in the nearby control area as reflected in OTU richness, evenness (Shannon-Wiener index) and dominance (Simpson index) for total plankton community and its four subcategories when Gracilaria biomass reached the maximum, while no such a significant difference was observed before seaweed inoculation. Our laboratory experiment using an artificial phytoplankton community of nine species observed the same effects of Gracilaria exposure. Principal component analysis and principal coordinates analysis showed the plankton community structure in cultivation area markedly differed from the control area when Gracilaria biomass reached its maximum. Redundancy analysis showed that G. lemaneiformis was the critical factor in controlling the dynamics of eukaryotic plankton communities in the studied coastal ecosystem. Our results explicitly demonstrated G. lemaneiformis cultivation could enhance biodiversity of plankton community via allelopathy, which prevents one or several plankton species from blooming and consequently maintains a relatively higher biodiversity. Our study provided further support for using large-scale G. lemaneiformis cultivation as an effective approach for improving costal ecosystem health.},
}

*Biodiversity
Biomass
China
Geography
Gracilaria/*growth & development
*Metagenomics
Phylogeny
Plankton/*genetics
Principal Component Analysis
RNA, Ribosomal, 28S/genetics
Seaweed/*growth & development

@article {pmid28607352,
year = {2017},
author = {Zhou, J and Jiang, X and Wei, D and Zhao, B and Ma, M and Chen, S and Cao, F and Shen, D and Guan, D and Li, J},
title = {Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {3267},
pmid = {28607352},
issn = {2045-2322},
mesh = {Bacteria/*classification/genetics ; Biodiversity ; China ; Crops, Agricultural ; Fertilizers/*analysis ; Metagenome ; Metagenomics/methods ; Nitrogen/*analysis ; RNA, Ribosomal, 16S ; *Seasons ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.},
}

Bacteria/*classification/genetics
Biodiversity
China
Crops, Agricultural
Fertilizers/*analysis
Metagenome
Metagenomics/methods
Nitrogen/*analysis
RNA, Ribosomal, 16S
*Seasons
Soil/*chemistry
*Soil Microbiology

@article {pmid30793504,
year = {2019},
author = {Kwon, YM and Patra, AK and Chiura, HX and Kim, SJ},
title = {Production of extracellular vesicles with light-induced proton pump activity by proteorhodopsin-containing marine bacteria.},
journal = {MicrobiologyOpen},
volume = {},
number = {},
pages = {e808},
doi = {10.1002/mbo3.808},
pmid = {30793504},
issn = {2045-8827},
support = {2019M00700//MABIK/ ; },
abstract = {The production and release of extracellular vesicles (EVs) is a common process occurring in various types of bacteria. However, little is known regarding the functions of EVs derived from marine bacteria. We observed that during cell growth, Sediminicola sp. YIK13, a proteorhodopsin (PR)-containing marine flavobacterium, produces EVs (S13EVs). Transmission electron microscopy showed that Sediminicola sp. YIK13 released two spherical vesicle types, with mono- and/or bi-layered membranes, in the culture. Interestingly, the S13EVs have an orange pigment, indicating the presence of putative carotenoid and PR pigments ascribed to the parental cells. The S13EVs demonstrated the same PR-derived absorption peak spectrum and light-induced proton pump activity as the parental cells. Western blot (immunoblot) analysis of the S13EVs revealed the presence of PR. We confirmed the 16S rRNA gene, pro gene, and genes required for chromophore retinal synthesis, namely blh and crtI, in the DNA packaged into these vesicles. In addition, by metagenomic sequencing, we found microbial rhodopsin-related genes in vesicles derived from natural aquatic environments. Our results suggest that EVs as well potentially pursue horizontal gene transfer of diverse microbial rhodopsin genes in marine ecosystems.},
}

@article {pmid30625669,
year = {2019},
author = {Costeira, R and Doherty, R and Allen, CCR and Larkin, MJ and Kulakov, LA},
title = {Analysis of viral and bacterial communities in groundwater associated with contaminated land.},
journal = {The Science of the total environment},
volume = {656},
number = {},
pages = {1413-1426},
doi = {10.1016/j.scitotenv.2018.11.429},
pmid = {30625669},
issn = {1879-1026},
mesh = {Bacteria/classification/*genetics ; Groundwater/*microbiology/virology ; *Metagenome ; *Microbiota ; Northern Ireland ; Soil Pollutants/*analysis ; Viruses/classification/*genetics ; },
abstract = {This work aimed at the comprehensive analysis of total microbial communities inhabiting a typical hydrocarbon-polluted site, where chemical characteristics of the groundwater were readily available. To achieve this, a joint metagenomic characterization of bacteria and viruses surrounding a contaminant plume was performed over a one-year period. The results presented demonstrated that both potential hydrocarbon degraders and their bacteriophages were dominant around the plume, and that the viral and bacterial diversities found at the site were probably influenced by the pH of the groundwater. Niche-specific and dispersed associations between phages and bacteria were identified. The niche phage-host associations were found at the edge of the site and at the core of the plume where pH was the highest (9.52). The identified host populations included several classes of bacteria (e.g. Clostridia and Proteobacteria). Thirty-six viral generalists were also discovered, with BGW-G9 having the broadest host range across 23 taxa, including Pseudomonas, Polycyclovorans, Methylocaldum and Candidatus Magnetobacterium species. The phages with broad host ranges are presumed to have significant effects on prokaryotic production and horizontal gene transfer, and therefore impact the biodegradation processes conducted by various bacteria of the environment studied. This study for the first time characterized the phages and their bacterial hosts associated with a contaminant plume.},
}

Bacteria/classification/*genetics
Groundwater/*microbiology/virology
*Metagenome
*Microbiota
Northern Ireland
Soil Pollutants/*analysis
Viruses/classification/*genetics

@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.

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 "CLAsificador MEtagenomico", 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.

CONCLUSIONS: We developed a tool that can be used to extract genomes (or parts of them) from a complex metagenome.},
}

*Algorithms
Colombia
Genes, Bacterial
Genetic Markers
*Genome, Bacterial
*Metagenomics
Microbiota
Phylogeny
Sequence Analysis, DNA/*methods
Xanthomonadaceae/*classification/*genetics

@article {pmid30338752,
year = {2018},
author = {Abranches, J and Zeng, L and Kajfasz, JK and Palmer, SR and Chakraborty, B and Wen, ZT and Richards, VP and Brady, LJ and Lemos, JA},
title = {Biology of Oral Streptococci.},
journal = {Microbiology spectrum},
volume = {6},
number = {5},
pages = {},
pmid = {30338752},
issn = {2165-0497},
support = {R01 DE022559/DE/NIDCR NIH HHS/United States ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; },
mesh = {Carbohydrate Metabolism ; Dental Caries/microbiology ; Endocarditis/microbiology ; Fermentation ; Humans ; Hydrogen Peroxide/metabolism ; Metagenomics ; Microbiota/physiology ; Mouth/*microbiology ; Phylogeny ; Streptococcus/classification/genetics/pathogenicity/*physiology ; Streptococcus gordonii/metabolism ; Streptococcus mutans ; Streptococcus salivarius/metabolism ; },
abstract = {Bacteria belonging to the genus Streptococcus are the first inhabitants of the oral cavity, which can be acquired right after birth and thus play an important role in the assembly of the oral microbiota. In this article, we discuss the different oral environments inhabited by streptococci and the species that occupy each niche. Special attention is given to the taxonomy of Streptococcus, because this genus is now divided into eight distinct groups, and oral species are found in six of them. Oral streptococci produce an arsenal of adhesive molecules that allow them to efficiently colonize different tissues in the mouth. Also, they have a remarkable ability to metabolize carbohydrates via fermentation, thereby generating acids as byproducts. Excessive acidification of the oral environment by aciduric species such as Streptococcus mutans is directly associated with the development of dental caries. However, less acid-tolerant species such as Streptococcus salivarius and Streptococcus gordonii produce large amounts of alkali, displaying an important role in the acid-base physiology of the oral cavity. Another important characteristic of certain oral streptococci is their ability to generate hydrogen peroxide that can inhibit the growth of S. mutans. Thus, oral streptococci can also be beneficial to the host by producing molecules that are inhibitory to pathogenic species. Lastly, commensal and pathogenic streptococci residing in the oral cavity can eventually gain access to the bloodstream and cause systemic infections such as infective endocarditis.},
}

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

@article {pmid30192933,
year = {2018},
author = {Li, F and Chen, C and Wei, W and Wang, Z and Dai, J and Hao, L and Song, L and Zhang, X and Zeng, L and Du, H and Tang, H and Liu, N and Yang, H and Wang, J and Madsen, L and Brix, S and Kristiansen, K and Xu, X and Li, J and Wu, R and Jia, H},
title = {The metagenome of the female upper reproductive tract.},
journal = {GigaScience},
volume = {7},
number = {10},
pages = {},
pmid = {30192933},
issn = {2047-217X},
mesh = {Biodiversity ; Computational Biology/methods ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Reproductive Tract Infections/*microbiology ; Vagina/microbiology ; },
abstract = {Background: The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking.

Results: We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. Direct annotation of sequencing reads identified the taxonomy of bacteria, archaea, fungi and viruses, confirming and extending the results from our previous study. We replicated our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of the 20GB raw data. After filtering, vaginal microorganisms were well covered in the generated reproductive tract gene catalogue, while the more diverse upper reproductive tract microbiota would require greater depth of sequencing and more samples to meet the full coverage scale.

Conclusions: We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.},
}

Biodiversity
Computational Biology/methods
Female
High-Throughput Nucleotide Sequencing
Humans
*Metagenome
*Metagenomics/methods
*Microbiota
Reproductive Tract Infections/*microbiology
Vagina/microbiology

@article {pmid30168288,
year = {2018},
author = {Minich, JJ and Zhu, Q and Xu, ZZ and Amir, A and Ngochera, M and Simwaka, M and Allen, EE and Zidana, H and Knight, R},
title = {Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus).},
journal = {MicrobiologyOpen},
volume = {7},
number = {6},
pages = {e00716},
doi = {10.1002/mbo3.716},
pmid = {30168288},
issn = {2045-8827},
mesh = {Animal Feed/analysis/microbiology ; Animals ; Aquaculture ; Bacteria/classification/genetics/*isolation & purification ; Catfishes/*growth & development/metabolism ; Cattle ; Livestock ; Manure/analysis/*microbiology ; Microbiota ; Ponds/analysis/*microbiology ; Poultry ; Swine ; Tilapia/*growth & development/metabolism ; },
abstract = {The majority of seafood is farmed, with most finfish coming from freshwater ponds. Ponds are often fertilized to promote microbial productivity as a natural feed source to fish. To understand if pond fertilization with livestock manure induces a probiotic or prebiotic effect, we communally reared tilapia (Oreochromis shiranus), and North African catfish (Clarias gariepinus), for 4 weeks under seven manure treatments including layer chicken, broiler chicken, guinea fowl, quail, pig, cow, vs. commercial feed to evaluate microbial community dynamics of the manure, pond water, and fish feces using 16S and 18S rRNA marker genes along with metagenome sequencing. Catfish growth, but not tilapia, was positively associated with plankton abundance (p = 0.0006, R2 = 0.4887) and greatest in ponds fertilized with quail manure (ANOVA, p < 0.05). Manure was unique and influenced the 16S microbiome in pond water, tilapia gut, and catfish gut and 18S community in pond water and catfish guts (PERMANOVA, p = 0.001). On average, 18.5%, 18.6%, and 45.3% of manure bacteria sOTUs, (sub-operational taxonomic units), were present in the water column, catfish feces, and tilapia feces which comprised 3.7%, 12.8%, and 10.9% of the total microbial richness of the communities, respectively. Antibiotic resistance genes were highest in the manure and water samples followed by tilapia feces and lowest in catfish feces (p < 0.0001). In this study, we demonstrate how the bacterial and eukaryotic microbial composition of fish ponds are influenced by specific livestock manure inputs and that the gut microbiome of tilapia is more sensitive and responsive than catfish to these changes. We conclude that animal manure used as fertilizer induces a primarily prebiotic effect on the pond ecosystem rather than a direct probiotic effect on fish.},
}

Animal Feed/analysis/microbiology
Animals
Aquaculture
Bacteria/classification/genetics/*isolation & purification
Catfishes/*growth & development/metabolism
Cattle
Livestock
Manure/analysis/*microbiology
Microbiota
Ponds/analysis/*microbiology
Poultry
Swine
Tilapia/*growth & development/metabolism

@article {pmid29652573,
year = {2018},
author = {Laudadio, I and Fulci, V and Palone, F and Stronati, L and Cucchiara, S and Carissimi, C},
title = {Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome.},
journal = {Omics : a journal of integrative biology},
volume = {22},
number = {4},
pages = {248-254},
doi = {10.1089/omi.2018.0013},
pmid = {29652573},
issn = {1557-8100},
mesh = {Adolescent ; Child ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The analysis of microbiota composition in humans, animals, and built environments is important because of emerging roles and applications in a broad range of disease and ecological phenotypes. Next Generation Sequencing is the current method of choice to characterize microbial community composition. The taxonomic profile of a microbial community can be obtained either by shotgun analysis of random DNA fragments or through 16S ribosomal RNA gene (rDNA) amplicon sequencing. It has been previously shown that the 16S rDNA amplicon sequencing approach yields quantitatively and qualitatively different results compared to shotgun metagenomics when the two techniques are used to assess microbial community composition on the same samples. However, most of such comparisons were either based on the recovery of 16S rDNA sequences in the shotgun metagenomics data or limited to a single microbiome or synthetic samples. Direct comparison of shotgun metagenomics and 16S rDNA amplicon sequencing on the same samples was performed only once in the recent literature, suggesting that the two methods yield comparable results. Here, we set out to compare the outcome of these two alternative approaches to the microbiome characterization in human gut microbiomes from stool samples. To this end, we processed six different samples with both techniques. We report here that shotgun next generation sequencing metagenomics allows much deeper characterization of the microbiome complexity, allowing identification of a larger number of species for each sample, compared to 16S rDNA amplicon sequencing. Further comparative studies in independent samples are called for.},
}

Adolescent
Child
Computational Biology/methods
Female
*Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing
Humans
Male
*Metagenome
*Metagenomics/methods
*RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid30777011,
year = {2019},
author = {Feng, Y and Ramnarine, VR and Bell, R and Volik, S and Davicioni, E and Hayes, VM and Ren, S and Collins, CC},
title = {Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {146},
doi = {10.1186/s12864-019-5457-z},
pmid = {30777011},
issn = {1471-2164},
support = {CSC201606325044//China Scholarship Council/ ; 201012TFF//Terry Fox Foundation/ ; T2013-01//Prostate Cancer Canada/ ; 81472397//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Prostate cancer (PCa) is the most common malignant neoplasm among men in many countries. Since most precancerous and cancerous tissues show signs of inflammation, chronic bacterial prostatitis has been hypothesized to be a possible etiology. However, establishing a causal relationship between microbial inflammation and PCa requires a comprehensive analysis of the prostate microbiome. The aim of this study was to characterize the microbiome in prostate tissue of PCa patients and investigate its association with tumour clinical characteristics as well as host expression profiles.

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.

CONCLUSIONS: This is the first study of the human prostate microbiome employing an integrated metagenomics and metatranscriptomics approach. In this Chinese cohort, both metagenome and metatranscriptome analyses showed a non-sterile microenvironment in the prostate of PCa patients, but we did not find links between the microbiome and local progression of PCa. However, the correlated expression of Pseudomonas genes and human small RNA genes may provide tantalizing preliminary evidence that Pseudomonas infection may impede metastasis.},
}

@article {pmid30031771,
year = {2018},
author = {Wade, RM and Sherwood, AR},
title = {Updating Plakobranchus cf. ianthobapsus (Gastropoda, Sacoglossa) host use: Diverse algal-animal interactions revealed by NGS with implications for invasive species management.},
journal = {Molecular phylogenetics and evolution},
volume = {128},
number = {},
pages = {172-181},
doi = {10.1016/j.ympev.2018.07.010},
pmid = {30031771},
issn = {1095-9513},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; Gastropoda/*genetics/*parasitology ; Hawaii ; *High-Throughput Nucleotide Sequencing ; *Host-Parasite Interactions ; *Introduced Species ; Likelihood Functions ; Metagenomics ; Phylogeny ; Principal Component Analysis ; },
abstract = {Sacoglossa, the "sap sucking" sea slugs, are highly specialized herbivores and the only metazoans that exhibit kleptoplasty, the sequestration and retention of chloroplasts from algae. Plakobranchus is one of the most generalistic herbivores within this order, with as many as 12 reported "algal host" (i.e. kleptoplast source) species. However, kleptoplast diversity studies conducted on Plakobranchus to date most likely underestimated the full diversity of kleptoplast sources within the studied populations due to limitations of the molecular techniques employed. Here, we apply a high throughput sequencing technique to assess kleptoplast diversity of Plakobranchus cf. ianthobapsus' from 10 sites across the Main Hawaiian Islands during winter and summer seasons. In so doing, we effectively used P. cf. ianthobapsus as a novel sampling tool to explore diminutive algal communities, including the current distribution of the invasive alga "Avrainvillea amadelpha." Our results show that P. cf. ianthobapsus sequesters chloroplasts from 23 algal species from across the siphonous green algal order Bryopsidales. We identified "Avrainvillea amadelpha" and Codium edule as new host species for P. cf. ianthobapusus, but their rarity among the data suggests they were most likely less preferential as hosts and were possibly utilized due to low abundance or unavailability of more preferable species, and therefore a response to starvation risk. Additionally, the identification of the highly invasive siphonous green alga "A. amadelpha" as a kleptoplast source provides new fine-scale range and distribution data for this problematic species. Overall kleptoplast diversity does not differ among sites, except in a coral-dominated, (i.e. not algal dominated) environment, suggesting that siphonous algal assemblages are common in algal-dominated ecosystems in the Hawaiian Islands. Diversity dissimilarity among seasons was recovered from the majority of sites sampled, supporting the need for seasonal data collection in algal diversity assessments. This case study using metabarcoding of sacoglossan kleptoplasts provides deeper insights into these plant-animal interactions with a better understanding of host use than previous studies using traditional molecular methods and illustrates how algal diversity studies on the scale of plastids can have implications for understanding algal community structure and invasive species dynamics.},
}

Animals
Biodiversity
DNA Barcoding, Taxonomic
Gastropoda/*genetics/*parasitology
Hawaii
*High-Throughput Nucleotide Sequencing
*Host-Parasite Interactions
*Introduced Species
Likelihood Functions
Metagenomics
Phylogeny
Principal Component Analysis

@article {pmid29165844,
year = {2018},
author = {Lassalle, F and Spagnoletti, M and Fumagalli, M and Shaw, L and Dyble, M and Walker, C and Thomas, MG and Bamberg Migliano, A and Balloux, F},
title = {Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet.},
journal = {Molecular ecology},
volume = {27},
number = {1},
pages = {182-195},
doi = {10.1111/mec.14435},
pmid = {29165844},
issn = {1365-294X},
support = {BB/H008802/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Department of Health/United Kingdom ; MR/N010760/1//Medical Research Council/United Kingdom ; },
mesh = {Biodiversity ; *Diet, Paleolithic ; *Farmers ; Genetics, Population ; Geography ; *Host-Pathogen Interactions ; Humans ; *Microbiota/genetics ; Mouth/*microbiology ; Philippines ; Principal Component Analysis ; Species Specificity ; },
abstract = {Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in close proximity in the Philippines. Deep shotgun sequencing of salivary DNA generated high-coverage microbiomes along with human genomes. Comparing these microbiomes with publicly available data from individuals living on a Western diet revealed that abundance ratios of core species were significantly correlated with subsistence strategy, with hunter-gatherers and Westerners occupying either end of a gradient of Neisseria against Haemophilus, and traditional farmers falling in between. Species found preferentially in hunter-gatherers included microbes often considered as oral pathogens, despite their hosts' apparent good oral health. Discriminant analysis of gene functions revealed vitamin B5 autotrophy and urease-mediated pH regulation as candidate adaptations of the microbiome to the hunter-gatherer and Western diets, respectively. These results suggest that major transitions in diet selected for different communities of commensals and likely played a role in the emergence of modern oral pathogens.},
}

Biodiversity
*Diet, Paleolithic
*Farmers
Genetics, Population
Geography
*Host-Pathogen Interactions
Humans
*Microbiota/genetics
Mouth/*microbiology
Philippines
Principal Component Analysis
Species Specificity

@article {pmid29113023,
year = {2018},
author = {Andújar, C and Arribas, P and Gray, C and Bruce, C and Woodward, G and Yu, DW and Vogler, AP},
title = {Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill.},
journal = {Molecular ecology},
volume = {27},
number = {1},
pages = {146-166},
doi = {10.1111/mec.14410},
pmid = {29113023},
issn = {1365-294X},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; *Environmental Monitoring ; *Fresh Water ; High-Throughput Nucleotide Sequencing ; Invertebrates/*drug effects ; *Metagenomics ; Pesticides/*toxicity ; Species Specificity ; Water Pollutants, Chemical/*toxicity ; },
abstract = {Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species-level resolution is difficult to obtain. Next-generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 "barcode" and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in the River Kennet (southern England). Operational taxonomic unit (OTU) recovery was tested under 72 parameters (read denoising, filtering, pair merging and clustering). Similar taxonomic profiles were obtained under a broad range of parameters. The SSU marker recovered Platyhelminthes and Nematoda, missed by cox1, while Rotifera were only amplified with cox1. A reference set was created from all available barcode entries for Arthropoda in the BOLD database and clustered into OTUs. The River Kennet metabarcoding produced matches to 207 of these reference OTUs, five times the number of species recognized with morphological monitoring. The increase was due to the following: greater taxonomic resolution (e.g., splitting a single morphotaxon "Chironomidae" into 55 named OTUs); splitting of Linnaean binomials into multiple molecular OTUs; and the use of a filtration-flotation protocol for extraction of minute specimens (meiofauna). Community analyses revealed strong differences between "impacted" vs. "control" samples, detectable with each gene marker, for each major taxonomic group, and for meio- and macrofaunal samples separately. Thus, highly resolved taxonomic data can be extracted at a fraction of the time and cost of traditional nonmolecular methods, opening new avenues for freshwater invertebrate biodiversity monitoring and molecular ecology.},
}

Animals
Biodiversity
DNA Barcoding, Taxonomic/*methods
*Environmental Monitoring
*Fresh Water
High-Throughput Nucleotide Sequencing
Invertebrates/*drug effects
*Metagenomics
Pesticides/*toxicity
Species Specificity
Water Pollutants, Chemical/*toxicity

@article {pmid28779076,
year = {2017},
author = {Yin, D and Du, E and Yuan, J and Gao, J and Wang, Y and Aggrey, SE and Guo, Y},
title = {Supplemental thymol and carvacrol increases ileum Lactobacillus population and reduces effect of necrotic enteritis caused by Clostridium perfringes in chickens.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {7334},
pmid = {28779076},
issn = {2045-2322},
mesh = {Animals ; Chickens ; Clostridium Infections/*veterinary ; Clostridium perfringens/*drug effects ; Dietary Supplements ; Enterocolitis, Necrotizing/*veterinary ; Gastrointestinal Microbiome ; Ileum/microbiology ; Lactobacillus/*drug effects/genetics ; Male ; Metagenome ; Metagenomics/methods ; Monoterpenes/*pharmacology ; Poultry Diseases/*drug therapy/*microbiology/mortality/pathology ; Thymol/*pharmacology ; },
abstract = {Necrotic enteritis (NE) caused by Clostridium perfringens is one of the most detrimental infectious diseases in poultry. This study examined the effect of blends of essential oils (BEOs) (25% thymol and 25% carvacrol) on NE and bacterial dynamics and functions in chicks challenged with C. perfringens. Chicks were assigned to a Control diet and BEOs diet (Control diet + 120 mg/kg BEOs), were challenged with C. perfringens from days 14 to 20 and were killed on day 21 for assessment. Supplementation with BEOs decreased the mortality, alleviated gut lesions, and decreased the virulence factors of pathogenic bacteria (VF 0073-ClpE, VF0124-LPS, and VF0350-BSH). Lack of supplementation also changed the nutrient and immunological dynamics of host microbiota in responding to C. perfringens infection. Adding BEOs changed the host ileum microbial population by increasing the numbers of Lactobacillus crispatus and Lactobacillus agilis, and decreasing Lactobacillus salivarius and Lactobacillus johnsonii. The functional roles of these changing host bacterial populations coupled with the putative reduced pathogenicity of C. perfringens by BEOs contributed to the reduction in gut lesions and mortality in infected chickens. It suggests that dietary supplementation with BEOs could significantly reduce the impact of NE caused by C. perfringens on broilers.},
}

Animals
Chickens
Clostridium Infections/*veterinary
Clostridium perfringens/*drug effects
Dietary Supplements
Enterocolitis, Necrotizing/*veterinary
Gastrointestinal Microbiome
Ileum/microbiology
Lactobacillus/*drug effects/genetics
Male
Metagenome
Metagenomics/methods
Monoterpenes/*pharmacology
Poultry Diseases/*drug therapy/*microbiology/mortality/pathology
Thymol/*pharmacology

@article {pmid28775301,
year = {2017},
author = {Erwin, PM and Rhodes, RG and Kiser, KB and Keenan-Bateman, TF and McLellan, WA and Pabst, DA},
title = {High diversity and unique composition of gut microbiomes in pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {7205},
pmid = {28775301},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Sperm Whale ; Symbiosis ; *Whales ; },
abstract = {Mammals host diverse bacterial and archaeal symbiont communities (i.e. microbiomes) that play important roles in digestive and immune system functioning, yet cetacean microbiomes remain largely unexplored, in part due to sample collection difficulties. Here, fecal samples from stranded pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales were used to characterize the gut microbiomes of two closely-related species with similar diets. 16S rRNA gene sequencing revealed diverse microbial communities in kogiid whales dominated by Firmicutes and Bacteroidetes. Core symbiont taxa were affiliated with phylogenetic lineages capable of fermentative metabolism and sulfate respiration, indicating potential symbiont contributions to energy acquisition during prey digestion. The diversity and phylum-level composition of kogiid microbiomes differed from those previously reported in toothed whales, which exhibited low diversity communities dominated by Proteobacteria and Actinobacteria. Community structure analyses revealed distinct gut microbiomes in K. breviceps and K. sima, driven by differential relative abundances of shared taxa, and unique microbiomes in kogiid hosts compared to other toothed and baleen whales, driven by differences in symbiont membership. These results provide insight into the diversity, composition and structure of kogiid gut microbiomes and indicate that host identity plays an important role in structuring cetacean microbiomes, even at fine-scale taxonomic levels.},
}

Animals
*Biodiversity
*Gastrointestinal Microbiome
Metagenome
Metagenomics/methods
Phylogeny
*Sperm Whale
Symbiosis
*Whales

@article {pmid28720895,
year = {2017},
author = {Liu, J and Techtmann, SM and Woo, HL and Ning, D and Fortney, JL and Hazen, TC},
title = {Rapid Response of Eastern Mediterranean Deep Sea Microbial Communities to Oil.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {5762},
pmid = {28720895},
issn = {2045-2322},
mesh = {Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; Biodiversity ; Geography ; Mediterranean Sea ; Metagenomics/methods ; Microbiota/*drug effects/genetics ; Petroleum/*toxicity ; Petroleum Pollution/*analysis ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; },
abstract = {Deep marine oil spills like the Deepwater Horizon (DWH) in the Gulf of Mexico have the potential to drastically impact marine systems. Crude oil contamination in marine systems remains a concern, especially for countries around the Mediterranean Sea with off shore oil production. The goal of this study was to investigate the response of indigenous microbial communities to crude oil in the deep Eastern Mediterranean Sea (E. Med.) water column and to minimize potential bias associated with storage and shifts in microbial community structure from sample storage. 16S rRNA amplicon sequencing was combined with GeoChip metagenomic analysis to monitor the microbial community changes to the crude oil and dispersant in on-ship microcosms set up immediately after water collection. After 3 days of incubation at 14 °C, the microbial communities from two different water depths: 824 m and 1210 m became dominated by well-known oil degrading bacteria. The archaeal population and the overall microbial community diversity drastically decreased. Similarly, GeoChip metagenomic analysis revealed a tremendous enrichment of genes related to oil biodegradation, which was consistent with the results from the DWH oil spill. These results highlight a rapid microbial adaption to oil contamination in the deep E. Med., and indicate strong oil biodegradation potential.},
}

Archaea/classification/genetics/metabolism
Bacteria/classification/genetics/metabolism
Biodegradation, Environmental
Biodiversity
Geography
Mediterranean Sea
Metagenomics/methods
Microbiota/*drug effects/genetics
Petroleum/*toxicity
Petroleum Pollution/*analysis
Population Dynamics
RNA, Ribosomal, 16S/genetics
Seawater/*microbiology
Sequence Analysis, DNA
*Water Microbiology

@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.},
}

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