@article {pmid30308944,
year = {2018},
author = {Fehlbaum, S and Prudence, K and Kieboom, J and Heerikhuisen, M and van den Broek, T and Schuren, FHJ and Steinert, RE and Raederstorff, D},
title = {In Vitro Fermentation of Selected Prebiotics and Their Effects on the Composition and Activity of the Adult Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {19},
number = {10},
pages = {},
pmid = {30308944},
issn = {1422-0067},
mesh = {*Biodiversity ; Dietary Fiber ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; *Prebiotics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Recently, the concept of prebiotics has been revisited to expand beyond non-digestible oligosaccharides, and the requirements for selective stimulation were extended to include microbial groups other than, and additional to, bifidobacteria and lactobacilli. Here, the gut microbiota-modulating effects of well-known and novel prebiotics were studied. An in vitro fermentation screening platform (i-screen) was inoculated with adult fecal microbiota, exposed to different dietary fibers that had a range of concentrations (inulin, alpha-linked galacto-oligosaccharides (alpha-GOS), beta-linked GOS, xylo-oligosaccharides (XOS) from corn cobs and high-fiber sugar cane, and beta-glucan from oats), and compared to a positive fructo-oligosaccharide (FOS) control and a negative control (no fiber addition). All dietary fibers displayed prebiotic activity, with beta-glucan showing more distinct effects on the microbial composition and metabolism compared to the other fibers. Beta-glucan induced the growth of Prevotella and Roseburia with a concomitant increase in propionate production. Inulin and both forms of GOS and XOS had a strong bifidogenic effect on the microbial composition. A dose-response effect was observed for butyrate when exposed to beta-glucan and inulin. The findings of this study support the potential for alpha-GOS, XOS, and oat beta-glucan to serve as novel prebiotics, due to their association with the positive shifts in microbiome composition and short-chain fatty acid production that point to potential health benefits.},
}

*Biodiversity
Dietary Fiber
Fatty Acids, Volatile/metabolism
Feces/microbiology
Fermentation
*Gastrointestinal Microbiome
Humans
Metagenome
Metagenomics/methods
*Prebiotics
RNA, Ribosomal, 16S/genetics

@article {pmid30250208,
year = {2018},
author = {Pärnänen, K and Karkman, A and Hultman, J and Lyra, C and Bengtsson-Palme, J and Larsson, DGJ and Rautava, S and Isolauri, E and Salminen, S and Kumar, H and Satokari, R and Virta, M},
title = {Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {3891},
pmid = {30250208},
issn = {2041-1723},
mesh = {Anti-Bacterial Agents/*adverse effects ; Antibiotic Prophylaxis/adverse effects ; Breast Feeding ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*genetics ; Humans ; Infant ; Interspersed Repetitive Sequences/*genetics ; Maternal Inheritance ; Metagenomics ; Milk, Human/*microbiology ; Phylogeny ; Time Factors ; },
abstract = {The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers. MGEs in mothers' breast milk are also shared with their own infants. Termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers, which have the potential to affect microbial community composition, are associated with higher abundances of specific ARGs, the composition of which is largely shaped by bacterial phylogeny in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but microbiota composition still strongly impacts the overall resistance load.},
}

Anti-Bacterial Agents/*adverse effects
Antibiotic Prophylaxis/adverse effects
Breast Feeding
Drug Resistance, Bacterial/*genetics
Feces/microbiology
Female
Gastrointestinal Microbiome/drug effects/*genetics
Humans
Infant
Interspersed Repetitive Sequences/*genetics
Maternal Inheritance
Metagenomics
Milk, Human/*microbiology
Phylogeny
Time Factors

@article {pmid30143202,
year = {2018},
author = {Shikata, A and Sermsathanaswadi, J and Thianheng, P and Baramee, S and Tachaapaikoon, C and Waeonukul, R and Pason, P and Ratanakhanokchai, K and Kosugi, A},
title = {Characterization of an Anaerobic, Thermophilic, Alkaliphilic, High Lignocellulosic Biomass-Degrading Bacterial Community, ISHI-3, Isolated from Biocompost.},
journal = {Enzyme and microbial technology},
volume = {118},
number = {},
pages = {66-75},
doi = {10.1016/j.enzmictec.2018.07.001},
pmid = {30143202},
issn = {1879-0909},
mesh = {Alkalies/chemistry ; Animals ; Bacteria, Anaerobic/growth & development ; *Biomass ; Cattle ; *Composting ; Lignin/*metabolism ; Metagenome ; *Microbial Consortia ; Oryza/*metabolism/microbiology ; Phylogeny ; Temperature ; Zea mays/*metabolism/microbiology ; },
abstract = {The generation of a complex microbial consortium is a promising approach for efficient biomass decomposition. An anaerobic thermophilic alkaliphilic microbial consortium with efficient degradation ability was screened from bovine manure compost using non-pretreated milling corn stover (CS) and rice straw (RS). A stable microbial consortium ISHI-3 with high degradation ability for CS and RS was isolated by the roll tube technique. ISHI-3 comprised Herbivorax saccincola and bacteria belonging to the classes Pelotomaculum, Tepidanaerobacter, and Tepidimicrobium, as determined by DGGE of the PCR-generated 16S rRNA genes. Furthermore, metagenomics analysis using a 16S rRNA library was carried out to determine the bacterial distribution during degradation of CS and RS. H. saccincola and bacteria belonging to Pelotomaculum were relatively abundant in the beginning to middle periods of culture with CS and RS whereas bacteria belonging to Tepidanaerobacter and Tepidimicrobium gradually increased in the population during the later stages. To understand the role of non-cellulolytic bacteria in the consortium, novel strains ET1 and GL4, which were most closely related to Tepidimicrobium ferriphilum and Tepidanaerobacter acetatoxydans, were isolated from ISHI-3. Based on their carbon source usage, morphology, and phylogenetic analysis, we propose that strains ET1 and GL4 should be classified as a novel genus or species. Bacteria ET1 and GL4 can utilize different organic compounds as carbon and energy sources such as organic acids, alcohols, sugars, and amino acids, showing a preference for organic acids and alcohols rather than sugars such as glucose and cellobiose. These results indicated that ET1 and GL4 help to accelerate efficient lignocellulose degradation of H. saccincola.},
}

Alkalies/chemistry
Animals
Bacteria, Anaerobic/growth & development
*Biomass
Cattle
*Composting
Lignin/*metabolism
Metagenome
*Microbial Consortia
Oryza/*metabolism/microbiology
Phylogeny
Temperature
Zea mays/*metabolism/microbiology

@article {pmid30353943,
year = {2018},
author = {Sonoda, A and Kamiyama, N and Ozaka, S and Gendo, Y and Ozaki, T and Hirose, H and Noguchi, K and Saechue, B and Sachi, N and Sakai, K and Mizukami, K and Hidano, S and Murakami, K and Kobayashi, T},
title = {Oral administration of antibiotics results in fecal occult bleeding due to metabolic disorders and defective proliferation of the gut epithelial cell in mice.},
journal = {Genes to cells : devoted to molecular & cellular mechanisms},
volume = {23},
number = {12},
pages = {1043-1055},
doi = {10.1111/gtc.12649},
pmid = {30353943},
issn = {1365-2443},
support = {//Suzuken Memorial Foundation/ ; 15K08953//Japan Society for the Promotion of Science/ ; 15K19577//Japan Society for the Promotion of Science/ ; 16K01872//Japan Society for the Promotion of Science/ ; 17H04649//Japan Society for the Promotion of Science/ ; 17H17104//Japan Society for the Promotion of Science/ ; 17K08695//Japan Society for the Promotion of Science/ ; 17K08889//Japan Society for the Promotion of Science/ ; 17K15954//Japan Society for the Promotion of Science/ ; 17K16346//Japan Society for the Promotion of Science/ ; //GlaxoSmithKline/ ; },
mesh = {Administration, Oral ; Ampicillin/administration & dosage/pharmacology ; Animals ; Anti-Bacterial Agents/*administration & dosage/*adverse effects ; Antimicrobial Cationic Peptides/metabolism ; Butyric Acid/pharmacology ; Carbohydrate Metabolism/drug effects ; Cecum/microbiology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Colon/*pathology ; Colonic Neoplasms/pathology ; Cytokines/metabolism ; Epithelial Cells/*pathology ; Glutamine/administration & dosage ; Lipid Metabolism/drug effects ; Macrophages/drug effects/metabolism ; Metabolic Diseases/*complications ; Metabolome/drug effects ; Metagenomics ; Mice ; Microbiota/drug effects/genetics ; *Occult Blood ; RAW 264.7 Cells ; Regeneration/drug effects ; Sodium Glutamate/administration & dosage ; Species Specificity ; Vancomycin/administration & dosage/pharmacology ; },
abstract = {Antibiotics sometimes exert adverse effects on the pathogenesis of colitis due to the dysbiosis resulting from the disruption of gut homeostasis. However, the precise mechanisms underlying colitogenic effects of antibiotic-induced colitis are largely unknown. Here, we show a novel murine fecal occult bleeding model induced by the combinatorial treatment of ampicillin and vancomycin, which is accompanied by an enlarged cecum, upregulation of pro-inflammatory cytokines IL-6 and IL-12, a reduction in Ki-67-positive epithelial cell number and an increase in the apoptotic cell number in the colon. Moreover, gas chromatography-tandem mass analysis showed that various kinds of metabolites, including glutamic acid and butyric acid, were significantly decreased in the cecal contents. In addition, abundance of butyric acid producer Clostridiales was dramatically reduced in the enlarged cecum. Interestingly, supplementation of monosodium glutamate or its precursor glutamine suppressed colonic IL-6 and IL-12, protected from cell apoptosis and prevented fecal occult blood indicating that the reduced level of glutamic acid is a possible mechanism of antibiotic-induced fecal occult bleeding. Our data showed a novel mechanism of antibiotic-induced fecal occult bleeding providing a new insight into the clinical application of glutamic acid for the treatment of antibiotic-induced colitis.},
}

Administration, Oral
Ampicillin/administration & dosage/pharmacology
Animals
Anti-Bacterial Agents/*administration & dosage/*adverse effects
Antimicrobial Cationic Peptides/metabolism
Butyric Acid/pharmacology
Carbohydrate Metabolism/drug effects
Cecum/microbiology
Cell Line, Tumor
Cell Proliferation/drug effects
Colon/*pathology
Colonic Neoplasms/pathology
Cytokines/metabolism
Epithelial Cells/*pathology
Glutamine/administration & dosage
Lipid Metabolism/drug effects
Macrophages/drug effects/metabolism
Metabolic Diseases/*complications
Metabolome/drug effects
Metagenomics
Mice
Microbiota/drug effects/genetics
*Occult Blood
RAW 264.7 Cells
Regeneration/drug effects
Sodium Glutamate/administration & dosage
Species Specificity
Vancomycin/administration & dosage/pharmacology

@article {pmid30036363,
year = {2018},
author = {Chai, H and Jiang, H and Lin, L and Liu, L},
title = {A marginalized two-part Beta regression model for microbiome compositional data.},
journal = {PLoS computational biology},
volume = {14},
number = {7},
pages = {e1006329},
pmid = {30036363},
issn = {1553-7358},
mesh = {Animals ; Colony Count, Microbial ; Likelihood Functions ; *Logistic Models ; Metagenomics ; Mice ; *Microbiota ; Skin/*microbiology ; },
abstract = {In microbiome studies, an important goal is to detect differential abundance of microbes across clinical conditions and treatment options. However, the microbiome compositional data (quantified by relative abundance) are highly skewed, bounded in [0, 1), and often have many zeros. A two-part model is commonly used to separate zeros and positive values explicitly by two submodels: a logistic model for the probability of a specie being present in Part I, and a Beta regression model for the relative abundance conditional on the presence of the specie in Part II. However, the regression coefficients in Part II cannot provide a marginal (unconditional) interpretation of covariate effects on the microbial abundance, which is of great interest in many applications. In this paper, we propose a marginalized two-part Beta regression model which captures the zero-inflation and skewness of microbiome data and also allows investigators to examine covariate effects on the marginal (unconditional) mean. We demonstrate its practical performance using simulation studies and apply the model to a real metagenomic dataset on mouse skin microbiota. We find that under the proposed marginalized model, without loss in power, the likelihood ratio test performs better in controlling the type I error than those under conventional methods.},
}

Animals
Colony Count, Microbial
Likelihood Functions
*Logistic Models
Metagenomics
Mice
*Microbiota
Skin/*microbiology

@article {pmid30017197,
year = {2018},
author = {He, F and Liu, D and Zhai, J and Zhang, L and Ma, Y and Xu, Y and Rong, K and Ma, J},
title = {Metagenomic analysis revealed the effects of goat milk feeding and breast feeding on the gut microbiome of Amur tiger cubs.},
journal = {Biochemical and biophysical research communications},
volume = {503},
number = {4},
pages = {2590-2596},
doi = {10.1016/j.bbrc.2018.07.020},
pmid = {30017197},
issn = {1090-2104},
mesh = {Animals ; Animals, Newborn ; Bacteria/isolation & purification ; Feeding Behavior ; *Gastrointestinal Microbiome ; *Goats/microbiology ; Metagenomics/*methods ; *Milk ; *Tigers/microbiology ; },
abstract = {BACKGROUND: Ingredients in breast milk can help establish a healthy community of microorganisms in the infant gut, but no research exists regarding the effects of goat milk feeding and breast feeding on the gut microbiome of the Amur tiger, which is one of the most endangered species in the world.

METHODS: In this study, we used whole-metagenome shotgun sequencing to analyze the effects of two different feeding patterns, goat milk feeding and breast feeding, on the composition and functional structures of gut microbiota in Amur tiger cubs.

RESULTS: Goat milk-fed cubs have fewer beneficial bacteria and more pathogenic bacteria and a higher microbial diversity in their gut than breastfed cubs. A total of 15 genera showed statistically significant differences; the relative abundances of Streptomyces scabiei, Streptomyces avermitilis and Streptomyces davawensis were significantly decreased, whereas those of Niabella soli, Aeromonas media and Brochothrix thermosphacta were significantly increased in the goat milk-fed group compared with those in the breastfed group. At the functional level, carbohydrate metabolism, translation and replication and repair decreased, and amino acid metabolism, membrane transport and metabolism of cofactors and vitamins increased in the gut microbiota of goat milk-fed cubs compared with breastfed cubs.

CONCLUSION: Our results indicate for the first time that the different milk feeding patterns of goat milk feeding and breast feeding can change the composition and functional structures of gut microbiota in Amur tiger cubs and that breastfed tiger cubs and goat milk-fed tiger cubs have distinct microbiotas in their guts.},
}

Animals
Animals, Newborn
Bacteria/isolation & purification
Feeding Behavior
*Gastrointestinal Microbiome
*Goats/microbiology
Metagenomics/*methods
*Milk
*Tigers/microbiology

@article {pmid29890228,
year = {2018},
author = {Poussin, C and Sierro, N and Boué, S and Battey, J and Scotti, E and Belcastro, V and Peitsch, MC and Ivanov, NV and Hoeng, J},
title = {Interrogating the microbiome: experimental and computational considerations in support of study reproducibility.},
journal = {Drug discovery today},
volume = {23},
number = {9},
pages = {1644-1657},
doi = {10.1016/j.drudis.2018.06.005},
pmid = {29890228},
issn = {1878-5832},
mesh = {Animals ; Computational Biology/*methods ; Crowdsourcing ; Data Accuracy ; Humans ; *Metagenome/genetics ; Metagenomics/*methods ; *Microbiota/genetics ; Reproducibility of Results ; *Research Design ; Workflow ; },
abstract = {The microbiome is an important factor in human health and disease and is investigated to develop novel therapeutics. Metagenomics leverages advances in sequencing technologies and computational analysis to identify and quantify the microorganisms present in a sample. This field has, however, not yet reached maturity and the international metagenomics community, aware of the current limitations and of the necessity for standardization, has started investigating sources of variability in experimental and computational workflows. The first studies have already resulted in the identification of crucial steps and factors affecting metagenomics data quality, quantification and interpretation. This review summarizes experimental and computational considerations for interrogating the microbiome and establishing reproducible and robust analysis workflows.},
}

Animals
Computational Biology/*methods
Crowdsourcing
Data Accuracy
Humans
*Metagenome/genetics
Metagenomics/*methods
*Microbiota/genetics
Reproducibility of Results
*Research Design
Workflow

@article {pmid29554948,
year = {2018},
author = {Walsh, AM and Crispie, F and O'Sullivan, O and Finnegan, L and Claesson, MJ and Cotter, PD},
title = {Species classifier choice is a key consideration when analysing low-complexity food microbiome data.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {50},
pmid = {29554948},
issn = {2049-2618},
support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; 11/PI/1137//Science Foundation Ireland/Ireland ; 13/SIRG/2160//Science Foundation Ireland/Ireland ; },
mesh = {Bacteria/classification/*genetics ; Base Sequence/genetics ; Computational Biology/methods ; DNA, Bacterial/*genetics ; Food Microbiology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with respect to choice of species classification tool, platform, or sequencing depth. Here, we benchmarked the performances of three high-throughput short-read sequencing platforms, the Illumina MiSeq, NextSeq 500, and Ion Proton, for shotgun metagenomics of food microbiota. Briefly, we sequenced six kefir DNA samples and a mock community DNA sample, the latter constructed by evenly mixing genomic DNA from 13 food-related bacterial species. A variety of bioinformatic tools were used to analyse the data generated, and the effects of sequencing depth on these analyses were tested by randomly subsampling reads.

RESULTS: Compositional analysis results were consistent between the platforms at divergent sequencing depths. However, we observed pronounced differences in the predictions from species classification tools. Indeed, PERMANOVA indicated that there was no significant differences between the compositional results generated by the different sequencers (p = 0.693, R2 = 0.011), but there was a significant difference between the results predicted by the species classifiers (p = 0.01, R2 = 0.127). The relative abundances predicted by the classifiers, apart from MetaPhlAn2, were apparently biased by reference genome sizes. Additionally, we observed varying false-positive rates among the classifiers. MetaPhlAn2 had the lowest false-positive rate, whereas SLIMM had the greatest false-positive rate. Strain-level analysis results were also similar across platforms. Each platform correctly identified the strains present in the mock community, but accuracy was improved slightly with greater sequencing depth. Notably, PanPhlAn detected the dominant strains in each kefir sample above 500,000 reads per sample. Again, the outputs from functional profiling analysis using SUPER-FOCUS were generally accordant between the platforms at different sequencing depths. Finally, and expectedly, metagenome assembly completeness was significantly lower on the MiSeq than either on the NextSeq (p = 0.03) or the Proton (p = 0.011), and it improved with increased sequencing depth.

CONCLUSIONS: Our results demonstrate a remarkable similarity in the results generated by the three sequencing platforms at different sequencing depths, and, in fact, the choice of bioinformatics methodology had a more evident impact on results than the choice of sequencer did.},
}

Bacteria/classification/*genetics
Base Sequence/genetics
Computational Biology/methods
DNA, Bacterial/*genetics
Food Microbiology/*methods
High-Throughput Nucleotide Sequencing/*methods
Metagenome/genetics
Metagenomics/*methods
Microbiota/*genetics
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA/*methods

@article {pmid29499759,
year = {2018},
author = {Eng, A and Borenstein, E},
title = {Taxa-function robustness in microbial communities.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {45},
pmid = {29499759},
issn = {2049-2618},
support = {DP2 AT007802/AT/NCCIH NIH HHS/United States ; DP2 AT007802-01//National Institutes of Health (US)/International ; },
mesh = {Bacteria/*classification/*genetics ; Biodiversity ; Cellular Microenvironment/*physiology ; Computer Simulation ; Environment ; Female ; Gastrointestinal Tract/microbiology ; Humans ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Vagina/microbiology ; },
abstract = {BACKGROUND: The species composition of a microbial community is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies. These perturbations to a community's taxonomic profile naturally also alter the community's functional profile-the aggregate set of genes encoded by community members-ultimately altering the community's overall functional capacities. The magnitude of such functional changes and the specific shift that will occur in each function, however, are strongly dependent on how genes are distributed across community members' genomes. This gene distribution, in turn, is determined by the taxonomic composition of the community and would markedly differ, for example, between communities composed of species with similar genomic content vs. communities composed of species whose genomes encode relatively distinct gene sets. Combined, these observations suggest that community functional robustness to taxonomic perturbations could vary widely across communities with different compositions, yet, to date, a systematic study of the inherent link between community composition and robustness is lacking.

RESULTS: In this study, we examined how a community's taxonomic composition influences the robustness of that community's functional profile to taxonomic perturbation (here termed taxa-function robustness) across a wide array of environments. Using a novel simulation-based computational model to quantify this taxa-function robustness in host-associated and non-host-associated communities, we find notable differences in robustness between communities inhabiting different body sites, including significantly higher robustness in gut communities compared to vaginal communities that cannot be attributed solely to differences in species richness. We additionally find between-site differences in the robustness of specific functions, some of which are potentially related to site-specific environmental conditions. These taxa-function robustness differences are most strongly associated with differences in overall functional redundancy, though other aspects of gene distribution also influence taxa-function robustness in certain body environments, and are sufficient to cluster communities by environment. Further analysis revealed a correspondence between our robustness estimates and taxonomic and functional shifts observed across human-associated communities.

CONCLUSIONS: Our analysis approach revealed intriguing taxa-function robustness variation across environments and identified features of community and gene distribution that impact robustness. This approach could be further applied for estimating taxa-function robustness in novel communities and for informing the design of synthetic communities with specific robustness requirements.},
}

Bacteria/*classification/*genetics
Biodiversity
Cellular Microenvironment/*physiology
Computer Simulation
Environment
Female
Gastrointestinal Tract/microbiology
Humans
Metagenomics
Microbiota/*genetics
Phylogeny
RNA, Ribosomal, 16S/genetics
Vagina/microbiology

@article {pmid29482646,
year = {2018},
author = {Louca, S and Doebeli, M and Parfrey, LW},
title = {Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {41},
pmid = {29482646},
issn = {2049-2618},
mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Base Sequence/genetics ; Gene Dosage/*genetics ; Genome, Bacterial/genetics ; Humans ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; },
abstract = {The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology. Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions of bacterial and archaeal taxa in microbial communities. Because different organisms contain different 16S gene copy numbers (GCNs), sequence variant counts are biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods and based on sequenced genomes, in order to correct for these biases. However, the accuracy of those predictions has not been independently assessed. Here, we systematically evaluate the predictability of 16S GCNs across bacterial and archaeal clades, based on ∼ 6,800 public sequenced genomes and using several phylogenetic methods. Further, we assess the accuracy of GCNs predicted by three recently published tools (PICRUSt, CopyRighter, and PAPRICA) over a wide range of taxa and for 635 microbial communities from varied environments. We find that regardless of the phylogenetic method tested, 16S GCNs could only be accurately predicted for a limited fraction of taxa, namely taxa with closely to moderately related representatives (≲15% divergence in the 16S rRNA gene). Consistent with this observation, we find that all considered tools exhibit low predictive accuracy when evaluated against completely sequenced genomes, in some cases explaining less than 10% of the variance. Substantial disagreement was also observed between tools (R2<0.5) for the majority of tested microbial communities. The nearest sequenced taxon index (NSTI) of microbial communities, i.e., the average distance to a sequenced genome, was a strong predictor for the agreement between GCN prediction tools on non-animal-associated samples, but only a moderate predictor for animal-associated samples. We recommend against correcting for 16S GCNs in microbiome surveys by default, unless OTUs are sufficiently closely related to sequenced genomes or unless a need for true OTU proportions warrants the additional noise introduced, so that community profiles remain interpretable and comparable between studies.},
}

Archaea/classification/*genetics
Bacteria/classification/*genetics
Base Sequence/genetics
Gene Dosage/*genetics
Genome, Bacterial/genetics
Humans
Metagenomics/methods
Microbiota/*genetics
Phylogeny
RNA, Ribosomal, 16S/*genetics
Sequence Analysis, DNA

@article {pmid29482639,
year = {2018},
author = {Marotz, CA and Sanders, JG and Zuniga, C and Zaramela, LS and Knight, R and Zengler, K},
title = {Improving saliva shotgun metagenomics by chemical host DNA depletion.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {42},
pmid = {29482639},
issn = {2049-2618},
support = {R21 AR071731/AR/NIAMS NIH HHS/United States ; AR071731/AR/NIAMS NIH HHS/United States ; n/a//Center for Microbiome Innovation/International ; },
mesh = {Azides/*chemistry ; Bacteria/genetics ; DNA/*chemistry ; Fungi/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Propidium/*analogs & derivatives/chemistry ; Saliva/*microbiology ; Sequence Analysis, DNA ; Viruses/genetics ; },
abstract = {BACKGROUND: Shotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencing approaches that assess taxonomy but not function and are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in microbial populations because few DNA sequence reads are from the microbial component. We developed and optimized a novel method for enriching microbial DNA from human oral samples and compared its efficiency and potential taxonomic bias with commercially available kits.

RESULTS: Three commercially available host depletion kits were directly compared with size filtration and a novel method involving osmotic lysis and treatment with propidium monoazide (lyPMA) in human saliva samples. We evaluated the percentage of shotgun metagenomic sequencing reads aligning to the human genome, and taxonomic biases of those not aligning, compared to untreated samples. lyPMA was the most efficient method of removing host-derived sequencing reads compared to untreated sample (8.53 ± 0.10% versus 89.29 ± 0.03%). Furthermore, lyPMA-treated samples exhibit the lowest taxonomic bias compared to untreated samples.

CONCLUSION: Osmotic lysis followed by PMA treatment is a cost-effective, rapid, and robust method for enriching microbial sequence data in shotgun metagenomics from fresh and frozen saliva samples and may be extensible to other host-derived sample types.},
}

Azides/*chemistry
Bacteria/genetics
DNA/*chemistry
Fungi/genetics
High-Throughput Nucleotide Sequencing
Humans
Metagenomics/*methods
Microbiota/*genetics
Propidium/*analogs & derivatives/chemistry
Saliva/*microbiology
Sequence Analysis, DNA
Viruses/genetics

@article {pmid29469169,
year = {2018},
author = {Fountain, MT and Bennett, J and Cobo-Medina, M and Conde Ruiz, R and Deakin, G and Delgado, A and Harrison, R and Harrison, N},
title = {Alimentary microbes of winter-form Drosophila suzukii.},
journal = {Insect molecular biology},
volume = {27},
number = {3},
pages = {383-392},
doi = {10.1111/imb.12377},
pmid = {29469169},
issn = {1365-2583},
mesh = {Animals ; DNA, Ribosomal Spacer/analysis ; Drosophila/*microbiology ; England ; *Gastrointestinal Microbiome ; *Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seasons ; },
abstract = {Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a damaging pest of fruit. Reproductively diapausing adults overwinter in woodlands and remain active on warmer winter days. It is unknown if this adult phase of the lifecycle feeds during the winter period, and what the food source may be. This study characterized the flora in the digestive tract of D. suzukii using a metagenomics approach. Live D. suzukii were trapped in four woodlands in the south of England and their guts dissected for DNA extraction and amplicon-based metagenomics sequencing (internal transcribed spacer and 16S rRNA). Analysis at genus and family taxonomic levels showed high levels of diversity with no differences in digestive tract bacterial or fungal biota between woodland sites of winter-form D. suzukii. Female D. suzukii at one site appeared to have higher bacterial diversity in the alimentary canal than males, but there was a site, sex interaction. Many of the biota were associated with cold, wet climatic conditions and decomposition. This study provides the first evidence that winter-form D. suzukii may be opportunistic feeders during the winter period and are probably exploiting food sources associated with moisture on decomposing vegetation during this time. A core gut microbiome has been identified for winter-form D. suzukii.},
}

Animals
DNA, Ribosomal Spacer/analysis
Drosophila/*microbiology
England
*Gastrointestinal Microbiome
*Metagenome
RNA, Bacterial/analysis
RNA, Ribosomal, 16S/analysis
Seasons

@article {pmid28866243,
year = {2018},
author = {Heeney, DD and Gareau, MG and Marco, ML},
title = {Intestinal Lactobacillus in health and disease, a driver or just along for the ride?.},
journal = {Current opinion in biotechnology},
volume = {49},
number = {},
pages = {140-147},
pmid = {28866243},
issn = {1879-0429},
support = {R01 AT009365/AT/NCCIH NIH HHS/United States ; },
mesh = {Animals ; Behavior ; Biodiversity ; Cognition ; *Disease ; *Health ; Humans ; Intestines/*microbiology ; Lactobacillus/*physiology ; },
abstract = {Metagenomics and related methods have led to significant advances in our understanding of the human microbiome. Members of the genus Lactobacillus, although best understood for essential roles in food fermentations and applications as probiotics, have also come to the fore in a number of untargeted gut microbiome studies in humans and animals. Even though Lactobacillus is only a minor member of the human colonic microbiota, the proportions of those bacteria are frequently either positively or negatively correlated with human disease and chronic conditions. Recent findings on Lactobacillus species in human and animal microbiome research, together with the increased knowledge on probiotic and other ingested lactobacilli, have resulted in new perspectives on the importance of this genus to human health.},
}

Animals
Behavior
Biodiversity
Cognition
*Disease
*Health
Humans
Intestines/*microbiology
Lactobacillus/*physiology

@article {pmid29793542,
year = {2018},
author = {Li, LG and Yin, X and Zhang, T},
title = {Tracking antibiotic resistance gene pollution from different sources using machine-learning classification.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {93},
pmid = {29793542},
issn = {2049-2618},
support = {172099/14E//Hong Kong General Research Fund/International ; },
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; China ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Machine Learning ; Metagenomics ; Sewage/*microbiology ; Soil Microbiology ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) has been a worldwide public health concern. Current widespread AMR pollution has posed a big challenge in accurately disentangling source-sink relationship, which has been further confounded by point and non-point sources, as well as endogenous and exogenous cross-reactivity under complicated environmental conditions. Because of insufficient capability in identifying source-sink relationship within a quantitative framework, traditional antibiotic resistance gene (ARG) signatures-based source-tracking methods would hardly be a practical solution.

RESULTS: By combining broad-spectrum ARG profiling with machine-learning classification SourceTracker, here we present a novel way to address the question in the era of high-throughput sequencing. Its potential in extensive application was firstly validated by 656 global-scale samples covering diverse environmental types (e.g., human/animal gut, wastewater, soil, ocean) and broad geographical regions (e.g., China, USA, Europe, Peru). Its potential and limitations in source prediction as well as effect of parameter adjustment were then rigorously evaluated by artificial configurations with representative source proportions. When applying SourceTracker in region-specific analysis, excellent performance was achieved by ARG profiles in two sample types with obvious different source compositions, i.e., influent and effluent of wastewater treatment plant. Two environmental metagenomic datasets of anthropogenic interference gradient further supported its potential in practical application. To complement general-profile-based source tracking in distinguishing continuous gradient pollution, a few generalist and specialist indicator ARGs across ecotypes were identified in this study.

CONCLUSION: We demonstrated for the first time that the developed source-tracking platform when coupling with proper experiment design and efficient metagenomic analysis tools will have significant implications for assessing AMR pollution. Following predicted source contribution status, risk ranking of different sources in ARG dissemination will be possible, thereby paving the way for establishing priority in mitigating ARG spread and designing effective control strategies.},
}

Animals
Anti-Bacterial Agents/*pharmacology
Bacteria/*drug effects/*genetics
China
Drug Resistance, Microbial/*genetics
Gastrointestinal Microbiome/*genetics
High-Throughput Nucleotide Sequencing
Humans
*Machine Learning
Metagenomics
Sewage/*microbiology
Soil Microbiology

@article {pmid29793532,
year = {2018},
author = {Bilen, M and Dufour, JC and Lagier, JC and Cadoret, F and Daoud, Z and Dubourg, G and Raoult, D},
title = {The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {94},
pmid = {29793532},
issn = {2049-2618},
mesh = {Actinobacteria/isolation & purification ; Archaea/*classification/genetics/*isolation & purification ; Bacteria/*classification/genetics/*isolation & purification ; Bacteroidetes/isolation & purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Firmicutes/isolation & purification ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics ; Proteobacteria/isolation & purification ; },
abstract = {After a decade of research and metagenomic analyses, our knowledge of the human microbiota appears to have reached a plateau despite promising results. In many studies, culture has proven to be essential in describing new prokaryotic species and filling metagenomic gaps. In 2015, only 2172 different prokaryotic species were reported to have been isolated at least once from the human body as pathogens or commensals. In this review, we update the previous repertoire by reporting the different species isolated from the human body to date, increasing it by 28% to reach a total of 2776 species associated with human beings. They have been classified into 11 different phyla, mostly the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Finally, culturomics contributed up to 66.2% towards updating this repertoire by reporting 400 species, of which 288 were novel. This demonstrates the need to continue the culturing work, which seems essential in order to decipher the hidden human microbial content.},
}

Actinobacteria/isolation & purification
Archaea/*classification/genetics/*isolation & purification
Bacteria/*classification/genetics/*isolation & purification
Bacteroidetes/isolation & purification
DNA, Archaeal/genetics
DNA, Bacterial/genetics
Firmicutes/isolation & purification
Gastrointestinal Microbiome/*genetics
Humans
Metagenomics
Proteobacteria/isolation & purification

@article {pmid29789015,
year = {2018},
author = {Panebianco, C and Andriulli, A and Pazienza, V},
title = {Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {92},
pmid = {29789015},
issn = {2049-2618},
support = {RC1703GA31//Ministero della Salute/International ; RC1503GA40//Ministero della Salute/International ; },
mesh = {Antineoplastic Agents/*metabolism/*therapeutic use ; Bacteria/*metabolism ; Dysbiosis/*chemically induced ; Gastrointestinal Microbiome/*physiology ; Humans ; Intestines/microbiology ; Neoplasms/*drug therapy/microbiology ; Prebiotics ; Probiotics/*therapeutic use ; Synbiotics ; },
abstract = {Cancer is a major health burden worldwide, and despite continuous advances in medical therapies, resistance to standard drugs and adverse effects still represent an important cause of therapeutic failure. There is a growing evidence that gut bacteria can affect the response to chemo- and immunotherapeutic drugs by modulating either efficacy or toxicity. Moreover, intratumor bacteria have been shown to modulate chemotherapy response. At the same time, anticancer treatments themselves significantly affect the microbiota composition, thus disrupting homeostasis and exacerbating discomfort to the patient. Here, we review the existing knowledge concerning the role of the microbiota in mediating chemo- and immunotherapy efficacy and toxicity and the ability of these therapeutic options to trigger dysbiotic condition contributing to the severity of side effects. In addition, we discuss the use of probiotics, prebiotics, synbiotics, postbiotics, and antibiotics as emerging strategies for manipulating the microbiota in order to improve therapeutic outcome or at least ensure patients a better quality of life all along of anticancer treatments.},
}

Antineoplastic Agents/*metabolism/*therapeutic use
Bacteria/*metabolism
Dysbiosis/*chemically induced
Gastrointestinal Microbiome/*physiology
Humans
Intestines/microbiology
Neoplasms/*drug therapy/microbiology
Prebiotics
Probiotics/*therapeutic use
Synbiotics

@article {pmid29636439,
year = {2018},
author = {Brown, CT and Xiong, W and Olm, MR and Thomas, BC and Baker, R and Firek, B and Morowitz, MJ and Hettich, RL and Banfield, JF},
title = {Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.},
journal = {mBio},
volume = {9},
number = {2},
pages = {},
pmid = {29636439},
issn = {2150-7511},
support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R01 GM103600/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/*chemistry/classification/genetics ; Biota ; Enterocolitis, Necrotizing/microbiology/pathology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; *Hospitalization ; Humans ; Infant, Newborn ; *Infant, Premature ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Proteome/*analysis ; Proteomics ; },
abstract = {During the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC), a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants. In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context.IMPORTANCE Humans are colonized by microbes at birth, a process that is important to health and development. However, much remains to be known about the fine-scale microbial dynamics that occur during the colonization period. We conducted a genome-resolved study of microbial community composition, replication rates, and proteomes during the first 3 months of life of both healthy and sick premature infants. Infants were found to be colonized by similar microbes, but each underwent a distinct colonization trajectory. Interestingly, related microbes colonizing different infants were found to have distinct proteomes, indicating that microbiome function is not only driven by which organisms are present, but also largely depends on microbial responses to the unique set of physiological conditions in the infant gut.},
}

Bacteria/*chemistry/classification/genetics
Biota
Enterocolitis, Necrotizing/microbiology/pathology
Feces/microbiology
Female
*Gastrointestinal Microbiome
*Hospitalization
Humans
Infant, Newborn
*Infant, Premature
Male
Metagenome
Metagenomics
*Microbiota
Proteome/*analysis
Proteomics

@article {pmid28730353,
year = {2018},
author = {Vieira, FR and Pecchia, JA},
title = {An Exploration into the Bacterial Community under Different Pasteurization Conditions during Substrate Preparation (Composting-Phase II) for Agaricus bisporus Cultivation.},
journal = {Microbial ecology},
volume = {75},
number = {2},
pages = {318-330},
pmid = {28730353},
issn = {1432-184X},
support = {005707/2012-05//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Agaricus/*growth & development/metabolism ; Bacteria/classification/genetics/growth & development/*isolation & purification ; Biodiversity ; Composting ; Culture Media/*chemistry/metabolism ; DNA, Bacterial/genetics ; Hot Temperature ; Pasteurization/instrumentation/*methods ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; },
abstract = {Substrate preparation (i.e., composting) for Agaricus bisporus cultivation is the most critical point of mushroom production. Among many factors involved in the composting process, the microbial ecology of the system is the underlying drive of composting and can be influenced by composting management techniques. Pasteurization temperature at the beginning of phase II, in theory, may influence the bacterial community and subsequently the "selectivity" and nutrition of the final substrate. Therefore, this hypothesis was tested by simulation in bioreactors under different pasteurization conditions (57 °C/6 h, 60 °C/2 h, and 68 °C/2 h), simulating conditions adopted by many producers. Bacterial diversity, based on 16S ribosomal RNA obtained by high-throughput sequencing and classified in operational taxonomic units (OTUs), was greater than previously reported using culture-dependent methods. Alpha diversity estimators show a lower diversity of OTUs under a high-temperature pasteurization condition. Bacillales order shows a relatively higher OTU abundance under a high-pasteurization temperature, which also was related to high ammonia emission measurements. On the other hand, beta diversity analysis showed no significantly changes in the bacterial community structure under different conditions. Agaricus bisporus mycelium growth during a standard spawn run period was significantly slower in the compost pasteurized at high temperature. Since the bacterial community structure was not greatly affected by different pasteurization conditions but by-products left (e.g., ammonia) at the end of compost conditioning varied, further studies need to be conducted to determine the functional role of the microbial communities found during substrate preparation for Agaricus bisporus cultivation.},
}

Agaricus/*growth & development/metabolism
Bacteria/classification/genetics/growth & development/*isolation & purification
Biodiversity
Composting
Culture Media/*chemistry/metabolism
DNA, Bacterial/genetics
Hot Temperature
Pasteurization/instrumentation/*methods
RNA, Ribosomal, 16S/genetics
Soil/*chemistry
Soil Microbiology

@article {pmid30413473,
year = {2019},
author = {Coscolín, C and Katzke, N and García-Moyano, A and Navarro-Fernández, J and Almendral, D and Martínez-Martínez, M and Bollinger, A and Bargiela, R and Gertler, C and Chernikova, TN and Rojo, D and Barbas, C and Tran, H and Golyshina, OV and Koch, R and Yakimov, MM and Bjerga, GEK and Golyshin, PN and Jaeger, KE and Ferrer, M},
title = {Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {2},
pages = {},
doi = {10.1128/AEM.02404-18},
pmid = {30413473},
issn = {1098-5336},
abstract = {Amination of bulky ketones, particularly in (R) configuration, is an attractive chemical conversion; however, known ω-transaminases (ω-TAs) show insufficient levels of performance. By applying two screening methods, we discovered 10 amine transaminases from the class III ω-TA family that were 38% to 76% identical to homologues. We present examples of such enzymes preferring bulky ketones over keto acids and aldehydes with stringent (S) selectivity. We also report representatives from the class III ω-TAs capable of converting (R) and (S) amines and bulky ketones and one that can convert amines with longer alkyl substituents. The preference for bulky ketones was associated with the presence of a hairpin region proximal to the conserved Arg414 and residues conforming and close to it. The outward orientation of Arg414 additionally favored the conversion of (R) amines. This configuration was also found to favor the utilization of putrescine as an amine donor, so that class III ω-TAs with Arg414 in outward orientation may participate in vivo in the catabolism of putrescine. The positioning of the conserved Ser231 also contributes to the preference for amines with longer alkyl substituents. Optimal temperatures for activity ranged from 45 to 65°C, and a few enzymes retained ≥50% of their activity in water-soluble solvents (up to 50% [vol/vol]). Hence, our results will pave the way to design, in the future, new class III ω-TAs converting bulky ketones and (R) amines for the production of high-value products and to screen for those converting putrescine.IMPORTANCE Amine transaminases of the class III ω-TAs are key enzymes for modification of chemical building blocks, but finding those capable of converting bulky ketones and (R) amines is still challenging. Here, by an extensive analysis of the substrate spectra of 10 class III ω-TAs, we identified a number of residues playing a role in determining the access and positioning of bulky ketones, bulky amines, and (R)- and (S) amines, as well as of environmentally relevant polyamines, particularly putrescine. The results presented can significantly expand future opportunities for designing (R)-specific class III ω-TAs to convert valuable bulky ketones and amines, as well as for deepening the knowledge into the polyamine catabolic pathways.},
}

@article {pmid29988102,
year = {2018},
author = {Sfanos, KS and Markowski, MC and Peiffer, LB and Ernst, SE and White, JR and Pienta, KJ and Antonarakis, ES and Ross, AE},
title = {Compositional differences in gastrointestinal microbiota in prostate cancer patients treated with androgen axis-targeted therapies.},
journal = {Prostate cancer and prostatic diseases},
volume = {21},
number = {4},
pages = {539-548},
pmid = {29988102},
issn = {1476-5608},
support = {16CHAL13//Prostate Cancer Foundation (PCF)/International ; 16CHAL13//Prostate Cancer Foundation (PCF)/International ; 16CHAL13//Prostate Cancer Foundation (PCF)/International ; W81XWH-13-PCRP-CCA//U.S. Department of Defense (DOD)/International ; },
mesh = {Aged ; Aged, 80 and over ; Androgen Antagonists/*pharmacology/therapeutic use ; Androgens/*metabolism ; Antineoplastic Agents, Hormonal/*pharmacology/therapeutic use ; Biodiversity ; Cross-Sectional Studies ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Molecular Targeted Therapy ; Prostatic Neoplasms/drug therapy/metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: It is well known that the gastrointestinal (GI) microbiota can influence the metabolism, pharmacokinetics, and toxicity of cancer therapies. Conversely, the effect of cancer treatments on the composition of the GI microbiota is poorly understood. We hypothesized that oral androgen receptor axis-targeted therapies (ATT), including bicalutamide, enzalutamide, and abiraterone acetate, may be associated with compositional differences in the GI microbiota.

METHODS: We profiled the fecal microbiota in a cross-sectional study of 30 patients that included healthy male volunteers and men with different clinical states of prostate cancer (i.e., localized, biochemically recurrent, and metastatic disease) using 16S rDNA amplicon sequencing. Functional inference of identified taxa was performed using PICRUSt.

RESULTS: We report a significant difference in alpha diversity in GI microbiota among men with versus without a prostate cancer diagnosis. Further analysis identified significant compositional differences in the GI microbiota of men taking ATT, including a greater abundance of species previously linked to response to anti-PD-1 immunotherapy such as Akkermansia muciniphila and Ruminococcaceae spp. In functional analyses, we found an enriched representation of bacterial gene pathways involved in steroid biosynthesis and steroid hormone biosynthesis in the fecal microbiota of men taking oral ATT.

CONCLUSIONS: There are measurable differences in the GI microbiota of men receiving oral ATT. We speculate that oral hormonal therapies for prostate cancer may alter the GI microbiota, influence clinical responses to ATT, and/or potentially modulate the antitumor effects of future therapies including immunotherapy. Given our findings, larger, longitudinal studies are warranted.},
}

Aged
Aged, 80 and over
Androgen Antagonists/*pharmacology/therapeutic use
Androgens/*metabolism
Antineoplastic Agents, Hormonal/*pharmacology/therapeutic use
Biodiversity
Cross-Sectional Studies
Gastrointestinal Microbiome/*drug effects
Humans
Male
Metagenome
Metagenomics/methods
Middle Aged
Molecular Targeted Therapy
Prostatic Neoplasms/drug therapy/metabolism/*microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid30619130,
year = {2018},
author = {Timmers, PHA and Vavourakis, CD and Kleerebezem, R and Damsté, JSS and Muyzer, G and Stams, AJM and Sorokin, DY and Plugge, CM},
title = {Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3039},
doi = {10.3389/fmicb.2018.03039},
pmid = {30619130},
issn = {1664-302X},
abstract = {Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H2 and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was 'Candidatus Syntrophonatronum acetioxidans,' and a near-complete draft genome of this SAOB was reconstructed. 'Ca. S. acetioxidans' has all genes necessary for operating the Wood-Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na+-dependent ATP synthase and marker genes for 'salt-out' strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of 'Ca. S. acetioxidans' showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA gene amplicon datasets of the soda lake sediments showed a high similarity of reads to 'Ca. S. acetioxidans' with abundance as high as 1.3% of all reads, whereas aceticlastic methanogens and acetate oxidizing sulfate-reducers were not abundant (≤0.1%) or could not be detected. These combined results indicate that SAO is the primary anaerobic acetate oxidizing pathway at extreme haloalkaline conditions performed by haloalkaliphilic syntrophic consortia.},
}

@article {pmid30342053,
year = {2018},
author = {Vallianou, NG and Stratigou, T and Tsagarakis, S},
title = {Microbiome and diabetes: Where are we now?.},
journal = {Diabetes research and clinical practice},
volume = {146},
number = {},
pages = {111-118},
doi = {10.1016/j.diabres.2018.10.008},
pmid = {30342053},
issn = {1872-8227},
mesh = {Animals ; Diabetes Mellitus, Type 2/*microbiology ; Dysbiosis/*microbiology ; Fecal Microbiota Transplantation/*methods ; Gastrointestinal Microbiome/*genetics ; Humans ; Mice ; Prebiotics/*microbiology ; Probiotics/*metabolism ; },
abstract = {Alterations in the diversity or structure of gut microbiota known as dysbiosis, may affect metabolic activities, resulting in metabolic disorders, such as obesity and diabetes. The development of more sophisticated methods, such as metagenomics sequencing, PCR-denaturing gradient gel electrophoresis, microarrays and fluorescence in situ hybridization, has expanded our knowledge on gut microbiome. Dysbiosis has been related to increased plasma concentrations of gut microbiota-derived lipopolysaccharide (LPS), which triggers the production of a variety of cytokines and the recruitment of inflammatory cells. Metabolomics have demonstrated that butyrate and propionate suppress weight gain in mice with high fat diet-induced obesity, and acetate has been proven to reduce food intake in healthy mice. The role of prebiotics, probiotics, genetically modified bacteria and fecal microbiota transplantation, as potential therapeutic challenges for type 2 diabetes will be discussed in this review.},
}

Animals
Diabetes Mellitus, Type 2/*microbiology
Dysbiosis/*microbiology
Fecal Microbiota Transplantation/*methods
Gastrointestinal Microbiome/*genetics
Humans
Mice
Prebiotics/*microbiology
Probiotics/*metabolism

@article {pmid28659635,
year = {2017},
author = {Hosomi, K and Ohno, H and Murakami, H and Natsume-Kitatani, Y and Tanisawa, K and Hirata, S and Suzuki, H and Nagatake, T and Nishino, T and Mizuguchi, K and Miyachi, M and Kunisawa, J},
title = {Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4339},
pmid = {28659635},
issn = {2045-2322},
mesh = {Adult ; Bacteria/classification/genetics ; *Biodiversity ; Feces/microbiology ; Female ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Young Adult ; },
abstract = {Metagenomic analysis based on the 16S rRNA gene is generally performed to examine the diversity and abundance of commensal bacteria in feces, which is now recognized to be associated with human health and diseases. Guanidine thiocyanate (GuSCN) solution is used as a less onerous way compared with a frozen method to transport and stock fecal samples at room temperature for DNA analysis; however, optimal methods to measure fecal bacterial composition in GuSCN solution remain to be investigated. Here, we examined the influence of various factors such as pretreatment (e.g., removing GuSCN solution and washing feces with phosphate-buffered saline (PBS) before mechanical lysis), fecal concentration in the GuSCN solution, storage time, and position of fecal subsampling on the 16S rRNA-based analysis of fecal bacteria in GuSCN solution. We found that pretreatment and fecal concentration affected the bacterial composition, and a little change was noted with subsampling position. Based on these results, we propose a basic protocol, including fecal sampling, sample storage, and DNA extraction, for the 16S rRNA-based analysis of bacterial composition in feces suspended in GuSCN solution.},
}

Adult
Bacteria/classification/genetics
*Biodiversity
Feces/microbiology
Female
Humans
Male
*Metagenome
*Metagenomics/methods
*Microbiota
Middle Aged
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Young Adult

@article {pmid30240699,
year = {2018},
author = {Harris, L and van Zyl, LJ and Kirby-McCullough, BM and Damelin, LH and Tiemessen, CT and Trindade, M},
title = {Identification and sequence analysis of two novel cryptic plasmids isolated from the vaginal mucosa of South African women.},
journal = {Plasmid},
volume = {98},
number = {},
pages = {56-62},
doi = {10.1016/j.plasmid.2018.09.008},
pmid = {30240699},
issn = {1095-9890},
mesh = {DNA, Bacterial/*genetics ; Female ; Humans ; Lactobacillus/classification/*genetics/*isolation & purification/metabolism ; Microbiota ; Mucous Membrane/*microbiology ; Phylogeny ; Plasmids/chemistry/*genetics ; Sequence Analysis, DNA ; South Africa/epidemiology ; Vagina/*microbiology ; Vaginosis, Bacterial/epidemiology/*microbiology ; },
abstract = {The vaginal mucosa is dominated by Gram positive, rod shaped lactobacilli which serve as a natural barrier against infection. In both healthy- and bacterial vaginosis (BV)-infected women Lactobacillus crispatus and Lactobacillus jensenii have been found to be the predominant Lactobacillus species. Many studies have been conducted to assess factors influencing lactobacilli dominance in the vaginal microbiome. In the present study two plasmids, pLc4 and pLc17, isolated from vaginal Lactobacillus strains of both healthy and BV-infected women were characterized. The smaller plasmid, pLc4 (4224 bp), was detected in both L. crispatus and L. jensenii strains, while pLc17 was only detected in L. crispatus. Based on its nucleotide sequence pLc4 appears highly novel, with its replication protein having 44% identity to the replication initiation protein of pSMQ173b_03. Phylogenetic analysis with other Rolling Circle Replication plasmids confirmed that pLc4 shows a low degree of similarity to these plasmids. Plasmid pLc17 (16,663 bp) appears to carry both a RCR replicon and a theta replicon, which is rare in naturally occurring plasmids. pLc4 was maintained at a high copy number of 29, while pLc17 appears to be a medium copy number plasmid maintained at 11 copies per chromosome. While sequence analysis is a valuable tool to study cryptic plasmids, further function-based analysis will be required in order to fully elucidate the role of these plasmids within the vaginal milieu.},
}

DNA, Bacterial/*genetics
Female
Humans
Lactobacillus/classification/*genetics/*isolation & purification/metabolism
Microbiota
Mucous Membrane/*microbiology
Phylogeny
Plasmids/chemistry/*genetics
Sequence Analysis, DNA
South Africa/epidemiology
Vagina/*microbiology
Vaginosis, Bacterial/epidemiology/*microbiology

@article {pmid30309375,
year = {2018},
author = {Zepeda Mendoza, ML and Roggenbuck, M and Manzano Vargas, K and Hansen, LH and Brunak, S and Gilbert, MTP and Sicheritz-Pontén, T},
title = {Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.},
journal = {Acta veterinaria Scandinavica},
volume = {60},
number = {1},
pages = {61},
pmid = {30309375},
issn = {1751-0147},
support = {R52-A5062//Lundbeckfonden/ ; },
mesh = {Adaptation, Biological ; Animals ; Animals, Wild/microbiology ; Bacteria/classification/genetics/*isolation & purification ; Falconiformes/*microbiology/physiology ; *Feeding Behavior ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Skin/*microbiology ; },
abstract = {BACKGROUND: Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut.

RESULTS: We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut.

CONCLUSIONS: Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.},
}

Adaptation, Biological
Animals
Animals, Wild/microbiology
Bacteria/classification/genetics/*isolation & purification
Falconiformes/*microbiology/physiology
*Feeding Behavior
Gastrointestinal Tract/*microbiology
*Microbiota
Skin/*microbiology

@article {pmid30091981,
year = {2018},
author = {Bradley, PH and Nayfach, S and Pollard, KS},
title = {Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.},
journal = {PLoS computational biology},
volume = {14},
number = {8},
pages = {e1006242},
pmid = {30091981},
issn = {1553-7358},
support = {T32 GM067547/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/genetics ; Gastrointestinal Microbiome/*genetics/physiology ; Gene Expression Regulation, Bacterial/genetics ; Genes, Microbial/genetics ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; },
abstract = {The mechanisms by which different microbes colonize the healthy human gut versus other body sites, the gut in disease states, or other environments remain largely unknown. Identifying microbial genes influencing fitness in the gut could lead to new ways to engineer probiotics or disrupt pathogenesis. We approach this problem by measuring the statistical association between a species having a gene and the probability that the species is present in the gut microbiome. The challenge is that closely related species tend to be jointly present or absent in the microbiome and also share many genes, only a subset of which are involved in gut adaptation. We show that this phylogenetic correlation indeed leads to many false discoveries and propose phylogenetic linear regression as a powerful solution. To apply this method across the bacterial tree of life, where most species have not been experimentally phenotyped, we use metagenomes from hundreds of people to quantify each species' prevalence in and specificity for the gut microbiome. This analysis reveals thousands of genes potentially involved in adaptation to the gut across species, including many novel candidates as well as processes known to contribute to fitness of gut bacteria, such as acid tolerance in Bacteroidetes and sporulation in Firmicutes. We also find microbial genes associated with a preference for the gut over other body sites, which are significantly enriched for genes linked to fitness in an in vivo competition experiment. Finally, we identify gene families associated with higher prevalence in patients with Crohn's disease, including Proteobacterial genes involved in conjugation and fimbria regulation, processes previously linked to inflammation. These gene targets may represent new avenues for modulating host colonization and disease. Our strategy of combining metagenomics with phylogenetic modeling is general and can be used to identify genes associated with adaptation to any environment.},
}

Bacteria/genetics
Gastrointestinal Microbiome/*genetics/physiology
Gene Expression Regulation, Bacterial/genetics
Genes, Microbial/genetics
Humans
Metagenome
Metagenomics/*methods
Microbiota/genetics
Phylogeny

@article {pmid30504906,
year = {2018},
author = {Wampach, L and Heintz-Buschart, A and Fritz, JV and Ramiro-Garcia, J and Habier, J and Herold, M and Narayanasamy, S and Kaysen, A and Hogan, AH and Bindl, L and Bottu, J and Halder, R and Sjöqvist, C and May, P and Andersson, AF and de Beaufort, C and Wilmes, P},
title = {Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {5091},
doi = {10.1038/s41467-018-07631-x},
pmid = {30504906},
issn = {2041-1723},
mesh = {Cesarean Section ; Delivery, Obstetric ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; In Vitro Techniques ; Infant, Newborn ; Infectious Disease Transmission, Vertical ; Interleukin-18/metabolism ; Lipopolysaccharides/metabolism ; Metagenomics/methods ; Pregnancy ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {The rate of caesarean section delivery (CSD) is increasing worldwide. It remains unclear whether disruption of mother-to-neonate transmission of microbiota through CSD occurs and whether it affects human physiology. Here we perform metagenomic analysis of earliest gut microbial community structures and functions. We identify differences in encoded functions between microbiomes of vaginally delivered (VD) and CSD neonates. Several functional pathways are over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis. We link these enriched functions to individual-specific strains, which are transmitted from mothers to neonates in case of VD. The stimulation of primary human immune cells with LPS isolated from early stool samples of VD neonates results in higher levels of tumour necrosis factor (TNF-α) and interleukin 18 (IL-18). Accordingly, the observed levels of TNF-α and IL-18 in neonatal blood plasma are higher after VD. Taken together, our results support that CSD disrupts mother-to-neonate transmission of specific microbial strains, linked functional repertoires and immune-stimulatory potential during a critical window for neonatal immune system priming.},
}

Cesarean Section
Delivery, Obstetric
Female
Gastrointestinal Microbiome/genetics/*physiology
Humans
In Vitro Techniques
Infant, Newborn
Infectious Disease Transmission, Vertical
Interleukin-18/metabolism
Lipopolysaccharides/metabolism
Metagenomics/methods
Pregnancy
Tumor Necrosis Factor-alpha/metabolism

@article {pmid30459421,
year = {2018},
author = {Xu, J and Zhang, Y and Zhang, P and Trivedi, P and Riera, N and Wang, Y and Liu, X and Fan, G and Tang, J and Coletta-Filho, HD and Cubero, J and Deng, X and Ancona, V and Lu, Z and Zhong, B and Roper, MC and Capote, N and Catara, V and Pietersen, G and Vernière, C and Al-Sadi, AM and Li, L and Yang, F and Xu, X and Wang, J and Yang, H and Jin, T and Wang, N},
title = {The structure and function of the global citrus rhizosphere microbiome.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {4894},
pmid = {30459421},
issn = {2041-1723},
mesh = {Bacteria/classification/genetics ; Citrus/*microbiology ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/genetics ; Metagenome/genetics ; Metagenomics/classification/methods ; Microbiota/*genetics ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; },
abstract = {Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.},
}

Bacteria/classification/genetics
Citrus/*microbiology
DNA, Ribosomal Spacer/genetics
Fungi/classification/genetics
Metagenome/genetics
Metagenomics/classification/methods
Microbiota/*genetics
Phylogeny
Plant Roots/*microbiology
RNA, Ribosomal, 16S/genetics
*Rhizosphere
*Soil Microbiology

@article {pmid30308248,
year = {2018},
author = {Hessler, T and Harrison, STL and Huddy, RJ},
title = {Stratification of microbial communities throughout a biological sulphate reducing up-flow anaerobic packed bed reactor, revealed through 16S metagenomics.},
journal = {Research in microbiology},
volume = {169},
number = {10},
pages = {543-551},
doi = {10.1016/j.resmic.2018.09.003},
pmid = {30308248},
issn = {1769-7123},
mesh = {Anaerobiosis ; Bacteria/classification/*genetics/isolation & purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Bioreactors/*microbiology ; DNA, Bacterial/genetics ; Genome, Bacterial ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sulfur Compounds/*metabolism ; },
abstract = {Biological sulphate reduction (BSR) is a promising low-cost treatment of acid rock drainage effluents. In this paper, the system performance and microbial ecology of a lactate supplemented BSR up-flow anaerobic packed bed reactor (UAPBR) are evaluated across reactor height and compared to a continuous stirred tank reactor (CSTR). The biomass concentrations of planktonic and biofilm communities were quantified and subsequently characterised by 16S rRNA gene amplicon sequencing. The defined microbial communities were shown to correlate with differing availability of lactate, volatile fatty acids produced from lactate degradation and sulphate concentration. The UAPBR was able to achieve near complete sulphate conversion at a 4-day hydraulic residence time (HRT) at a sulphate feed concentration of 10.41 mM (1 g/L). The high volumetric sulphate reduction rate of 0.184 mM/L.h achieved in the first third of the reactor was attributed to OTUs present in the planktonic and biofilm communities. While the scavenging of sulphate within the final third of the UAPBR was attributed to an acetate oxidising genus of SRB which was not detected in the lactate-fed CSTR. The detailed analyses of the microbial communities throughout the UAPBR and CSTR contribute to the growing understanding of the impact of the microbial communities of BSR reactors on system performance.},
}

Anaerobiosis
Bacteria/classification/*genetics/isolation & purification/*metabolism
Biodegradation, Environmental
Biodiversity
Bioreactors/*microbiology
DNA, Bacterial/genetics
Genome, Bacterial
Metagenomics
Oxidation-Reduction
Phylogeny
RNA, Ribosomal, 16S/*genetics
Sulfur Compounds/*metabolism

@article {pmid30597002,
year = {2018},
author = {Choi, I and Ponsero, AJ and Bomhoff, M and Youens-Clark, K and Hartman, JH and Hurwitz, BL},
title = {Libra: scalable k-mer based tool for massive all-vs-all metagenome comparisons.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giy165},
pmid = {30597002},
issn = {2047-217X},
abstract = {Background: Shotgun metagenomics provides powerful insights into microbial community biodiversity and function. Yet, inferences from metagenomic studies are often limited by dataset size and complexity and are restricted by the availability and completeness of existing databases. De novo comparative metagenomics enables the comparison of metagenomes based on their total genetic content.

Results: We developed a tool called Libra that performs an all-vs-all comparison of metagenomes for precise clustering based on their k-mer content. Libra uses a scalable Hadoop framework for massive metagenome comparisons, Cosine Similarity for calculating the distance using sequence composition and abundance while normalizing for sequencing depth, and a web-based implementation in iMicrobe (http://imicrobe.us) that uses the CyVerse advanced cyberinfrastructure to promote broad use of the tool by the scientific community.

Conclusions: A comparison of Libra to equivalent tools using both simulated and real metagenomic datasets, ranging from 80 million to 4.2 billion reads, reveals that methods commonly implemented to reduce compute time for large datasets-such as data reduction, read count normalization, and presence/absence distance metrics-greatly diminish the resolution of large-scale comparative analyses. In contrast, Libra uses all of the reads to calculate k-mer abundance in a Hadoop architecture that can scale to any size dataset to enable global-scale analyses and link microbial signatures to biological processes.},
}

@article {pmid30479342,
year = {2018},
author = {Ramani, S and Stewart, CJ and Laucirica, DR and Ajami, NJ and Robertson, B and Autran, CA and Shinge, D and Rani, S and Anandan, S and Hu, L and Ferreon, JC and Kuruvilla, KA and Petrosino, JF and Venkataram Prasad, BV and Bode, L and Kang, G and Estes, MK},
title = {Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {5010},
pmid = {30479342},
issn = {2041-1723},
support = {R01 AI036040/AI/NIAID NIH HHS/United States ; R01 AI105101/AI/NIAID NIH HHS/United States ; R37 AI036040/AI/NIAID NIH HHS/United States ; },
mesh = {Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Milk, Human/*chemistry/*microbiology ; Oligosaccharides/*metabolism ; Rotavirus/pathogenicity ; Rotavirus Infections/immunology/*microbiology ; Rotavirus Vaccines/immunology ; },
abstract = {Neonatal rotavirus infections are predominantly asymptomatic. While an association with gastrointestinal symptoms has been described in some settings, factors influencing differences in clinical presentation are not well understood. Using multidisciplinary approaches, we show that a complex interplay between human milk oligosaccharides (HMOs), milk microbiome, and infant gut microbiome impacts neonatal rotavirus infections. Validating in vitro studies where HMOs are not decoy receptors for neonatal strain G10P[11], population studies show significantly higher levels of Lacto-N-tetraose (LNT), 2'-fucosyllactose (2'FL), and 6'-siallylactose (6'SL) in milk from mothers of rotavirus-positive neonates with gastrointestinal symptoms. Further, these HMOs correlate with abundance of Enterobacter/Klebsiella in maternal milk and infant stool. Specific HMOs also improve the infectivity of a neonatal strain-derived rotavirus vaccine. This study provides molecular and translational insight into host factors influencing neonatal rotavirus infections and identifies maternal components that could promote the performance of live, attenuated rotavirus vaccines.},
}

Feces/microbiology
*Gastrointestinal Microbiome
Humans
Infant, Newborn
Milk, Human/*chemistry/*microbiology
Oligosaccharides/*metabolism
Rotavirus/pathogenicity
Rotavirus Infections/immunology/*microbiology
Rotavirus Vaccines/immunology

@article {pmid30478343,
year = {2018},
author = {Regan, T and Barnett, MW and Laetsch, DR and Bush, SJ and Wragg, D and Budge, GE and Highet, F and Dainat, B and de Miranda, JR and Watson, M and Blaxter, M and Freeman, TC},
title = {Characterisation of the British honey bee metagenome.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {4995},
pmid = {30478343},
issn = {2041-1723},
mesh = {Animals ; Bees/*genetics/microbiology ; Contig Mapping ; Genetic Variation ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; Symbiosis/genetics ; United Kingdom ; },
abstract = {The European honey bee (Apis mellifera) plays a major role in pollination and food production. Honey bee health is a complex product of the environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of these factors will help manage modern challenges to bee health. Here we used DNA sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from across Britain. Low heterozygosity was observed in many Scottish colonies which had high similarity to the native dark bee. Colonies exhibited high diversity in composition and relative abundance of individual microbiome taxa. Most non-bee sequences were derived from known honey bee commensal bacteria or pathogens. However, DNA was also detected from additional fungal, protozoan and metazoan species. To classify cobionts lacking genomic information, we developed a novel network analysis approach for clustering orphan DNA contigs. Our analyses shed light on microbial communities associated with honey bees and demonstrate the power of high-throughput, directed metagenomics for identifying novel biological threats in agroecosystems.},
}

Animals
Bees/*genetics/microbiology
Contig Mapping
Genetic Variation
*Metagenome
Metagenomics
Microbiota/genetics
Sequence Analysis, DNA
Symbiosis/genetics
United Kingdom

@article {pmid29902201,
year = {2018},
author = {Li, X and Naser, SA and Khaled, A and Hu, H and Li, X},
title = {When old metagenomic data meet newly sequenced genomes, a case study.},
journal = {PloS one},
volume = {13},
number = {6},
pages = {e0198773},
pmid = {29902201},
issn = {1932-6203},
support = {R15 GM123407/GM/NIGMS NIH HHS/United States ; },
mesh = {Colitis/genetics/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; *Metagenomics ; *Whole Genome Sequencing ; },
abstract = {Dozens of computational methods are developed to identify species present in a metagenomic dataset. Many of these computational methods depend on available sequenced microbial species, which are still far from being representative. To see how newly sequenced genomes affect the analysis results, we re-analyzed a shotgun metagenomic dataset composed of twelve colitis free metagenomic samples and ten colitis-related metagenomic samples. Unexpectedly, we identified at least two new phyla that may relate to colitis development in patients, together with the phylum identified previously. Compared with the previously identified phylum that differed between the two types of samples, the differences associated with the two new phyla are statistically more significant. Moreover, the abundance of the two new phyla correlates more with the severity of colitis. Surprisingly, even by repeating the analyses implemented in the previous study, we found that at least one main conclusion in the previous study is not supported. Our study indicates the importance of re-analysis of the generated metagenomic datasets and the necessity of considering multiple updated tools in metagenomic studies. It also sheds light on the limitations of the popular tools used currently and the importance to infer the presence of taxa without relying upon available sequenced genomes.},
}

Colitis/genetics/*microbiology
Feces/microbiology
Gastrointestinal Microbiome/*genetics
Humans
*Metagenome
*Metagenomics
*Whole Genome Sequencing

@article {pmid29899081,
year = {2019},
author = {Aron-Wisnewsky, J and Prifti, E and Belda, E and Ichou, F and Kayser, BD and Dao, MC and Verger, EO and Hedjazi, L and Bouillot, JL and Chevallier, JM and Pons, N and Le Chatelier, E and Levenez, F and Ehrlich, SD and Dore, J and Zucker, JD and Clément, K},
title = {Major microbiota dysbiosis in severe obesity: fate after bariatric surgery.},
journal = {Gut},
volume = {68},
number = {1},
pages = {70-82},
doi = {10.1136/gutjnl-2018-316103},
pmid = {29899081},
issn = {1468-3288},
mesh = {Adult ; *Bariatric Surgery ; Biomarkers/blood ; Chromatography, Liquid ; Comorbidity ; Dysbiosis/*etiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Mass Spectrometry ; Metagenomics ; Obesity, Morbid/*microbiology/*surgery ; Phenotype ; Prospective Studies ; Risk Factors ; },
abstract = {OBJECTIVES: Decreased gut microbial gene richness (MGR) and compositional changes are associated with adverse metabolism in overweight or moderate obesity, but lack characterisation in severe obesity. Bariatric surgery (BS) improves metabolism and inflammation in severe obesity and is associated with gut microbiota modifications. Here, we characterised severe obesity-associated dysbiosis (ie, MGR, microbiota composition and functional characteristics) and assessed whether BS would rescue these changes.

DESIGN: Sixty-one severely obese subjects, candidates for adjustable gastric banding (AGB, n=20) or Roux-en-Y-gastric bypass (RYGB, n=41), were enrolled. Twenty-four subjects were followed at 1, 3 and 12 months post-BS. Gut microbiota and serum metabolome were analysed using shotgun metagenomics and liquid chromatography mass spectrometry (LC-MS). Confirmation groups were included.

RESULTS: Low gene richness (LGC) was present in 75% of patients and correlated with increased trunk-fat mass and comorbidities (type 2 diabetes, hypertension and severity). Seventy-eight metagenomic species were altered with LGC, among which 50% were associated with adverse body composition and metabolic phenotypes. Nine serum metabolites (including glutarate, 3-methoxyphenylacetic acid and L-histidine) and functional modules containing protein families involved in their metabolism were strongly associated with low MGR. BS increased MGR 1 year postsurgery, but most RYGB patients remained with low MGR 1 year post-BS, despite greater metabolic improvement than AGB patients.

CONCLUSIONS: We identified major gut microbiota alterations in severe obesity, which include decreased MGR and related functional pathways linked with metabolic deteriorations. The lack of full rescue post-BS calls for additional strategies to improve the gut microbiota ecosystem and microbiome-host interactions in severe obesity.

TRIAL REGISTRATION NUMBER: NCT01454232.},
}

Adult
*Bariatric Surgery
Biomarkers/blood
Chromatography, Liquid
Comorbidity
Dysbiosis/*etiology
Female
*Gastrointestinal Microbiome
Humans
Male
Mass Spectrometry
Metagenomics
Obesity, Morbid/*microbiology/*surgery
Phenotype
Prospective Studies
Risk Factors

@article {pmid29690922,
year = {2018},
author = {Jaenicke, S and Albaum, SP and Blumenkamp, P and Linke, B and Stoye, J and Goesmann, A},
title = {Flexible metagenome analysis using the MGX framework.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {76},
pmid = {29690922},
issn = {2049-2618},
mesh = {*Database Management Systems ; *Metagenome ; Metagenomics/*methods ; Microbiota ; Reproducibility of Results ; User-Computer Interface ; Workflow ; },
abstract = {BACKGROUND: The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as metagenomics; in particular, the recent advances in sequencing technologies have enabled researchers to study even the most complex communities. Metagenome analysis, the assignment of sequences to taxonomic and functional entities, however, remains a tedious task: large amounts of data need to be processed. There are a number of approaches addressing particular aspects, but scientific questions are often too specific to be answered by a general-purpose method.

RESULTS: We present MGX, a flexible and extensible client/server-framework for the management and analysis of metagenomic datasets; MGX features a comprehensive set of adaptable workflows required for taxonomic and functional metagenome analysis, combined with an intuitive and easy-to-use graphical user interface offering customizable result visualizations. At the same time, MGX allows to include own data sources and devise custom analysis pipelines, thus enabling researchers to perform basic as well as highly specific analyses within a single application.

CONCLUSIONS: With MGX, we provide a novel metagenome analysis platform giving researchers access to the most recent analysis tools. MGX covers taxonomic and functional metagenome analysis, statistical evaluation, and a wide range of visualizations easing data interpretation. Its default taxonomic classification pipeline provides equivalent or superior results in comparison to existing tools.},
}

*Database Management Systems
*Metagenome
Metagenomics/*methods
Microbiota
Reproducibility of Results
User-Computer Interface
Workflow

@article {pmid29685174,
year = {2018},
author = {Fan, X and Peters, BA and Jacobs, EJ and Gapstur, SM and Purdue, MP and Freedman, ND and Alekseyenko, AV and Wu, J and Yang, L and Pei, Z and Hayes, RB and Ahn, J},
title = {Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {59},
pmid = {29685174},
issn = {2049-2618},
support = {R01 CA159036/CA/NCI NIH HHS/United States ; U01CA182370/CA/NCI NIH HHS/United States ; R21CA183887/CA/NCI NIH HHS/United States ; Pancreas Cancer Action Network Career Development Award//American Association for Cancer Research/International ; P30CA016087/CA/NCI NIH HHS/United States ; R03CA159414/CA/NCI NIH HHS/United States ; R01CA159036/CA/NCI NIH HHS/United States ; R01CA164964/CA/NCI NIH HHS/United States ; R01 CA164964/CA/NCI NIH HHS/United States ; },
mesh = {Adult ; Aged ; Aged, 80 and over ; *Alcohol Drinking ; Female ; Humans ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Public Health Surveillance ; RNA, Ribosomal, 16S/genetics ; United States ; },
abstract = {BACKGROUND: Dysbiosis of the oral microbiome can lead to local oral disease and potentially to cancers of the head, neck, and digestive tract. However, little is known regarding exogenous factors contributing to such microbial imbalance.

RESULTS: We examined the impact of alcohol consumption on the oral microbiome in a cross-sectional study of 1044 US adults. Bacterial 16S rRNA genes from oral wash samples were amplified, sequenced, and assigned to bacterial taxa. We tested the association of alcohol drinking level (non-drinker, moderate drinker, or heavy drinker) and type (liquor, beer, or wine) with overall microbial composition and individual taxon abundance. The diversity of oral microbiota and overall bacterial profiles differed between heavy drinkers and non-drinkers (α-diversity richness p = 0.0059 and β-diversity unweighted UniFrac p = 0.0036), and abundance of commensal order Lactobacillales tends to be decreased with higher alcohol consumption (fold changes = 0.89 and 0.94 for heavy and moderate drinkers, p trend = 0.005 [q = 0.064]). Additionally, certain genera were enriched in subjects with higher alcohol consumption, including Actinomyces, Leptotrichia, Cardiobacterium, and Neisseria; some of these genera contain oral pathogens, while Neisseria can synthesize the human carcinogen acetaldehyde from ethanol. Wine drinkers may differ from non-drinkers in microbial diversity and profiles (α-diversity richness p = 0.048 and β-diversity unweighted UniFrac p = 0.059) after controlling for drinking amount, while liquor and beer drinkers did not. All significant differences between drinkers and non-drinkers remained after exclusion of current smokers.

CONCLUSIONS: Our results, from a large human study of alcohol consumption and the oral microbiome, indicate that alcohol consumption, and heavy drinking in particular, may influence the oral microbiome composition. These findings may have implications for better understanding the potential role that oral bacteria play in alcohol-related diseases.},
}

Adult
Aged
Aged, 80 and over
*Alcohol Drinking
Female
Humans
Male
Metagenome
Metagenomics
*Microbiota
Middle Aged
Mouth/*microbiology
Public Health Surveillance
RNA, Ribosomal, 16S/genetics
United States

@article {pmid29684865,
year = {2018},
author = {Kurokawa, S and Kishimoto, T and Mizuno, S and Masaoka, T and Naganuma, M and Liang, KC and Kitazawa, M and Nakashima, M and Shindo, C and Suda, W and Hattori, M and Kanai, T and Mimura, M},
title = {The effect of fecal microbiota transplantation on psychiatric symptoms among patients with irritable bowel syndrome, functional diarrhea and functional constipation: An open-label observational study.},
journal = {Journal of affective disorders},
volume = {235},
number = {},
pages = {506-512},
doi = {10.1016/j.jad.2018.04.038},
pmid = {29684865},
issn = {1573-2517},
mesh = {Adult ; Anxiety Disorders/*psychology ; Constipation/psychology/*therapy ; Depressive Disorder/*psychology ; Diarrhea/psychology/*therapy ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; Gastrointestinal Diseases ; Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/psychology/*therapy ; Male ; Middle Aged ; },
abstract = {BACKGROUNDS: The intestinal microbiota is considered as a potential common underpinning pathophysiology of Functional Gastrointestinal Disorders (FGIDs) and psychiatric disorders such as depression and anxiety. Fecal Microbiota Transplantation (FMT) has been reported to have therapeutic effects on diseases related to dysbiosis, but few studies have evaluated its effect on psychiatric symptoms.

METHODS: We followed 17 patients with either Irritable Bowel Syndrome (IBS), Functional Diarrhea (FDr) or Functional Constipation (FC) who underwent FMT for the treatment of gastrointestinal symptoms and observation of psychiatric symptoms. Changes in Hamilton Rating Scale for Depression (HAM-D) and subscale of sleep-related items, Hamilton Rating Scale for Anxiety (HAM-A) and Quick Inventory for Depressive Symptoms (QIDS) between baseline and 4 weeks after FMT, and relationship with the intestinal microbiota were measured.

RESULTS: At baseline, 12 out of 17 patients were rated with HAM-D ≥ 8. Significant improvement in HAM-D total and sleep subscale score, HAM-A and QIDS were observed (p = 0.007, p = 0.007, p = 0.01, p = 0.007, respectively). Baseline Shannon index indicated that microbiota showed lower diversity in patients with HAM-D ≥ 8 compared to those of healthy donors and patients with HAM-D < 8. There was a significant correlation between baseline Shannon index and HAM-D score, and a correlation between Shannon index change and HAM-D improvement after FMT.

LIMITATIONS: The small sample size with no control group.

CONCLUSIONS: Our results suggest that depression and anxiety symptoms may be improved by FMT regardless of gastrointestinal symptom change in patients with IBS, FDr and FC, and the increase of microbiota diversity may help to improve patient's mood.},
}

Adult
Anxiety Disorders/*psychology
Constipation/psychology/*therapy
Depressive Disorder/*psychology
Diarrhea/psychology/*therapy
*Fecal Microbiota Transplantation
Feces/*microbiology
Female
Gastrointestinal Diseases
Gastrointestinal Microbiome
Humans
Irritable Bowel Syndrome/psychology/*therapy
Male
Middle Aged

@article {pmid29669589,
year = {2018},
author = {Coelho, LP and Kultima, JR and Costea, PI and Fournier, C and Pan, Y and Czarnecki-Maulden, G and Hayward, MR and Forslund, SK and Schmidt, TSB and Descombes, P and Jackson, JR and Li, Q and Bork, P},
title = {Similarity of the dog and human gut microbiomes in gene content and response to diet.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {72},
pmid = {29669589},
issn = {2049-2618},
support = {686070//Horizon 2020 Framework Programme (BE)/International ; },
mesh = {Animals ; *Diet ; Dogs ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; Mice ; *Microbiota ; Obesity ; Swine ; },
abstract = {BACKGROUND: Gut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metagenomics to investigate the relationship between the gut metagenomes of dogs, humans, mice, and pigs.

RESULTS: We present a dog gut microbiome gene catalog containing 1,247,405 genes (based on 129 metagenomes and a total of 1.9 terabasepairs of sequencing data). Based on this catalog and taxonomic abundance profiling, we show that the dog microbiome is closer to the human microbiome than the microbiome of either pigs or mice. To investigate this similarity in terms of response to dietary changes, we report on a randomized intervention with two diets (high-protein/low-carbohydrate vs. lower protein/higher carbohydrate). We show that diet has a large and reproducible effect on the dog microbiome, independent of breed or sex. Moreover, the responses were in agreement with those observed in previous human studies.

CONCLUSIONS: We conclude that findings in dogs may be predictive of human microbiome results. In particular, a novel finding is that overweight or obese dogs experience larger compositional shifts than lean dogs in response to a high-protein diet.},
}

Animals
*Diet
Dogs
Feces/microbiology
*Gastrointestinal Microbiome
Humans
*Metagenome
*Metagenomics/methods
Mice
*Microbiota
Obesity
Swine

@article {pmid29661230,
year = {2018},
author = {Gomez-Silvan, C and Leung, MHY and Grue, KA and Kaur, R and Tong, X and Lee, PKH and Andersen, GL},
title = {A comparison of methods used to unveil the genetic and metabolic pool in the built environment.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {71},
pmid = {29661230},
issn = {2049-2618},
support = {G-2015-13977//Alfred P. Sloan Foundation/International ; 11276116//Research Grants Council, University Grants Committee/International ; },
mesh = {*Built Environment ; *Environmental Microbiology ; Humans ; *Metabolomics/methods ; *Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting.

RESULTS: We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community.

CONCLUSIONS: Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.},
}

*Built Environment
*Environmental Microbiology
Humans
*Metabolomics/methods
*Metagenomics/methods
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid29642940,
year = {2018},
author = {Dai, Z and Coker, OO and Nakatsu, G and Wu, WKK and Zhao, L and Chen, Z and Chan, FKL and Kristiansen, K and Sung, JJY and Wong, SH and Yu, J},
title = {Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {70},
pmid = {29642940},
issn = {2049-2618},
support = {766613, 14106145, 14111216//RGC-GRF/International ; 2016YFC1303200//135 Program Project China/International ; 2013CB531401//973 Program China/International ; 2014BAI09B05//National Key Technology R&D Program/International ; },
mesh = {Aged ; Bacteria/*classification/*genetics ; Cell Transformation, Neoplastic ; Colorectal Neoplasms/diagnosis/*etiology ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Gene Ontology ; Humans ; Male ; *Metagenome ; *Metagenomics/methods ; Middle Aged ; },
abstract = {BACKGROUND: Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort the structure of microbial dysbiosis in CRC and lead to inconsistent results among studies. In this regard, our study targeted at exploring changes in gut microbiota that are universal across populations at species level.

RESULTS: Based on the combined analysis of 526 metagenomic samples from Chinese, Austrian, American, and German and French cohorts, seven CRC-enriched bacteria (Bacteroides fragilis, Fusobacterium nucleatum, Porphyromonas asaccharolytica, Parvimonas micra, Prevotella intermedia, Alistipes finegoldii, and Thermanaerovibrio acidaminovorans) have been identified across populations. The seven enriched bacterial markers classified cases from controls with an area under the receiver-operating characteristics curve (AUC) of 0.80 across the different populations. Abundance correlation analysis demonstrated that CRC-enriched and CRC-depleted bacteria respectively formed their own mutualistic networks, in which the latter was disjointed in CRC. The CRC-enriched bacteria have been found to be correlated with lipopolysaccharide and energy biosynthetic pathways.

CONCLUSIONS: Our study identified potential diagnostic bacterial markers that are robust across populations, indicating their potential universal use for non-invasive CRC diagnosis. We also elucidated the ecological networks and functional capacities of CRC-associated microbiota.},
}

Aged
Bacteria/*classification/*genetics
Cell Transformation, Neoplastic
Colorectal Neoplasms/diagnosis/*etiology
Computational Biology/methods
Female
*Gastrointestinal Microbiome
Gene Ontology
Humans
Male
*Metagenome
*Metagenomics/methods
Middle Aged

@article {pmid29631628,
year = {2018},
author = {Mason, MR and Chambers, S and Dabdoub, SM and Thikkurissy, S and Kumar, PS},
title = {Characterizing oral microbial communities across dentition states and colonization niches.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {67},
pmid = {29631628},
issn = {2049-2618},
support = {T32-DE014320/DE/NIDCR NIH HHS/United States ; R01 DE022579/DE/NIDCR NIH HHS/United States ; F30- DE024940/DE/NIDCR NIH HHS/United States ; F30 DE024940/DE/NIDCR NIH HHS/United States ; T32 DE014320/DE/NIDCR NIH HHS/United States ; R01-DE022579/DE/NIDCR NIH HHS/United States ; },
mesh = {Biodiversity ; Cross-Sectional Studies ; *Dentition ; Gingiva/microbiology ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; },
abstract = {METHODS: The present study aimed to identify patterns and processes in acquisition of oral bacteria and to characterize the microbiota of different dentition states and habitats. Mucosal, salivary, supragingival, and subgingival biofilm samples were collected from orally and systemically healthy children and mother-child dyads in predentate, primary, mixed, and permanent dentitions. 16S rRNA gene sequences were compared to the Human Oral Microbiome Database (HOMD). Functional potential was inferred using PICRUSt.

RESULTS: Unweighted and weighted UniFrac distances were significantly smaller between each mother-predentate dyad than infant-unrelated female dyads. Predentate children shared a median of 85% of species-level operational taxonomic units (s-OTUs) and 100% of core s-OTUs with their mothers. Maternal smoking, but not gender, mode of delivery, feeding habits, or type of food discriminated between predentate microbial profiles. The primary dentition demonstrated expanded community membership, structure, and function when compared to the predentate stage, as well as significantly lower similarity between mother-child dyads. The primary dentition also included 85% of predentate core s-OTUs. Subsequent dentitions exhibited over 90% similarity to the primary dentition in phylogenetic and functional structure. Species from the predentate mucosa as well as new microbial assemblages were identified in the primary supragingival and subgingival microbiomes. All individuals shared 65% of species between supragingival and subgingival habitats; however, the salivary microbiome exhibited less than 35% similarity to either habitat.

CONCLUSIONS: Within the limitations of a cross-sectional study design, we identified two definitive stages in oral bacterial colonization: an early predentate imprinting and a second wave with the eruption of primary teeth. Bacterial acquisition in the oral microbiome is influenced by the maternal microbiome. Personalization begins with the eruption of primary teeth; however, this is limited to phylogeny; functionally, individuals exhibit few differences, suggesting that microbial assembly may follow a defined schematic that is driven by the functional requirements of the ecosystem. This early microbiome forms the foundation upon which newer communities develop as more colonization niches emerge, and expansion of biodiversity is attributable to both introduction of new species and increase in abundance of predentate organisms.},
}

Biodiversity
Cross-Sectional Studies
*Dentition
Gingiva/microbiology
Humans
Metagenome
Metagenomics/methods
*Microbiota
Mouth/*microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Saliva/microbiology

@article {pmid29631623,
year = {2018},
author = {Shkoporov, AN and Ryan, FJ and Draper, LA and Forde, A and Stockdale, SR and Daly, KM and McDonnell, SA and Nolan, JA and Sutton, TDS and Dalmasso, M and McCann, A and Ross, RP and Hill, C},
title = {Reproducible protocols for metagenomic analysis of human faecal phageomes.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {68},
pmid = {29631623},
issn = {2049-2618},
support = {SFI/14/SP APC/B3032//Science Foundation Ireland/Ireland ; SFI/12/RC/2273//Science Foundation Ireland/Ireland ; N/A//Janssen Biotech, Inc/International ; },
mesh = {Bacteria/classification/genetics ; Bacteriophages/*genetics ; Feces/*virology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; },
abstract = {BACKGROUND: Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing. The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing.

RESULTS: Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at + 4 °C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples.

CONCLUSIONS: The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results.},
}

Bacteria/classification/genetics
Bacteriophages/*genetics
Feces/*virology
*Gastrointestinal Microbiome
Humans
*Metagenome
*Metagenomics/methods
RNA, Ribosomal, 16S/genetics
Reproducibility of Results

@article {pmid29615108,
year = {2018},
author = {Cornuault, JK and Petit, MA and Mariadassou, M and Benevides, L and Moncaut, E and Langella, P and Sokol, H and De Paepe, M},
title = {Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {65},
pmid = {29615108},
issn = {2049-2618},
mesh = {Animals ; Bacteriophages/*physiology/ultrastructure ; Biodiversity ; Colitis/etiology ; DNA Damage ; Dysbiosis ; Faecalibacterium prausnitzii/*virology ; *Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Inflammatory Bowel Diseases/etiology ; Metagenome ; Metagenomics/methods ; Mice ; Retroelements ; Symbiosis ; },
abstract = {BACKGROUND: Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases.

METHODS: We identified 18 prophages in 15 genomes of F. prausnitzii, used comparative genomics to define eight phage clades, and annotated the genome of the type phage of each clade. For two of the phages, we studied prophage induction in vitro and in vivo in mice. Finally, we aligned reads from already published viral metagenomic data onto the newly identified phages.

RESULTS: We show that each phage clade represents a novel viral genus and that a surprisingly large fraction of them (10 of the 18 phages) codes for a diversity-generating retroelement, which could contribute to their adaptation to the digestive tract environment. We obtained either experimental or in silico evidence of activity for at least one member of each genus. In addition, four of these phages are either significantly more prevalent or more abundant in stools of IBD patients than in those of healthy controls.

CONCLUSION: Since IBD patients generally have less F. prausnitzii in their microbiota than healthy controls, the higher prevalence or abundance of some of its phages may indicate that they are activated during disease. This in turn suggests that phages could trigger or aggravate F. prausnitzii depletion in patients. Our results show that prophage detection in sequenced strains of the microbiota can usefully complement viral metagenomic studies.},
}

Animals
Bacteriophages/*physiology/ultrastructure
Biodiversity
Colitis/etiology
DNA Damage
Dysbiosis
Faecalibacterium prausnitzii/*virology
*Gastrointestinal Microbiome
Genome, Viral
Humans
Inflammatory Bowel Diseases/etiology
Metagenome
Metagenomics/methods
Mice
Retroelements
Symbiosis

@article {pmid29609653,
year = {2018},
author = {De Vrieze, J and Pinto, AJ and Sloan, WT and Ijaz, UZ},
title = {The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {63},
pmid = {29609653},
issn = {2049-2618},
support = {NE/L011956/1//Natural Environment Research Council/International ; EP/M016811/1//Engineering and Physical Sciences Research Council/International ; },
mesh = {*Anaerobiosis ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing.

RESULTS: A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles.

CONCLUSIONS: In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion.},
}

*Anaerobiosis
Archaea/classification/genetics
Bacteria/classification/genetics
Biodiversity
Metagenomics/methods
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid29587880,
year = {2018},
author = {Gasc, C and Peyret, P},
title = {Hybridization capture reveals microbial diversity missed using current profiling methods.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {61},
pmid = {29587880},
issn = {2049-2618},
mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; *Metagenome ; *Metagenomics/methods ; *Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Soil Microbiology ; },
abstract = {BACKGROUND: Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method has resulted in the discovery of many unexpected evolutionary lineages. However, amplicon sequencing is subject to numerous biases, with some taxa being missed, and is limited by the read length of second-generation sequencing platforms, which drastically reduces the phylogenetic resolution.

RESULTS: Here, we describe a hybridization capture strategy that allows the enrichment of 16S rRNA genes from metagenomic samples and enables an exhaustive identification and a complete reconstruction of the biomarker. Applying this approach to a microbial mock community and a soil sample, we demonstrated that hybridization capture is able to reveal greater microbial diversity than 16S rDNA amplicon sequencing and shotgun sequencing. The reconstruction of full-length 16S rRNA genes facilitated the improvement of phylogenetic resolution and the discovery of novel prokaryotic taxa.

CONCLUSIONS: Our results demonstrate that hybridization capture can lead to major breakthroughs in our understanding of microbial diversity, overcoming the limitations of conventional 16S rRNA gene studies. If applied to a broad range of environmental samples, this innovative approach could reveal the undescribed diversity of the still underexplored microbial communities and could provide a better understanding of ecosystem function.},
}

Archaea/classification/genetics
Bacteria/classification/genetics
*Biodiversity
*Metagenome
*Metagenomics/methods
*Nucleic Acid Hybridization
Phylogeny
RNA, Ribosomal, 16S/genetics
Reproducibility of Results
Soil Microbiology

@article {pmid29106455,
year = {2018},
author = {Maarala, AI and Bzhalava, Z and Dillner, J and Heljanko, K and Bzhalava, D},
title = {ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {6},
pages = {928-935},
doi = {10.1093/bioinformatics/btx702},
pmid = {29106455},
issn = {1367-4811},
mesh = {Algorithms ; Computers ; *Genome, Viral ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods ; *Software ; Viruses/*genetics ; },
abstract = {Motivation: Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and cheaper than ever before. However, the traditional sequential genome analysis algorithms, tools, and platforms are inefficient for performing large-scale metagenomic studies on ever-growing sample data volumes. Currently, there is an urgent need for scalable analysis pipelines that enable harnessing all the power of parallel computation in computing clusters and in cloud computing environments. We propose ViraPipe, a scalable metagenome analysis pipeline that is able to analyze thousands of human microbiomes in parallel in tolerable time. The pipeline is tuned for analyzing viral metagenomes and the software is applicable for other metagenomic analyses as well. ViraPipe integrates parallel BWA-MEM read aligner, MegaHit De novo assembler, and BLAST and HMMER3 sequence search tools. We show the scalability of ViraPipe by running experiments on mining virus related genomes from NGS datasets in a distributed Spark computing cluster.

Results: ViraPipe analyses 768 human samples in 210 minutes on a Spark computing cluster comprising 23 nodes and 1288 cores in total. The speedup of ViraPipe executed on 23 nodes was 11x compared to the sequential analysis pipeline executed on a single node. The whole process includes parallel decompression, read interleaving, BWA-MEM read alignment, filtering and normalizing of non-human reads, De novo contigs assembling, and searching of sequences with BLAST and HMMER3 tools.

Contact: ilari.maarala@aalto.fi.

https://github.com/NGSeq/ViraPipe.},
}

Algorithms
Computers
*Genome, Viral
High-Throughput Nucleotide Sequencing/*methods
Humans
Metagenome
Metagenomics/*methods
Microbiota/genetics
Sequence Analysis, DNA/methods
Sequence Analysis, RNA/methods
*Software
Viruses/*genetics

@article {pmid28642609,
year = {2017},
author = {Banerjee, S and Tian, T and Wei, Z and Peck, KN and Shih, N and Chalian, AA and O'Malley, BW and Weinstein, GS and Feldman, MD and Alwine, J and Robertson, ES},
title = {Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4036},
pmid = {28642609},
issn = {2045-2322},
support = {P30 CA016520/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Bacteria/classification/genetics ; Carcinoma, Squamous Cell/epidemiology/*etiology ; Computational Biology/methods ; Host-Parasite Interactions ; Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth Neoplasms/epidemiology/*etiology ; Mutagenesis, Insertional ; Oropharyngeal Neoplasms/epidemiology/*etiology ; Parasites/classification/genetics ; Reproducibility of Results ; },
abstract = {The microbiome is fundamentally one of the most unique organs in the human body. Dysbiosis can result in critical inflammatory responses and result in pathogenesis contributing to neoplastic events. We used a pan-pathogen array technology (PathoChip) coupled with next-generation sequencing to establish microbial signatures unique to human oral and oropharyngeal squamous cell carcinomas (OCSCC/OPSCC). Signatures for DNA and RNA viruses including oncogenic viruses, gram positive and negative bacteria, fungi and parasites were detected. Cluster and topological analyses identified 2 distinct groups of microbial signatures related to OCSCCs/OPSCCs. Results were validated by probe capture next generation sequencing; the data from which also provided a comprehensive map of integration sites and chromosomal hotspots for micro-organism genomic insertions. Identification of these microbial signatures and their integration sites may provide biomarkers for OCSCC/OPSCC diagnosis and prognosis as well as novel avenues for study of their potential role in OCSCCs/OPSCCs.},
}

Animals
Bacteria/classification/genetics
Carcinoma, Squamous Cell/epidemiology/*etiology
Computational Biology/methods
Host-Parasite Interactions
Host-Pathogen Interactions
Humans
Metagenome
Metagenomics/methods
*Microbiota
Mouth Neoplasms/epidemiology/*etiology
Mutagenesis, Insertional
Oropharyngeal Neoplasms/epidemiology/*etiology
Parasites/classification/genetics
Reproducibility of Results

@article {pmid30258040,
year = {2018},
author = {Taft, DH and Liu, J and Maldonado-Gomez, MX and Akre, S and Huda, MN and Ahmad, SM and Stephensen, CB and Mills, DA},
title = {Bifidobacterial Dominance of the Gut in Early Life and Acquisition of Antimicrobial Resistance.},
journal = {mSphere},
volume = {3},
number = {5},
pages = {},
pmid = {30258040},
issn = {2379-5042},
support = {S10 RR029668/RR/NCRR NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; F32 HD093185/HD/NICHD NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; R01 AT007079/AT/NCCIH NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/*pharmacology ; Bangladesh ; Bifidobacterium/genetics/*physiology ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; Probiotics/therapeutic use ; Regression Analysis ; },
abstract = {Bifidobacterium species are important commensals capable of dominating the infant gut microbiome, in part by producing acids that suppress growth of other taxa. Bifidobacterium species are less prone to possessing antimicrobial resistance (AMR) genes (ARGs) than other taxa that may colonize infants. Given that AMR is a growing public health crisis and ARGs are present in the gut microbiome of humans from early life, this study examines the correlation between a Bifidobacterium-dominated infant gut microbiome and AMR levels, measured by a culture-independent metagenomic approach both in early life and as infants become toddlers. In general, Bifidobacterium dominance is associated with a significant reduction in AMR in a Bangladeshi cohort, both in the number of acquired AMR genes present and in the abundance of AMR genes. However, by year 2, Bangladeshi infants had no significant differences in AMR related to their early-life Bifidobacterium levels. A generalized linear model including all infants in a previously published Swedish cohort found a significant negative association between log-transformed total AMR and Bifidobacterium levels, thus confirming the relationship between Bifidobacterium levels and AMR. In both cohorts, there was no change between early-life and later-life AMR abundance in high-Bifidobacterium infants but a significant reduction in AMR abundance in low-Bifidobacterium infants. These results support the hypothesis that early Bifidobacterium dominance of the infant gut microbiome may help reduce colonization by taxa containing ARGs.IMPORTANCE Infants are vulnerable to an array of infectious diseases, and as the gut microbiome may serve as a reservoir of AMR for pathogens, reducing the levels of AMR in infants is important to infant health. This study demonstrates that high levels of Bifidobacterium are associated with reduced levels of AMR in early life and suggests that probiotic interventions to increase infant Bifidobacterium levels have the potential to reduce AMR in infants. However, this effect is not sustained at year 2 of age in Bangladeshi infants, underscoring the need for more detailed studies of the biogeography and timing of infant AMR acquisition.},
}

Anti-Bacterial Agents/*pharmacology
Bangladesh
Bifidobacterium/genetics/*physiology
DNA, Bacterial/genetics
Drug Resistance, Bacterial/*genetics
Feces/microbiology
Female
*Gastrointestinal Microbiome
Humans
Infant
Male
Metagenomics
Probiotics/therapeutic use
Regression Analysis

@article {pmid30232167,
year = {2018},
author = {Ingala, MR and Simmons, NB and Perkins, SL},
title = {Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals.},
journal = {mSphere},
volume = {3},
number = {5},
pages = {},
pmid = {30232167},
issn = {2379-5042},
mesh = {Animals ; Chiroptera/*microbiology ; *Diet ; Ecology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; *Metagenomics ; Phylogeny ; },
abstract = {Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome.},
}

Animals
Chiroptera/*microbiology
*Diet
Ecology
Gastrointestinal Microbiome/genetics/*physiology
Humans
*Metagenomics
Phylogeny

@article {pmid30185512,
year = {2018},
author = {Rohwer, RR and Hamilton, JJ and Newton, RJ and McMahon, KD},
title = {TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.},
journal = {mSphere},
volume = {3},
number = {5},
pages = {},
pmid = {30185512},
issn = {2379-5042},
mesh = {Algorithms ; Animals ; Bacteria/*classification ; DNA, Bacterial/genetics ; Databases as Topic ; *Databases, Genetic ; Ecosystem ; Fresh Water/*microbiology ; *Metagenomics ; Mice ; *Microbial Consortia ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set's sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at https://www.github.com/McMahonLab/TaxAssIMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.},
}

Algorithms
Animals
Bacteria/*classification
DNA, Bacterial/genetics
Databases as Topic
*Databases, Genetic
Ecosystem
Fresh Water/*microbiology
*Metagenomics
Mice
*Microbial Consortia
*Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid29543361,
year = {2018},
author = {Malone, EW and Perkin, JS and Leckie, BM and Kulp, MA and Hurt, CR and Walker, DM},
title = {Which species, how many, and from where: Integrating habitat suitability, population genomics, and abundance estimates into species reintroduction planning.},
journal = {Global change biology},
volume = {24},
number = {8},
pages = {3729-3748},
doi = {10.1111/gcb.14126},
pmid = {29543361},
issn = {1365-2486},
mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources ; Fishes/*genetics ; Genetic Variation ; Metagenomics ; Population Density ; Rivers ; },
abstract = {Extirpated organisms are reintroduced into their former ranges worldwide to combat species declines and biodiversity losses. The growing field of reintroduction biology provides guiding principles for reestablishing populations, though criticisms remain regarding limited integration of initial planning, modeling frameworks, interdisciplinary collaborations, and multispecies approaches. We used an interdisciplinary, multispecies, quantitative framework to plan reintroductions of three fish species into Abrams Creek, Great Smoky Mountains National Park, USA. We first assessed the appropriateness of habitat at reintroduction sites for banded sculpin (Cottus carolinae), greenside darter (Etheostoma blennioides), and mottled sculpin (Cottus bairdii) using species distribution modeling. Next, we evaluated the relative suitability of nine potential source stock sites using population genomics, abundance estimates, and multiple-criteria decision analysis (MCDA) based on known correlates of reintroduction success. Species distribution modeling identified mottled sculpin as a poor candidate, but banded sculpin and greenside darter as suitable candidates for reintroduction based on species-habitat relationships and habitats available in Abrams Creek. Genotyping by sequencing revealed acceptable levels of genetic diversity at all candidate source stock sites, identified population clusters, and allowed for estimating the number of fish that should be included in translocations. Finally, MCDA highlighted priorities among candidate source stock sites that were most likely to yield successful reintroductions based on differential weightings of habitat assessment, population genomics, and the number of fish available for translocation. Our integrative approach represents a unification of multiple recent advancements in the field of reintroduction biology and highlights the benefit of shifting away from simply choosing nearby populations for translocation to an information-based science with strong a priori planning coupled with several suggested posteriori monitoring objectives. Our framework can be applied to optimize reintroduction successes for a multitude of organisms and advances in the science of reintroduction biology by simultaneously addressing a variety of past criticisms of the field.},
}

Animals
*Biodiversity
Conservation of Natural Resources
Fishes/*genetics
Genetic Variation
Metagenomics
Population Density
Rivers

@article {pmid29355422,
year = {2018},
author = {Mira, A},
title = {Oral Microbiome Studies: Potential Diagnostic and Therapeutic Implications.},
journal = {Advances in dental research},
volume = {29},
number = {1},
pages = {71-77},
doi = {10.1177/0022034517737024},
pmid = {29355422},
issn = {1544-0737},
mesh = {Bacteria/classification ; Biofilms/classification ; Biomarkers/analysis ; Dental Caries/immunology/*microbiology/*prevention & control ; Humans ; In Situ Hybridization, Fluorescence/methods ; Metagenomics ; Microbiota/*physiology ; Microfluidics ; Mouth/*microbiology ; Prebiotics ; Probiotics/pharmacology ; Saliva/microbiology ; },
abstract = {Understanding the microbiology of dental caries is not a mere academic exercise; it provides the basis for preventive, diagnostic, and treatment strategies and gives the dentist a theoretical framework to become a better professional. The last years have seen the development of new research methodologies, ranging from high-throughput sequencing or "omics" techniques to new fluorescence microscopy applications and microfluidics, which have allowed the study of the oral microbiome to an unprecedented level of detail. Those studies have provided new insights about oral biofilm formation, biomarkers of caries risk, microbial etiology, appropriate sampling, identification of health-associated bacteria, and new anticaries strategies, among others. Several pitfalls are associated with the new technologies, including a small number of samples per study group, elevated cost, and genus- or species-based analyses that do not take into consideration intraspecies variability. However, the new data strongly suggest that saliva may not be an appropriate sample for etiological studies or for bacterial caries-risk tests, that microbial composition alone may be insufficient to predict caries risk, and that antimicrobial or immunization strategies targeting single species are unlikely to be effective. Strategies directed toward modulation of the oral biofilm, such as pre- and probiotics, emerge as promising new approaches to prevent tooth decay.},
}

Bacteria/classification
Biofilms/classification
Biomarkers/analysis
Dental Caries/immunology/*microbiology/*prevention & control
Humans
In Situ Hybridization, Fluorescence/methods
Metagenomics
Microbiota/*physiology
Microfluidics
Mouth/*microbiology
Prebiotics
Probiotics/pharmacology
Saliva/microbiology

@article {pmid29092015,
year = {2018},
author = {Olekhnovich, EI and Vasilyev, AT and Ulyantsev, VI and Kostryukova, ES and Tyakht, AV},
title = {MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {3},
pages = {434-444},
doi = {10.1093/bioinformatics/btx681},
pmid = {29092015},
issn = {1367-4811},
mesh = {Algorithms ; Bacteria/*genetics ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics/*methods ; *Software ; },
abstract = {Motivation: Antibiotic resistance is an important global public health problem. Human gut microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens.

Results: We developed MetaCherchant-an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph. The algorithm was validated on a number of simulated and published datasets, as well as applied to new 'shotgun' metagenomes of gut microbiota from patients with Helicobacter pylori who underwent antibiotic therapy. Genomic context was reconstructed for several major resistance genes. Taxonomic annotation of the context suggests that within a single metagenome, the resistance genes can be contained in genomes of multiple species. MetaCherchant allows reconstruction of mobile elements with resistance genes within the genomes of bacteria using metagenomic data. Application of MetaCherchant in differential mode produced specific graph structures suggesting the evidence of possible resistance gene transmission within a mobile element that occurred as a result of the antibiotic therapy. MetaCherchant is a promising tool giving researchers an opportunity to get an insight into dynamics of resistance transmission in vivo basing on metagenomic data.

Source code and binaries are freely available for download at https://github.com/ctlab/metacherchant. The code is written in Java and is platform-independent.

Cotanct: ulyantsev@rain.ifmo.ru.

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

Algorithms
Bacteria/*genetics
Drug Resistance, Bacterial/*genetics
Gastrointestinal Microbiome/*genetics
Humans
Metagenomics/*methods
*Software

@article {pmid28968799,
year = {2018},
author = {Äijö, T and Müller, CL and Bonneau, R},
title = {Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {3},
pages = {372-380},
pmid = {28968799},
issn = {1367-4811},
mesh = {Bacteria/genetics/*isolation & purification ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; *Models, Statistical ; RNA, Ribosomal, 16S/*analysis ; Sequence Analysis, DNA/methods ; },
abstract = {Motivation: The number of microbial and metagenomic studies has increased drastically due to advancements in next-generation sequencing-based measurement techniques. Statistical analysis and the validity of conclusions drawn from (time series) 16S rRNA and other metagenomic sequencing data is hampered by the presence of significant amount of noise and missing data (sampling zeros). Accounting uncertainty in microbiome data is often challenging due to the difficulty of obtaining biological replicates. Additionally, the compositional nature of current amplicon and metagenomic data differs from many other biological data types adding another challenge to the data analysis.

Results: To address these challenges in human microbiome research, we introduce a novel probabilistic approach to explicitly model overdispersion and sampling zeros by considering the temporal correlation between nearby time points using Gaussian Processes. The proposed Temporal Gaussian Process Model for Compositional Data Analysis (TGP-CODA) shows superior modeling performance compared to commonly used Dirichlet-multinomial, multinomial and non-parametric regression models on real and synthetic data. We demonstrate that the nonreplicative nature of human gut microbiota studies can be partially overcome by our method with proper experimental design of dense temporal sampling. We also show that different modeling approaches have a strong impact on ecological interpretation of the data, such as stationarity, persistence and environmental noise models.

A Stan implementation of the proposed method is available under MIT license at https://github.com/tare/GPMicrobiome.

Contact: taijo@flatironinstitute.org or rb113@nyu.edu.

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

Bacteria/genetics/*isolation & purification
Gastrointestinal Microbiome/*genetics
*Genome, Bacterial
High-Throughput Nucleotide Sequencing/methods
Humans
Metagenomics/*methods
*Models, Statistical
RNA, Ribosomal, 16S/*analysis
Sequence Analysis, DNA/methods

@article {pmid30581574,
year = {2019},
author = {Angelakis, E and Bachar, D and Yasir, M and Musso, D and Djossou, F and Melenotte, C and Robert, C and Davoust, B and Gaborit, B and Azhar, EI and Bibi, F and Dutour, A and Raoult, D},
title = {Comparison of the gut microbiota of obese individuals from different geographic origins.},
journal = {New microbes and new infections},
volume = {27},
number = {},
pages = {40-47},
doi = {10.1016/j.nmni.2018.11.005},
pmid = {30581574},
issn = {2052-2975},
abstract = {Few studies have examined the interaction of human geography, microbial community structure and obesity. We tested obese adult volunteers from France, Saudi Arabia, French Polynesia and from a traditional population in the village of Trois-Sauts in French Guiana by sequencing the V3-V4 region. We also sequenced homemade fermented cachiri beers that were obtained from the traditional Amazonian population and are highly consumed by this population. We found that French and Saudis had significantly less richness and biodiversity in their gut microbiota than Amazonians and Polynesians (p <0.05). Principle coordinate analysis of the overall composition of the genera communities revealed that the microbiomes of Amazonians clustered independently from the other obese individuals. Moreover, we found that Amazonians presented significantly stricter anaerobic genera than the Saudis, French and Polynesians (p < 0.001). Polynesians presented significantly lower relative abundance of Lactobacillus sp. than French (p 0.01) and Saudis (p 0.05). Treponema berlinense and Treponema succinifaciens were only present in the gut microbiome of Amazonians. The cachiri beers presented significantly more bacterial species in common with the gut microbiome of Amazonians (p < 0.005). Obese individuals with different origins present modifications in their gut microbiota, and we provide evidence that the cachiri beers influenced the gut microbiome of Amazonians.},
}

@article {pmid30138419,
year = {2018},
author = {Oliveira, JL and Cury, JC and Gurgel-Gonçalves, R and Bahia, AC and Monteiro, FA},
title = {Field-collected Triatoma sordida from central Brazil display high microbiota diversity that varies with regard to developmental stage and intestinal segmentation.},
journal = {PLoS neglected tropical diseases},
volume = {12},
number = {8},
pages = {e0006709},
pmid = {30138419},
issn = {1935-2735},
mesh = {Animals ; Bacteria/*classification ; Brazil ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Male ; Nymph ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Triatoma/growth & development/*microbiology ; },
abstract = {BACKGROUND/METHODOLOGY: Triatomine bugs are the vectors of Trypanosoma cruzi, the agent of Chagas disease. Vector control has for decades relied upon insecticide spraying, but insecticide resistance has recently emerged in several triatomine populations. One alternative strategy to reduce T. cruzi transmission is paratransgenesis, whereby symbiotic bacteria are genetically engineered to produce T. cruzi-killing proteins in the vector's gut. This approach requires in-depth knowledge of the vectors' natural gut microbiota. Here, we use metagenomics (16S rRNA 454 pyrosequencing) to describe the gut microbiota of field-caught Triatoma sordida-likely the most common peridomestic triatomine in Brazil. For large nymphs (4th and 5th stage) and adults, we also studied separately the three main digestive-tract segments-anterior midgut, posterior midgut, and hindgut.

PRINCIPAL FINDINGS: Bacteria of four phyla (12 genera) were present in both nymphs (all five stages) and adults, thus defining T. sordida's 'bacterial core': Actinobacteria (Brevibacterium, Corynebacterium, Dietzia, Gordonia, Nitriliruptor, Nocardia, Nocardiopsis, Rhodococcus, and Williamsia), Proteobacteria (Pseudomonas and Sphingobium), and Firmicutes (Staphylococcus). We found some clear differences in bacterial composition and relative abundance among development stages; overall, Firmicutes and Proteobacteria increased, but Actinobacteria decreased, through development. Finally, the bacterial microbiotas of the bugs' anterior midgut, posterior midgut, and hindgut were sharply distinct.

CONCLUSIONS/SIGNIFICANCE: Our results identify the 'bacterial core set' of T. sordida and reveal important gut microbiota differences among development stages-particularly between 1st-3rd stage nymphs and adults. Further, we show that, within any given development stage, the vectors' gut cannot be regarded as a single homogeneous environment. Cultivable, non-pathogenic 'core' bacterial species may now be tested as candidates for paratransgenic control of T. cruzi transmission by T. sordida.},
}

Animals
Bacteria/*classification
Brazil
Female
*Gastrointestinal Microbiome
Gastrointestinal Tract/*microbiology
Male
Nymph
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Triatoma/growth & development/*microbiology

@article {pmid29667264,
year = {2018},
author = {Xu, Y and Jia, YH and Chen, L and Huang, WM and Yang, DQ},
title = {Metagenomic analysis of oral microbiome in young children aged 6-8 years living in a rural isolated Chinese province.},
journal = {Oral diseases},
volume = {24},
number = {6},
pages = {1115-1125},
doi = {10.1111/odi.12871},
pmid = {29667264},
issn = {1601-0825},
mesh = {Child ; China ; Dentition, Mixed ; Female ; Humans ; Male ; Metagenomics ; *Microbiota ; Mouth/*microbiology ; *Rural Population ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The mixed dentition is an important transition period from primary teeth to permanent teeth. However, the caries prevalence of first permanent molar in mixed dentitions was about 30%, which almost represent the caries rate of permanent teeth in this period of time. Therefore, we assessed the oral bacterial profiles in young children (age 6-8) with mixed dentition with or without first molar caries for providing the research basis of caries etiology.

METHODS: We collected samples of supragingival plaque and saliva from the children living in Guizhou, a rural isolated province in China. Then, we performed DNA extraction and purification followed by 454 pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA and compared our results with those of previous research.

RESULTS: (i) We analyzed 48,320 unique sequences that represented 18 phyla, 29 classes, 44 orders, 74 families, 129 genera, 15,003 species-level OUT in plaque and saliva samples; (ii) longitudinally, there was the "healthy core microbiome" between healthy deciduous dentition and early mixed dentition, for example, Neisseria, Porphyromonas, Selenomonas etc.; (iii) horizontally, there also existed the "healthy core microbiome" in early mixed dentition, for example, Neisseria, Streptococcus, Prevotella etc.; (iv) the dominant bacteria detected by Lefse in caries group including Actinomycetaceae, Streptobacillus (p < 0.05) and those in caries-free group including Gammaproteobacteria, Pasteurellaceae, Aggregatibacter, Chloroflexi, (p < 0.05).

CONCLUSIONS: The oral cavity is a highly heterogeneous ecosystem with the "healthy core microbiome" in children, although microbial composition shifts along with aging. In addition, the abundance and diversity of microbiota vary between caries and caries-free groups verify the ecological plaque hypothesis.},
}

Child
China
Dentition, Mixed
Female
Humans
Male
Metagenomics
*Microbiota
Mouth/*microbiology
*Rural Population
Sequence Analysis, DNA

@article {pmid28592823,
year = {2017},
author = {Cardoso, DC and Sandionigi, A and Cretoiu, MS and Casiraghi, M and Stal, L and Bolhuis, H},
title = {Comparison of the active and resident community of a coastal microbial mat.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2969},
pmid = {28592823},
issn = {2045-2322},
mesh = {Bacteria/classification/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Seawater ; *Water Microbiology ; },
abstract = {Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potential stable pool of extracellular DNA. Here we focused on the active microbial community by comparing 16S rRNA sequences obtained from the ribosomal RNA pool with gene sequences obtained from the DNA fraction. In addition, we aimed to establish an optimal and feasible sampling protocol that takes potential spatial and temporal heterogeneity into account. The coastal microbial mat investigated here was sampled randomly and at regular time points during one 24-h period. DNA and RNA was extracted and after conversion of the RNA fraction to cDNA, the V1-V3 and the V3-V4 regions of the 16S rRNA gene were targeted for high-throughput amplicon sequencing. We show that the community composition varies little in time and space whereas two amplified 16S regions gave significant different results. The largest differences were found when comparing the "resident community" (DNA) with the "active community" (cDNA/RNA); in the latter, Cyanobacteria dominated for almost 95% while they represented 60% of the resident fraction.},
}

Bacteria/classification/genetics
Metagenome
Metagenomics/methods
*Microbiota
RNA, Ribosomal, 16S/genetics
*Seawater
*Water Microbiology

@article {pmid28083919,
year = {2018},
author = {Ishihara, K},
title = {New approach for studying mobile genes using metagenomic analysis.},
journal = {Oral diseases},
volume = {24},
number = {4},
pages = {494-496},
doi = {10.1111/odi.12640},
pmid = {28083919},
issn = {1601-0825},
mesh = {Bacteria/*genetics ; Drug Resistance, Bacterial/genetics ; Fiji ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Humans ; *Metagenome ; Metagenomics ; Mouth/*microbiology ; Mouth Diseases/*microbiology ; North America ; },
}

Bacteria/*genetics
Drug Resistance, Bacterial/genetics
Fiji
Gastrointestinal Microbiome/genetics
Gene Transfer, Horizontal
Humans
*Metagenome
Metagenomics
Mouth/*microbiology
Mouth Diseases/*microbiology
North America

@article {pmid29227468,
year = {2018},
author = {Beaulaurier, J and Zhu, S and Deikus, G and Mogno, I and Zhang, XS and Davis-Richardson, A and Canepa, R and Triplett, EW and Faith, JJ and Sebra, R and Schadt, EE and Fang, G},
title = {Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.},
journal = {Nature biotechnology},
volume = {36},
number = {1},
pages = {61-69},
pmid = {29227468},
issn = {1546-1696},
support = {R01 GM114472/GM/NIGMS NIH HHS/United States ; },
mesh = {Algorithms ; Bacteria/genetics ; Cluster Analysis ; DNA Methylation/*genetics ; Environmental Microbiology ; Genome, Bacterial/genetics ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Plasmids/genetics ; Sequence Analysis, DNA ; },
abstract = {Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing. Our method takes advantage of these endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins. We validate our method using synthetic and real microbiome sequences. In addition to genome binning, we show that our method links plasmids and other mobile genetic elements to their host species in a real microbiome sample. Incorporation of DNA methylation information into shotgun metagenomics analyses will complement existing methods to enable more accurate sequence binning.},
}

Algorithms
Bacteria/genetics
Cluster Analysis
DNA Methylation/*genetics
Environmental Microbiology
Genome, Bacterial/genetics
Humans
Metagenome/*genetics
*Metagenomics
Microbiota/*genetics
Plasmids/genetics
Sequence Analysis, DNA

@article {pmid30559737,
year = {2018},
author = {Gong, Z and Liang, Y and Wang, M and Jiang, Y and Yang, Q and Xia, J and Zhou, X and You, S and Gao, C and Wang, J and He, J and Shao, H and McMinn, A},
title = {Viral Diversity and Its Relationship With Environmental Factors at the Surface and Deep Sea of Prydz Bay, Antarctica.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2981},
doi = {10.3389/fmicb.2018.02981},
pmid = {30559737},
issn = {1664-302X},
abstract = {A viral metagenomic analysis of five surface and two bottom water (878 meters below surface, mbs, and 3,357 mbs) samples from Prydz Bay, was conducted during February-March 2015. The results demonstrated that most of the DNA viruses were dsDNA viruses (79.73-94.06%, except at PBI1, 37.51%). Of these, Caudovirales (Siphoviridae, Myoviridae, and Podoviridae) phages were most abundant in surface seawater (67.67-71.99%), while nucleocytoplasmic large DNA viruses (NCLDVs) (Phycodnaviridae, Mimiviridae, and Pandoraviridae accounted for >30% of dsDNA viruses) were most abundant in the bottom water (3,357 mbs). Of the ssDNA viruses, Microviridae was the dominant family in PBI2, PBI3, PBOs, and PBI4b (57.09-87.55%), while Inoviridae (58.16%) was the dominant family in PBI1. Cellulophaga phages (phi38:1 and phi10:1) and Flavobacterium phage 11b, infecting the possible host strains affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, were abundant in surface water dsDNA viromes. The long contig (PBI2_1_C) from the viral metagenomes were most similar to the genome architectures of Cellulophaga phage phi10:1 and Flavobacterium phage 11b from the Arctic Ocean. Comparative analysis showed that the surface viral community of Prydz Bay could be clearly separated from other marine and freshwater environments. The deep sea viral community was similar to the deep sea viral metagenome at A Long-term Oligotrophic Habitat Assessment Station (ALOHA, at 22°45'N, 158°00'W). The multivariable analysis indicated that nutrients probably played an important role in shaping the local viral community structure. This study revealed the preliminary characteristics of the viral community in Prydz Bay, from both the surface and the deep sea. It provided evidence of the relationships between the virome and the environment in Prydz Bay and provided the first data from the deep sea viral community of the Southern Ocean.},
}

@article {pmid30048915,
year = {2018},
author = {Milanović, V and Osimani, A and Garofalo, C and De Filippis, F and Ercolini, D and Cardinali, F and Taccari, M and Aquilanti, L and Clementi, F},
title = {Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE.},
journal = {International journal of food microbiology},
volume = {286},
number = {},
pages = {66-74},
doi = {10.1016/j.ijfoodmicro.2018.07.022},
pmid = {30048915},
issn = {1879-3460},
mesh = {Acetic Acid/*analysis ; Bacteria/*classification/genetics/*isolation & purification ; Biodiversity ; Fermentation ; Metagenomics ; Microbiota/genetics ; Molecular Typing ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Wine/*microbiology ; },
abstract = {The production of traditional vinegar is usually carried out using the so-called "seed vinegar" or "mother of vinegar" that is composed of an undefined and complex pool of microorganisms deriving from a previous vinegar production. To date, there have been relatively few studies on the microbiota of seed vinegars. The present study was carried out to discover the bacterial biota of seed vinegar samples used in the homemade production of local vinegars obtained from the acetic fermentation of white wine. The seed vinegar samples were subjected to viable counting and advanced molecular analyses, namely, Illumina sequencing and PCR-DGGE. The adopted polyphasic approach allowed the bacterial diversity of the analyzed samples to be profiled, thus revealing the presence of acetic acid bacteria ascribed to the genera Acetobacter, Gluconacetobacter, Gluconobacter and Komagataeibacter. Moreover, other microbial genera as Pseudomonas, Bacillus and Clostridium were abundantly found in almost all the samples, together with other minority genera. The results of viable counting confirmed the well-acknowledged limitations inherent with acetic acid bacteria recovery on plate growth media. The overall results confirmed that seed vinegars have a complex and heterogeneous biodiversity, thus encouraging their exploitation for the isolation and future technological characterization of cultures to be selected for the manufacture of mixed starter cultures.},
}

Acetic Acid/*analysis
Bacteria/*classification/genetics/*isolation & purification
Biodiversity
Fermentation
Metagenomics
Microbiota/genetics
Molecular Typing
Polymerase Chain Reaction
RNA, Ribosomal, 16S/genetics
Wine/*microbiology

@article {pmid29446650,
year = {2018},
author = {Guilhot, E and Khelaifia, S and La Scola, B and Raoult, D and Dubourg, G},
title = {Methods for culturing anaerobes from human specimen.},
journal = {Future microbiology},
volume = {13},
number = {},
pages = {369-381},
doi = {10.2217/fmb-2017-0170},
pmid = {29446650},
issn = {1746-0921},
mesh = {Antioxidants ; Bacteria, Anaerobic/*growth & development/*isolation & purification ; Bacteriological Techniques ; Coculture Techniques ; Culture Media/chemistry ; Humans ; Metagenomics ; *Microbiota ; Single-Cell Analysis ; Specimen Handling ; },
abstract = {Anaerobes represent the dominating population in the human gut microbiota and play a key role in gut homeostasis. In addition, several anaerobes are now considered as probiotics and they remain essential to several processes in the field of biotechnology. With the implementation of MALDI-TOF MS in routine laboratories, anaerobes are no longer neglected in clinical microbiology, as their identification is made easy. However, the isolation and identification of anaerobic bacteria, remains time consuming, fastidious and costly. Various strategies have been developed, from sampling to culturing human specimens, which will be discussed in this paper. Also, particular attention is paid to isolating species with special medical importance, as for contribution to the field of culturomics.},
}

Antioxidants
Bacteria, Anaerobic/*growth & development/*isolation & purification
Bacteriological Techniques
Coculture Techniques
Culture Media/chemistry
Humans
Metagenomics
*Microbiota
Single-Cell Analysis
Specimen Handling

@article {pmid29255284,
year = {2018},
author = {Costea, PI and Hildebrand, F and Arumugam, M and Bäckhed, F and Blaser, MJ and Bushman, FD and de Vos, WM and Ehrlich, SD and Fraser, CM and Hattori, M and Huttenhower, C and Jeffery, IB and Knights, D and Lewis, JD and Ley, RE and Ochman, H and O'Toole, PW and Quince, C and Relman, DA and Shanahan, F and Sunagawa, S and Wang, J and Weinstock, GM and Wu, GD and Zeller, G and Zhao, L and Raes, J and Knight, R and Bork, P},
title = {Enterotypes in the landscape of gut microbial community composition.},
journal = {Nature microbiology},
volume = {3},
number = {1},
pages = {8-16},
pmid = {29255284},
issn = {2058-5276},
support = {MR/M50161X/1//Medical Research Council/United Kingdom ; P30 AI045008/AI/NIAID NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; UH2 DK083981/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Biodiversity ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.},
}

Animals
Bacteria/*classification/genetics
Bacterial Typing Techniques
Biodiversity
Gastrointestinal Microbiome/*genetics
Gastrointestinal Tract/*microbiology
Humans
*Metagenome
Metagenomics
RNA, Ribosomal, 16S/genetics

@article {pmid29133882,
year = {2018},
author = {Yutin, N and Makarova, KS and Gussow, AB and Krupovic, M and Segall, A and Edwards, RA and Koonin, EV},
title = {Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.},
journal = {Nature microbiology},
volume = {3},
number = {1},
pages = {38-46},
pmid = {29133882},
issn = {2058-5276},
support = {Z01 LM000073-12/NULL/Intramural NIH HHS/United States ; },
mesh = {Bacteriophages/*classification/*genetics ; Bacteroidetes/virology ; Databases, Protein ; Gastrointestinal Microbiome/*genetics ; Genome, Viral/genetics ; *Genomics ; Humans ; *Metagenomics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, Protein ; Viral Proteins/chemistry/genetics ; },
abstract = {Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery 1-3 . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome 4 . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study. Here we combine a comprehensive search of genomic and metagenomic databases with sensitive methods for protein sequence analysis to identify an expansive, diverse group of bacteriophages related to crAssphage and predict the functions of the majority of phage proteins, in particular those that comprise the structural, replication and expression modules. Most, if not all, of the crAss-like phages appear to be associated with diverse bacteria from the phylum Bacteroidetes, which includes some of the most abundant bacteria in the human gut microbiome and that are also common in various other habitats. These findings provide for experimental characterization of the most abundant but poorly understood members of the human-associated virome.},
}

Bacteriophages/*classification/*genetics
Bacteroidetes/virology
Databases, Protein
Gastrointestinal Microbiome/*genetics
Genome, Viral/genetics
*Genomics
Humans
*Metagenomics
Models, Genetic
Molecular Sequence Data
Phylogeny
Sequence Analysis, Protein
Viral Proteins/chemistry/genetics

@article {pmid29109478,
year = {2018},
author = {Kolinko, S and Wu, YW and Tachea, F and Denzel, E and Hiras, J and Gabriel, R and Bäcker, N and Chan, LJG and Eichorst, SA and Frey, D and Chen, Q and Azadi, P and Adams, PD and Pray, TR and Tanjore, D and Petzold, CJ and Gladden, JM and Simmons, BA and Singer, SW},
title = {A bacterial pioneer produces cellulase complexes that persist through community succession.},
journal = {Nature microbiology},
volume = {3},
number = {1},
pages = {99-107},
doi = {10.1038/s41564-017-0052-z},
pmid = {29109478},
issn = {2058-5276},
support = {S10 OD018530/OD/NIH HHS/United States ; },
mesh = {Bacteria/*classification/*enzymology/metabolism ; Bacterial Proteins/analysis/isolation & purification ; Biological Evolution ; Cellulase/*analysis/isolation & purification ; Cellulose/*metabolism ; Composting ; Genome, Bacterial/genetics ; Glycoside Hydrolases/analysis/isolation & purification ; Glycosylation ; Heterotrophic Processes ; Metagenomics ; Microbial Consortia/*physiology ; Models, Biological ; Multienzyme Complexes/*analysis/isolation & purification ; *Phylogeny ; Soil Microbiology ; },
abstract = {Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.},
}

Bacteria/*classification/*enzymology/metabolism
Bacterial Proteins/analysis/isolation & purification
Biological Evolution
Cellulase/*analysis/isolation & purification
Cellulose/*metabolism
Composting
Genome, Bacterial/genetics
Glycoside Hydrolases/analysis/isolation & purification
Glycosylation
Heterotrophic Processes
Metagenomics
Microbial Consortia/*physiology
Models, Biological
Multienzyme Complexes/*analysis/isolation & purification
*Phylogeny
Soil Microbiology

@article {pmid28588309,
year = {2017},
author = {Jiang, S and Xie, S and Lv, D and Wang, P and He, H and Zhang, T and Zhou, Y and Lin, Q and Zhou, H and Jiang, J and Nie, J and Hou, F and Chen, Y},
title = {Alteration of the gut microbiota in Chinese population with chronic kidney disease.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2870},
pmid = {28588309},
issn = {2045-2322},
mesh = {Adult ; Aged ; Bacteria/classification/genetics ; Biomarkers ; Butyrates/metabolism ; Case-Control Studies ; China/epidemiology ; Computational Biology/methods ; Female ; *Gastrointestinal Microbiome ; Humans ; Kidney Failure, Chronic/epidemiology ; Kidney Function Tests ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Population Surveillance ; Renal Insufficiency, Chronic/diagnosis/*epidemiology/metabolism ; },
abstract = {We evaluated differences in the compositions of faecal microbiota between 52 end stage renal disease (ESRD) patients and 60 healthy controls in southern China using quantitative real-time polymerase chain reaction (qPCR) and high-throughput sequencing (16S ribosomal RNA V4-6 region) methods. The absolute quantification of total bacteria was significantly reduced in ESRD patients (p < 0.01). In three enterotypes, Prevotella was enriched in the healthy group whereas Bacteroides were prevalent in the ESRD group (LDA score > 4.5). 11 bacterial taxa were significantly overrepresented in samples from ESRD and 22 bacterial taxa were overrepresented in samples from healthy controls. The butyrate producing bacteria, Roseburia, Faecalibacterium, Clostridium, Coprococcus and Prevotella were reduced in the ESRD group (LDA values > 2.0). Canonical correspondence analysis (CCA) indicated that Cystatin C (CysC), creatinine and eGFR appeared to be the most important environmental parameters to influence the overall microbial communities. In qPCR analysis, The butyrate producing species Roseburia spp., Faecalibacterium prausnitzii, Prevotella and Universal bacteria, were negatively related to CRP and CysC. Total bacteria in faeces were reduced in patients with ESRD compared to that in healthy individuals. The enterotypes change from Prevotella to Bacteroides in ESRD patients. The gut microbiota was associated with the inflammatory state and renal function of chronic kidney disease.},
}

Adult
Aged
Bacteria/classification/genetics
Biomarkers
Butyrates/metabolism
Case-Control Studies
China/epidemiology
Computational Biology/methods
Female
*Gastrointestinal Microbiome
Humans
Kidney Failure, Chronic/epidemiology
Kidney Function Tests
Male
Metagenome
Metagenomics/methods
Middle Aged
Population Surveillance
Renal Insufficiency, Chronic/diagnosis/*epidemiology/metabolism

@article {pmid28588199,
year = {2017},
author = {Gomez-Arango, LF and Barrett, HL and McIntyre, HD and Callaway, LK and Morrison, M and Nitert, MD},
title = {Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2860},
pmid = {28588199},
issn = {2045-2322},
mesh = {Adult ; Biomarkers ; Female ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Mouth/*microbiology ; Obesity/*etiology ; Overweight/*etiology ; Phylogeny ; Placenta/*microbiology ; Pregnancy ; *Pregnancy Complications ; },
abstract = {A distinct bacterial signature of the placenta was reported, providing evidence that the fetus does not develop in a sterile environment. The oral microbiome was suggested as a possible source of the bacterial DNA present in the placenta based on similarities to the oral non-pregnant microbiome. Here, the possible origin of the placental microbiome was assessed, examining the gut, oral and placental microbiomes from the same pregnant women. Microbiome profiles from 37 overweight and obese pregnant women were examined by 16SrRNA sequencing. Fecal and oral contributions to the establishment of the placental microbiome were evaluated. Core phylotypes between body sites and metagenome predictive functionality were determined. The placental microbiome showed a higher resemblance and phylogenetic proximity with the pregnant oral microbiome. However, similarity decreased at lower taxonomic levels and microbiomes clustered based on tissue origin. Core genera: Prevotella, Streptococcus and Veillonella were shared between all body compartments. Pathways encoding tryptophan, fatty-acid metabolism and benzoate degradation were highly enriched specifically in the placenta. Findings demonstrate that the placental microbiome exhibits a higher resemblance with the pregnant oral microbiome. Both oral and gut microbiomes contribute to the microbial seeding of the placenta, suggesting that placental colonization may have multiple niche sources.},
}

Adult
Biomarkers
Female
*Gastrointestinal Microbiome
Humans
Metagenome
Metagenomics/methods
Mouth/*microbiology
Obesity/*etiology
Overweight/*etiology
Phylogeny
Placenta/*microbiology
Pregnancy
*Pregnancy Complications

@article {pmid28584301,
year = {2017},
author = {Pootakham, W and Mhuantong, W and Yoocha, T and Putchim, L and Sonthirod, C and Naktang, C and Thongtham, N and Tangphatsornruang, S},
title = {High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2774},
pmid = {28584301},
issn = {2045-2322},
mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/*genetics ; Biodiversity ; *Metagenomics/methods ; *Microbiota ; Phylogeny ; Phylogeography ; *RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Thailand ; },
abstract = {Coral reefs are a complex ecosystem consisting of coral animals and a vast array of associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their fundamental roles in fitness and survival of the host animal. The scleractinian coral Porites lutea is one of the dominant reef-builders in the Indo-West Pacific. Currently, very little is known about the composition and structure of bacterial communities across P. lutea reefs. The purpose of this study is twofold: to demonstrate the advantages of using PacBio circular consensus sequencing technology in microbial community studies and to investigate the diversity and structure of P. lutea-associated microbiome in the Indo-Pacific. This is the first metagenomic study of marine environmental samples that utilises the PacBio sequencing system to capture full-length 16S rRNA sequences. We observed geographically distinct coral-associated microbial profiles between samples from the Gulf of Thailand and Andaman Sea. Despite the geographical and environmental impacts on the coral-host interactions, we identified a conserved community of bacteria that were present consistently across diverse reef habitats. Finally, we demonstrated the superior performance of full-length 16S rRNA sequences in resolving taxonomic uncertainty of coral associates at the species level.},
}

Animals
Anthozoa/*microbiology
Bacteria/*classification/*genetics
Biodiversity
*Metagenomics/methods
*Microbiota
Phylogeny
Phylogeography
*RNA, Ribosomal, 16S
Sequence Analysis, DNA
Thailand

@article {pmid28536449,
year = {2017},
author = {Choi, S and Song, H and Tripathi, BM and Kerfahi, D and Kim, H and Adams, JM},
title = {Effect of experimental soil disturbance and recovery on structure and function of soil community: a metagenomic and metagenetic approach.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2260},
pmid = {28536449},
issn = {2045-2322},
mesh = {Biodiversity ; *Biota ; Ecosystem ; *Metagenome ; *Metagenomics/methods ; Microbiota ; *Soil ; *Soil Microbiology ; },
abstract = {There has been little study of effects of disturbance on soil biota combining closely controlled experimental conditions and DNA-based methods. We sampled pots of soil at varying times following an initial simulated mass mortality event. Soil DNA was extracted at intervals up to 24 weeks after the event, and shotgun metagenomes sequenced using NextSeq. Compared to initial conditions, we found: consistent, sequential changes in functional metagenome and community structure over time, indicating successional niche differentiation amongst soil biota. As predicted, early successional systems had greater abundance of genes associated with motility, but fewer genes relating to DNA/RNA/protein metabolism, cell division and cell cycle. Contrary to predictions, there were no significant differences in cell signaling, virulence and defense-related genes. Also, stress related genes were less abundant in later succession. The early successional system had lower taxonomic diversity but higher functional gene diversity. Over time, community characteristics changed progressively, but by the end of the experiment had not returned to the 'original' state of the system before disturbance. Results indicated a predictable sequence of gene functions and taxa following disturbance, analogous to ecosystem succession for large organisms. It is unclear if and when the system would return to its pre-disturbance state.},
}

Biodiversity
*Biota
Ecosystem
*Metagenome
*Metagenomics/methods
Microbiota
*Soil
*Soil Microbiology

@article {pmid30155977,
year = {2018},
author = {Bálint, M and Nowak, C and Márton, O and Pauls, SU and Wittwer, C and Aramayo, JL and Schulze, A and Chambert, T and Cocchiararo, B and Jansen, M},
title = {Accuracy, limitations and cost efficiency of eDNA-based community survey in tropical frogs.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1415-1426},
doi = {10.1111/1755-0998.12934},
pmid = {30155977},
issn = {1755-0998},
support = {//USGS Amphibian Research and Monitoring Initiative/ ; //Globetrotter/ ; //Erika and Walter Datz-Stiftung/ ; LOEWE - Landes-Offensive zur Entwicklung Wissens//Hessisches Ministerium für Wissenschaft und Kunst/ ; //Ministry of Higher Education/ ; },
mesh = {Amphibians/*classification/*genetics ; Animals ; *Biota ; Bolivia ; Costs and Cost Analysis ; DNA Barcoding, Taxonomic/economics/*methods ; Metagenomics/economics/*methods ; Tropical Climate ; },
abstract = {Rapid environmental change in highly biodiverse tropical regions demands efficient biomonitoring programmes. While existing metrics of species diversity and community composition rely on encounter-based survey data, eDNA recently emerged as alternative approach. Costs and ecological value of eDNA-based methods have rarely been evaluated in tropical regions, where high species richness is accompanied by high functional diversity (e.g., the use of different microhabitats by different species and life stages). We first tested whether estimation of tropical frogs' community structure derived from eDNA data is compatible with expert field assessments. Next, we evaluated whether eDNA is a financially viable solution for biodiversity monitoring in tropical regions. We applied eDNA metabarcoding to investigate frog species occurrence in five ponds in the Chiquitano dry forest region in Bolivia and compared our data with a simultaneous visual and audio encounter survey (VAES). We found that taxon lists and community structure generated with eDNA and VAES correspond closely, and most deviations are attributable to different species' life histories. Cost efficiency of eDNA surveys was mostly influenced by the richness of local fauna and the number of surveyed sites: VAES may be less costly in low-diversity regions, but eDNA quickly becomes more cost-efficient in high-diversity regions with many sites sampled. The results highlight that eDNA is suitable for large-scale biodiversity surveys in high-diversity areas if life history is considered, and certain precautions in sampling, genetic analyses and data interpretation are taken. We anticipate that spatially extensive, standardized eDNA biodiversity surveys will quickly emerge in the future.},
}

Amphibians/*classification/*genetics
Animals
*Biota
Bolivia
Costs and Cost Analysis
DNA Barcoding, Taxonomic/economics/*methods
Metagenomics/economics/*methods
Tropical Climate

@article {pmid30129704,
year = {2018},
author = {Macher, JN and Vivancos, A and Piggott, JJ and Centeno, FC and Matthaei, CD and Leese, F},
title = {Comparison of environmental DNA and bulk-sample metabarcoding using highly degenerate cytochrome c oxidase I primers.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1456-1468},
doi = {10.1111/1755-0998.12940},
pmid = {30129704},
issn = {1755-0998},
mesh = {Aquatic Organisms/classification/*genetics ; DNA/chemistry/*genetics/isolation & purification ; DNA Barcoding, Taxonomic/*methods ; DNA Primers/*genetics ; Electron Transport Complex IV/*genetics ; *Fresh Water ; Metagenomics/*methods ; New Zealand ; Rivers ; },
abstract = {Freshwater biodiversity provides important ecosystem services and is at the core of water quality monitoring worldwide. To assess freshwater biodiversity, genetic methods such as metabarcoding are increasingly used as they are faster and allow better taxonomic resolution than manual identification methods. Either sampled organisms are used directly for "bulk metabarcoding," or water is filtered and the extracted environmental DNA serves as a proxy for biodiversity via "eDNA metabarcoding." Despite the advantages of both methods, questions remain regarding their comparability and applicability for routine biomonitoring and stressor impact assessment. Therefore, we compared metabarcoding results from bulk and eDNA samples taken from 19 streams spanning a wide gradient of farming intensities in New Zealand. We performed PCR with highly degenerate cytochrome c oxidase I primers and sequenced libraries on an Illumina MiSeq. The inferred community composition differed strongly between the two methods. More taxa were captured by eDNA than bulk-sample metabarcoding (5,819 vs. 1,483), but more of the commonly used invertebrate bioindicator taxa (mayflies, stoneflies and caddisflies) were found in bulk (47) than eDNA samples (37). Catchment-wide and local land use impacts on communities were detected better by eDNA metabarcoding, especially for non-metazoan taxa. Our findings imply that bulk-sample metabarcoding resembles classical freshwater biomonitoring approaches better, as more indicator macroinvertebrate taxa are captured. However, eDNA metabarcoding might be better suited to infer the impact of stressors on stream ecosystems at larger scales, as many new and potentially more informative taxa are registered. We therefore suggest exploring both methods in future assessments of stream biodiversity.},
}

Aquatic Organisms/classification/*genetics
DNA/chemistry/*genetics/isolation & purification
DNA Barcoding, Taxonomic/*methods
DNA Primers/*genetics
Electron Transport Complex IV/*genetics
*Fresh Water
Metagenomics/*methods
New Zealand
Rivers

@article {pmid30106226,
year = {2018},
author = {Heeger, F and Bourne, EC and Baschien, C and Yurkov, A and Bunk, B and Spröer, C and Overmann, J and Mazzoni, CJ and Monaghan, MT},
title = {Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1500-1514},
doi = {10.1111/1755-0998.12937},
pmid = {30106226},
issn = {1755-0998},
support = {SAW-2014-IGB-1//Leibniz Association/ ; },
mesh = {Aquatic Organisms/classification/genetics ; Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/*genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Fungal/*genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {DNA metabarcoding is widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints limit most studies to marker lengths below 600 base pairs (bp). Longer sequencing reads of several thousand bp are now possible with third-generation sequencing. Increased marker lengths provide greater taxonomic resolution and allow for phylogenetic methods of classification, but longer reads may be subject to higher rates of sequencing error and chimera formation. In addition, most bioinformatics tools for DNA metabarcoding were designed for short reads and are therefore unsuitable. Here, we used Pacific Biosciences circular consensus sequencing (CCS) to DNA-metabarcode environmental samples using a ca. 4,500 bp marker that included most of the eukaryote SSU and LSU rRNA genes and the complete ITS region. We developed an analysis pipeline that reduced error rates to levels comparable to short-read platforms. Validation using a mock community indicated that our pipeline detected 98% of chimeras de novo. We recovered 947 OTUs from water and sediment samples from a natural lake, 848 of which could be classified to phylum, 397 to genus and 330 to species. By allowing for the simultaneous use of three databases (Unite, SILVA and RDP LSU), long-read DNA metabarcoding provided better taxonomic resolution than any single marker. We foresee the use of long reads enabling the cross-validation of reference sequences and the synthesis of ribosomal rRNA gene databases. The universal nature of the rRNA operon and our recovery of >100 nonfungal OTUs indicate that long-read DNA metabarcoding holds promise for studies of eukaryotic diversity more broadly.},
}

Aquatic Organisms/classification/genetics
Cluster Analysis
DNA Barcoding, Taxonomic/*methods
DNA, Fungal/chemistry/genetics
DNA, Ribosomal Spacer/chemistry/genetics
Fungi/*classification/*genetics
Metagenomics/*methods
Phylogeny
RNA, Fungal/*genetics
RNA, Ribosomal/genetics
RNA, Ribosomal, 18S/genetics
Sequence Analysis, DNA

@article {pmid30014577,
year = {2018},
author = {Cordier, T and Forster, D and Dufresne, Y and Martins, CIM and Stoeck, T and Pawlowski, J},
title = {Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1381-1391},
doi = {10.1111/1755-0998.12926},
pmid = {30014577},
issn = {1755-0998},
support = {316030_150817//Swiss Network for International Studies/ ; 31003A_179125//Swiss National Science Foundation/ ; STO414/15-1//Deutsche Forschungsgemeinschaft/ ; //Carl Zeiss Foundation/ ; //NVIDIA GPU grant program/ ; },
mesh = {Bacteria/*classification ; *Biodiversity ; Biomarkers/analysis ; Computer Simulation ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring/*methods ; Eukaryota/*classification ; Metagenomics/*methods ; RNA, Ribosomal/genetics ; *Supervised Machine Learning ; },
abstract = {Biodiversity monitoring is the standard for environmental impact assessment of anthropogenic activities. Several recent studies showed that high-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) could overcome many limitations of the traditional morphotaxonomy-based bioassessment. Recently, we demonstrated that supervised machine learning (SML) can be used to predict accurate biotic indices values from eDNA metabarcoding data, regardless of the taxonomic affiliation of the sequences. However, it is unknown to which extent the accuracy of such models depends on taxonomic resolution of molecular markers or how SML compares with metabarcoding approaches targeting well-established bioindicator species. In this study, we address these issues by training predictive models upon five different ribosomal bacterial and eukaryotic markers and measuring their performance to assess the environmental impact of marine aquaculture on independent data sets. Our results show that all tested markers are yielding accurate predictive models and that they all outperform the assessment relying solely on taxonomically assigned sequences. Remarkably, we did not find any significant difference in the performance of the models built using universal eukaryotic or prokaryotic markers. Using any molecular marker with a taxonomic range broad enough to comprise different potential bioindicator taxa, SML approach can overcome the limits of taxonomy-based eDNA bioassessment.},
}

Bacteria/*classification
*Biodiversity
Biomarkers/analysis
Computer Simulation
DNA Barcoding, Taxonomic/*methods
Environmental Monitoring/*methods
Eukaryota/*classification
Metagenomics/*methods
RNA, Ribosomal/genetics
*Supervised Machine Learning

@article {pmid29978606,
year = {2018},
author = {Xiong, W and Zhan, A},
title = {Testing clustering strategies for metabarcoding-based investigation of community-environment interactions.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1326-1338},
doi = {10.1111/1755-0998.12922},
pmid = {29978606},
issn = {1755-0998},
support = {31572228//National Natural Science Foundation of China/ ; ZDRW-ZS-2016-5-6//The Key Research Program of the Chinese Academy of Sciences/ ; 2015//The Innovation in Cross-functional Team Program of the Chinese Academy of Sciences/ ; 2015ZX07201-008-09//Water Pollution Control and Treatment Special Project/ ; 15K01ESPCR//The State Key Joint Laboratory of Environment Simulation and Pollution Control (RCEES, Chinese Academy of Sciences)/ ; 2017M620927//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; China ; *Cluster Analysis ; Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; *Environmental Exposure ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Rivers ; Water Pollutants/toxicity ; Zooplankton/drug effects ; },
abstract = {The degradation of freshwater ecosystems has become a common ecological and environmental problem globally. Owing to the complexity of biological communities, there remain tremendous technical challenges for investigating influence of environmental stressors (e.g., chemical pollution) on biological communities. High-throughput sequencing-based metabarcoding provides a powerful tool to reveal complex interactions between environments and biological communities. Among many technical issues, the clustering strategies for operational taxonomic units (OTUs) which are crucial for assessing biodiversity of communities, may affect final conclusions. Here, we used zooplankton communities along an environmental pollution gradient in the Chaobai River in Northern China to test different clustering strategies, including nonclustering and clustering with varied thresholds. Our results showed that though the number of OTUs estimated by nonclustering strategies and clustering strategies with divergence thresholds of 99%-97% largely varied, they were able to identify the same set of significant environmental and spatial variables responsible for geographical distributions of zooplankton communities. In addition, the ecological conclusions obtained by clustering thresholds of 99%-97% were consistent with nonclustering strategies, where for all eight clustering scenarios we detected that species sorting predicted by environmental variables overrode dispersal as the dominant factor in structuring zooplankton communities. However, clustering with the divergence thresholds of <95% affected the environmental and spatial variables identified. We conclude that both newly developed nonclustering methods and traditional clustering methods with divergence thresholds ≥97% were reliable to reveal mechanisms of complex community-environment interactions, although different clustering strategies could lead to largely varied biodiversity estimates such as those for α-diversity.},
}

Animals
China
*Cluster Analysis
Computational Biology/*methods
DNA Barcoding, Taxonomic/*methods
*Environmental Exposure
Environmental Monitoring/*methods
Metagenomics/*methods
Rivers
Water Pollutants/toxicity
Zooplankton/drug effects

@article {pmid29877042,
year = {2018},
author = {Schnell, IB and Bohmann, K and Schultze, SE and Richter, SR and Murray, DC and Sinding, MS and Bass, D and Cadle, JE and Campbell, MJ and Dolch, R and Edwards, DP and Gray, TNE and Hansen, T and Hoa, ANQ and Noer, CL and Heise-Pavlov, S and Sander Pedersen, AF and Ramamonjisoa, JC and Siddall, ME and Tilker, A and Traeholt, C and Wilkinson, N and Woodcock, P and Yu, DW and Bertelsen, MF and Bunce, M and Gilbert, MTP},
title = {Debugging diversity - a pan-continental exploration of the potential of terrestrial blood-feeding leeches as a vertebrate monitoring tool.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1282-1298},
doi = {10.1111/1755-0998.12912},
pmid = {29877042},
issn = {1755-0998},
support = {DNRF94//Danish National Research Foundation/ ; //University of Copenhagen/ ; FT0991741//Australian Research Council Future Fellowship/ ; //KfW Bankengruppe/ ; //WWF Germany/ ; DFF-5051-00140//The Danish Council for Independent Research/ ; 31400470//National Natural Science Foundation of China/ ; 41661144002//National Natural Science Foundation of China/ ; 2012FY110800//Ministry of Science and Technology of China/ ; GREKF13-13//State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology/ ; GREKF14-13//State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology/ ; GREKF16-09//State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology/ ; },
mesh = {Amphibians/parasitology ; Animals ; Birds/parasitology ; Blood Chemical Analysis/*methods ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring/*methods ; High-Throughput Nucleotide Sequencing/methods ; Leeches/*growth & development ; Mammals/parasitology ; Metagenomics/*methods ; Reptiles/parasitology ; },
abstract = {The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and amphibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate biodiversity.},
}

Amphibians/parasitology
Animals
Birds/parasitology
Blood Chemical Analysis/*methods
DNA Barcoding, Taxonomic/*methods
Environmental Monitoring/*methods
High-Throughput Nucleotide Sequencing/methods
Leeches/*growth & development
Mammals/parasitology
Metagenomics/*methods
Reptiles/parasitology

@article {pmid29551526,
year = {2018},
author = {Santos, JC and Tarvin, RD and O'Connell, LA and Blackburn, DC and Coloma, LA},
title = {Diversity within diversity: Parasite species richness in poison frogs assessed by transcriptomics.},
journal = {Molecular phylogenetics and evolution},
volume = {125},
number = {},
pages = {40-50},
doi = {10.1016/j.ympev.2018.03.015},
pmid = {29551526},
issn = {1095-9513},
mesh = {Animals ; Anura/*genetics/*parasitology ; Biodiversity ; *Gene Expression Profiling ; Genetic Speciation ; Host-Parasite Interactions/genetics ; Parasites/*physiology ; Phylogeny ; Poisons ; Species Specificity ; Transcriptome/genetics ; },
abstract = {Symbionts (e.g., endoparasites and commensals) play an integral role in their host's ecology, yet in many cases their diversity is likely underestimated. Although endoparasites are traditionally characterized using morphology, sequences of conserved genes, and shotgun metagenomics, host transcriptomes constitute an underused resource to identify these organisms' diversity. By isolating non-host transcripts from host transcriptomes, individual host tissues can now simultaneously reveal their endoparasite species richness (i.e., number of different taxa) and provide insights into parasite gene expression. These approaches can be used in host taxa whose endoparasites are mostly unknown, such as those of tropical amphibians. Here, we focus on the poison frogs (Dendrobatidae) as hosts, which are a Neotropical clade known for their bright coloration and defensive alkaloids. These toxins are an effective protection against vertebrate predators (e.g., snakes and birds), bacteria, and skin-biting ectoparasites (e.g., mosquitoes); however, little is known about their deterrence against eukaryotic endoparasites. With de novo transcriptomes of dendrobatids, we developed a bioinformatics pipeline for endoparasite identification that uses host annotated RNA-seq data and set of a priori parasite taxonomic terms, which are used to mine for specific endoparasites. We found a large community of helminths and protozoans that were mostly restricted to the digestive tract and a few systemic parasites (e.g., Trypanosoma). Contrary to our expectations, all dendrobatid frogs regardless of the presence of alkaloid defenses have endoparasites, with their highest species richness located in the frog digestive tract. Some of these organisms (e.g., roundworms) might prove to be generalists, as they were not found to be co-diversifying with their frog hosts. We propose that endoparasites may escape poison frogs' chemical defenses by colonizing tissues with fewer alkaloids than the frog's skin, where most toxins are stored.},
}

Animals
Anura/*genetics/*parasitology
Biodiversity
*Gene Expression Profiling
Genetic Speciation
Host-Parasite Interactions/genetics
Parasites/*physiology
Phylogeny
Poisons
Species Specificity
Transcriptome/genetics

@article {pmid29396546,
year = {2018},
author = {Gonzalez-Martinez, A and Sihvonen, M and Muñoz-Palazon, B and Rodriguez-Sanchez, A and Mikola, A and Vahala, R},
title = {Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {2208},
pmid = {29396546},
issn = {2045-2322},
mesh = {Archaea/classification/genetics/*isolation & purification ; Arctic Regions ; Bacteria/classification/genetics/*isolation & purification ; Bioreactors/*microbiology ; *Biota ; Finland ; Fungi/classification/genetics/*isolation & purification ; Metagenomics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/microbiology ; Waste Water/*microbiology ; Water Purification ; },
abstract = {Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.},
}

Archaea/classification/genetics/*isolation & purification
Arctic Regions
Bacteria/classification/genetics/*isolation & purification
Bioreactors/*microbiology
*Biota
Finland
Fungi/classification/genetics/*isolation & purification
Metagenomics
Real-Time Polymerase Chain Reaction
Sequence Analysis, DNA
Sewage/microbiology
Waste Water/*microbiology
Water Purification

@article {pmid29395346,
year = {2018},
author = {Limborg, MT and Alberdi, A and Kodama, M and Roggenbuck, M and Kristiansen, K and Gilbert, MTP},
title = {Applied Hologenomics: Feasibility and Potential in Aquaculture.},
journal = {Trends in biotechnology},
volume = {36},
number = {3},
pages = {252-264},
doi = {10.1016/j.tibtech.2017.12.006},
pmid = {29395346},
issn = {1879-3096},
mesh = {Animals ; *Aquaculture ; Epigenomics ; *Feasibility Studies ; Fishes/*microbiology ; Food Industry ; Gastrointestinal Microbiome/genetics/immunology ; Genome, Microbial/genetics/immunology ; Humans ; Immune System/immunology/microbiology ; *Metagenomics ; Proteomics ; Transcriptome ; },
abstract = {Aquaculture will play an essential role in feeding a growing human population, but several biological challenges impede sustainable growth of production. Emerging evidence across all areas of life has revealed the importance of the intimate biological interactions between animals and their associated gut microbiota. Based on challenges in aquaculture, we leverage current knowledge in molecular biology and host microbiota interactions to propose an applied holo-omic framework that integrates molecular data including genomes, transcriptomes, epigenomes, proteomes, and metabolomes for analyzing fish and their gut microbiota as interconnected and coregulated systems. With an eye towards aquaculture, we discuss the feasibility and potential of our holo-omic framework to improve growth, health, and sustainability in any area of food production, including livestock and agriculture.},
}

Animals
*Aquaculture
Epigenomics
*Feasibility Studies
Fishes/*microbiology
Food Industry
Gastrointestinal Microbiome/genetics/immunology
Genome, Microbial/genetics/immunology
Humans
Immune System/immunology/microbiology
*Metagenomics
Proteomics
Transcriptome

@article {pmid29330424,
year = {2018},
author = {Cui, X and Ye, L and Li, J and Jin, L and Wang, W and Li, S and Bao, M and Wu, S and Li, L and Geng, B and Zhou, X and Zhang, J and Cai, J},
title = {Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {635},
pmid = {29330424},
issn = {2045-2322},
mesh = {Adult ; Aged ; Bacteria/*classification/genetics/isolation & purification ; Butyrates/analysis ; Dysbiosis/*diagnosis ; Female ; Gastrointestinal Microbiome ; Heart Failure/*complications ; Humans ; Male ; Metabolomics/*methods ; Metagenomics/*methods ; Methylamines/analysis ; Middle Aged ; Phylogeny ; },
abstract = {Previous studies suggested a possible gut microbiota dysbiosis in chronic heart failure (CHF). However, direct evidence was lacking. In this study, we investigated the composition and metabolic patterns of gut microbiota in CHF patients to provide direct evidence and comprehensive understanding of gut microbiota dysbiosis in CHF. We enrolled 53 CHF patients and 41 controls. Metagenomic analyses of faecal samples and metabolomic analyses of faecal and plasma samples were then performed. We found that the composition of gut microbiota in CHF was significantly different from controls. Faecalibacterium prausnitzii decrease and Ruminococcus gnavus increase were the essential characteristics in CHF patients' gut microbiota. We also observed an imbalance of gut microbes involved in the metabolism of protective metabolites such as butyrate and harmful metabolites such as trimethylamine N-oxide in CHF patients. Metabolic features of both faecal and plasma samples from CHF patients also significantly changed. Moreover, alterations in faecal and plasma metabolic patterns correlated with gut microbiota dysbiosis in CHF. Taken together, we found that CHF was associated with distinct gut microbiota dysbiosis and pinpointed the specific core bacteria imbalance in CHF, along with correlations between changes in certain metabolites and gut microbes.},
}

Adult
Aged
Bacteria/*classification/genetics/isolation & purification
Butyrates/analysis
Dysbiosis/*diagnosis
Female
Gastrointestinal Microbiome
Heart Failure/*complications
Humans
Male
Metabolomics/*methods
Metagenomics/*methods
Methylamines/analysis
Middle Aged
Phylogeny

@article {pmid29194469,
year = {2018},
author = {McIver, LJ and Abu-Ali, G and Franzosa, EA and Schwager, R and Morgan, XC and Waldron, L and Segata, N and Huttenhower, C},
title = {bioBakery: a meta'omic analysis environment.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {7},
pages = {1235-1237},
pmid = {29194469},
issn = {1367-4811},
support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; },
mesh = {Metagenomics/*methods ; Microbiota/*genetics ; Reproducibility of Results ; *Software ; Workflow ; },
abstract = {Summary: bioBakery is a meta'omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured analysis modules also joined into workflows for reproducibility.

bioBakery (http://huttenhower.sph.harvard.edu/biobakery) is publicly available for local installation as individual modules and as a virtual machine image. Each individual module has been developed to perform a particular task (e.g. quantitative taxonomic profiling or statistical analysis), and they are provided with source code, tutorials, demonstration data, and validation results; the bioBakery virtual image includes the entire suite of modules and their dependencies pre-installed. Images are available for both Amazon EC2 and Google Compute Engine. All software is open source under the MIT license. bioBakery is actively maintained with a support group at biobakery-users@googlegroups.com and new tools being added upon their release.

Contact: chuttenh@hsph.harvard.edu.

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

Metagenomics/*methods
Microbiota/*genetics
Reproducibility of Results
*Software
Workflow

@article {pmid29040406,
year = {2018},
author = {Pericard, P and Dufresne, Y and Couderc, L and Blanquart, S and Touzet, H},
title = {MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {4},
pages = {585-591},
doi = {10.1093/bioinformatics/btx644},
pmid = {29040406},
issn = {1367-4811},
mesh = {Algorithms ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Metagenome ; Metagenomics/methods ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; *Software ; },
abstract = {Motivation: Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution.

Results: We designed MATAM, a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. The method implements a stepwise process based on construction and analysis of a read overlap graph. It is applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes. We show that MATAM outperforms other available methods in terms of low error rates and recovered fractions and is suitable to provide improved assemblies for precise taxonomic assignments.

https://github.com/bonsai-team/matam.

Contact: pierre.pericard@gmail.com or helene.touzet@univ-lille1.fr.

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

Algorithms
Gastrointestinal Microbiome/*genetics
High-Throughput Nucleotide Sequencing/*methods
Humans
*Metagenome
Metagenomics/methods
*Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA/methods
*Software

@article {pmid28588195,
year = {2017},
author = {Kang, J and Ma, X and He, S},
title = {Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2813},
pmid = {28588195},
issn = {2045-2322},
mesh = {Animals ; Catfishes/*genetics ; Genome/genetics ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; },
abstract = {Advances in genome scanning using high-throughput sequencing technologies has led to a revolution in studies of non-model organisms. The glyptosternoid fish Creteuchiloglanis macropterus, is widely distributed in the main stem and tributaries of the Nujiang River basin. Here, we analyzed IIB restriction-site-associated DNA (2b-RAD) sequences and mitochondrial DNA sequences, to assess the genomic signature of adaptation by detecting and estimating the degree of genetic differentiation among ten Creteuchiloglanis macropterus populations from the Nujiang River. The analyses revealed significant population differentiation among the up-tributaries, main stem, mid-tributary and low-tributary. Annotation of contigs containing outlier SNPs revealed that the candidate genes showed significant enrichment in several important biological process terms between up-tributaries and low-tributary, and exhibited prominent enrichment in the term macromolecular metabolic process between all tributaries and the main stem. Population dynamics analyses indicated that the Late Pleistocene glaciations strongly influenced the demographic history of C. macropterus. Our results provide strong evidence for the utility of RAD-seq in population genetics studies, and our generated SNP resource should provide a valuable tool for population genomics studies of C. macropterus in the future.},
}

Animals
Catfishes/*genetics
Genome/genetics
High-Throughput Nucleotide Sequencing
*Metagenomics
Polymorphism, Single Nucleotide/genetics
Sequence Analysis, DNA

@article {pmid28539641,
year = {2017},
author = {Alessi, AM and Bird, SM and Bennett, JP and Oates, NC and Li, Y and Dowle, AA and Polikarpov, I and Young, JPW and McQueen-Mason, SJ and Bruce, NC},
title = {Revealing the insoluble metasecretome of lignocellulose-degrading microbial communities.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2356},
pmid = {28539641},
issn = {2045-2322},
support = {BB/1018492/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K020358/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J014443/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Biomass ; Lignin/*metabolism ; Mass Spectrometry ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota ; Oryza/growth & development/microbiology ; Proteome/genetics/*metabolism ; Proteomics/*methods ; Transcriptome/genetics ; Triticum/growth & development/microbiology ; },
abstract = {Microbial communities metabolize plant biomass using secreted enzymes; however, identifying extracellular proteins tightly bound to insoluble lignocellulose in these microbiomes presents a challenge, as the rigorous extraction required to elute these proteins also lyses the microbes associated with the plant biomass releasing intracellular proteins that contaminate the metasecretome. Here we describe a technique for targeting the extracellular proteome, which was used to compare the metasecretome and meta-surface-proteome of two lignocellulose-degrading communities grown on wheat straw and rice straw. A combination of mass spectrometry-based proteomics coupled with metatranscriptomics enabled the identification of a unique secretome pool from these lignocellulose-degrading communities. This method enabled us to efficiently discriminate the extracellular proteins from the intracellular proteins by improving detection of actively secreted and transmembrane proteins. In addition to the expected carbohydrate active enzymes, our new method reveals a large number of unknown proteins, supporting the notion that there are major gaps in our understanding of how microbial communities degrade lignocellulosic substrates.},
}

Biomass
Lignin/*metabolism
Mass Spectrometry
Metagenome/genetics
Metagenomics/methods
*Microbiota
Oryza/growth & development/microbiology
Proteome/genetics/*metabolism
Proteomics/*methods
Transcriptome/genetics
Triticum/growth & development/microbiology

@article {pmid30522530,
year = {2018},
author = {Edlund, A and Yang, Y and Yooseph, S and He, X and Shi, W and McLean, JS},
title = {Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {217},
doi = {10.1186/s40168-018-0591-4},
pmid = {30522530},
issn = {2049-2618},
support = {R00DE024543//National Institute of Dental and Craniofacial Research/ ; K99DE024543//National Institute of Dental and Craniofacial Research/ ; 1R01DE023810//National Institute of Dental and Craniofacial Research/ ; 1R01DE023810//National Institute of Dental and Craniofacial Research/ ; 1R01DE023810//National Institute of Dental and Craniofacial Research/ ; 1R01DE020102//National Institute of Dental and Craniofacial Research/ ; 1R01DE020102//National Institute of Dental and Craniofacial Research/ ; 1R01DE020102//National Institute of Dental and Craniofacial Research/ ; 1R01DE026186//National Institute of Dental and Craniofacial Research/ ; 1R01DE026186//National Institute of Dental and Craniofacial Research/ ; 1R01DE026186//National Institute of Dental and Craniofacial Research/ ; R01GM095373//National Institute of General Medical Sciences/ ; },
abstract = {BACKGROUND: Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processes such as co-aggregation, competition for space and resources, and by bacterially produced reactive agents. Knowledge on the dynamics of assembly within complex communities is very limited and derives mainly from studies composed of a limited number of bacterial species. To fill current knowledge gaps, we applied parallel metagenomic and metatranscriptomic analyses during assembly and maturation of an in vitro oral biofilm. This model system has previously demonstrated remarkable reproducibility in taxonomic composition across replicate samples during maturation.

RESULTS: Time course analysis of the biofilm maturation was performed by parallel sampling every 2-3 h for 24 h for both DNA and RNA. Metagenomic analyses revealed that community taxonomy changed most dramatically between three and six hours of growth when pH dropped from 6.5 to 5.5. By applying comparative metatranscriptome analysis we could identify major shifts in overall community activities between six and nine hours of growth when pH dropped below 5.5, as 29,015 genes were significantly up- or down- expressed. Several of the differentially expressed genes showed unique activities for individual bacterial genomes and were associated with pyruvate and lactate metabolism, two-component signaling pathways, production of antibacterial molecules, iron sequestration, pH neutralization, protein hydrolysis, and surface attachment. Our analysis also revealed several mechanisms responsible for the niche expansion of the cariogenic pathogen Lactobacillus fermentum.

CONCLUSION: It is highly regarded that acidic conditions in dental plaque cause a net loss of enamel from teeth. Here, as pH drops below 5.5 pH to 4.7, we observe blooms of cariogenic lactobacilli, and a transition point of many bacterial gene expression activities within the community. To our knowledge, this represents the first study of the assembly and maturation of a complex oral bacterial biofilm community that addresses gene level functional responses over time.},
}

@article {pmid30394652,
year = {2018},
author = {Borton, MA and Daly, RA and O'Banion, B and Hoyt, DW and Marcus, DN and Welch, S and Hastings, SS and Meulia, T and Wolfe, RA and Booker, AE and Sharma, S and Cole, DR and Wunch, K and Moore, JD and Darrah, TH and Wilkins, MJ and Wrighton, KC},
title = {Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale.},
journal = {Environmental microbiology},
volume = {20},
number = {12},
pages = {4596-4611},
doi = {10.1111/1462-2920.14467},
pmid = {30394652},
issn = {1462-2920},
support = {1342701//National Science Foundation Dimensions of Biodiversity/ ; FE0024297//Department of Energy's National Energy Technology Laboratory/ ; //U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//Office of Science of the U.S. Department of Energy/ ; },
abstract = {About 60% of natural gas production in the United States comes from hydraulic fracturing of unconventional reservoirs, such as shales or organic-rich micrites. This process inoculates and enriches for halotolerant microorganisms in these reservoirs over time, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of methanogens across unconventional reservoirs, and report that members of genus Methanohalophilus are recovered from every hydraulically fractured unconventional reservoir sampled by metagenomics. We provide the first genomic sequencing of three isolate genomes, as well as two metagenome assembled genomes (MAGs). Utilizing six other previously sequenced isolate genomes and MAGs, we perform comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in CRISPR-Cas systems of Methanohalophilus, with genomes from geographically distinct unconventional reservoirs sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic methane production in hydraulically fractured unconventional reservoirs.},
}

@article {pmid29739908,
year = {2018},
author = {Gladieux, P},
title = {Updates in the Language of Histoplasma Biodiversity.},
journal = {mBio},
volume = {9},
number = {3},
pages = {},
pmid = {29739908},
issn = {2150-7511},
mesh = {*Biodiversity ; Biological Evolution ; Genetic Speciation ; *Histoplasma ; Humans ; Metagenomics ; Phylogeny ; },
abstract = {In a recent article, Sepúlveda et al. (mBio 8:e01339-17, 2017, https://doi.org/10.1128/mBio.01339-17) investigated the genetic structure and evolutionary history of the human pathogen Histoplasma Using whole-genome resequencing data, Sepúlveda et al. found that the Histoplasma genus is composed of at least four strongly differentiated lineages. Their tour de force is to use a smart combination of population genomic approaches to show that the advanced stage of intraspecific divergence observed within Histoplasma does not simply reflect population structure, but instead results from previously unidentified speciation events. The four independently evolving Histoplasma lineages are elevated to the species status and assigned names. The newly described species exhibit medically important differences in phenotype, and these findings, therefore, have important epidemiological implications. This work provides a blueprint for phylogenomic species recognition in fungi, opening the way for a new age of enlightenment in which fungal species are diagnosed using highly discriminatory tools within a hypothesis-testing framework.},
}

*Biodiversity
Biological Evolution
Genetic Speciation
*Histoplasma
Humans
Metagenomics
Phylogeny

@article {pmid29668334,
year = {2018},
author = {Amrane, S and Raoult, D and Lagier, JC},
title = {Metagenomics, culturomics, and the human gut microbiota.},
journal = {Expert review of anti-infective therapy},
volume = {16},
number = {5},
pages = {373-375},
doi = {10.1080/14787210.2018.1467268},
pmid = {29668334},
issn = {1744-8336},
mesh = {Culture Techniques/*methods ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; },
}

Culture Techniques/*methods
Gastrointestinal Microbiome/*physiology
High-Throughput Nucleotide Sequencing/methods
Humans
Metagenomics/*methods

@article {pmid30384903,
year = {2018},
author = {Huang, X and Zhu, J and Cai, Z and Lao, Y and Jin, H and Yu, K and Zhang, B and Zhou, J},
title = {Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach.},
journal = {Microbiological research},
volume = {217},
number = {},
pages = {1-13},
doi = {10.1016/j.micres.2018.08.015},
pmid = {30384903},
issn = {1618-0623},
mesh = {Acyltransferases/genetics/metabolism ; Bacteria/classification/*genetics/*metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Carbon-Sulfur Lyases/genetics/metabolism ; China ; Dinoflagellida/growth & development/*microbiology ; Eutrophication/physiology ; Marine Biology ; Metagenomics/*methods ; Microbiota/*genetics/*physiology ; Phylogeny ; Proteobacteria/genetics/metabolism ; Quorum Sensing/*genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis ; Sequence Analysis, Protein ; Sequence Homology ; Symbiosis ; Transcription Factors/genetics/metabolism ; },
abstract = {The complicated relationships among environmental microorganisms are regulated by quorum sensing (QS). Understanding QS-based signals could shed light on the interactions between microbial communities in certain environments. Although QS characteristics have been widely discussed, few studies have been conducted on the role of QS in phycospheric microorganisms. Here, we used metagenomics to examine the profile of AI-1 (AinS, HdtS, LuxI) and AI-2 (LuxS) autoinducers from a deeply sequenced microbial database, obtained from a complete dinoflagellate bloom. A total of 3001 putative AI-1 homologs and 130 AI-2 homologs were identified. The predominant member among the AI groups was HdtS. The abundance of HdtS, AinS, and LuxS increased as the bloom developed, whereas the abundance of LuxI showed the opposite trend. Phylogenetic analysis suggested that HdtS and LuxI synthase originated mainly from alpha-, beta-, and gamma-Proteobacteria, whereas AinS synthase originated solely from Vibrionales. In comparison to AI-1, the sequences related to AI-2 (LuxS) demonstrated a much wider taxonomic coverage. Some significant correlations were found between dominant species and QS signals. In addition to the QS, we also performed parallel analysis of the quorum quenching (QQ) sequences. In comparison to QS, the relative abundance of QQ signals was lower; however, an obvious frequency correlation was observed. These results suggested that QS and QQ signals co-participate in regulating microbial communities during an algal bloom. These data helped to reveal the characteristic behavior of algal symbiotic bacteria, and facilitated a better understanding of microbial dynamics during an algal bloom event from a chemical ecological perspective.},
}

Acyltransferases/genetics/metabolism
Bacteria/classification/*genetics/*metabolism
Bacterial Physiological Phenomena
Bacterial Proteins/genetics/metabolism
Carbon-Sulfur Lyases/genetics/metabolism
China
Dinoflagellida/growth & development/*microbiology
Eutrophication/physiology
Marine Biology
Metagenomics/*methods
Microbiota/*genetics/*physiology
Phylogeny
Proteobacteria/genetics/metabolism
Quorum Sensing/*genetics/*physiology
RNA, Ribosomal, 16S/genetics
Seawater/microbiology
Sequence Analysis
Sequence Analysis, Protein
Sequence Homology
Symbiosis
Transcription Factors/genetics/metabolism

@article {pmid27188959,
year = {2016},
author = {Angelakis, E and Bachar, D and Henrissat, B and Armougom, F and Audoly, G and Lagier, JC and Robert, C and Raoult, D},
title = {Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {26276},
pmid = {27188959},
issn = {2045-2322},
mesh = {Bacteria/genetics ; DNA, Bacterial/genetics/*isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Kwashiorkor/microbiology ; *Metagenomics ; Obesity/microbiology ; Polysaccharides/*chemistry ; Polysaccharides, Bacterial/chemistry ; Protein-Energy Malnutrition/microbiology ; },
abstract = {Exopolysaccharides produced by bacterial species and present in feces are extremely inhibitory to DNA restriction and can cause discrepancies in metagenomic studies. We determined the effects of different DNA extraction methods on the apparent composition of the gut microbiota using Illumina MiSeq deep sequencing technology. DNA was extracted from the stool from an obese female using 10 different methods and the choice of DNA extraction method affected the proportional abundance at the phylum level, species richness (Chao index, 227 to 2,714) and diversity (non parametric Shannon, 1.37 to 4.4). Moreover DNA was extracted from stools obtained from 83 different individuals by the fastest extraction assay and by an extraction assay that degradated exopolysaccharides. The fastest extraction method was able to detect 68% to 100% genera and 42% to 95% species whereas the glycan degradation extraction method was able to detect 56% to 93% genera and 25% to 87% species. To allow a good liberation of DNA from exopolysaccharides commonly presented in stools, we recommend the mechanical lysis of stools plus glycan degradation, used here for the first time. Caution must be taken in the interpretation of current metagenomic studies, as the efficiency of DNA extraction varies widely among stool samples.},
}

Bacteria/genetics
DNA, Bacterial/genetics/*isolation & purification
Feces/microbiology
Female
Gastrointestinal Microbiome/*genetics
High-Throughput Nucleotide Sequencing
Humans
Kwashiorkor/microbiology
*Metagenomics
Obesity/microbiology
Polysaccharides/*chemistry
Polysaccharides, Bacterial/chemistry
Protein-Energy Malnutrition/microbiology

@article {pmid30532085,
year = {2018},
author = {Chen, B and Yu, T and Xie, S and Du, K and Liang, X and Lan, Y and Sun, C and Lu, X and Shao, Y},
title = {Comparative shotgun metagenomic data of the silkworm Bombyx mori gut microbiome.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180285},
doi = {10.1038/sdata.2018.285},
pmid = {30532085},
issn = {2052-4463},
abstract = {Lepidoptera (butterflies and moths) is a major insect order including important pollinators and agricultural pests, however their microbiomes are little studied. Here, using next-generation sequencing (NGS)-based shotgun metagenomics, we characterize both the biodiversity and functional potential of gut microbiota of a lepidopteran model insect, the silkworm Bombyx mori. Two metagenomes, including the standard inbred strain Dazao (P50) and an improved hybrid strain Qiufeng × Baiyu (QB) widely used in commercial silk production, were generated, containing 45,505,084 and 69,127,002 raw reads, respectively. Taxonomic analysis revealed that a total of 663 bacterial species were identified in P50 silkworms, while 322 unique species in QB silkworms. Notably, Enterobacter, Acinetobacter and Enterococcus were dominated in both strains. The further functional annotation was performed by both BlastP and MG-RAST against various databases including Nr, COG, KEGG, CAZy and SignalP, which revealed >5 × 106 protein-coding genes. These datasets not only provide first insights into all bacterial genes in silkworm guts, but also help to generate hypotheses for subsequently testing functional traits of gut microbiota in an important insect group.},
}

@article {pmid30528276,
year = {2018},
author = {Ramos-Barbero, MD and Martin-Cuadrado, AB and Viver, T and Santos, F and Martinez-Garcia, M and Antón, J},
title = {Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly.},
journal = {Systematic and applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.syapm.2018.11.001},
pmid = {30528276},
issn = {1618-0984},
abstract = {Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next generation sequencing, are democratizing this powerful approach that is spreading from specialized research groups to the general public. Using metagenomes from hypersaline environments, as well as mock metagenomes composed of Archaea and Bacteria frequently found in these systems, we have analyzed the advantages and difficulties of the binning process in these extreme environments to tackle microbial population diversity. These extreme systems harbor relatively low species diversity but high intraspecific diversity, which can compromise metagenome assembly and therefore the whole binning process. The main goal is to compare the output of the binning process with what is previously known from the analyzed samples, based on years of study using different approaches. Several scenarios have been analyzed in detail: (i) a good quality bin from a species highly abundant in the environment; (ii) an intermediate quality bin with incongruences that can be solved by further analyses and manual curation, and (iii) a low-quality bin to investigate the failure to recover a very abundant microbial genome as well as some possible solutions. The latter can be considered the "great metagenomics anomaly" and is mainly due to assembly problems derived from the microdiversity of naturally co-existing populations in nature.},
}

@article {pmid30372979,
year = {2019},
author = {Park, SE and Seo, SH and Kim, EJ and Byun, S and Na, CS and Son, HS},
title = {Changes of microbial community and metabolite in kimchi inoculated with different microbial community starters.},
journal = {Food chemistry},
volume = {274},
number = {},
pages = {558-565},
doi = {10.1016/j.foodchem.2018.09.032},
pmid = {30372979},
issn = {1873-7072},
mesh = {Bacteria/metabolism ; Brassica/metabolism/*microbiology ; *Fermentation ; Fermented Foods/*microbiology ; *Food Microbiology ; *Microbiota ; },
abstract = {Gas chromatography mass spectrometry-based metabolomics and next generation sequencing-based metagenomics were applied to investigate the effect of different microbial community starters (MCSs) on kimchi fermentation. Profiles of metabolites and microbial community in kimchi were remarkably different from those on the first day of fermentation according to MCS used. Kimchi inoculated with MCS5 or MCS10 had relatively higher levels of lactic acid, leucine, propanedioic acid, serine, glycerol, erythritol, and sorbitol but lower levels of butanedioic acid, glyceric acid, myo-inositol, xylose, fructose, and talose compared to control kimchi or kimchi inoculated with MCS1. Microbial communities of kimchi inoculated with MCS1, MCS5, and MCS10 were characterized by high ratios of Leuconostoc, Lactobacillus plantarum, and Lactobacillus brevis, respectively. The microbial community of kimchi formed on the first day of fermentation was stable for 50 days, suggesting that microbial communities containing multiple microorganisms can be used as starters to obtain desired quality of kimchi.},
}

Bacteria/metabolism
Brassica/metabolism/*microbiology
*Fermentation
Fermented Foods/*microbiology
*Food Microbiology
*Microbiota

@article {pmid30173738,
year = {2018},
author = {Stroebel, C and Alexander, T and Workentine, ML and Timsit, E},
title = {Effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of recently weaned beef cattle.},
journal = {Veterinary microbiology},
volume = {223},
number = {},
pages = {126-133},
doi = {10.1016/j.vetmic.2018.08.007},
pmid = {30173738},
issn = {1873-2542},
mesh = {Animals ; Bacteria/genetics/*isolation & purification ; Bovine Respiratory Disease Complex/*microbiology ; Cattle ; DNA, Bacterial/chemistry/genetics ; Female ; *Metagenomics ; *Microbiota ; Moraxella/genetics/isolation & purification ; Mycoplasma/genetics/isolation & purification ; Nasopharynx/microbiology ; RNA, Ribosomal, 16S/chemistry/genetics ; Trachea/microbiology ; Transportation ; Weaning ; },
abstract = {The objective was to study effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of feedlot cattle. Two groups of 30 Angus-cross heifers were studied from weaning to 28 d after arrival at a feedlot. For each group, half the heifers were either transported directly to a feedlot after weaning (RANC) or transported to and co-mingled at an auction market for 24 h before being placed in a feedlot (AUCT). Deep nasal swabs (DNS) and trans-tracheal aspirates (TTA) were collected at weaning (d0) and at on-arrival processing at the feedlot (d2). At 7 (d9) and 28 d (d30) after arrival, DNS were repeated. The DNA was extracted from DNS and TTA and the V4 region of the 16S rRNA gene sequenced (MiSeq). Alpha diversity analysis did not reveal differences between AUCT and RANC. However, bacterial diversity decreased over time in the nasopharynx, especially at d9. Although beta-diversity was not different between AUCT and RANC, interval after arrival and feedlot where heifers were placed affected composition of the nasopharyngeal bacterial communities. In both groups, a large increase in Mycoplasma was observed after arrival; in one group, Mycoplasma bovis was dominant at d9 and remained dominant until d30. However, in the other group, Mycoplasma dispar dominated at d9 and was replaced by Moraxella at d30. We concluded that transportation to and co-mingling at an auction market for 24 h did not significantly influence diversity or composition of nasopharyngeal or tracheal bacterial communities.},
}

Animals
Bacteria/genetics/*isolation & purification
Bovine Respiratory Disease Complex/*microbiology
Cattle
DNA, Bacterial/chemistry/genetics
Female
*Metagenomics
*Microbiota
Moraxella/genetics/isolation & purification
Mycoplasma/genetics/isolation & purification
Nasopharynx/microbiology
RNA, Ribosomal, 16S/chemistry/genetics
Trachea/microbiology
Transportation
Weaning