@article {pmid32645030,
year = {2020},
author = {Vancuren, SJ and Dos Santos, SJ and Hill, JE and , },
title = {Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling.},
journal = {PloS one},
volume = {15},
number = {7},
pages = {e0235682},
pmid = {32645030},
issn = {1932-6203},
support = {//CIHR/Canada ; },
mesh = {Bacteria/genetics ; Chaperonin 60/*genetics ; DNA Barcoding, Taxonomic/*methods ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Vagina/microbiology ; },
abstract = {Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.},
}

Bacteria/genetics
Chaperonin 60/*genetics
DNA Barcoding, Taxonomic/*methods
Female
High-Throughput Nucleotide Sequencing/methods
Humans
Metagenomics/*methods
Microbiota/*genetics
Vagina/microbiology

@article {pmid32007292,
year = {2020},
author = {Santos-Cortez, RLP and Bhutta, MF and Earl, JP and Hafrén, L and Jennings, M and Mell, JC and Pichichero, ME and Ryan, AF and Tateossian, H and Ehrlich, GD},
title = {Panel 3: Genomics, precision medicine and targeted therapies.},
journal = {International journal of pediatric otorhinolaryngology},
volume = {130 Suppl 1},
number = {},
pages = {109835},
doi = {10.1016/j.ijporl.2019.109835},
pmid = {32007292},
issn = {1872-8464},
support = {R01 DC015688/DC/NIDCD NIH HHS/United States ; R01 DC012595/DC/NIDCD NIH HHS/United States ; R01 DC002148/DC/NIDCD NIH HHS/United States ; R01 DC000129/DC/NIDCD NIH HHS/United States ; MC_UP_1503/1/MRC_/Medical Research Council/United Kingdom ; R01 DC015004/DC/NIDCD NIH HHS/United States ; R01 AI080935/AI/NIAID NIH HHS/United States ; R13 DC017389/DC/NIDCD NIH HHS/United States ; },
mesh = {Animals ; Ear, Middle/*microbiology ; Genetic Predisposition to Disease/*genetics ; Genomics ; Humans ; Microbiota/genetics ; Otitis Media/drug therapy/*genetics/*microbiology/prevention & control ; Precision Medicine ; },
abstract = {OBJECTIVE: To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media.

DATA SOURCES: PubMed articles published since the last meeting in June 2015 up to June 2019.

REVIEW METHODS: A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members.

CONCLUSION: Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media.

IMPLICATIONS FOR PRACTICE: In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics.},
}

Animals
Ear, Middle/*microbiology
Genetic Predisposition to Disease/*genetics
Genomics
Humans
Microbiota/genetics
Otitis Media/drug therapy/*genetics/*microbiology/prevention & control
Precision Medicine

@article {pmid31977194,
year = {2020},
author = {Chevrette, MG and Handelsman, J},
title = {From Metagenomes to Molecules: Innovations in Functional Metagenomics Unlock Hidden Chemistry in the Human Microbiome.},
journal = {Biochemistry},
volume = {59},
number = {6},
pages = {729-730},
doi = {10.1021/acs.biochem.0c00033},
pmid = {31977194},
issn = {1520-4995},
mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota ; },
}

Humans
Metagenome
*Metagenomics
*Microbiota

@article {pmid31879084,
year = {2020},
author = {Marsh, RL and Aho, C and Beissbarth, J and Bialasiewicz, S and Binks, M and Cervin, A and Kirkham, LS and Lemon, KP and Slack, MPE and Smith-Vaughan, HC},
title = {Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures.},
journal = {International journal of pediatric otorhinolaryngology},
volume = {130 Suppl 1},
number = {},
pages = {109836},
doi = {10.1016/j.ijporl.2019.109836},
pmid = {31879084},
issn = {1872-8464},
support = {R01 GM117174/GM/NIGMS NIH HHS/United States ; R13 DC017389/DC/NIDCD NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bacteria ; Disease Models, Animal ; Ear, Middle/*microbiology ; Humans ; *Microbiota/drug effects ; Nasopharynx/microbiology ; Otitis Media/*microbiology ; Smoking ; Vaccines/pharmacology ; },
abstract = {OBJECTIVE: To perform a comprehensive review of otitis media microbiome literature published between 1st July 2015 and 30th June 2019.

DATA SOURCES: PubMed database, National Library of Medicine.

REVIEW METHODS: Key topics were assigned to each panel member for detailed review. Draft reviews were collated and circulated for discussion when the panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019. The final draft was prepared with input from all panel members.

CONCLUSIONS: Much has been learned about the different types of bacteria (including commensals) present in the upper respiratory microbiome, but little is known about the virome and mycobiome. A small number of studies have investigated the middle ear microbiome; however, current data are often limited by small sample sizes and methodological heterogeneity between studies. Furthermore, limited reporting of sample collection methods mean that it is often difficult to determine whether bacteria detected in middle ear fluid specimens originated from the middle ear or the external auditory canal. Recent in vitro studies suggest that bacterial interactions in the nasal/nasopharyngeal microbiome may affect otitis media pathogenesis by modifying otopathogen behaviours. Impacts of environmental pressures (e.g. smoke, nutrition) and clinical interventions (e.g. vaccination, antibiotics) on the upper respiratory and middle ear microbiomes remain poorly understood as there are few data.

IMPLICATIONS FOR PRACTICE: Advances in understanding bacterial dynamics in the upper airway microbiome are driving development of microbiota-modifying therapies to prevent or treat disease (e.g. probiotics). Further advances in otitis media microbiomics will likely require technological improvements that overcome the current limitations of OMICs technologies when applied to low volume and low biomass specimens that potentially contain high numbers of host cells. Improved laboratory models are needed to elucidate mechanistic interactions among the upper respiratory and middle ear microbiomes. Minimum reporting standards are critically needed to improve inter-study comparisons and enable future meta-analyses.},
}

Animals
Anti-Bacterial Agents/pharmacology
*Bacteria
Disease Models, Animal
Ear, Middle/*microbiology
Humans
*Microbiota/drug effects
Nasopharynx/microbiology
Otitis Media/*microbiology
Smoking
Vaccines/pharmacology

@article {pmid31722195,
year = {2019},
author = {Hertel, J and Harms, AC and Heinken, A and Baldini, F and Thinnes, CC and Glaab, E and Vasco, DA and Pietzner, M and Stewart, ID and Wareham, NJ and Langenberg, C and Trenkwalder, C and Krüger, R and Hankemeier, T and Fleming, RMT and Mollenhauer, B and Thiele, I},
title = {Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease.},
journal = {Cell reports},
volume = {29},
number = {7},
pages = {1767-1777.e8},
doi = {10.1016/j.celrep.2019.10.035},
pmid = {31722195},
issn = {2211-1247},
support = {MC_UU_12015/1/MRC_/Medical Research Council/United Kingdom ; MR/N003284/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Aged ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Parkinson Disease/*microbiology ; Sulfur/*metabolism ; },
abstract = {Parkinson's disease (PD) exhibits systemic effects on the human metabolism, with emerging roles for the gut microbiome. Here, we integrate longitudinal metabolome data from 30 drug-naive, de novo PD patients and 30 matched controls with constraint-based modeling of gut microbial communities derived from an independent, drug-naive PD cohort, and prospective data from the general population. Our key results are (1) longitudinal trajectory of metabolites associated with the interconversion of methionine and cysteine via cystathionine differed between PD patients and controls; (2) dopaminergic medication showed strong lipidomic signatures; (3) taurine-conjugated bile acids correlated with the severity of motor symptoms, while low levels of sulfated taurolithocholate were associated with PD incidence in the general population; and (4) computational modeling predicted changes in sulfur metabolism, driven by A. muciniphila and B. wadsworthia, which is consistent with the changed metabolome. The multi-omics integration reveals PD-specific patterns in microbial-host sulfur co-metabolism that may contribute to PD severity.},
}

Aged
Female
*Gastrointestinal Microbiome
Humans
Longitudinal Studies
Male
Middle Aged
Parkinson Disease/*microbiology
Sulfur/*metabolism

@article {pmid31689942,
year = {2019},
author = {Sommers, P and Fontenele, RS and Kringen, T and Kraberger, S and Porazinska, DL and Darcy, JL and Schmidt, SK and Varsani, A},
title = {Single-Stranded DNA Viruses in Antarctic Cryoconite Holes.},
journal = {Viruses},
volume = {11},
number = {11},
pages = {},
pmid = {31689942},
issn = {1999-4915},
mesh = {Antarctic Regions ; DNA Viruses/classification/*genetics/isolation & purification ; DNA, Circular ; *DNA, Single-Stranded ; DNA, Viral/genetics ; Fresh Water/virology ; Genome, Viral/genetics ; Ice Cover/*virology ; Metagenomics ; Microbiota/genetics ; Microviridae/classification/genetics/isolation & purification ; Open Reading Frames ; Phylogeny ; Viral Proteins/genetics ; },
abstract = {Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.},
}

Antarctic Regions
DNA Viruses/classification/*genetics/isolation & purification
DNA, Circular
*DNA, Single-Stranded
DNA, Viral/genetics
Fresh Water/virology
Genome, Viral/genetics
Ice Cover/*virology
Metagenomics
Microbiota/genetics
Microviridae/classification/genetics/isolation & purification
Open Reading Frames
Phylogeny
Viral Proteins/genetics

@article {pmid31504188,
year = {2020},
author = {Kim, KJ and Park, J and Park, SC and Won, S},
title = {Phylogenetic tree-based microbiome association test.},
journal = {Bioinformatics (Oxford, England)},
volume = {36},
number = {4},
pages = {1000-1006},
doi = {10.1093/bioinformatics/btz686},
pmid = {31504188},
issn = {1367-4811},
mesh = {Bacteria ; Humans ; Metagenomics ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {MOTIVATION: Ecological patterns of the human microbiota exhibit high inter-subject variation, with few operational taxonomic units (OTUs) shared across individuals. To overcome these issues, non-parametric approaches, such as the Mann-Whitney U-test and Wilcoxon rank-sum test, have often been used to identify OTUs associated with host diseases. However, these approaches only use the ranks of observed relative abundances, leading to information loss, and are associated with high false-negative rates. In this study, we propose a phylogenetic tree-based microbiome association test (TMAT) to analyze the associations between microbiome OTU abundances and disease phenotypes. Phylogenetic trees illustrate patterns of similarity among different OTUs, and TMAT provides an efficient method for utilizing such information for association analyses. The proposed TMAT provides test statistics for each node, which are combined to identify mutations associated with host diseases.

RESULTS: Power estimates of TMAT were compared with existing methods using extensive simulations based on real absolute abundances. Simulation studies showed that TMAT preserves the nominal type-1 error rate, and estimates of its statistical power generally outperformed existing methods in the considered scenarios. Furthermore, TMAT can be used to detect phylogenetic mutations associated with host diseases, providing more in-depth insight into bacterial pathology.

The 16S rRNA amplicon sequencing metagenomics datasets for colorectal carcinoma and myalgic encephalomyelitis/chronic fatigue syndrome are available from the European Nucleotide Archive (ENA) database under project accession number PRJEB6070 and PRJEB13092, respectively. TMAT was implemented in the R package. Detailed information is available at http://healthstat.snu.ac.kr/software/tmat.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

Bacteria
Humans
Metagenomics
*Microbiota
*Phylogeny
RNA, Ribosomal, 16S

@article {pmid31275319,
year = {2019},
author = {Trachsel, J and Briggs, C and Gabler, NK and Allen, HK and Loving, CL},
title = {Dietary Resistant Potato Starch Alters Intestinal Microbial Communities and Their Metabolites, and Markers of Immune Regulation and Barrier Function in Swine.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {1381},
pmid = {31275319},
issn = {1664-3224},
mesh = {Animals ; *Biomarkers ; Computational Biology/methods ; *Diet ; *Gastrointestinal Microbiome/immunology ; Immunoglobulin A/immunology ; Immunohistochemistry ; *Immunomodulation ; Immunophenotyping ; Intestinal Mucosa/immunology/metabolism/microbiology ; *Metabolome ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Models, Biological ; Phenotype ; *Solanum tuberosum/chemistry ; *Starch/chemistry ; Swine ; },
abstract = {Interactions between diet, the microbiota, and the host set the ecological conditions in the gut and have broad implications for health. Prebiotics are dietary compounds that may shift conditions toward health by promoting the growth of beneficial microbes that produce metabolites capable of modulating host cells. This study's objective was to assess how a dietary prebiotic could impact host tissues via modulation of the intestinal microbiota. Pigs fed a diet amended with 5% resistant potato starch (RPS) exhibited alterations associated with gut health relative to swine fed an unamended control diet (CON). RPS intake increased abundances of anaerobic Clostridia in feces and several tissues, as well as intestinal concentrations of butyrate. Functional gene amplicons suggested bacteria similar to Anaerostipes hadrus were stimulated by RPS intake. The CON treatment exhibited increased abundances of several genera of Proteobacteria (which utilize respiratory metabolisms) in several intestinal locations. RPS intake increased the abundance of regulatory T cells in the cecum, but not periphery, and cecal immune status alterations were indicative of enhanced mucosal defenses. A network analysis of host and microbial changes in the cecum revealed that regulatory T cells positively correlated with butyrate concentration, luminal IgA concentration, expression of IL-6 and DEF1B, and several mucosa-associated bacterial taxa. Thus, the administration of RPS modulated the microbiota and host immune status, altering markers of cecal barrier function and immunological tolerance, and suggesting a reduced niche for bacterial respiration.},
}

Animals
*Biomarkers
Computational Biology/methods
*Diet
*Gastrointestinal Microbiome/immunology
Immunoglobulin A/immunology
Immunohistochemistry
*Immunomodulation
Immunophenotyping
Intestinal Mucosa/immunology/metabolism/microbiology
*Metabolome
Metabolomics/methods
Metagenome
Metagenomics/methods
Models, Biological
Phenotype
*Solanum tuberosum/chemistry
*Starch/chemistry
Swine

@article {pmid32705341,
year = {2020},
author = {Gupta, P and Vakhlu, J and Sharma, YP and Imchen, M and Kumavath, R},
title = {Metagenomic insights into the fungal assemblages of the northwest Himalayan cold desert.},
journal = {Extremophiles : life under extreme conditions},
volume = {24},
number = {5},
pages = {749-758},
doi = {10.1007/s00792-020-01191-z},
pmid = {32705341},
issn = {1433-4909},
support = {DST-SERB/2018/001085//Department science and technology/ ; BT/PR11727/BCE/08/720/2008//DBT-SRF/ ; CSIR (9/100/0177) 2K13-EMR-I//CSIR-SRF/ ; },
mesh = {Antarctic Regions ; Arctic Regions ; Biodiversity ; *Fungi/genetics ; *Metagenome ; *Mycobiome ; },
abstract = {Psychrophilic fungi are a critical biotic component in cold deserts that serves a central role in nutrient recycling and biogeochemical cycles. Despite their ecological significance, culture-independent studies on psychrophilic mycobiome are limited. In the present study, the fungal diversity patterns across the Drass, an Indian cold desert in the Himalaya, were indexed by targeted amplicon pyrosequencing (ITS). In the Drass dataset, Ascomycota was represented by 92 genera, while 22 genera represented Basidiomycota. The most abundant genus was Conocybe (20.46%). Most of the identified genera were reported in the literature to be prolific extracellular hydrolytic enzyme producers. To identify whether the Drass fungal assemblages share similarities to other cold deserts, these were further compared to Antarctic and Arctic cold deserts. Comparative analysis across the three cold deserts indicated the dominance of Dikarya (Ascomycota and Basidiomycota). The observed alpha diversity, Shannon index as well as Pielou's evenness was highest in the Antarctic followed by Drass and Arctic datasets. The genera Malassezia, Preussia, Pseudogymnoascus, Cadophora, Geopora, Monodictys, Tetracladium, Titaea, Mortierella, and Cladosporium were common to all the cold deserts. Furthermore, Conocybe was represented predominantly in Drass. Interestingly, the genus Conocybe has not been previously reported from any other studies on Antarctic or Arctic biomes. To the best of our knowledge, this is the first fungal metagenome study in Drass soil. Our analysis shows that despite the similarities of low temperature among the cold deserts, a significant differential abundance of fungal communities prevails in the global cold deserts.},
}

Antarctic Regions
Arctic Regions
Biodiversity
*Fungi/genetics
*Metagenome
*Mycobiome

@article {pmid32648690,
year = {2019},
author = {Deaton, J and Yu, FB and Quake, SR},
title = {Mini-Metagenomics and Nucleotide Composition Aid the Identification and Host Association of Novel Bacteriophage Sequences.},
journal = {Advanced biosystems},
volume = {3},
number = {11},
pages = {e1900108},
doi = {10.1002/adbi.201900108},
pmid = {32648690},
issn = {2366-7478},
mesh = {Bacteriophages/*genetics/isolation & purification ; *Biodiversity ; *Genome, Viral ; *Metagenomics ; *Sequence Analysis, DNA ; },
abstract = {A broad spectrum of metagenomic and single cell sequencing techniques have become popular for dissecting environmental microbial diversity, leading to the characterization of thousands of novel microbial lineages. In addition to recovering bacterial and archaeal genomes, metagenomic assembly can also produce genomes of viruses that infect microbial cells. Because of their diversity, lack of marker genes, and small genome size, identifying novel bacteriophage sequences from metagenomic data is often challenging, especially when the objective is to establish phage-host relationships. The present work describes a computational approach that uses supervised learning to classify metagenomic contigs as phage or non-phage as well as assigning phage taxonomy based on tetranucleotide frequencies. Furthermore, the method assigns phage-host relationships using co-occurrence statistics derived from a recently developed mini-metagenomic experimental technique. This work evaluates method performance at identifying viral contigs and predicting taxonomic classification using publicly available references. Then, using two mini-metagenomic datasets, over 100 novel phage contigs from hot spring samples of Yellowstone National Park are identified and assigned to putative microbial hosts. Results of this work demonstrate the value of combining viral sequence identification with mini-metagenomic experimental methods to understand the microbial ecosystem.},
}

Bacteriophages/*genetics/isolation & purification
*Biodiversity
*Genome, Viral
*Metagenomics
*Sequence Analysis, DNA

@article {pmid31480274,
year = {2019},
author = {A Duarte, M and F Silva, JM and R Brito, C and S Teixeira, D and L Melo, F and M Ribeiro, B and Nagata, T and S Campos, F},
title = {Faecal Virome Analysis of Wild Animals from Brazil.},
journal = {Viruses},
volume = {11},
number = {9},
pages = {},
pmid = {31480274},
issn = {1999-4915},
mesh = {Animals ; Animals, Wild/*virology ; Birds/virology ; Brazil/epidemiology ; Epidemiological Monitoring ; Feces/*virology ; Genome, Viral/genetics ; Mammals/virology ; Microbiota/*genetics ; Phylogeny ; Viruses/classification/genetics/isolation & purification ; },
abstract = {The Brazilian Cerrado fauna shows very wide diversity and can be a potential viral reservoir. Therefore, the animal's susceptibility to some virus can serve as early warning signs of potential human virus diseases. Moreover, the wild animal virome of this biome is unknown. Based on this scenario, high-throughput sequencing contributes a robust tool for the identification of known and unknown virus species in this environment. In the present study, faeces samples from cerrado birds (Psittacara leucophthalmus, Amazona aestiva, and Sicalis flaveola) and mammals (Didelphis albiventris, Sapajus libidinosus, and Galictis cuja) were collected at the Veterinary Hospital, University of Brasília. Viral nucleic acid was extracted, submitted to random amplification, and sequenced by Illumina HiSeq platform. The reads were de novo assembled, and the identities of the contigs were evaluated by Blastn and tblastx searches. Most viral contigs analyzed were closely related to bacteriophages. Novel archaeal viruses of the Smacoviridae family were detected. Moreover, sequences of members of Adenoviridae, Anelloviridae, Circoviridae, Caliciviridae, and Parvoviridae families were identified. Complete and nearly complete genomes of known anelloviruses, circoviruses, and parvoviruses were obtained, as well as putative novel species. We demonstrate that the metagenomics approach applied in this work was effective for identification of known and putative new viruses in faeces samples from Brazilian Cerrado fauna.},
}

Animals
Animals, Wild/*virology
Birds/virology
Brazil/epidemiology
Epidemiological Monitoring
Feces/*virology
Genome, Viral/genetics
Mammals/virology
Microbiota/*genetics
Phylogeny
Viruses/classification/genetics/isolation & purification

@article {pmid31000244,
year = {2019},
author = {Rocchetti, G and Senizza, A and Gallo, A and Lucini, L and Giuberti, G and Patrone, V},
title = {In vitro large intestine fermentation of gluten-free rice cookies containing alfalfa seed (Medicago sativa L.) flour: A combined metagenomic/metabolomic approach.},
journal = {Food research international (Ottawa, Ont.)},
volume = {120},
number = {},
pages = {312-321},
doi = {10.1016/j.foodres.2019.03.003},
pmid = {31000244},
issn = {1873-7145},
mesh = {Cooking ; DNA, Bacterial/genetics/isolation & purification ; Edible Grain/chemistry ; Fatty Acids, Volatile/analysis ; Fermentation ; Flour/*analysis ; Gastrointestinal Microbiome ; Glutens/analysis ; Intestine, Large/*metabolism ; Lignans/analysis ; Medicago sativa/*chemistry ; *Metabolomics ; *Metagenomics ; Oryza/*chemistry ; Phenols/analysis ; Polyphenols/analysis ; RNA, Ribosomal, 16S/genetics/isolation & purification ; Seeds/*chemistry ; Sequence Analysis, DNA ; },
abstract = {Alfalfa seed flour (ASF) at different inclusion levels (0% as control, 30% and 45% w/w) was used to prepare rice flour-based gluten-free (GF) cookies (CK). Samples underwent a simulated in vitro digestion and fermentation process. The comprehensive changes in the phenolic profiles were evaluated during 48 h of fermentation by means of untargeted UHPLC-QTOF mass spectrometry followed by multivariate statistics. Furthermore, the modifications in microbial profile and the production of short chain fatty acids (SCFA) were investigated. Cookies presenting 30% (30-CK) and 45% (45-CK) ASF possessed the greater total phenolic content when compared to the control, being 0.42 and 0.56 mg/g versus 0.15 mg/g, respectively. The orthogonal projection to latent structure discriminant analysis, applied to untargeted metabolomics-based data, showed a clear modulation of the profile in phenolic metabolites over time (from 8 up to 48 h of in vitro fermentation). In this regard, the in vitro fermentation of 30-CK and 45-CK resulted in the maximum increase in lignans and phenolic acids, whose bioaccessibility at 24 h of in vitro fermentation was 16.2% and 12.2%, respectively. In addition, the metagenomic sequencing approach allowed to identify in Clostridiaceae, Ruminococcaceae, Lachnospiraceae and Streptococcaceae the most represented bacterial populations during the in vitro fermentation. A greater total SCFA production (p < .05) was recorded overtime for all ASF-enriched cookies when compared to the control. Therefore, ASF proved to be an excellent alternative to common non-wheat cereal flours (such as pseudocereals or legumes) for improving possible health-promoting properties in GF cookie formulation.},
}

Cooking
DNA, Bacterial/genetics/isolation & purification
Edible Grain/chemistry
Fatty Acids, Volatile/analysis
Fermentation
Flour/*analysis
Gastrointestinal Microbiome
Glutens/analysis
Intestine, Large/*metabolism
Lignans/analysis
Medicago sativa/*chemistry
*Metabolomics
*Metagenomics
Oryza/*chemistry
Phenols/analysis
Polyphenols/analysis
RNA, Ribosomal, 16S/genetics/isolation & purification
Seeds/*chemistry
Sequence Analysis, DNA

@article {pmid32912302,
year = {2020},
author = {Saary, P and Mitchell, AL and Finn, RD},
title = {Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {244},
doi = {10.1186/s13059-020-02155-4},
pmid = {32912302},
issn = {1474-760X},
support = {BB/M011755/1, BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Core Funds//EMBL/ ; },
abstract = {Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets. We demonstrate that our method outperforms current genome quality estimators, particularly for estimating contamination, and have applied EukCC to datasets derived from two different environments to enable the identification of novel eukaryote genomes, including one from the human skin.},
}

@article {pmid31542415,
year = {2019},
author = {Tackmann, J and Matias Rodrigues, JF and von Mering, C},
title = {Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data.},
journal = {Cell systems},
volume = {9},
number = {3},
pages = {286-296.e8},
doi = {10.1016/j.cels.2019.08.002},
pmid = {31542415},
issn = {2405-4720},
support = {/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Algorithms ; Biodiversity ; Computational Biology/*methods ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; *Microbial Interactions ; Microbiota/*physiology ; Models, Statistical ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {The availability of large-scale metagenomic sequencing data can facilitate the understanding of microbial ecosystems in unprecedented detail. However, current computational methods for predicting ecological interactions are hampered by insufficient statistical resolution and limited computational scalability. They also do not integrate metadata, which can reduce the interpretability of predicted ecological patterns. Here, we present FlashWeave, a computational approach based on a flexible Probabilistic Graphical Model framework that integrates metadata and predicts direct microbial interactions from heterogeneous microbial abundance data sets with hundreds of thousands of samples. FlashWeave outperforms state-of-the-art methods on diverse benchmarking challenges in terms of runtime and accuracy. We use FlashWeave to analyze a cross-study data set of 69,818 publicly available human gut samples and produce, to the best of our knowledge, the largest and most diverse network of predicted, direct gastrointestinal microbial interactions to date. FlashWeave is freely available for download here: https://github.com/meringlab/FlashWeave.jl.},
}

Algorithms
Biodiversity
Computational Biology/*methods
Ecosystem
High-Throughput Nucleotide Sequencing
Humans
Metagenome
Metagenomics
*Microbial Interactions
Microbiota/*physiology
Models, Statistical
RNA, Ribosomal, 16S/*genetics

@article {pmid30778155,
year = {2019},
author = {Ata, B and Yildiz, S and Turkgeldi, E and Brocal, VP and Dinleyici, EC and Moya, A and Urman, B},
title = {The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {2204},
pmid = {30778155},
issn = {2045-2322},
mesh = {Adult ; Case-Control Studies ; Cervix Uteri/*microbiology ; Endometriosis/*diagnosis/etiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Severity of Illness Index ; Vagina/*microbiology ; Young Adult ; },
abstract = {Dysbiosis in the genital tract or gut microbiome can be associated with endometriosis. We sampled vaginal, cervical and gut microbiota from 14 women with histology proven stage 3/4 endometriosis and 14 healthy controls. The V3 and V4 regions of the 16S rRNA gene were amplified following the 16S Metagenomic Sequencing Library Preparation. Despite overall similar vaginal, cervical and intestinal microbiota composition between stage 3/4 endometriosis group and controls, we observed differences at genus level. The complete absence of Atopobium in the vaginal and cervical microbiota of the stage 3/4 endometriosis group was noteworthy. In the cervical microbiota, Gardnerella, Streptococcus, Escherichia, Shigella, and Ureoplasma, all of which contain potentially pathogenic species, were increased in stage 3/4 endometriosis. More women in the stage 3/4 endometriosis group had Shigella/Escherichia dominant stool microbiome. Further studies can clarify whether the association is causal, and whether dysbiosis leads to endometriosis or endometriosis leads to dysbiosis.},
}

Adult
Case-Control Studies
Cervix Uteri/*microbiology
Endometriosis/*diagnosis/etiology
Female
*Gastrointestinal Microbiome
Humans
Metagenome
Metagenomics/methods
*Microbiota
Severity of Illness Index
Vagina/*microbiology
Young Adult

@article {pmid32899763,
year = {2020},
author = {El-Hossary, EM and Abdel-Halim, M and Ibrahim, ES and Pimentel-Elardo, SM and Nodwell, JR and Handoussa, H and Abdelwahab, MF and Holzgrabe, U and Abdelmohsen, UR},
title = {Natural Products Repertoire of the Red Sea.},
journal = {Marine drugs},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/md18090457},
pmid = {32899763},
issn = {1660-3397},
abstract = {Marine natural products have achieved great success as an important source of new lead compounds for drug discovery. The Red Sea provides enormous diversity on the biological scale in all domains of life including micro- and macro-organisms. In this review, which covers the literature to the end of 2019, we summarize the diversity of bioactive secondary metabolites derived from Red Sea micro- and macro-organisms, and discuss their biological potential whenever applicable. Moreover, the diversity of the Red Sea organisms is highlighted as well as their genomic potential. This review is a comprehensive study that compares the natural products recovered from the Red Sea in terms of ecological role and pharmacological activities.},
}

@article {pmid32899230,
year = {2020},
author = {Iacono, R and Cobucci-Ponzano, B and De Lise, F and Curci, N and Maurelli, L and Moracci, M and Strazzulli, A},
title = {Spatial Metagenomics of Three Geothermal Sites in Pisciarelli Hot Spring Focusing on the Biochemical Resources of the Microbial Consortia.},
journal = {Molecules (Basel, Switzerland)},
volume = {25},
number = {17},
pages = {},
doi = {10.3390/molecules25174023},
pmid = {32899230},
issn = {1420-3049},
support = {ASI N. 2019-3-U.0//Agenzia Spaziale Italiana/ ; },
abstract = {Terrestrial hot springs are of great interest to the general public and to scientists alike due to their unique and extreme conditions. These have been sought out by geochemists, astrobiologists, and microbiologists around the globe who are interested in their chemical properties, which provide a strong selective pressure on local microorganisms. Drivers of microbial community composition in these springs include temperature, pH, in-situ chemistry, and biogeography. Microbes in these communities have evolved strategies to thrive in these conditions by converting hot spring chemicals and organic matter into cellular energy. Following our previous metagenomic analysis of Pisciarelli hot springs (Naples, Italy), we report here the comparative metagenomic study of three novel sites, formed in Pisciarelli as result of recent geothermal activity. This study adds comprehensive information about phylogenetic diversity within Pisciarelli hot springs by peeking into possible mechanisms of adaptation to biogeochemical cycles, and high applicative potential of the entire set of genes involved in the carbohydrate metabolism in this environment (CAZome). This site is an excellent model for the study of biodiversity on Earth and biosignature identification, and for the study of the origin and limits of life.},
}

@article {pmid32555605,
year = {2020},
author = {Shamsaddini, A and Dadkhah, K and Gillevet, PM},
title = {BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline.},
journal = {PloS one},
volume = {15},
number = {6},
pages = {e0234860},
pmid = {32555605},
issn = {1932-6203},
mesh = {Animals ; Bacteria/*classification/genetics ; Computational Biology/*methods ; Datasets as Topic ; *Gastrointestinal Microbiome ; Metagenomics/*methods ; Mice ; RNA, Ribosomal, 16S/genetics ; *Software ; },
abstract = {Current microbiome applications require substantial bioinformatics expertise to execute. As microbiome clinical diagnostics are being developed, there is a critical need to implement computational tools and applications that are user-friendly for the medical community to understand microbiome correlation with the health. To address this need, we have developed BiomMiner (pronounced as "biominer"), an automated pipeline that provides a comprehensive analysis of microbiome data. The pipeline finds taxonomic signatures of microbiome data and compiles actionable clinical report that allows clinicians and biomedical scientists to efficiently perform statistical analysis and data mining on the large microbiome datasets. BiomMiner generates web-enabled visualization of the analysis results and is specifically designed to facilitate the use of microbiome datasets in clinical applications.},
}

Animals
Bacteria/*classification/genetics
Computational Biology/*methods
Datasets as Topic
*Gastrointestinal Microbiome
Metagenomics/*methods
Mice
RNA, Ribosomal, 16S/genetics
*Software

@article {pmid32043695,
year = {2020},
author = {He, Z and Pan, L and Zhang, M and Zhang, M and Huang, F and Gao, S},
title = {Metagenomic comparison of structure and function of microbial community between water, effluent and shrimp intestine of higher place Litopenaeus vannamei ponds.},
journal = {Journal of applied microbiology},
volume = {129},
number = {2},
pages = {243-255},
doi = {10.1111/jam.14610},
pmid = {32043695},
issn = {1365-2672},
support = {KLM2017005//Key Laboratory of Mariculture, Ministry Education, Ocean University of China (OUC)/ ; 20160359//Bio-Form Biotechnology Co. LTD/ ; },
mesh = {Animals ; Bacteria/classification/genetics/isolation & purification ; Intestines/*microbiology ; Metagenome ; Microbiota/genetics/*physiology ; Penaeidae/*microbiology ; Ponds/*microbiology ; RNA, Ribosomal, 16S/genetics ; Shellfish/*microbiology ; Waste Water/microbiology ; },
abstract = {AIMS: The present study aimed to reveal microbial relationship between shrimp intestine and ambient in higher place shrimp ponds from the aspects of composition and function.

METHODS AND RESULTS: Metagenome and 16S rRNA gene sequencing were used to compare microbial compositions and functions of water, effluent and shrimp intestine in higher place Litopenaeus vannamei ponds. Although the three groups had similar dominant phyla, such as Proteobacteria, Bacteroidetes and Tenericutes, their bacterial compositions at the genus level were obviously different. Compared to effluent and intestine, the relative abundance of Vibrio as common opportunistic pathogen for shrimp was significantly higher in water. However, cluster analysis showed that intestinal microbial composition was more similar to that of effluent than water. Metagenomic data showed that the predominant microbial functions in the three groups were mostly related to energy production and biosynthesis, while carbohydrate metabolism was relatively enriched in intestinal microbiota. More importantly, Proteobacteria played a critical role in carbon metabolism and biosynthesis of amino acids in the three habitats, and Vibrio had the most functions related to bacterial virulence and infection.

CONCLUSIONS: Shrimp intestinal microbiota had a close correlation with the ambient microbiota in both structure and function. As the most dominant phylum, Proteobacteria was very important for microbiota communication and nutrient cycling in higher place shrimp ponds. Moreover, due to the pathogenicity, it was necessary to monitor the abundant changes of Vibrio in water to decrease the risk of shrimp disease outbreaks.

These above results may be helpful to comprehensively understand the characteristics and functions of microbiota in higher place shrimp ponds, thereby providing basic information for developing the management strategies of entire microbiota to sustain shrimp health.},
}

Animals
Bacteria/classification/genetics/isolation & purification
Intestines/*microbiology
Metagenome
Microbiota/genetics/*physiology
Penaeidae/*microbiology
Ponds/*microbiology
RNA, Ribosomal, 16S/genetics
Shellfish/*microbiology
Waste Water/microbiology

@article {pmid31443379,
year = {2019},
author = {Imanishi, I and Uchiyama, J and Tsukui, T and Hisatsune, J and Ide, K and Matsuzaki, S and Sugai, M and Nishifuji, K},
title = {Therapeutic Potential of an Endolysin Derived from Kayvirus S25-3 for Staphylococcal Impetigo.},
journal = {Viruses},
volume = {11},
number = {9},
pages = {},
pmid = {31443379},
issn = {1999-4915},
mesh = {Administration, Cutaneous ; Animals ; Anti-Bacterial Agents/administration & dosage/pharmacology ; Bacteriolysis ; Caudovirales/*metabolism/pathogenicity ; Endopeptidases/administration & dosage/genetics/*pharmacology ; Genes, Bacterial ; Genes, Viral ; Impetigo/*drug therapy/microbiology ; Metagenomics ; Mice ; Microbiota/genetics ; Pseudomonas aeruginosa/virology ; RNA, Ribosomal, 16S ; Recombinant Proteins/administration & dosage/pharmacology ; Skin/microbiology/pathology ; Staphylococcal Infections/drug therapy ; Staphylococcus Phages/metabolism/pathogenicity ; *Staphylococcus aureus/drug effects/virology ; Staphylococcus epidermidis/virology ; Streptococcus mitis/virology ; },
abstract = {Impetigo is a contagious skin infection predominantly caused by Staphylococcus aureus. Decontamination of S. aureus from the skin is becoming more difficult because of the emergence of antibiotic-resistant strains. Bacteriophage endolysins are less likely to invoke resistance and can eliminate the target bacteria without disturbance of the normal microflora. In this study, we investigated the therapeutic potential of a recombinant endolysin derived from kayvirus S25-3 against staphylococcal impetigo in an experimental setting. First, the recombinant S25-3 endolysin required an incubation period of over 15 minutes to exhibit efficient bactericidal effects against S. aureus. Second, topical application of the recombinant S25-3 endolysin decreased the number of intraepidermal staphylococci and the size of pustules in an experimental mouse model of impetigo. Third, treatment with the recombinant S25-3 endolysin increased the diversity of the skin microbiota in the same mice. Finally, we revealed the genus-specific bacteriolytic effect of recombinant S25-3 endolysin against staphylococci, particularly S. aureus, among human skin commensal bacteria. Therefore, topical treatment with recombinant S25-3 endolysin can be a promising disease management procedure for staphylococcal impetigo by efficient bacteriolysis of S. aureus while improving the cutaneous bacterial microflora.},
}

Administration, Cutaneous
Animals
Anti-Bacterial Agents/administration & dosage/pharmacology
Bacteriolysis
Caudovirales/*metabolism/pathogenicity
Endopeptidases/administration & dosage/genetics/*pharmacology
Genes, Bacterial
Genes, Viral
Impetigo/*drug therapy/microbiology
Metagenomics
Mice
Microbiota/genetics
Pseudomonas aeruginosa/virology
RNA, Ribosomal, 16S
Recombinant Proteins/administration & dosage/pharmacology
Skin/microbiology/pathology
Staphylococcal Infections/drug therapy
Staphylococcus Phages/metabolism/pathogenicity
*Staphylococcus aureus/drug effects/virology
Staphylococcus epidermidis/virology
Streptococcus mitis/virology

@article {pmid31009062,
year = {2019},
author = {Zhang, J and Lin, W},
title = {Scalable estimation and regularization for the logistic normal multinomial model.},
journal = {Biometrics},
volume = {75},
number = {4},
pages = {1098-1108},
doi = {10.1111/biom.13071},
pmid = {31009062},
issn = {1541-0420},
mesh = {Algorithms ; Computer Simulation ; Gastrointestinal Microbiome/genetics ; Humans ; *Logistic Models ; Metagenomics/*methods ; Methods ; Sequence Analysis ; Stochastic Processes ; },
abstract = {Clustered multinomial data are prevalent in a variety of applications such as microbiome studies, where metagenomic sequencing data are summarized as multinomial counts for a large number of bacterial taxa per subject. Count normalization with ad hoc zero adjustment tends to result in poor estimates of abundances for taxa with zero or small counts. To account for heterogeneity and overdispersion in such data, we suggest using the logistic normal multinomial (LNM) model with an arbitrary correlation structure to simultaneously estimate the taxa compositions by borrowing information across subjects. We overcome the computational difficulties in high dimensions by developing a stochastic approximation EM algorithm with Hamiltonian Monte Carlo sampling for scalable parameter estimation in the LNM model. The ill-conditioning problem due to unstructured covariance is further mitigated by a covariance-regularized estimator with a condition number constraint. The advantages of the proposed methods are illustrated through simulations and an application to human gut microbiome data.},
}

Algorithms
Computer Simulation
Gastrointestinal Microbiome/genetics
Humans
*Logistic Models
Metagenomics/*methods
Methods
Sequence Analysis
Stochastic Processes

@article {pmid30771735,
year = {2019},
author = {Petersen, C and Wankhade, UD and Bharat, D and Wong, K and Mueller, JE and Chintapalli, SV and Piccolo, BD and Jalili, T and Jia, Z and Symons, JD and Shankar, K and Anandh Babu, PV},
title = {Dietary supplementation with strawberry induces marked changes in the composition and functional potential of the gut microbiome in diabetic mice.},
journal = {The Journal of nutritional biochemistry},
volume = {66},
number = {},
pages = {63-69},
pmid = {30771735},
issn = {1873-4847},
support = {R03 AG052848/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; Diabetes Mellitus, Experimental/diet therapy/*microbiology ; Dietary Supplements ; *Fragaria ; Gastrointestinal Microbiome/*physiology ; Male ; Metabolic Networks and Pathways ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Receptors, Leptin/genetics ; },
abstract = {Gut microbiota contributes to the biological activities of berry anthocyanins by transforming them into bioactive metabolites, and anthocyanins support the growth of specific bacteria, indicating a two-way relationship between anthocyanins and microbiota. In the present study, we tested the hypothesis that strawberry supplementation alters gut microbial ecology in diabetic db/db mice. Control (db/+) and diabetic (db/db) mice (7 weeks old) consumed standard diet or diet supplemented with 2.35% freeze-dried strawberry (db/db + SB) for 10 weeks. Colon contents were used to isolate bacterial DNA. V4 variable region of 16S rRNA gene was amplified. Data analyses were performed using standardized pipelines (QIIME 1.9 and R packages). Differences in predictive metagenomics function were identified by PICRUSt. Principal coordinate analyses confirmed that the microbial composition was significantly influenced by both host genotype and strawberry consumption. Further, α-diversity indices and β-diversity were different at the phylum and genus levels, and genus and operational taxonomical units levels, respectively (P<.05). At the phylum level, strawberry supplementation decreased the abundance of Verrucomicrobia in db/db + SB vs. db/db mice (P<.05). At the genus level, db/db mice exhibited a decrease in the abundance of Bifidobacterium, and strawberry supplementation increased Bifidobacterium in db/db + SB vs. db/db mice (P<.05). PICRUSt revealed significant differences in 45 predicted metabolic functions among the 3 groups. Our study provides evidence for marked changes in the composition and functional potential of the gut microbiome with strawberry supplementation in diabetic mice. Importantly, strawberry supplementation increased the abundance of beneficial bacteria Bifidobacterium which play a pivotal role in the metabolism of anthocyanins.},
}

Animals
Diabetes Mellitus, Experimental/diet therapy/*microbiology
Dietary Supplements
*Fragaria
Gastrointestinal Microbiome/*physiology
Male
Metabolic Networks and Pathways
Mice, Inbred C57BL
Mice, Mutant Strains
Receptors, Leptin/genetics

@article {pmid32897356,
year = {2020},
author = {Bandini, F and Misci, C and Taskin, E and Cocconcelli, PS and Puglisi, E},
title = {Biopolymers modulate microbial communities in municipal organic waste digestion.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaa183},
pmid = {32897356},
issn = {1574-6941},
abstract = {The development of biopolymers has raised issues about their recalcitrance in the environment. Their disposal is mainly carried out with the organic fraction of municipal solid waste (OFMSW) through thermophilic anaerobic digestion and aerobic composting, bioprocesses aimed at turning organic matter into biogas and compost. However, the effects of biopolymers on OFMSW treatment, on the final compost and on the microbial communities involved are partly unexplored. In this study, the OFMSW treatment was reproduced on a laboratory-scale respecting real plant conditions and testing the impacts of mixing polylactic acid (PLA) and starch-based bioplastic (SBB) separately. The dynamics of bacterial, archaeal and fungal communities during the process was screened by high-throughput sequencing (HTS) of phylogenetic amplicons. SBB showed a minor and heterogeneous microbial diversity between the anaerobic and aerobic phases. Contrariwise, PLA treatment resulted in wider and more diverse bacterial and fungal communities for the compost and the aerobic biofilm. Since the biodiversity in compost may play a crucial role in its stability and safety, the modulation of environmental microbial communities induced by higher concentrations of PLA in OFMSW treatment can pose relevant issues.},
}

@article {pmid32514171,
year = {2020},
author = {Chng, KR and Li, C and Bertrand, D and Ng, AHQ and Kwah, JS and Low, HM and Tong, C and Natrajan, M and Zhang, MH and Xu, L and Ko, KKK and Ho, EXP and Av-Shalom, TV and Teo, JWP and Khor, CC and , and Chen, SL and Mason, CE and Ng, OT and Marimuthu, K and Ang, B and Nagarajan, N},
title = {Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment.},
journal = {Nature medicine},
volume = {26},
number = {6},
pages = {941-951},
doi = {10.1038/s41591-020-0894-4},
pmid = {32514171},
issn = {1546-170X},
mesh = {Beds/microbiology ; Biofilms ; Cross Infection/drug therapy/*microbiology/transmission ; Disinfection ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Equipment Contamination ; Equipment and Supplies, Hospital/*microbiology ; Geographic Mapping ; Humans ; *Infection Control ; Metagenomics ; Microbiota/*genetics ; Opportunistic Infections/drug therapy/microbiology/transmission ; Patients' Rooms ; Singapore ; Spatio-Temporal Analysis ; Tertiary Care Centers ; },
abstract = {Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.},
}

Beds/microbiology
Biofilms
Cross Infection/drug therapy/*microbiology/transmission
Disinfection
Drug Resistance, Bacterial/*genetics
Drug Resistance, Multiple, Bacterial/genetics
Equipment Contamination
Equipment and Supplies, Hospital/*microbiology
Geographic Mapping
Humans
*Infection Control
Metagenomics
Microbiota/*genetics
Opportunistic Infections/drug therapy/microbiology/transmission
Patients' Rooms
Singapore
Spatio-Temporal Analysis
Tertiary Care Centers

@article {pmid32042169,
year = {2020},
author = {Moss, EL and Maghini, DG and Bhatt, AS},
title = {Complete, closed bacterial genomes from microbiomes using nanopore sequencing.},
journal = {Nature biotechnology},
volume = {38},
number = {6},
pages = {701-707},
doi = {10.1038/s41587-020-0422-6},
pmid = {32042169},
issn = {1546-1696},
support = {R01 AI148623/AI/NIAID NIH HHS/United States ; P50 AG047366/AG/NIA NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; },
mesh = {Adult ; Animals ; DNA, Bacterial/analysis/genetics ; Dogs ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/*genetics ; Humans ; Metagenomics/*methods ; Mice ; Nanopore Sequencing/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation.},
}

Adult
Animals
DNA, Bacterial/analysis/genetics
Dogs
Feces/microbiology
Gastrointestinal Microbiome/*genetics
Genome, Bacterial/*genetics
Humans
Metagenomics/*methods
Mice
Nanopore Sequencing/*methods
Sequence Analysis, DNA/*methods

@article {pmid31167953,
year = {2020},
author = {Bonning, BC},
title = {The Insect Virome: Opportunities and Challenges.},
journal = {Current issues in molecular biology},
volume = {34},
number = {},
pages = {1-12},
doi = {10.21775/cimb.034.001},
pmid = {31167953},
issn = {1467-3045},
mesh = {Animals ; Biodiversity ; Genome, Viral ; Host-Pathogen Interactions/genetics/immunology ; Insect Viruses/*classification/*genetics ; Insecta/genetics/immunology/*virology ; Invertebrates ; Metagenomics ; Microbiota ; },
abstract = {The insect virome is composed of a myriad of viruses. Both field populations and laboratory colonies of insects harbour diverse viruses, including viruses that infect the insect itself, viruses of microbes associated with the insect, and viruses associated with ingested materials. Metagenomics analysis for identification of virus-derived sequences has allowed for new appreciation of the extent and diversity of the insect virome. The complex interactions between insect viruses and host antiviral immune pathways (RNA interference and apoptosis), and between viruses and other members of the microbiome (e.g. Wolbachia) are becoming apparent. In this chapter, an overview of the diversity of viruses in insects and recent virus discovery research for specific insects and insect-derived cell lines is provided. The opportunities and challenges associated with the insect virome, including the potential impacts of viruses on both research and insect management programs are also addressed.},
}

Animals
Biodiversity
Genome, Viral
Host-Pathogen Interactions/genetics/immunology
Insect Viruses/*classification/*genetics
Insecta/genetics/immunology/*virology
Invertebrates
Metagenomics
Microbiota

@article {pmid32890633,
year = {2020},
author = {Joulian, C and Fonti, V and Chapron, S and Bryan, CG and Guezennec, AG},
title = {Bioleaching of pyritic coal wastes: bioprospecting and efficiency of selected consortia.},
journal = {Research in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.resmic.2020.08.002},
pmid = {32890633},
issn = {1769-7123},
abstract = {Pyrite-bearing coal wastes are responsible of the formation of acid mine drainage (AMD), and their management to mitigate environmental impacts is a challenge to the coal mine industry in Europe and worldwide. The European CEReS project sought to develop a generic co-processing strategy to reuse and recycle coal wastes, based on removal of AMD generating potential through bioleaching. Chemolitoautotrophic iron- and sulfur-oxidizing microbial consortia were enriched from a Polish coal waste at 30°C and 48°C, but not 42°C. Pyrite leaching yield, determined from bioleaching tests in 2-L stirred bioreactors, was best with the 48°C endogenous consortium (80%), then the 42°C exogenous BRGM-KCC consortium (71%), and finally the 30°C endogenous consortium (50%). 16S rRNA gene-targeted metagenomics from five surface locations on the dump waste revealed a microbial community adapted to the site context, composed of iron- and/or sulfur-oxidizing genera thriving in low pH and metal rich environments and involved in AMD generation. All together, the results confirmed the predisposition of the pyritic coal waste to bioleaching and the potential of endogenous microorganisms for efficient bioleaching at 48°C. The good leaching yields open the perspective to optimize further and scale-up the bioleaching process.},
}

@article {pmid32884659,
year = {2020},
author = {Saccò, M and Blyth, AJ and Humphreys, WF and Cooper, SJB and Austin, AD and Hyde, J and Mazumder, D and Hua, Q and White, NE and Grice, K},
title = {Refining trophic dynamics through multi-factor Bayesian mixing models: A case study of subterranean beetles.},
journal = {Ecology and evolution},
volume = {10},
number = {16},
pages = {8815-8826},
doi = {10.1002/ece3.6580},
pmid = {32884659},
issn = {2045-7758},
abstract = {Food web dynamics are vital in shaping the functional ecology of ecosystems. However, trophic ecology is still in its infancy in groundwater ecosystems due to the cryptic nature of these environments. To unravel trophic interactions between subterranean biota, we applied an interdisciplinary Bayesian mixing model design (multi-factor BMM) based on the integration of faunal C and N bulk tissue stable isotope data (δ13C and δ15N) with radiocarbon data (Δ14C), and prior information from metagenomic analyses. We further compared outcomes from multi-factor BMM with a conventional isotope double proxy mixing model (SIA BMM), triple proxy (δ13C, δ15N, and Δ14C, multi-proxy BMM), and double proxy combined with DNA prior information (SIA + DNA BMM) designs. Three species of subterranean beetles (Paroster macrosturtensis, Paroster mesosturtensis, and Paroster microsturtensis) and their main prey items Chiltoniidae amphipods (AM1: Scutachiltonia axfordi and AM2: Yilgarniella sturtensis), cyclopoids and harpacticoids from a calcrete in Western Australia were targeted. Diet estimations from stable isotope only models (SIA BMM) indicated homogeneous patterns with modest preferences for amphipods as prey items. Multi-proxy BMM suggested increased-and species-specific-predatory pressures on amphipods coupled with high rates of scavenging/predation on sister species. SIA + DNA BMM showed marked preferences for amphipods AM1 and AM2, and reduced interspecific scavenging/predation on Paroster species. Multi-factorial BMM revealed the most precise estimations (lower overall SD and very marginal beetles' interspecific interactions), indicating consistent preferences for amphipods AM1 in all the beetles' diets. Incorporation of genetic priors allowed crucial refining of the feeding preferences, while integration of more expensive radiocarbon data as a third proxy (when combined with genetic data) produced more precise outcomes but close dietary reconstruction to that from SIA + DNA BMM. Further multidisciplinary modeling from other groundwater environments will help elucidate the potential behind these designs and bring light to the feeding ecology of one the most vital ecosystems worldwide.},
}

@article {pmid32615432,
year = {2020},
author = {Yang, L and Hou, K and Zhang, B and Ouyang, C and Lin, A and Xu, S and Ke, D and Fang, L and Chen, Q and Wu, J and Yan, C and Lian, Y and Jiang, T and He, J and Wang, H and Fu, Y and Xiao, C and Chen, Z},
title = {Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut.},
journal = {The Science of the total environment},
volume = {741},
number = {},
pages = {140423},
doi = {10.1016/j.scitotenv.2020.140423},
pmid = {32615432},
issn = {1879-1026},
mesh = {Cost-Benefit Analysis ; Feces ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Specimen Handling ; Temperature ; },
abstract = {With the increasing researches on the role of gut microbiota in human health and disease, appropriate storage method of fecal samples at ambient temperature would conveniently guarantee the precise and reliable microbiota results. Nevertheless, less choice of stabilizer that is cost-efficient and feasible to be used in longer preservation period obstructed the large-scale metagenomics studies. Here, we evaluated the efficacy of a guanidine isothiocyanate-based reagent method EffcGut and compared it with the other already used storage method by means of 16S rRNA gene sequencing technology. We found that guanidine isothiocyanate-based reagent method at ambient temperature was not inferior to OMNIgene·GUT OM-200 and it could retain the similar bacterial community as that of -80 °C within 24 weeks. Furthermore, bacterial diversity and community structure difference were compared among different sample fraction (supernatant, suspension and precipitate) preserved in EffcGut and -80 °C. We found that supernatant under the preservation of EffcGut retained the similar community structure and composition as that of the low temperature preservation method.},
}

Cost-Benefit Analysis
Feces
Humans
*Microbiota
RNA, Ribosomal, 16S
*Specimen Handling
Temperature

@article {pmid32589643,
year = {2020},
author = {Ajene, IJ and Khamis, FM and van Asch, B and Pietersen, G and Rasowo, BA and Ombura, FL and Wairimu, AW and Akutse, KS and Sétamou, M and Mohamed, S and Ekesi, S},
title = {Microbiome diversity in Diaphorina citri populations from Kenya and Tanzania shows links to China.},
journal = {PloS one},
volume = {15},
number = {6},
pages = {e0235348},
pmid = {32589643},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; China ; Drug Resistance, Microbial/genetics ; Hemiptera/*microbiology ; Insect Vectors/microbiology ; Kenya ; *Microbiota/drug effects/genetics ; *Phylogeny ; Plant Diseases/microbiology ; Sequence Analysis ; Symbiosis ; Tanzania ; },
abstract = {The Asian citrus psyllid (Diaphorina citri) is a key pest of Citrus spp. worldwide, as it acts as a vector for "Candidatus Liberibacter asiaticus (Las)", the bacterial pathogen associated with the destructive Huanglongbing (HLB) disease. Recent detection of D. citri in Africa and reports of Las-associated HLB in Ethiopia suggest that the citrus industry on the continent is under imminent threat. Endosymbionts and gut bacteria play key roles in the biology of arthropods, especially with regards to vector-pathogen interactions and resistance to antibiotics. Thus, we aim to profile the bacterial genera and to identify antibiotic resistance genes within the microbiome of different populations worldwide of D. citri. The metagenome of D. citri was sequenced using the Oxford Nanopore full-length 16S metagenomics protocol, and the "What's in my pot" (WIMP) analysis pipeline. Microbial diversity within and between D. citri populations was assessed, and antibiotic resistance genes were identified using the WIMP-ARMA workflow. The most abundant genera were key endosymbionts of D. citri ("Candidatus Carsonella", "Candidatus Profftella", and Wolbachia). The Shannon diversity index showed that D. citri from Tanzania had the highest diversity of bacterial genera (1.92), and D. citri from China had the lowest (1.34). The Bray-Curtis dissimilarity showed that China and Kenya represented the most diverged populations, while the populations from Kenya and Tanzania were the least diverged. The WIMP-ARMA analyses generated 48 CARD genes from 13 bacterial species in each of the populations. Spectinomycin resistance genes were the most frequently found, with an average of 65.98% in all the populations. These findings add to the knowledge on the diversity of the African D. citri populations and the probable introduction source of the psyllid in these African countries.},
}

Animals
*Biodiversity
China
Drug Resistance, Microbial/genetics
Hemiptera/*microbiology
Insect Vectors/microbiology
Kenya
*Microbiota/drug effects/genetics
*Phylogeny
Plant Diseases/microbiology
Sequence Analysis
Symbiosis
Tanzania

@article {pmid31543403,
year = {2019},
author = {Yuan, J and Chen, C and Cui, J and Lu, J and Yan, C and Wei, X and Zhao, X and Li, N and Li, S and Xue, G and Cheng, W and Li, B and Li, H and Lin, W and Tian, C and Zhao, J and Han, J and An, D and Zhang, Q and Wei, H and Zheng, M and Ma, X and Li, W and Chen, X and Zhang, Z and Zeng, H and Ying, S and Wu, J and Yang, R and Liu, D},
title = {Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae.},
journal = {Cell metabolism},
volume = {30},
number = {4},
pages = {675-688.e7},
doi = {10.1016/j.cmet.2019.08.018},
pmid = {31543403},
issn = {1932-7420},
mesh = {Animals ; Ethanol/*metabolism ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Hep G2 Cells ; Humans ; Klebsiella pneumoniae/*metabolism/pathogenicity ; Male ; Mice ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*microbiology ; },
abstract = {The underlying etiology of nonalcoholic fatty liver disease (NAFLD) is believed to be quite varied. Changes in the gut microbiota have been investigated and are believed to contribute to at least some cases of the disease, though a causal relationship remains unclear. Here, we show that high-alcohol-producing Klebsiella pneumoniae (HiAlc Kpn) is associated with up to 60% of individuals with NAFLD in a Chinese cohort. Transfer of clinical isolates of HiAlc Kpn by oral gavage into mice induced NAFLD. Likewise, fecal microbiota transplant (FMT) into mice using a HiAlc-Kpn-strain-containing microbiota isolated from an individual with NASH induced NAFLD. However, selective elimination of the HiAlc Kpn strain before FMT prevented NAFLD in the recipient mice. These results suggest that at least in some cases of NAFLD an alteration in the gut microbiome drives the condition due to excess endogenous alcohol production.},
}

Animals
Ethanol/*metabolism
Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
Hep G2 Cells
Humans
Klebsiella pneumoniae/*metabolism/pathogenicity
Male
Mice
Mice, Inbred C57BL
Non-alcoholic Fatty Liver Disease/*microbiology

@article {pmid31523007,
year = {2019},
author = {Cabral, DJ and Penumutchu, S and Reinhart, EM and Zhang, C and Korry, BJ and Wurster, JI and Nilson, R and Guang, A and Sano, WH and Rowan-Nash, AD and Li, H and Belenky, P},
title = {Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome.},
journal = {Cell metabolism},
volume = {30},
number = {4},
pages = {800-823.e7},
pmid = {31523007},
issn = {1932-7420},
support = {P20 GM109035/GM/NIGMS NIH HHS/United States ; P20 GM121344/GM/NIGMS NIH HHS/United States ; S10 OD023461/OD/NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; },
mesh = {Amoxicillin/*pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteroides thetaiotaomicron/*drug effects/*metabolism ; Dietary Fiber/metabolism ; *Drug Resistance, Bacterial ; Female ; Gastrointestinal Microbiome/*drug effects ; Glucose/metabolism ; Mice ; Mice, Inbred C57BL ; Polysaccharides/metabolism ; },
abstract = {Although antibiotics disturb the structure of the gut microbiota, factors that modulate these perturbations are poorly understood. Bacterial metabolism is an important regulator of susceptibility in vitro and likely plays a large role within the host. We applied a metagenomic and metatranscriptomic approach to link antibiotic-induced taxonomic and transcriptional responses within the murine microbiome. We found that antibiotics significantly alter the expression of key metabolic pathways at the whole-community and single-species levels. Notably, Bacteroides thetaiotaomicron, which blooms in response to amoxicillin, upregulated polysaccharide utilization. In vitro, we found that the sensitivity of this bacterium to amoxicillin was elevated by glucose and reduced by polysaccharides. Accordingly, we observed that dietary composition affected the abundance and expansion of B. thetaiotaomicron, as well as the extent of microbiome disruption with amoxicillin. Our work indicates that the metabolic environment of the microbiome plays a role in the response of this community to antibiotics.},
}

Amoxicillin/*pharmacology
Animals
Anti-Bacterial Agents/*pharmacology
Bacteroides thetaiotaomicron/*drug effects/*metabolism
Dietary Fiber/metabolism
*Drug Resistance, Bacterial
Female
Gastrointestinal Microbiome/*drug effects
Glucose/metabolism
Mice
Mice, Inbred C57BL
Polysaccharides/metabolism

@article {pmid31888048,
year = {2019},
author = {Sakanaka, M and Gotoh, A and Yoshida, K and Odamaki, T and Koguchi, H and Xiao, JZ and Kitaoka, M and Katayama, T},
title = {Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation.},
journal = {Nutrients},
volume = {12},
number = {1},
pages = {},
pmid = {31888048},
issn = {2072-6643},
support = {18K14379; 19K15732; 19K22277; 201860637; 17J08530//Japan Society for the Promotion of Science/ ; },
mesh = {*Bifidobacterium/enzymology/genetics/metabolism ; Breast Feeding ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Genome, Bacterial/genetics ; Humans ; Infant ; Metagenomics ; *Milk, Human/chemistry/metabolism ; Oligosaccharides/*metabolism ; },
abstract = {The infant's gut microbiome is generally rich in the Bifidobacterium genus. The mother's milk contains natural prebiotics, called human milk oligosaccharides (HMOs), as the third most abundant solid component after lactose and lipids, and of the different gut microbes, infant gut-associated bifidobacteria are the most efficient in assimilating HMOs. Indeed, the fecal concentration of HMOs was found to be negatively correlated with the fecal abundance of Bifidobacterium in infants. Given these results, two HMO molecules, 2'-fucosyllactose and lacto-N-neotetraose, have recently been industrialized to fortify formula milk. As of now, however, our knowledge about the HMO consumption pathways in infant gut-associated bifidobacteria is still incomplete. The recent studies indicate that HMO assimilation abilities significantly vary among different Bifidobacterium species and strains. Therefore, to truly maximize the effects of prebiotic and probiotic supplementation in commercialized formula, we need to understand HMO consumption behaviors of bifidobacteria in more detail. In this review, we summarized how different Bifidobacterium species/strains are equipped with varied gene sets required for HMO assimilation. We then examined the correlation between the abundance of the HMO-related genes and bifidobacteria-rich microbiota formation in the infant gut through data mining analysis of a deposited fecal microbiome shotgun sequencing dataset. Finally, we shortly described future perspectives on HMO-related studies.},
}

*Bifidobacterium/enzymology/genetics/metabolism
Breast Feeding
Feces/microbiology
Female
*Gastrointestinal Microbiome/genetics/physiology
Genome, Bacterial/genetics
Humans
Infant
Metagenomics
*Milk, Human/chemistry/metabolism
Oligosaccharides/*metabolism

@article {pmid30741985,
year = {2019},
author = {Vera-Gargallo, B and Chowdhury, TR and Brown, J and Fansler, SJ and Durán-Viseras, A and Sánchez-Porro, C and Bailey, VL and Jansson, JK and Ventosa, A},
title = {Spatial distribution of prokaryotic communities in hypersaline soils.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {1769},
pmid = {30741985},
issn = {2045-2322},
mesh = {Animals ; Biodiversity ; Chemical Phenomena ; Geologic Sediments/microbiology ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; *Prokaryotic Cells ; *Salinity ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Increasing salinization in wetland systems is a major threat to ecosystem services carried out by microbial communities. Thus, it is paramount to understand how salinity drives both microbial community structures and their diversity. Here we evaluated the structure and diversity of the prokaryotic communities from a range of highly saline soils (EC1:5 from 5.96 to 61.02 dS/m) from the Odiel Saltmarshes and determined their association with salinity and other soil physicochemical features by analyzing 16S rRNA gene amplicon data through minimum entropy decomposition (MED). We found that these soils harbored unique communities mainly composed of halophilic and halotolerant taxa from the phyla Euryarchaeota, Proteobacteria, Balneolaeota, Bacteroidetes and Rhodothermaeota. In the studied soils, several site-specific properties were correlated with community structure and individual abundances of particular sequence variants. Salinity had a secondary role in shaping prokaryotic communities in these highly saline samples since the dominant organisms residing in them were already well-adapted to a wide range of salinities. We also compared ESV-based results with OTU-clustering derived ones, showing that, in this dataset, no major differences in ecological outcomes were obtained by the employment of one or the other method.},
}

Animals
Biodiversity
Chemical Phenomena
Geologic Sediments/microbiology
Metagenome
Metagenomics/methods
Mice
*Microbiota
*Prokaryotic Cells
*Salinity
Soil/*chemistry
*Soil Microbiology

@article {pmid32867361,
year = {2020},
author = {Xue, CX and Liu, J and Lea-Smith, DJ and Rowley, G and Lin, H and Zheng, Y and Zhu, XY and Liang, J and Ahmad, W and Todd, JD and Zhang, XH},
title = {Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth.},
journal = {Microorganisms},
volume = {8},
number = {9},
pages = {},
doi = {10.3390/microorganisms8091309},
pmid = {32867361},
issn = {2076-2607},
abstract = {The Earth's oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0-10,500 m) in the Mariana Trench, the deepest natural point in the Earth's oceans. We recovered 726 metagenome-assembled genomes (MAGs) affiliated to 27 phyla. Overall, biodiversity increased in line with increased depth. In addition, the genome size of MAGs at ≥4000 m layers was slightly larger compared to those at 0-2000 m. As expected, surface waters were the main source of primary production, predominantly from Cyanobacteria. Intriguingly, microbes conducting an unusual form of nitrogen metabolism were identified in the deepest waters (>10,000 m), as demonstrated by an enrichment of genes encoding proteins involved in dissimilatory nitrate to ammonia conversion (DNRA), nitrogen fixation and urea transport. These likely facilitate the survival of ammonia-oxidizing archaea α lineage, which are typically present in environments with a high ammonia concentration. In addition, the microbial potential for oxidative phosphorylation and the glyoxylate shunt was enhanced in >10,000 m waters. This study provides novel insights into how microbial communities and their genetic potential for biogeochemical cycling differs through the Challenger deep water column, and into the unique adaptive lifestyle of microbes in the Earth's deepest seawater.},
}

@article {pmid32867028,
year = {2020},
author = {Marin-Gómez, W and Grande, MJ and Pérez-Pulido, R and Galvez, A and Lucas, R},
title = {Changes in the Bacterial Diversity of Human Milk during Late Lactation Period (Weeks 21 to 48).},
journal = {Foods (Basel, Switzerland)},
volume = {9},
number = {9},
pages = {},
doi = {10.3390/foods9091184},
pmid = {32867028},
issn = {2304-8158},
support = {RS-AGR230//Universidad de Jaén/ ; },
abstract = {Breast milk from a single mother was collected during a 28-week lactation period. Bacterial diversity was studied by amplicon sequencing analysis of the V3-V4 variable region of the 16S rRNA gene. Firmicutes and Proteobacteria were the main phyla detected in the milk samples, followed by Actinobacteria and Bacteroidetes. The proportion of Firmicutes to Proteobacteria changed considerably depending on the sampling week. A total of 411 genera or higher taxons were detected in the set of samples. Genus Streptococcus was detected during the 28-week sampling period, at relative abundances between 2.0% and 68.8%, and it was the most abundant group in 14 of the samples. Carnobacterium and Lactobacillus had low relative abundances. At the genus level, bacterial diversity changed considerably at certain weeks within the studied period. The weeks or periods with lowest relative abundance of Streptococcus had more diverse bacterial compositions including genera belonging to Proteobacteria that were poorly represented in the rest of the samples.},
}

@article {pmid32857738,
year = {2020},
author = {Wang, J and Zhou, J},
title = {The effects of offshore petroleum exploitation on microbial community and antibiotic resistome of adjacent marine sediments.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {81},
number = {12},
pages = {2501-2510},
doi = {10.2166/wst.2020.289},
pmid = {32857738},
issn = {0273-1223},
mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Genes, Bacterial ; Geologic Sediments ; Humans ; *Microbiota ; *Petroleum ; },
abstract = {The exploitation of petroleum in offshore areas is becoming more prosperous due to the increasing human demand for oil. However, the effects of offshore petroleum exploitation on the microbial community in the surrounding environment are still not adequately understood. In the present study, variations in the composition, function, and antibiotic resistance of the microbial community in marine sediments adjacent to an offshore petroleum exploitation platform were analyzed by a metagenomics-based method. Significant shifts in the microbial community composition were observed in sediments impacted by offshore petroleum exploitation. Nitrosopumilales was enriched in marine sediments with the activities of offshore petroleum exploitation compared to the control sediments. The abundances of function genes involved in carbon, butanoate, methane, and fatty acid metabolism in sediment microbial communities also increased due to the offshore petroleum exploitation. Offshore petroleum exploitation resulted in the propagation of some antibiotic resistance genes (ARGs), including a multidrug transporter, smeE, and arnA, in marine sediments via horizontal gene transfer mediated by class I integrons. However, the total abundance and diversity of ARGs in marine sediments were not significantly affected by offshore petroleum exploitation. This study is the first attempt to analyze the impact of offshore petroleum exploitation on the spread of antibiotic resistance.},
}

Anti-Bacterial Agents
Bacteria/genetics
Genes, Bacterial
Geologic Sediments
Humans
*Microbiota
*Petroleum

@article {pmid32554026,
year = {2020},
author = {Appolinario, LR and Tschoeke, D and Calegario, G and Barbosa, LH and Moreira, MA and Albuquerque, ALS and Thompson, CC and Thompson, FL},
title = {Oil leakage induces changes in microbiomes of deep-sea sediments of Campos Basin (Brazil).},
journal = {The Science of the total environment},
volume = {740},
number = {},
pages = {139556},
doi = {10.1016/j.scitotenv.2020.139556},
pmid = {32554026},
issn = {1879-1026},
mesh = {Brazil ; Geologic Sediments ; Hydrocarbons ; Metagenomics ; *Microbiota ; *Petroleum ; },
abstract = {The Campos Basin (100,000 km2) is located on the continental shelf of southeastern Brazil. Despite the significant oil and gas industrial activities underway in the Campos Basin, scarce information is available regarding the hydrocarbon contents and microbial communities in the deep-sea sediments. To gain new insights on these aspects, we first obtained deep-sea sediment samples with different degrees of oil exposure. We obtained samples from a seabed fissure (N = 28), surroundings (250 m to 500 m from the fissure; N = 24), and a control area (N = 4). We used shotgun metagenomics to characterize the taxonomic and metabolic diversity and analyzed biogeochemical parameters (metal and oil concentration) of all samples. The high levels of unresolved complex mixture of hydrocarbons in the fissure indicate a potentially recent petrogenic contribution in these sediments. The fissure area was found to have a higher abundance of hydrocarbonoclastic bacterial genera and hydrocarbon degradation genes. These bacteria may be used as biosensors of sediment contamination. The effects of oil contamination, mainly around the fissure, are less clear at 250 m and 500 m, suggesting that the surroundings may not have been heavily affected by the oil leakage. Our study demonstrates that metagenomics can disclose biosensors for environmental monitoring.},
}

Brazil
Geologic Sediments
Hydrocarbons
Metagenomics
*Microbiota
*Petroleum

@article {pmid32521370,
year = {2020},
author = {Kang, X and Cui, Y and Shen, T and Yan, M and Tu, W and Shoaib, M and Xiang, Q and Zhao, K and Gu, Y and Chen, Q and Li, S and Liang, Y and Ma, M and Zou, L and Yu, X},
title = {Changes of root microbial populations of natively grown plants during natural attenuation of V-Ti magnetite tailings.},
journal = {Ecotoxicology and environmental safety},
volume = {201},
number = {},
pages = {110816},
doi = {10.1016/j.ecoenv.2020.110816},
pmid = {32521370},
issn = {1090-2414},
mesh = {Biodegradation, Environmental ; China ; Ferrosoferric Oxide/analysis/*toxicity ; Metagenomics ; Microbiota/*drug effects/genetics ; Mining ; Plant Roots/*microbiology ; Poaceae/growth & development/microbiology ; Rhizobium ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/analysis/*toxicity ; Titanium/analysis/*toxicity ; Typhaceae/growth & development/microbiology ; Vanadium/analysis/*toxicity ; },
abstract = {Mine tailings contain dangerously high levels of toxic metals which pose a constant threat to local ecosystems. Few naturally grown native plants can colonize tailings site and the existence of their root-associated microbial populations is poorly understood. The objective of this study was to give further insights into the interactions between native plants and their microbiota during natural attenuation of abandoned V-Ti magnetite mine tailings. In the present work, we first examined the native plants' potential for phytoremediation using plant/soil analytical methods and then investigated the root microbial communities and their inferred functions using 16 S rRNA-based metagenomics. It was found that in V-Ti magnetite mine tailings the two dominant plants Bothriochloa ischaemum and Typha angustifolia were able to increase available nitrogen in the rhizosphere soil by 23.3% and 53.7% respectively. The translocation factors (TF) for both plants indicated that B. ischaemum was able to accumulate Pb (TF = 1.212), while T. angustifolia was an accumulator of Mn (TF = 2.502). The microbial community structure was more complex in the soil associated with T. angustifolia than with B. ischaemum. The presence of both plants significantly reduced the population of Acinetobacter. Specifically, B. ischaemum enriched Massilia, Opitutus and Hydrogenophaga species while T. angustifolia significantly increased rhizobia species. Multivariate analyses revealed that among all tested soil variables Fe and total organic carbon (TOC) could be the key factors in shaping the microbial structure. The putative functional analysis indicated that soil sample of B. ischaemum was abundant with nitrate/nitrite reduction-related functions while that of T. angustifolia was rich in nitrogen fixing functions. The results indicate that these native plants host a diverse range of soil microbes, whose community structure can be shaped by plant types and soil variables. It is also possible that these plants can be used to improve soil nitrogen content and serve as bioaccumulators for Pb or Mn for phytoremediation purposes.},
}

Biodegradation, Environmental
China
Ferrosoferric Oxide/analysis/*toxicity
Metagenomics
Microbiota/*drug effects/genetics
Mining
Plant Roots/*microbiology
Poaceae/growth & development/microbiology
Rhizobium
Rhizosphere
Soil/chemistry
Soil Microbiology
Soil Pollutants/analysis/*toxicity
Titanium/analysis/*toxicity
Typhaceae/growth & development/microbiology
Vanadium/analysis/*toxicity

@article {pmid31611361,
year = {2019},
author = {Guitor, AK and Raphenya, AR and Klunk, J and Kuch, M and Alcock, B and Surette, MG and McArthur, AG and Poinar, HN and Wright, GD},
title = {Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes.},
journal = {Antimicrobial agents and chemotherapy},
volume = {64},
number = {1},
pages = {},
pmid = {31611361},
issn = {1098-6596},
support = {MT-14981//CIHR/Canada ; PJT-156214//CIHR/Canada ; },
mesh = {Bacteria/drug effects/genetics/isolation & purification ; DNA Probes/genetics ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/genetics ; Genome, Bacterial ; Humans ; *Metagenome ; Metagenomics/methods ; Microbiota/drug effects/genetics ; Whole Genome Sequencing ; },
abstract = {Identification of the nucleotide sequences encoding antibiotic resistance elements and determination of their association with antibiotic resistance are critical to improve surveillance and monitor trends in antibiotic resistance. Current methods to study antibiotic resistance in various environments rely on extensive deep sequencing or laborious culturing of fastidious organisms, both of which are heavily time-consuming operations. An accurate and sensitive method to identify both rare and common resistance elements in complex metagenomic samples is needed. Referencing the sequences in the Comprehensive Antibiotic Resistance Database, we designed a set of 37,826 probes to specifically target over 2,000 nucleotide sequences associated with antibiotic resistance in clinically relevant bacteria. Testing of this probe set on DNA libraries generated from multidrug-resistant bacteria to selectively capture resistance genes reproducibly produced higher numbers of reads on target at a greater length of coverage than shotgun sequencing. We also identified additional resistance gene sequences from human gut microbiome samples that sequencing alone was not able to detect. Our method to capture the resistome enables a sensitive means of gene detection in diverse environments where genes encoding antibiotic resistance represent less than 0.1% of the metagenome.},
}

Bacteria/drug effects/genetics/isolation & purification
DNA Probes/genetics
Databases, Genetic
Drug Resistance, Bacterial/*genetics
Drug Resistance, Multiple, Bacterial/genetics
Feces/microbiology
Gastrointestinal Microbiome/drug effects/genetics
Genome, Bacterial
Humans
*Metagenome
Metagenomics/methods
Microbiota/drug effects/genetics
Whole Genome Sequencing

@article {pmid31592688,
year = {2019},
author = {Colman, DR and Lindsay, MR and Amenabar, MJ and Boyd, ES},
title = {The Intersection of Geology, Geochemistry, and Microbiology in Continental Hydrothermal Systems.},
journal = {Astrobiology},
volume = {19},
number = {12},
pages = {1505-1522},
doi = {10.1089/ast.2018.2016},
pmid = {31592688},
issn = {1557-8070},
mesh = {Bacterial Proteins/genetics/metabolism ; Biological Evolution ; Extremophiles/*isolation & purification/physiology ; Geologic Sediments/analysis/chemistry/*microbiology ; Hot Springs/chemistry/*microbiology ; Hot Temperature/adverse effects ; Hydrogen-Ion Concentration ; *Metagenome ; Microbiota/*physiology ; Oxidation-Reduction ; Sulfur/metabolism ; Thermodynamics ; Water Microbiology ; },
abstract = {Decompressional boiling of ascending hydrothermal waters and separation into a vapor (gas) and a liquid phase drive extensive variation in the geochemical composition of hot spring waters. Yet little is known of how the process of phase separation influences the distribution of microbial metabolisms in springs. Here, we determined the variation in protein coding genes in 51 metagenomes from chemosynthetic hot spring communities that span geochemical gradients in Yellowstone National Park. The 51 metagenomes could be divided into 5 distinct groups that correspond to low and high temperatures and acidic and circumneutral/alkaline springs. A fifth group primarily comprised metagenomes from springs with moderate acidity and that are influenced by elevated volcanic gas input. Protein homologs putatively involved in the oxidation of sulfur compounds, a process that leads to acidification of spring waters, in addition to those involved in the reduction of sulfur compounds were enriched in metagenomes from acidic springs sourced by vapor phase gases. Metagenomes from springs with evidence for elevated volcanic gas input were enriched in protein homologs putatively involved in oxidation of those gases, including hydrogen and methane. Finally, metagenomes from circumneutral/alkaline springs sourced by liquid phase waters were enriched in protein homologs putatively involved in heterotrophy and respiration of oxidized nitrogen compounds and oxygen. These results indicate that the geological process of phase separation shapes the ecology of thermophilic communities through its influence on the availability of nutrients in the form of gases, solutes, and minerals. Microbial acidification of hot spring waters further influences the kinetic and thermodynamic stabilities of nutrients and their bioavailability. These data therefore provide an important framework to understand how geological processes have shaped the evolutionary history of chemosynthetic thermophiles and how these organisms, in turn, have shaped their geochemical environments.},
}

Bacterial Proteins/genetics/metabolism
Biological Evolution
Extremophiles/*isolation & purification/physiology
Geologic Sediments/analysis/chemistry/*microbiology
Hot Springs/chemistry/*microbiology
Hot Temperature/adverse effects
Hydrogen-Ion Concentration
*Metagenome
Microbiota/*physiology
Oxidation-Reduction
Sulfur/metabolism
Thermodynamics
Water Microbiology

@article {pmid31122082,
year = {2019},
author = {McCombe, PA and Henderson, RD and Lee, A and Lee, JD and Woodruff, TM and Restuadi, R and McRae, A and Wray, NR and Ngo, S and Steyn, FJ},
title = {Gut microbiota in ALS: possible role in pathogenesis?.},
journal = {Expert review of neurotherapeutics},
volume = {19},
number = {9},
pages = {785-805},
doi = {10.1080/14737175.2019.1623026},
pmid = {31122082},
issn = {1744-8360},
mesh = {Amyotrophic Lateral Sclerosis/*etiology/*microbiology ; Animals ; Dysbiosis/*complications ; *Gastrointestinal Microbiome ; Humans ; },
abstract = {Introduction: The gut microbiota has important roles in maintaining human health. The microbiota and its metabolic byproducts could play a role in the pathogenesis of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Areas covered: The authors evaluate the methods of assessing the gut microbiota, and also review how the gut microbiota affects the various physiological functions of the gut. The authors then consider how gut dysbiosis could theoretically affect the pathogenesis of ALS. They present the current evidence regarding the composition of the gut microbiota in ALS and in rodent models of ALS. Finally, the authors review therapies that could improve gut dysbiosis in the context of ALS. Expert opinion: Currently reported studies suggest some instances of gut dysbiosis in ALS patients and mouse models; however, these studies are limited, and more information with well-controlled larger datasets is required to make a definitive judgment about the role of the gut microbiota in ALS pathogenesis. Overall this is an emerging field that is worthy of further investigation. The authors advocate for larger studies using modern metagenomic techniques to address the current knowledge gaps.},
}

Amyotrophic Lateral Sclerosis/*etiology/*microbiology
Animals
Dysbiosis/*complications
*Gastrointestinal Microbiome
Humans

@article {pmid32601270,
year = {2020},
author = {Fremin, BJ and Sberro, H and Bhatt, AS},
title = {MetaRibo-Seq measures translation in microbiomes.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {3268},
pmid = {32601270},
issn = {2041-1723},
support = {P50 AG047366/AG/NIA NIH HHS/United States ; },
mesh = {Metagenomics ; Microbiota/*genetics ; Protein Biosynthesis/genetics ; RNA-Seq/*methods ; },
abstract = {No method exists to measure large-scale translation of genes in uncultured organisms in microbiomes. To overcome this limitation, we develop MetaRibo-Seq, a method for simultaneous ribosome profiling of tens to hundreds of organisms in microbiome samples. MetaRibo-Seq was benchmarked against gold-standard Ribo-Seq in a mock microbial community and applied to five different human fecal samples. Unlike RNA-Seq, Ribo-Seq signal of a predicted gene suggests it encodes a translated protein. We demonstrate two applications of this technique: First, MetaRibo-Seq identifies small genes, whose identification until now has been challenging. For example, MetaRibo-Seq identifies 2,091 translated, previously unannotated small protein families from five fecal samples, more than doubling the number of small proteins predicted to exist in this niche. Second, the combined application of RNA-Seq and MetaRibo-Seq identifies differences in the translation of transcripts. In summary, MetaRibo-Seq enables comprehensive translational profiling in microbiomes and identifies previously unannotated small proteins.},
}

Metagenomics
Microbiota/*genetics
Protein Biosynthesis/genetics
RNA-Seq/*methods

@article {pmid30733472,
year = {2019},
author = {Zhang, W and Li, J and Lu, S and Han, N and Miao, J and Zhang, T and Qiang, Y and Kong, Y and Wang, H and Gao, T and Liu, Y and Li, X and Peng, X and Chen, X and Zhao, X and Che, J and Zhang, L and Chen, X and Zhang, Q and Hu, M and Li, Q and Kan, B},
title = {Gut microbiota community characteristics and disease-related microorganism pattern in a population of healthy Chinese people.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {1594},
pmid = {30733472},
issn = {2045-2322},
mesh = {Adolescent ; China ; *Disease ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; *Healthy Volunteers ; Humans ; Male ; Middle Aged ; Young Adult ; },
abstract = {China's population accounts for about 1/5th of the world's total population. Owing to differences in environment, race, living habits, and other factors, the structure of the intestinal flora of Chinese individuals is expected to have unique features; however, this has not been thoroughly examined. Here, we collected faecal samples from healthy adults living in three cities of China and investigated their gut microbiome using metagenomics and bioinformatics technology. We found that 11 core bacterial genera were present in all of the Chinese faecal samples; moreover, several patient characteristics (age, region, body mass index, physical exercise, smoking habits, and alcoholic drink, and yogurt consumption) were found to have different effects on the gut microbiome of healthy Chinese people. We also examined the distribution patterns of disease-related microorganisms (DRMs), revealing which DRMs can potentially be used as markers for assessment of health risk. We also developed a program called "Guthealthy" for evaluating the health status associated with the microbiome and DRM pattern in the faecal samples. The microbiota data obtained in this study will provide a basis for a healthy gut microbiome composition in the Chinese population.},
}

Adolescent
China
*Disease
Feces/microbiology
Female
*Gastrointestinal Microbiome
*Healthy Volunteers
Humans
Male
Middle Aged
Young Adult

@article {pmid30696861,
year = {2019},
author = {Okazaki, F and Zang, L and Nakayama, H and Chen, Z and Gao, ZJ and Chiba, H and Hui, SP and Aoki, T and Nishimura, N and Shimada, Y},
title = {Microbiome Alteration in Type 2 Diabetes Mellitus Model of Zebrafish.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {867},
pmid = {30696861},
issn = {2045-2322},
mesh = {Animals ; Bacteria/genetics ; Diabetes Mellitus/*genetics/metabolism/*microbiology ; Disease Models, Animal ; Gastrointestinal Microbiome/*genetics ; Glucose Intolerance/genetics ; Male ; Metagenome/genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Zebrafish/microbiology ; },
abstract = {Understanding the gut microbiota in metabolic disorders, including type 2 diabetes mellitus (T2DM), is now gaining importance due to its potential role in disease risk and progression. We previously established a zebrafish model of T2DM, which shows glucose intolerance with insulin resistance and responds to anti-diabetic drugs. In this study, we analysed the gut microbiota of T2DM zebrafish by deep sequencing the 16S rRNA V3-V4 hypervariable regions, and imputed a functional profile using predictive metagenomic tools. While control and T2DM zebrafish were fed with the same kind of feed, the gut microbiota in T2DM group was less diverse than that of the control. Predictive metagenomics profiling using PICRUSt revealed functional alternation of the KEGG pathways in T2DM zebrafish. Several amino acid metabolism pathways (arginine, proline, and phenylalanine) were downregulated in the T2DM group, similar to what has been previously reported in humans. In summary, we profiled the gut microbiome in T2DM zebrafish, which revealed functional similarities in gut bacterial environments between these zebrafish and T2DM affected humans. T2DM zebrafish can become an alternative model organism to study host-bacterial interactions in human obesity and related diseases.},
}

Animals
Bacteria/genetics
Diabetes Mellitus/*genetics/metabolism/*microbiology
Disease Models, Animal
Gastrointestinal Microbiome/*genetics
Glucose Intolerance/genetics
Male
Metagenome/genetics
Metagenomics/methods
RNA, Ribosomal, 16S/genetics
Zebrafish/microbiology

@article {pmid32703166,
year = {2020},
author = {Kondratenko, Y and Korobeynikov, A and Lapidus, A},
title = {CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities.},
journal = {BMC bioinformatics},
volume = {21},
number = {Suppl 12},
pages = {303},
doi = {10.1186/s12859-020-03591-6},
pmid = {32703166},
issn = {1471-2105},
support = {19-16-00049//Russian Science Foundation/ ; },
mesh = {Databases, Genetic ; *High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/genetics ; *Molecular Sequence Annotation ; RNA, Ribosomal, 16S/genetics ; *Software ; },
abstract = {BACKGROUND: Illumina paired-end reads are often used for 16S analysis in metagenomic studies. Since DNA fragment size is usually smaller than the sum of lengths of paired reads, reads can be merged for downstream analysis. In spite of development of several tools for merging of paired-end reads, poor quality at the 3' ends within the overlapping region prevents the accurate combining of significant portion of read pairs. Recently CD-HIT-OTU-Miseq was presented as a new approach for 16S analysis using the paired-end reads, it completely avoids the reads merging process due to separate clustering of paired reads. CD-HIT-OTU-Miseq is a set of tools which are supposed to be successively launched by auxiliary shell scripts. This launch mode is not suitable for processing of big amounts of data generated in modern omics experiments. To solve this issue we created CDSnake - Snakemake pipeline utilizing CD-HIT tools for easier consecutive launch of CD-HIT-OTU-Miseq tools for complete processing of paired end reads in metagenomic studies. Usage of pipeline make 16S analysis easier due to one-command launch and helps to yield reproducible results.

RESULTS: We benchmarked our pipeline against two commonly used pipelines for OTU retrieval, incorporated into popular workflow for microbiome analysis, QIIME2 - DADA2 and deblur. Three mock datasets having highly overlapping paired-end 2 × 250 bp reads were used for benchmarking - Balanced, HMP, and Extreme. CDSnake outputted less OTUs than DADA2 and deblur. However, on Balanced and HMP datasets number of OTUs outputted by CDSnake was closer to real number of strains which were used for mock community generation, than those outputted by DADA2 and deblur. Though generally slower than other pipelines, CDSnake outputted higher total counts, preserving more information from raw data. Inheriting this properties from original CD-HIT-OTU-MiSeq utilities, CDSnake made their usage handier due to simple scalability, easier automated runs and other Snakemake benefits.

CONCLUSIONS: We developed Snakemake pipeline for OTU-MiSeq utilities, which simplified and automated data analysis. Benchmarking showed that this approach is capable to outperform popular tools in certain conditions.},
}

Databases, Genetic
*High-Throughput Nucleotide Sequencing
Humans
Microbiota/genetics
*Molecular Sequence Annotation
RNA, Ribosomal, 16S/genetics
*Software

@article {pmid32497143,
year = {2020},
author = {Wang, S and Yan, Z and Wang, P and Zheng, X and Fan, J},
title = {Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area.},
journal = {PloS one},
volume = {15},
number = {6},
pages = {e0234128},
pmid = {32497143},
issn = {1932-6203},
mesh = {Bacteria/classification/*genetics/*metabolism ; *Biodiversity ; China ; Geologic Sediments/*microbiology ; *Metagenomics ; Seawater/*microbiology ; },
abstract = {Qinhuangdao coastal area is an important mariculture area in North China. Microbial communities play an important role in driving biogeochemical cycle and energy flow. It is necessary to identify the microbial communities and their functions in the coastal mariculture area of Qinhuangdao. In this study, the microbial community compositions and their metabolic potentials in the sediments and their surrounding seawaters of Qinhuangdao mariculture area were uncovered by the 16S rRNA gene amplicon sequencing and metagenomic shotgun sequencing approaches. The results of amplicon sequencing showed that Gammaproteobacteria and Alphaproteobacteria were predominant classes. Our datasets showed a clear shift in microbial taxonomic groups and the metabolic pathways in the sediments and surrounding seawaters. Metagenomic analysis showed that purine metabolism, ABC transporters, and pyrimidine metabolism were the most abundant pathways. Genes related to two-component system, TCA cycle and nitrogen metabolism exhibited higher abundance in sediments compared with those in seawaters. The presence of cadmium-resistant genes and ABC transporters suggested the ability of microorganisms to resist the toxicity of cadmium. In summary, this study provides comprehensive and significant differential signatures in the microbial community and metabolic pathways in Qinhuangdao mariculture area, and can develop effective microbial indicators to monitor mariculture area in the future.},
}

Bacteria/classification/*genetics/*metabolism
*Biodiversity
China
Geologic Sediments/*microbiology
*Metagenomics
Seawater/*microbiology

@article {pmid31629686,
year = {2019},
author = {Cao, L and Gurevich, A and Alexander, KL and Naman, CB and Leão, T and Glukhov, E and Luzzatto-Knaan, T and Vargas, F and Quinn, R and Bouslimani, A and Nothias, LF and Singh, NK and Sanders, JG and Benitez, RAS and Thompson, LR and Hamid, MN and Morton, JT and Mikheenko, A and Shlemov, A and Korobeynikov, A and Friedberg, I and Knight, R and Venkateswaran, K and Gerwick, WH and Gerwick, L and Dorrestein, PC and Pevzner, PA and Mohimani, H},
title = {MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities.},
journal = {Cell systems},
volume = {9},
number = {6},
pages = {600-608.e4},
pmid = {31629686},
issn = {2405-4720},
support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; R01 GM107550/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; R01 GM097509/GM/NIGMS NIH HHS/United States ; DP2 GM137413/GM/NIGMS NIH HHS/United States ; T32 CA009523/CA/NCI NIH HHS/United States ; },
mesh = {Computational Biology/*methods ; Genomics/methods ; Humans ; Microbiota/*genetics ; Peptides/chemistry ; Protein Processing, Post-Translational/*genetics ; Ribosomes/genetics ; Software ; },
abstract = {Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.},
}

Computational Biology/*methods
Genomics/methods
Humans
Microbiota/*genetics
Peptides/chemistry
Protein Processing, Post-Translational/*genetics
Ribosomes/genetics
Software

@article {pmid31533247,
year = {2019},
author = {Modha, S and Hughes, J and Bianco, G and Ferguson, HM and Helm, B and Tong, L and Wilkie, GS and Kohl, A and Schnettler, E},
title = {Metaviromics Reveals Unknown Viral Diversity in the Biting Midge Culicoides impunctatus.},
journal = {Viruses},
volume = {11},
number = {9},
pages = {},
pmid = {31533247},
issn = {1999-4915},
support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/12 and MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Ceratopogonidae/*virology ; Europe ; Genetic Variation ; Genome, Viral/*genetics ; Insect Vectors/*virology ; Metagenomics ; Phylogeny ; RNA Viruses/classification/*genetics ; },
abstract = {Biting midges (Culicoides species) are vectors of arboviruses and were responsible for the emergence and spread of Schmallenberg virus (SBV) in Europe in 2011 and are likely to be involved in the emergence of other arboviruses in Europe. Improved surveillance and better understanding of risks require a better understanding of the circulating viral diversity in these biting insects. In this study, we expand the sequence space of RNA viruses by identifying a number of novel RNA viruses from Culicoides impunctatus (biting midge) using a meta-transcriptomic approach. A novel metaviromic pipeline called MetaViC was developed specifically to identify novel virus sequence signatures from high throughput sequencing (HTS) datasets in the absence of a known host genome. MetaViC is a protein centric pipeline that looks for specific protein signatures in the reads and contigs generated as part of the pipeline. Several novel viruses, including an alphanodavirus with both segments, a novel relative of the Hubei sobemo-like virus 49, two rhabdo-like viruses and a chuvirus, were identified in the Scottish midge samples. The newly identified viruses were found to be phylogenetically distinct to those previous known. These findings expand our current knowledge of viral diversity in arthropods and especially in these understudied disease vectors.},
}

Animals
Ceratopogonidae/*virology
Europe
Genetic Variation
Genome, Viral/*genetics
Insect Vectors/*virology
Metagenomics
Phylogeny
RNA Viruses/classification/*genetics

@article {pmid32835181,
year = {2020},
author = {Kirubakaran, R and ArulJothi, KN and Revathi, S and Shameem, N and Parray, JA},
title = {Emerging priorities for microbial metagenome research.},
journal = {Bioresource technology reports},
volume = {11},
number = {},
pages = {100485},
doi = {10.1016/j.biteb.2020.100485},
pmid = {32835181},
issn = {2589-014X},
abstract = {Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.},
}

@article {pmid32098813,
year = {2020},
author = {Waterworth, SC and Flórez, LV and Rees, ER and Hertweck, C and Kaltenpoth, M and Kwan, JC},
title = {Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
pmid = {32098813},
issn = {2150-7511},
mesh = {Animals ; Bacteria/genetics ; Biological Products ; Burkholderia/genetics ; Coleoptera/*microbiology ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome Size ; Genome, Bacterial/*genetics ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; Symbiosis/*genetics/physiology ; },
abstract = {Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont's genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.IMPORTANCE Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation-bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that the symbiont has acquired genes from other bacteria despite going through genome reduction, suggesting that isolation has not yet played a major role in this case of genome reduction, with horizontal gene gains still offering a potential route for adaptation.},
}

Animals
Bacteria/genetics
Biological Products
Burkholderia/genetics
Coleoptera/*microbiology
Evolution, Molecular
*Gene Transfer, Horizontal
Genome Size
Genome, Bacterial/*genetics
Metagenomics
Microbiota/*genetics
Multigene Family
Symbiosis/*genetics/physiology

@article {pmid31373933,
year = {2019},
author = {Raj, AS and Shanahan, ER and Tran, CD and Bhat, P and Fletcher, LM and Vesey, DA and Morrison, M and Holtmann, G and Macdonald, GA},
title = {Dysbiosis of the Duodenal Mucosal Microbiota Is Associated With Increased Small Intestinal Permeability in Chronic Liver Disease.},
journal = {Clinical and translational gastroenterology},
volume = {10},
number = {8},
pages = {e00068},
pmid = {31373933},
issn = {2155-384X},
mesh = {Adult ; Aged ; Chronic Disease ; DNA, Bacterial/isolation & purification ; Disease Progression ; Duodenum/microbiology/*pathology ; Dysbiosis/diagnosis/microbiology/*pathology ; Female ; Gastrointestinal Microbiome/genetics ; Humans ; Intestinal Mucosa/microbiology/*pathology ; Liver/*pathology ; Liver Diseases/complications/*diagnosis/microbiology/pathology ; Male ; Middle Aged ; Permeability ; RNA, Ribosomal, 16S/genetics ; },
abstract = {OBJECTIVES: Chronic liver disease (CLD) is associated with both alterations of the stool microbiota and increased small intestinal permeability. However, little is known about the role of the small intestinal mucosa-associated microbiota (MAM) in CLD. The aim of this study was to evaluate the relationship between the duodenal MAM and both small intestinal permeability and liver disease severity in CLD.

METHODS: Subjects with CLD and a disease-free control group undergoing routine endoscopy underwent duodenal biopsy to assess duodenal MAM by 16S rRNA gene sequencing. Small intestinal permeability was assessed by a dual sugar (lactulose: rhamnose) assay. Other assessments included transient elastography, endotoxemia, serum markers of hepatic inflammation, dietary intake, and anthropometric measurements.

RESULTS: Forty-six subjects (35 with CLD and 11 controls) were assessed. In subjects with CLD, the composition (P = 0.02) and diversity (P < 0.01) of the duodenal MAM differed to controls. Constrained multivariate analysis and linear discriminate effect size showed this was due to Streptococcus-affiliated lineages. Small intestinal permeability was significantly higher in CLD subjects compared to controls. In CLD, there were inverse correlations between microbial diversity and both increased small intestinal permeability (r = -0.41, P = 0.02) and serum alanine aminotransferase (r = -0.35, P = 0.04). Hepatic stiffness was not associated with the MAM.

DISCUSSION: In CLD, there is dysbiosis of the duodenal MAM and an inverse correlation between microbial diversity and small intestinal permeability.

TRANSLATIONAL IMPACT: Strategies to ameliorate duodenal MAM dysbiosis may ameliorate intestinal barrier dysfunction and liver injury in CLD.},
}

Adult
Aged
Chronic Disease
DNA, Bacterial/isolation & purification
Disease Progression
Duodenum/microbiology/*pathology
Dysbiosis/diagnosis/microbiology/*pathology
Female
Gastrointestinal Microbiome/genetics
Humans
Intestinal Mucosa/microbiology/*pathology
Liver/*pathology
Liver Diseases/complications/*diagnosis/microbiology/pathology
Male
Middle Aged
Permeability
RNA, Ribosomal, 16S/genetics

@article {pmid31229556,
year = {2020},
author = {Parvathi, A and Jasna, V and Aswathy, VK and Aparna, S and Nathan, VK and Jyothibabu, R},
title = {Dominance of Wolbachia sp. in the deep-sea sediment bacterial metataxonomic sequencing analysis in the Bay of Bengal, Indian Ocean.},
journal = {Genomics},
volume = {112},
number = {1},
pages = {1030-1041},
doi = {10.1016/j.ygeno.2019.06.019},
pmid = {31229556},
issn = {1089-8646},
mesh = {Alphaproteobacteria/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Firmicutes/isolation & purification ; Geologic Sediments/chemistry/*microbiology ; High-Throughput Nucleotide Sequencing ; Indian Ocean ; Metagenomics ; Oceans and Seas ; Proteobacteria/isolation & purification ; Sequence Analysis, DNA ; Wolbachia/genetics/*isolation & purification ; },
abstract = {The Bay of Bengal, located in the north-eastern part of the Indian Ocean is world's largest bay occupying an area of ~8,39,000 mile2. The variability in bacterial community structure and function in sediment ecosystems of the Bay of Bengal is examined by Illumina high-throughput metagenomic sequencing. Of five metataxonomics data sets presented, two (SD1 and SD2) were from stations close to the shore and three (SD4, SD5, and SD6) were from the deep-sea (~3000 m depth). Phylum Proteobacteria (90.27 to 92.52%) dominated the deep-sea samples, whereas phylum Firmicutes (65.35 to 90.98%) dominated the coastal samples. Comparative analysis showed that coastal and deep-sea sediments showed distinct microbial communities. Wolbachia species, belonging to class Alphaproteobacteria was the most dominant species in the deep-sea sediments. The gene functions of bacterial communities were predicted for deep-sea and coastal sediment ecosystems. The results indicated that deep-sea sediment bacterial communities were involved in metabolic activities like dehalogenation and sulphide oxidation.},
}

Alphaproteobacteria/isolation & purification
Bacteria/classification/genetics/isolation & purification
Biodiversity
Firmicutes/isolation & purification
Geologic Sediments/chemistry/*microbiology
High-Throughput Nucleotide Sequencing
Indian Ocean
Metagenomics
Oceans and Seas
Proteobacteria/isolation & purification
Sequence Analysis, DNA
Wolbachia/genetics/*isolation & purification

@article {pmid31219825,
year = {2019},
author = {Knudsen, C and Neyrinck, AM and Lanthier, N and Delzenne, NM},
title = {Microbiota and nonalcoholic fatty liver disease: promising prospects for clinical interventions?.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {22},
number = {5},
pages = {393-400},
doi = {10.1097/MCO.0000000000000584},
pmid = {31219825},
issn = {1473-6519},
mesh = {Animals ; Biomedical Research ; Disease Progression ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolomics ; Metagenomics ; Mice ; *Non-alcoholic Fatty Liver Disease/physiopathology/therapy ; Rats ; },
abstract = {PURPOSE OF REVIEW: Nonalcoholic fatty liver disease (NAFLD) is becoming the most important cause of chronic liver disease in Western countries but no pharmacological therapy is currently available. Growing evidence suggests that the microbiota plays a role in the occurrence and evolution of this disease, namely through the production of bioactive metabolites.

RECENT FINDINGS: Omics technologies (metagenomic, metabolomic, and phenomic data) allow providing a robust prediction of steatosis. More than just correlations, causative effects of certain bacterial metabolites have been evidenced in vitro and in rodent models. Butyrate has been shown to be a potent metabolic and inflammatory modulator in the liver. Several aromatic amino-acids such as phenylacetic acid, imidazole propionate, and 3-(4-hydroxyphenyl)lactate have been identified as potential inducers of steatosis and hepatic inflammation, whereas indolic compounds (indole and indole-3-acetate) seem to preserve liver integrity. Current clinical trials aim at evaluating the efficacy of novel approaches (functional foods, prebiotic and probiotics, and fecal microbial transplants).

SUMMARY: The microbiota brings new hopes in the management of nonalcoholic fatty liver diseases, including nonalcoholic steatohepatitis. Adequate intervention studies in targeted patients are needed to unravel the relevance of such approaches in the management of those liver diseases.},
}

Animals
Biomedical Research
Disease Progression
Gastrointestinal Microbiome/*physiology
Humans
Metabolomics
Metagenomics
Mice
*Non-alcoholic Fatty Liver Disease/physiopathology/therapy
Rats

@article {pmid31134711,
year = {2019},
author = {You, YA and Kwon, EJ and Choi, SJ and Hwang, HS and Choi, SK and Lee, SM and Kim, YJ},
title = {Vaginal microbiome profiles of pregnant women in Korea using a 16S metagenomics approach.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {82},
number = {1},
pages = {e13124},
doi = {10.1111/aji.13124},
pmid = {31134711},
issn = {1600-0897},
support = {HI14C0306//Korea Health Industry Development Institute/International ; 1-2016-1388-001-1//Intramural research funds from Ewha womans University/International ; 2016R1A6A3A11932253//The National Research Foundation of Korea/International ; HI18C0378//Ministry of Health & Welfare of the Republic of Korea/International ; },
mesh = {Adult ; Bacteria/classification/genetics ; Female ; Fetal Membranes, Premature Rupture/*microbiology ; Humans ; Metagenomics ; Microbiota/*genetics ; Obstetric Labor, Premature/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S ; Republic of Korea ; Vagina/*microbiology ; },
abstract = {PROBLEM: The stability and dominance of Lactobacillus spp. in vaginal fluid are important for reproductive health. However, the characterization of the vaginal microbiota of women with preterm labor (PTL) or preterm premature rupture of membranes (P-PROM), and its association with preterm birth (PTB) are poorly understood.

METHOD OF STUDY: We collected vaginal fluid from women at risk of PTB (n = 58) in five university hospitals in Korea. We performed a hierarchical clustering analysis and classification according to the Lactobacillus spp. and Lactobacillus abundance using Illumina MiSeq sequencing of 16S rRNA gene amplicons.

RESULTS: Women at risk for PTB caused by P-PROM had greater bacterial richness and diversity at the time of admission than those with PTL (P < 0.05). However, they were not significantly different between term and preterm samples. In the classification by Lactobacillus spp., the community commonly dominated by Bacteroides and Lactobacillus crispatus was found for the first time in pregnant women in Korea, and all women with this community delivered preterm. Intriguingly, women with an abundance of Weissella in a Bacteroides-dominant community delivered at term. Moreover, in the classification by Lactobacillus proportion, the abundances of Weissella and Rickettsiales were associated with term deliveries, but the abundances of Bacteroides and Escherichia-Shigella were associated with PTBs (P < 0.05).

CONCLUSION: This result suggests that Lactobacillus abundance-based classification of vaginal fluid may reveal the microbiome associated with PTB. Further studies are needed to investigate the mechanism underlying the link between the microbiome and PTB.},
}

Adult
Bacteria/classification/genetics
Female
Fetal Membranes, Premature Rupture/*microbiology
Humans
Metagenomics
Microbiota/*genetics
Obstetric Labor, Premature/*microbiology
Pregnancy
RNA, Ribosomal, 16S
Republic of Korea
Vagina/*microbiology

@article {pmid32814564,
year = {2020},
author = {Vidanaarachchi, R and Shaw, M and Tang, SL and Halgamuge, S},
title = {IMPARO: inferring microbial interactions through parameter optimisation.},
journal = {BMC molecular and cell biology},
volume = {21},
number = {Suppl 1},
pages = {34},
doi = {10.1186/s12860-020-00269-y},
pmid = {32814564},
issn = {2661-8850},
abstract = {BACKGROUND: Microbial Interaction Networks (MINs) provide important information for understanding bacterial communities. MINs can be inferred by examining microbial abundance profiles. Abundance profiles are often interpreted with the Lotka Volterra model in research. However existing research fails to consider a biologically meaningful underlying mathematical model for MINs or to address the possibility of multiple solutions.

RESULTS: In this paper we present IMPARO, a method for inferring microbial interactions through parameter optimisation. We use biologically meaningful models for both the abundance profile, as well as the MIN. We show how multiple MINs could be inferred with similar reconstructed abundance profile accuracy, and argue that a unique solution is not always satisfactory. Using our method, we successfully inferred clear interactions in the gut microbiome which have been previously observed in in-vitro experiments.

CONCLUSIONS: IMPARO was used to successfully infer microbial interactions in human microbiome samples as well as in a varied set of simulated data. The work also highlights the importance of considering multiple solutions for MINs.},
}

@article {pmid32791721,
year = {2020},
author = {Butler, ÉM and Chiavaroli, V and Derraik, JGB and Grigg, CP and Wilson, BC and Walker, N and OʼSullivan, JM and Cutfield, WS},
title = {Maternal bacteria to correct abnormal gut microbiota in babies born by C-section.},
journal = {Medicine},
volume = {99},
number = {30},
pages = {e21315},
pmid = {32791721},
issn = {1536-5964},
mesh = {Adult ; Anthropometry/methods ; Asthma/epidemiology/etiology ; Bacterial Physiological Phenomena ; Body Composition ; Case-Control Studies ; Celiac Disease/epidemiology/etiology ; Cesarean Section/*adverse effects ; Delivery, Obstetric/trends ; Feces ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenomics/methods ; Microbiota/genetics/*physiology ; New Zealand/epidemiology ; Pediatric Obesity/epidemiology/etiology ; Placebos/*administration & dosage ; Pregnancy ; Vagina/*microbiology ; },
abstract = {INTRODUCTION: There is evidence that caesarean section (CS) is associated with increased risk of childhood obesity, asthma, and coeliac disease. The gut microbiota of CS-born babies differs to those born vaginally, possibly due to reduced exposure to maternal vaginal bacteria during birth. Vaginal seeding is a currently unproven practice intended to reduce such differences, so that the gut microbiota of CS-born babies is similar to that of babies born vaginally. Our pilot study, which uses oral administration as a novel form of vaginal seeding, will assess the degree of maternal strain transfer and overall efficacy of the procedure for establishing normal gut microbiota development.

METHODS AND ANALYSIS: Protocol for a single-blinded, randomized, placebo-controlled pilot study of a previously untested method of vaginal seeding (oral administration) in 30 CS-born babies. A sample of maternal vaginal bacteria is obtained prior to CS, and mixed with 5 ml sterile water to obtain a supernatant. Healthy babies are randomized at 1:1 to receive active treatment (3 ml supernatant) or placebo (3 ml sterile water). A reference group of 15 non-randomized vaginal-born babies are also being recruited. Babies' stool samples will undergo whole metagenomic shotgun sequencing to identify potential differences in community structure between CS babies receiving active treatment compared to those receiving placebo at age 1 month (primary outcome). Secondary outcomes include differences in overall gut community between CS groups (24 hours, 3 months); similarity of CS-seeded and placebo gut profiles to vaginally-born babies (24 hours, 1 and 3 months); degree of maternal vaginal strain transfer in CS-born babies (24 hours, 1 and 3 months); anthropometry (1 and 3 months) and body composition (3 months).

ETHICS AND DISSEMINATION: Ethics approval by the Northern A Health and Disability Ethics Committee (18/NTA/49). Results will be published in peer-reviewed journals and presented at international conferences.

REGISTRATION: Australian New Zealand Clinical Trials Registry (ACTRN12618000339257).},
}

Adult
Anthropometry/methods
Asthma/epidemiology/etiology
Bacterial Physiological Phenomena
Body Composition
Case-Control Studies
Celiac Disease/epidemiology/etiology
Cesarean Section/*adverse effects
Delivery, Obstetric/trends
Feces
Female
Humans
Infant
Infant, Newborn
Male
Metagenomics/methods
Microbiota/genetics/*physiology
New Zealand/epidemiology
Pediatric Obesity/epidemiology/etiology
Placebos/*administration & dosage
Pregnancy
Vagina/*microbiology

@article {pmid32004459,
year = {2020},
author = {Zhou, W and Spoto, M and Hardy, R and Guan, C and Fleming, E and Larson, PJ and Brown, JS and Oh, J},
title = {Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.},
journal = {Cell},
volume = {180},
number = {3},
pages = {454-470.e18},
pmid = {32004459},
issn = {1097-4172},
support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; F30 DE027870/DE/NIDCR NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; T90 DE021989/DE/NIDCR NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; U19 AI142733/AI/NIAID NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; R43 AR073562/AR/NIAMS NIH HHS/United States ; },
mesh = {Adult ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; *Evolution, Molecular ; Female ; *Gene Transfer, Horizontal ; Healthy Volunteers ; Host Microbial Interactions/*genetics ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Phylogeny ; *Polymorphism, Single Nucleotide ; Skin/*microbiology ; Staphylococcus epidermidis/*genetics/isolation & purification/pathogenicity ; Virulence/genetics ; Young Adult ; },
abstract = {Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the evolutionary trajectory and functional distribution of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S. epidermidis genomes from 5 healthy individuals, we found that skin S. epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.},
}

Adult
DNA, Bacterial/genetics
Drug Resistance, Bacterial/genetics
*Evolution, Molecular
Female
*Gene Transfer, Horizontal
Healthy Volunteers
Host Microbial Interactions/*genetics
Humans
Male
Microbiota/*genetics
Middle Aged
Phylogeny
*Polymorphism, Single Nucleotide
Skin/*microbiology
Staphylococcus epidermidis/*genetics/isolation & purification/pathogenicity
Virulence/genetics
Young Adult

@article {pmid31585992,
year = {2019},
author = {Peña-Gonzalez, A and Soto-Girón, MJ and Smith, S and Sistrunk, J and Montero, L and Páez, M and Ortega, E and Hatt, JK and Cevallos, W and Trueba, G and Levy, K and Konstantinidis, KT},
title = {Metagenomic Signatures of Gut Infections Caused by Different Escherichia coli Pathotypes.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {24},
pages = {},
pmid = {31585992},
issn = {1098-5336},
support = {K01 AI103544/AI/NIAID NIH HHS/United States ; },
mesh = {Case-Control Studies ; Child ; Child, Preschool ; Diarrhea/microbiology ; Disease Outbreaks ; Ecuador ; Escherichia coli/genetics/isolation & purification/*metabolism/pathogenicity ; Escherichia coli Infections/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Infant ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Virulence/genetics ; Virulence Factors/genetics ; },
abstract = {Escherichia coli is a leading contributor to infectious diarrhea and child mortality worldwide, but it remains unknown how alterations in the gut microbiome vary for distinct E. coli pathotype infections and whether these signatures can be used for diagnostic purposes. Further, the majority of enteric diarrheal infections are not diagnosed with respect to their etiological agent(s) due to technical challenges. To address these issues, we devised a novel approach that combined traditional, isolate-based and molecular-biology techniques with metagenomics analysis of stool samples and epidemiological data. Application of this pipeline to children enrolled in a case-control study of diarrhea in Ecuador showed that, in about half of the cases where an E. coli pathotype was detected by culture and PCR, E. coli was likely not the causative agent based on the metagenome-derived low relative abundance, the level of clonality, and/or the virulence gene content. Our results also showed that diffuse adherent E. coli (DAEC), a pathotype that is generally underrepresented in previous studies of diarrhea and thus, thought not to be highly virulent, caused several small-scale diarrheal outbreaks across a rural to urban gradient in Ecuador. DAEC infections were uniquely accompanied by coelution of large amounts of human DNA and conferred significant shifts in the gut microbiome composition relative to controls or infections caused by other E. coli pathotypes. Our study shows that diarrheal infections can be efficiently diagnosed for their etiological agent and categorized based on their effects on the gut microbiome using metagenomic tools, which opens new possibilities for diagnostics and treatment.IMPORTANCEE. coli infectious diarrhea is an important contributor to child mortality worldwide. However, diagnosing and thus treating E. coli infections remain challenging due to technical and other reasons associated with the limitations of the traditional culture-based techniques and the requirement to apply Koch's postulates. In this study, we integrated traditional microbiology techniques with metagenomics and epidemiological data in order to identify cases of diarrhea where E. coli was most likely the causative disease agent and evaluate specific signatures in the disease-state gut microbiome that distinguish between diffuse adherent, enterotoxigenic, and enteropathogenic E. coli pathotypes. Therefore, our methodology and results should be highly relevant for diagnosing and treating diarrheal infections and have important applications in public health.},
}

Case-Control Studies
Child
Child, Preschool
Diarrhea/microbiology
Disease Outbreaks
Ecuador
Escherichia coli/genetics/isolation & purification/*metabolism/pathogenicity
Escherichia coli Infections/*microbiology
Feces/microbiology
Gastrointestinal Microbiome/genetics/*physiology
Humans
Infant
*Metagenome
RNA, Ribosomal, 16S/genetics
Virulence/genetics
Virulence Factors/genetics

@article {pmid31307001,
year = {2019},
author = {Wang, J and Khokhar, I and Ren, C and Li, X and Wang, J and Fan, S and Jia, Y and Yan, Y},
title = {Characterization and 16S metagenomic analysis of organophosphorus flame retardants degrading consortia.},
journal = {Journal of hazardous materials},
volume = {380},
number = {},
pages = {120881},
doi = {10.1016/j.jhazmat.2019.120881},
pmid = {31307001},
issn = {1873-3336},
mesh = {Flame Retardants/*metabolism ; *Metagenomics ; *Microbial Consortia ; Organophosphorus Compounds/*metabolism ; Rhodococcus/metabolism ; Sphingomonadaceae/metabolism ; },
abstract = {Three bacterial consortia, named YC-SY1, YC-BJ1 and YC-GZ1, were enriched from different areas of China. Bacterial consortia YC-SY1, YC-BJ1 and YC-GZ1 could efficiently degrade triphenyl phosphate (TPhP) (100 mg/L) by approximately 79.4%, 99.8% and 99.6%, tricresyl phosphate (TCrP) by 90.6%, 91.9% and 96.3%, respectively, within 4 days. And they could retain high degrading efficiency under a broad range of temperature (15-40 ℃), pH (6.0-10.0) and salinity (0-4%). A total of 10 bacterial isolates were selected and investigated their degradation capacity. Among these isolates, two were significantly superior to the others. Strain Rhodococcus sp. YC-JH2 could utilize TPhP (50 mg/L) as sole carbon source for growth with 37.36% degradation within 7 days. Strain Sphingopyxis sp. YC-JH3 could efficiently degrade 96.2% of TPhP (50 mg/L) within 7 days, except that no cell growth was observed. Combined with 16S diversity analysis, our results suggest that the effective components of three bacterial consortia responsible for TPhP and TCrP degradation were almost the same, that is, bacteria capable of degrading TPhP and TCrP are limited, in this study, the most efficient component is Sphingopyxis. This study provides abundant microorganism sources for research on organophosphorus flame retardants (OPFRs) metabolism and bioremediation towards OPFRs-contaminated environments.},
}

Flame Retardants/*metabolism
*Metagenomics
*Microbial Consortia
Organophosphorus Compounds/*metabolism
Rhodococcus/metabolism
Sphingomonadaceae/metabolism

@article {pmid32806340,
year = {2020},
author = {Banchi, E and Ametrano, CG and Tordoni, E and Stanković, D and Ongaro, S and Tretiach, M and Pallavicini, A and Muggia, L and , },
title = {Environmental DNA assessment of airborne plant and fungal seasonal diversity.},
journal = {The Science of the total environment},
volume = {738},
number = {},
pages = {140249},
doi = {10.1016/j.scitotenv.2020.140249},
pmid = {32806340},
issn = {1879-1026},
mesh = {*DNA Barcoding, Taxonomic ; *Environmental DNA ; Fungi/genetics ; Italy ; Seasons ; },
abstract = {Environmental DNA (eDNA) metabarcoding and metagenomics analyses can improve taxonomic resolution in biodiversity studies. Only recently, these techniques have been applied in aerobiology, to target bacteria, fungi and plants in airborne samples. Here, we present a nine-month aerobiological study applying eDNA metabarcoding in which we analyzed simultaneously airborne diversity and variation of fungi and plants across five locations in North and Central Italy. We correlated species composition with the ecological characteristics of the sites and the seasons. The most abundant taxa among all sites and seasons were the fungal genera Cladosporium, Alternaria, and Epicoccum and the plant genera Brassica, Corylus, Cupressus and Linum, the latter being much more variable among sites. PERMANOVA and indicator species analyses showed that the plant diversity from air samples is significantly correlated with seasons, while that of fungi varied according to the interaction between seasons and sites. The results consolidate the performance of a new eDNA metabarcoding pipeline for the simultaneous amplification and analysis of airborne plant and fungal particles. They also highlight the promising complementarity of this approach with more traditional biomonitoring frameworks and routine reports of air quality provided by environmental agencies.},
}

*DNA Barcoding, Taxonomic
*Environmental DNA
Fungi/genetics
Italy
Seasons

@article {pmid32717520,
year = {2020},
author = {Flores-Orozco, D and Patidar, R and Levin, DB and Sparling, R and Kumar, A and Çiçek, N},
title = {Effect of mesophilic anaerobic digestion on the resistome profile of dairy manure.},
journal = {Bioresource technology},
volume = {315},
number = {},
pages = {123889},
doi = {10.1016/j.biortech.2020.123889},
pmid = {32717520},
issn = {1873-2976},
mesh = {Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/drug effects ; Genes, Bacterial ; *Manure ; Microbiota/*drug effects ; },
abstract = {The effect of mesophilic anaerobic digestion (AD) on the resistome profile of manures from two different dairy farms was evaluated using a metagenomic approach. A total of 187 unique Antibiotic resistance genes (ARGs) for 17 different classes of antibiotics were detected in raw (undigested) manures. The results indicate that regardless of the origin of the dairy manure, mesophilic AD was capable of reducing or enriching the relative abundance of some ARGs. The main driver of these changes was strongly correlated with the evolution of the microbial community during the AD process. Putative ARG hosts were suggested by analyses of the co-occurrence of microbial groups and ARGs. Finally, network analyses revealed that mesophilic AD could also reduce the co-occurrence of different groups of ARGs potentially located in the same genetic elements. Our results provide valuable insights into the microbial mechanisms driving the diversity and abundance of ARGs during mesophilic AD.},
}

Anaerobiosis
Anti-Bacterial Agents/pharmacology
Drug Resistance, Microbial/drug effects
Genes, Bacterial
*Manure
Microbiota/*drug effects

@article {pmid31235833,
year = {2019},
author = {Pham, TP and Tidjani Alou, M and Bachar, D and Levasseur, A and Brah, S and Alhousseini, D and Sokhna, C and Diallo, A and Wieringa, F and Million, M and Raoult, D},
title = {Gut Microbiota Alteration is Characterized by a Proteobacteria and Fusobacteria Bloom in Kwashiorkor and a Bacteroidetes Paucity in Marasmus.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {9084},
doi = {10.1038/s41598-019-45611-3},
pmid = {31235833},
issn = {2045-2322},
mesh = {Bacteroidetes/*isolation & purification ; Biodiversity ; Case-Control Studies ; Female ; Fusobacteria/*isolation & purification ; *Gastrointestinal Microbiome ; Humans ; Kwashiorkor/*microbiology ; Male ; Protein-Energy Malnutrition/*microbiology ; Proteobacteria/*isolation & purification ; },
abstract = {Kwashiorkor and marasmus are considered to be two different clinical diseases resulting from severe malnutrition, but this distinction has been questioned. In a previous study comparing children with kwashiorkor and healthy children from Niger and Senegal, we found a dramatic gut microbiota alteration with a predominant depletion of anaerobes and enrichment in Proteobacteria and Fusobacteria in kwashiorkor. However, it remained unknown whether this association was related to malnutrition or was a specific feature of kwashiorkor. In this continuation study, we added 7 new marasmus subjects and 71,162 new colonies from the same countries. Our results showed that, compared to marasmus, the kwashiorkor gut microbiota was characterized by an increased proportion of Proteobacteria (culturomics, Marasmus 5.0%, Kwashiorkor 16.7%, p < 0.0001; metagenomics, Marasmus 14.7%, Kwashiorkor 22.0%, p = 0.001), but there was a decreased proportion of Bacteroidetes in marasmus (culturomics, Marasmus 0.8%, Kwashiorkor 6.5%, p = 0.001; metagenomics, Marasmus 5.4%, Kwashiorkor 7.0%, p = 0.03). Fusobacterium was more frequently cultured from kwashiorkor. All detected potential pathogenic species were enriched in the kwashiorkor gut microbiota. These results provide a biological basis to support the usage of an antibiotic therapy more effective in suppressing the overgrowth of bacterial communities resistant to penicillin, combined with antioxidants and probiotics for nutritional recovery therapies, particularly for kwashiorkor.},
}

Bacteroidetes/*isolation & purification
Biodiversity
Case-Control Studies
Female
Fusobacteria/*isolation & purification
*Gastrointestinal Microbiome
Humans
Kwashiorkor/*microbiology
Male
Protein-Energy Malnutrition/*microbiology
Proteobacteria/*isolation & purification

@article {pmid32803809,
year = {2020},
author = {Thompson, AR and Geisen, S and Adams, BJ},
title = {Shotgun metagenomics reveal a diverse assemblage of protists in a model Antarctic soil ecosystem.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15198},
pmid = {32803809},
issn = {1462-2920},
abstract = {The soils of the McMurdo Dry Valleys (MDV) of Antarctica are established models for understanding fundamental processes in soil ecosystem functioning (e.g. ecological tipping points, community structuring, and nutrient cycling) because the extreme physical environment drastically reduces biodiversity and ecological complexity. Understanding the functioning of MDV soils requires in-depth knowledge of the diversity of MDV soil species. Protists, which contribute significantly to soil ecosystem functioning worldwide, remain poorly characterized in the MDV. To better assess the diversity of MDV protists, we performed shotgun metagenomics on 18 sites representing a variety of landscape features and edaphic variables. Our results show MDV soil protists are diverse at both the genus (155 of 281 eukaryote genera) and family (120) levels, but comprise only 6% of eukaryotic reads. Protists are structured by moisture, total N, and distance from the local coast, and possess limited richness in arid (<5% moisture) and at high elevation sites, known drivers of communities in the MDV. High relative diversity and broad distribution of protists in our study promotes these organisms as key members of MDV soil microbiomes and the MDV as a useful system for understanding the contribution of soil protists to the structure of soil microbiomes. SIGNIFICANCE: The McMurdo Dry Valley ecosystem is an established model for understanding the relationship between soil biodiversity and fundamental ecosystem processes, but the diversity and physical drivers of protists in this system are poorly understood. This paper lays the groundwork for integrating the biodiversity and ecology of soil protists into a comprehensive ecological framework of the McMurdo Dry Valley ecosystem and contributes to our understanding of the biodiversity of protist communities in polar regions. This article is protected by copyright. All rights reserved.},
}

@article {pmid32461638,
year = {2020},
author = {Polster, SP and Sharma, A and Tanes, C and Tang, AT and Mericko, P and Cao, Y and Carrión-Penagos, J and Girard, R and Koskimäki, J and Zhang, D and Stadnik, A and Romanos, SG and Lyne, SB and Shenkar, R and Yan, K and Lee, C and Akers, A and Morrison, L and Robinson, M and Zafar, A and Bittinger, K and Kim, H and Gilbert, JA and Kahn, ML and Shen, L and Awad, IA},
title = {Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2659},
pmid = {32461638},
issn = {2041-1723},
support = {F30 NS100252/NS/NINDS NIH HHS/United States ; U54 NS065705/NS/NINDS NIH HHS/United States ; P01 NS092521/NS/NINDS NIH HHS/United States ; R01 NS100949/NS/NINDS NIH HHS/United States ; R01 HL094326/HL/NHLBI NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; },
mesh = {Adolescent ; Adult ; Biomarkers/blood ; Brain Neoplasms/complications/diagnosis/microbiology ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Hemangioma, Cavernous/*complications/diagnosis ; Humans ; Intestines/microbiology/pathology ; Male ; Metagenomics ; Middle Aged ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {Cavernous angiomas (CA) are common vascular anomalies causing brain hemorrhage. Based on mouse studies, roles of gram-negative bacteria and altered intestinal homeostasis have been implicated in CA pathogenesis, and pilot study had suggested potential microbiome differences between non-CA and CA individuals based on 16S rRNA gene sequencing. We here assess microbiome differences in a larger cohort of human subjects with and without CA, and among subjects with different clinical features, and conduct more definitive microbial analyses using metagenomic shotgun sequencing. Relative abundance of distinct bacterial species in CA patients is shown, consistent with postulated permissive microbiome driving CA lesion genesis via lipopolysaccharide signaling, in humans as in mice. Other microbiome differences are related to CA clinical behavior. Weighted combinations of microbiome signatures and plasma inflammatory biomarkers enhance associations with disease severity and hemorrhage. This is the first demonstration of a sensitive and specific diagnostic microbiome in a human neurovascular disease.},
}

Adolescent
Adult
Biomarkers/blood
Brain Neoplasms/complications/diagnosis/microbiology
DNA, Bacterial/genetics
Feces/microbiology
Female
Gastrointestinal Microbiome/*genetics
Hemangioma, Cavernous/*complications/diagnosis
Humans
Intestines/microbiology/pathology
Male
Metagenomics
Middle Aged
Pilot Projects
RNA, Ribosomal, 16S/genetics
Young Adult

@article {pmid32354993,
year = {2020},
author = {Chakraborty, A and Ruff, SE and Dong, X and Ellefson, ED and Li, C and Brooks, JM and McBee, J and Bernard, BB and Hubert, CRJ},
title = {Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {20},
pages = {11029-11037},
pmid = {32354993},
issn = {1091-6490},
mesh = {Alkanes/metabolism ; Archaea/classification/metabolism ; Bacteria/classification/metabolism ; Biodiversity ; Geologic Sediments/chemistry/*microbiology ; Gulf of Mexico ; Hydrocarbons/*metabolism ; Metagenome ; Metagenomics ; Microbiota/*physiology ; Petroleum/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; },
abstract = {Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sediments from the deep-water Eastern Gulf of Mexico to assess whether hydrocarbon fluid migration is a mechanism for upward microbial dispersal. While 132 of these sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well-known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the uncultivated bacterial phyla Atribacteria and Aminicenantes and the archaeal order Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of nonrespiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. These results point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.},
}

Alkanes/metabolism
Archaea/classification/metabolism
Bacteria/classification/metabolism
Biodiversity
Geologic Sediments/chemistry/*microbiology
Gulf of Mexico
Hydrocarbons/*metabolism
Metagenome
Metagenomics
Microbiota/*physiology
Petroleum/metabolism
Phylogeny
RNA, Ribosomal, 16S/genetics
Seawater/chemistry/*microbiology

@article {pmid31588624,
year = {2019},
author = {Zhao, F and Zhou, G and Liu, X and Song, S and Xu, X and Hooiveld, G and Müller, M and Liu, L and Kristiansen, K and Li, C},
title = {Dietary Protein Sources Differentially Affect the Growth of Akkermansia muciniphila and Maintenance of the Gut Mucus Barrier in Mice.},
journal = {Molecular nutrition & food research},
volume = {63},
number = {23},
pages = {e1900589},
doi = {10.1002/mnfr.201900589},
pmid = {31588624},
issn = {1613-4133},
mesh = {Animals ; Dietary Proteins/*pharmacology ; Energy Metabolism ; *Gastrointestinal Microbiome ; Male ; Mice ; Mice, Inbred C57BL ; Mucus/*metabolism ; Soybean Proteins/pharmacology ; Verrucomicrobia/*growth & development ; },
abstract = {SCOPE: The gut microbiota plays an essential role in linking diet to host health. The specific role of different dietary proteins on the gut microbiota and health is less understood. Here, the impact of proteins derived from chicken and soy on the gut microbiota and host gut barrier in C57BL/6 mice is investigated.

METHODS AND RESULTS: Specific-pathogen-free and germ-free mice are assigned to either a chicken- or a soy protein-based diet for 4 weeks. Compared with a chicken-protein-based diet, intake of a soy-protein-based diet reduces the abundance of A. muciniphila and the number of goblet cells, lowers the level of Muc2 mRNA, and decreases the thickness of the mucus layer in the colon of specific-pathogen-free mice. In germ-free mice, colonization with A. muciniphila combined with intake of a chicken-protein-based diet results in a higher expression of the Muc2 mRNA in colon, and surprisingly, an increased potential for oxidative phosphorylation in A. muciniphila compared with colonized mice fed a soy-protein-based diet.

CONCLUSION: These findings suggest possible mutually beneficial interactions between the growth and function of A. muciniphila and host mucus barrier in response to intake of a chicken-protein-based diet contrasting the intake of a soy-protein-based diet.},
}

Animals
Dietary Proteins/*pharmacology
Energy Metabolism
*Gastrointestinal Microbiome
Male
Mice
Mice, Inbred C57BL
Mucus/*metabolism
Soybean Proteins/pharmacology
Verrucomicrobia/*growth & development

@article {pmid31330855,
year = {2019},
author = {Deng, L and Silins, R and Castro-Mejía, JL and Kot, W and Jessen, L and Thorsen, J and Shah, S and Stokholm, J and Bisgaard, H and Moineau, S and Nielsen, DS},
title = {A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples.},
journal = {Viruses},
volume = {11},
number = {7},
pages = {},
pmid = {31330855},
issn = {1999-4915},
support = {//CIHR/Canada ; },
mesh = {Bacteriophages/classification/genetics ; Computational Biology/methods ; Feces/*virology ; *Gastrointestinal Microbiome ; Humans ; Infant ; *Metagenome ; *Metagenomics/methods ; },
abstract = {The human gut microbiome (GM) plays an important role in human health and diseases. However, while substantial progress has been made in understanding the role of bacterial inhabitants of the gut, much less is known regarding the viral component of the GM. Bacteriophages (phages) are viruses attacking specific host bacteria and likely play important roles in shaping the GM. Although metagenomic approaches have led to the discoveries of many new viruses, they remain largely uncultured as their hosts have not been identified, which hampers our understanding of their biological roles. Existing protocols for isolation of viromes generally require relatively high input volumes and are generally more focused on extracting nucleic acids of good quality and purity for down-stream analysis, and less on purifying viruses with infective capacity. In this study, we report the development of an efficient protocol requiring low sample input yielding purified viromes containing phages that are still infective, which also are of sufficient purity for genome sequencing. We validated the method through spiking known phages followed by plaque assays, qPCR, and metagenomic sequencing. The protocol should facilitate the process of culturing novel viruses from the gut as well as large scale studies on gut viromes.},
}

Bacteriophages/classification/genetics
Computational Biology/methods
Feces/*virology
*Gastrointestinal Microbiome
Humans
Infant
*Metagenome
*Metagenomics/methods

@article {pmid31323792,
year = {2019},
author = {Santiago-Rodriguez, TM and Hollister, EB},
title = {Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut.},
journal = {Viruses},
volume = {11},
number = {7},
pages = {},
pmid = {31323792},
issn = {1999-4915},
mesh = {Adaptation, Biological ; Animals ; Bacteria/genetics/virology ; Bacteriolysis ; Bacteriophages/physiology ; *Disease Susceptibility ; Dysbiosis ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; *Host-Pathogen Interactions ; Humans ; Metagenomics/methods ; Microbial Interactions ; *Microbiota ; *Viruses/classification/genetics ; },
abstract = {The virome is comprised of endogenous retroviruses, eukaryotic viruses, and bacteriophages and is increasingly being recognized as an essential part of the human microbiome. The human virome is associated with Type-1 diabetes (T1D), Type-2 diabetes (T2D), Inflammatory Bowel Disease (IBD), Human Immunodeficiency Virus (HIV) infection, and cancer. Increasing evidence also supports trans-kingdom interactions of viruses with bacteria, small eukaryotes and host in disease progression. The present review focuses on virus ecology and biology and how this translates mostly to human gut virome research. Current challenges in the field and how the development of bioinformatic tools and controls are aiding to overcome some of these challenges are also discussed. Finally, the present review also focuses on how human gut virome research could result in translational and clinical studies that may facilitate the development of therapeutic approaches.},
}

Adaptation, Biological
Animals
Bacteria/genetics/virology
Bacteriolysis
Bacteriophages/physiology
*Disease Susceptibility
Dysbiosis
Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing
*Host-Pathogen Interactions
Humans
Metagenomics/methods
Microbial Interactions
*Microbiota
*Viruses/classification/genetics

@article {pmid31278253,
year = {2019},
author = {Visnovska, T and Biggs, PJ and Schmeier, S and Frizelle, FA and Purcell, RV},
title = {Metagenomics and transcriptomics data from human colorectal cancer.},
journal = {Scientific data},
volume = {6},
number = {1},
pages = {116},
doi = {10.1038/s41597-019-0117-3},
pmid = {31278253},
issn = {2052-4463},
mesh = {Aged ; Aged, 80 and over ; Bacteria/classification ; Colorectal Neoplasms/*genetics/*microbiology ; DNA Barcoding, Taxonomic ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; RNA-Seq ; *Transcriptome ; },
abstract = {Colorectal cancer is a heterogenous and mostly sporadic disease, the development of which is associated with microbial dysbiosis. Recent advances in subtype classification have successfully stratified the disease using molecular profiling. To understand potential relationships between molecular mechanisms differentiating the subtypes of colorectal cancer and composition of gut microbial community, we classified a set of 34 tumour samples into molecular subtypes using RNA-sequencing gene expression profiles and determined relative abundances of bacterial taxonomic groups. To identify bacterial community composition, 16S rRNA amplicon metabarcoding was used as well as whole genome metagenomics of the non-human part of RNA-sequencing data. The generated data expands the collection of the data sources related to the disease and connects molecular aspects of the cancer with environmental impact of microbial community.},
}

Aged
Aged, 80 and over
Bacteria/classification
Colorectal Neoplasms/*genetics/*microbiology
DNA Barcoding, Taxonomic
Female
*Gastrointestinal Microbiome
Humans
Male
*Metagenomics
Middle Aged
RNA, Ribosomal, 16S/genetics
RNA-Seq
*Transcriptome

@article {pmid31199864,
year = {2019},
author = {Luiken, REC and Van Gompel, L and Munk, P and Sarrazin, S and Joosten, P and Dorado-García, A and Borup Hansen, R and Knudsen, BE and Bossers, A and Wagenaar, JA and Aarestrup, FM and Dewulf, J and Mevius, DJ and Heederik, DJJ and Smit, LAM and Schmitt, H and , },
title = {Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {74},
number = {9},
pages = {2596-2604},
pmid = {31199864},
issn = {1460-2091},
mesh = {Animals ; Anti-Infective Agents/pharmacology/*therapeutic use ; Bacteria/*drug effects/genetics ; Chickens/*microbiology ; Computational Biology ; Cross-Sectional Studies ; Drug Resistance, Bacterial/*drug effects ; Europe ; Farms ; Feces/microbiology ; *Metagenomics ; Microbiota/*drug effects/genetics ; Risk Factors ; },
abstract = {OBJECTIVES: To determine associations between farm- and flock-level antimicrobial usage (AMU), farm biosecurity status and the abundance of faecal antimicrobial resistance genes (ARGs) on broiler farms.

METHODS: In the cross-sectional pan-European EFFORT study, conventional broiler farms were visited and faeces, AMU information and biosecurity records were collected. The resistomes of pooled faecal samples were determined by metagenomic analysis for 176 farms. A meta-analysis approach was used to relate total and class-specific ARGs (expressed as fragments per kb reference per million bacterial fragments, FPKM) to AMU (treatment incidence per DDD, TIDDDvet) per country and subsequently across all countries. In a similar way, the association between biosecurity status (Biocheck.UGent) and the resistome was explored.

RESULTS: Sixty-six (38%) flocks did not report group treatments but showed a similar resistome composition and roughly similar ARG levels to antimicrobial-treated flocks. Nevertheless, we found significant positive associations between β-lactam, tetracycline, macrolide and lincosamide, trimethoprim and aminoglycoside antimicrobial flock treatments and ARG clusters conferring resistance to the same class. Similar associations were found with purchased products. In gene-level analysis for β-lactams and macrolides, lincosamides and streptogramins, a significant positive association was found with the most abundant gene clusters blaTEM and erm(B). Little evidence was found for associations with biosecurity.

CONCLUSIONS: The faecal microbiome in European broilers contains a high diversity of ARGs, even in the absence of current antimicrobial selection pressure. Despite this, the relative abundance of genes and the composition of the resistome is positively related to AMU in European broiler farms for several antimicrobial classes.},
}

Animals
Anti-Infective Agents/pharmacology/*therapeutic use
Bacteria/*drug effects/genetics
Chickens/*microbiology
Computational Biology
Cross-Sectional Studies
Drug Resistance, Bacterial/*drug effects
Europe
Farms
Feces/microbiology
*Metagenomics
Microbiota/*drug effects/genetics
Risk Factors

@article {pmid32179689,
year = {2020},
author = {Bonilla-Rosso, G and Steiner, T and Wichmann, F and Bexkens, E and Engel, P},
title = {Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {13},
pages = {7355-7362},
pmid = {32179689},
issn = {1091-6490},
mesh = {Animals ; Bacteria/genetics ; Bacteriophages/genetics ; Bees/genetics/*microbiology/*virology ; Bifidobacterium/isolation & purification/virology ; Gastrointestinal Microbiome ; Metagenome ; Microbiota ; Symbiosis/physiology ; },
abstract = {The honey bee gut microbiota influences bee health and has become an important model to study the ecology and evolution of microbiota-host interactions. Yet, little is known about the phage community associated with the bee gut, despite its potential to modulate bacterial diversity or to govern important symbiotic functions. Here we analyzed two metagenomes derived from virus-like particles, analyzed the prevalence of the identified phages across 73 bacterial metagenomes from individual bees, and tested the host range of isolated phages. Our results show that the honey bee gut virome is composed of at least 118 distinct clusters corresponding to both temperate and lytic phages and representing novel genera with a large repertoire of unknown gene functions. We find that the phage community is prevalent in honey bees across space and time and targets the core members of the bee gut microbiota. The large number and high genetic diversity of the viral clusters seems to mirror the high extent of strain-level diversity in the bee gut microbiota. We isolated eight lytic phages that target the core microbiota member Bifidobacterium asteroides, but that exhibited different host ranges at the strain level, resulting in a nested interaction network of coexisting phages and bacterial strains. Collectively, our results show that the honey bee gut virome consists of a complex and diverse phage community that likely plays an important role in regulating strain-level diversity in the bee gut and that holds promise as an experimental model to study bacteria-phage dynamics in natural microbial communities.},
}

Animals
Bacteria/genetics
Bacteriophages/genetics
Bees/genetics/*microbiology/*virology
Bifidobacterium/isolation & purification/virology
Gastrointestinal Microbiome
Metagenome
Microbiota
Symbiosis/physiology

@article {pmid31252683,
year = {2019},
author = {Lawrence, D and Baldridge, MT and Handley, SA},
title = {Phages and Human Health: More Than Idle Hitchhikers.},
journal = {Viruses},
volume = {11},
number = {7},
pages = {},
pmid = {31252683},
issn = {1999-4915},
support = {R01 OD024917/OD/NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; R01 OD024917/NH/NIH HHS/United States ; },
mesh = {Animals ; Bacteriophages/classification/genetics/*isolation & purification/physiology ; Gastrointestinal Tract/*virology ; Genome, Viral ; Health ; Humans ; *Microbiota ; },
abstract = {Bacteriophages, or phages, are viruses that infect bacteria and archaea. Phages have diverse morphologies and can be coded in DNA or RNA and as single or double strands with a large range of genome sizes. With the increasing use of metagenomic sequencing approaches to analyze complex samples, many studies generate massive amounts of "viral dark matter", or sequences of viral origin unable to be classified either functionally or taxonomically. Metagenomic analysis of phages is still in its infancy, and uncovering novel phages continues to be a challenge. Work over the past two decades has begun to uncover key roles for phages in different environments, including the human gut. Recent studies in humans have identified expanded phage populations in both healthy infants and in inflammatory bowel disease patients, suggesting distinct phage activity during development and in specific disease states. In this review, we examine our current knowledge of phage biology and discuss recent efforts to improve the analysis and discovery of novel phages. We explore the roles phages may play in human health and disease and discuss the future of phage research.},
}

Animals
Bacteriophages/classification/genetics/*isolation & purification/physiology
Gastrointestinal Tract/*virology
Genome, Viral
Health
Humans
*Microbiota

@article {pmid30957268,
year = {2019},
author = {Tian, M and Chen, M and Bao, Y and Xu, C and Qin, Q and Zhang, W and He, Y and Shao, Q},
title = {Microbial contributions to bronchial asthma occurrence in children: A metagenomic study.},
journal = {Journal of cellular biochemistry},
volume = {120},
number = {8},
pages = {13853-13860},
doi = {10.1002/jcb.28658},
pmid = {30957268},
issn = {1097-4644},
mesh = {Adolescent ; Asthma/*epidemiology/*microbiology ; Bacteria/*genetics ; Biodiversity ; Case-Control Studies ; Child ; Child, Preschool ; Female ; Humans ; Male ; *Metagenomics ; },
abstract = {Bronchial asthma, a common chronic respiratory disease in children, is traditionally regarded as a noninfectious disease. Current hypotheses, however, argue that asthma can be caused by microbial infection. We, therefore, hypothesize that a variety of microbes are more commonly found in the sputum of children with asthma, and these microbes may contribute to the occurrence and development of asthma. The present study proposes to use metagenomic approach to explore microbial diversity and to identify the microbial community characteristics of sputum from children with asthma. We found that microbial communities in the sputum of children differed significantly between asthmatics and controls. Kruskal-Wallis testing showed that 16 phyla, 104 genera, and 159 species were significantly downregulated, whereas two phyla including Platyhelminthes phylum and Chordata phylum, two genera including Spirometra genus and Homo sapiens, and the Spirometra erinaceieuropaei species were significantly upregulated in asthma patients compared with controls (P < 0.05). Among them, H. sapiens and S. erinaceieuropaei exhibited 2.3- and 2.0-fold overabundance in asthmatics vs controls, respectively. Meanwhile, metastats assay demonstrated that 31 phyla, 400 genera, and 813 species were significantly downregulated, whereas two phyla, 10 genera, and 16 species were significantly upregulated in asthma patients compared with controls (P < 0.05). Among them, Tetrahymena thermophila and Candidatus Zinderia insecticola exhibited 4.7-fold overabundance in asthmatics vs controls. Our study establishes a link between microbial infection and the mechanisms leading to asthma development, which will be useful for developing novel diagnostic biomarkers and aiding in the prevention and control of asthma.},
}

Adolescent
Asthma/*epidemiology/*microbiology
Bacteria/*genetics
Biodiversity
Case-Control Studies
Child
Child, Preschool
Female
Humans
Male
*Metagenomics

@article {pmid32130435,
year = {2020},
author = {Tikariha, H and Purohit, HJ},
title = {Unfolding microbial community intelligence in aerobic and anaerobic biodegradation processes using metagenomics.},
journal = {Archives of microbiology},
volume = {202},
number = {6},
pages = {1269-1274},
doi = {10.1007/s00203-020-01839-6},
pmid = {32130435},
issn = {1432-072X},
mesh = {Aerobiosis ; Anaerobiosis ; *Biodegradation, Environmental ; Bioreactors/*microbiology ; *Metagenomics ; Microbiota/*physiology ; Sewage/*microbiology ; Waste Water/*microbiology ; },
abstract = {Environmental factors and available nutrients influence microbial communities, and with that, there exists a dynamic shift in community structure and hierarchy in wastewater treatment systems. Of the various factors, the availability and gradient of oxygen selectively enrich a typical microbial community and also form the community stratification which could be established through metagenomics studies. In recent years, metagenomics with various sets of bioinformatics tools has assisted in exploration and better insight into the organization and relation of the taxonomical and functional composition and associate physiological intelligence of the microbial communities. The microbial communities, under defined conditions acquire a typical hierarchy with flexible but active network of the metabolic route, which ensures the survival needs of every member residing in that community and their abundance. This knowledge of community functional organization defines the rule in designing and improving biodegradation processes in case of both aerobic and anaerobic systems.},
}

Aerobiosis
Anaerobiosis
*Biodegradation, Environmental
Bioreactors/*microbiology
*Metagenomics
Microbiota/*physiology
Sewage/*microbiology
Waste Water/*microbiology

@article {pmid31870316,
year = {2019},
author = {Deutscher, AT and Chapman, TA and Shuttleworth, LA and Riegler, M and Reynolds, OL},
title = {Tephritid-microbial interactions to enhance fruit fly performance in sterile insect technique programs.},
journal = {BMC microbiology},
volume = {19},
number = {Suppl 1},
pages = {287},
pmid = {31870316},
issn = {1471-2180},
mesh = {Animals ; *Bacterial Physiological Phenomena ; Domestication ; Female ; Gastrointestinal Microbiome ; Insect Control ; Male ; Pest Control, Biological ; Sexual Behavior, Animal/*physiology ; Tephritidae/microbiology/*physiology ; },
abstract = {BACKGROUND: The Sterile Insect Technique (SIT) is being applied for the management of economically important pest fruit flies (Diptera: Tephritidae) in a number of countries worldwide. The success and cost effectiveness of SIT depends upon the ability of mass-reared sterilized male insects to successfully copulate with conspecific wild fertile females when released in the field.

METHODS: We conducted a critical analysis of the literature about the tephritid gut microbiome including the advancement of methods for the identification and characterization of microbiota, particularly next generation sequencing, the impacts of irradiation (to induce sterility of flies) and fruit fly rearing, and the use of probiotics to manipulate the fruit fly gut microbiota.

RESULTS: Domestication, mass-rearing, irradiation and handling, as required in SIT, may change the structure of the fruit flies' gut microbial community compared to that of wild flies under field conditions. Gut microbiota of tephritids are important in their hosts' development, performance and physiology. Knowledge of how mass-rearing and associated changes of the microbial community impact the functional role of the bacteria and host biology is limited. Probiotics offer potential to encourage a gut microbial community that limits pathogens, and improves the quality of fruit flies.

CONCLUSIONS: Advances in technologies used to identify and characterize the gut microbiota will continue to expand our understanding of tephritid gut microbial diversity and community composition. Knowledge about the functions of gut microbes will increase through the use of gnotobiotic models, genome sequencing, metagenomics, metatranscriptomics, metabolomics and metaproteomics. The use of probiotics, or manipulation of the gut microbiota, offers significant opportunities to enhance the production of high quality, performing fruit flies in operational SIT programs.},
}

Animals
*Bacterial Physiological Phenomena
Domestication
Female
Gastrointestinal Microbiome
Insect Control
Male
Pest Control, Biological
Sexual Behavior, Animal/*physiology
Tephritidae/microbiology/*physiology

@article {pmid31850241,
year = {2019},
author = {Wang, J and Gu, X and Yang, J and Wei, Y and Zhao, Y},
title = {Gut Microbiota Dysbiosis and Increased Plasma LPS and TMAO Levels in Patients With Preeclampsia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {409},
pmid = {31850241},
issn = {2235-2988},
mesh = {Adult ; Biomarkers ; Case-Control Studies ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Lipopolysaccharides/*blood ; Metagenome ; Metagenomics/methods ; Methylamines/*blood ; Pre-Eclampsia/*blood/*etiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Objective: To characterize the gut microbiota in patients with preeclampsia (PE) compared with healthy controls. Methods: We analyzed and compared the microbiota communities in the feces of 48 PE patients with 48 age-, gestational weeks-, and pre-pregnancy body mass index-matched healthy controls using 16S rRNA gene sequencing, and also we tested fecal and plasma lipopolysaccharide (LPS) and plasma trimethylamine-N-oxide (TMAO) concentration levels in the two groups. Results: Compared with the control group, microbial alpha diversity was lower in the PE group, but there was no statistically significant difference between the two groups. At the phylum level, Firmicutes (51.64% PE vs. 59.62% Control, P < 0.05), Bacteroidetes (40.51% PE vs. 34.81% Control, P< 0.05), Proteobacteria (4.51% PE vs. 2.56% Control, P < 0.05), and Actinobacteria (2.90% PE vs. 1.77% Control, P < 0.05), exhibited significant differences between the PE group and the control group. LEfSe analysis found 17 differentially abundant taxa between the two groups. PICRUSt analysis found that in the KEGG pathways, the microbial gene functions related to LPS biosynthesis were higher in the fecal microbiome of the PE group. The fecal and plasma LPS concentrations and plasma TMAO concentrations of PE patients were higher than those of the healthy controls. Conclusion: PE patients had gut microbiota dysbiosis and increased plasma LPS and TMAO levels, which will lead to a better understanding of the relationship between the gut microbiota and PE.},
}

Adult
Biomarkers
Case-Control Studies
*Dysbiosis
Feces/microbiology
Female
*Gastrointestinal Microbiome
Humans
Lipopolysaccharides/*blood
Metagenome
Metagenomics/methods
Methylamines/*blood
Pre-Eclampsia/*blood/*etiology
Pregnancy
RNA, Ribosomal, 16S/genetics

@article {pmid31492669,
year = {2019},
author = {Zhou, K and Zhang, R and Sun, J and Zhang, W and Tian, RM and Chen, C and Kawagucci, S and Xu, Y},
title = {Potential Interactions between Clade SUP05 Sulfur-Oxidizing Bacteria and Phages in Hydrothermal Vent Sponges.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {22},
pages = {},
pmid = {31492669},
issn = {1098-5336},
mesh = {Animals ; Bacteriophages/*classification/metabolism ; Genome, Bacterial ; *Hydrothermal Vents ; Metabolic Networks and Pathways ; Metagenomics ; Microbiota ; Oxidation-Reduction ; Phylogeny ; Porifera/*microbiology/*virology ; RNA, Ribosomal, 16S/genetics ; Sulfur/metabolism ; Sulfur-Reducing Bacteria/*virology ; *Symbiosis ; },
abstract = {In deep-sea hydrothermal vent environments, sulfur-oxidizing bacteria belonging to the clade SUP05 are crucial symbionts of invertebrate animals. Marine viruses, as the most abundant biological entities in the ocean, play essential roles in regulating the sulfur metabolism of the SUP05 bacteria. To date, vent sponge-associated SUP05 and their phages have not been well documented. The current study analyzed microbiomes of Haplosclerida sponges from hydrothermal vents in the Okinawa Trough and recovered the dominant SUP05 genome, designated VS-SUP05. Phylogenetic analysis showed that VS-SUP05 was closely related to endosymbiotic SUP05 strains from mussels living in deep-sea hydrothermal vent fields. Homology and metabolic pathway comparisons against free-living and symbiotic SUP05 strains revealed that the VS-SUP05 genome shared many features with the deep-sea mussel symbionts. Supporting a potentially symbiotic lifestyle, the VS-SUP05 genome contained genes involved in the synthesis of essential amino acids and cofactors that are desired by the host. Analysis of sponge-associated viral sequences revealed putative VS-SUP05 phages, all of which were double-stranded viruses belonging to the families Myoviridae, Siphoviridae, Podoviridae, and Microviridae Among the phage sequences, one contig contained metabolic genes (iscR, iscS, and iscU) involved in iron-sulfur cluster formation. Interestingly, genome sequence comparison revealed horizontal transfer of the iscS gene among phages, VS-SUP05, and other symbiotic SUP05 strains, indicating an interaction between marine phages and SUP05 symbionts. Overall, our findings confirm the presence of SUP05 bacteria and their phages in sponges from deep-sea vents and imply a beneficial interaction that allows adaptation of the host sponge to the hydrothermal vent environment.IMPORTANCE Chemosynthetic SUP05 bacteria dominate the microbial communities of deep-sea hydrothermal vents around the world, SUP05 bacteria utilize reduced chemical compounds in vent fluids and commonly form symbioses with invertebrate organisms. This symbiotic relationship could be key to adapting to such unique and extreme environments. Viruses are the most abundant biological entities on the planet and have been identified in hydrothermal vent environments. However, their interactions with the symbiotic microbes of the SUP05 clade, along with their role in the symbiotic system, remain unclear. Here, using metagenomic sequence-based analyses, we determined that bacteriophages may support metabolism in SUP05 bacteria and play a role in the sponge-associated symbiosis system in hydrothermal vent environments.},
}

Animals
Bacteriophages/*classification/metabolism
Genome, Bacterial
*Hydrothermal Vents
Metabolic Networks and Pathways
Metagenomics
Microbiota
Oxidation-Reduction
Phylogeny
Porifera/*microbiology/*virology
RNA, Ribosomal, 16S/genetics
Sulfur/metabolism
Sulfur-Reducing Bacteria/*virology
*Symbiosis

@article {pmid32774330,
year = {2020},
author = {Khamis, FM and Ombura, FLO and Akutse, KS and Subramanian, S and Mohamed, SA and Fiaboe, KKM and Saijuntha, W and Van Loon, JJA and Dicke, M and Dubois, T and Ekesi, S and Tanga, CM},
title = {Insights in the Global Genetics and Gut Microbiome of Black Soldier Fly, Hermetia illucens: Implications for Animal Feed Safety Control.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1538},
doi = {10.3389/fmicb.2020.01538},
pmid = {32774330},
issn = {1664-302X},
abstract = {The utilization of the black soldier fly (BSF) Hermetia illucens L. for recycling organic waste into high-quality protein and fat biomass for animal feeds has gained momentum worldwide. However, information on the genetic diversity and environmental implications on safety of the larvae is limited. This study delineates genetic variability and unravels gut microbiome complex of wild-collected and domesticated BSF populations from six continents using mitochondrial COI gene and 16S metagenomics. All sequences generated from the study linked to H. illucens accessions KM967419.1, FJ794355.1, FJ794361.1, FJ794367.1, KC192965.1, and KY817115.1 from GenBank. Phylogenetic analyses of the sequences generated from the study and rooted by GenBank accessions of Hermetia albitarsis Fabricius and Hermetia sexmaculata Macquart separated all samples into three branches, with H. illucens and H. sexmaculata being closely related. Genetic distances between H. illucens samples from the study and GenBank accessions of H. illucens ranged between 0.0091 and 0.0407 while H. sexmaculata and H. albitarsis samples clearly separated from all H. illucens by distances of 0.1745 and 0.1903, respectively. Genetic distance matrix was used to generate a principal coordinate plot that further confirmed the phylogenetic clustering. Haplotype network map demonstrated that Australia, United States 1 (Rhode Island), United States 2 (Colorado), Kenya, and China shared a haplotype, while Uganda shared a haplotype with GenBank accession KC192965 BSF from United States. All other samples analyzed had individual haplotypes. Out of 481,695 reads analyzed from 16S metagenomics, four bacterial families (Enterobactereaceae, Dysgonomonadaceae, Wohlfahrtiimonadaceae, and Enterococcaceae) were most abundant in the BSF samples. Alpha-diversity, as assessed by Shannon index, showed that the Kenyan and Thailand populations had the highest and lowest microbe diversity, respectively; while microbial diversity assessed through Bray Curtis distance showed United States 3 (Maysville) and Netherlands populations to be the most dissimilar. Our findings on genetic diversity revealed slight phylogeographic variation between BSF populations across the globe. The 16S data depicted larval gut bacterial families with economically important genera that might pose health risks to both animals and humans. This study recommends pre-treatment of feedstocks and postharvest measures of the harvested BSF larvae to minimize risk of pathogen contamination along the insect-based feed value chain.},
}

@article {pmid30770850,
year = {2019},
author = {Kouchaki, S and Tapinos, A and Robertson, DL},
title = {A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {2159},
pmid = {30770850},
issn = {2045-2322},
support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; BB/M001121/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 555 (MC_UU_1201412)//RCUK | Medical Research Council (MRC)/International ; },
mesh = {Algorithms ; Bacteria/*classification/*genetics ; Computational Biology/*methods ; Gastrointestinal Microbiome ; Metagenomics/*methods ; Microbiota ; *Sequence Homology, Nucleic Acid ; },
abstract = {Algorithms in bioinformatics use textual representations of genetic information, sequences of the characters A, T, G and C represented computationally as strings or sub-strings. Signal and related image processing methods offer a rich source of alternative descriptors as they are designed to work in the presence of noisy data without the need for exact matching. Here we introduce a method, multi-resolution local binary patterns (MLBP) adapted from image processing to extract local 'texture' changes from nucleotide sequence data. We apply this feature space to the alignment-free binning of metagenomic data. The effectiveness of MLBP is demonstrated using both simulated and real human gut microbial communities. Sequence reads or contigs can be represented as vectors and their 'texture' compared efficiently using machine learning algorithms to perform dimensionality reduction to capture eigengenome information and perform clustering (here using randomized singular value decomposition and BH-tSNE). The intuition behind our method is the MLBP feature vectors permit sequence comparisons without the need for explicit pairwise matching. We demonstrate this approach outperforms existing methods based on k-mer frequencies. The signal processing method, MLBP, thus offers a viable alternative feature space to textual representations of sequence data. The source code for our Multi-resolution Genomic Binary Patterns method can be found at https://github.com/skouchaki/MrGBP .},
}

Algorithms
Bacteria/*classification/*genetics
Computational Biology/*methods
Gastrointestinal Microbiome
Metagenomics/*methods
Microbiota
*Sequence Homology, Nucleic Acid

@article {pmid30554441,
year = {2019},
author = {Curtis, K and Stewart, CJ and Robinson, M and Molfese, DL and Gosnell, SN and Kosten, TR and Petrosino, JF and De La Garza, R and Salas, R},
title = {Insular resting state functional connectivity is associated with gut microbiota diversity.},
journal = {The European journal of neuroscience},
volume = {50},
number = {3},
pages = {2446-2452},
pmid = {30554441},
issn = {1460-9568},
support = {//McNair Medical Institute/International ; //Toomim Family Fund/International ; //Pilot Award from the Core for Advanced MR Imaging at Baylor College of Medicine/International ; P30 CA125123/CA/NCI NIH HHS/United States ; 19295//NARSAD/International ; I01 CX000994/CX/CSRD VA/United States ; VHA5I01CX000994//the Veteran Health Administration/International ; R03 DA029167/DA/NIDA NIH HHS/United States ; K01 DA026539/DA/NIDA NIH HHS/United States ; DA09167//National Institute of Health/International ; DA026539//National Institute of Health/International ; 5P30CA0125123/BC/NCI NIH HHS/United States ; },
mesh = {Adult ; Cerebral Cortex/*diagnostic imaging/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Magnetic Resonance Imaging/methods ; Male ; Nerve Net/*diagnostic imaging/*physiology ; Rest/*physiology ; Young Adult ; },
abstract = {The gut microbiota has recently gained attention as a possible modulator of brain activity. A number of reports suggest that the microbiota may be associated with neuropsychiatric conditions such as major depressive disorder, autism and anxiety. The gut microbiota is thought to influence the brain via vagus nerve signalling, among other possible mechanisms. The insula processes and integrates these vagal signals. To determine if microbiota diversity and structure modulate brain activity, we collected faecal samples and examined insular function using resting state functional connectivity (RSFC). Thirty healthy participants (non-smokers, tobacco smokers and electronic cigarette users, n = 10 each) were studied. We found that the RSFC between the insula and several regions (frontal pole left, lateral occipital cortex right, lingual gyrus right and cerebellum 4, 5 and vermis 9) were associated with bacterial microbiota diversity and structure. In addition, two specific bacteria genera, Prevotella and Bacteroides, were specifically different in tobacco smokers and also associated with insular connectivity. In conclusion, we show that insular connectivity is associated with microbiome diversity, structure and at least two specific bateria genera. Furthemore, this association is potentially modulated by tobacco smoking, although the sample sizes for the different smoking groups were small and this result needs validation in a larger cohort. While replication is necessary, the microbiota is a readily accessible therapeutic target for modulating insular connectivity, which has previously been shown to be abnormal in anxiety and tobacco use disorders.},
}

Adult
Cerebral Cortex/*diagnostic imaging/*physiology
Female
Gastrointestinal Microbiome/*physiology
Humans
Magnetic Resonance Imaging/methods
Male
Nerve Net/*diagnostic imaging/*physiology
Rest/*physiology
Young Adult

@article {pmid32039051,
year = {2019},
author = {Tong, Y and Zheng, L and Qing, P and Zhao, H and Li, Y and Su, L and Zhang, Q and Zhao, Y and Luo, Y and Liu, Y},
title = {Oral Microbiota Perturbations Are Linked to High Risk for Rheumatoid Arthritis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {475},
pmid = {32039051},
issn = {2235-2988},
mesh = {Arthritis, Rheumatoid/*epidemiology ; Bacteria/classification/genetics ; Biodiversity ; Case-Control Studies ; China ; Dysbiosis/*complications ; Female ; *Host Microbial Interactions ; Humans ; Male ; Metagenomics ; Middle Aged ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; Risk Assessment ; },
abstract = {Oral microbial dysbiosis is known to increase susceptibility of an individual to develop rheumatoid arthritis (RA). Individuals at-risk of RA may undergo different phases of disease progression. In this study, we aim to investigate whether and whereby the oral microbiome communities alter prior to symptoms of RA. Seventy-nine saliva samples were collected from 29 high-risk individuals, who were positive for anti-citrullinated protein antibodies (ACPA) and have no clinical arthritis, 27 RA patients and 23 healthy controls (HCs). The salivary microbiome was examined using 16S ribosomal RNA gene sequencing. Alpha and beta diversity analysis and the linear discriminant analysis were applied to examine the bacterial diversity, community structure and discriminatory taxa between three groups, respectively. The correlation between salivary bacteria and autoantibodies were analyzed. In the "pre-clinical" stages, salivary microbial diversity was significantly reduced comparing to RA patients and HCs. In contrast to HCs, like RA patients, individuals at high-risk for RA showed a reduction in the abundance of genus Defluviitaleaceae_UCG-011 and the species Neisseria oralis, but an expansion of Prevotella_6. Unexpectedly, the relative abundance of Porphyromonas gingivalis, reported as opportunistic pathogens for RA development, was significantly decreased in high-risk individuals. Additionally, we identified four genera in the saliva from high-risk individuals positively correlated with serum ACPA titers, and the other two genera inversely displayed. In summary, we observed a characteristic compositional change of salivary microbes in individuals at high-risk for RA, suggesting that oral microbiota dysbiosis occurs in the "pre-clinical" stage of RA and are correlated with systemic autoimmune features.},
}

Arthritis, Rheumatoid/*epidemiology
Bacteria/classification/genetics
Biodiversity
Case-Control Studies
China
Dysbiosis/*complications
Female
*Host Microbial Interactions
Humans
Male
Metagenomics
Middle Aged
Mouth/*microbiology
RNA, Ribosomal, 16S/genetics
Risk Assessment

@article {pmid31888470,
year = {2019},
author = {Goloshchapov, OV and Olekhnovich, EI and Sidorenko, SV and Moiseev, IS and Kucher, MA and Fedorov, DE and Pavlenko, AV and Manolov, AI and Gostev, VV and Veselovsky, VA and Klimina, KM and Kostryukova, ES and Bakin, EA and Shvetcov, AN and Gumbatova, ED and Klementeva, RV and Shcherbakov, AA and Gorchakova, MV and Egozcue, JJ and Pawlowsky-Glahn, V and Suvorova, MA and Chukhlovin, AB and Govorun, VM and Ilina, EN and Afanasyev, BV},
title = {Long-term impact of fecal transplantation in healthy volunteers.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {312},
pmid = {31888470},
issn = {1471-2180},
mesh = {Adult ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Time Factors ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) has been recently approved by FDA for the treatment of refractory recurrent clostridial colitis (rCDI). Success of FTM in treatment of rCDI led to a number of studies investigating the effectiveness of its application in the other gastrointestinal diseases. However, in the majority of studies the effects of FMT were evaluated on the patients with initially altered microbiota. The aim of our study was to estimate effects of FMT on the gut microbiota composition in healthy volunteers and to monitor its long-term outcomes.

RESULTS: We have performed a combined analysis of three healthy volunteers before and after capsule FMT by evaluating their general condition, adverse clinical effects, changes of basic laboratory parameters, and several immune markers. Intestinal microbiota samples were evaluated by 16S rRNA gene and shotgun sequencing. The data analysis demonstrated profound shift towards the donor microbiota taxonomic composition in all volunteers. Following FMT, all the volunteers exhibited gut colonization with donor gut bacteria and persistence of this effect for almost ∼1 year of observation. Transient changes of immune parameters were consistent with suppression of T-cell cytotoxicity. FMT was well tolerated with mild gastrointestinal adverse events, however, one volunteer developed a systemic inflammatory response syndrome.

CONCLUSIONS: The FMT leads to significant long-term changes of the gut microbiota in healthy volunteers with the shift towards donor microbiota composition and represents a relatively safe procedure to the recipients without long-term adverse events.},
}

Adult
*Fecal Microbiota Transplantation
Feces/*microbiology
Female
*Gastrointestinal Microbiome
Healthy Volunteers
Humans
Male
Middle Aged
RNA, Ribosomal, 16S/genetics
Time Factors

@article {pmid31653789,
year = {2019},
author = {Kleyer, H and Tecon, R and Or, D},
title = {Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {1},
pages = {},
pmid = {31653789},
issn = {1098-5336},
mesh = {*Bacteria/classification/genetics/isolation & purification ; Metagenome ; Metagenomics ; Microbial Interactions ; Microbiota/*genetics ; Phylogeny ; Porosity ; RNA, Ribosomal, 16S ; Soil/chemistry ; *Soil Microbiology ; Water ; },
abstract = {The complexity of natural soils presents a challenge to the systematic identification and disentanglement of governing processes that shape natural bacterial communities. Studies have highlighted the critical role of the soil aqueous phase in shaping interactions among soil bacterial communities. To quantify and improve the attributability of soil aqueous-phase effects, we introduced a synthetic and traceable bacterial community to simple porous microcosms and subjected the community to constant or dynamic hydration conditions. The results were expressed in terms of absolute abundance and show species-specific responses to hydration and nutrient conditions. Hydration dynamics exerted a significant influence on the fraction of less-abundant species, especially after extended incubation periods. Phylogenetic relationships did not explain the group of most abundant species. The ability to quantify species-level dynamics in a bacterial community offers an important step toward deciphering the links between community composition and functions in dynamic terrestrial environments.IMPORTANCE The composition and activity of soil bacteria are central to various ecosystem services and soil biogeochemical cycles. A key factor for soil bacterial activity is soil hydration, which is in a constant state of change due to rainfall, drainage, plant water uptake, and evaporation. These dynamic changes in soil hydration state affect the structure and function of soil bacterial communities in complex ways often unobservable in natural soil. We designed an experimental system that retains the salient features of hydrated soil yet enables systematic evaluation of changes in a representative bacterial community in response to cycles of wetting and drying. The study shows that hydration cycles affect community abundance, yet most changes in composition occur with the less-abundant species (while the successful ones remain dominant). This research offers a new path for an improved understanding of bacterial community assembly in natural environments, including bacterial growth, maintenance, and death, with a special focus on the role of hydrological factors.},
}

*Bacteria/classification/genetics/isolation & purification
Metagenome
Metagenomics
Microbial Interactions
Microbiota/*genetics
Phylogeny
Porosity
RNA, Ribosomal, 16S
Soil/chemistry
*Soil Microbiology
Water

@article {pmid30989200,
year = {2019},
author = {Ye, L and Chan, EWC and Chen, S},
title = {Selective and suppressive effects of antibiotics on donor and recipient bacterial strains in gut microbiota determine transmission efficiency of blaNDM-1-bearing plasmids.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {74},
number = {7},
pages = {1867-1875},
doi = {10.1093/jac/dkz137},
pmid = {30989200},
issn = {1460-2091},
mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage ; Escherichia coli/*drug effects/genetics ; Gastrointestinal Microbiome/*drug effects ; Gene Transfer, Horizontal/*drug effects ; Klebsiella pneumoniae/*drug effects/genetics ; Male ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rats, Sprague-Dawley ; beta-Lactamases/*genetics ; },
abstract = {OBJECTIVES: To test whether antibiotics of different functional categories exhibit differential potential in promoting transmission of MDR-encoding plasmids among members of the gut microbiome.

METHODS: Rats inoculated with blaNDM-1-bearing Klebsiella pneumoniae were subjected to treatment with different types of antibiotics. The structural changes in the gastrointestinal (GI) tract microbiome were determined by 16S rRNA sequencing and analysis. In addition, the efficiency of transmission of blaNDM-1-bearing plasmids to different subtypes of GI tract Escherichia coli was also confirmed in vitro.

RESULTS: We showed that drugs that are commonly used to treat Gram-negative bacterial infections, such as ampicillin and amoxicillin, could enrich both carbapenem-resistant Enterobacteriaceae (CRE) and antibiotic-susceptible E. coli in the GI tract, thereby promoting transmission of the blaNDM-1-bearing plasmid in the gut microbiome. In contrast, meropenem was found to minimize the population of CRE in the gut microbiome, hence treatment with this drug exhibited drastically lower potential to promote transmission of the blaNDM-1-bearing plasmid to the recipient strains. We further showed that an increased population size of Proteobacteria due to a suppressive effect on Firmicutes is a key factor in enhancing the efficiency of transmission of the blaNDM-1-bearing plasmid and hence dissemination of carbapenem-resistant strains.

CONCLUSIONS: This study depicted for the first time the effect of different antibiotics on the structure of the rat GI tract microbiome, which in turn determined the pattern and rate of transmission of the blaNDM-1-bearing plasmid. Such findings can help establish new guidelines for prudent antibiotic usage to minimize the chance of dissemination of mobile resistance elements among members of the GI tract microbiome.},
}

Animals
Anti-Bacterial Agents/*administration & dosage
Escherichia coli/*drug effects/genetics
Gastrointestinal Microbiome/*drug effects
Gene Transfer, Horizontal/*drug effects
Klebsiella pneumoniae/*drug effects/genetics
Male
Metagenomics
RNA, Ribosomal, 16S/genetics
Rats, Sprague-Dawley
beta-Lactamases/*genetics

@article {pmid30887528,
year = {2019},
author = {Mauras, A and Wopereis, H and Yeop, I and Esber, N and Delannoy, J and Labellie, C and Reygner, J and Kapel, N and Slump, R and van Eijndthoven, T and Rutten, L and Knol, J and Garssen, J and Harthoorn, LF and Butel, MJ and Bajaj-Elliott, M and Hartog, A and Waligora-Dupriet, AJ},
title = {Gut microbiota from infant with cow's milk allergy promotes clinical and immune features of atopy in a murine model.},
journal = {Allergy},
volume = {74},
number = {9},
pages = {1790-1793},
pmid = {30887528},
issn = {1398-9995},
support = {//Danone Nutricia Research/International ; },
mesh = {Animals ; Cattle ; Disease Models, Animal ; *Disease Susceptibility ; *Gastrointestinal Microbiome/immunology ; Humans ; Hypersensitivity, Immediate/*etiology ; Infant ; Metagenomics/methods ; Mice ; Milk Hypersensitivity/*etiology ; },
}

Animals
Cattle
Disease Models, Animal
*Disease Susceptibility
*Gastrointestinal Microbiome/immunology
Humans
Hypersensitivity, Immediate/*etiology
Infant
Metagenomics/methods
Mice
Milk Hypersensitivity/*etiology

@article {pmid30239621,
year = {2019},
author = {Zinter, MS and Dvorak, CC and Mayday, MY and Iwanaga, K and Ly, NP and McGarry, ME and Church, GD and Faricy, LE and Rowan, CM and Hume, JR and Steiner, ME and Crawford, ED and Langelier, C and Kalantar, K and Chow, ED and Miller, S and Shimano, K and Melton, A and Yanik, GA and Sapru, A and DeRisi, JL},
title = {Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {68},
number = {11},
pages = {1847-1855},
pmid = {30239621},
issn = {1537-6591},
support = {K12 HD068371/HD/NICHD NIH HHS/United States ; K23 HL133437/HL/NHLBI NIH HHS/United States ; K23 HL138461/HL/NHLBI NIH HHS/United States ; L60 MD010865/MD/NIMHD NIH HHS/United States ; K12 HD000850/HD/NICHD NIH HHS/United States ; },
mesh = {Adolescent ; Bacteria/genetics ; Child ; Child, Preschool ; Female ; Fungi/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Immunocompromised Host ; Lung/*microbiology/*virology ; Lung Diseases/diagnosis/*microbiology/*virology ; Male ; *Metagenome ; Metagenomics ; Microbiota ; Missed Diagnosis ; Pilot Projects ; Retrospective Studies ; Viruses/genetics ; },
abstract = {BACKGROUND: Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next-generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children.

METHODS: We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children's hospitals from 2014-2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort.

RESULTS: We identified a rich cross-domain pulmonary microbiome that contained bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33-0.72 vs median, 0.96; IQR, 0.94-0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001).

CONCLUSIONS: An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.},
}

Adolescent
Bacteria/genetics
Child
Child, Preschool
Female
Fungi/genetics
High-Throughput Nucleotide Sequencing
Humans
*Immunocompromised Host
Lung/*microbiology/*virology
Lung Diseases/diagnosis/*microbiology/*virology
Male
*Metagenome
Metagenomics
Microbiota
Missed Diagnosis
Pilot Projects
Retrospective Studies
Viruses/genetics

@article {pmid31488869,
year = {2019},
author = {Amrane, S and Hocquart, M and Afouda, P and Kuete, E and Pham, TP and Dione, N and Ngom, II and Valles, C and Bachar, D and Raoult, D and Lagier, JC},
title = {Metagenomic and culturomic analysis of gut microbiota dysbiosis during Clostridium difficile infection.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {12807},
pmid = {31488869},
issn = {2045-2322},
mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/growth & development/*isolation & purification/metabolism ; Bacteroides/isolation & purification ; Bifidobacterium/isolation & purification ; Biological Therapy ; Clostridium Infections/*microbiology/therapy ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Middle Aged ; Molecular Typing ; },
abstract = {Recently, cocktail of bacteria were proposed in order to treat Clostridium difficile infection (CDI), but these bacteriotherapies were selected more by chance than experimentation. We propose to comprehensively explore the gut microbiota of patients with CDI compared to healthy donors in order to propose a consortium of bacteria for treating C. difficile. We compared stool samples composition from 11 CDI patients and 8 healthy donors using two techniques: metagenomics, 16S V3-V4 region amplification and sequencing and culturomics, high throughout culture using six culture conditions and MALDI-TOF identification. By culturomics, we detected 170 different species in the CDI group and 275 in the control group. Bacteroidetes were significantly underrepresented in the CDI group (p = 0.007). By metagenomics, 452 different operational taxonomic units assigned to the species level were detected in the CDI group compared to 522 in the control group. By these two techniques, we selected 37 bacteria only found in control group in more than 75% of the samples and/or with high relative abundance, 10 of which have already been tested in published bacteriotherapies against CDI, and 3 of which (Bifidobacterium adolescentis, Bifidobacterium longum and Bacteroides ovatus) have been detected by these two techniques. This controlled number of bacteria could be administrated orally in a non-invasive way in order to treat CDI.},
}

Adult
Aged
Aged, 80 and over
Bacteria/classification/growth & development/*isolation & purification/metabolism
Bacteroides/isolation & purification
Bifidobacterium/isolation & purification
Biological Therapy
Clostridium Infections/*microbiology/therapy
Feces/microbiology
Female
*Gastrointestinal Microbiome
Humans
Male
Metagenomics
Middle Aged
Molecular Typing

@article {pmid31081685,
year = {2019},
author = {Thombre, RS and Shivakarthik, E and Sivaraman, B and Vaishampayan, PA and Seuylemezian, A and Meka, JK and Vijayan, S and Kulkarni, PP and Pataskar, T and Patil, BS},
title = {Survival of Extremotolerant Bacteria from the Mukundpura Meteorite Impact Crater.},
journal = {Astrobiology},
volume = {19},
number = {6},
pages = {785-796},
doi = {10.1089/ast.2018.1928},
pmid = {31081685},
issn = {1557-8070},
mesh = {Acidobacteria/genetics/isolation & purification/radiation effects ; Actinobacteria/genetics/isolation & purification/radiation effects ; Bacillus/genetics/isolation & purification/radiation effects ; DNA, Bacterial/isolation & purification ; High-Energy Shock Waves/*adverse effects ; Metagenomics ; *Meteoroids ; Microbial Viability/*radiation effects ; Microbiota/genetics/*radiation effects ; Origin of Life ; Proteobacteria/genetics/isolation & purification/radiation effects ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; },
abstract = {Carbonaceous meteorites provide clues with regard to prebiotic chemistry and the origin of life. Geological Survey of India recorded a carbonaceous chondrite meteorite fall in Mukundpura, India, on June 6, 2017. We conducted a study to investigate the microbial community that survived the meteorite impact. 16S rRNA metagenomic sequencing indicates the presence of Actinobacteria, Proteobacteria, and Acidobacteria in meteorite impact soil. Comparative phylogenetic analysis revealed an intriguing abundance of class Bacilli in the impact soil. Bacillus thermocopriae IR-1, a moderately thermotolerant organism, was isolated from a rock, impacted by the Mukundpura meteorite. We investigated the resilience of B. thermocopriae IR-1 to environmental stresses and impact shock in a Reddy shock tube. Bacillus thermocopriae IR-1 survived (28.82% survival) the effect of shock waves at a peak shock pressure of 300 kPa, temperature 400 K, and Mach number of 1.47. This investigation presents the first report on the effect of impact shock on B. thermocopriae IR-1. The study is also the first report on studying the microbial diversity and isolation of bacteria from impact crater soil immediately after meteorite impact event.},
}

Acidobacteria/genetics/isolation & purification/radiation effects
Actinobacteria/genetics/isolation & purification/radiation effects
Bacillus/genetics/isolation & purification/radiation effects
DNA, Bacterial/isolation & purification
High-Energy Shock Waves/*adverse effects
Metagenomics
*Meteoroids
Microbial Viability/*radiation effects
Microbiota/genetics/*radiation effects
Origin of Life
Proteobacteria/genetics/isolation & purification/radiation effects
RNA, Ribosomal, 16S/genetics
*Soil Microbiology

@article {pmid30962186,
year = {2019},
author = {Shah, NB and Allegretti, AS and Nigwekar, SU and Kalim, S and Zhao, S and Lelouvier, B and Servant, F and Serena, G and Thadhani, RI and Raj, DS and Fasano, A},
title = {Blood Microbiome Profile in CKD : A Pilot Study.},
journal = {Clinical journal of the American Society of Nephrology : CJASN},
volume = {14},
number = {5},
pages = {692-701},
pmid = {30962186},
issn = {1555-905X},
mesh = {Adult ; Aged ; Cross-Sectional Studies ; DNA, Bacterial/*blood ; Female ; *Gastrointestinal Microbiome ; Glomerular Filtration Rate ; Humans ; Male ; Metagenomics ; Middle Aged ; Pilot Projects ; RNA, Ribosomal, 16S/analysis ; Renal Insufficiency, Chronic/blood/*microbiology/physiopathology ; },
abstract = {BACKGROUND AND OBJECTIVES: The association between gut dysbiosis, high intestinal permeability, and endotoxemia-mediated inflammation is well established in CKD. However, changes in the circulating microbiome in patients with CKD have not been studied. In this pilot study, we compare the blood microbiome profile between patients with CKD and healthy controls using 16S ribosomal DNA sequencing.

Blood bacterial DNA was studied in buffy coat samples quantitatively by 16S PCR and qualitatively by 16S targeted metagenomic sequencing using a molecular pipeline specifically optimized for blood samples in a cross-sectional study comparing 20 nondiabetic patients with CKD and 20 healthy controls.

RESULTS: There were 22 operational taxonomic units significantly different between the two groups. 16S metagenomic sequencing revealed a significant reduction in α diversity (Chao1 index) in the CKD group compared with healthy controls (127±18 versus 145±31; P=0.04). Proteobacteria phylum, Gammaproteobacteria class, and Enterobacteriaceae and Pseudomonadaceae families were more abundant in the CKD group compared with healthy controls. Median 16S ribosomal DNA levels did not significantly differ between CKD and healthy groups (117 versus 122 copies/ng DNA; P=0.38). GFR correlated inversely with the proportion of Proteobacteria (r=-0.54; P≤0.01).

CONCLUSIONS: Our pilot study demonstrates qualitative differences in the circulating microbiome profile with lower α diversity and significant taxonomic variations in the blood microbiome in patients with CKD compared with healthy controls.},
}

Adult
Aged
Cross-Sectional Studies
DNA, Bacterial/*blood
Female
*Gastrointestinal Microbiome
Glomerular Filtration Rate
Humans
Male
Metagenomics
Middle Aged
Pilot Projects
RNA, Ribosomal, 16S/analysis
Renal Insufficiency, Chronic/blood/*microbiology/physiopathology

@article {pmid30329017,
year = {2019},
author = {Graspeuntner, S and Waschina, S and Künzel, S and Twisselmann, N and Rausch, TK and Cloppenborg-Schmidt, K and Zimmermann, J and Viemann, D and Herting, E and Göpel, W and Baines, JF and Kaleta, C and Rupp, J and Härtel, C and Pagel, J},
title = {Gut Dysbiosis With Bacilli Dominance and Accumulation of Fermentation Products Precedes Late-onset Sepsis in Preterm Infants.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {69},
number = {2},
pages = {268-277},
doi = {10.1093/cid/ciy882},
pmid = {30329017},
issn = {1537-6591},
mesh = {Anaerobiosis ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dysbiosis/*complications ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; *Infant, Premature ; Male ; *Metabolome ; Metabolomics ; Metagenomics ; Neonatal Sepsis/*pathology ; Phylogeny ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Gut dysbiosis has been suggested as a major risk factor for the development of late-onset sepsis (LOS), a main cause of mortality and morbidity in preterm infants. We aimed to assess specific signatures of the gut microbiome, including metabolic profiles, in preterm infants <34 weeks of gestation preceding LOS.

METHODS: In a single-center cohort, fecal samples from preterm infants were prospectively collected during the period of highest vulnerability for LOS (days 7, 14, and 21 of life). Following 16S rRNA gene profiling, we assessed microbial community function using microbial metabolic network modeling. Data were adjusted for gestational age and use of probiotics.

RESULTS: We studied stool samples from 71 preterm infants with LOS and 164 unaffected controls (no LOS/necrotizing enterocolitis). In most cases, the bacteria isolated in diagnostic blood culture corresponded to the genera in the gut microbiome. LOS cases had a decelerated development of microbial diversity. Before onset of disease, LOS cases had specific gut microbiome signatures with higher abundance of Bacilli (specifically coagulase-negative Staphylococci) and a lack of anaerobic bacteria. In silico modeling of bacterial community metabolism suggested accumulation of the fermentation products ethanol and formic acid in LOS cases before the onset of disease.

CONCLUSIONS: Intestinal dysbiosis preceding LOS is characterized by an accumulation of Bacilli and their fermentation products and a paucity of anaerobic bacteria. Early microbiome and metabolic patterns may become a valuable biomarker to guide individualized prevention strategies of LOS in highly vulnerable populations.},
}

Anaerobiosis
Cluster Analysis
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Dysbiosis/*complications
Feces/chemistry/microbiology
*Gastrointestinal Microbiome
Humans
Infant
Infant, Newborn
*Infant, Premature
Male
*Metabolome
Metabolomics
Metagenomics
Neonatal Sepsis/*pathology
Phylogeny
Prospective Studies
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid32724224,
year = {2020},
author = {Vu, D and Groenewald, M and Verkley, G},
title = {Convolutional neural networks improve fungal classification.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {12628},
doi = {10.1038/s41598-020-69245-y},
pmid = {32724224},
issn = {2045-2322},
support = {BEK/BPR-2009/137964-U//Fonds Economische Structuurversterking (FES), Dutch Minister of Education, Culture and Science/ ; },
abstract = {Sequence classification plays an important role in metagenomics studies. We assess the deep neural network approach for fungal sequence classification as it has emerged as a successful paradigm for big data classification and clustering. Two deep learning-based classifiers, a convolutional neural network (CNN) and a deep belief network (DBN) were trained using our recently released barcode datasets. Experimental results show that CNN outperformed the traditional BLAST classification and the most accurate machine learning based Ribosomal Database Project (RDP) classifier on datasets that had many of the labels present in the training datasets. When classifying an independent dataset namely the "Top 50 Most Wanted Fungi", CNN and DBN assigned less sequences than BLAST. However, they could assign much more sequences than the RDP classifier. In terms of efficiency, it took the machine learning classifiers up to two seconds to classify a test dataset while it was 53 s for BLAST. The result of the current study will enable us to speed up the taxonomic assignments for the fungal barcode sequences generated at our institute as ~ 70% of them still need to be validated for public release. In addition, it will help to quickly provide a taxonomic profile for metagenomics samples.},
}

@article {pmid32002757,
year = {2020},
author = {Galloway-Peña, J and Hanson, B},
title = {Tools for Analysis of the Microbiome.},
journal = {Digestive diseases and sciences},
volume = {65},
number = {3},
pages = {674-685},
doi = {10.1007/s10620-020-06091-y},
pmid = {32002757},
issn = {1573-2568},
mesh = {Animals ; Computational Biology/*methods/trends ; High-Throughput Nucleotide Sequencing/*methods/trends ; Humans ; Machine Learning/trends ; Metagenomics/*methods/trends ; Microbiota/*physiology ; Sequence Analysis, DNA/*methods/trends ; },
abstract = {Over the past decade, it has become exceedingly clear that the microbiome is a critical factor in human health and disease and thus should be investigated to develop innovative treatment strategies. The field of metagenomics has come a long way in leveraging the advances of next-generation sequencing technologies resulting in the capability to identify and quantify all microorganisms present in human specimens. However, the field of metagenomics is still in its infancy, specifically in regard to the limitations in computational analysis, statistical assessments, standardization, and validation due to vast variability in the cohorts themselves, experimental design, and bioinformatic workflows. This review summarizes the methods, technologies, computational tools, and model systems for characterizing and studying the microbiome. We also discuss important considerations investigators must make when interrogating the involvement of the microbiome in health and disease in order to establish robust results and mechanistic insights before moving into therapeutic design and intervention.},
}

Animals
Computational Biology/*methods/trends
High-Throughput Nucleotide Sequencing/*methods/trends
Humans
Machine Learning/trends
Metagenomics/*methods/trends
Microbiota/*physiology
Sequence Analysis, DNA/*methods/trends

@article {pmid31619307,
year = {2020},
author = {Elokil, AA and Magdy, M and Melak, S and Ishfaq, H and Bhuiyan, A and Cui, L and Jamil, M and Zhao, S and Li, S},
title = {Faecal microbiome sequences in relation to the egg-laying performance of hens using amplicon-based metagenomic association analysis.},
journal = {Animal : an international journal of animal bioscience},
volume = {14},
number = {4},
pages = {706-715},
doi = {10.1017/S1751731119002428},
pmid = {31619307},
issn = {1751-732X},
mesh = {Actinobacteria/genetics/isolation & purification ; Animals ; Bacteria/*genetics/isolation & purification ; Chickens/*microbiology/physiology ; Cyanobacteria/genetics/isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Genotype ; Metagenome/*genetics ; *Metagenomics ; Ovum ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Exploring the composition and structure of the faecal microbial community improves the understanding of the role of the gut microbiota in the gastrointestinal function and the egg-laying performance of hens. Therefore, detection of hen-microbial interactions can explore a new breeding marker for the selection of egg production due to the important role of the gut microbiome in the host's metabolism and health. Recently, the gut microbiota has been recognised as a regulator of host performance, which has led to investigations of the productive effects of changes in the faecal microbiome in various animals. In the present study, a metagenomics analysis was applied to characterise the composition and structural diversity of faecal microbial communities under two selections of egg-laying performance, high (H, n = 30) and low (L, n = 30), using 16S rRNA-based metagenomic association analysis. The most abundant bacterial compositions were estimated based on the operational classification units among samples and between the groups from metagenomic data sets. The results indicated that Firmicutes phylum has higher significant (P < 0.01) in the H group than in the L group. In addition, higher relative abundance phyla of Bacteroides and Fusobacteria were estimated in the H group than the L group, contrasting the phyla of Actinobacteria, Cyanobacteria and Proteobacteria were more relative abundance in the L group. The families (Lactobacillus, Bifidobacterium, Acinetobacter, Flavobacteriaceae, Lachnoclostridum and Rhodococcus) were more abundant in the H group based on the comparison between the H and L groups. Meanwhile, three types of phyla (Proteobacteria, Actinobacteria and Cyanobacteria) and six families (Acinetobacter, Avibacterium, Clostridium, Corynebacterium, Helicobacter and Peptoclostridium) were more abundant in the L group (P < 0.01). Overall, the selection of genotypes has enriched a relationship between the gut microbiota and the egg-laying performance. These findings suggest that the faecal microbiomes of chickens with high egg-laying performance have more diverse activities than those of chickens with low egg-laying performance, which may be related to the metabolism and health of the host and egg production variation.},
}

Actinobacteria/genetics/isolation & purification
Animals
Bacteria/*genetics/isolation & purification
Chickens/*microbiology/physiology
Cyanobacteria/genetics/isolation & purification
Feces/microbiology
Female
Gastrointestinal Microbiome/*genetics
Genotype
Metagenome/*genetics
*Metagenomics
Ovum
Proteobacteria/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid30445563,
year = {2019},
author = {Ramos-Sevillano, E and Wade, WG and Mann, A and Gilbert, A and Lambkin-Williams, R and Killingley, B and Nguyen-Van-Tam, JS and Tang, CM},
title = {The Effect of Influenza Virus on the Human Oropharyngeal Microbiome.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {68},
number = {12},
pages = {1993-2002},
pmid = {30445563},
issn = {1537-6591},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Biodiversity ; Case-Control Studies ; Humans ; Influenza, Human/etiology ; Metagenome ; Metagenomics/methods ; *Microbial Interactions ; *Microbiota ; Oropharynx/*microbiology ; *Orthomyxoviridae ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Secondary bacterial infections are an important cause of morbidity and mortality associated with influenza infections. As bacterial disease can be caused by a disturbance of the host microbiome, we examined the impact of influenza on the upper respiratory tract microbiome in a human challenge study.

METHODS: The dynamics and ecology of the throat microbiome were examined following an experimental influenza challenge of 52 previously-healthy adult volunteers with influenza A/Wisconsin/67/2005 (H3N2) by intranasal inoculation; 35 healthy control subjects were not subjected to the viral challenge. Serial oropharyngeal samples were taken over a 30-day period, and the V1-V3 region of the bacterial 16S ribosomal RNA sequences were amplified and sequenced to determine the composition of the microbiome. The carriage of pathogens was also detected.

RESULTS: Of the 52 challenged individuals, 43 developed proven influenza infections, 33 of whom became symptomatic. None of the controls developed influenza, although 22% reported symptoms. The diversity of bacterial communities remained remarkably stable following the acquisition of influenza, with no significant differences over time between individuals with influenza and those in the control group. Influenza infection was not associated with perturbation of the microbiome at the level of phylum or genus. There was no change in colonization rates with Streptococcus pneumoniae or Neisseria meningitidis.

CONCLUSIONS: The throat microbiota is resilient to influenza infection, indicating the robustness of the upper-airway microbiome.},
}

Biodiversity
Case-Control Studies
Humans
Influenza, Human/etiology
Metagenome
Metagenomics/methods
*Microbial Interactions
*Microbiota
Oropharynx/*microbiology
*Orthomyxoviridae
RNA, Ribosomal, 16S/genetics