@article {pmid31982944,
year = {2020},
author = {Wang, Y and Cui, X and Chen, X and Yang, S and Ling, Y and Song, Q and Zhu, S and Sun, L and Li, C and Li, Y and Deng, X and Delwart, E and Zhang, W},
title = {A recombinant infectious bronchitis virus from a chicken with a spike gene closely related to that of a turkey coronavirus.},
journal = {Archives of virology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00705-019-04488-3},
pmid = {31982944},
issn = {1432-8798},
support = {2017YFC1200201//National Key Research and Development Programs of China/ ; BE2017693//Jiangsu Provincial Key Research and Development Projects/ ; 81741062//National Natural Science Foundation of China/ ; 201810299587W//Student's Platform for Innovation and Entrepreneurship Training Program/ ; No//Blood Systems Research Institute/ ; BE2016663//Jiangsu social development project/ ; },
abstract = {Using viral metagenomics, the complete genome sequence of an infectious bronchitis virus (IBV) strain (named ahysx-1) from a fecal sample from a healthy chicken in Anhui province, China, was determined. The genome sequence of ahysx-1 was found to be very similar to that of IBV strain ck/CH/LLN/131040 (KX252787), except for the spike gene region, which is similar to that of a turkey coronavirus strain (EU022526), suggesting that ahysx-1 is a recombinant. Recombination analysis and phylogenetic analysis based on the genomic sequences of ahysx-1 and other related strains confirmed that ahysx-1 appears to be a recombinant resulting from a recombination event that occurred between a chicken coronavirus and a turkey coronavirus. Further studies need to be performed to determine whether this recombinant IBV strain is pathogenic and whether it is transmitted between chickens and turkeys.},
}

@article {pmid31982930,
year = {2020},
author = {Chen, YT and Zeng, Y and Wang, HZ and Zheng, D and Kamagata, Y and Narihiro, T and Nobu, MK and Tang, YQ},
title = {Different Interspecies Electron Transfer Patterns during Mesophilic and Thermophilic Syntrophic Propionate Degradation in Chemostats.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-020-01485-x},
pmid = {31982930},
issn = {1432-184X},
support = {2016YFE0127700//Ministry of Science and Technology of the People's Republic of China/ ; 51678378//National Natural Science Foundation of China/ ; 41701295//National Natural Science Foundation of China/ ; 2018M643480//Postdoctoral Research Foundation of China/ ; 2018SCUH0023//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Propionate is one of the major intermediates in anaerobic digestion of organic waste to CO2 and CH4. In methanogenic environments, propionate is degraded through a mutualistic interaction between symbiotic propionate oxidizers and methanogens. Although temperature heavily influences the microbial ecology and performance of methanogenic processes, its effect on syntrophic interaction during propionate degradation remains poorly understood. In this study, metagenomics and metatranscriptomics were employed to compare mesophilic and thermophilic propionate degradation communities. Mesophilic propionate degradation involved multiple syntrophic organisms (Syntrophobacter, Smithella, and Syntrophomonas), pathways, interactions, and preference toward formate-based electron transfer to methanogenic partners (i.e., Methanoculleus). In thermophilic propionate degradation, one syntrophic organism predominated (Pelotomaculum), interspecies H2 transfer played a major role, and phylogenetically and metabolically diverse H2-oxidizing methanogens were present (i.e., Methanoculleus, Methanothermobacter, and Methanomassiliicoccus). This study showed that microbial interactions, metabolic pathways, and niche diversity are distinct between mesophilic and thermophilic microbial communities responsible for syntrophic propionate degradation.},
}

@article {pmid31980604,
year = {2020},
author = {Roberts, LW and Harris, PNA and Forde, BM and Ben Zakour, NL and Catchpoole, E and Stanton-Cook, M and Phan, MD and Sidjabat, HE and Bergh, H and Heney, C and Gawthorne, JA and Lipman, J and Allworth, A and Chan, KG and Chong, TM and Yin, WF and Schembri, MA and Paterson, DL and Beatson, SA},
title = {Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {466},
doi = {10.1038/s41467-019-14139-5},
pmid = {31980604},
issn = {2041-1723},
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to characterise a hospital outbreak of blaIMP-4 carbapenemase-producing E. hormaechei. Using Illumina sequencing, we determined that all outbreak strains were sequence type 90 (ST90) and near-identical. Comparison to publicly available data linked all outbreak isolates to a 2013 isolate from the same ward, suggesting an environmental source in the hospital. Using Pacific Biosciences sequencing, we resolved the complete context of the blaIMP-4 gene on a large IncHI2 plasmid carried by all IMP-4-producing strains across different hospitals. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaechei and the IncHI2 plasmid within the hospital plumbing. Finally, Oxford Nanopore sequencing rapidly resolved the true relationship of subsequent isolates to the initial outbreak. Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak.},
}

@article {pmid31980038,
year = {2020},
author = {Keren, R and Lawrence, JE and Zhuang, W and Jenkins, D and Banfield, JF and Alvarez-Cohen, L and Zhou, L and Yu, K},
title = {Increased replication of dissimilatory nitrate-reducing bacteria leads to decreased anammox bioreactor performance.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {7},
doi = {10.1186/s40168-020-0786-3},
pmid = {31980038},
issn = {2049-2618},
support = {ECC-1028962//Engineering Research Center for ReInventing the Nation's Water Infrastructure/ ; DGE 1106400//National Science Foundation Graduate Research Fellowship/ ; },
abstract = {BACKGROUND: Anaerobic ammonium oxidation (anammox) is a biological process employed to remove reactive nitrogen from wastewater. While a substantial body of literature describes the performance of anammox bioreactors under various operational conditions and perturbations, few studies have resolved the metabolic roles of their core microbial community members.

RESULTS: Here, we used metagenomics to study the microbial community of a laboratory-scale anammox bioreactor from inoculation, through a performance destabilization event, to robust steady-state performance. Metabolic analyses revealed that nutrient acquisition from the environment is selected for in the anammox community. Dissimilatory nitrate reduction to ammonium (DNRA) was the primary nitrogen removal pathway that competed with anammox. Increased replication of bacteria capable of DNRA led to the out-competition of anammox bacteria, and the loss of the bioreactor's nitrogen removal capacity. These bacteria were highly associated with the anammox bacterium and considered part of the core microbial community.

CONCLUSIONS: Our findings highlight the importance of metabolic interdependencies related to nitrogen- and carbon-cycling within anammox bioreactors and the potentially detrimental effects of bacteria that are otherwise considered core microbial community members.},
}

@article {pmid31980025,
year = {2020},
author = {Lee, H and Lee, HK and Min, SK and Lee, WH},
title = {16S rDNA microbiome composition pattern analysis as a diagnostic biomarker for biliary tract cancer.},
journal = {World journal of surgical oncology},
volume = {18},
number = {1},
pages = {19},
doi = {10.1186/s12957-020-1793-3},
pmid = {31980025},
issn = {1477-7819},
support = {2017R1C1B5017902//National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning/ ; NRF-2017M3A9F3047497//National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning/ ; },
abstract = {BACKGROUND: The aim of this study is to investigate the composition of microbiota in biliary tract cancer patients and healthy adults by metagenome analysis and evaluate its potential values as biomarkers for biliary tract cancer.

METHODS: Patients who were diagnosed with biliary tract cancer or benign inflammation were enrolled in this study. The control group consisted of healthy adults who presented with no history of significant medical issues. We isolated bacteria-derived extracellular vesicles in the plasma. The microbiome composition was investigated with 16S rDNA metagenome analysis. We evaluated each microbiome to ensure suitability for the biliary tract cancer prediction model.

RESULTS: A total of 155 patients were included in this study: 24 patients with diagnosed biliary tract cancers, 43 diagnosed with cholecystitis or cholangitis, and 88 healthy adults. The microbiome composition pattern of the biliary tract cancer differed from the microbiome composition pattern seen in healthy adult group in beta diversity analysis. The percent composition of microbiota was found to be different from the phylum to genus level. Differences in the composition of the Bifidobacteriaceae and Pseudomonaceae families and Corynebacteriaceae Corynebacterium, Oxalobacteraceae Ralstonia and Comamonadaceae Comamonas species may be used to develop predictive models for biliary tract cancer.

CONCLUSION: Biliary tract cancer patients have altered microbiome composition, which represents a promising biomarker to differentiate malignant biliary tract disease from normal control group.},
}

@article {pmid31979034,
year = {2020},
author = {Connelly, S and Fanelli, B and Hasan, NA and Colwell, RR and Kaleko, M},
title = {SYN-007, an Orally Administered Beta-Lactamase Enzyme, Protects the Gut Microbiome from Oral Amoxicillin/Clavulanate without Adversely Affecting Antibiotic Systemic Absorption in Dogs.},
journal = {Microorganisms},
volume = {8},
number = {2},
pages = {},
doi = {10.3390/microorganisms8020152},
pmid = {31979034},
issn = {2076-2607},
abstract = {Beta-lactamases, enzymes produced by bacteria to degrade beta-lactam antibiotics, have been harnessed as therapeutics to protect the gut microbiome from damage caused by antibiotics. Proof-of-concept of this approach using SYN-004 (ribaxamase), a beta-lactamase formulated for oral delivery with intravenous (IV) penicillins and cephalosporins, was demonstrated with animal models and in humans. Ribaxamase degraded ceftriaxone in the gastrointestinal tract, protected the gut microbiome, significantly reduced the incidence of Clostridioidesdifficile disease and attenuated emergence of antibiotic resistant organisms. SYN-007 is a delayed release formulation of ribaxamase intended for use with oral beta-lactams. In dogs treated with oral amoxicillin, SYN-007 diminished antibiotic-mediated microbiome disruption and reduced the emergence of antibiotic resistance without altering amoxicillin systemic absorption. Here, SYN-007 function in the presence of clavulanate, a beta-lactamase inhibitor, was investigated. Dogs received amoxicillin (40 mg/kg, orally (PO), three times a day (TID)) or the combined antibiotic/beta-lactamase inhibitor, amoxicillin/clavulanate (40 mg/kg amoxicillin, 5.7 mg/kg clavulanate, PO, TID) +/- SYN-007 (10 mg, PO, TID) for five days. Serum amoxicillin levels were not significantly different +/- SYN-007 compared to amoxicillin alone or amoxicillin/clavulanate alone as controls for both first and last doses, indicating SYN-007 did not interfere with systemic absorption of the antibiotic. Whole genome shotgun metagenomics analyses of the fecal microbiomes demonstrated both amoxicillin and amoxicillin/clavulanate significantly reduced diversity and increased the frequency of antibiotic resistance genes. Microbiome damage appeared more severe with amoxicillin/clavulanate. In contrast, with SYN-007, microbiome diversity was not significantly altered, and frequency of antibiotic resistance genes did not increase. Importantly, SYN-007 functioned in the presence of clavulanate to protect the gut microbiome indicating that SYN-007 activity was not inhibited by clavulanate in the dog gastrointestinal tract. SYN-007 has the potential to expand microbiome protection to beta-lactam/beta-lactamase inhibitor combinations delivered orally or systemically.},
}

@article {pmid31978775,
year = {2020},
author = {Grzesiak, J and Kaczyńska, A and Gawor, J and Żuchniewicz, K and Aleksandrzak-Piekarczyk, T and Gromadka, R and Zdanowski, MK},
title = {A smelly business: Microbiology of Adélie penguin guano (Point Thomas rookery, Antarctica).},
journal = {The Science of the total environment},
volume = {714},
number = {},
pages = {136714},
doi = {10.1016/j.scitotenv.2020.136714},
pmid = {31978775},
issn = {1879-1026},
abstract = {Adélie penguins (Pygoscelis adeliae) are the most numerous flightless bird group breeding in coastal areas of Maritime and Continental Antarctica. Their activity leaves a mark on the land in the form of large guano deposits. This guano is an important nutrient source for terrestrial habitats of ice-free Antarctic areas, most notably by being the source of ammonia vapors which feed the surrounding grass, lichen and algae communities. Although investigated by researchers, the fate of the guano-associated microbial community and its role in decomposition processes remain vague. Therefore, by employing several direct community assessment methods combined with a broad culture-based approach we provide data on bacterial numbers, their activity and taxonomic affiliation in recently deposited and decayed Adélie penguin guano sampled at the Point Thomas rookery in Maritime Antarctica (King George Island). Our research indicates that recently deposited guano harbored mostly bacteria of penguin gut origin, presumably inactive in cold rookery settings. This material was rich in mesophilic enzymes active also at low temperatures, likely mediating early stage decomposition. Fresh guano colonization by environmental bacteria was minor, accomplished mostly by ammonia scavenging Jeotgalibaca sp. cells. Decayed guano contained 10-fold higher bacterial numbers with cold-active enzymes dominating the samples. Guano was colonized by uric-acid degrading and lipolytic Psychrobacter spp. and proteolytic Chryseobacterium sp. among others. Several spore-forming bacteria of penguin gut origin persisted in highly decomposed material, most notably uric-acid fermenting members of the Gottschalkiaceae family.},
}

@article {pmid31978735,
year = {2019},
author = {Rusiñol, M and Martínez-Puchol, S and Timoneda, N and Fernández-Cassi, X and Pérez-Cataluña, A and Fernández-Bravo, A and Moreno-Mesonero, L and Moreno, Y and Alonso, JL and Figueras, MJ and Abril, JF and Bofill-Mas, S and Girones, R},
title = {Metagenomic analysis of viruses, bacteria and protozoa in irrigation water.},
journal = {International journal of hygiene and environmental health},
volume = {224},
number = {},
pages = {113440},
doi = {10.1016/j.ijheh.2019.113440},
pmid = {31978735},
issn = {1618-131X},
abstract = {Viruses (e.g., noroviruses and hepatitis A and E virus), bacteria (e.g., Salmonella spp. and pathogenic Escherichia coli) and protozoa (e.g., Cryptosporidium parvum and Giardia intestinalis) are well-known contributors to food-borne illnesses linked to contaminated fresh produce. As agricultural irrigation increases the total amount of water used annually, reclaimed water is a good alternative to reduce dependency on conventional irrigation water sources. European guidelines have established acceptable concentrations of certain pathogens and/or indicators in irrigation water, depending on the irrigation system used and the irrigated crop. However, the incidences of food-borne infections are known to be underestimated and all the different pathogens contributing to these infections are not known. Next-generation sequencing (NGS) enables the determination of the viral, bacterial and protozoan populations present in a water sample, providing an opportunity to detect emerging pathogens and develop improved tools for monitoring the quality of irrigation water. This is a descriptive study of the virome, bacteriome and parasitome present in different irrigation water sources. We applied the same concentration method for all the studied samples and specific metagenomic approaches to characterize both DNA and RNA viruses, bacteria and protozoa. In general, most of the known viral species corresponded to plant viruses and bacteriophages. Viral diversity in river water varied over the year, with higher bacteriophage prevalences during the autumn and winter. Reservoir water contained Enterobacter cloacae, an opportunistic human pathogen and an indicator of fecal contamination, as well as Naegleria australiensis and Naegleria clarki. Hepatitis E virus and Naegleria fowleri, emerging human pathogens, were detected in groundwater. Reclaimed water produced in a constructed wetland system presented a virome and bacteriome that resembled those of freshwater samples (river and reservoir water). Viral, bacterial and protozoan pathogens were occasionally detected in the different irrigation water sources included in this study, justifying the use of improved NGS techniques to get a comprehensive evaluation of microbial species and potential environmental health hazards associated to irrigation water.},
}

@article {pmid31978162,
year = {2020},
author = {Chung, YW and Gwak, HJ and Moon, S and Rho, M and Ryu, JH},
title = {Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0227886},
doi = {10.1371/journal.pone.0227886},
pmid = {31978162},
issn = {1932-6203},
abstract = {BACKGROUND: Microbial communities of the mouse gut have been extensively studied; however, their functional roles and regulation are yet to be elucidated. Metagenomic and metatranscriptomic analyses may allow us a comprehensive profiling of bacterial composition and functions of the complex gut microbiota. The present study aimed to investigate the active functions of the microbial communities in the murine cecum by analyzing both metagenomic and metatranscriptomic data on specific bacterial species within the microbial communities, in addition to the whole microbiome.

RESULTS: Bacterial composition of the healthy mouse gut microbiome was profiled using the following three different approaches: 16S rRNA-based profiling based on amplicon and shotgun sequencing data, and genome-based profiling based on shotgun sequencing data. Consistently, Bacteroidetes, Firmicutes, and Deferribacteres emerged as the major phyla. Based on NCBI taxonomy, Muribaculaceae, Lachnospiraceae, and Deferribacteraceae were the predominant families identified in each phylum. The genes for carbohydrate metabolism were upregulated in Muribaculaceae, while genes for cofactors and vitamin metabolism and amino acid metabolism were upregulated in Deferribacteraceae. The genes for translation were commonly enhanced in all three families. Notably, combined analysis of metagenomic and metatranscriptomic sequencing data revealed that the functions of translation and metabolism were largely upregulated in all three families in the mouse gut environment. The ratio of the genes in the metagenome and their expression in the metatranscriptome indicated higher expression of carbohydrate metabolism in Muribaculum, Duncaniella, and Mucispirillum.

CONCLUSIONS: We demonstrated a fundamental methodology for linking genomic and transcriptomic datasets to examine functional activities of specific bacterial species in a complicated microbial environment. We investigated the normal flora of the mouse gut using three different approaches and identified Muribaculaceae, Lachnospiraceae, and Deferribacteraceae as the predominant families. The functional distribution of these families was reflected in the entire microbiome. By comparing the metagenomic and metatranscriptomic data, we found that the expression rates differed for different functional categories in the mouse gut environment. Application of these methods to track microbial transcription in individuals over time, or before and after administration of a specific stimulus will significantly facilitate future development of diagnostics and treatments.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.0c00033},
pmid = {31977194},
issn = {1520-4995},
}

@article {pmid31977019,
year = {2020},
author = {Warsi, O and Knopp, M and Surkov, S and Hultqvist, JJ and Andersson, DI},
title = {Evolution of a new function by fusion between phage DNA and a bacterial gene.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaa007},
pmid = {31977019},
issn = {1537-1719},
abstract = {Mobile genetic elements, such as plasmids, phages and transposons, are important sources for evolution of novel functions. In this study, we performed a large-scale screening of metagenomic phage libraries for their ability to suppress temperature-sensitive S. Typhimurium mutants to examine how phage DNA could confer evolutionary novelty to bacteria. We identified an insert encoding 23 amino acids from a phage, that when fused with a bacterial DNA-binding repressor protein (LacI) resulted in the formation of a chimeric protein that localized to the outer membrane. This relocalization of the chimeric protein resulted in increased membrane vesicle formation and an associated suppression of the temperature-sensitivity of the bacterium. Both the host LacI protein and the extracellular 23 amino acids stretch are necessary for the generation of the novel phenotype. Furthermore, mutational analysis of the chimeric protein showed that although the native repressor function of the LacI protein is maintained in this chimeric structure, it is not necessary for the new function. Thus, our study demonstrates how a gene fusion between foreign DNA and bacterial DNA can generate novelty without compromising the native function of a given gene.},
}

@article {pmid31976742,
year = {2020},
author = {Maggiori, C and Stromberg, J and Blanco, Y and Goordial, J and Cloutis, E and García-Villadangos, M and Parro, V and Whyte, L},
title = {The Limits, Capabilities, and Potential for Life Detection with MinION Sequencing in a Paleochannel Mars Analog.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ast.2018.1964},
pmid = {31976742},
issn = {1557-8070},
abstract = {No instrument capable of direct life detection has been included on a mission payload to Mars since NASA's Viking missions in the 1970s. This prevents us from discovering whether life is or ever was present on Mars. DNA is an ideal target biosignature since it is unambiguous, nonspecific, and readily detectable with nanopore sequencing. Here, we present a proof-of-concept utilization of the Oxford Nanopore Technologies (ONT) MinION sequencer for direct life detection and show how it can complement results from established space mission instruments. We used nanopore sequencing data from the MinION to detect and characterize the microbial life in a set of paleochannels near Hanksville, UT, with supporting data from X-ray diffraction, reflectance spectroscopy, Raman spectroscopy, and Life Detector Chip (LDChip) microarray immunoassay analyses. These paleochannels are analogs to martian sinuous ridges. The MinION-generated metagenomes reveal a rich microbial community dominated by bacteria and containing radioresistant, psychrophilic, and halophilic taxa. With spectral data and LDChip immunoassays, these metagenomes were linked to the surrounding Mars analog environment and potential metabolisms (e.g., methane production and perchlorate reduction). This shows a high degree of synergy between these techniques for detecting and characterizing biosignatures. We also resolved a prospective lower limit of ∼0.001 ng of DNA required for successful sequencing. This work represents the first determination of the MinION's DNA detection limits beyond ONT recommendations and the first whole metagenome analysis of a sinuous ridge analog.},
}

@article {pmid31976084,
year = {2020},
author = {Obbard, DJ and Shi, M and Roberts, KE and Longdon, B and Dennis, AB},
title = {A new lineage of segmented RNA viruses infecting animals.},
journal = {Virus evolution},
volume = {6},
number = {1},
pages = {vez061},
doi = {10.1093/ve/vez061},
pmid = {31976084},
issn = {2057-1577},
abstract = {Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called 'dark' virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose 'dark' virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.},
}

@article {pmid31975740,
year = {2020},
author = {Sakandar, HA and Huang, W and Kubow, S and Sadiq, FA and Imran, M},
title = {Comparison of bacterial communities in gliadin-degraded sourdough (Khamir) sample and non-degraded sample.},
journal = {Journal of food science and technology},
volume = {57},
number = {1},
pages = {375-380},
doi = {10.1007/s13197-019-04030-y},
pmid = {31975740},
issn = {0022-1155},
abstract = {The study was undertaken to investigate the comparison lying between bacterial communities in autochthonous gliadin-degraded sourdough sample (D13) and non-degraded sample (D50). Degree of gliadin degradation in various samples was determined by Fourier transform infrared spectroscopy and represented samples were selected for 16 S rDNA sequence analysis by Illumina Miseq platform. It was observed, that Proteobacteria (50.65%) and Actinobacteria (6.70%) phyla were more abundant as compared with Firmicutes (42.53%) in D13, however, Firmicutes (83.44) were more abundant, comparatively, in D50 than Proteobacteria (14.97%). Lower taxonomic levels surfaced its more prominent effects. It had been also observed that Lactobacillus genera was the core genera (50.37%) followed by Weissella (27.15%) and Psychrobacter (21.53%) in D50 and D13, respectively. Shannon and Simpson indices indicated that degraded sample had more bacterial diversity and richness compared with non-degraded sample.},
}

@article {pmid31974429,
year = {2020},
author = {Radjabzadeh, D and Boer, CG and Beth, SA and van der Wal, P and Kiefte-De Jong, JC and Jansen, MAE and Konstantinov, SR and Peppelenbosch, MP and Hays, JP and Jaddoe, VWV and Ikram, MA and Rivadeneira, F and van Meurs, JBJ and Uitterlinden, AG and Medina-Gomez, C and Moll, HA and Kraaij, R},
title = {Diversity, compositional and functional differences between gut microbiota of children and adults.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {1040},
doi = {10.1038/s41598-020-57734-z},
pmid = {31974429},
issn = {2045-2322},
abstract = {The gut microbiota has been shown to play diverse roles in human health and disease although the underlying mechanisms have not yet been fully elucidated. Large cohort studies can provide further understanding into inter-individual differences, with more precise characterization of the pathways by which the gut microbiota influences human physiology and disease processes. Here, we aimed to profile the stool microbiome of children and adults from two population-based cohort studies, comprising 2,111 children in the age-range of 9 to 12 years (the Generation R Study) and 1,427 adult individuals in the range of 46 to 88 years of age (the Rotterdam Study). For the two cohorts, 16S rRNA gene profile datasets derived from the Dutch population were generated. The comparison of the two cohorts showed that children had significantly lower gut microbiome diversity. Furthermore, we observed higher relative abundances of genus Bacteroides in children and higher relative abundances of genus Blautia in adults. Predicted functional metagenome analysis showed an overrepresentation of the glycan degradation pathways, riboflavin (vitamin B2), pyridoxine (vitamin B6) and folate (vitamin B9) biosynthesis pathways in children. In contrast, the gut microbiome of adults showed higher abundances of carbohydrate metabolism pathways, beta-lactam resistance, thiamine (vitamin B1) and pantothenic (vitamin B5) biosynthesis pathways. A predominance of catabolic pathways in children (valine, leucine and isoleucine degradation) as compared to biosynthetic pathways in adults (valine, leucine and isoleucine biosynthesis) suggests a functional microbiome switch to the latter in adult individuals. Overall, we identified compositional and functional differences in gut microbiome between children and adults in a population-based setting. These microbiome profiles can serve as reference for future studies on specific human disease susceptibility in childhood, adulthood and specific diseased populations.},
}

@article {pmid31974406,
year = {2020},
author = {Aarestrup, J and Bjerregaard, LG and Meyle, KD and Pedersen, DC and Gjærde, LK and Jensen, BW and Baker, JL},
title = {Birthweight, childhood overweight, height and growth and adult cancer risks: a review of studies using the Copenhagen School Health Records Register.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41366-020-0523-9},
pmid = {31974406},
issn = {1476-5497},
abstract = {BACKGROUND: Most identified risk factors for cancer primarily occur in adulthood. As cancers generally have long latency periods, it is possible that risk factors acting earlier in life and accumulation of risks across the life course are important. Thus, focusing only on adult overweight as a modifiable risk factor may overlook childhood as an important aetiologic time window when body size is relevant for future cancer risks. The objective of this study was to review the evidence for associations between birthweight, body mass index (BMI), height and growth from 7-13 years and adult cancer risks based on studies using the Copenhagen School Health Records Register.

METHODS: The register contains measured anthropometric information on 372,636 children born in 1930-1989. All studies examining associations between early life body size and risks of adult cancer (until 85 years, diagnosed in 1968-2015) were included, comprising 31 studies on 16 different cancer sites. Cancer diagnoses were retrieved via individual-level linkages to the Danish Cancer Registry.

RESULTS: Birthweight was differentially associated with bladder, breast, colon, glioma, Hodgkin's disease, liver, kidney (renal cell), melanoma, ovarian, rectal, testicular and thyroid cancer. BMI in childhood was positively associated with risks of bladder (only late childhood), colon, endometrial, kidney, liver, oesophageal (only late childhood), ovarian, pancreatic (<70 years), prostate (only before childhood height adjustment) and thyroid cancer, whereas it was inversely associated with breast cancer. Child height was positively associated with breast, colon, endometrial, glioma, Hodgkin's disease, kidney, melanoma, oesophageal (only women), ovarian, prostate, testicular and thyroid cancer and inversely associated with bladder cancer. Greater than average increases in childhood BMI or linear growth at ages 7-13 increased risks of several cancers.

CONCLUSIONS: Early life body size and growth are associated with many, but not all adult cancers, suggesting that the aetiology of several cancers may lie earlier in life than previously thought.},
}

@article {pmid31248008,
year = {2019},
author = {Steury, RA and Currey, MC and Cresko, WA and Bohannan, BJM},
title = {Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback.},
journal = {Genes},
volume = {10},
number = {7},
pages = {},
doi = {10.3390/genes10070484},
pmid = {31248008},
issn = {2073-4425},
support = {P50GM098911/NH/NIH HHS/United States ; R24RR032670/NH/NIH HHS/United States ; },
mesh = {Animals ; Environment ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Host Microbial Interactions ; Metagenomics ; Microbiota ; Oregon ; Smegmamorpha/genetics/*microbiology ; },
abstract = {Much of animal-associated microbiome research has been conducted in&nbsp;species&nbsp;for which little is known of their natural ecology and evolution.&nbsp;Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host genetic variation and the environment both influence microbiome variation.&nbsp;The few studies that have&nbsp;related&nbsp;population genetic&nbsp;and microbiome variation in wild populations&nbsp;have been constrained by observation-based kinship data or&nbsp;incomplete genomic information. Here we&nbsp;integrate population genomic&nbsp;and microbiome analyses&nbsp;in wild threespine stickleback fish distributed throughout western Oregon, USA. We found that gut microbiome diversity and composition partitioned more among than within wild host populations and was better explained by host population genetic divergence than&nbsp;by environment and geography. We also identified gut microbial taxa that were most differentially abundant across environments and across genetically divergent populations. Our findings highlight the benefits of studies that investigate host-associated microbiomes in wild organisms.},
}

Animals
Environment
Gastrointestinal Microbiome/*genetics
*Genetic Variation
Genetics, Population
Geography
Host Microbial Interactions
Metagenomics
Microbiota
Oregon
Smegmamorpha/genetics/*microbiology

@article {pmid30282116,
year = {2019},
author = {Taylor, SL and O'Farrell, HE and Simpson, JL and Yang, IA and Rogers, GB},
title = {The contribution of respiratory microbiome analysis to a treatable traits model of care.},
journal = {Respirology (Carlton, Vic.)},
volume = {24},
number = {1},
pages = {19-28},
doi = {10.1111/resp.13411},
pmid = {30282116},
issn = {1440-1843},
mesh = {Airway Management/*methods ; Humans ; Metagenomics/methods ; Microbiological Phenomena ; *Microbiota/drug effects/physiology ; Models, Organizational ; Patient Care Management/*organization & administration ; *Pulmonary Disease, Chronic Obstructive/immunology/microbiology/physiopathology/therapy ; Respiratory System/*microbiology ; },
abstract = {The composition of the airway microbiome in patients with chronic airway diseases, such as severe asthma, chronic obstructive pulmonary disease (COPD), bronchiectasis and cystic fibrosis (CF), has the potential to inform a precision model of clinical care. Patients with these conditions share overlapping disease characteristics, including airway inflammation and airflow limitation. The clinical management of chronic respiratory conditions is increasingly moving away from a one-size-fits-all model based on primary diagnosis, towards care targeting individual disease traits, and is particularly useful for subgroups of patients who respond poorly to conventional therapies. Respiratory microbiome analysis is an important potential contributor to such a 'treatable traits' approach, providing insight into both microbial drivers of airways disease, and the selective characteristics of the changing lower airway environment. We explore the potential to integrate respiratory microbiome analysis into a treatable traits model of clinical care and provide a practical guide to the application and clinical interpretation of respiratory microbiome analysis.},
}

Airway Management/*methods
Humans
Metagenomics/methods
Microbiological Phenomena
*Microbiota/drug effects/physiology
Models, Organizational
Patient Care Management/*organization & administration
*Pulmonary Disease, Chronic Obstructive/immunology/microbiology/physiopathology/therapy
Respiratory System/*microbiology

@article {pmid31972701,
year = {2020},
author = {Azar, MM and Gaston, DC and Kotton, CN and Malinis, MF},
title = {Emerging microbiology diagnostics for transplant infections: On the cusp of a paradigm shift.},
journal = {Transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1097/TP.0000000000003123},
pmid = {31972701},
issn = {1534-6080},
abstract = {In light of the heightened risk for infection associated with solid organ and hematopoietic stem cell transplantation, rapid and accurate microbiology diagnostics are essential to the practice of transplant clinicians, including infectious diseases specialists. In the last decade, diagnostic microbiology has seen a shift towards culture-independent techniques including single-target and multiplexed molecular testing, mass-spectrometry, and magnetic resonance-based methods which have together greatly expanded the array of pathogens identified, increased processing speed and throughput, allowed for detection of resistance determinants, and ultimately improved the outcomes of infected transplant recipients. More recently, a newer generation of diagnostics with immense potential has emerged, including multiplexed molecular panels directly applicable to blood and blood culture specimens, next-generation metagenomics and gas chromatography mass spectrometry. Though these methods have some recognized drawbacks, many have already demonstrated improved diagnostic sensitivity and a positive impact on clinical outcomes in transplant and immunocompromised patients.},
}

@article {pmid31971995,
year = {2020},
author = {Ben Maamar, S and Glawe, AJ and Brown, TK and Hellgeth, N and Hu, J and Wang, JP and Huttenhower, C and Hartmann, EM},
title = {Mobilizable antibiotic resistance genes are present in dust microbial communities.},
journal = {PLoS pathogens},
volume = {16},
number = {1},
pages = {e1008211},
doi = {10.1371/journal.ppat.1008211},
pmid = {31971995},
issn = {1553-7374},
abstract = {The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.},
}

@article {pmid31971861,
year = {2020},
author = {Yang, J and Li, D and Yang, Z and Dai, W and Feng, X and Liu, Y and Jiang, Y and Li, P and Li, Y and Tang, B and Zhou, Q and Qiu, C and Zhang, C and Xu, X and Feng, S and Wang, D and Wang, H and Wang, W and Zheng, Y and Zhang, L and Wang, W and Zhou, K and Li, S and Yu, P},
title = {Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/19490976.2020.1712986},
pmid = {31971861},
issn = {1949-0984},
abstract = {Colorectal cancer (CRC) causes high morbidity and mortality worldwide, and noninvasive gut microbiome (GM) biomarkers are promising for early CRC diagnosis. However, the GM varies significantly based on ethnicity, diet and living environment, suggesting varied GM biomarker performance in different regions. We performed a metagenomic association analysis on stools from 52 patients and 55 corresponding healthy family members who lived together to identify GM biomarkers for CRC in Chongqing, China. The GM of patients differed significantly from that of healthy controls. A total of 22 microbial genes were included as screening biomarkers with high accuracy in additional 46 cases and 40 randomly selected healthy adults in Chongqing (area under the receive-operation curve (AUC) = 0.905, 95% CI 0.832-0.977). The classifier based on the identified 22 biomarkers also performed well in the cohort from Hong Kong (AUC = 0.811, 95% CI 0.715-0.907) and French (AUC = 0.859, 95% CI 0.773-0.944) populations. Quantitative PCR was applied for measuring three selected biomarkers in the classification of CRC patients in independent Chongqing population containing 30 cases and 30 controls and the best biomarker from Coprobacillus performed well with high AUC (0.930, 95% CI 0.904-0.955). This study revealed increased sensitivity and applicability of our GM biomarkers compared with previous biomarkers significantly promoting the early diagnosis of CRC.},
}

@article {pmid31971461,
year = {2020},
author = {Schmidt, JW and Vikram, A and Miller, E and Jones, SA and Arthur, TM},
title = {In-Feed Tylosin Phosphate Administration to Feedlot Cattle Minimally Affects Antimicrobial Resistance.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {350-364},
doi = {10.4315/0362-028X.JFP-19-342},
pmid = {31971461},
issn = {1944-9097},
abstract = {The macrolide class antimicrobial tylosin (trade name Tylan) is approved by the U.S. Food and Drug Administration for continuous inclusion in feed for liver abscess prevention. To address concerns that this antimicrobial application may threaten human health, a population of feedlot steers was split into a control treatment (n = 42) and a tylosin treatment (n = 42). Feed rations were identical except for the inclusion of tylosin at 60 to 90 mg per head per day. Fecal swab (n = 335), pen surface material (n = 256), feed (n = 56), and water trough (n = 32) samples were obtained over four sample occasions: November (1 day before the start of tylosin inclusion in feed), January (80 days of tylosin in feed), April (167 days), and June (253 days). These samples were cultured for Escherichia coli, tetracycline-resistant E. coli, third-generation cephalosporin-resistant E. coli, Enterococcus, tetracycline-resistant Enterococcus, and erythromycin-resistant Enterococcus. Metagenomic DNA was isolated from each June fecal swab and pen surface material sample. Metagenomic DNA samples were pooled by pen for 14 fecal and 14 pen surface material samples. Quantitative PCR was employed to assess the abundances of the following 10 antimicrobial resistance genes: aac(6')-Ie-aph(2″)-Ia, aadA1, blaCMY-2, blaCTX-M, blaKPC-2, erm(B), mecA, tet(A), tet(B), and tet(M). Nasal swab samples (n = 335) were obtained from each steer during each sample period and cultured for the presence of Staphylococcus aureus and methicillin-resistant S. aureus. Of these measurements, only January and June mean fecal swab erythromycin-resistant Enterococcus colony counts for tylosin-treated cattle were significantly higher (P ≤ 0.05) than the range of mean values for control treatments. These results suggest that in-feed tylosin through the end of finishing has a narrow and minimal antimicrobial resistance impact.},
}

@article {pmid31968684,
year = {2020},
author = {Carrai, M and Van Brussel, K and Shi, M and Li, CX and Chang, WS and Munday, JS and Voss, K and McLuckie, A and Taylor, D and Laws, A and Holmes, EC and Barrs, VR and Beatty, JA},
title = {Identification of A Novel Papillomavirus Associated with Squamous Cell Carcinoma in A Domestic Cat.},
journal = {Viruses},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/v12010124},
pmid = {31968684},
issn = {1999-4915},
support = {D15FE-001//Morris Animal Foundation/ ; FL170100022//Australian Research Council/ ; },
abstract = {Papillomaviruses infect the skin and mucosal surfaces of diverse animal hosts with consequences ranging from asymptomatic colonization to highly malignant epithelial cancers. Increasing evidence suggests a role for papillomaviruses in the most common cutaneous malignancy of domestic cats, squamous cell carcinoma (SCC). Using total DNA sequencing we identified a novel feline papillomavirus in a nasal biopsy taken from a cat presenting with both nasal cavity lymphoma and recurrent squamous cell carcinoma affecting the nasal planum. We designate this novel virus as Felis catus papillomavirus 6 (FcaPV6). The complete FcaPV6 7453 bp genome was similar to those of other feline papillomaviruses and phylogenetic analysis revealed that it was most closely related to FcaPV3, although was distinct enough to represent a new viral type. Classification of FcaPV6 in a new genus alongside FcaPVs 3, 4 and 5 is supported. Archived excisional biopsy of the SCC, taken 20 months prior to presentation, was intensely positive on p16 immunostaining. FcaPV6, amplified using virus-specific, but not consensus, PCR, was the only papillomavirus detected in DNA extracted from the SCC. Conversely, renal lymphoma, sampled at necropsy two months after presentation, tested negative on FcaPV6-specific PCR. In sum, using metagenomics we demonstrate the presence of a novel feline papillomavirus in association with cutaneous squamous cell carcinoma.},
}

@article {pmid31968354,
year = {2020},
author = {Schulz, F and Roux, S and Paez-Espino, D and Jungbluth, S and Walsh, D and Denef, VJ and McMahon, KD and Konstantinidis, KT and Eloe-Fadrosh, EA and Kyrpides, N and Woyke, T},
title = {Giant virus diversity and host interactions through global metagenomics.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-020-1957-x},
pmid = {31968354},
issn = {1476-4687},
abstract = {Current knowledge about the nucleocytoplasmic large DNA viruses (NCLDV) is largely derived from viral isolates co-cultivated with protists and algae. Building on the rapidly increasing wealth of publicly available metagenome data, we reconstructed 2,074 NCLDV genomes from sampling sites spanning the globe. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysing 58,023 metagenomic major capsid proteins of large and giant viruses revealed global distribution patterns and underlined their cosmopolitan nature. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, revealing host reprogramming as a likely common strategy in the NCLDV. Furthermore, horizontal gene transfer inferences connected viral lineages to diverse eukaryotic hosts. We anticipate that the vast diversity of NCLDV revealed here on a global scale will establish giant viruses as key ecosystem players across Earth's biomes, associated with most major eukaryotic lineages.},
}

@article {pmid31968006,
year = {2020},
author = {Nott, MA and Driscoll, HE and Takeda, M and Vangala, M and Corsi, SR and Tighe, SW},
title = {Advanced biofilm analysis in streams receiving organic deicer runoff.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0227567},
doi = {10.1371/journal.pone.0227567},
pmid = {31968006},
issn = {1932-6203},
abstract = {Prolific heterotrophic biofilm growth is a common occurrence in airport receiving streams containing deicers and anti-icers, which are composed of low-molecular weight organic compounds. This study investigated biofilm spatiotemporal patterns and responses to concurrent and antecedent (i.e., preceding biofilm sampling) environmental conditions at stream sites upstream and downstream from Milwaukee Mitchell International Airport in Milwaukee, Wisconsin, during two deicing seasons (2009-2010; 2010-2011). Biofilm abundance and community composition were investigated along spatial and temporal gradients using field surveys and microarray analyses, respectively. Given the recognized role of Sphaerotilus in organically enriched environments, additional analyses were pursued to specifically characterize its abundance: a consensus sthA sequence was determined via comparison of whole metagenome sequences with a previously identified sthA sequence, the primers developed for this gene were used to characterize relative Sphaerotilus abundance using quantitative real-time PCR, and a Sphaerotilus strain was isolated to validate the determined sthA sequence. Results indicated that biofilm abundance was stimulated by elevated antecedent chemical oxygen demand concentrations, a surrogate for deicer concentrations, with minimal biofilm volumes observed when antecedent chemical oxygen demand concentrations remained below 48 mg/L. Biofilms were composed of diverse communities (including sheathed bacterium Thiothrix) whose composition appeared to shift in relation to antecedent temperature and chemical oxygen demand. The relative abundance of sthA correlated most strongly with heterotrophic biofilm volume (positive) and dissolved oxygen (negative), indicating that Sphaerotilus was likely a consistent biofilm member and thrived under low oxygen conditions. Additional investigations identified the isolate as a new strain of Sphaerotilus montanus (strain KMKE) able to use deicer components as carbon sources and found that stream dissolved oxygen concentrations related inversely to biofilm volume as well as to antecedent temperature and chemical oxygen demand. The airport setting provides insight into potential consequences of widescale adoption of organic deicers for roadway deicing.},
}

@article {pmid31965894,
year = {2020},
author = {Lee, NY and Yoon, SJ and Han, DH and Gupta, H and Youn, GS and Shin, MJ and Ham, YL and Kwak, MJ and Kim, BY and Yu, JS and Lee, DY and Park, TS and Park, SH and Kim, BK and Joung, HC and Choi, IS and Hong, JT and Kim, DJ and Han, SH and Suk, KT},
title = {Lactobacillus and Pediococcus ameliorate progression of non-alcoholic fatty liver disease through modulation of the gut microbiome.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/19490976.2020.1712984},
pmid = {31965894},
issn = {1949-0984},
abstract = {Targeting the gut-liver axis by modulating the gut-microbiome can be a promising therapeutic approach in nonalcoholic fatty liver disease (NAFLD). The aim of this study was to evaluate the effects of single species and a combination of Lactobacillus and Pediococcus in NAFLD mice model. Six-week male C57BL/6J mice were divided into 9 groups (n = 10/group; normal, Western diet, and 7 Western diet-strains [109 CFU/g, 8 weeks]). The strains used were L. bulgaricus, L. casei, L. helveticus, P. pentosaceus KID7, and three combinations (1: L. casei+L. helveticus, 2: L. casei+L. helveticus+P. pentosaceus KID7, and 3: L. casei+L. helveticus+L. bulgaricus). Liver/Body weight ratio, serum and stool analysis, liver pathology, and metagenomics by 16S rRNA-sequencing were examined. In the liver/body ratio, L. bulgaricus (5.1 ± 0.5), L. helveticus (5.2 ± 0.4), P. pentosaceus KID7 (5.5 ± 0.5), and combination1 and 2 (4.2 ± 0.6 and 4.8 ± 0.7) showed significant reductions compared with Western (6.2 ± 0.6)(p < 0.001). In terms of cholesterol and steatosis/inflammation/NAFLD activity, all groups except for L. casei were associated with an improvement (p < .05). The elevated level of tumor necrosis factor-α/interleukin-1β (pg/ml) in Western (65.8 ± 7.9/163.8 ± 12.2) was found to be significantly reduced in L. bulgaricus (24.2 ± 1.0/58.9 ± 15.3), L. casei (35.6 ± 2.1/62.9 ± 6.0), L. helveticus (43.4 ± 3.2/53.6 ± 7.5), and P. pentosaceus KID7 (22.9 ± 3.4/59.7 ± 12.2)(p < 0.01). Cytokines were improved in the combination groups. In metagenomics, each strains revealed a different composition and elevated Firmicutes/Bacteroidetes ratio in the western (47.1) was decreased in L. bulgaricus (14.5), L. helveticus (3.0), and P. pentosaceus KID7 (13.3). L. bulgaricus, L. casei, L. helveticus, and P. pentosaceus KID7 supplementation can improve NAFLD-progression by modulating gut-microbiome and inflammatory pathway.},
}

@article {pmid31965841,
year = {2019},
author = {Rianda, D and Agustina, R and Setiawan, EA and Manikam, NRM},
title = {Effect of probiotic supplementation on cognitive function in children and adolescents: a systematic review of randomised trials.},
journal = {Beneficial microbes},
volume = {10},
number = {8},
pages = {873-882},
doi = {10.3920/BM2019.0068},
pmid = {31965841},
issn = {1876-2891},
abstract = {Available reviews have shown potential effects of probiotics on neurobehavioral outcomes through 'gut-brain axis' mechanism in adults. However, reviews on cognitive function in children and adolescents are lacking. Therefore, we conducted a systematic review of randomised controlled trials (RCTs) of the effect of probiotic supplementation on cognitive function in children and adolescents. A search of four databases (Cochrane Central Register of Controlled Trials, PsycARTICLES, Scopus, PubMed) was conducted to identify RCTs published from January 1990 to December 2018. Seven studies met the inclusion criteria and their cognitive outcomes were analysed. Only one study found a positive result with Lactobacillus rhamnosus GG (LGG) 1×1010 cfu supplementation with outcomes on attention deficit hyperactivity disorder (ADHD) or Asperger syndrome (AS) manifestations as diagnosed using the International Classification of Diseases-10 criteria. The supplementations were administered to Finnish mothers for 4 weeks before delivery and continuously given for 6 months after delivery if they breastfed, or to the children. ADHD or AS was diagnosed at the age of 13 years in 17.1% children in the placebo and none in the probiotic group (P=0.008). This study found significant differences in species composition and number of cells belonging to the genus Bifidobacterium between healthy children and children who later developed ADHD or AS at different time points. Six remaining studies with varying strains, durations of intervention, start-time of administration, and outcomes demonstrated no difference in cognition after probiotic supplementation. Metagenomic analyses on gut microbiota composition were not performed in any of these studies. In conclusion, the favourable effect of probiotic supplementation on cognitive function in children and adolescents was observed in one study with LGG supplementation by a risk reduction of developing ADHD or AS (i.e. autism). More long-term and follow-up trials using probiotics identifying the effect on cognition are warranted before routine use.},
}

@article {pmid31965701,
year = {2020},
author = {Muñoz-Arenas, LC and Fusaro, C and Hernández-Guzmán, M and Dendooven, L and Estrada-Torres, A and Navarro-Noya, YE},
title = {Soil microbial diversity drops with land use change in a high mountain temperate forest: a metagenomics survey.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12822},
pmid = {31965701},
issn = {1758-2229},
abstract = {Land-use change has been identified as the most severe threat to biodiversity. Soils are important biodiversity reservoirs, but to what extent conversion of high altitude temperate forest to arable land affects taxonomic and functional soil biodiversity is still largely unknown. Shotgun metagenomics was used to determine the taxonomic and functional diversity of Bacteria, Archaea and DNA Virus in terms of effective number of species in high altitude temperate Oak and Pine-oak forest and arable soils from Mexico. Generally, the soil ecosystem maintained its microbial species richness notwithstanding land-use change. Archaea diversity was not affected by land-use change, but the bacterial diversity decreased with 45-55% when the oak forest was converted to arable land and 65-75% when the pine-oak forest was. Loss in bacterial diversity as a result of land-use change was positively correlated (R2 = 0.41) with the 10 to 25% loss in functional diversity. The archaeal communities were evener than the bacterial ones, which might explain their different response to land-use change. We expected a decrease in DNA viral communities as the bacterial diversity decreased, i.e. their potential hosts. However, a higher viral diversity was found in the arable than in the forest soils. It was found that converting high altitude oak and pine-oak forests to arable land more than halved the bacterial diversity, but did not affect the archaeal and even increased the viral diversity. This article is protected by copyright. All rights reserved.},
}

@article {pmid31965087,
year = {2020},
author = {Deng, X and Achari, A and Federman, S and Yu, G and Somasekar, S and Bártolo, I and Yagi, S and Mbala-Kingebeni, P and Kapetshi, J and Ahuka-Mundeke, S and Muyembe-Tamfum, JJ and Ahmed, AA and Ganesh, V and Tamhankar, M and Patterson, JL and Ndembi, N and Mbanya, D and Kaptue, L and McArthur, C and Muñoz-Medina, JE and Gonzalez-Bonilla, CR and López, S and Arias, CF and Arevalo, S and Miller, S and Stone, M and Busch, M and Hsieh, K and Messenger, S and Wadford, DA and Rodgers, M and Cloherty, G and Faria, NR and Thézé, J and Pybus, OG and Neto, Z and Morais, J and Taveira, N and Hackett, JR and Chiu, CY},
title = {Author Correction: Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-020-0671-7},
pmid = {31965087},
issn = {2058-5276},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid31964767,
year = {2020},
author = {Diener, C and Gibbons, SM and Resendis-Antonio, O},
title = {MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
doi = {10.1128/mSystems.00606-19},
pmid = {31964767},
issn = {2379-5077},
abstract = {Compositional changes in the gut microbiota have been associated with a variety of medical conditions such as obesity, Crohn's disease, and diabetes. However, connecting microbial community composition to ecosystem function remains a challenge. Here, we introduce MICOM, a customizable metabolic model of the human gut microbiome. By using a heuristic optimization approach based on L2 regularization, we were able to obtain a unique set of realistic growth rates that corresponded well with observed replication rates. We integrated adjustable dietary and taxon abundance constraints to generate personalized metabolic models for individual metagenomic samples. We applied MICOM to a balanced cohort of metagenomes from 186 people, including a metabolically healthy population and individuals with type 1 and type 2 diabetes. Model results showed that individual bacterial genera maintained conserved niche structures across humans, while the community-level production of short-chain fatty acids (SCFAs) was heterogeneous and highly individual specific. Model output revealed complex cross-feeding interactions that would be difficult to measure in vivo Metabolic interaction networks differed somewhat consistently between healthy and diabetic subjects. In particular, MICOM predicted reduced butyrate and propionate production in a diabetic cohort, with restoration of SCFA production profiles found in healthy subjects following metformin treatment. Overall, we found that changes in diet or taxon abundances have highly personalized effects. We believe MICOM can serve as a useful tool for generating mechanistic hypotheses for how diet and microbiome composition influence community function. All methods are implemented in an open-source Python package, which is available at https://github.com/micom-dev/micomIMPORTANCE The bacterial communities that live within the human gut have been linked to health and disease. However, we are still just beginning to understand how those bacteria interact and what potential interventions to our gut microbiome can make us healthier. Here, we present a mathematical modeling framework (named MICOM) that can recapitulate the growth rates of diverse bacterial species in the gut and can simulate metabolic interactions within microbial communities. We show that MICOM can unravel the ecological rules that shape the microbial landscape in our gut and that a given dietary or probiotic intervention can have widely different effects in different people.},
}

@article {pmid31964729,
year = {2020},
author = {Flannery, JE and Stagaman, K and Burns, AR and Hickey, RJ and Roos, LE and Giuliano, RJ and Fisher, PA and Sharpton, TJ},
title = {Gut Feelings Begin in Childhood: the Gut Metagenome Correlates with Early Environment, Caregiving, and Behavior.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
doi = {10.1128/mBio.02780-19},
pmid = {31964729},
issn = {2150-7511},
abstract = {Psychosocial environments impact normative behavioral development in children, increasing the risk of problem behaviors and psychiatric disorders across the life span. Converging evidence demonstrates that early normative development is affected by the gut microbiome, which itself can be altered by early psychosocial environments. However, much of our understanding of the gut microbiome's role in early development stems from nonhuman animal models and predominately focuses on the first years of life, during peri- and postnatal microbial colonization. As a first step to identify if these findings translate to humans and the extent to which these relationships are maintained after initial microbial colonization, we conducted a metagenomic investigation among a cross-sectional sample of early school-aged children with a range of adverse experiences and caregiver stressors and relationships. Our results indicate that the taxonomic and functional composition of the gut microbiome correlates with behavior during a critical period of child development. Furthermore, our analysis reveals that both socioeconomic risk exposure and child behaviors associate with the relative abundances of specific taxa (e.g., Bacteroides and Bifidobacterium species) as well as functional modules encoded in their genomes (e.g., monoamine metabolism) that have been linked to cognition and health. While we cannot infer causality within this study, these findings suggest that caregivers may moderate the gut microbiome's link to environment and behaviors beyond the first few years of life.IMPORTANCE Childhood is a formative period of behavioral and biological development that can be modified, for better or worse, by the psychosocial environment that is in part determined by caregivers. Not only do our own genes and the external environment influence such developmental trajectories, but the community of microbes living in, on, and around our bodies-the microbiome-plays an important role as well. By surveying the gut microbiomes of a cross-sectional cohort of early school-aged children with a range of psychosocial environments and subclinical mental health symptoms, we demonstrated that caregiving behaviors modified the child gut microbiome's association to socioeconomic risk and behavioral dysregulation.},
}

@article {pmid31963525,
year = {2020},
author = {García-López, R and Cornejo-Granados, F and Lopez-Zavala, AA and Sánchez-López, F and Cota-Huízar, A and Sotelo-Mundo, RR and Guerrero, A and Mendoza-Vargas, A and Gómez-Gil, B and Ochoa-Leyva, A},
title = {Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota.},
journal = {Microorganisms},
volume = {8},
number = {1},
pages = {},
doi = {10.3390/microorganisms8010134},
pmid = {31963525},
issn = {2076-2607},
support = {IA203118, IN215520//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; 2019 CIC-UNAM-CIAD, 2019 CIC-UNAM-UNISON//Actividades de Intercambio Académico UNAM-CIC/ ; },
abstract = {The shrimp has become the most valuable traded marine product in the world, and its microbiota plays an essential role in its development and overall health status. Massive high-throughput sequencing techniques using several hypervariable regions of the 16S rRNA gene are broadly applied in shrimp microbiota studies. However, it is essential to consider that the use of different hypervariable regions can influence the obtained data and the interpretation of the results. The present study compares the shrimp microbiota structure and composition obtained by three types of amplicons: one spanning both the V3 and V4 hypervariable regions (V3V4), one for the V3 region only (V3), and one for the V4 region only (V4) using the same experimental and bioinformatics protocols. Twenty-four samples from hepatopancreas and intestine were sequenced and evaluated using the GreenGenes and silva reference databases for clustering and taxonomic classification. In general, the V3V4 regions resulted in higher richness and diversity, followed by V3 and V4. All three regions establish an apparent clustering effect that discriminates between the two analyzed organs and describe a higher richness for the intestine and a higher diversity for the hepatopancreas samples. Proteobacteria was the most abundant phyla overall, and Cyanobacteria was more common in the intestine, whereas Firmicutes and Actinobacteria were more prevalent in hepatopancreas samples. Also, the genus Vibrio was significantly abundant in the intestine, as well as Acinetobacter and Pseudomonas in the hepatopancreas suggesting these taxa as markers for their respective organs independently of the sequenced region. The use of a single hypervariable region such as V3 may be a low-cost alternative that enables an adequate description of the shrimp microbiota, allowing for the development of strategies to continually monitor the microbial communities and detect changes that could indicate susceptibility to pathogens under real aquaculture conditions while the use of the full V3V4 regions can contribute to a more in-depth characterization of the microbial composition.},
}

@article {pmid31963501,
year = {2020},
author = {Mancabelli, L and Milani, C and Lugli, GA and Fontana, F and Turroni, F and van Sinderen, D and Ventura, M},
title = {The Impact of Primer Design on Amplicon-Based Metagenomic Profiling Accuracy: Detailed Insights into Bifidobacterial Community Structure.},
journal = {Microorganisms},
volume = {8},
number = {1},
pages = {},
doi = {10.3390/microorganisms8010131},
pmid = {31963501},
issn = {2076-2607},
abstract = {Next Generation Sequencing (NGS) technologies have overcome the limitations of cultivation-dependent approaches and allowed detailed study of bacterial populations that inhabit the human body. The consortium of bacteria residing in the human intestinal tract, also known as the gut microbiota, impacts several physiological processes important for preservation of the health status of the host. The most widespread microbiota profiling method is based on amplification and sequencing of a variable portion of the 16S rRNA gene as a universal taxonomic marker among members of the Bacteria domain. Despite its popularity and obvious advantages, this 16S rRNA gene-based approach comes with some important limitations. In particular, the choice of the primer pair for amplification plays a major role in defining the accuracy of the reconstructed bacterial profiles. In the current study, we performed an in silico PCR using all currently described 16S rRNA gene-targeting primer pairs (PP) in order to assess their efficiency. Our results show that V3, V4, V5, and V6 were the optimal regions on which to design 16S rRNA metagenomic primers. In detail, PP39 (Probio_Uni/Probio_Rev), PP41 (341F/534R), and PP72 (970F/1050R) were the most suitable primer pairs with an amplification efficiency of >98.5%. Furthermore, the Bifidobacterium genus was examined as a test case for accurate evaluation of intra-genus performances at subspecies level. Intriguingly, the in silico analysis revealed that primer pair PP55 (527f/1406r) was unable to amplify the targeted region of any member of this bacterial genus, while several other primer pairs seem to rather inefficiently amplify the target region of the main bifidobacterial taxa. These results highlight that selection of a 16S rRNA gene-based PP should be done with utmost care in order to avoid biases in microbiota profiling results.},
}

@article {pmid31963239,
year = {2020},
author = {Burton, KJ and Krüger, R and Scherz, V and Münger, LH and Picone, G and Vionnet, N and Bertelli, C and Greub, G and Capozzi, F and Vergères, G},
title = {Trimethylamine-N-Oxide Postprandial Response in Plasma and Urine Is Lower After Fermented Compared to Non-Fermented Dairy Consumption in Healthy Adults.},
journal = {Nutrients},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/nu12010234},
pmid = {31963239},
issn = {2072-6643},
support = {14/JP-HDHL/B3076//Joint Programming Initiative A healthy diet for a healthy life/ ; 170280//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {Trimethylamine-N-oxide (TMAO) can be produced by the gut microbiota from dietary substrates and is associated with cardiovascular disease. While dairy products contain TMAO precursors, the effect of fermented dairy on TMAO metabolism remains unclear. We used plasma and urine samples collected for two randomised cross-over studies to evaluate the effects of fermented dairy consumption on TMAO metabolism. In Study 1, thirteen healthy young men tested a yogurt and an acidified milk during postprandial tests and a two-week daily intervention. In Study 2, ten healthy adults tested milk and cheese during postprandial tests. TMAO and five related metabolites were measured in plasma and urine by LC-MS/MS and NMR. Faecal microbiota composition was assessed in Study 1 (16S rRNA metagenomics sequencing). Fermented milk products were associated with lower postprandial TMAO responses than non-fermented milks in urine (Study 1, p = 0.01; Study 2, p = 0.02) and in plasma, comparing yogurt and acidified milk (Study 1, p = 0.04). Daily consumption of dairy products did not differentially affect fasting TMAO metabolites. Significant correlations were observed between microbiota taxa and circulating or urinary TMAO concentrations. Fermentation of dairy products appear, at least transiently, to affect associations between dairy products and circulating TMAO levels.},
}

@article {pmid31963174,
year = {2020},
author = {Kwok, KTT and Nieuwenhuijse, DF and Phan, MVT and Koopmans, MPG},
title = {Virus Metagenomics in Farm Animals: A Systematic Review.},
journal = {Viruses},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/v12010107},
pmid = {31963174},
issn = {1999-4915},
support = {91217040//ZonMw/ ; 643476//Horizon 2020/ ; 799417//Horizon 2020/ ; },
abstract = {A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the "FAIR" (Findable, Accessible, Interoperable, and Reusable) data principles.},
}

@article {pmid31757825,
year = {2020},
author = {Frankel-Bricker, J and Buerki, S and Feris, KP and White, MM},
title = {Influences of a Prolific Gut Fungus (Zancudomyces culisetae) on Larval and Adult Mosquito (Aedes aegypti)-Associated Microbiota.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {3},
pages = {},
doi = {10.1128/AEM.02334-19},
pmid = {31757825},
issn = {1098-5336},
abstract = {Adult mosquitoes inherit a bacterial community from larvae via transstadial transmission, an understudied process that may influence host-microbe interactions. Microbes contribute to important host life history traits, and analyzing transmitted microbial communities, the interrelationship between larval and adult-associated microbiota, and factors influencing host-microbe relationships provides targets for research. During its larval stage, the yellow fever mosquito (Aedes aegypti) hosts the trichomycete gut fungus Zancudomyces culisetae, and fungal colonization coincides with environmental perturbations in the digestive tract microecosystem. Natural populations are differentially exposed to fungi, thereby potentially harboring distinct microbiota and experiencing disparate host-microbe interactions. This study's objectives were to characterize larval and initial adult microbiomes, investigate variation in diversity and distribution of microbial communities across individuals, and assess whether larval fungal colonization impacted microbiomes at these developmental stages. Laboratory-based fungal infestation assays, sequencing of 16S rRNA gene amplicons, and bacterial load quantification protocols revealed that initial adult microbiomes varied in diversity and distribution. Larval fungal colonization had downstream effects on initial adult microbiomes, significantly reducing microbial community variation, shifting relative abundances of certain bacterial families, and influencing transstadial transmission outcomes of particular genera. Further, abundances of several families consistently decreased in adults relative to levels in larvae, possibly reflecting impacts of host development on specific bacterial taxa. These findings demonstrated that a prolific gut fungus impacted mosquito-associated microbiota at two developmental stages in an insect connected with global human health.IMPORTANCE Mosquitoes are widespread vectors of numerous human pathogens and harbor microbiota known to affect host phenotypic traits. However, little research has directly investigated how bacterial communities associated with larvae and adults are connected. We characterized whole-body bacterial communities in mosquito larvae preceding pupation and in newly emerged adults, and investigated whether a significant biotic factor, fungal colonization of the larval hindgut, impacted these microbiomes. Results showed that fungal colonization reduced microbial community variation across individuals and differentially impacted the outcomes of transstadial transmission for certain bacterial genera, revealing downstream effects of the fungus on initial adult microbiomes. The importance of our research is in providing a thorough comparative analysis of whole-body microbiota harbored in larvae and adults of the yellow fever mosquito (Aedes aegypti) and in demonstrating the important role a widespread gut fungus played in a host-associated microbiome.},
}

@article {pmid31454888,
year = {2019},
author = {Borghi, E and Vignoli, A},
title = {Rett Syndrome and Other Neurodevelopmental Disorders Share Common Changes in Gut Microbial Community: A Descriptive Review.},
journal = {International journal of molecular sciences},
volume = {20},
number = {17},
pages = {},
doi = {10.3390/ijms20174160},
pmid = {31454888},
issn = {1422-0067},
mesh = {Animals ; Biodiversity ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Neurodevelopmental Disorders/diagnosis/*etiology ; Phenotype ; Rett Syndrome/diagnosis/*etiology ; },
abstract = {In this narrative review, we summarize recent pieces of evidence of the role of microbiota alterations in Rett syndrome (RTT). Neurological problems are prominent features of the syndrome, but the pathogenic mechanisms modulating its severity are still poorly understood. Gut microbiota was recently demonstrated to be altered both in animal models and humans with different neurodevelopmental disorders and/or epilepsy. By investigating gut microbiota in RTT cohorts, a less rich microbial community was identified which was associated with alterations of fecal microbial short-chain fatty acids. These changes were positively correlated with severe clinical outcomes. Indeed, microbial metabolites can play a crucial role both locally and systemically, having dynamic effects on host metabolism and gene expression in many organs. Similar alterations were found in patients with autism and down syndrome as well, suggesting a potential common pathway of gut microbiota involvement in neurodevelopmental disorders.},
}

Animals
Biodiversity
Dysbiosis
*Gastrointestinal Microbiome
Humans
Metagenome
Metagenomics/methods
Neurodevelopmental Disorders/diagnosis/*etiology
Phenotype
Rett Syndrome/diagnosis/*etiology

@article {pmid31962124,
year = {2020},
author = {Niu, J and Li, XL and Wu, YL and Sun, QZ and Zhang, W and Cao, M and Wang, JJ},
title = {RNA virome screening in diverse but ecologically related citrus pests reveals potential virus-host interactions.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {107329},
doi = {10.1016/j.jip.2020.107329},
pmid = {31962124},
issn = {1096-0805},
abstract = {As an evergreen ecosystem, citrus orchards have specialized pest species and stable ecological homeostasis; thus, they provide an ideal model for investigating RNA viromes in diverse but ecologically related species. For this purpose, we collected specialized citrus pests from three classes of invertebrates, Insecta, Arachnida, and Gastropoda and we constructed two kinds of libraries (RNA and small RNA) for the pests by deep sequencing. In total, six virus-derived sequences were identified, including four Picornavirales, one Jingchuvirales and one Nidovirales. The picornavirus-derived small RNAs showed significant small RNA peaks and symmetric distribution patterns along the genome, which suggests these viruses infected the hosts and triggered host antiviral immunity RNA interference. Screening of virus-derived sequences in multiple species of citrus pests (n=10 per species) showed that Eotetranychus kankitus picorna-like virus and Tetranychus urticae mivirus may be present in multiple pests. Our investigation in citrus pests confirmed that RNA viruses revealed by metagenomics could impact host immunity (e.g. RNAi). An approach with parallel deep sequencing of RNAs and small RNAs is useful not only for viral discoveries but also for understanding virus-host interactions of ecologically related but divergent pest species.},
}

@article {pmid31961856,
year = {2020},
author = {Wise, EL and Márquez, S and Mellors, J and Paz, V and Atkinson, B and Gutierrez, B and Zapata, S and Coloma, J and Pybus, OG and Jackson, SK and Trueba, G and Fejer, G and Logue, CH and Pullan, ST},
title = {Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing.},
journal = {PLoS neglected tropical diseases},
volume = {14},
number = {1},
pages = {e0007897},
doi = {10.1371/journal.pntd.0007897},
pmid = {31961856},
issn = {1935-2735},
abstract = {Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published qRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an qRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68-99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens.},
}

@article {pmid31961432,
year = {2020},
author = {Jones, CMA and Connors, J and Dunn, KA and Bielawski, JP and Comeau, AM and Langille, MGI and Van Limbergen, J},
title = {Bacterial Taxa and Functions Are Predictive of Sustained Remission Following Exclusive Enteral Nutrition in Pediatric Crohn's Disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaa001},
pmid = {31961432},
issn = {1536-4844},
abstract = {BACKGROUND: The gut microbiome is extensively involved in induction of remission in pediatric Crohn's disease (CD) patients by exclusive enteral nutrition (EEN). In this follow-up study of pediatric CD patients undergoing treatment with EEN, we employ machine learning models trained on baseline gut microbiome data to distinguish patients who achieved and sustained remission (SR) from those who did not achieve remission nor relapse (non-SR) by 24 weeks.

METHODS: A total of 139 fecal samples were obtained from 22 patients (8-15 years of age) for up to 96 weeks. Gut microbiome taxonomy was assessed by 16S rRNA gene sequencing, and functional capacity was assessed by metagenomic sequencing. We used standard metrics of diversity and taxonomy to quantify differences between SR and non-SR patients and to associate gut microbial shifts with fecal calprotectin (FCP), and disease severity as defined by weighted Pediatric Crohn's Disease Activity Index. We used microbial data sets in addition to clinical metadata in random forests (RFs) models to classify treatment response and predict FCP levels.

RESULTS: Microbial diversity did not change after EEN, but species richness was lower in low-FCP samples (<250 µg/g). An RF model using microbial abundances, species richness, and Paris disease classification was the best at classifying treatment response (area under the curve [AUC] = 0.9). KEGG Pathways also significantly classified treatment response with the addition of the same clinical data (AUC = 0.8). Top features of the RF model are consistent with previously identified IBD taxa, such as Ruminococcaceae and Ruminococcus gnavus.

CONCLUSIONS: Our machine learning approach is able to distinguish SR and non-SR samples using baseline microbiome and clinical data.},
}

@article {pmid31961065,
year = {2020},
author = {Dunn, CM and Velasco, C and Rivas, A and Andrews, M and Garman, C and Jacob, PB and Jeffries, MA},
title = {Identification of cartilage microbial DNA signatures and associations with knee and hip osteoarthritis.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.41210},
pmid = {31961065},
issn = {2326-5205},
abstract = {OBJECTIVES: Alterations of the gut microbiota have been implicated in many forms of arthritis, but an examination of cartilage microbial patterns have not been performed. The objective of this study was to characterize the microbial DNA profile of articular cartilage and determine changes associated with osteoarthritis (OA).

METHODS: 16s rRNA gene deep sequencing was performed on eroded and intact cartilage samples from knee and hip OA patients and cadaveric controls. Microbial DNA diversity was assessed, groups compared, and metagenomic profiles reconstructed. Confirmation was performed in an independent cohort by clade-specific qPCR. Human results were compared to cartilage from OA-susceptible C57BL6 and OA-resistant MRL/MpJ mice. Germ-free C57BL6 mouse cartilage was analyzed as a methodological control.

RESULTS: Alpha diversity was reduced in human OA vs. control (p<0.0001), and in hip samples vs. knees (p<0.0001). Numerous clades were different in human OA vs. controls, similar findings were noted in murine B6 vs. MRL comparisons. Hip samples were microbiologically distinct from knee samples. OA microbial DNA demonstrated increased Gram-negative constituents (p=0.02). Functional analysis demonstrated increases in lipopolysaccharide production (p=9.9E-3), phosphatidylinositol signaling (p=4.2E-4), and nitrogen metabolism (p=8E-3) and decreases in sphingolipid metabolism (p=7.7E-4) associated with OA.

CONCLUSIONS: Our study reveals a microbial DNA signature in human and mouse cartilage. We find alterations in this signature, including increases in Gram-negative constituents, during the development and progression of human OA. Furthermore, we identified strain-specific signatures within mouse cartilage that mirror human patterns. The establishment and potential pathogenic role of these DNA signatures deserve further study.},
}

@article {pmid31960273,
year = {2020},
author = {Wan, P and Chen, J},
title = {A Calm, Dispassionate Look at Skin Microbiota in Atopic Dermatitis: An Integrative Literature Review.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
doi = {10.1007/s13555-020-00352-4},
pmid = {31960273},
issn = {2193-8210},
support = {YJ-SCMC2017-12//Foundation of Shanghai Children's Medical Center, School of Medicine, Shanghai Jiaotong University/ ; },
abstract = {Atopic dermatitis (AD) is a chronic common inflammatory skin disorder with clinical characteristics of pruritic, dry, and recurrent flares that involve the whole body. Recent studies have demonstrated that the skin microbiota, characterized by an overgrowth of Staphylococcus aureus (S. aureus), plays a critical role in the manifestation of AD. There is striking evidence that skin microbiota can modulate the development and progression of AD. Therefore, more and more therapeutic approaches are adopted for modifying skin microbiota. Here we discuss the role of skin microbiota in the etiology and maintenance of AD; furthermore, we summarize the effects of therapeutic treatments on skin microbiota in AD based on published literature. With the help of the theoretical guidance suggested by microbial metagenome analysis, the reconstitution of microbiota should be a promising way to harness the pathogens of AD and could be used as a brand-new therapeutic strategy in clinical trials. We believe that the targeted therapy of dysbiosis in AD may possibly become a unique approach to an integrated treatment program in the near future.},
}

@article {pmid31960092,
year = {2020},
author = {Jongman, M and Carmichael, PC and Bill, M},
title = {Technological Advances in Phytopathogen Detection and Metagenome Profiling Techniques.},
journal = {Current microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00284-020-01881-z},
pmid = {31960092},
issn = {1432-0991},
abstract = {The use of advanced molecular methods in plant pathology and applied microbiology has necessitated for more accurate, rapid detection and identification of plant pathogens. This is particularly significant given accelerated emergence of virulence that leads to increased prevalence of plant pathogens. Thus, the capacity to contain plant pathogens and ultimately disease progression is key to ensuring crop biosecurity and overall food security. Of recent, research on pathogens utilizes a holistic approach focusing on elucidating growth dynamics within the entire biome rather than studying individual or closely related isolates in unison. This has advanced knowledge and information of microbial ecosystem within natural environments in the twenty first century. Applied technological platforms used for rapid detection and profiling microbial biomes in this regard include digital PCR, pyrosequencing, Illumina, DNA microarray and barcoding, Ion torrent, and nanopore. These technologies have been applied in various fields including human health and medicine, marine and animal biology, crop production and water quality research, to mention but a few. Although much has been done and achieved through the development of several technologies, more accuracy is required to circumvent the shortfalls still experienced. This includes integrating existing methods with new applications such as viability PCRs and microbial viability testing. Hence, this review provides critical analysis of some widely used latest technologies in rapid detection and identification of plant pathogens, and profiling plant associated microbiomes that reveal growth dynamics and population diversity. The advantages and limitations of the technologies are also discussed.},
}

@article {pmid31959971,
year = {2020},
author = {Fornelos, N and Franzosa, EA and Bishai, J and Annand, JW and Oka, A and Lloyd-Price, J and Arthur, TD and Garner, A and Avila-Pacheco, J and Haiser, HJ and Tolonen, AC and Porter, JA and Clish, CB and Sartor, RB and Huttenhower, C and Vlamakis, H and Xavier, RJ},
title = {Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-019-0655-7},
pmid = {31959971},
issn = {2058-5276},
support = {P01DK094779//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P40OD010995//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R24DK110499//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54DK102557//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R24DK110499//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54DK102557//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AT009708//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Inflammatory bowel diseases (IBD) are associated with alterations in gut microbial abundances and lumenal metabolite concentrations, but the effects of specific metabolites on the gut microbiota in health and disease remain largely unknown. Here, we analysed the influences of metabolites that are differentially abundant in IBD on the growth and physiology of gut bacteria that are also differentially abundant in IBD. We found that N-acylethanolamines (NAEs), a class of endogenously produced signalling lipids elevated in the stool of IBD patients and a T-cell transfer model of colitis, stimulated growth of species over-represented in IBD and inhibited that of species depleted in IBD in vitro. Using metagenomic sequencing, we recapitulated the effects of NAEs in complex microbial communities ex vivo, with Proteobacteria blooming and Bacteroidetes declining in the presence of NAEs. Metatranscriptomic analysis of the same communities identified components of the respiratory chain as important for the metabolism of NAEs, and this was verified using a mutant deficient for respiratory complex I. In this study, we identified NAEs as a class of metabolites that are elevated in IBD and have the potential to shift gut microbiota towards an IBD-like composition.},
}

@article {pmid31959969,
year = {2020},
author = {Whelan, FJ and Waddell, B and Syed, SA and Shekarriz, S and Rabin, HR and Parkins, MD and Surette, MG},
title = {Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-019-0643-y},
pmid = {31959969},
issn = {2058-5276},
support = {RN214668 - 315549//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; GA #: 793818//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; },
abstract = {Amplicon sequencing (for example, of the 16S rRNA gene) identifies the presence and relative abundance of microbial community members. However, metagenomic sequencing is needed to identify the genetic content and functional potential of a community. Metagenomics is challenging in samples dominated by host DNA, such as those from the skin, tissue and respiratory tract. Here, we combine advances in amplicon and metagenomic sequencing with culture-enriched molecular profiling to study the human microbiota. Using the cystic fibrosis lung as an example, we cultured an average of 82.13% of the operational taxonomic units representing 99.3% of the relative abundance identified in direct sequencing of sputum samples; importantly, culture enrichment identified 63.3% more operational taxonomic units than direct sequencing. We developed the PLate Coverage Algorithm (PLCA) to determine a representative subset of culture plates on which to conduct culture-enriched metagenomics, resulting in the recovery of greater taxonomic diversity-including of low-abundance taxa-with better metagenome-assembled genomes, longer contigs and better functional annotations when compared to culture-independent methods. The PLCA is also applied as a proof of principle to a previously published gut microbiota dataset. Culture-enriched molecular profiling can be used to better understand the role of the human microbiota in health and disease.},
}

@article {pmid31959912,
year = {2020},
author = {Retchless, AC and Kretz, CB and Rodriguez-Rivera, LD and Chen, A and Soeters, HM and Whaley, MJ and Wang, X},
title = {Oropharyngeal microbiome of a college population following a meningococcal disease outbreak.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {632},
doi = {10.1038/s41598-020-57450-8},
pmid = {31959912},
issn = {2045-2322},
abstract = {Asymptomatic oropharyngeal carriage of Neisseria meningitidis peaks in adolescence and young adulthood. Following a meningococcal disease outbreak at a U.S. college, we profiled the oropharyngeal microbiomes of 158 students to identify associations between bacterial community composition and meningococcal carriage or risk factors for carriage, including male gender, smoking, and frequent social mixing. Metagenomic shotgun sequencing identified 268 bacterial taxa at the genus or species level, with Streptococcus, Veillonella, and Rothia species being most abundant. Microbiome composition showed weak associations with meningococcal carriage and risk factors for carriage. N. meningitidis abundance was positively correlated with that of Fusobacterium nucleatum, consistent with hypothesized propionic acid cross-feeding. Additional species had positive abundance correlations with N. meningitidis, including Aggregatibacter aphrophilus, Campylobacter rectus, Catonella morbi, Haemophilus haemolyticus, and Parvimonas micra. N. meningitidis abundance was negatively correlated with unidentified Veillonella species. Several of these species are commonly found in dental plaque, while N. meningitidis is primarily found in the pharynx, suggesting that ecological interactions extend throughout the oral cavity. Although risk factors for meningococcal carriage do not strongly impact most bacterial species in the oropharynx, variation in the upper respiratory tract microbiome may create conditions that are more or less favorable for N. meningitidis carriage.},
}

@article {pmid31959785,
year = {2020},
author = {Moreno-Pino, M and Cristi, A and Gillooly, JF and Trefault, N},
title = {Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {645},
doi = {10.1038/s41598-020-57464-2},
pmid = {31959785},
issn = {2045-2322},
abstract = {Relatively little is known about the role of sponge microbiomes in the Antarctic marine environment, where sponges may dominate the benthic landscape. Specifically, we understand little about how taxonomic and functional diversity contributes to the symbiotic lifestyle and aids in nutrient cycling. Here we use functional metagenomics to investigate the community composition and metabolic potential of microbiomes from two abundant Antarctic sponges, Leucetta antarctica and Myxilla sp. Genomic and taxonomic analyses show that both sponges harbor a distinct microbial community with high fungal abundance, which differs from the surrounding seawater. Functional analyses reveal both sponge-associated microbial communities are enriched in functions related to the symbiotic lifestyle (e.g., CRISPR system, Eukaryotic-like proteins, and transposases), and in functions important for nutrient cycling. Both sponge microbiomes possessed genes necessary to perform processes important to nitrogen cycling (i.e., ammonia oxidation, nitrite oxidation, and denitrification), and carbon fixation. The latter indicates that Antarctic sponge microorganisms prefer light-independent pathways for CO2 fixation mediated by chemoautotrophic microorganisms. Together, these results show how the unique metabolic potential of two Antarctic sponge microbiomes help these sponge holobionts survive in these inhospitable environments, and contribute to major nutrient cycles of these ecosystems.},
}

@article {pmid31959775,
year = {2020},
author = {Cooper, RO and Cressler, CE},
title = {Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {652},
doi = {10.1038/s41598-019-57367-x},
pmid = {31959775},
issn = {2045-2322},
abstract = {The keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions. However, the bacterial species present and functions associated with their genomes are not well understood. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota of Daphnia magna. We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in Daphnia magna. Genes involved in host colonization and immune system evasion were detected across the MAGs. Some metabolic pathways were specific to some MAGs, including sulfur oxidation, nitrate reduction, and flagellar assembly. Amino acid exporters were identified in MAGs identified as important for host fitness, and pathways for key vitamin biosynthesis and export were identified across MAGs. In total, our examination of functions in these MAGs shows a diversity of nutrient acquisition and metabolism pathways present that may benefit the host, as well as genomic signatures of host association and immune system evasion.},
}

@article {pmid31780826,
year = {2019},
author = {Tang, L},
title = {Exploring the chemical space of the human microbiome.},
journal = {Nature methods},
volume = {16},
number = {12},
pages = {1201},
doi = {10.1038/s41592-019-0671-9},
pmid = {31780826},
issn = {1548-7105},
mesh = {Humans ; Metagenome ; *Microbiota ; },
}

Humans
Metagenome
*Microbiota

@article {pmid31957879,
year = {2020},
author = {Arıkan, M and Mitchell, AL and Finn, RD and Gürel, F},
title = {Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics.},
journal = {Journal of food science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1750-3841.14992},
pmid = {31957879},
issn = {1750-3841},
support = {215Z672//Türkiye Bilimsel ve Teknolojik Araştirma Kurumu/ ; 20138//Bilimsel Araştirma Projeleri Birimi, Istanbul Üniversitesi/ ; BB/M011755/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //European Molecular Biology Laboratory/ ; },
abstract = {Kombucha, a fermented tea generated from the co-culture of yeasts and bacteria, has gained worldwide popularity in recent years due to its potential benefits to human health. As a result, many studies have attempted to characterize both its biochemical properties and microbial composition. Here, we have applied a combination of whole metagenome sequencing (WMS) and amplicon (16S rRNA and Internal Transcribed Spacer 1 [ITS1]) sequencing to investigate the microbial communities of homemade Kombucha fermentations from day 3 to day 15. We identified the dominant bacterial genus as Komagataeibacter and dominant fungal genus as Zygosaccharomyces in all samples at all time points. Furthermore, we recovered three near complete Komagataeibacter genomes and one Zygosaccharomyces bailii genome and then predicted their functional properties. Also, we determined the broad taxonomic and functional profile of plasmids found within the Kombucha microbial communities. Overall, this study provides a detailed description of the taxonomic and functional systems of the Kombucha microbial community. Based on this, we conject that the functional complementarity enables metabolic cross talks between Komagataeibacter species and Z. bailii, which helps establish the sustained a relatively low diversity ecosystem in Kombucha.},
}

@article {pmid31956680,
year = {2020},
author = {Srivastava, R and Srivastava, AK and Ramteke, PW and Gupta, VK and Srivastava, AK},
title = {Metagenome dataset of wheat rhizosphere from Ghazipur region of Eastern Uttar Pradesh.},
journal = {Data in brief},
volume = {28},
number = {},
pages = {105094},
doi = {10.1016/j.dib.2019.105094},
pmid = {31956680},
issn = {2352-3409},
abstract = {Wheat is the major crop in India and like other crops also subjected to influence by microbial communities of the rhizospheric region which are extremely diverse and undoubtedly play a central role in the nutrient cycle, plant productivity and growth promotion. In order to know how changes in the rhizospheric microbial community can make an impact on overall crop function, wheat rhizospheric soil samples from Ghazipur (25.913824 N 83.529715 E) regions of Eastern Uttar Pradesh (Eastern Indogangatic Plain), were collected and analyzed. Full length 16S rRNA gene amplification sequencing was performed to reveal the bacterial community in wheat rhizosphere. A total of 51,909 read were analyzed, out of that only 44,125 reads were classified and 7784 were unclassified using oxford nanopore sequencing and EPI2ME data analysis platform. MinION oxford nanopore sequencing uncovered that dominant phyla were Proteobacteria (68%), followed by firmicutes (13%), bacteroidetes (3%), actinobacteria (3%) and acidobacteria (3%). The data is available at the NCBI - Sequence Read Archive (SRA) with accession number: SRX5275271.},
}

@article {pmid31956606,
year = {2019},
author = {Katagiri, S and Shiba, T and Tohara, H and Yamaguchi, K and Hara, K and Nakagawa, K and Komatsu, K and Watanabe, K and Ohsugi, Y and Maekawa, S and Iwata, T},
title = {Re-initiation of Oral Food Intake Following Enteral Nutrition Alters Oral and Gut Microbiota Communities.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {434},
doi = {10.3389/fcimb.2019.00434},
pmid = {31956606},
issn = {2235-2988},
abstract = {Stroke is associated with multiple forms of disability, including dysphagia. Post-stroke dysphagia increases the risks of pneumonia and mortality and often results in cessation of oral feeding. However, appropriate rehabilitation methods can eventually lead to resumption of oral food intake. This study tried to clarify that re-initiating oral food intake could modify the composition of oral/gut microbial communities in patients with dysphagia. From 78 patients with sub-acute stage of stroke, 11 complete tube feeding subjects without taking antibiotics were enrolled and received rehabilitation for re-initiation of oral food intake, and 8 subjects were brought back to complete oral feeding. Oral and gut microbiota community profiles were evaluated using 16S rRNA sequencing of the saliva and feces samples before and after re-initiation of oral food intake in patients recovering from enteral nutrition under the same nutrient condition. Standard nutrition in the hospital was 1,840 kcal, including protein = 75 g, fat = 45 g, and carbohydrates = 280 g both for tube and oral feeding subjects. Oral food intake increased oral and gut microbiome diversity and altered the composition of the microbiome. Oral and gut microbiome compositions were drastically different; however, the abundance of family Carnobacteriaceae and genus Granulicatella was increased in both the oral and gut microbiome after re-initiation of oral food intake. Although oral microbiota showed more significant changes than the gut microbiota, metagenome prediction revealed the presence of more differentially enriched pathways in the gut. In addition, simpler co-occurrence networks of oral and gut microbiomes, indicating improved dysbiosis of the microbiome, were observed during oral feeding as compared to that during tube feeding. Oral food intake affects oral and gut microbiomes in patients recovering from enteral nutrition. Rehabilitation for dysphagia can modify systemic health by increasing the diversity and altering the composition and co-occurrence network structure of oral and gut microbial communities.},
}

@article {pmid31956235,
year = {2019},
author = {Benderli, NC and Ogai, K and Lloyd, YM and Arios, JP and Jiyarom, B and Awanakam, AH and Esemu, LF and Hori, A and Megnekou, R and Leke, RGF and Kuraishi, T and Okamoto, S and Ekali, GL},
title = {Feasibility of microbial sample collection on the skin from people in Yaoundé, Cameroon.},
journal = {Drug discoveries & therapeutics},
volume = {13},
number = {6},
pages = {360-364},
doi = {10.5582/ddt.2019.01075},
pmid = {31956235},
issn = {1881-784X},
abstract = {Characterization of microbial communities in the skin in healthy individuals and diseased patients holds valuable information for understanding pathogenesis of skin diseases and as a source for developing novel therapies. Notably, resources regarding skin microbiome are limited in developing countries where skin disorders from infectious diseases are extremely common. A simple method for sample collection and processing for skin microbiome studies in such countries is crucial. The aim of this study is to confirm the feasibility of collecting skin microbiota from individuals in Yaoundé, a capital city of Cameroon, and subsequent extraction of bacterial DNA in a resource limited setting. Skin swabs from several individuals in Yaoundé were successfully obtained, and sufficient amount of bacterial 16S ribosomal RNA-coding DNA was collected, which was confirmed by quantitative PCR. The median copy number of 16S ribosomal RNA gene varied across participants and collection sites, with significantly more copies in samples collected from the forehead compared to the left and right forearm, or back. This study demonstrated that collecting surface skin microbes using our swabbing method is feasible in a developing country. We further showed that even with limited resources, we could collect sufficient amount of skin microbiota from the inhabitants in Yaoundé where no studies of skin microbiome were reported, which can be passed to further metagenomic analysis such as next generation sequencing.},
}

@article {pmid31536448,
year = {2019},
author = {Chen, Z and Lin, S and Jiang, Y and Liu, L and Jiang, J and Chen, S and Tong, Y and Wang, P},
title = {Effects of Bread Yeast Cell Wall Beta-Glucans on Mice with Loperamide-Induced Constipation.},
journal = {Journal of medicinal food},
volume = {22},
number = {10},
pages = {1009-1021},
doi = {10.1089/jmf.2019.4407},
pmid = {31536448},
issn = {1557-7600},
mesh = {Acetylcholinesterase/metabolism ; Animals ; Constipation/chemically induced/*drug therapy ; Defecation/drug effects ; *Gastrointestinal Microbiome ; Gastrointestinal Transit/drug effects ; Loperamide/*adverse effects ; Male ; Metagenome ; Mice ; Mice, Inbred BALB C ; Mucin-2/metabolism ; Saccharomyces cerevisiae/*chemistry ; Serotonin/metabolism ; Substance P/metabolism ; Zonula Occludens-1 Protein/metabolism ; beta-Glucans/*pharmacology ; },
abstract = {Constipation is a common gastrointestinal disorder characterized by changes in intestinal habits. Increasing evidence indicates that long-term use of irritant laxatives causes serious side effects. Meanwhile, more than 50% of patients are dissatisfied with sense of use of non-prescriptional laxatives. β-glucans are natural polysaccharides widely found in yeast, fungus, and plants, which have been reported to exhibit various pharmacological effects. The aim of this study was to characterize the effect of β-glucans extracted from the bread yeast cell wall on loperamide-induced constipation mice. Forty mice were fed with loperamide (10 mg/kg) to make the constipation model and a diet supplemented with 2.5, 5, and 10 mg/kg β-glucan. We assessed the defecation frequency, intestinal transit function of mice, as well as used high-throughput sequencing to analyze the intestinal microbiota composition and functional biological profiles data. Meanwhile, we detected expression of neurotransmitters including acetylcholinesterase, substance P, and serotonin (5-HT) and expression of tight junction protein (TJP) including zonula occludens-1 and mucin-2 in distal colon to characterize the possible molecular mechanisms. β-glucans significantly enhanced intestinal motility and provided a possibility to regulate the expression of neurotransmitters and TJP in mice. The intestinal microecological portion of the treatment group partially recovered and was closer to the normal group. This study showed that β-glucans can influence the intestinal microbiota and restore microecological balance to regulate the express of neurotransmitters and TJP to recover intestinal epithelial mechanical barrier. We suggested that β-glucans could be used as an active nutritional supplement to protect the damaged intestinal barrier and help patients who have constipation complications and dysbiosis.},
}

Acetylcholinesterase/metabolism
Animals
Constipation/chemically induced/*drug therapy
Defecation/drug effects
*Gastrointestinal Microbiome
Gastrointestinal Transit/drug effects
Loperamide/*adverse effects
Male
Metagenome
Mice
Mice, Inbred BALB C
Mucin-2/metabolism
Saccharomyces cerevisiae/*chemistry
Serotonin/metabolism
Substance P/metabolism
Zonula Occludens-1 Protein/metabolism
beta-Glucans/*pharmacology

@article {pmid31955296,
year = {2020},
author = {Al Kadi, M and Jung, N and Ito, S and Kameoka, S and Hishida, T and Motooka, D and Nakamura, S and Iida, T and Okuzaki, D},
title = {UNAGI: an automated pipeline for nanopore full-length cDNA sequencing uncovers novel transcripts and isoforms in yeast.},
journal = {Functional & integrative genomics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10142-020-00732-1},
pmid = {31955296},
issn = {1438-7948},
support = {10636830//Japan Society for the Promotion of Science/ ; JPMJCR15G1//Core Research for Evolutional Science and Technology/ ; },
abstract = {Sequencing the entire RNA molecule leads to a better understanding of the transcriptome architecture. SMARTer (Switching Mechanism at 5'-End of RNA Template) is a technology aimed at generating full-length cDNA from low amounts of mRNA for sequencing by short-read sequencers such as those from Illumina. However, short read sequencing such as Illumina technology includes fragmentation that results in bias and information loss. Here, we built a pipeline, UNAGI or UNAnnotated Gene Identifier, to process long reads obtained with nanopore sequencing and compared this pipeline with the standard Illumina pipeline by studying the Saccharomyces cerevisiae transcriptome in full-length cDNA samples generated from two different biological samples: haploid and diploid cells. Additionally, we processed the long reads with another long read tool, FLAIR. Our strand-aware method revealed significant differential gene expression that was masked in Illumina data by antisense transcripts. Our pipeline, UNAGI, outperformed the Illumina pipeline and FLAIR in transcript reconstruction (sensitivity and specificity of 80% and 40% vs. 18% and 34% and 79% and 32%, respectively). Moreover, UNAGI discovered 3877 unannotated transcripts including 1282 intergenic transcripts while the Illumina pipeline discovered only 238 unannotated transcripts. For isoforms profiling, UNAGI also outperformed the Illumina pipeline and FLAIR in terms of sensitivity (91% vs. 82% and 63%, respectively). But the low accuracy of nanopore sequencing led to a closer gap in terms of specificity with Illumina pipeline (70% vs. 63%) and to a huge gap with FLAIR (70% vs 0.02%).},
}

@article {pmid31955099,
year = {2020},
author = {Martínez-Puchol, S and Rusiñol, M and Fernández-Cassi, X and Timoneda, N and Itarte, M and Andrés, C and Antón, A and Abril, JF and Girones, R and Bofill-Mas, S},
title = {Characterisation of the sewage virome: comparison of NGS tools and occurrence of significant pathogens.},
journal = {The Science of the total environment},
volume = {713},
number = {},
pages = {136604},
doi = {10.1016/j.scitotenv.2020.136604},
pmid = {31955099},
issn = {1879-1026},
abstract = {NGS techniques are excellent tools to monitor and identify viral pathogens circulating among the population with some limitations that need to be overcome, especially in complex matrices. Sewage contains a high amount of other microorganisms that could interfere when trying to sequence viruses for which random PCR amplifications are needed before NGS. The selection of appropriate NGS tools is important for reliable identification of viral diversity among the population. We have compared different NGS methodologies (Untargeted Viral Metagenomics, Target Enrichment Sequencing and Amplicon Deep Sequencing) for the detection and characterisation of viruses in urban sewage, focusing on three important human pathogens: papillomaviruses, adenoviruses and enteroviruses. A full picture of excreted viruses was obtained by applying Untargeted Viral Metagenomics, which detected members of four different vertebrate viral families in addition to bacteriophages, plant viruses and viruses infecting other hosts. Target Enrichment Sequencing, using specific vertebrate viral probes, allowed the detection of up to eight families containing human viruses, with high variety of types within the families and with a high genome coverage. By applying Amplicon Deep Sequencing, the diversity of enteroviruses, adenoviruses and papillomaviruses observed was higher than when applying the other two strategies and this technique allowed the subtyping of an enterovirus A71 C1 strain related to a brainstem encephalitis outbreak occurring at the same time in the sampling area. From the data obtained, we concluded that the different strategies studied provided different levels of analysis: TES is the best strategy to obtain a broad picture of human viruses present in complex samples such as sewage. Other NGS strategies are useful for studying the virome of complex samples when also targeting viruses infecting plants, bacteria, invertebrates or fungi (Untargeted Viral Metagenomics) or when observing the variety within a sole viral family is the objective of the study (Amplicon Deep Sequencing).},
}

@article {pmid31954761,
year = {2020},
author = {Monguí, A and Lozano, GL and Handelsman, J and Restrepo, S and Junca, H},
title = {Design and validation of a transposon that promotes expression of genes in episomal DNA.},
journal = {Journal of biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiotec.2020.01.007},
pmid = {31954761},
issn = {1873-4863},
abstract = {Functional metagenomics, or the cloning and expression of DNA isolated directly from environmental samples, represents a source of novel compounds with biotechnological potential. However, attempts to identify such compounds in metagenomic libraries are generally inefficient in part due to lack of expression of heterologous DNA. In this research, the TnC_T7 transposon was developed to supply transcriptional machinery during functional analysis of metagenomic libraries. TnC_T7 contains bidirectional T7 promoters, the gene encoding the T7 RNA polymerase (T7RNAP), and a kanamycin resistance gene. The T7 RNA polymerase gene is regulated by the inducible arabinose promoter (PBAD), thereby facilitating inducible expression of genes adjacent to the randomly integrating transposon. The high processivity of T7RNAP should make this tool particularly useful for obtaining gene expression in long inserts. TnC_T7 functionality was validated by conducting in vitro transposition of pKR-C12 or fosmid pF076_GFPmut3*, carrying metagenomic DNA from soil. We identified transposon insertions that enhanced GFP expression in both vectors, including insertions in which the promoter delivered by the transposon was located as far as 8.7 kb from the GFP gene, indicating the power of the high processivity of the T7 polymerase. The results gathered in this research demonstrate the potential of TnC_T7 to enhance gene expression in functional metagenomic studies.},
}

@article {pmid31953381,
year = {2020},
author = {Vich Vila, A and Collij, V and Sanna, S and Sinha, T and Imhann, F and Bourgonje, AR and Mujagic, Z and Jonkers, DMAE and Masclee, AAM and Fu, J and Kurilshikov, A and Wijmenga, C and Zhernakova, A and Weersma, RK},
title = {Impact of commonly used drugs on the composition and metabolic function of the gut microbiota.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {362},
doi = {10.1038/s41467-019-14177-z},
pmid = {31953381},
issn = {2041-1723},
support = {016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; D16-14//Maag Lever Darm Stichting (Dutch Digestive Foundation)/ ; },
abstract = {The human gut microbiota has now been associated with drug responses and efficacy, while chemical compounds present in these drugs can also impact the gut bacteria. However, drug-microbe interactions are still understudied in the clinical context, where polypharmacy and comorbidities co-occur. Here, we report relations between commonly used drugs and the gut microbiome. We performed metagenomics sequencing of faecal samples from a population cohort and two gastrointestinal disease cohorts. Differences between users and non-users were analysed per cohort, followed by a meta-analysis. While 19 of 41 drugs are found to be associated with microbial features, when controlling for the use of multiple medications, proton-pump inhibitors, metformin, antibiotics and laxatives show the strongest associations with the microbiome. We here provide evidence for extensive changes in taxonomy, metabolic potential and resistome in relation to commonly used drugs. This paves the way for future studies and has implications for current microbiome studies by demonstrating the need to correct for multiple drug use.},
}

@article {pmid31953342,
year = {2020},
author = {Steinke, L and Slysz, GW and Lipton, MS and Klatt, C and Moran, JJ and Romine, MF and Wood, JM and Anderson, G and Bryant, DA and Ward, DM},
title = {Short-term stable isotope probing of proteins reveals taxa incorporating inorganic carbon in a hot spring microbial mat.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.01829-19},
pmid = {31953342},
issn = {1098-5336},
abstract = {The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consist of oxygenic cyanobacteria (Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (Ci), but some evidence suggests that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of Ci incorporation into different taxa, mat samples were incubated with 13C-bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of 13C-label incorporation. 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. 1,417 peptides, derived from 720 proteins, were detectably labeled with 13C. Most 13C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins involved in photosynthesis, Ci fixation, and N2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for Ci fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to Ci fixation. Other taxa showed much lower 13C-bicarbonate incorporation.Importance Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Protein-SIP permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in Ci fixation. Because this pathway imparts a lower degree of selection of isotopically heavy Ci than does the Calvin-Benson-Bassham Cycle, the results suggest a mechanism for why the natural abundance of 13C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the 13C/12C ratios of mat biomass will help geochemists interpret the 13C/12C ratios of organic carbon in the fossil record.},
}

@article {pmid31953333,
year = {2020},
author = {Riiser, ES and Haverkamp, THA and Varadharajan, S and Borgan, Ø and Jakobsen, KS and Jentoft, S and Star, B},
title = {Metagenomic shotgun analyses reveal complex patterns of intra- and interspecific variation in the intestinal microbiomes of codfishes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02788-19},
pmid = {31953333},
issn = {1098-5336},
abstract = {The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we use metagenomic shotgun sequencing of individual specimens to compare the intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) -that have distinct behavior and habitats- and three Gadidae species that occupy a range of ecological niches. Interestingly, we find significantly diverged microbiomes amongst the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species' comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet or a combination there-off comprise major drivers of the intestinal community composition of codfishes.Importance The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g. diet, temperature or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observe distinct microbiomes amongst two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation are more variable. For instance, we do not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii) whose lineages have evolutionary separated over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.},
}

@article {pmid31953253,
year = {2020},
author = {Erawijantari, PP and Mizutani, S and Shiroma, H and Shiba, S and Nakajima, T and Sakamoto, T and Saito, Y and Fukuda, S and Yachida, S and Yamada, T},
title = {Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2019-319188},
pmid = {31953253},
issn = {1468-3288},
abstract = {OBJECTIVE: Recent evidence points to the gut microbiome's involvement in postoperative outcomes, including after gastrectomy. Here, we investigated the influence of gastrectomy for gastric cancer on the gut microbiome and metabolome, and how it related to postgastrectomy conditions.

DESIGN: We performed shotgun metagenomics sequencing and capillary electrophoresis time-of-flight mass spectrometry-based metabolomics analyses on faecal samples collected from participants with a history of gastrectomy for gastric cancer (n=50) and compared them with control participants (n=56).

RESULTS: The gut microbiota in the gastrectomy group showed higher species diversity and richness (p<0.05), together with greater abundance of aerobes, facultative anaerobes and oral microbes. Moreover, bile acids such as genotoxic deoxycholic acid and branched-chain amino acids were differentially abundant between the two groups (linear discriminant analysis (LDA) effect size (LEfSe): p<0.05, q<0.1, LDA>2.0), as were also Kyoto Encyclopedia of Genes and Genomes modules involved in nutrient transport and organic compounds biosynthesis (LEfSe: p<0.05, q<0.1, LDA>2.0).

CONCLUSION: Our results reveal alterations of gut microbiota after gastrectomy, suggesting its association with postoperative comorbidities. The multi-omic approach applied in this study could complement the follow-up of patients after gastrectomy.},
}

@article {pmid31952524,
year = {2020},
author = {Blahak, S and Jenckel, M and Höper, D and Beer, M and Hoffmann, B and Schlottau, K},
title = {Investigations into the presence of nidoviruses in pythons.},
journal = {Virology journal},
volume = {17},
number = {1},
pages = {6},
doi = {10.1186/s12985-020-1279-5},
pmid = {31952524},
issn = {1743-422X},
abstract = {BACKGROUND: Pneumonia and stomatitis represent severe and often fatal diseases in different captive snakes. Apart from bacterial infections, paramyxo-, adeno-, reo- and arenaviruses cause these diseases. In 2014, new viruses emerged as the cause of pneumonia in pythons. In a few publications, nidoviruses have been reported in association with pneumonia in ball pythons and a tiger python. The viruses were found using new sequencing methods from the organ tissue of dead animals.

METHODS: Severe pneumonia and stomatitis resulted in a high mortality rate in a captive breeding collection of green tree pythons. Unbiased deep sequencing lead to the detection of nidoviral sequences. A developed RT-qPCR was used to confirm the metagenome results and to determine the importance of this virus. A total of 1554 different boid snakes, including animals suffering from respiratory diseases as well as healthy controls, were screened for nidoviruses. Furthermore, in addition to two full-length sequences, partial sequences were generated from different snake species.

RESULTS: The assembled full-length snake nidovirus genomes share only an overall genome sequence identity of less than 66.9% to other published snake nidoviruses and new partial sequences vary between 99.89 and 79.4%. Highest viral loads were detected in lung samples. The snake nidovirus was not only present in diseased animals, but also in snakes showing no typical clinical signs.

CONCLUSIONS: Our findings further highlight the possible importance of snake nidoviruses in respiratory diseases and proof multiple circulating strains with varying disease potential. Nidovirus detection in clinical healthy individuals might represent testing during the incubation period or reconvalescence. Our investigations show new aspects of nidovirus infections in pythons. Nidoviruses should be included in routine diagnostic workup of diseased reptiles.},
}

@article {pmid31952477,
year = {2020},
author = {Narayan, NR and Weinmaier, T and Laserna-Mendieta, EJ and Claesson, MJ and Shanahan, F and Dabbagh, K and Iwai, S and DeSantis, TZ},
title = {Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {56},
doi = {10.1186/s12864-019-6427-1},
pmid = {31952477},
issn = {1471-2164},
abstract = {BACKGROUND: Shotgun metagenomic sequencing reveals the potential in microbial communities. However, lower-cost 16S ribosomal RNA (rRNA) gene sequencing provides taxonomic, not functional, observations. To remedy this, we previously introduced Piphillin, a software package that predicts functional metagenomic content based on the frequency of detected 16S rRNA gene sequences corresponding to genomes in regularly updated, functionally annotated genome databases. Piphillin (and similar tools) have previously been evaluated on 16S rRNA data processed by the clustering of sequences into operational taxonomic units (OTUs). New techniques such as amplicon sequence variant error correction are in increased use, but it is unknown if these techniques perform better in metagenomic content prediction pipelines, or if they should be treated the same as OTU data in respect to optimal pipeline parameters.

RESULTS: To evaluate the effect of 16S rRNA sequence analysis method (clustering sequences into OTUs vs amplicon sequence variant error correction into amplicon sequence variants (ASVs)) on the ability of Piphillin to predict functional metagenomic content, we evaluated Piphillin-predicted functional content from 16S rRNA sequence data processed through OTU clustering and error correction into ASVs compared to corresponding shotgun metagenomic data. We show a strong correlation between metagenomic data and Piphillin-predicted functional content resulting from both 16S rRNA sequence analysis methods. Differential abundance testing with Piphillin-predicted functional content exhibited a low false positive rate (< 0.05) while capturing a large fraction of the differentially abundant features resulting from corresponding metagenomic data. However, Piphillin prediction performance was optimal at different cutoff parameters depending on 16S rRNA sequence analysis method. Using data analyzed with amplicon sequence variant error correction, Piphillin outperformed comparable tools, for instance exhibiting 19% greater balanced accuracy and 54% greater precision compared to PICRUSt2.

CONCLUSIONS: Our results demonstrate that raw Illumina sequences should be processed for subsequent Piphillin analysis using amplicon sequence variant error correction (with DADA2 or similar methods) and run using a 99% ID cutoff for Piphillin, while sequences generated on platforms other than Illumina should be processed via OTU clustering (e.g., UPARSE) and run using a 96% ID cutoff for Piphillin. Piphillin is publicly available for academic users (Piphillin server. http://piphillin.secondgenome.com/.).},
}

@article {pmid31952112,
year = {2020},
author = {Chorna, N and Romaguera, J and Godoy-Vitorino, F},
title = {Cervicovaginal Microbiome and Urine Metabolome Paired Analysis Reveals Niche Partitioning of the Microbiota in Patients with Human Papilloma Virus Infections.},
journal = {Metabolites},
volume = {10},
number = {1},
pages = {},
doi = {10.3390/metabo10010036},
pmid = {31952112},
issn = {2218-1989},
support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; 2U54MD007587, U54MD007600/MD/NIMHD NIH HHS/United States ; },
abstract = {In this study, we evaluate the association between vaginal and cervical human papillomavirus infections high-risk types (HPV+H), negative controls (HPV-), the bacterial biota, and urinary metabolites via integration of metagenomics, metabolomics, and bioinformatics analysis. We recently proposed that testing urine as a biofluid could be a non-invasive method for the detection of cervical HPV+H infections by evaluating the association between cervical HPV types and a total of 24 urinary metabolites identified in the samples. As a follow-up study, we expanded the analysis by pairing the urine metabolome data with vaginal and cervical microbiota in selected samples from 19 Puerto Rican women diagnosed with HPV+H infections and HPV- controls, using a novel comprehensive framework, Model-based Integration of Metabolite Observations and Species Abundances 2 (MIMOSA2). This approach enabled us to estimate the functional activities of the cervicovaginal microbiome associated with HPV+H infections. Our results suggest that HPV+H infections could induce changes in physicochemical properties of the genital tract through which niche partitioning may occur. As a result, Lactobacillus sp. enrichment coincided with the depletion of L. iners and Shuttleworthia, which dominate under normal physiological conditions. Changes in the diversity of microbial species in HPV+H groups influence the capacity of new community members to produce or consume metabolites. In particular, the functionalities of four metabolic enzymes were predicted to be associated with the microbiota, including acylphosphatase, prolyl aminopeptidase, prolyl-tRNA synthetase, and threonyl-tRNA synthetase. Such metabolic changes may influence systemic health effects in women at risk of developing cervical cancer. Overall, even assuming the limitation of the power due to the small sample number, our study adds to current knowledge by suggesting how microbial taxonomic and metabolic shifts induced by HPV infections may influence the maintenance of microbial homeostasis and indicate that HPV+H infections may alter the ecological balance of the cervicovaginal microbiota, resulting in higher bacterial diversity.},
}

@article {pmid31949936,
year = {2019},
author = {Ng, C and Li, H and Wu, WKK and Wong, SH and Yu, J},
title = {Genomics and metagenomics of colorectal cancer.},
journal = {Journal of gastrointestinal oncology},
volume = {10},
number = {6},
pages = {1164-1170},
doi = {10.21037/jgo.2019.06.04},
pmid = {31949936},
issn = {2078-6891},
abstract = {Colorectal cancer (CRC) is a common cancer globally. It is a complex disease influenced by genetic and environmental factors. Early studies on familial cases have identified major genes involved in CRC, such as proto-oncogenes KRAS, PIK3CA and BRAF, and tumour-suppressor genes APC and TP53. These genes have provided valuable insight into the molecular pathogenesis of CRC, and some have made ways to clinical utility to help diagnose cancer syndromes, prognosticate oncological outcomes and predict treatment responses. While these genetic factors are important, recent studies have suggested contribution of microorganisms to colorectal carcinogenesis. Observational studies, animal experiments and translational works have identified several microorganisms as potential carcinogenic bacteria, such as Fusobacterium nucleatum and Peptostreptococcus anaerobius. With the advent of sequencing technology and bioinformatics, more genomic and metagenomic factors are being uncovered as important players in CRC carcinogenesis. This article aims to review recent genomic and metagenomic discoveries relating to CRC.},
}

@article {pmid31948964,
year = {2020},
author = {Tse, EHY and Zhang, LY and Lau, SL and Chan, MC},
title = {Genome Sequence of a Human Norovirus GII.4 Hong Kong[P31] Variant in Hong Kong, China.},
journal = {Microbiology resource announcements},
volume = {9},
number = {3},
pages = {},
doi = {10.1128/MRA.01391-19},
pmid = {31948964},
issn = {2576-098X},
abstract = {We report the nearly complete genome of a norovirus GII.4 Hong Kong[P31] variant (GII strain Hu/HK/2019/GII.4 Hong Kong[P31]/CUHK-NS-2200) that was detected in a patient with gastroenteritis in August 2019. The genome was sequenced by metagenomic next-generation sequencing and was found to have 92.8% nucleotide similarity to the closest GII.4 norovirus sequence in GenBank.},
}

@article {pmid31948958,
year = {2020},
author = {Stüken, A and Haverkamp, THA},
title = {Metagenomic Sequences of Three Drinking Water and Two Shower Hose Biofilm Samples Treated with or without Copper-Silver Ionization.},
journal = {Microbiology resource announcements},
volume = {9},
number = {3},
pages = {},
doi = {10.1128/MRA.01220-19},
pmid = {31948958},
issn = {2576-098X},
abstract = {We announce five shotgun metagenomics data sets from two Norwegian premise plumbing systems. The samples were shotgun sequenced on two lanes of an Illumina HiSeq 3000 instrument (THRUplex chemistry, 151 bp, paired-end reads), providing an extensive resource for sequence analyses of tap water and biofilm microbial communities.},
}

@article {pmid31948613,
year = {2020},
author = {Knight, SJ and Karon, O and Goddard, MR},
title = {Small scale fungal community differentiation in a vineyard system.},
journal = {Food microbiology},
volume = {87},
number = {},
pages = {103358},
doi = {10.1016/j.fm.2019.103358},
pmid = {31948613},
issn = {1095-9998},
abstract = {Microbes influence the quality of agricultural commodities and contribute to their distinctive sensorial attributes. Increasingly studies have demonstrated not only differential geographic patterns in microbial communities and populations, but that these contribute to valuable regionally distinct agricultural product identities, the most well-known example being wine. However, little is understood about microbial geographic patterns at scales of less than 100 km. For wine, single vineyards are the smallest (and most valuable) scale at which wine is asserted to differ; however, it is unknown whether microbes play any role in agricultural produce differentiation at this scale. Here we investigate whether vineyard fungal communities and yeast populations driving the spontaneous fermentation of fruit from these same vineyards are differentiated using metagenomics and population genetics. Significant differentiation of fungal communities was revealed between four Central Otago (New Zealand) Pinot Noir vineyard sites. However, there was no vineyard demarcation between fermenting populations of S. cerevisiae. Overall, this provides evidence that vineyard microbiomes potentially contribute to vineyard specific attributes in wine. Understanding the scale at which microbial communities are differentiated, and how these communities influence food product attributes has direct economic implications for industry and could inform sustainable management practices that maintain and enhance microbial diversity.},
}

@article {pmid31947979,
year = {2020},
author = {Purkamo, L and Kietäväinen, R and Nuppunen-Puputti, M and Bomberg, M and Cousins, C},
title = {Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context.},
journal = {Life (Basel, Switzerland)},
volume = {10},
number = {1},
pages = {},
doi = {10.3390/life10010002},
pmid = {31947979},
issn = {2075-1729},
support = {2016-2018//Jenny ja Antti Wihurin Rahasto/ ; RENGAS//KYT2018/ ; BIKES//KYT22/ ; C.Cousins//Royal Society of Edinburgh/ ; },
abstract = {The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhäsalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhäsalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. One of the most common OTUs detected from Otaniemi could only be classified to phylum level, highlighting the uncharacterized nature of the deep biosphere in bedrock. Chemoheterotrophy, fermentation and nitrogen cycling are potentially significant metabolisms in these ultradeep environments. To conclude, this study provides information on microbial ecology of low biomass, carbon-depleted and energy-deprived deep subsurface environment. This information is useful in the prospect of finding life in other planetary bodies.},
}

@article {pmid31232514,
year = {2019},
author = {Matesanz, S and Pescador, DS and Pías, B and Sánchez, AM and Chacón-Labella, J and Illuminati, A and de la Cruz, M and López-Angulo, J and Marí-Mena, N and Vizcaíno, A and Escudero, A},
title = {Estimating belowground plant abundance with DNA metabarcoding.},
journal = {Molecular ecology resources},
volume = {19},
number = {5},
pages = {1265-1277},
doi = {10.1111/1755-0998.13049},
pmid = {31232514},
issn = {1755-0998},
support = {CGL2015-66809-P//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; },
mesh = {*Biota ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Metagenomics/*methods ; Plant Roots/classification/genetics ; Plants/*classification/*genetics ; },
abstract = {Most work on plant community ecology has been performed above ground, neglecting the processes that occur in the soil. DNA metabarcoding, in which multiple species are computationally identified in bulk samples, can help to overcome the logistical limitations involved in sampling plant communities belowground. However, a major limitation of this methodology is the quantification of species' abundances based on the percentage of sequences assigned to each taxon. Using root tissues of five dominant species in a semi-arid Mediterranean shrubland (Bupleurum fruticescens, Helianthemum cinereum, Linum suffruticosum, Stipa pennata and Thymus vulgaris), we built pairwise mixtures of relative abundance (20%, 50% and 80% biomass), and implemented two methods (linear model fits and correction indices) to improve estimates of root biomass. We validated both methods with multispecies mixtures that simulate field-collected samples. For all species, we found a positive and highly significant relationship between the percentage of sequences and biomass in the mixtures (R2 = .44-.66), but the equations for each species (slope and intercept) differed among them, and two species were consistently over- and under-estimated. The correction indices greatly improved the estimates of biomass percentage for all five species in the multispecies mixtures, and reduced the overall error from 17% to 6%. Our results show that, through the use of post-sequencing quantification methods on mock communities, DNA metabarcoding can be effectively used to determine not only species' presence but also their relative abundance in field samples of root mixtures. Importantly, knowledge of these aspects will allow us to study key, yet poorly understood, belowground processes.},
}

*Biota
DNA Barcoding, Taxonomic/*methods
DNA, Plant/genetics
Metagenomics/*methods
Plant Roots/classification/genetics
Plants/*classification/*genetics

@article {pmid31058458,
year = {2019},
author = {McCartney-Melstad, E and Gidiş, M and Shaffer, HB},
title = {An empirical pipeline for choosing the optimal clustering threshold in RADseq studies.},
journal = {Molecular ecology resources},
volume = {19},
number = {5},
pages = {1195-1204},
doi = {10.1111/1755-0998.13029},
pmid = {31058458},
issn = {1755-0998},
support = {//U.S. Fish and Wildlife Service/ ; 1257648//Division of Environmental Biology (National Science Foundation)/ ; //The Scientific and Technological Council of Turkey (TUBITAK)/ ; //Bureau of Reclamation/ ; //California Department of Transportation/ ; },
mesh = {Animals ; *Cluster Analysis ; Computational Biology/*methods ; Genetics, Population/*methods ; Metagenomics/*methods ; *Phylogeny ; Ranidae/classification/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Genomic data are increasingly used for high resolution population genetic studies including those at the forefront of biological conservation. A key methodological challenge is determining sequence similarity clustering thresholds for RADseq data when no reference genome is available. These thresholds define the maximum permitted divergence among allelic variants and the minimum divergence among putative paralogues and are central to downstream population genomic analyses. Here we develop a novel set of metrics to determine sequence similarity thresholds that maximize the correct separation of paralogous regions and minimize oversplitting naturally occurring allelic variation within loci. These metrics empirically identify the threshold value at which true alleles at opposite ends of several major axes of genetic variation begin to incorrectly separate into distinct clusters, allowing researchers to choose thresholds just below this value. We test our approach on a recently published data set for the protected foothill yellow-legged frog (Rana boylii). The metrics recover a consistent pattern of roughly 96% similarity as a threshold above which genetic divergence and data missingness become increasingly correlated. We provide scripts for assessing different clustering thresholds and discuss how this approach can be applied across a wide range of empirical data sets.},
}

Animals
*Cluster Analysis
Computational Biology/*methods
Genetics, Population/*methods
Metagenomics/*methods
*Phylogeny
Ranidae/classification/genetics
Sequence Analysis, DNA/*methods

@article {pmid31945533,
year = {2019},
author = {Wang, J and Yuan, S and Tang, L and Pan, X and Pu, X and Li, R and Shen, C},
title = {Contribution of heavy metal in driving microbial distribution in a eutrophic river.},
journal = {The Science of the total environment},
volume = {712},
number = {},
pages = {136295},
doi = {10.1016/j.scitotenv.2019.136295},
pmid = {31945533},
issn = {1879-1026},
abstract = {Urban rivers represent an important source of freshwater. Accelerated urban development has resulted in imbalances in the water ecological environment and even eutrophication. Moreover, both natural and anthropogenic sources result in frequent heavy metal pollution in urban rivers. However, the combined impact of eutrophication and heavy metal pollution on the diversity and structure of the river microbial communities has not been adequately addressed. The microbial community distribution and predicted functions were examined in six water and sediment samples from the Laojingshui (LJS) River using metagenomic sequencing. The results showed that there were distinct differences in the microbial composition along the river. Redundancy analysis (RDA) revealed that the redox potential (Eh) was the most influential factor, explaining 76.5% of the variation (p = 0.002), and the heavy metals Zn and Cu explained 4.5 and 3.9%, respectively (p < 0.05). The results revealed that high nitrogen and phosphorus concentrations may have affected the proliferation of opportunistic plant species, such as Eichhornia crassipes, but Eh and heavy metals may have had greater impacts than N and P on the microorganisms in the water and sediment. The sensitivities of Deltaproteobacteria, Acidobacteria, Gemmatimonadetes and Nitrospira were most significant under Zn and Cu contamination when accompanied by eutrophic conditions. The expression ratio of the CYS (Cystain) gene might explain why the spatial distribution of each metal differed. This study suggests that heavy metals in eutrophication water continue to be the main factors determining the composition of microbial community, so the treatment of eutrophic water still needs to attach great importance to the complex pollution of heavy metals.},
}

@article {pmid31945519,
year = {2019},
author = {Meenatchi, R and Thinesh, T and Brindangnanam, P and Hassan, S and Kiran, GS and Selvin, J},
title = {Revealing the impact of global mass bleaching on coral microbiome through 16S rRNA gene-based metagenomic analysis.},
journal = {Microbiological research},
volume = {233},
number = {},
pages = {126408},
doi = {10.1016/j.micres.2019.126408},
pmid = {31945519},
issn = {1618-0623},
abstract = {Coral bleaching, a phenomenon by which the expulsion of corals' alveolate endosymbiont (zooxanthellae) occurs when experiencing thermal stress is the major cause for devastation of corals. However, apart from this obligate symbiont of Scleractinian corals, there are different kinds of microbes that exist as stable, transient or sporadic members of the holobiont which reside within various microhabitats in the coral structures. Thus, this study aims to profile the coral bacterial community composition among different coral genera (thermally-sensitive (Acropora digetifera and A. noblis) and thermally resistant (Favites abdita) coral genera analyzed by field monitoring surveys) and also in a particular coral genus (thermally sensitive coral-A. digetifera) at two different sampling times (March 2016 and January 2017). A total of about 608695 paired end reads were obtained through Illumina MiSeq Sequencing platform. The alpha diversity indices (ACE, Chao1 and Shannon) were found to be higher in A. nobilis, followed by A. digetifera and Favites abdita, and the corresponding Simpson values were also found to follow the same trend, indicating that the samples are both rich in species diversity and species evenness. Proteobacteria was found to be the most dominant phylum and Gammaproteobacteria was the predominant class present in all the coral genera studied as also during different sampling time periods. As Vibrionaceae was previously reported to increase its abundance during bleaching stress conditions, bacterial profiling among different coral genera showed the presence of 86 % Vibrionaceae in A. digetifera colonies, and it was 93 % in A. digetifera samples collected during March 2016 whereas, it was found to decrease significantly (7 %) in same tagged colonies collected during January 2017. Thus, profiling of microbiome is of prime importance while studying the holobiont organism like the corals. Stress levels experienced by Palk Bay are even depicted in this microbiome study showing high alpha diversity indices that should alarm reef managers to pay attention to this precious stress tolerant reef community.},
}

@article {pmid31945518,
year = {2019},
author = {Puvar, AC and Nathani, NM and Shaikh, I and Bhatt, AD and Bhargava, P and Joshi, CG and Joshi, MN},
title = {Bacterial line of defense in Dirinaria lichen from two different ecosystems: First genomic insights of its mycobiont Dirinaria sp. GBRC AP01.},
journal = {Microbiological research},
volume = {233},
number = {},
pages = {126407},
doi = {10.1016/j.micres.2019.126407},
pmid = {31945518},
issn = {1618-0623},
abstract = {Lichens have been widely studied for their symbiotic properties and for the secondary metabolites production by its fungal symbiont. Recent molecular studies have confirmed coexistence of bacteria along with the fungal and algal symbionts. Direct nucleic acid study by -omics approaches is providing better insights into their structural and functional dynamics. However, genomic analysis of individual members of lichen is difficult by the conventional approach. Hence, genome assembly from metagenome data needs standardization in the eukaryotic system like lichens. The present study aimed at metagenomic characterization of rock associated lichen Dirinaria collected from Kutch and Dang regions of Gujarat, followed by genome reconstruction and annotation of the mycobiont Dirinaria. The regions considered in the study are eco-geographically highly variant. The results revealed higher alpha diversity in the dry region Kutch as compared to the tropical forest associated lichen from Dang. Ascomycota was the most abundant eukaryote while Proteobacteria dominated the bacterial population. There were 23 genera observed only in the Kutch lichen (KL) and one genus viz., Candidatus Vecturithrix unique to the Dang lichen (DL). The exclusive bacterial genera in the Kutch mostly belonged to groups reported for stress tolerance and earlier isolated from lithobionts of extreme niches. The assembled data of KL & DL were further used for genome reconstruction of Dirinaria sp. using GC and tetra-pentamer parameters and reassembly that resulted into a final draft genome of 31.7 Mb and 9556 predicted genes. Twenty-eight biosynthesis gene clusters were predicted that included genes for polyketide, indole and terpene synthesis. Association analysis of bacteria and mycobiont revealed 8 pathways specific to bacteria with implications in lichen symbiosis and environment interaction. The study provides the first draft genome of the entire fungal Dirinaria genus and provides insights into the Dirinaria lichen metagenome from Gujarat region.},
}

@article {pmid31944684,
year = {2020},
author = {Wang, X and Chen, Z and Mu, Q and Wu, X and Zhang, J and Mao, D and Luo, Y and Alvarez, PJJ},
title = {Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.9b04116},
pmid = {31944684},
issn = {1520-5851},
abstract = {An expanding list of chemicals may permeabilize bacterial cells and facilitate horizontal gene transfer (HGT), which enhances propagation of antibiotic resistance genes (ARGs) in the environment. Previous studies showed that 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]), an ionic liquid, can facilitate HGT of some ARGs among bacteria. However, the dynamic response of a wider range of ARGs and associated mobile genetic elements (MGEs) in different environments is unknown. Here, we used metagenomic tools to study shifts of the resistome and microbiome in both sediments and freshwater microcosms exposed to [BMIm][PF6]. Exposure for 16 h to 0.1 or 1.0 g/L significantly enriched more than 207 ARG subtypes primarily encoding efflux pumps in freshwater microcosms, as well as cultivable antibiotic-resistant bacteria. This resistome enrichment was attributed to HGT facilitated by MGEs (428 plasmids, 61 integron-integrase genes, and 45 gene cassettes were enriched), as well as to HGT-related functional genes. Interestingly, resistome enrichment occurred fast (within 16 h) after [BMIm][PF6] exposure, before any significant changes in bacterial community structure. Similar ARG enrichment occurred in sediment microcosms exposed to [BMIm][PF6] for 28 d, and this longer exposure affected the microbial community structure (e.g., Proteobacteria abundance increased significantly). Overall, this study suggests that [BMIm][PF6] releases could rapidly enrich the antibiotic resistome in receiving environments by increasing HGT and fortuitously selecting for efflux pump genes, thus contributing to ARG propagation.},
}

@article {pmid31943734,
year = {2020},
author = {Magnuson, E and Mykytczuk, NCS and Pellerin, A and Goordial, J and Twine, SM and Wing, B and Foote, SJ and Fulton, K and Whyte, LG},
title = {Thiomicrorhabdus streamers and sulfur cycling in perennial hypersaline cold springs in the Canadian high Arctic.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14916},
pmid = {31943734},
issn = {1462-2920},
abstract = {The Gypsum Hill (GH) springs on Axel Heiberg Island in the Canadian high Arctic are host to chemolithoautotrophic, sulfur-oxidizing streamers that flourish in the high Arctic winter in water temperatures from -1.3-7°C with ~8% salinity in a high Arctic winter environment with air temperatures commonly less than -40°C and an average annual air temperature of -15°C. Metagenome sequencing and binning of streamer samples produced a 96% complete Thiomicrorhabdus sp. metagenome-assembled genome representing a possible new species or subspecies. This is the most cold- and salt-extreme source environment for a Thiomicrorhabdus genome yet described. Metaproteomic and metatranscriptomic analysis attributed nearly all gene expression in the streamers to the Thiomicrorhabdus sp. and suggested that it is active in CO2 fixation and oxidation of sulfide to elemental sulfur. In situ geochemical and isotopic analyses of the fractionation of multiple sulfur isotopes determined the biogeochemical transformation of sulfur from its source in Carboniferous evaporites to biotic processes occurring in the sediment and streamers. These complementary molecular tools provided a functional link between the geochemical substrates and the collective traits and activity that define the microbial community's interactions within a unique polar saline habitat where Thiomicrorhabdus-dominated streamers form and flourish. This article is protected by copyright. All rights reserved.},
}

@article {pmid31943422,
year = {2020},
author = {Li, R and Li, X and Huang, T and Wang, Y and Xue, M and Sun, S and Yan, D and Song, G and Sun, G and Li, M},
title = {Influence of cecotrophy on fat metabolism mediated by caecal microorganisms in New Zealand white rabbits.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.13309},
pmid = {31943422},
issn = {1439-0396},
support = {2018YFD0502203//National Key R&D Program of China/ ; S2013-08-G01//Henan Agriculture Research System/ ; },
abstract = {Cecotrophy is a special behaviour of rabbits. Eating soft faeces can improve feed efficiency and maintain gut flora in rabbits. In our previous study, we found that fasting from soft faeces significantly reduced growth rate and total cholesterol (TC) in New Zealand white rabbits (NZW rabbits), thereby resulting in lower values for body weight and fat deposition in the soft faeces fasting group than in the control group. However, it has not been demonstrated whether cecotrophy by NZW rabbits can regulate lipid metabolism by changing the diversity of caecal microorganisms. In this study, thirty-six 28-day-old weaned NZW female rabbits were randomly divided into two groups (the soft faeces fasting group and the control group) and fed to 90 days. Rabbits in the experimental group were treated with an Elizabeth circle to prevent them from eating their soft faeces. Then, the caecal contents of three rabbits from the soft faeces fasting group and three rabbits from the control group were collected for metagenomic sequencing. We found that the abundance of Bacteroides increased, while Ruminococcus decreased, compared with the control group after fasting from soft faeces. Relative abundance was depressed for genes related to metabolic pathways such as ascorbate and aldarate metabolism, riboflavin metabolism and bile secretion. Moreover, there was a general correlation between variation in microbial diversity and fat deposition. Bacteroides affects body weight and TC by participating in the riboflavin metabolism pathway. By investigating the effect of cecotrophy on caecal microorganisms of rabbits, we identified the key microorganisms that regulate the rapid growth performance of NZW rabbits, which may provide useful reference for the future research and development of microecological preparations for NZW rabbits.},
}

@article {pmid31942944,
year = {2020},
author = {Hogan, CA and Yang, S and Garner, OB and Green, DA and Gomez, CA and Dien Bard, J and Pinsky, BA and Banaei, N},
title = {Clinical Impact of Metagenomic Next-Generation Sequencing of Plasma Cell-Free DNA for the Diagnosis of Infectious Diseases: A Multicenter Retrospective Cohort Study.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaa035},
pmid = {31942944},
issn = {1537-6591},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA has emerged as an attractive diagnostic modality allowing broad-range pathogen detection, noninvasive sampling, and earlier diagnosis. However, little is known about its real-world clinical impact as used in routine practice.

METHODS: We performed a retrospective cohort study of all patients for whom plasma mNGS (Karius test) was performed for all indications at 5 U.S. institutions over 1.5 years. Comprehensive chart review was performed, and standardized assessment of clinical impact of the mNGS based on the treating team's interpretation of Karius results and patient management was established.

RESULTS: A total of 82 Karius tests were evaluated, from 39 (47.6%) adults and 43 (52.4%) children and a total of 53 (64.6%) immunocompromised patients. Karius positivity rate was 50/82 (61.0%), with 25 (50.0%) showing two or more organisms (range, 2-8). The Karius test results led to positive impact in 6 (7.3%), negative impact in 3 (3.7%), no impact in 71 (86.6%), and was indeterminate in 2 (2.4%). Cases with positive Karius result and clinical impact involved bacteria and/or fungi but not DNA viruses or parasites. In 10 patients who underwent 16 additional repeated tests, only one was associated with clinical impact.

CONCLUSIONS: The real-world impact of the Karius test as currently used in routine clinical practice is limited. Further studies are needed to identify high-yield patient populations, define the complementary role of mNGS to conventional microbiological methods and how best to integrate mNGS into current testing algorithms.},
}

@article {pmid31942942,
year = {2020},
author = {Babady, NE},
title = {Clinical Metagenomics for Bloodstream Infections: Is The Juice Worth The Squeeze?.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaa041},
pmid = {31942942},
issn = {1537-6591},
}

@article {pmid31942889,
year = {2020},
author = {Xing, C and Chen, J and Zheng, X and Chen, L and Chen, M and Wang, L and Li, X},
title = {Functional metagenomic exploration identifies novel prokaryotic copper resistance genes from the soil microbiome.},
journal = {Metallomics : integrated biometal science},
volume = {},
number = {},
pages = {},
doi = {10.1039/c9mt00273a},
pmid = {31942889},
issn = {1756-591X},
abstract = {Functional metagenomics is a premise-free approach for exploring metal resistance genes, enabling more profound effects on the development of bioremediation tools than pure culture based selection. Six soil metagenomic libraries were screened for copper (Cu) resistance genes in the current study through conventional functional genomics. Clones from the six metagenomic libraries were randomly selected from solid medium supplied with Cu, resulting in 411 Cu resistance clones. Thirty-five clones with the strongest Cu resistance were sequenced and 12 unique sequences harboring 25 putative open reading frames were obtained. It is inferred by bioinformatic analysis that putative genes carried by these recombinant plasmids probably function in the pathways of responding to Cu stress, including energy metabolism, integral components of membrane, ion transport/chelation, protein/amino acid metabolism, carbohydrate/fatty acid metabolism, signal transduction and DNA binding. The sequenced clones were re-transformed into Escherichia coli strain DH5α, and the host's biomass and the metal sorption under Cu stress were subsequently determined. The results showed that the biomass of eight of the clones was significantly increased, whereas four of them were significantly reduced. A negative correlation (R = 0.86) was found between the biomass and Cu sorption capacity. The 12 positive clones were further transferred into a Cu-sensitive E. coli strain (ΔCopA), among which nine restored the host's Cu resistance substantially. The Cu resistant genes explored in this study by functional metagenomics possess a potential capacity for developing novel bioremediation strategies, and the findings imply a vast diversity of microbial Cu resistance genetic factors in soil yet to be discovered.},
}

@article {pmid31942261,
year = {2020},
author = {Chen, Q and Meyer, WA and Zhang, Q and White, JF},
title = {16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8417},
doi = {10.7717/peerj.8417},
pmid = {31942261},
issn = {2167-8359},
abstract = {Turfgrass investigators have observed that plantings of grass seeds produced in moist climates produce seedling stands that show greater stand evenness with reduced disease compared to those grown from seeds produced in dry climates. Grass seeds carry microbes on their surfaces that become endophytic in seedlings and promote seedling growth. We hypothesize that incomplete development of the microbiome associated with the surface of seeds produced in dry climates reduces the performance of seeds. Little is known about the influence of moisture on the structure of this microbial community. We conducted metagenomic analysis of the bacterial communities associated with seeds of three turf species (Festuca rubra, Lolium arundinacea, and Lolium perenne) from low moisture (LM) and high moisture (HM) climates. The bacterial communities were characterized by Illumina high-throughput sequencing of 16S rRNA V3-V4 regions. We performed seed germination tests and analyzed the correlations between the abundance of different bacterial groups and seed germination at different taxonomy ranks. Climate appeared to structure the bacterial communities associated with seeds. LM seeds vectored mainly Proteobacteria (89%). HM seeds vectored a denser and more diverse bacterial community that included Proteobacteria (50%) and Bacteroides (39%). At the genus level, Pedobacter (20%), Sphingomonas (13%), Massilia (12%), Pantoea (12%) and Pseudomonas (11%) were the major genera in the bacterial communities regardless of climate conditions. Massilia, Pantoea and Pseudomonas dominated LM seeds, while Pedobacter and Sphingomonas dominated HM seeds. The species of turf seeds did not appear to influence bacterial community composition. The seeds of the three turf species showed a core microbiome consisting of 27 genera from phyla Actinobacteria, Bacteroidetes, Patescibacteria and Proteobacteria. Differences in seed-vectored microbes, in terms of diversity and density between high and LM climates, may result from effects of moisture level on the colonization of microbes and the development of microbe community on seed surface tissues (adherent paleas and lemmas). The greater diversity and density of seed vectored microbes in HM climates may benefit seedlings by helping them tolerate stress and fight disease organisms, but this dense microbial community may also compete with seedlings for nutrients, slowing or modulating seed germination and seedling growth.},
}

@article {pmid31941900,
year = {2020},
author = {Siranosian, BA and Tamburini, FB and Sherlock, G and Bhatt, AS},
title = {Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {280},
doi = {10.1038/s41467-019-14103-3},
pmid = {31941900},
issn = {2041-1723},
support = {Clinical Investigator Award//Damon Runyon Cancer Research Foundation (Cancer Research Fund of the Damon Runyon-Walter Winchell Foundation)/ ; R01AI148623//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {CrAss-like phages are double-stranded DNA viruses that are prevalent in human gut microbiomes. Here, we analyze gut metagenomic data from mother-infant pairs and patients undergoing fecal microbiota transplantation to evaluate the patterns of acquisition, transmission and strain diversity of crAss-like phages. We find that crAss-like phages are rarely detected at birth but are increasingly prevalent in the infant microbiome after one month of life. We observe nearly identical genomes in 50% of cases where the same crAss-like clade is detected in both the mother and the infant, suggesting vertical transmission. In cases of putative transmission of prototypical crAssphage (p-crAssphage), we find that a subset of strains present in the mother are detected in the infant, and that strain diversity in infants increases with time. Putative tail fiber proteins are enriched for nonsynonymous strain variation compared to other genes, suggesting a potential evolutionary benefit to maintaining strain diversity in specific genes. Finally, we show that p-crAssphage can be acquired through fecal microbiota transplantation.},
}

@article {pmid31941778,
year = {2020},
author = {Zhang, C and Wang, Z and Cai, J and Yan, X and Zhang, F and Wu, J and Xu, L and Zhao, Z and Hu, T and Tu, C and He, B},
title = {Seroreactive profiling of filoviruses in Chinese bats reveals extensive infection of diverse viruses.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JVI.02042-19},
pmid = {31941778},
issn = {1098-5514},
abstract = {Southern China is a hotspot of emerging infectious diseases, in which dwell diverse species of bats, a large group of flying mammals considered natural reservoirs for zoonotic viruses. Recently, divergent filoviruses (FiVs) have been identified in bats within this region, which pose a potential risk to public health, but their true infection situation in bats remains largely unclear. Here, 689 archived bat serum samples were analyzed by ELISA, western blot and neutralization assay to investigate the seroprevalence and cross-reactivity of four divergent FiVs and two other viruses (Rabies virus and Tuhoko pararubulavirus 1) of different families within the order Mononegavirales Results showed no cross-antigenicity between FiVs and other mononegaviruses, but different cross-reactivity among the FiVs themselves. The total FiV seroreactive rate was 36.3% (250/689), with infection by the indigenous Chinese FiV DH04 or antigenically-related one being the most widely and the most highly prevalent. Further viral metagenomic analysis of fruit bat tissues also identified the gene sequence of a novel FiV. These results indicate the likely prevalence of other so far unidentified FiVs within Chinese bat population, with frugivorous Rousettus leschenaulti and Eonycteris spelaea bats and insectivorous Myotis horsfieldii and M. schreibersi bats being their major reservoirs.IMPORTANCE Bats are natural hosts of many FiVs, from which diverse FiVs were serologically or virologically detected in Africa, Europe and East Asia. Recently, very divergent FiVs were identified in Chinese bat population, but their antigenic relationship with other known FiVs remains unknown. Here we conducted serological characterization and investigation of Chinese indigenous FiVs and prototypes of other viruses in bats. Results indicated that Chinese indigenous FiVs are antigenically distant to other FiVs and infection of novel or multiple FiVs occurred in Chinese bats with FiV DH04 or antigenically-related one being the most widely and the most highly prevalent. Additionally, besides Rousettus leschenaulti and Eonycteris spelaea bats, the insectivorous Myotis horsfieldii and M. schreibersi bats are highly preferential hosts of FiVs. Seroreactive and viral metagenomic results indicated that more as yet unknown bat-borne FiVs circulate in the Southern China, and to uncover them further investigation and timely surveillance is needed.},
}

@article {pmid31941452,
year = {2020},
author = {Pinto, OHB and Silva, TF and Vizzotto, CS and Santana, RH and Lopes, FAC and Silva, BS and Thompson, FL and Kruger, RH},
title = {Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {13},
doi = {10.1186/s12866-020-1698-x},
pmid = {31941452},
issn = {1471-2180},
support = {0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 0//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 0//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 0//Fundação de Apoio à Pesquisa do Distrito Federal/ ; },
abstract = {BACKGROUND: Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume.

RESULTS: The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25.

CONCLUSIONS: Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.},
}

@article {pmid31941046,
year = {2020},
author = {Hierweger, MM and Werder, S and Seuberlich, T},
title = {Parainfluenza Virus 5 Infection in Neurological Disease and Encephalitis of Cattle.},
journal = {International journal of molecular sciences},
volume = {21},
number = {2},
pages = {},
doi = {10.3390/ijms21020498},
pmid = {31941046},
issn = {1422-0067},
support = {31003A_163438//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; MON-108//Bundesamt für Lebensmittelsicherheit und Veterinärwesen/ ; },
abstract = {The etiology of viral encephalitis in cattle often remains unresolved, posing a potential risk for animal and human health. In metagenomics studies of cattle with bovine non-suppurative encephalitis, parainfluenza virus 5 (PIV5) was identified in three brain samples. Interestingly, in two of these animals, bovine herpesvirus 6 and bovine astrovirus CH13 were additionally found. We investigated the role of PIV5 in bovine non-suppurative encephalitis and further characterized the three cases. With traditional sequencing methods, we completed the three PIV5 genomes, which were compared to one another. However, in comparison to already described PIV5 strains, unique features were revealed, like an 81 nucleotide longer open reading frame encoding the small hydrophobic (SH) protein. With in situ techniques, we demonstrated PIV5 antigen and RNA in one animal and found a broad cell tropism of PIV5 in the brain. Comparative quantitative analyses revealed a high viral load of PIV5 in the in situ positive animal and therefore, we propose that PIV5 was probably the cause of the disease. With this study, we clearly show that PIV5 is capable of naturally infecting different brain cell types in cattle in vivo and therefore it is a probable cause of encephalitis and neurological disease in cattle.},
}

@article {pmid31940944,
year = {2020},
author = {Du, XP and Cai, ZH and Zuo, P and Meng, FX and Zhu, JM and Zhou, J},
title = {Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom.},
journal = {Microorganisms},
volume = {8},
number = {1},
pages = {},
doi = {10.3390/microorganisms8010107},
pmid = {31940944},
issn = {2076-2607},
support = {41976126//Jin Zhou/ ; },
abstract = {Viruses are key biogeochemical engines in the regulation of the dynamics of phytoplankton. However, there has been little research on viral communities in relation to algal blooms. Using the virMine tool, we analyzed viral information from metagenomic data of field dinoflagellate (Gymnodinium catenatum) blooms at different stages. Species identification indicated that phages were the main species. Unifrac analysis showed clear temporal patterns in virioplankton dynamics. The viral community was dominated by Siphoviridae, Podoviridae, and Myoviridae throughout the whole bloom cycle. However, some changes were observed at different phases of the bloom; the relatively abundant Siphoviridae and Myoviridae dominated at pre-bloom and peak bloom stages, while at the post-bloom stage, the members of Phycodnaviridae and Microviridae were more abundant. Temperature and nutrients were the main contributors to the dynamic structure of the viral community. Some obvious correlations were found between dominant viral species and host biomass. Functional analysis indicated some functional genes had dramatic response in algal-associated viral assemblages, especially the CAZyme encoding genes. This work expands the existing knowledge of algal-associated viruses by characterizing viral composition and function across a complete algal bloom cycle. Our data provide supporting evidence that viruses participate in dinoflagellate bloom dynamics under natural conditions.},
}

@article {pmid31940838,
year = {2020},
author = {Bastaraud, A and Cecchi, P and Handschumacher, P and Altmann, M and Jambou, R},
title = {Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys?.},
journal = {International journal of environmental research and public health},
volume = {17},
number = {2},
pages = {},
doi = {10.3390/ijerph17020480},
pmid = {31940838},
issn = {1660-4601},
abstract = {A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new 'plastic context.' We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.},
}

@article {pmid31940381,
year = {2020},
author = {Breusing, C and Franke, M and Young, CR},
title = {Intra-host symbiont diversity in eastern Pacific cold seep tubeworms identified by the 16S-V6 region, but undetected by the 16S-V4 region.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0227053},
doi = {10.1371/journal.pone.0227053},
pmid = {31940381},
issn = {1932-6203},
abstract = {Vestimentiferan tubeworms are key taxa in deep-sea chemosynthetic habitats worldwide. As adults they obtain their nutrition through their sulfide-oxidizing bacterial endosymbionts, which are acquired from the environment. Although horizontal transmission should favor infections by various symbiotic microbes, the current paradigm holds that every tubeworm harbors only one endosymbiotic 16S rRNA phylotype. Although previous studies based on traditional Sanger sequencing have questioned these findings, population level high-throughput analyses of the symbiont 16S diversity are still missing. To get further insights into the symbiont genetic variation and uncover hitherto hidden diversity we applied state-of-the-art 16S-V4 amplicon sequencing to populations of the co-occurring tubeworm species Lamellibrachia barhami and Escarpia spicata that were collected during E/V Nautilus and R/V Western Flyer cruises to cold seeps in the eastern Pacific Ocean. In agreement with earlier work our sequence data indicated that L. barhami and E. spicata share one monomorphic symbiont phylotype. However, complementary CARD-FISH analyses targeting the 16S-V6 region implied the existence of an additional phylotype in L. barhami. Our results suggest that the V4 region might not be sufficiently variable to investigate diversity in the intra-host symbiont population at least in the analyzed sample set. This is an important finding given that this region has become the standard molecular marker for high-throughput microbiome analyses. Further metagenomic research will be necessary to solve these issues and to uncover symbiont diversity that is hidden below the 16S rRNA level.},
}

@article {pmid31940321,
year = {2020},
author = {Honap, TP and Sankaranarayanan, K and Schnorr, SL and Ozga, AT and Warinner, C and Lewis, CM},
title = {Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0226930},
doi = {10.1371/journal.pone.0226930},
pmid = {31940321},
issn = {1932-6203},
abstract = {CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as compared to industrialized, urban populations. Statistical comparisons showed no association of crAssphage prevalence with variables such as age, sex, body mass index, and health status of individuals. Phylogenetic analyses show that crAssphage strains reconstructed from the same individual over multiple time-points, cluster together. CrAssphage strains from individuals from the same study population do not always cluster together. Some evidence of clustering is seen at the level of broadly defined geographic regions, however, the relative positions of these clusters within the crAssphage phylogeny are not well-supported. We hypothesize that this lack of strong biogeographic structuring is suggestive of an expansion event within crAssphage. Using a Bayesian dating approach, we estimate that this expansion has occurred fairly recently. Overall, we determine that crAssphage presence is associated with an industrialized lifestyle and the absence of strong biogeographic structuring within global crAssphage strains is likely due to a recent population expansion within this bacteriophage.},
}

@article {pmid31940146,
year = {2020},
author = {Nair, RR and Rangaswamy, B and Sarojini, BSI and Joseph, V},
title = {Anaerobic ammonia-oxidizing bacteria in tropical bioaugmented zero water exchange aquaculture ponds.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-020-07663-1},
pmid = {31940146},
issn = {1614-7499},
abstract = {Bioaugmented zero water exchange aquaculture production systems (ZWEAPS) maintained with minimal or no water exchange prevent the ammonia accumulation in the system, leading to environmental sustainability and biosecurity. The microbes in the bioaugmented ZWEAPS plays a major role in maintaining low levels of ammonia through ammonia oxidation and nitrite oxidation. The comprehensive understanding on anammox population in the systems will provide an insight on the environmental factors controlling the functional anammox bacterial communities for potential biostimulation and augmented ammonia removal in ZWEAPS. The sediment metagenome of such three tropical bioaugmented ZWE shrimp culture ponds were analysed to determine the diversity, distribution and abundance of anaerobic ammonia-oxidizing (anammox) bacteria based on hydrazine oxidoreductase (hzo) gene as a phylogenetic marker. The restriction fragment length polymorphism (RFLP) phylotypes from the clone libraries were identified with maximum distribution to Candidatus Kuenenia, as the dominant population in the study sites with high ammonia load followed by Candidatus Scalindua. The environmental factors associated with the abundance and diversity of the anammox population were analysed using RDA and Pearson correlation. The samples of final culturing period (75th day) of TCR-S ZWE pond was observed with the highest operational taxonomic unit (OTU)-based diversity, where comparatively higher ammonia (water 0.71 mg L-1 and sediment 1.21 mg L-1) was recorded among the study sites. The gene abundance of the anammox population ranged from 106 to 107 copies per gram of sediment, in spite of less diversity. The physiochemical factors such as ammonia, nitrite, redox potential and the total organic carbon indicated a strong and positive correlation to the abundance and distribution of the anammox population, which highlights the importance of anammox communities and the potential of biostimulation for ammonia removal in the aquaculture systems.},
}

@article {pmid31937679,
year = {2020},
author = {Weissman, JL and Johnson, PLF},
title = {Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
doi = {10.1128/mSystems.00752-19},
pmid = {31937679},
issn = {2379-5077},
abstract = {A diversity of clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems provide adaptive immunity to bacteria and archaea through recording "memories" of past viral infections. Recently, many novel CRISPR-associated proteins have been discovered via computational studies, but those studies relied on biased and incomplete databases of assembled genomes. We avoided these biases and applied a network theory approach to search for novel CRISPR-associated genes by leveraging subtle ecological cooccurrence patterns identified from environmental metagenomes. We validated our method using existing annotations and discovered 32 novel CRISPR-associated gene families. These genes span a range of putative functions, with many potentially regulating the response to infection.IMPORTANCE Every branch on the tree of life, including microbial life, faces the threat of viral pathogens. Over the course of billions of years of coevolution, prokaryotes have evolved a great diversity of strategies to defend against viral infections. One of these is the CRISPR adaptive immune system, which allows microbes to "remember" past infections in order to better fight them in the future. There has been much interest among molecular biologists in CRISPR immunity because this system can be repurposed as a tool for precise genome editing. Recently, a number of comparative genomics approaches have been used to detect novel CRISPR-associated genes in databases of genomes with great success, potentially leading to the development of new genome-editing tools. Here, we developed novel methods to search for these distinct classes of genes directly in environmental samples ("metagenomes"), thus capturing a more complete picture of the natural diversity of CRISPR-associated genes.},
}

@article {pmid31937678,
year = {2020},
author = {Olm, MR and Crits-Christoph, A and Diamond, S and Lavy, A and Matheus Carnevali, PB and Banfield, JF},
title = {Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
doi = {10.1128/mSystems.00731-19},
pmid = {31937678},
issn = {2379-5077},
abstract = {Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of nonsynonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, two methods for estimating homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full-length 16S rRNA genes were least useful, in part because they were underrecovered from metagenomes. However, many ribosomal proteins displayed both high metagenomic recoverability and species discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination.IMPORTANCE There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.},
}

@article {pmid31937673,
year = {2020},
author = {Alcalá-Briseño, RI and Casarrubias-Castillo, K and López-Ley, D and Garrett, KA and Silva-Rosales, L},
title = {Network Analysis of the Papaya Orchard Virome from Two Agroecological Regions of Chiapas, Mexico.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
doi = {10.1128/mSystems.00423-19},
pmid = {31937673},
issn = {2379-5077},
abstract = {The study of complex ecological interactions, such as those among host, pathogen, and vector communities, can help to explain host ranges and the emergence of novel pathogens. We evaluated the viromes of papaya orchards, including weed and insect viromes, to identify common viruses in intensive production of papaya in the Pacific Coastal Plain and the Central Depression of Chiapas, Mexico. Samples of papaya cultivar Maradol, susceptible to papaya ringspot virus (PRSV), were categorized by symptoms by local farmers (papaya ringspot symptoms, non-PRSV symptoms, or asymptomatic). These analyses revealed the presence of 61 viruses, where only 4 species were shared among both regions, 16 showed homology to known viruses, and 36 were homologous with genera including Potyvirus, Comovirus, and Tombusvirus (RNA viruses) and Begomovirus and Mastrevirus (DNA viruses). We analyzed the network of associations between viruses and host-location combinations, revealing ecological properties of the network, such as an asymmetric nested pattern, and compared the observed network to null models of network association. Understanding the network structure informs management strategies, for example, revealing the potential role of PRSV in asymptomatic papaya and that weeds may be an important pathogen reservoir. We identify three key management implications: (i) each region may need a customized management strategy; (ii) visual assessment of papaya may be insufficient for PRSV, requiring diagnostic assays; and (iii) weed control within orchards may reduce the risk of virus spread to papaya. Network analysis advances understanding of host-pathogen interactions in the agroecological landscape.IMPORTANCE Virus-virus interactions in plants can modify host symptoms. As a result, disease management strategies may be unsuccessful if they are based solely on visual assessment and diagnostic assays for known individual viruses. Papaya ringspot virus is an important limiting factor for papaya production and likely has interactions with other viruses that are not yet known. Using high-throughput sequencing, we recovered known and novel RNA and DNA viruses from papaya orchards in Chiapas, Mexico, and categorized them by host and, in the case of papaya, symptom type: asymptomatic papaya, papaya with ringspot virus symptoms, papaya with nonringspot symptoms, weeds, and insects. Using network analysis, we demonstrated virus associations within and among host types and described the ecological community patterns. Recovery of viruses from weeds and asymptomatic papaya suggests the need for additional management attention. These analyses contribute to the understanding of the community structure of viruses in the agroecological landscape.},
}

@article {pmid31937645,
year = {2020},
author = {Subramaniam, K and Behringer, DC and Bojko, J and Yutin, N and Clark, AS and Bateman, KS and van Aerle, R and Bass, D and Kerr, RC and Koonin, EV and Stentiford, GD and Waltzek, TB},
title = {A New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic Biomes.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
doi = {10.1128/mBio.02938-19},
pmid = {31937645},
issn = {2150-7511},
abstract = {Panulirus argus virus 1 (PaV1) is the only known virus infecting the Caribbean spiny lobster (Panulirus argus) from the Caribbean Sea. Recently, related viruses, Dikerogammarus haemobaphes virus 1 (DhV1) and Carcinus maenas virus 1 (CmV1), have been detected in the demon shrimp (Dikerogammarus haemobaphes) and the European shore crab (Carcinus maenas), respectively, from sites in the United Kingdom. The virion morphology of these crustacean viruses is similar to that of iridoviruses. However, unlike iridoviruses and other nucleocytoplasmic large DNA viruses (NCLDVs), these viruses complete their morphogenesis in the host cell nucleus rather than in the cytoplasm. To date, these crustacean viruses have remained unclassified due to a lack of genomic data. Using an Illumina MiSeq sequencer, we sequenced the complete genomes of PaV1, CmV1, and DhV1. Comparative genome analysis shows that these crustacean virus genomes encode the 10 hallmark proteins previously described for the NCLDVs of eukaryotes, strongly suggesting that they are members of this group. With a size range of 70 to 74 kb, these are the smallest NCLDV genomes identified to date. Extensive gene loss, divergence of gene sequences, and the accumulation of low-complexity sequences reflect the extreme degradation of the genomes of these "minimal" NCLDVs rather than any direct relationship with the NCLDV ancestor. Phylogenomic analysis supports the classification of these crustacean viruses as a distinct family, "Mininucleoviridae," within the pitho-irido-Marseille branch of the NCLDVs.IMPORTANCE Recent genomic and metagenomic studies have led to a dramatic expansion of the known diversity of nucleocytoplasmic large DNA viruses (NCLDVs) of eukaryotes, which include giant viruses of protists and important pathogens of vertebrates, such as poxviruses. However, the characterization of viruses from nonmodel hosts still lags behind. We sequenced the complete genomes of three viruses infecting crustaceans, the Caribbean spiny lobster, demon shrimp, and European shore crab. These viruses have the smallest genomes among the known NCLDVs, with losses of many core genes, some of which are shared with iridoviruses. The deterioration of the transcription apparatus is compatible with microscopic and ultrastructural observations indicating that these viruses replicate in the nucleus of infected cells rather than in the cytoplasm. Phylogenomic analysis indicates that these viruses are sufficiently distinct from all other NCLDVs to justify the creation of a separate family, for which we propose the name "Mininucleoviridae" (i.e., small viruses reproducing in the cell nucleus).},
}

@article {pmid31936703,
year = {2020},
author = {Kang, S and You, HJ and Lee, YG and Jeong, Y and Johnston, TV and Baek, NI and Ku, S and Ji, GE},
title = {Production, Structural Characterization, and In Vitro Assessment of the Prebiotic Potential of Butyl-Fructooligosaccharides.},
journal = {International journal of molecular sciences},
volume = {21},
number = {2},
pages = {},
doi = {10.3390/ijms21020445},
pmid = {31936703},
issn = {1422-0067},
support = {2017R1A2B2012390//National Research Foundation of Korea/ ; NRF-2017M3A9F3041747//National Research Foundation of Korea/ ; },
abstract = {Short-chain fatty acids (SCFAs), especially butyrate, produced in mammalian intestinal tracts via fermentation of dietary fiber, are known biofunctional compounds in humans. However, the variability of fermentable fiber consumed on a daily basis and the diversity of gut microbiota within individuals often limits the production of short-chain fatty acids in the human gut. In this study, we attempted to enhance the butyrate levels in human fecal samples by utilizing butyl-fructooligosaccharides (B-FOS) as a novel prebiotic substance. Two major types of B-FOS (GF3-1B and GF3-2B), composed of short-chain fructooligosaccharides (FOS) bound to one or two butyric groups by ester bonds, were synthesized. Qualitative analysis of these B-FOS using Fourier transform infrared (FT-IR) spectroscopy, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), nuclear magnetic resonance (NMR) and low-resolution fast-atom bombardment mass spectra (LR-FAB-MS), showed that the chemical structure of GF3-1B and GF3-2B were [O-(1-buty-β-D-fru-(2→1)-O-β-D-fru-(2→1)-O-β-D-fru-O-α-D-glu] and [O-(1-buty)-β-D-fru-(2→1)-O-β-D-fru-(2→1)-O-(4-buty)-β-D-fru-O-α-D-glu], respectively. The ratio of these two compounds was approximately 5:3. To verify their biofunctionality as prebiotic oligosaccharides, proliferation and survival patterns of human fecal microbiota were examined in vitro via 16S rRNA metagenomics analysis compared to a positive FOS control and a negative control without a carbon source. B-FOS treatment showed different enrichment patterns on the fecal microbiota community during fermentation, and especially stimulated the growth of major butyrate producing bacterial consortia and modulated specific butyrate producing pathways with significantly enhanced butyrate levels. Furthermore, the relative abundance of Fusobacterium and ammonia production with related metabolic genes were greatly reduced with B-FOS and FOS treatment compared to the control group. These findings indicate that B-FOS differentially promotes butyrate production through the enhancement of butyrate-producing bacteria and their metabolic genes, and can be applied as a novel prebiotic compound in vivo.},
}

@article {pmid31935465,
year = {2020},
author = {O' Donovan, CM and Connor, B and Madigan, SM and Cotter, PD and O' Sullivan, O},
title = {Instances of altered gut microbiomes among Irish cricketers over periods of travel in the lead up to the 2016 World Cup: A sequencing analysis.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {101553},
doi = {10.1016/j.tmaid.2020.101553},
pmid = {31935465},
issn = {1873-0442},
abstract = {BACKGROUND: Changes and stresses experienced during travel have the potential to impact the gut microbiome, with travel implicated in the spread of antibiotic resistance genes across continents. The possibility of gut microbiome-mediated negative impacts arising from travel, and consequences for peak performance, would be of particular concern for elite athletes.

METHODS: Faecal samples were collected from male (N = 14) and female (N = 7) cricket players during the build-up to the 2016 Cricket World Cup. Baseline and post-travel samples were collected from all participants and subjected to 16S rRNA amplicon sequencing. Samples from a subset of participants (N = 4) were analysed by shotgun metagenomic sequencing.

RESULTS: Analysis revealed a single travel time point as having the potential to have an impact on the gut microbiome. Reductions in alpha diversity following travel were observed, accompanied by shifts in the taxonomic profile of the gut microbiome. Antibiotic resistance and virulence genes were also identified as undergoing changes following travel.

CONCLUSIONS: This study reveals that periods of travel, in particular following gastrointestinal distress, may result in gut microbiome disruption. While this analysis was completed in athletes, the findings are applicable to all travelling individuals and considerations should be made surrounding travel in an attempt to reduce these changes.},
}

@article {pmid31934655,
year = {2019},
author = {Orłowska, A and Iwan, E and Smreczak, M and Rola, J},
title = {Evaluation of Direct Metagenomics and Target Enriched Approaches for High-throughput Sequencing of Field Rabies Viruses.},
journal = {Journal of veterinary research},
volume = {63},
number = {4},
pages = {471-479},
pmid = {31934655},
issn = {2450-7393},
abstract = {Introduction: High-throughput sequencing (HTS) identifies random viral fragments in environmental samples metagenomically. High reliability gains it broad application in virus evolution, host-virus interaction, and pathogenicity studies. Deep sequencing of field samples with content of host genetic material and bacteria often produces insufficient data for metagenomics and must be preceded by target enrichment. The main goal of the study was the evaluation of HTS for complete genome sequencing of field-case rabies viruses (RABVs).

Material and Methods: The material was 23 RABVs isolated mainly from red foxes and one European bat lyssavirus-1 isolate propagated in neuroblastoma cells. Three methods of RNA isolation were tested for the direct metagenomics and RABV-enriched approaches. Deep sequencing was performed with a MiSeq sequencer (Illumina) and reagent v3 kit. Bioinformatics data were evaluated by Kraken and Centrifuge software and de novo assembly was done with metaSPAdes.

Results: Testing RNA extraction procedures revealed the deep sequencing scope superiority of the combined TRIzol/column method. This HTS methodology made it possible to obtain complete genomes of all the RABV isolates collected in the field. Significantly greater rates of RABV genome coverages (over 5,900) were obtained with RABV enrichment. Direct metagenomic studies sequenced the full length of 6 out of 16 RABV isolates with a medium coverage between 1 and 71.

Conclusion: Direct metagenomics gives the most realistic illustration of the field sample microbiome, but with low coverage. For deep characterisation of viruses, e.g. for spatial and temporal phylogeography during outbreaks, target enrichment is recommended as it covers sequences much more completely.},
}

@article {pmid31933014,
year = {2020},
author = {Aguirre-Garrido, JF and Martínez-Abarca, F and Montiel-Lugo, D and Hernández-Soto, LM and Ramírez-Saad, H},
title = {Metagenomic analyses uncover the differential effect of azide treatment on bacterial community structure by enriching a specific Cyanobacteria present in a saline-alkaline environmental sample.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10123-020-00119-z},
pmid = {31933014},
issn = {1618-1905},
support = {BIO2017-82244-P//Ministerio de Ciencia, Innovación y Universidades/ ; 710228//Consejo Nacional de Ciencia y Tecnología/ ; 291062//Consejo Nacional de Ciencia y Tecnología/ ; },
abstract = {Treatment of environmental samples under field conditions may require the application of chemical preservatives, although their use sometimes produces changes in the microbial communities. Sodium azide, a commonly used preservative, is known to differentially affect the growth of bacteria. Application of azide and darkness incubation to Isabel soda lake water samples induced changes in the structure of the bacterial community, as assessed by partial 16S rRNA gene pyrosequencing. Untreated water samples (WU) were dominated by gammaproteobacterial sequences accounting for 86%, while in the azide-treated (WA) samples, this group was reduced to 33% abundance, and cyanobacteria-related sequences became dominant with 53%. Shotgun sequencing and genome recruitment analyses pointed to Halomonas campanensis strain LS21 (genome size 4.07 Mbp) and Synechococcus sp. RS9917 (2.58 Mbp) as the higher recruiting genomes from the sequence reads of WA and WU environmental libraries, respectively, covering nearly the complete genomes. Combined treatment of water samples with sodium azide and darkness has proven effective on the selective enrichment of a cyanobacterial group. This approach may allow the complete (or almost-complete) genome sequencing of Cyanobacteria from metagenomic DNA of different origins, and thus increasing the number of the underrepresented cyanobacterial genomes in the databases.},
}

@article {pmid31933013,
year = {2020},
author = {Xu, Y and Zhang, G and Ding, H and Ci, D and Dai, L and Zhang, Z},
title = {Influence of salt stress on the rhizosphere soil bacterial community structure and growth performance of groundnut (Arachis hypogaea L.).},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10123-020-00118-0},
pmid = {31933013},
issn = {1618-1905},
support = {2018YFD1000906//the National Key R&D Program of China/ ; CXGC2018E21//the Agricultural Scientific and the Technological Innovation Project of Shandong Academy of Agricultural Sciences/ ; },
abstract = {Soil salinity is regarded as severe environmental stress that can change the composition of rhizosphere soil bacterial community and import a plethora of harms to crop plants. However, relatively little is known about the relationship between salt stress and root microbial communities in groundnuts. The goal of this study was to assess the effect of salt stress on groundnut growth performance and rhizosphere microbial community structure. Statistical analysis exhibited that salt stress indeed affected groundnut growth and pod yield. Further taxonomic analysis showed that the bacterial community predominantly consisted of phyla Proteobacteria, Actinobacteria, Saccharibacteria, Chloroflexi, Acidobacteria, and Cyanobacteria. Among these bacteria, numbers of Cyanobacteria and Acidobacteria mainly increased, while that of Actinobacteria and Chloroflexi decreased after salt treatment via taxonomic and qPCR analysis. Moreover, Sphingomonas and Microcoleus as the predominant genera in salt-treated rhizosphere soils might enhance salt tolerance as plant growth-promoting rhizobacteria. Metagenomic profiling showed that series of sequences related to signaling transduction, posttranslational modification, and chaperones were enriched in the salt-treated soils, which may have implications for plant survival and salt tolerance. These data will help us better understand the symbiotic relationship between the dominant microbial community and groundnuts and form the foundation for further improvement of salt tolerance of groundnuts via modification of soil microbial community.},
}

@article {pmid31932713,
year = {2020},
author = {Deng, X and Achari, A and Federman, S and Yu, G and Somasekar, S and Bártolo, I and Yagi, S and Mbala-Kingebeni, P and Kapetshi, J and Ahuka-Mundeke, S and Muyembe-Tamfum, JJ and Ahmed, AA and Ganesh, V and Tamhankar, M and Patterson, JL and Ndembi, N and Mbanya, D and Kaptue, L and McArthur, C and Muñoz-Medina, JE and Gonzalez-Bonilla, CR and López, S and Arias, CF and Arevalo, S and Miller, S and Stone, M and Busch, M and Hsieh, K and Messenger, S and Wadford, DA and Rodgers, M and Cloherty, G and Faria, NR and Thézé, J and Pybus, OG and Neto, Z and Morais, J and Taveira, N and R Hackett, J and Chiu, CY},
title = {Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-019-0637-9},
pmid = {31932713},
issn = {2058-5276},
support = {204311/Z/16/Z//Wellcome Trust (Wellcome)/ ; R33-AI129455//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01-HL105704//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; },
abstract = {Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use.},
}