@article {pmid32227523,
year = {2020},
author = {Hiramatsu, Y and Suzuki, K and Motooka, D and Nakamura, S and Horiguchi, Y},
title = {Expression of small RNAs of Bordetella pertussis colonizing murine tracheas.},
journal = {Microbiology and immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1348-0421.12791},
pmid = {32227523},
issn = {1348-0421},
abstract = {We performed RNA sequencing on Bordetella pertussis, the causative agent of whooping cough, and identified 9 novel small RNAs (sRNAs) that were transcribed during the bacterial colonization of murine tracheas. Among them, four sRNAs were more strongly expressed in vivo than in vitro. Moreover, the expression of 8 sRNAs was not regulated by the BvgAS two-component system, which is the master regulator for the expression of genes contributing to the bacterial infection. The present results suggest a BvgAS-independent gene regulatory system involving the sRNAs that is active during B. pertussis infection. This article is protected by copyright. All rights reserved.},
}

@article {pmid32226996,
year = {2020},
author = {Chen, M and Guo, WL and Li, QY and Xu, JX and Cao, YJ and Liu, B and Yu, XD and Rao, PF and Ni, L and Lv, XC},
title = {The protective mechanism of Lactobacillus plantarum FZU3013 against non-alcoholic fatty liver associated with hyperlipidemia in mice fed a high-fat diet.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/c9fo03003d},
pmid = {32226996},
issn = {2042-650X},
abstract = {Lactobacillus plantarum FZU3013, a probiotic previously isolated from the traditional brewing process of Hongqu rice wine, may have the beneficial effect of improving the disorders of lipid metabolism. This study aimed to investigate the role of L. plantarum FZU3013 in improving non-alcoholic fatty liver (NAFL) associated with hyperlipidemia in mice fed a high-fat diet. The results indicated that L. plantarum FZU3013 intervention significantly reduced the HFD-induced body weight gain and the abnormal levels of serum total triglycerides (TG), total cholesterol (TC) and low-density lipoprotein (LDL-C), and inhibited the excessive accumulation of liver lipids. In addition, L. plantarum FZU3013 also promoted the excretion of bile acids through feces. Metagenomic and multivariate statistical analysis revealed that L. plantarum FZU3013 made significant structural changes in the intestinal microbiome of the mice fed with HFD, in particular by modulating the relative abundance of some function related microbial phylotypes. Furthermore, ultra-performance liquid chromatography with quadruple-time of flight mass spectrometry (UPLC-QTOF/MS)-based liver metabolomics demonstrated that L. plantarum FZU3013 had a significant regulatory effect on the composition of liver metabolites in hyperlipidemic mice, especially on the levels of some important biomarkers involved in the pathways of glycerophospholipid metabolism, fatty acid degradation, fatty acid elongation, glycerolipid metabolism, primary bile acid biosynthesis, arachidonic acid metabolism, etc. Moreover, L. plantarum FZU3013 regulated the mRNA expression levels of the genes responsible for liver lipid and cholesterol metabolism. L. plantarum FZU3013 intervention increased the hepatic mRNA levels of cholesterol 7α-hydroxylase (CYP7A1) and the bile salt export pump (BSEP), suggesting enhanced bile acid synthesis and excretion from the liver. These findings present new evidence supporting that L. plantarum FZU3013 has the potential to improve lipid metabolism disorders through modulating specific intestinal microbial phylotypes and regulating hepatic lipid metabolism related genes, therefore it could be used as a potential functional food for the prevention of NAFL and hyperlipidemia.},
}

@article {pmid32226422,
year = {2020},
author = {Chen, ML and Becraft, ED and Pachiadaki, M and Brown, JM and Jarett, JK and Gasol, JM and Ravin, NV and Moser, DP and Nunoura, T and Herndl, GJ and Woyke, T and Stepanauskas, R},
title = {Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {376},
doi = {10.3389/fmicb.2020.00376},
pmid = {32226422},
issn = {1664-302X},
abstract = {Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.},
}

@article {pmid32224841,
year = {2020},
author = {Ko, G and Kim, PG and Cho, Y and Jeong, S and Kim, JY and Kim, KH and Lee, HY and Han, J and Yu, N and Ham, S and Jang, I and Kang, B and Shin, S and Kim, L and Lee, SW and Nam, D and Kim, JF and Kim, N and Kim, SY and Lee, S and Roh, TY and Lee, B},
title = {Bioinformatics services for analyzing massive genomic datasets.},
journal = {Genomics & informatics},
volume = {18},
number = {1},
pages = {e8},
doi = {10.5808/GI.2020.18.1.e8},
pmid = {32224841},
issn = {1598-866X},
support = {2014M3C9A3064552//National Research Foundation of Korea/ ; 2014M3C9A3065221//National Research Foundation of Korea/ ; 2014M3C9A3064548//National Research Foundation of Korea/ ; 2014M3C9A3068554//National Research Foundation of Korea/ ; 2014M3C9A3068822//National Research Foundation of Korea/ ; 2019M3C9A5069653//National Research Foundation of Korea/ ; },
abstract = {The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www.bioexpress.re.kr/.},
}

@article {pmid32224328,
year = {2020},
author = {Kotay, SM and Parikh, HI and Barry, K and Gweon, HS and Guilford, W and Carroll, J and Mathers, AJ},
title = {Nutrients influence the dynamics of Klebsiella pneumoniae carbapenemase producing enterobacterales in transplanted hospital sinks.},
journal = {Water research},
volume = {176},
number = {},
pages = {115707},
doi = {10.1016/j.watres.2020.115707},
pmid = {32224328},
issn = {1879-2448},
abstract = {Antimicrobial resistance has been recognized as a threat to human health. The role of hospital sinks acting as a reservoir for some of the most concerning antibiotic resistant organisms, carbapenemase producing Enterobacterales (CPE) is evident but not well understood. Strategies to prevent establishment, interventions to eliminate these reservoirs and factors which drive persistence of CPE are not well established. We use a uniquely designed sink lab to transplant CPE colonized hospital sink plumbing with an aim to understand CPE dynamics in a controlled setting, notably exploiting both molecular and culture techniques. After ex situ installation the CPE population in the sink plumbing drop from previously detectable to undetectable levels. The addition of nutrients is followed by a quick rebound in CPE detection in the sinks after as many as 37 days. We did not however detect a significant shift in microbial community structure or the overall resistance gene carriage in longitudinal samples from a subset of these transplanted sinks using whole shotgun metagenomic sequencing. Comparing nutrient types in a benchtop culture study model, protein rich nutrients appear to be the most supportive for CPE growth and biofilm formation ability. The role of nutrients exposure is determining factor for maintaining a high bioburden of CPE in the sink drains and P-traps. Therefore, limiting nutrient disposal into sinks has reasonable potential with regard to decreasing the CPE wastewater burden, especially in hospitals seeking to control an environmental reservoir.},
}

@article {pmid32222544,
year = {2020},
author = {Jia, S and Bian, K and Shi, P and Ye, L and Liu, CH},
title = {Metagenomic profiling of antibiotic resistance genes and their associations with bacterial community during multiple disinfection regimes in a full-scale drinking water treatment plant.},
journal = {Water research},
volume = {176},
number = {},
pages = {115721},
doi = {10.1016/j.watres.2020.115721},
pmid = {32222544},
issn = {1879-2448},
abstract = {For comprehensive insights into the effects of multiple disinfection regimes on antibiotic resistome in drinking water, this study utilized metagenomic approaches to reveal the changing patterns of antibiotic resistance genes (ARGs) and bacterial community as well as their associations. A total of 297 ARGs within 17 types were detected in the drinking water, and their total relative abundance ranged from 195.49 ± 24.85 to 626.31 ± 38.61 copies of ARGs per cell. The total ARG abundance was significantly increased after the antimicrobial resin and ultraviolet (AR/UV) disinfection while significantly decreased after the ozone and chlorine (O3/Cl2) disinfection and remained stable after AR/Cl2 disinfection. Overall, 18 ARGs including bacA, mexT, and blaOXA-12, mainly affiliated to bacitracin, multidrug, and beta-lactam, were persistent and discriminative during all the disinfection strategies in drinking water, and they were considered as key ARGs that represent the antibiotic resistome during drinking water disinfection. Additionally, possible hosts of 50% key ARGs were revealed based on co-occurrence network. During multiple disinfection processes, the change of Fusobacteriales and Aeromonadaceae in abundance mainly contributed to the abundance shift of bacA, and Pseudomonas mainly increased the abundance of mexT. These findings indicated that bacterial community shift may be the key factor driving the change of antibiotic resistome during disinfection. The strong association between antibiotic resistome alteration and bacterial community shift proposed in this study may enhance our understanding of the underlying mechanism of the disinfection effects on antibiotic resistance and benefit effective measures to improve safety of drinking water.},
}

@article {pmid32222508,
year = {2020},
author = {Aalto, SL and Suurnäkki, S and von Ahnen, M and Siljanen, HMP and Pedersen, PB and Tiirola, M},
title = {Nitrate removal microbiology in woodchip bioreactors: A case-study with full-scale bioreactors treating aquaculture effluents.},
journal = {The Science of the total environment},
volume = {723},
number = {},
pages = {138093},
doi = {10.1016/j.scitotenv.2020.138093},
pmid = {32222508},
issn = {1879-1026},
abstract = {Woodchip bioreactors are viable low-cost nitrate (NO3-) removal applications for treating agricultural and aquaculture discharges. The active microbial biofilms growing on woodchips are conducting nitrogen (N) removal, reducing NO3- while oxidizing the carbon (C) from woodchips. However, bioreactor age, and changes in the operating conditions or in the microbial community might affect the NO3- removal as well as potentially promote nitrous oxide (N2O) production through either incomplete denitrification or dissimilatory NO3- reduction to ammonium (DNRA). Here, we combined stable isotope approach, amplicon sequencing, and captured metagenomics for studying the potential NO3- removal rates, and the abundance and community composition of microbes involved in N transformation processes in the three different full-scale woodchip bioreactors treating recirculating aquaculture system (RAS) effluents. We confirmed denitrification producing di‑nitrogen gas (N2) to be the primary NO3- removal pathway, but found that 6% of NO3- could be released as N2O under high NO3- concentrations and low amounts of bioavailable C, whereas DNRA rates tend to increase with the C amount. The abundance of denitrifiers was equally high between the studied bioreactors, yet the potential NO3- removal rates were linked to the denitrifying community diversity. The same core proteobacterial groups were driving the denitrification, while Bacteroidetes dominated the DNRA carrying microbes in all the three bioreactors studied. Altogether, our results suggest that woodchip bioreactors have a high genetic potential for NO3- removal through a highly abundant and diverse denitrifying community, but that the rates and dynamics between the NO3- removal pathways depend on the other factors (e.g., bioreactor design, operating conditions, and the amount of bioavailable C in relation to the incoming NO3- concentrations).},
}

@article {pmid32222272,
year = {2020},
author = {Desbrousses, C and Archer, F and Colin, A and Bobet-Erny, A and Champavère, A and Gros, E and Beurdeley, P and Cruvellier, S and Tardy, F and Eloit, M},
title = {High-Throughput Sequencing (HTS) of newly synthetized RNAs enables one shot detection and identification of live mycoplasmas and differentiation from inert nucleic acids.},
journal = {Biologicals : journal of the International Association of Biological Standardization},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biologicals.2020.03.002},
pmid = {32222272},
issn = {1095-8320},
abstract = {Mycoplasma contamination threatens both the safety of biologics produced in cell substrates as well as the quality of scientific results based on cell-culture observations. Methods currently used to detect contamination of cells include culture, enzymatic activity, immunofluorescence and PCR but suffer from some limitations. High throughput sequencing (HTS) can be used to identify microbes like mycoplasmas in biologics since it enables an unbiased approach to detection without the need to design specific primers to pre-amplify target sequences but it does not enable the confirmation of microbial infection since this could reflect carryover of inert sequences. In order to unambiguously differentiate the presence of live or dead mycoplasmas in biological products, the present method was developed based on metabolic RNA labelling of newly synthetized mycoplasmal RNAs. HTS of labelled RNA detected A549 cell infection with Acholeplasma laidlawii in a manner similar to both PCR and culture and demonstrated that this technique can unambiguously identify bacterial species and differentiates infected cells from cells exposed to a high inoculum of heat-inactivated mycoplasmas. This method therefore combines the advantage of culture (that detects only live microorganisms) with those of molecular tests (rapidity) together with a very broad range of bacterial detection and identification.},
}

@article {pmid31830070,
year = {2019},
author = {Khilyas, IV and Sorokina, AV and Elistratova, AA and Markelova, MI and Siniagina, MN and Sharipova, MR and Shcherbakova, TA and D'Errico, ME and Cohen, MF},
title = {Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0225929},
pmid = {31830070},
issn = {1932-6203},
mesh = {Asbestos, Serpentine/*analysis ; Biodiversity ; Computational Biology/methods ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Minerals/*analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Russia ; *Soil Microbiology ; Spectrum Analysis ; },
abstract = {Endolithic microbial communities survive nutrient and energy deficient conditions while contributing to the weathering of their mineral substrate. This study examined the mineral composition and microbial communities of fully serpentinized weathered rock from 0.1 to 6.5 m depth at a site within the Khalilovsky massif, Orenburg Region, Southern Ural Mountains, Russia. The mineral composition includes a major content of serpentinite family (mostly consisting of lizardite and chrysotile), magnesium hydrocarbonates (hydromagnesite with lesser amounts of hydrotalcite and pyroaurite) concentrated in the upper layers, and clay minerals. We found that the deep-seated weathered serpentinites are chrysotile-type minerals, while the middle and surface serpentinites mostly consist of lizardite and chrysotile types. Microbial community analysis, based on 16S rRNA gene sequencing, showed a similar diversity of phyla throughout the depth profile. The dominant bacterial phyla were the Actinobacteria (of which unclassified genera in the orders Acidimicrobiales and Actinomycetales were most numerous), Chloroflexi (dominated by an uncultured P2-11E order) and the Proteobacteria (predominantly class Betaproteobacteria). Densities of several groups of bacteria were negatively correlated with depth. Occurrence of the orders Actinomycetales, Gaiellales, Solirubrobacterales, Rhizobiales and Burkholderiales were positively correlated with depth. Our findings show that endolithic microbial communities of the Khalilovsky massif have similar diversity to those of serpentine soils and rocks, but are substantially different from those of the aqueous environments of actively serpentinizing systems.},
}

Asbestos, Serpentine/*analysis
Biodiversity
Computational Biology/methods
Geologic Sediments/*chemistry/*microbiology
Metagenome
Metagenomics/methods
*Microbiota
Minerals/*analysis
Phylogeny
RNA, Ribosomal, 16S/genetics
Russia
*Soil Microbiology
Spectrum Analysis

@article {pmid31800638,
year = {2019},
author = {Choi, S and Lee, JG and Lee, AR and Eun, CS and Han, DS and Park, CH},
title = {Helicobacter pylori antibody and pepsinogen testing for predicting gastric microbiome abundance.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0225961},
pmid = {31800638},
issn = {1932-6203},
mesh = {Adult ; Antibodies, Bacterial/*immunology ; Bacterial Load ; Comorbidity ; Female ; Helicobacter Infections/diagnosis/*immunology/*metabolism/*microbiology ; Helicobacter pylori/*immunology ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Pepsinogen A/*metabolism ; Prognosis ; Serologic Tests ; Stomach Neoplasms/etiology ; },
abstract = {BACKGROUND: Although the high-throughput sequencing technique is useful for evaluating gastric microbiome, it is difficult to use clinically. We aimed to develop a predictive model for gastric microbiome based on serologic testing.

METHODS: This study was designed to analyze sequencing data obtained from the Hanyang University Gastric Microbiome Cohort, which was established initially to investigate gastric microbial composition according to the intragastric environment. We evaluated the relationship between the relative abundance of potential gastric cancer-associated bacteria (nitrosating/nitrate-reducing bacteria or type IV secretion system [T4SS] protein gene-contributing bacteria) and serologic markers (IgG anti-Helicobacter pylori [HP] antibody or pepsinogen [PG] levels).

RESULTS: We included 57 and 26 participants without and with HP infection, respectively. The relative abundance of nitrosating/nitrate-reducing bacteria was 4.9% and 3.6% in the HP-negative and HP-positive groups, respectively, while that of T4SS protein gene-contributing bacteria was 20.5% and 6.5% in the HP-negative and HP-positive groups, respectively. The relative abundance of both nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria increased exponentially as PG levels decreased. Advanced age (only for nitrosating/nitrate-reducing bacteria), a negative result of IgG anti-HP antibody, low PG levels, and high Charlson comorbidity index were associated with a high relative abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria. The adjusted coefficient of determination (R2) was 53.7% and 70.0% in the model for nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria, respectively.

CONCLUSION: Not only the negative results of IgG anti-HP antibody but also low PG levels were associated with a high abundance of nitrosating/nitrate-reducing bacteria and T4SS protein gene-contributing bacteria.},
}

Adult
Antibodies, Bacterial/*immunology
Bacterial Load
Comorbidity
Female
Helicobacter Infections/diagnosis/*immunology/*metabolism/*microbiology
Helicobacter pylori/*immunology
Humans
Male
Metagenome
Metagenomics/methods
*Microbiota
Middle Aged
Pepsinogen A/*metabolism
Prognosis
Serologic Tests
Stomach Neoplasms/etiology

@article {pmid31477884,
year = {2019},
author = {Perkel, JM},
title = {Workflow systems turn raw data into scientific knowledge.},
journal = {Nature},
volume = {573},
number = {7772},
pages = {149-150},
doi = {10.1038/d41586-019-02619-z},
pmid = {31477884},
issn = {1476-4687},
mesh = {Cloud Computing ; Computational Biology/*methods ; *Data Analysis ; Information Dissemination/*methods ; *Knowledge ; Metagenomics/methods ; Registries ; Reproducibility of Results ; Software/standards/*supply & distribution ; },
}

Cloud Computing
Computational Biology/*methods
*Data Analysis
Information Dissemination/*methods
*Knowledge
Metagenomics/methods
Registries
Reproducibility of Results
Software/standards/*supply & distribution

@article {pmid31363173,
year = {2019},
author = {Pérez-Carrascal, OM and Terrat, Y and Giani, A and Fortin, N and Greer, CW and Tromas, N and Shapiro, BJ},
title = {Coherence of Microcystis species revealed through population genomics.},
journal = {The ISME journal},
volume = {13},
number = {12},
pages = {2887-2900},
pmid = {31363173},
issn = {1751-7370},
mesh = {Brazil ; Canada ; Ecosystem ; Evolution, Molecular ; Fresh Water/microbiology ; Genome, Bacterial ; Metagenomics ; Microcystins/metabolism ; Microcystis/classification/*genetics/*isolation & purification/metabolism ; Phylogeny ; },
abstract = {Microcystis is a genus of freshwater cyanobacteria, which causes harmful blooms in ecosystems worldwide. Some Microcystis strains produce harmful toxins such as microcystin, impacting drinking water quality. Microcystis colony morphology, rather than genetic similarity, is often used to classify Microcystis into morphospecies. Yet colony morphology is a plastic trait, which can change depending on environmental and laboratory culture conditions, and is thus an inadequate criterion for species delineation. Furthermore, Microcystis populations are thought to disperse globally and constitute a homogeneous gene pool. However, this assertion is based on relatively incomplete characterization of Microcystis genomic diversity. To better understand these issues, we performed a population genomic analysis of 33 newly sequenced genomes mainly from Canada and Brazil. We identified 17 Microcystis clusters of genomic similarity, five of which correspond to monophyletic clades containing at least three newly sequenced genomes. Four out of these five clades match to named morphospecies. Notably, M. aeruginosa is paraphyletic, distributed across 12 genomic clusters, suggesting it is not a coherent species. A few clades of closely related isolates are specific to a unique geographic location, suggesting biogeographic structure over relatively short evolutionary time scales. Higher homologous recombination rates within than between clades further suggest that monophyletic groups might adhere to a Biological Species-like concept, in which barriers to gene flow maintain species distinctness. However, certain genes-including some involved in microcystin and micropeptin biosynthesis-are recombined between monophyletic groups in the same geographic location, suggesting local adaptation.},
}

Brazil
Canada
Ecosystem
Evolution, Molecular
Fresh Water/microbiology
Genome, Bacterial
Metagenomics
Microcystins/metabolism
Microcystis/classification/*genetics/*isolation & purification/metabolism
Phylogeny

@article {pmid31285337,
year = {2019},
author = {Greenlon, A and Chang, PL and Damtew, ZM and Muleta, A and Carrasquilla-Garcia, N and Kim, D and Nguyen, HP and Suryawanshi, V and Krieg, CP and Yadav, SK and Patel, JS and Mukherjee, A and Udupa, S and Benjelloun, I and Thami-Alami, I and Yasin, M and Patil, B and Singh, S and Sarma, BK and von Wettberg, EJB and Kahraman, A and Bukun, B and Assefa, F and Tesfaye, K and Fikre, A and Cook, DR},
title = {Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {30},
pages = {15200-15209},
pmid = {31285337},
issn = {1091-6490},
mesh = {Biological Evolution ; Cicer/*microbiology ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Mesorhizobium/classification/*genetics ; Metagenomics/methods ; Microbial Consortia/*genetics ; Nitrogen Fixation/physiology ; Phylogeny ; Phylogeography ; Soil/classification ; Soil Microbiology ; Symbiosis/genetics ; },
abstract = {Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.},
}

Biological Evolution
Cicer/*microbiology
Conjugation, Genetic
*Gene Transfer, Horizontal
*Genome, Bacterial
Mesorhizobium/classification/*genetics
Metagenomics/methods
Microbial Consortia/*genetics
Nitrogen Fixation/physiology
Phylogeny
Phylogeography
Soil/classification
Soil Microbiology
Symbiosis/genetics

@article {pmid31209046,
year = {2019},
author = {Rinker, DC and Specian, NK and Zhao, S and Gibbons, JG},
title = {Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {27},
pages = {13446-13451},
pmid = {31209046},
issn = {1091-6490},
mesh = {Adaptation, Physiological/genetics ; Animals ; *Biological Evolution ; Diet/*veterinary ; Ecology ; *Gene Dosage/genetics ; Metagenomics ; Ursidae/*genetics ; },
abstract = {Polar bear (Ursus maritimus) and brown bear (Ursus arctos) are recently diverged species that inhabit vastly differing habitats. Thus, analysis of the polar bear and brown bear genomes represents a unique opportunity to investigate the evolutionary mechanisms and genetic underpinnings of rapid ecological adaptation in mammals. Copy number (CN) differences in genomic regions between closely related species can underlie adaptive phenotypes and this form of genetic variation has not been explored in the context of polar bear evolution. Here, we analyzed the CN profiles of 17 polar bears, 9 brown bears, and 2 black bears (Ursus americanus). We identified an average of 318 genes per individual that showed evidence of CN variation (CNV). Nearly 200 genes displayed species-specific CN differences between polar bear and brown bear species. Principal component analysis of gene CN provides strong evidence that CNV evolved rapidly in the polar bear lineage and mainly resulted in CN loss. Olfactory receptors composed 47% of CN differentiated genes, with the majority of these genes being at lower CN in the polar bear. Additionally, we found significantly fewer copies of several genes involved in fatty acid metabolism as well as AMY1B, the salivary amylase-encoding gene in the polar bear. These results suggest that natural selection shaped patterns of CNV in response to the transition from an omnivorous to primarily carnivorous diet during polar bear evolution. Our analyses of CNV shed light on the genomic underpinnings of ecological adaptation during polar bear evolution.},
}

Adaptation, Physiological/genetics
Animals
*Biological Evolution
Diet/*veterinary
Ecology
*Gene Dosage/genetics
Metagenomics
Ursidae/*genetics

@article {pmid31143925,
year = {2019},
author = {Hundsdoerfer, AK and Lee, KM and Kitching, IJ and Mutanen, M},
title = {Genome-wide SNP Data Reveal an Overestimation of Species Diversity in a Group of Hawkmoths.},
journal = {Genome biology and evolution},
volume = {11},
number = {8},
pages = {2136-2150},
pmid = {31143925},
issn = {1759-6653},
mesh = {Animals ; *Evolution, Molecular ; *Genome ; Metagenomics/*methods ; Moths/*classification/*genetics ; Phylogeny ; *Polymorphism, Single Nucleotide ; Species Specificity ; },
abstract = {The interface between populations and evolving young species continues to generate much contemporary debate in systematics depending on the species concept(s) applied but which ultimately reduces to the fundamental question of "when do nondiscrete entities become distinct, mutually exclusive evolutionary units"? Species are perceived as critical biological entities, and the discovery and naming of new species is perceived by many authors as a major research aim for assessing current biodiversity before much of it becomes extinct. However, less attention is given to determining whether these names represent valid biological entities because this is perceived as both a laborious chore and an undesirable research outcome. The charismatic spurge hawkmoths (Hyles euphorbiae complex, HEC) offer an opportunity to study this less fashionable aspect of systematics. To elucidate this intriguing systematic challenge, we analyzed over 10,000 ddRAD single nucleotide polymorphisms from 62 individuals using coalescent-based and population genomic methodology. These genome-wide data reveal a clear overestimation of (sub)species-level diversity and demonstrate that the HEC taxonomy has been seriously oversplit. We conclude that only one valid species name should be retained for the entire HEC, namely Hyles euphorbiae, and we do not recognize any formal subspecies or other taxonomic subdivisions within it. Although the adoption of genetic tools has frequently revealed morphologically cryptic diversity, the converse, taxonomic oversplitting of species, is generally (and wrongly in our opinion) accepted as rare. Furthermore, taxonomic oversplitting is most likely to have taken place in intensively studied popular and charismatic organisms such as the HEC.},
}

Animals
*Evolution, Molecular
*Genome
Metagenomics/*methods
Moths/*classification/*genetics
Phylogeny
*Polymorphism, Single Nucleotide
Species Specificity

@article {pmid32221908,
year = {2020},
author = {Caraballo Guzmán, A and González Hurtado, MI and Cuesta-Astroz, Y and Torres, G},
title = {Metagenomic characterization of bacterial biofilm in four food processing plants in Colombia.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
doi = {10.1007/s42770-020-00260-x},
pmid = {32221908},
issn = {1678-4405},
support = {55965//Colciencias/ ; },
abstract = {Bacteria inside biofilms are more persistent and resistant to stress conditions found in the production environment of food processing plants, thus representing a constant risk for product safety and quality. Therefore, the aim of this study was to characterize, using 16S rRNA sequencing, the bacterial communities from biofilms found in four food processing plants (P1, P2, P3, and P4). In total, 50 samples from these four processing plants were taken after cleaning and disinfection processes. Four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroides represented over 94% of the operational taxonomic units found across these four plants. A total of 102 families and 189 genera were identified. Two genera, Pseudomonas spp. and Acinetobacter spp., were the most frequently found (93.47%) across the four plants. In P1, Pseudomonas spp. and Lactobacillus spp. were the dominant genera, whereas Lactobacillus spp. and Streptococcus spp. were identified in P2. On the other hand, biofilms found in P3 and P4 mainly consisted of Pseudomonas spp. and Acinetobacter spp. Our results indicate that different bacterial genera of interest to the food industry due to their ability to form biofilm and affect food quality can coexist inside biofilms, and as such, persist in production environments, representing a constant risk for manufactured foods. In addition, the core microbiota identified across processing plants evaluated was probably influenced by type of food produced and cleaning and disinfection processes performed in each one of these.},
}

@article {pmid32221408,
year = {2020},
author = {Wu, R and Chai, B and Cole, JR and Gunturu, SK and Guo, X and Tian, R and Gu, JD and Zhou, J and Tiedje, JM},
title = {Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-020-0635-1},
pmid = {32221408},
issn = {1751-7370},
support = {DE-SC0010715//U.S. Department of Energy (DOE)/ ; DE-FG02-99ER62848//U.S. Department of Energy (DOE)/ ; DBI-1356380//National Science Foundation (NSF)/ ; DBI-1759892//National Science Foundation (NSF)/ ; DBI-1356380//National Science Foundation (NSF)/ ; DBI-1759892//National Science Foundation (NSF)/ ; },
abstract = {There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus-host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus-host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.},
}

@article {pmid32220815,
year = {2020},
author = {Zhai, W and Qin, T and Li, L and Guo, T and Yin, X and Khan, MI and Hashmi, MZ and Liu, X and Tang, X and Xu, J},
title = {Abundance and diversity of microbial arsenic biotransformation genes in the sludge of full-scale anaerobic digesters from a municipal wastewater treatment plant.},
journal = {Environment international},
volume = {138},
number = {},
pages = {105535},
doi = {10.1016/j.envint.2020.105535},
pmid = {32220815},
issn = {1873-6750},
abstract = {Arsenic (As) is a potential contaminant in sewage sludge that may affect waste treatment and limit the use of these waste materials as soil amendments. Anaerobic digestion (AD) is an important and effective process for the treatment of sewage sludge and the chemical speciation of As is particularly important in sludge AD. However, the biotransformation genes of As in sludge during AD has not been fully explored. In this study, the influent and effluent sludge of anaerobic digester in a wastewater treatment plant (WWTP) was collected to investigate the species transformations of As, the abundance and diversity of As biotransformation genes was explored by real-time PCR (qPCR) and metagenomic sequencing, separately. The results showed that arsenite [As(III)] and arsenate [As(V)] were predominant in the influent sludge, whereas the relative abundance of monomethylarsenic acid (MMA) increased by 25.7% after digestion. As biotransformation genes were highly abundant, and the As(III) S-adenosylmethionine methyltransferase (arsM) gene was the predominant which significantly increased after AD by qPCR analysis. Metagenomic analysis indicated that the diversity of the arsM-like sequences also increased significantly after AD. Most of the arsM-like sequences in all the influent and effluent sludge samples were related to Bacteroidetes and Alphaproteobacteria. Furthermore, co-occurrence network analysis indicated a strong correlation between the microbial communities and As. This study provides a direct and reliable reference on As biotransformation genes and microbial community in the AD of sludge.},
}

@article {pmid32220197,
year = {2020},
author = {Du, R and Feng, Y and Liu, LN and Liu, YB and Ye, H and Lü, XJ and Wang, XH and Zong, ZY},
title = {[Pathogen Diagnosis of a Febrile HIV Case by the Metagenomic Next-generation Sequencing].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {51},
number = {2},
pages = {257-260},
doi = {10.12182/20200360605},
pmid = {32220197},
issn = {1672-173X},
abstract = {This study is aimed to explore the value of metagenomic next-generation sequencing (mNGS) in diagnosing pathogen in fever patients. It is often a challenge to identify the pathogen that caused the infection in the HIV patients with fever. How could the mNGS be helpful for pathogen diagnosis is unclear. Here we reported a case of human immunodeficiency virus (HIV) patient with 2-month period of fever. After routine clinical laboratory tests including the conventional smear, culture, serological tests and pathological examinations, the causal pathogen still remained undiagnosed. Then the lymph node biopsy tissue was subjected to broad-range polymerase chain reaction (PCR) and the peripheral blood was subjected to mNGS. At the same time, peripheral blood culture was carried out with an extension of culture time to acquire the pathogen. Results from both broad-range PCR and mNGS revealed the pathogen was Talaromyces marneffei. The isolate recovered from the peripheral blood culture was subjected to the whole-genome sequencing. Whole genome sequencing revealed that the antimicrobial resistance gene FLU1 existed in this pathogen's genome, but mNGS did not detect the FLU1 gene. Phylogenetic analysis based on whole genome sequence revealed that this isolate was far from other clones published in NCBI database. Here we reported a case of Talaromyces marneffei infection diagnosed by mNGS, showing that mNGS is helpful in etiological diagnosis for HIV patients with unexplained fever. However, application of mNGS in antimicrobial resistant genes detection and pathogen tracing need to be well-studied in the future.},
}

@article {pmid32219339,
year = {2020},
author = {Kyrgyzov, O and Prost, V and Gazut, S and Farcy, B and Brüls, T},
title = {Binning unassembled short reads based on k-mer abundance covariance using sparse coding.},
journal = {GigaScience},
volume = {9},
number = {4},
pages = {},
doi = {10.1093/gigascience/giaa028},
pmid = {32219339},
issn = {2047-217X},
abstract = {BACKGROUND: Sequence-binning techniques enable the recovery of an increasing number of genomes from complex microbial metagenomes and typically require prior metagenome assembly, incurring the computational cost and drawbacks of the latter, e.g., biases against low-abundance genomes and inability to conveniently assemble multi-terabyte datasets.

RESULTS: We present here a scalable pre-assembly binning scheme (i.e., operating on unassembled short reads) enabling latent genome recovery by leveraging sparse dictionary learning and elastic-net regularization, and its use to recover hundreds of metagenome-assembled genomes, including very low-abundance genomes, from a joint analysis of microbiomes from the LifeLines DEEP population cohort (n = 1,135, >1010 reads).

CONCLUSION: We showed that sparse coding techniques can be leveraged to carry out read-level binning at large scale and that, despite lower genome reconstruction yields compared to assembly-based approaches, bin-first strategies can complement the more widely used assembly-first protocols by targeting distinct genome segregation profiles. Read enrichment levels across 6 orders of magnitude in relative abundance were observed, indicating that the method has the power to recover genomes consistently segregating at low levels.},
}

@article {pmid32219088,
year = {2020},
author = {De, R and Mukhopadhyay, AK and Dutta, S},
title = {Molecular Analysis of Selected Resistance Determinants in Diarrheal Fecal Samples Collected From Kolkata, India Reveals an Abundance of Resistance Genes and the Potential Role of the Microbiota in Its Dissemination.},
journal = {Frontiers in public health},
volume = {8},
number = {},
pages = {61},
doi = {10.3389/fpubh.2020.00061},
pmid = {32219088},
issn = {2296-2565},
abstract = {Twenty-five diarrheal fecal samples from Kolkata were examined to determine the relative abundance of antimicrobial resistance genes (ARGs) against eight common classes of antibiotics with polymerase chain reaction (PCR) and Sanger sequencing. Relative abundance of an ARG was calculated as the percentage of fecal samples showing the presence of that particular ARG. The frequency of occurrence of resistance marker against each class of antibiotic was calculated as the percentage of fecal samples carrying at least one resistance marker for that particular class of antimicrobials. Antibiogram of Vibrio cholerae (V. cholerae) O1 strains isolated from four of these samples was obtained by disc diffusion method and was compared with the ARG profile of corresponding fecal samples from which the strains were isolated. A 464 bp amplicon of the V3-V4 region of bacterial 16S rDNA was obtained by PCR from 9 of these 25 samples using the primer pair S-D-Bact-0341-b-S-17 and S-D-Bact-0785-a-A-21 and sequenced to determine the major operational taxonomic unit (OTU). These 9 samples represented diarrhea due to diverse etiology and also unresolved etiology as determined by culture method. We conclude that the diarrheal intestinal microbiome has a common gene pool of ARGs against the major classes of antibiotics and may be serving as a reservoir of ARG dissemination. ARG profile of cholera stool showed that ARGs present in the gut of cholera patients may be transferred to the V. cholerae genome and pose a serious threat to the treatment of cholera by triggering resistance against potential drugs to which contemporary strains of V. cholerae were found to be sensitive in the present study. Fecal samples which were culture negative for diarrheal pathogens we tested also carried ARGs and OTU. Abundance of resistance markers against macrolides, tetracyclines, and aminoglycosides was the highest. Phylum Proteobacteria was the most abundant OTU suggesting proteobacterial blooms characteristic of disturbed gut microflora. Our study is the first comparative study of ARG profile of diarrheal samples with varying etiologic agent revealing the presence of ARGs against the most important classes of antibiotics in the gut of diarrheal patients by common, robust molecular methods, which are easily accessible by molecular epidemiological laboratories worldwide.},
}

@article {pmid32218527,
year = {2020},
author = {Lam, TT and Shum, MH and Zhu, HC and Tong, YG and Ni, XB and Liao, YS and Wei, W and Cheung, WY and Li, WJ and Li, LF and Leung, GM and Holmes, EC and Hu, YL and Guan, Y},
title = {Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-020-2169-0},
pmid = {32218527},
issn = {1476-4687},
abstract = {The ongoing outbreak of viral pneumonia in China and beyond is associated with a novel coronavirus, SARS-CoV-21. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection2. Although bats are likely reservoir hosts for SARS-CoV-2, the identity of any intermediate host that might have facilitated transfer to humans is unknown. Here, we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity to SARS-CoV-2 in the receptor-binding domain. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of novel coronaviruses and should be removed from wet markets to prevent zoonotic transmission.},
}

@article {pmid32218376,
year = {2020},
author = {Murphy, R},
title = {An Integrative Approach to Assessing Diet-Cancer Relationships.},
journal = {Metabolites},
volume = {10},
number = {4},
pages = {},
doi = {10.3390/metabo10040123},
pmid = {32218376},
issn = {2218-1989},
support = {17644//Michael Smith Foundation for Health Research/ ; 704735//Canadian Cancer Society Research Institute/ ; },
abstract = {The relationship between diet and cancer is often viewed with skepticism by the public and health professionals, despite a considerable body of evidence and general consistency in recommendations over the past decades. A systems biology approach which integrates 'omics' data including metabolomics, genetics, metagenomics, transcriptomics and proteomics holds promise for developing a better understanding of how diet affects cancer and for improving the assessment of diet through biomarker discovery thereby renewing confidence in diet-cancer links. This review discusses the application of multi-omics approaches to studies of diet and cancer. Considerations and challenges that need to be addressed to facilitate the investigation of diet-cancer relationships with multi-omic approaches are also discussed.},
}

@article {pmid32216300,
year = {2020},
author = {Sun, X and Kong, T and Haggblom, MM and Kolton, M and Li, F and Dong, Y and Huang, Y and Li, B and Sun, W},
title = {Chemolithoautotrophic diazotrophy dominates the nitrogen fixation process in mine tailings.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.9b07835},
pmid = {32216300},
issn = {1520-5851},
abstract = {Nutrient deficiency, especially bioavailable nitrogen deficiency, often impedes the bioremediation efforts of mining generated tailings. Biological nitrogen-fixation is a critical process necessary for the initial nitrogen buildup in tailings. Current knowledge regarding the diazotrophs that inhabit tailings is still in its infancy. Therefore, in this study, a comprehensive investigation combining geochemical characterization, sequence analyses, molecular techniques, and activity measurements was conducted to characterize the diazotrophic community residing in tailing environments. Significant differences between tailings and their adjacent soils in prokaryotic and diazotrophic communities were detected. Meanwhile, strong and significant correlations between the absolute abundance of the nitrogen fixation (nifH), carbon fixation (cbbL), sulfur oxidation (soxB), and arsenite oxidation (aioA) genes were observed in the tailings, but not in the soils. The reconstructed nif-containing metagenome-assembled genomes (MAGs) suggest that the carbon fixation and sulfur oxidation pathways were important for potential diazotrophs inhabiting the tailings. Activity measurements further confirmed that diazotrophs inhabiting tailings preferentially to use the inorganic electron donors (e.g., elemental sulfur) compared to organic electron donors (e.g., sucrose), while diazotrophs inhabiting soils preferred organic carbon sources. Collectively, these findings suggest that chemolithoautotrophic diazotrophs may play essential roles in acquiring nutrients and facilitating ecological succession in tailings.},
}

@article {pmid32215305,
year = {2020},
author = {Theerachat, M and Glinwong, C and Chulalaksananukul, W},
title = {Dataset of blood cockle (Anadara granosa) microbiota from coastal areas and earthen-pond farms around the upper Gulf of Thailand.},
journal = {Data in brief},
volume = {30},
number = {},
pages = {105393},
doi = {10.1016/j.dib.2020.105393},
pmid = {32215305},
issn = {2352-3409},
abstract = {The blood cockle (Anadara granosa), a bivalve mollusc, is a unique seafood item in Southeast Asia. Bivalve molluscs are filter feeders upon plankton, and so they may bioaccumulate microbes and heavy metals in their tissues. Bacteria survival can be enhanced by living inside the shell and they can subsequently infect humans and higher vertebrates after ingestion of the bivalve. This study presented a metagenomics analysis of the bacteria associated with A. granosa from six farms around the Gulf of Thailand. Three farms were located on the coast and the other three were from earthen ponds. Genomic DNA was extracted from the samples and analysed via sequencing of the V3-V4 region of the 16S rRNA gene, and then using a 97% DNA sequence similarity cut-off for designation of the operational taxonomic units. The environmental parameters, including temperature, pH, salinity, dissolved oxygen, and the concentration of three heavy metals (Cu, Cr, and Hg) and one metalloid (As) were investigated. The raw sequence data is available at the NCBI Sequence Read Archive accession number PRJNA592226. The Proteobacteria, Bacteroidetes and Cyanobacteria were common components of the microbiota in all six habitats and together comprised more than 77% of the relative abundance in all the samples. This is the first report on the microbiome in blood cockles in Thailand by a culture independent method. The data can be applied for efficiently controlling and improving seafood safety management.},
}

@article {pmid32213408,
year = {2020},
author = {Xing, L and Wang, Z and Gu, M and Yin, Q and Wu, G},
title = {Coupled effects of ferroferric oxide supplement and ethanol co-metabolism on the methanogenic oxidation of propionate.},
journal = {The Science of the total environment},
volume = {723},
number = {},
pages = {137992},
doi = {10.1016/j.scitotenv.2020.137992},
pmid = {32213408},
issn = {1879-1026},
abstract = {Direct interspecies electron transfer (DIET) is a new electron-transfer strategy for enhanced propionate degradation. Ethanol can enrich the DIET species of Geobacter and conductive ferroferric oxide (Fe3O4) can promote DIET. Therefore, coupled effects of ethanol and Fe3O4 on propionate degradation were investigated. The maximum CH4 production rate was increased by 81.4% by adding Fe3O4 when simultaneously fed with ethanol and propionate, while the improvement could not be observed without ethanol. The sludge conductivity and the electron transfer system activity by adding Fe3O4 were increased by 2.66 and 2.73 times, respectively. Besides, the relative abundance of functional microbes such as Geobacter, Syntrophobacter, Smithella, and Methanosaeta, and their functional genes were increased by the supplement of Fe3O4. The improvement of propionate degradation by adding Fe3O4 was largely attributed to the co-existence of ethanol degradation. The DIET between Geobacter and Methanosaeta might provide more energies or rapidly consume the oxidation products to promote the propionate degradation.},
}

@article {pmid32213246,
year = {2020},
author = {Averina, OV and Kovtun, AS and Polyakova, SI and Savilova, AM and Rebrikov, DV and Danilenko, VN},
title = {The bacterial neurometabolic signature of the gut microbiota of young children with autism spectrum disorders.},
journal = {Journal of medical microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1099/jmm.0.001178},
pmid = {32213246},
issn = {1473-5644},
abstract = {Introduction. The human gut microbiota is currently seen as an important factor that can promote autism spectrum disorder (ASD) development in children.Aim. This study aimed to detect differences in the taxonomic composition and content of bacterial genes encoding key enzymes involved in the metabolism of neuroactive biomarker compounds in the metagenomes of gut microbiota of children with ASD and neurotypical children.Methodology. A whole metagenome sequencing approach was used to obtain metagenomic data on faecal specimens of 36 children with ASD and 21 healthy neurotypical children of 3-5 years old. Taxonomic analysis was conducted using MetaPhlAn2. The developed bioinformatics algorithm and created catalogue of the orthologues were applied to identify bacterial genes of neuroactive compounds in the metagenomes. For the identification of metagenomic signatures of children with ASD, Wilcoxon's test and adjustment for multiple comparisons were used.Results. Statistically significant differences with decreases in average abundance in the microbiota of ASD children were found for the genera Barnesiella and Parabacteroides and species Alistipes putredinis, B. caccae, Bacteroides intestinihominis, Eubacterium rectale, Parabacteroides distasonis and Ruminococcus lactaris. Average relative abundances of the detected genes and neurometabolic signature approach did not reveal many significant differences in the metagenomes of the groups that were compared. We noted decreases in the abundance of genes linked to production of GABA, melatonine and butyric acid in the ASD metagenomes.Conclusion. For the first time, the neurometabolic signature of the gut microbiota of young children with ASD is presented. The data can help to provide a comparative assessment of the transcriptional and metabolomic activity of the identified genes.},
}

@article {pmid32211345,
year = {2020},
author = {Walkenhorst, MS and Reyes, L and Perez, G and Progulske-Fox, A and Brown, MB and Phillips, PL},
title = {A Uniquely Altered Oral Microbiome Composition Was Observed in Pregnant Rats With Porphyromonas gingivalis Induced Periodontal Disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {92},
doi = {10.3389/fcimb.2020.00092},
pmid = {32211345},
issn = {2235-2988},
abstract = {Porphyromonas gingivalis is an anaerobic bacterium commonly found in the oral cavity and associated with the development of periodontal disease. P. gingivalis has also been linked to several systemic vascular and inflammatory diseases including poor pregnancy outcomes. Little is known about the changes in the oral flora during pregnancy in connection to P. gingivalis infection. This pilot study aims to explore changes in the oral microbiome due to P. gingivalis inoculation and pregnancy in an in vivo rat model of periodontal disease. A metagenomic sequencing analysis targeting seven of the 16S rRNA gene variable regions was performed for oral samples collected at the following time points: baseline control (week 0), P. gingivalis inoculated (week 11), P. gingivalis inoculated and pregnant rat at necropsy (week 16). A second set of animals were also sampled to generate a sham-inoculated (week 11) control group. We found that the rat oral microbiome profiles were more similar to that of the human oral cavity compared to previous reports targeting one or two 16S variable regions. Overall, there appears to be a relatively stable core microbiome in the oral cavity. As expected, P. gingivalis induced periodontal disease resulted in oral microbiome dysbiosis. During pregnancy, some aspects of the oral microbiome shifted toward a more baseline-like profile. However, population analyses in terms of dissimilarity measures and especially metagenomic based predictions of select characteristics such as cell morphology, oxygen requirement, and major metabolite synthesis showed that pregnancy did not restore the composition of the oral microbiome. Rather, a uniquely altered oral microbiome composition was observed in pregnant rats with pre-established periodontal disease.},
}

@article {pmid32211343,
year = {2020},
author = {Xing, XW and Zhang, JT and Ma, YB and He, MW and Yao, GE and Wang, W and Qi, XK and Chen, XY and Wu, L and Wang, XL and Huang, YH and Du, J and Wang, HF and Wang, RF and Yang, F and Yu, SY},
title = {Metagenomic Next-Generation Sequencing for Diagnosis of Infectious Encephalitis and Meningitis: A Large, Prospective Case Series of 213 Patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {88},
doi = {10.3389/fcimb.2020.00088},
pmid = {32211343},
issn = {2235-2988},
abstract = {Purpose: We assessed the performance of metagenomic next-generation sequencing (mNGS) in the diagnosis of infectious encephalitis and meningitis. Methods: This was a prospective multicenter study. Cerebrospinal fluid samples from patients with viral encephalitis and/or meningitis, tuberculous meningitis, bacterial meningitis, fungal meningitis, and non-central nervous system (CNS) infections were subjected to mNGS. Results: In total, 213 patients with infectious and non-infectious CNS diseases were finally enrolled from November 2016 to May 2019; the mNGS-positive detection rate of definite CNS infections was 57.0%. At a species-specific read number (SSRN) ≥2, mNGS performance in the diagnosis of definite viral encephalitis and/or meningitis was optimal (area under the curve [AUC] = 0.659, 95% confidence interval [CI] = 0.566-0.751); the positivity rate was 42.6%. At a genus-specific read number ≥1, mNGS performance in the diagnosis of tuberculous meningitis (definite or probable) was optimal (AUC=0.619, 95% CI=0.516-0.721); the positivity rate was 27.3%. At SSRNs ≥5 or 10, the diagnostic performance was optimal for definite bacterial meningitis (AUC=0.846, 95% CI = 0.711-0.981); the sensitivity was 73.3%. The sensitivities of mNGS (at SSRN ≥2) in the diagnosis of cryptococcal meningitis and cerebral aspergillosis were 76.92 and 80%, respectively. Conclusion: mNGS of cerebrospinal fluid effectively identifies pathogens causing infectious CNS diseases. mNGS should be used in conjunction with conventional microbiological testing. Trial Registration: Chinese Clinical Trial Registry, ChiCTR1800020442.},
}

@article {pmid32211306,
year = {2020},
author = {Junior, JA and Vieira, YA and Cruz, IA and da Silva Vilar, D and Aguiar, MM and Torres, NH and Bharagava, RN and Lima, ÁS and de Souza, RL and Romanholo Ferreira, LF},
title = {Sequential degradation of raw vinasse by a laccase enzyme producing fungus Pleurotus sajor-caju and its ATPS purification.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {25},
number = {},
pages = {e00411},
doi = {10.1016/j.btre.2019.e00411},
pmid = {32211306},
issn = {2215-017X},
abstract = {This study evaluated simultaneously the raw vinasse degradation, an effluent from the sugar-alcohol industry, the laccase production by Pleurotus sajor-caju and its purification using aqueous two-phase systems (ATPS). To improve laccase production, different concentrations of inducers (ethanol and CuSO4) were added. The higher laccase production promoted an increase of 4-fold using 0.4 mM of CuSO4 as inducer, with maximum enzymatic activity of 539.3 U/L on the 3rd day of fermentation. The final treated vinasse had a decolorization of 92% and turbidity removal of 99% using CuSO4. Moreover, the produced laccase was then purified by ATPS in a single purification step, reaching 2.9-fold and recovered ≈ 99,9 %, in the top phase (PEG-rich phase) using 12 wt% of PEG 1500 + 20 wt% of citrate buffer + enzyme broth + water, at 25 °C. Thus, an integrated process of vinasse degradation, laccase production and purification with potential industrial application was proposed.},
}

@article {pmid32210948,
year = {2020},
author = {Sepulveda, J and Moeller, AH},
title = {The Effects of Temperature on Animal Gut Microbiomes.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {384},
doi = {10.3389/fmicb.2020.00384},
pmid = {32210948},
issn = {1664-302X},
abstract = {Temperature is a prominent abiotic environmental variable that drives the adaptive trajectories of animal lineages and structures the composition of animal communities. Global temperature regimes are expected to undergo rapid shifts in the next century, yet for many animal taxa we lack an understanding of the consequences of these predicted shifts for animal populations. In this review, we synthesize recent evidence that temperature variation shapes the composition and function of animal gut microbiomes, key regulators of host physiology, with potential consequences for host population responses to climate change. Several recent studies spanning a range of animal taxa, including Chordata, Arthropoda, and Mollusca, have reported repeatable associations between temperature and the community composition and function of the gut microbiome. In several cases, the same microbiome responses to temperature have been observed across distantly related animal taxa, suggesting the existence of conserved mechanisms underlying temperature-induced microbiome plasticity. Extreme temperatures can disrupt the stability of alpha-diversity within the gut microbiomes individual hosts and generate beta-diversity among microbiomes within host populations. Microbiome states resulting from extreme temperatures have been associated, and in some cases causally linked, with both beneficial and deleterious effects on host phenotypes. We propose routes by which temperature-induced changes in the gut microbiome may impact host fitness, including effects on colonization resistance in the gut, on host energy and nutrient assimilation, and on host life history traits. Cumulatively, available data indicate that disruption of the gut microbiome may be a mechanism by which changing temperatures will impact animal fitness in wild-living populations.},
}

@article {pmid32210932,
year = {2020},
author = {Korry, BJ and Cabral, DJ and Belenky, P},
title = {Metatranscriptomics Reveals Antibiotic-Induced Resistance Gene Expression in the Murine Gut Microbiota.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {322},
doi = {10.3389/fmicb.2020.00322},
pmid = {32210932},
issn = {1664-302X},
abstract = {Antibiotic resistance is a current and expanding threat to the practice of modern medicine. Antibiotic therapy has been shown to perturb the composition of the host microbiome with significant health consequences. In addition, the gut microbiome is known to be a reservoir of antibiotic resistance genes. Work has demonstrated that antibiotics can alter the collection of antibiotic resistance genes within the microbiome through selection and horizontal gene transfer. While antibiotics also have the potential to impact the expression of resistance genes, metagenomic-based pipelines currently lack the ability to detect these shifts. Here, we utilized a dual sequencing approach combining shotgun metagenomics and metatranscriptomics to profile how three antibiotics, amoxicillin, doxycycline, and ciprofloxacin, impact the murine gut resistome at the DNA and RNA level. We found that each antibiotic induced broad, but untargeted impacts on the gene content of the resistome. In contrast, changes in ARG transcript abundance were more targeted to the antibiotic treatment. Doxycycline and amoxicillin induced the expression of tetracycline and beta-lactamase resistance genes, respectively. Furthermore, the increased beta-lactamase resistance gene transcripts could contribute to an observed bloom of Bacteroides thetaiotaomicron during amoxicillin treatment. Based on these findings, we propose that the utilization of a dual sequencing methodology provides a unique capacity to fully understand the response of the resistome to antibiotic perturbation. In particular, the analysis of transcripts reveals that the expression and utilization of resistance genes is far narrower than their abundance at the genomic level would suggest.},
}

@article {pmid32210237,
year = {2020},
author = {Long, S and Yang, Y and Shen, C and Wang, Y and Deng, A and Qin, Q and Qiao, L},
title = {Metaproteomics characterizes human gut microbiome function in colorectal cancer.},
journal = {NPJ biofilms and microbiomes},
volume = {6},
number = {1},
pages = {14},
doi = {10.1038/s41522-020-0123-4},
pmid = {32210237},
issn = {2055-5008},
support = {81671849//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81671556//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18441901000//Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)/ ; 2016YFE0132400//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; },
abstract = {Pathogenesis of colorectal cancer (CRC) is associated with alterations in gut microbiome. Previous studies have focused on the changes of taxonomic abundances by metagenomics. Variations of the function of intestinal bacteria in CRC patients compared to healthy crowds remain largely unknown. Here we collected fecal samples from CRC patients and healthy volunteers and characterized their microbiome using quantitative metaproteomic method. We have identified and quantified 91,902 peptides, 30,062 gut microbial protein groups, and 195 genera of microbes. Among the proteins, 341 were found significantly different in abundance between the CRC patients and the healthy volunteers. Microbial proteins related to iron intake/transport; oxidative stress; and DNA replication, recombination, and repair were significantly alternated in abundance as a result of high local concentration of iron and high oxidative stress in the large intestine of CRC patients. Our study shows that metaproteomics can provide functional information on intestinal microflora that is of great value for pathogenesis research, and can help guide clinical diagnosis in the future.},
}

@article {pmid32210172,
year = {2020},
author = {Lukša, J and Vepštaitė-Monstavičė, I and Apšegaitė, V and Blažytė-Čereškienė, L and Stanevičienė, R and Strazdaitė-Žielienė, Ž and Ravoitytė, B and Aleknavičius, D and Būda, V and Mozūraitis, R and Servienė, E},
title = {Fungal Microbiota of Sea Buckthorn Berries at Two Ripening Stages and Volatile Profiling of Potential Biocontrol Yeasts.},
journal = {Microorganisms},
volume = {8},
number = {3},
pages = {},
doi = {10.3390/microorganisms8030456},
pmid = {32210172},
issn = {2076-2607},
support = {09.3.3-LMT-K-712-01-0099//Lietuvos Mokslo Taryba/ ; },
abstract = {Sea buckthorn, Hippophae rhamnoides L., has considerable potential for landscape reclamation, food, medicinal, and cosmetics industries. In this study, we analyzed fungal microorganism populations associated with carposphere of sea buckthorn harvested in Lithuania. An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to reveal the ripening-affected fungal community alterations on sea buckthorn berries. According to alpha and beta diversity analyses, depending on the ripening stage, sea buckthorn displayed significantly different fungal communities. Unripe berries were shown to be prevalent by Aureobasidium, Taphrina, and Cladosporium, while ripe berries were dominated by Aureobasidium and Metschnikowia. The selected yeast strains from unripe and mature berries were applied for volatile organic compounds identification by gas chromatography and mass spectrometry techniques. It was demonstrated that the patterns of volatiles of four yeast species tested were distinct from each other. The current study for the first time revealed the alterations of fungal microorganism communities colonizing the surface of sea buckthorn berries at different ripening stages. The novel information on specific volatile profiles of cultivable sea buckthorn-associated yeasts with a potential role in biocontrol is important for the development of the strategies for plant cultivation and disease management, as well as for the improvement of the quality and preservation of the postharvest berries. Management of the fungal microorganisms present on the surface of berries might be a powerful instrument for control of phytopathogenic and potentially antagonistic microorganisms affecting development and quality of the berries.},
}

@article {pmid32210160,
year = {2020},
author = {Melnikova, DI and Magarlamov, TY},
title = {The Microbial Community of Tetrodotoxin-Bearing and Non-Tetrodotoxin-Bearing Ribbon Worms (Nemertea) from the Sea of Japan.},
journal = {Marine drugs},
volume = {18},
number = {3},
pages = {},
doi = {10.3390/md18030177},
pmid = {32210160},
issn = {1660-3397},
abstract = {A potent marine toxin, tetrodotoxin (TTX), found in a great variety of marine and some terrestrial species, leaves intriguing questions about its origin and distribution in marine ecosystems. TTX-producing bacteria were found in the cultivable microflora of many TTX-bearing hosts, thereby providing strong support for the hypothesis that the toxin is of bacterial origin in these species. However, metagenomic studies of TTX-bearing animals addressing the whole microbial composition and estimating the contribution of TTX-producing bacteria to the overall toxicity of the host were not conducted. The present study is the first to characterize and compare the 16S rRNA gene data obtained from four TTX-bearing and four non-TTX-bearing species of marine ribbon worms. The statistical analysis showed that different nemertean species harbor distinct bacterial communities, while members of the same species mostly share more similar microbiomes. The bacterial species historically associated with TTX production were found in all studied samples but predominated in TTX-bearing nemertean species. This suggests that deeper knowledge of the microbiome of TTX-bearing animals is a key to understanding the origin of TTX in marine ecosystems.},
}

@article {pmid32209718,
year = {2020},
author = {Liu, MK and Tang, YM and Guo, XJ and Zhao, K and Penttinen, P and Tian, XH and Zhang, XY and Ren, DQ and Zhang, XP},
title = {Structural and Functional Changes in Prokaryotic Communities in Artificial Pit Mud during Chinese Baijiu Production.},
journal = {mSystems},
volume = {5},
number = {2},
pages = {},
doi = {10.1128/mSystems.00829-19},
pmid = {32209718},
issn = {2379-5077},
abstract = {The Chinese alcoholic beverage strong-flavor baijiu (SFB) gets its characteristic flavor during fermentation in cellars lined with pit mud. Microbes in the pit mud produce key precursors of flavor esters. The maturation time of natural pit mud of over 20 years has promoted attempts to produce artificial pit mud (APM) with a shorter maturation time. However, knowledge about the molecular basis of APM microbial dynamics and associated functional variation during SFB brewing is limited, and the role of this variability in high-quality SFB production remains poorly understood. We studied APM maturation in new cellars until the fourth brewing batch using 16S rRNA gene amplicon sequencing, quantitative PCR, metaproteomics, and metabolomics techniques. A total of 36 prokaryotic classes and 195 genera were detected. Bacilli and Clostridia dominated consistently, and the relative abundance of Bacilli decreased along with the APM maturation. Even though both amplicon sequencing and quantitative PCR showed increased abundance of Clostridia, the levels of most of the Clostridium proteins were similar in both the first- and fourth-batch APM samples. Six genera correlated with eight or more major flavor compounds in SFB samples. Functional prediction suggested that the prokaryotic communities in the fourth-batch APM samples were actively engaged in organic acid metabolism, and the detected higher concentrations of proteins and metabolites in the corresponding metabolic pathways supported the prediction. This multi-omics approach captured changes in the abundances of specific microbial species, proteins, and metabolites during APM maturation, which are of great significance for the optimization of APM culture technique.IMPORTANCE Strong-flavor baijiu (SFB) accounts for more than 70% of all Chinese liquor production. In the Chinese baijiu brewing industry, artificial pit mud (APM) has been widely used since the 1960s to construct fermentation cellars for production of high-quality SFB. To gain insights at the systems level into the mechanisms driving APM prokaryotic taxonomic and functional dynamics and into how this variation is connected with high-quality SFB production, we performed the first combined metagenomic, metaproteomic, and metabolomic analyses of this brewing microecosystem. Together, the multi-omics approach enabled us to develop a more complete picture of the changing metabolic processes occurring in APM microbial communities during high-quality SFB production, which will be helpful for further optimization of APM culture technique and improvement of SFB quality.},
}

@article {pmid32209716,
year = {2020},
author = {Rampelli, S and Soverini, M and D'Amico, F and Barone, M and Tavella, T and Monti, D and Capri, M and Astolfi, A and Brigidi, P and Biagi, E and Franceschi, C and Turroni, S and Candela, M},
title = {Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation.},
journal = {mSystems},
volume = {5},
number = {2},
pages = {},
doi = {10.1128/mSystems.00124-20},
pmid = {32209716},
issn = {2379-5077},
abstract = {The gut microbiome of long-lived people display an increasing abundance of subdominant species, as well as a rearrangement in health-associated bacteria, but less is known about microbiome functions. In order to disentangle the contribution of the gut microbiome to the complex trait of human longevity, we here describe the metagenomic change of the human gut microbiome along with aging in subjects with up to extreme longevity, including centenarians (aged 99 to 104 years) and semisupercentenarians (aged 105 to 109 years), i.e., demographically very uncommon subjects who reach the extreme limit of the human life span. According to our findings, the gut microbiome of centenarians and semisupercentenarians is more suited for xenobiotic degradation and shows a rearrangement in metabolic pathways related to carbohydrate, amino acid, and lipid metabolism. Collectively, our data go beyond the relationship between intestinal bacteria and physiological changes that occur with aging by detailing the shifts in the potential metagenomic functions of the gut microbiome of centenarians and semisupercentenarians as a response to progressive dietary and lifestyle modifications.IMPORTANCE The study of longevity may help us understand how human beings can delay or survive the most frequent age-related diseases and morbidities. In this scenario, the gut microbiome has been proposed as one of the variables to monitor and possibly support healthy aging. Indeed, the disruption of host-gut microbiome homeostasis has been associated with inflammation and intestinal permeability as well as a general decline in bone and cognitive health. Here, we performed a metagenomic assessment of fecal samples from semisupercentenarians, i.e., 105 to 109 years old, in comparison to young adults, the elderly, and centenarians, shedding light on the longest compositional and functional trajectory of the human gut microbiome with aging. In addition to providing a fine taxonomic resolution down to the species level, our study emphasizes the progressive age-related increase in degradation pathways of pervasive xenobiotics in Western societies, possibly as a result of a supportive process within the molecular continuum characterizing aging.},
}

@article {pmid32209694,
year = {2020},
author = {Teruya, S and Hiramatsu, Y and Nakamura, K and Fukui-Miyazaki, A and Tsukamoto, K and Shinoda, N and Motooka, D and Nakamura, S and Ishigaki, K and Shinzawa, N and Nishida, T and Sugihara, F and Maeda, Y and Horiguchi, Y},
title = {Bordetella Dermonecrotic Toxin Is a Neurotropic Virulence Factor That Uses CaV3.1 as the Cell Surface Receptor.},
journal = {mBio},
volume = {11},
number = {2},
pages = {},
doi = {10.1128/mBio.03146-19},
pmid = {32209694},
issn = {2150-7511},
abstract = {Dermonecrotic toxin (DNT) is one of the representative toxins produced by Bordetella pertussis, but its role in pertussis, B. pertussis infection, remains unknown. In this study, we identified the T-type voltage-gated Ca2+ channel CaV3.1 as the DNT receptor by CRISPR-Cas9-based genome-wide screening. As CaV3.1 is highly expressed in the nervous system, the neurotoxicity of DNT was examined. DNT affected cultured neural cells and caused flaccid paralysis in mice after intracerebral injection. No neurological symptoms were observed by intracerebral injection with the other major virulence factors of the organisms, pertussis toxin and adenylate cyclase toxin. These results indicate that DNT has aspects of the neurotropic virulence factor of B. pertussis The possibility of the involvement of DNT in encephalopathy, which is a complication of pertussis, is also discussed.IMPORTANCEBordetella pertussis, which causes pertussis, a contagious respiratory disease, produces three major protein toxins, pertussis toxin, adenylate cyclase toxin, and dermonecrotic toxin (DNT), for which molecular actions have been elucidated. The former two toxins are known to be involved in the emergence of some clinical symptoms and/or contribute to the establishment of bacterial infection. In contrast, the role of DNT in pertussis remains unclear. Our study shows that DNT affects neural cells through specific binding to the T-type voltage-gated Ca2+ channel that is highly expressed in the central nervous system and leads to neurological disorders in mice after intracerebral injection. These data raise the possibility of DNT as an etiological agent for pertussis encephalopathy, a severe complication of B. pertussis infection.},
}

@article {pmid32209692,
year = {2020},
author = {Storey, MA and Andreassend, SK and Bracegirdle, J and Brown, A and Keyzers, RA and Ackerley, DF and Northcote, PT and Owen, JG},
title = {Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts.},
journal = {mBio},
volume = {11},
number = {2},
pages = {},
doi = {10.1128/mBio.02997-19},
pmid = {32209692},
issn = {2150-7511},
abstract = {Marine sponges have been a prolific source of unique bioactive compounds that are presumed to act as a deterrent to predation. Many of these compounds have potential therapeutic applications; however, the lack of efficient and sustainable synthetic routes frequently limits clinical development. Here, we describe a metagenomic investigation of Mycale hentscheli, a chemically gifted marine sponge that possesses multiple distinct chemotypes. We applied shotgun metagenomic sequencing, hybrid assembly of short- and long-read data, and metagenomic binning to obtain a comprehensive picture of the microbiome of five specimens, spanning three chemotypes. Our data revealed multiple producing species, each having relatively modest secondary metabolomes, that contribute collectively to the chemical arsenal of the holobiont. We assembled complete genomes for multiple new genera, including two species that produce the cytotoxic polyketides pateamine and mycalamide, as well as a third high-abundance symbiont harboring a proteusin-type biosynthetic pathway that appears to encode a new polytheonamide-like compound. We also identified an additional 188 biosynthetic gene clusters, including a pathway for biosynthesis of peloruside. These results suggest that multiple species cooperatively contribute to defensive symbiosis in M. hentscheli and reveal that the taxonomic diversity of secondary-metabolite-producing sponge symbionts is larger and richer than previously recognized.IMPORTANCEMycale hentscheli is a marine sponge that is rich in bioactive small molecules. Here, we use direct metagenomic sequencing to elucidate highly complete and contiguous genomes for the major symbiotic bacteria of this sponge. We identify complete biosynthetic pathways for the three potent cytotoxic polyketides which have previously been isolated from M. hentscheli Remarkably, and in contrast to previous studies of marine sponges, we attribute each of these metabolites to a different producing microbe. We also find that the microbiome of M. hentscheli is stably maintained among individuals, even over long periods of time. Collectively, our data suggest a cooperative mode of defensive symbiosis in which multiple symbiotic bacterial species cooperatively contribute to the defensive chemical arsenal of the holobiont.},
}

@article {pmid32209105,
year = {2020},
author = {Sarkar, J and Dutta, A and Pal Chowdhury, P and Chakraborty, J and Dutta, TK},
title = {Characterization of a novel family VIII esterase EstM2 from soil metagenome capable of hydrolyzing estrogenic phthalates.},
journal = {Microbial cell factories},
volume = {19},
number = {1},
pages = {77},
doi = {10.1186/s12934-020-01336-x},
pmid = {32209105},
issn = {1475-2859},
abstract = {BACKGROUND: Microbes are rich sources of enzymes and esterases are one of the most important classes of enzymes because of their potential for application in the field of food, agriculture, pharmaceuticals and bioremediation. Due to limitations in their cultivation, only a small fraction of the complex microbial communities can be cultured from natural habitats. Thus to explore the catalytic potential of uncultured organisms, the metagenomic approach has turned out to be an effective alternative method for direct mining of enzymes of interest. Based on activity-based screening method, an esterase-positive clone was obtained from metagenomic libraries.

RESULTS: Functional screening of a soil metagenomic fosmid library, followed by transposon mutagenesis led to the identification of a 1179 bp esterase gene, estM2, that encodes a 392 amino acids long protein (EstM2) with a translated molecular weight of 43.12 kDa. Overproduction, purification and biochemical characterization of the recombinant protein demonstrated carboxylesterase activity towards short-chain fatty acyl esters with optimal activity for p-nitrophenyl butyrate at pH 8.0 and 37 °C. Amino acid sequence analysis and subsequent phylogenetic analysis suggested that EstM2 belongs to the family VIII esterases that bear modest similarities to class C β-lactamases. EstM2 possessed the conserved S-x-x-K motif of class C β-lactamases but did not exhibit β-lactamase activity. Guided by molecular docking analysis, EstM2 was shown to hydrolyze a wide range of di- and monoesters of alkyl-, aryl- and benzyl-substituted phthalates. Thus, EstM2 displays an atypical hydrolytic potential of biotechnological significance within family VIII esterases.

CONCLUSIONS: This study has led to the discovery of a new member of family VIII esterases. To the best of our knowledge, this is the first phthalate hydrolase (EstM2), isolated from a soil metagenomic library that belongs to a family possessing β-lactamase like catalytic triad. Based on its catalytic potential towards hydrolysis of both phthalate diesters and phthalate monoesters, this enzyme may find use to counter the growing pollution caused by phthalate-based plasticizers in diverse geological environment and in other aspects of biotechnological applications.},
}

@article {pmid32209031,
year = {2020},
author = {Sarma, SJ and Lei, Z and Rosenfeld, CS and Ericsson, A and Sumner, LW},
title = {Nontargeted fecal metabolomics: an emerging tool to probe the role of the gut-microbiome in host-health.},
journal = {Bioanalysis},
volume = {},
number = {},
pages = {},
doi = {10.4155/bio-2020-0010},
pmid = {32209031},
issn = {1757-6199},
}

@article {pmid31271261,
year = {2019},
author = {Martoni, CJ and Evans, M and Chow, CT and Chan, LS and Leyer, G},
title = {Impact of a probiotic product on bowel habits and microbial profile in participants with functional constipation: A randomized controlled trial.},
journal = {Journal of digestive diseases},
volume = {20},
number = {9},
pages = {435-446},
pmid = {31271261},
issn = {1751-2980},
mesh = {Adolescent ; Adult ; Aged ; Bacterial Typing Techniques ; Constipation/microbiology/physiopathology/*therapy ; Defecation/physiology ; Double-Blind Method ; Energy Intake/physiology ; Exercise/physiology ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Metagenome/physiology ; Middle Aged ; Probiotics/adverse effects/*therapeutic use ; Prospective Studies ; Psychometrics ; Quality of Life ; Treatment Outcome ; Young Adult ; },
abstract = {OBJECTIVE: To investigate the clinical efficacy of a multi-strain probiotic product on bowel habits and microbial profile in participants with functional constipation.

METHODS: This was a randomized, double-blind, placebo-controlled and parallel-arm study. Altogether 94 otherwise healthy adults aged 18 to 65 years with symptoms of functional constipation were randomized as part of the intention-to-treat population. The participants received a placebo or the probiotic product (1.5 × 1010 CFU/day), consisting of Lactobacillus acidophilus DDS-1, Bifidobacterium animalis subsp. lactis UABla-12, Bifidobacterium longum UABl-14 and Bifidobacterium bifidum UABb-10 over 4 weeks. Outcomes included the patient assessment of constipation-symptom (PAC-SYM) questionnaire, stool frequency and consistency, and microbial profile.

RESULTS: There were no significant between-group differences in the PAC-SYM score, despite significant within-group differences (P < 0.001) over the study period. The probiotic group showed a faster normalization of stool frequency and consistency, with most participants achieving a normalized profile after 1 week. Fecal samples of the probiotic group exhibited higher relative abundance of Ruminococcaceae (P = 0.0047), including the Ruminococcus genus, and lower relative abundance of Erysipelotrichaceae (P = 0.0172) at end-point compared with baseline. Placebo group samples showed similar abundance profiles over the study, with the exception of Clostridiaceae, which was lower at the study end-point (P = 0.0033). Among treated participants, all four probiotic strains were significantly more abundant after the intervention.

CONCLUSIONS: No significant differences were observed in symptomology, with both groups showing a more than 20% improvement. However, the probiotic helped modulate bowel function earlier than the placebo, with a corresponding shift to a more fibrolytic microbiota.},
}

Adolescent
Adult
Aged
Bacterial Typing Techniques
Constipation/microbiology/physiopathology/*therapy
Defecation/physiology
Double-Blind Method
Energy Intake/physiology
Exercise/physiology
Feces/microbiology
Gastrointestinal Microbiome/*physiology
Humans
Metagenome/physiology
Middle Aged
Probiotics/adverse effects/*therapeutic use
Prospective Studies
Psychometrics
Quality of Life
Treatment Outcome
Young Adult

@article {pmid31194675,
year = {2019},
author = {Bernstein, DB and Dewhirst, FE and Segrè, D},
title = {Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {31194675},
issn = {2050-084X},
support = {T32GM008764/GM/NIGMS NIH HHS/United States ; T32 GM008764/GM/NIGMS NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 GM121950/GM/NIGMS NIH HHS/United States ; DE-SC0012627//Biological and Environmental Research/International ; RGP0020/2016//Human Frontier Science Program/International ; NSFOCE-BSF 1635070//National Science Foundation/International ; HR0011-15-C-0091//Defense Advanced Research Projects Agency/International ; R37DE016937/DE/NIDCR NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; R01GM121950/GM/NIGMS NIH HHS/United States ; R01DE024468/DE/NIDCR NIH HHS/United States ; 1457695//National Science Foundation/International ; },
mesh = {Computational Biology ; Humans ; *Metabolic Networks and Pathways ; Metagenomics ; *Microbial Interactions ; *Microbiota ; Mouth/*microbiology ; },
abstract = {The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.},
}

Computational Biology
Humans
*Metabolic Networks and Pathways
Metagenomics
*Microbial Interactions
*Microbiota
Mouth/*microbiology

@article {pmid32208434,
year = {2020},
author = {Jangid, A and Fukuda, S and Seki, M and Horiuchi, T and Suzuki, Y and Taylor, TD and Ohno, H and Prakash, T},
title = {Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice.},
journal = {PloS one},
volume = {15},
number = {3},
pages = {e0228358},
doi = {10.1371/journal.pone.0228358},
pmid = {32208434},
issn = {1932-6203},
abstract = {Inflammatory bowel disease results from alterations in the immune system and intestinal microbiota. The role of intestinal epithelial cells (IECs) in maintaining gut homeostasis is well known and its perturbation often causes gastrointestinal disorders including IBD. The epithelial specific adaptor protein (AP)-1B is involved in the establishment of the polarity of IECs. Deficiency of the AP-1B μ subunit (Ap1m2-/-) leads to the development of chronic colitis in mice. However, how this deficiency affects the gut microbes and its potential functions remains elusive. To gain insights into the gut microbiome of Ap1m2-/- mice having the colitis phenotype, we undertook shotgun metagenomic sequencing analysis of knockout mice. We found important links to the microbial features involved in altering various physiological pathways, including carbohydrate metabolism, nutrient transportation, oxidative stress, and bacterial pathogenesis (cell motility). In addition, an increased abundance of sulfur-reducing and lactate-producing bacteria has been observed which may aggravate the colitis condition.},
}

@article {pmid32208227,
year = {2020},
author = {Liu, H and Hu, Z and Zhou, M and Zhang, H and Li, Z and Zhang, H and Hu, J and Yao, X and Lou, L and Xi, C and Zhu, L and Xu, X and Zheng, P and Hu, B},
title = {Airborne microorganisms exacerbate the formation of atmospheric ammonium and sulfate.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {263},
number = {Pt A},
pages = {114293},
doi = {10.1016/j.envpol.2020.114293},
pmid = {32208227},
issn = {1873-6424},
abstract = {Haze pollution is inseparable from the transformation of air pollutants especially the ammonium and sulfate. Chemical and physical processes play important roles in this transformation. However, the role of microbial processes has rarely been studied. In this report, we applied the cultivation-independent metagenomic approach to study airborne microorganisms, investigating the potential microbial-catalyzed transformation of ammonium and sulfate in PM2.5 samples. Functional genes predict that airborne microorganisms have the potential to catalyze ammonium formation but not ammonium oxidation since no ammoxidation genes were identified. We also found that the frequency of sulfate-forming genes was 1.56 times of those for sulfate-reducing genes. It was speculated that microbial metabolisms in the atmosphere could contribute to the accumulation of ammonium and sulfate. With the increase of PM2.5 concentration, the frequency of functional genes and the relative abundance of genera which involved in nitrogen and sulfur metabolisms increased. That suggested air pollution was conducive to the microbial-mediated formation of ammonium and sulfate. Overall, our results provided evidence for the possible role of microbial processes in the air pollutant transformation and brought a new perspective for studying the formation of secondary air pollutants.},
}

@article {pmid32208150,
year = {2020},
author = {Fuerst, JA},
title = {Microbial Evolution: Chlamydial Creatures from the Deep.},
journal = {Current biology : CB},
volume = {30},
number = {6},
pages = {R267-R269},
doi = {10.1016/j.cub.2020.01.086},
pmid = {32208150},
issn = {1879-0445},
abstract = {A metagenomic study of marine sediments from a hydrothermal vent field in the Arctic Mid-Ocean Ridge revealed wider diversity amongst members of the phylum Chlamydiae than was previously known. Unlike known chlamydiae, some of the newly described marine-sediment species may be potentially free-living.},
}

@article {pmid31437575,
year = {2019},
author = {Li, A and Wang, Y and Pei, L and Mehmood, K and Li, K and Qamar, H and Iqbal, M and Waqas, M and Liu, J and Li, J},
title = {Influence of dietary supplementation with Bacillus velezensis on intestinal microbial diversity of mice.},
journal = {Microbial pathogenesis},
volume = {136},
number = {},
pages = {103671},
doi = {10.1016/j.micpath.2019.103671},
pmid = {31437575},
issn = {1096-1208},
mesh = {Animals ; Bacillus/*growth & development/isolation & purification ; Cattle/microbiology ; Cecum/microbiology ; Diet/*methods ; Duodenum/microbiology ; *Gastrointestinal Microbiome ; Ileum/microbiology ; Jejunum/microbiology ; Metagenomics ; Mice ; Probiotics/*administration & dosage ; Tibet ; },
abstract = {Yaks are an aboriginal breed of the Qinghai-Tibet plateau (3000 m), which are highly adaptable to cold and hypoxic environments. It is noticed that hypoxia and hypothermia can induce changes in intestinal microbial structure in animals. Increasing evidences suggested that probiotics supplementation can improve the balance of gut microbiota of animals. However, so far, very few studies have emphasized on the probiotics isolated from yaks in the Qinghai-Tibet Plateau. Therefore, a potential probiotic strain Bacillus velezensis was isolated from yaks. In the present study, a total of 18 Kunming mice (15-18 g) were equally distributed into two groups; control and probiotic treated groups (1 × 109 CFU/day). During the experimental period, all the mice from both groups were given standard normal diet ad libitum. At the end of the experiment, mice were euthanized and the intestines (duodenum, jejunum, ileum, and cecum) were removed for high-throughput sequencing. The results demonstrated that Bacillus velezensis supplementation showed beneficial effects on the gut microbiota of mice. Specifically, Bacillus velezensis supplementation increased the population of Lactobacillus and Ruminococcus in the duodenum, and Candidatus Arthromitus in the jejunum. Additionally, Acinetobacter in the duodenum and Helicobacter in the cecum were decreased after feeding Bacillus velezensis. Altogether, these findings suggested that Bacillus velezensis isolated from Tibetan yaks can improve gut microbiota of mice.},
}

Animals
Bacillus/*growth & development/isolation & purification
Cattle/microbiology
Cecum/microbiology
Diet/*methods
Duodenum/microbiology
*Gastrointestinal Microbiome
Ileum/microbiology
Jejunum/microbiology
Metagenomics
Mice
Probiotics/*administration & dosage
Tibet

@article {pmid31201356,
year = {2019},
author = {Szafrański, SP and Kilian, M and Yang, I and Bei der Wieden, G and Winkel, A and Hegermann, J and Stiesch, M},
title = {Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches.},
journal = {The ISME journal},
volume = {13},
number = {10},
pages = {2500-2522},
pmid = {31201356},
issn = {1751-7370},
mesh = {Aggregatibacter/classification/*virology ; Bacteriophages/classification/genetics/isolation & purification/*physiology ; Base Composition ; Biodiversity ; Genome, Viral ; Genomics ; Haemophilus/classification/*virology ; Host Specificity ; Humans ; Lysogeny ; Metagenome ; Phylogeny ; Prophages/classification/genetics/isolation & purification/physiology ; },
abstract = {Aggregatibacter and Haemophilus species are relevant human commensals and opportunistic pathogens. Consequently, their bacteriophages may have significant impact on human microbial ecology and pathologies. Our aim was to reveal the prevalence and diversity of bacteriophages infecting Aggregatibacter and Haemophilus species that colonize the human body. Genome mining with comparative genomics, screening of clinical isolates, and profiling of metagenomes allowed characterization of 346 phages grouped in 52 clusters and 18 superclusters. Less than 10% of the identified phage clusters were represented by previously characterized phages. Prophage diversity patterns varied significantly for different phage types, host clades, and environmental niches. A more diverse phage community lysogenizes Haemophilus influenzae and Haemophilus parainfluenzae strains than Aggregatibacter actinomycetemcomitans and "Haemophilus ducreyi". Co-infections occurred more often in "H. ducreyi". Phages from Aggregatibacter actinomycetemcomitans preferably lysogenized strains of specific serotype. Prophage patterns shared by subspecies clades of different bacterial species suggest similar ecoevolutionary drivers. Changes in frequencies of DNA uptake signal sequences and guanine-cytosine content reflect phage-host long-term coevolution. Aggregatibacter and Haemophilus phages were prevalent at multiple oral sites. Together, these findings should help exploring the ecoevolutionary forces shaping virus-host interactions in the human microbiome. Putative lytic phages, especially phiKZ-like, may provide new therapeutic options.},
}

Aggregatibacter/classification/*virology
Bacteriophages/classification/genetics/isolation & purification/*physiology
Base Composition
Biodiversity
Genome, Viral
Genomics
Haemophilus/classification/*virology
Host Specificity
Humans
Lysogeny
Metagenome
Phylogeny
Prophages/classification/genetics/isolation & purification/physiology

@article {pmid32207614,
year = {2020},
author = {Hu, W and Liang, J and Ju, F and Wang, Q and Liu, R and Bai, Y and Liu, H and Qu, J},
title = {Metagenomics unravels differential microbiome composition and metabolic potential in rapid sand filters purifying surface water versus groundwater.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.9b07143},
pmid = {32207614},
issn = {1520-5851},
abstract = {Designed for retaining suspended particles, rapid sand filters (RSFs) are widely used in drinking water treatment. There is increasing evidence that microbial processes within RSFs contribute to the transformation and removal of organic carbon, nitrogen, and metal pollutants. Here, we linked microbial composition and functional profiles with treatment performance of 12 different RSFs that significantly removed influent ammonium and manganese (Mn). Metagenomic analyses showed chemoautotrophic or methanotrophic bacteria were prevalent in the groundwater filters, and chemoheterotrophic bacteria encoding more carbohydrate- and xenobiotic-metabolizing genes were more abundant in the surface water filters. Approximately 92% of ammonium was transformed into nitrate, with a critical contribution from comammox Nitrospira. The composition of comammox amoA differed between groundwater and surface water filters, with clade A dominating groundwater filters (78.0% ± 12.0%) and clade B dominating surface water filters (91.9% ± 8.9%). Further, we identified six bacterial genera encoding known Mn(II)-oxidizing genes in the RSFs, with Pseudomonas accounting for 71.1%. These Mn(II)-oxidizing bacteria might promote the Mn(II) oxidation and thus increase the removal of influent Mn. Overall, our study gave a comprehensive investigation on microbiome in RSFs and highlighted the roles of comammox and Mn(II)-oxidizing bacteria in water purification.},
}

@article {pmid32207561,
year = {2020},
author = {Shen, Y and Nie, J and Kuang, L and Zhang, J and Li, H},
title = {DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.13560},
pmid = {32207561},
issn = {1751-7915},
support = {CARS-27//Earmarked Fund for China Agriculture Research System/ ; GJFP2017003//National Program for Quality and Safety Risk Assessment of Agricultural Products of China/ ; GJFP2018003//National Program for Quality and Safety Risk Assessment of Agricultural Products of China/ ; CAAS-ASTIP//Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences/ ; },
abstract = {The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole-genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing-based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.},
}

@article {pmid32207218,
year = {2020},
author = {Newberry, E and Bhandari, R and Kemble, J and Sikora, E and Potnis, N},
title = {Genome-resolved metagenomics to study co-occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14989},
pmid = {32207218},
issn = {1462-2920},
abstract = {Assessment of pathogen diversity in agricultural fields is essential for informing management decisions and the development of resistant plant varieties. However, many population genomic studies have relied on culture-based approaches that do not provide quantitative assessment of pathogen populations at the field-level or the associated host microbiome. Here, we applied whole-genome shotgun sequencing of microbial DNA extracted directly from the washings of pooled leaf samples, collected from individual tomato and pepper fields in Alabama that displayed the classical symptoms of bacterial spot disease caused by Xanthomonas spp. Our results revealed that while the occurrence of both X. perforans and X. euvesicatoria within fields was limited, evidence of co-occurrence of up to three distinct X. perforans genotypes was obtained in seven of the ten tomato fields sampled. These population dynamics were accompanied by the corresponding type 3 secreted effector repertoires associated with the co-occurring X. perforans genotypes, indicating that metapopulation structure within fields should be considered when assessing the adaptive potential of X. perforans. Finally, analysis of microbial community composition revealed that co-occurrence of the bacterial spot pathogens Pseudomonas cichorii and Xanthomonas spp. is common in Alabama fields and provided evidence for the non-random association of several other human- and plant-opportunists. This article is protected by copyright. All rights reserved.},
}

@article {pmid32206831,
year = {2020},
author = {Mehta, O and Ghosh, TS and Kothidar, A and Gowtham, MR and Mitra, R and Kshetrapal, P and Wadhwa, N and Thiruvengadam, R and , and Nair, GB and Bhatnagar, S and Das, B},
title = {Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-020-01501-0},
pmid = {32206831},
issn = {1432-184X},
support = {No.BT/PR9983/MED/97/194/2013//Department of Biotechnology, Government of India/ ; },
abstract = {The trillions of microorganisms residing in the human body display varying degrees of compositional and functional diversities within and between individuals and contribute significantly to host physiology and susceptibility to disease. Microbial species present in the vaginal milieu of reproductive age women showed a large personal component and varies widely in different ethnic groups at the taxonomic, genomic, and functional levels. Lactobacillus iners, L. crispatus, L. gasseri, L. jensenii, and L. johnsonii are most frequently detected bacterial species in the vaginal milieu of reproductive age women. However, we currently lack (i) an understanding of the baseline vaginal microbiota of reproductive age Indian women, (ii) the extent of taxonomic and functional variations of vaginal microbiota between individuals and (iii) the genomic repertoires of the dominant vaginal microbiota associated with the Indian subjects. In our study, we analyzed the metagenome of high vaginal swab (HVS) samples collected from 40 pregnant Indian women enrolled in the GARBH-Ini cohort. Composition and abundance of bacterial species was characterized by pyrosequencing 16S rRNA gene. We identified 3067 OTUs with ≥ 10 reads from four different bacterial phyla. Several species of lactobacilli were clustered into three community state types (CSTs). L. iners, L. crispatus, L. gasseri, and L. jensenii are the most frequently detected Lactobacillus species in the vaginal environment of Indian women. Other than Lactobacillus, several species of Halomonas were also identified in the vaginal environment of most of the women sampled. To gain genomic and functional insights, we isolated several Lactobacillus species from the HVS samples and explored their whole genome sequences by shotgun sequencing. We analyzed the genome of dominant Lactobacillus species, L. iners, L. crispatus, L. gasseri, and L. paragesseri to represent the CSTs and identify functions that may influence the composition of complex vaginal microbial ecology. This study reports for the first time the vaginal microbial ecology of Indian women and genomic insights into L. iners, L. crispatus, L. gasseri, and L. paragesseri commonly found in the genital tract of reproductive age women.},
}

@article {pmid32206676,
year = {2020},
author = {Phadke, VK and Shantha, JG and O'Keefe, G},
title = {Relapsing Uveitis due to Human T-lymphotropic Virus Type 1 in a Patient Living With HIV Diagnosed by Metagenomic Deep Sequencing.},
journal = {Open forum infectious diseases},
volume = {7},
number = {3},
pages = {ofaa078},
doi = {10.1093/ofid/ofaa078},
pmid = {32206676},
issn = {2328-8957},
abstract = {HIV infection can result in vision loss from different causes, including HIV retinopathy and uveitis secondary to other infections, such as toxoplasmosis and viral retinitis. It is imperative to identify any infectious causes of uveitis to successfully treat the condition and prevent further vision loss. Metagenomic deep sequencing (MDS) is an emerging technology that presents an unbiased approach to the evaluation of clinical syndromes, including uveitis, that have not been diagnosed by pathogen-specific testing. Herein we present a case of a woman living with HIV with 11 years of relapsing bilateral uveitis refractory to systemic corticosteroid therapy who was diagnosed with human T-lymphotropic virus type 1 (HTLV-1)-associated uveitis by this technology. We also briefly review the literature of MDS as a diagnostic tool and the epidemiology, pathogenesis, and diagnosis of HTLV-1-associated uveitis.},
}

@article {pmid32205368,
year = {2020},
author = {Vorobev, A and Dupouy, M and Carradec, Q and Delmont, T and Annamale, A and Wincker, P and Pelletier, E},
title = {Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.253070.119},
pmid = {32205368},
issn = {1549-5469},
abstract = {Large scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta -omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ~37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ~12 thousand co-abundant gene groups (CAGs), encompassing ~7 million unigenes, including 924 metagenomics based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for an analysis of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.},
}

@article {pmid31825995,
year = {2019},
author = {Woloszynek, S and Mell, JC and Zhao, Z and Simpson, G and O'Connor, MP and Rosen, GL},
title = {Exploring thematic structure and predicted functionality of 16S rRNA amplicon data.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0219235},
pmid = {31825995},
issn = {1932-6203},
mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Crohn Disease/*microbiology ; Humans ; Metagenomics/*methods ; Microbiota ; Mouth Neoplasms/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Software ; Time Factors ; },
abstract = {Analysis of microbiome data involves identifying co-occurring groups of taxa associated with sample features of interest (e.g., disease state). Elucidating such relations is often difficult as microbiome data are compositional, sparse, and have high dimensionality. Also, the configuration of co-occurring taxa may represent overlapping subcommunities that contribute to sample characteristics such as host status. Preserving the configuration of co-occurring microbes rather than detecting specific indicator species is more likely to facilitate biologically meaningful interpretations. Additionally, analyses that use taxonomic relative abundances to predict the abundances of different gene functions aggregate predicted functional profiles across taxa. This precludes straightforward identification of predicted functional components associated with subsets of co-occurring taxa. We provide an approach to explore co-occurring taxa using "topics" generated via a topic model and link these topics to specific sample features (e.g., disease state). Rather than inferring predicted functional content based on overall taxonomic relative abundances, we instead focus on inference of functional content within topics, which we parse by estimating interactions between topics and pathways through a multilevel, fully Bayesian regression model. We apply our methods to three publicly available 16S amplicon sequencing datasets: an inflammatory bowel disease dataset, an oral cancer dataset, and a time-series dataset. Using our topic model approach to uncover latent structure in 16S rRNA amplicon surveys, investigators can (1) capture groups of co-occurring taxa termed topics; (2) uncover within-topic functional potential; (3) link taxa co-occurrence, gene function, and environmental/host features; and (4) explore the way in which sets of co-occurring taxa behave and evolve over time. These methods have been implemented in a freely available R package: https://cran.r-project.org/package=themetagenomics, https://github.com/EESI/themetagenomics.},
}

Bacteria/*classification/*genetics
*Biodiversity
Crohn Disease/*microbiology
Humans
Metagenomics/*methods
Microbiota
Mouth Neoplasms/*microbiology
Phylogeny
RNA, Ribosomal, 16S/*genetics
Sequence Analysis, DNA
Software
Time Factors

@article {pmid32203902,
year = {2020},
author = {Kim, E and Yulisa, A and Kim, S and Hwang, S},
title = {Monitoring microbial community structure and variations in a full-scale petroleum refinery wastewater treatment plant.},
journal = {Bioresource technology},
volume = {306},
number = {},
pages = {123178},
doi = {10.1016/j.biortech.2020.123178},
pmid = {32203902},
issn = {1873-2976},
abstract = {This research investigated the process efficiency and microbial communities and their diversity in a full-scale wastewater treatment plant (WWTP) fed with petroleum refining wastewater (PRW) that contained toxic hydrocarbon contaminants and carcinogens. Process parameters and bacterial community structures were monitored for six months to create a link between microbial dynamics and influent characteristics of petrochemical wastewater. The WWTP showed a stable process with efficiencies >70% for both soluble chemical oxygen demand (SCOD) and benzene removal. More than 30 genera were identified by metagenomic analysis, and the bacterial populations changed significantly during the operation period. Among them, genera Sulfuritalea (11.9 ± 3.5%), Ottowia (4.3 ± 2.2%), Thauera (3.1 ± 7.2%) and Hyphomicrobium (1.3 ± 0.7%) were dominant and important bacterial genera that may have been responsible for the degradation of aromatic compounds such as benzene and phenol.},
}

@article {pmid32203124,
year = {2020},
author = {Liang, JL and Liu, J and Jia, P and Yang, TT and Zeng, QW and Zhang, SC and Liao, B and Shu, WS and Li, JT},
title = {Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-020-0632-4},
pmid = {32203124},
issn = {1751-7370},
support = {41622106//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Little is known about the changes in soil microbial phosphorus (P) cycling potential during terrestrial ecosystem management and restoration, although much research aims to enhance soil P cycling. Here, we used metagenomic sequencing to analyse 18 soil microbial communities at a P-deficient degraded mine site in southern China where ecological restoration was implemented using two soil ameliorants and eight plant species. Our results show that the relative abundances of key genes governing soil microbial P-cycling potential were higher at the restored site than at the unrestored site, indicating enhancement of soil P cycling following restoration. The gcd gene, encoding an enzyme that mediates inorganic P solubilization, was predominant across soil samples and was a major determinant of bioavailable soil P. We reconstructed 39 near-complete bacterial genomes harboring gcd, which represented diverse novel phosphate-solubilizing microbial taxa. Strong correlations were found between the relative abundance of these genomes and bioavailable soil P, suggesting their contributions to the enhancement of soil P cycling. Moreover, 84 mobile genetic elements were detected in the scaffolds containing gcd in the 39 genomes, providing evidence for the role of phage-related horizontal gene transfer in assisting soil microbes to acquire new metabolic potential related to P cycling.},
}

@article {pmid32203121,
year = {2020},
author = {Campbell, TP and Sun, X and Patel, VH and Sanz, C and Morgan, D and Dantas, G},
title = {The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-020-0634-2},
pmid = {32203121},
issn = {1751-7370},
support = {Director's New Innovator Award//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI123394//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; Mallinckrodt Scholar Award//Edward Mallinckrodt, Jr. Foundation (Mallinckrodt Foundation)/ ; },
abstract = {The gut microbiome can vary across differences in host lifestyle, geography, and host species. By comparing closely related host species across varying lifestyles and geography, we can evaluate the relative contributions of these factors in structuring the composition and functions of the microbiome. Here we show that the gut microbial taxa, microbial gene family composition, and resistomes of great apes and humans are more related by host lifestyle than geography. We show that captive chimpanzees and gorillas are enriched for microbial genera commonly found in non-Westernized humans. Captive ape microbiomes also had up to ~34-fold higher abundance and up to ~5-fold higher richness of all antibiotic resistance genes compared with wild apes. Through functional metagenomics, we identified a number of novel antibiotic resistance genes, including a gene conferring resistance to colistin, an antibiotic of last resort. Finally, by comparing our study cohorts to human and ape gut microbiomes from a diverse range of environments and lifestyles, we find that the influence of host lifestyle is robust to various geographic locations.},
}

@article {pmid32203118,
year = {2020},
author = {Probst, AJ and Elling, FJ and Castelle, CJ and Zhu, Q and Elvert, M and Birarda, G and Holman, HN and Lane, KR and Ladd, B and Ryan, MC and Woyke, T and Hinrichs, KU and Banfield, JF},
title = {Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-020-0624-4},
pmid = {32203118},
issn = {1751-7370},
support = {G-2016-20166041//Alfred P. Sloan Foundation/ ; G-2016-20166041//Alfred P. Sloan Foundation/ ; },
abstract = {Sediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community.},
}

@article {pmid32202696,
year = {2020},
author = {Zhang, X and Ma, C and Zhang, W and Li, W and Yu, J and Xue, D and Wu, X and Deng, G},
title = {Shifts in microbial community, pathogenicity-related genes and antibiotic resistance genes during dairy manure piled up.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.13551},
pmid = {32202696},
issn = {1751-7915},
support = {2015BZ02//Key Technologies Research and Development Program of Ningxia/ ; 2017BN04//Key Project of Research and Development of Ningxia Hui Autonomous Region of China(the project of east-west cooperation)/ ; KJT2017002//The project for the cultivation of scientific and innovative talent/ ; ZKZD2017001//The Major Innovation Projects for building first-class Universities in China's Western Region/ ; },
abstract = {The uncomposted faeces of dairy cow are usually stacked on cow breeding farms, dried under natural conditions and then used as cow bedding material or they may be continuously piled up. However, no information is available to evaluate variations in the human and animal pathogen genes and antibiotic resistance during the accumulation of fresh faeces of dairy cow to manure. Here, we present the metagenomic analysis of fresh faeces and manure from a dairy farm in Ning Xia, showing a unique enrichment of human and animal pathogen genes and antibiotic resistance genes (ARGs) in manure. We found that manure accumulation could significantly increase the diversity and abundance of the pathogenic constituents. Furthermore, pathogens from manure could spread to the plant environment and enphytotic pathogens could affect the yield and quality of crops during the use of manure as a fertilizer. Levels of virulence genes and ARGs increased with the enrichment of microbes and pathogens when faeces accumulated to manure. Accumulated manure was also the transfer station of ARGs to enrich the ARGs in the environment, indicating the ubiquitous presence of environmental antibiotic resistance genes. Our results demonstrate that manure accumulation and usage without effective manure management is an unreasonable approach that could enrich pathogenic microorganisms and ARGs in the environment. The manure metagenome structure allows us to appreciate the overall influence and interaction of animal waste on water, soil and other areas impacted by faecal accumulation and the factors that influence pathogen occurrence in products from dairy cows.},
}

@article {pmid32202395,
year = {2020},
author = {Ruiz-Fernández, P and Ramírez-Flandes, S and Rodríguez-León, E and Ulloa, O},
title = {Autotrophic Carbon Fixation Pathways Along the Redox Gradient in Oxygen-Depleted Oceanic Waters.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12837},
pmid = {32202395},
issn = {1758-2229},
abstract = {Anoxic marine zones (AMZs), also known as 'oxygen-deficient zones', contribute to the loss of fixed nitrogen from the ocean by anaerobic microbial processes. While these microbial processes associated with the nitrogen cycle have been extensively studied, those linked to the carbon cycle in AMZs have received much less attention, particularly the autotrophic carbon fixation -a crucial component of the carbon cycle. Using metagenomic and metatranscriptomic data from major AMZs, we report an explicit partitioning of the marker genes associated with different autotrophic carbon fixation pathways along the redox gradient (from oxic to anoxic conditions) present in the water column of AMZs. Sequences related to the Calvin-Benson-Bassham cycle were found along the entire gradient, while those related to the reductive Acetyl-CoA pathway were restricted to suboxic and anoxic waters. Sequences putatively associated with the 3-hydroxypropionate/4-hydroxybutyrate cycle dominated in the upper and lower oxyclines. Genes related to the reductive tricarboxylic acid cycle were represented from dysoxic to anoxic waters. The taxonomic affiliation of the sequences is consistent with the presence of microorganisms involved in crucial steps of biogeochemical cycles in AMZs, such as the gamma-proteobacteria sulphur oxidisers, the anammox bacteria Candidatus Scalindua and the thaumarcheota ammonia oxidisers of the Marine Group I. This article is protected by copyright. All rights reserved.},
}

@article {pmid32201928,
year = {2020},
author = {Cai, M and Liu, Y and Yin, X and Zhou, Z and Friedrich, MW and Richter-Heitmann, T and Nimzyk, R and Kulkarni, A and Wang, X and Li, W and Pan, J and Yang, Y and Gu, JD and Li, M},
title = {Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11427-020-1679-1},
pmid = {32201928},
issn = {1869-1889},
abstract = {Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota". Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood-Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.},
}

@article {pmid32200751,
year = {2020},
author = {Quistad, SD and Doulcier, G and Rainey, PB},
title = {Experimental manipulation of selfish genetic elements links genes to microbial community function.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190681},
doi = {10.1098/rstb.2019.0681},
pmid = {32200751},
issn = {1471-2970},
abstract = {Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}

@article {pmid32200748,
year = {2020},
author = {VanInsberghe, D and Arevalo, P and Chien, D and Polz, MF},
title = {How can microbial population genomics inform community ecology?.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190253},
doi = {10.1098/rstb.2019.0253},
pmid = {32200748},
issn = {1471-2970},
abstract = {Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}

@article {pmid32200740,
year = {2020},
author = {Garcia, CA and Hagstrom, GI and Larkin, AA and Ustick, LJ and Levin, SA and Lomas, MW and Martiny, AC},
title = {Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190254},
doi = {10.1098/rstb.2019.0254},
pmid = {32200740},
issn = {1471-2970},
abstract = {Linking 'omics measurements with biogeochemical cycles is a widespread challenge in microbial community ecology. Here, we propose applying genomic adaptation as 'biosensors' for microbial investments to overcome nutrient stress. We then integrate this genomic information with a trait-based model to predict regional shifts in the elemental composition of marine plankton communities. We evaluated this approach using metagenomic and particulate organic matter samples from the Atlantic, Indian and Pacific Oceans. We find that our genome-based trait model significantly improves our prediction of particulate C : P (carbon : phosphorus) across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen and phosphorus stress. In many ecosystems, it can be very challenging to quantify microbial stress. Thus, a carefully calibrated genomic approach could become a widespread tool for understanding microbial responses to environmental changes and the biogeochemical outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}

@article {pmid32200735,
year = {2020},
author = {Rainey, PB and Quistad, SD},
title = {Toward a dynamical understanding of microbial communities.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190248},
doi = {10.1098/rstb.2019.0248},
pmid = {32200735},
issn = {1471-2970},
abstract = {The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}

@article {pmid32200634,
year = {2020},
author = {Zhang, C and Zheng, W and Huang, X and Bell, EW and Zhou, X and Zhang, Y},
title = {Protein structure and sequence re-analysis of 2019-nCoV genome refutes snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.0c00129},
pmid = {32200634},
issn = {1535-3907},
abstract = {As the infection of 2019-nCoV coronavirus is quickly developing into a global pneumonia epidemic, careful analysis of its transmission and cellular mechanisms is sorely needed. In this report, we first analyzed two recent studies which concluded that snakes are the intermediate hosts of 2019-nCoV and that the 2019-nCoV spike protein insertions shared a unique similarity to HIV-1. The re-implementation of the analyses, built on larger-scale datasets using state-of-the-art bioinformatics methods and databases, present however clear evidences rebutting these conclusions. Next, using metagenomic samples from Manis javanica we assembled a draft genome of the 2019-nCoV-like coronavirus, which shows 73% coverage and 91% sequence identity to the 2019-nCoV genome. In particular, the alignments of the spike surface glycoprotein receptor binding domain revealed 4-fold more variations in the bat coronavirus RaTG13 than those in the Manis coronavirus compared to 2019-nCoV, suggesting the pangolin as a missing link in the transmission of 2019-nCoV from bats to human.},
}

@article {pmid31521614,
year = {2019},
author = {Yamada, T and Hino, S and Iijima, H and Genda, T and Aoki, R and Nagata, R and Han, KH and Hirota, M and Kinashi, Y and Oguchi, H and Suda, W and Furusawa, Y and Fujimura, Y and Kunisawa, J and Hattori, M and Fukushima, M and Morita, T and Hase, K},
title = {Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis.},
journal = {EBioMedicine},
volume = {48},
number = {},
pages = {513-525},
pmid = {31521614},
issn = {2352-3964},
mesh = {Adult ; Animals ; Biomarkers ; Butyrates/metabolism ; Case-Control Studies ; Female ; Gastrointestinal Microbiome ; *Homeostasis ; Humans ; *Immunity, Mucosal ; Inflammatory Bowel Diseases/etiology/metabolism/pathology ; Intestinal Mucosa/*immunology/*metabolism ; Male ; Metagenome ; Metagenomics ; Mice ; Middle Aged ; Mucins/*metabolism ; Polysaccharides/*metabolism ; Symbiosis ; },
abstract = {BACKGROUND: The dysbiosis of gut microbiota has been implicated in the pathogenesis of inflammatory bowel diseases; however, the underlying mechanisms have not yet been elucidated. Heavily glycosylated mucin establishes a first-line barrier against pathogens and serves as a niche for microbial growth.

METHODS: To elucidate relationships among dysbiosis, abnormal mucin utilisation, and microbial metabolic dysfunction, we analysed short-chain fatty acids (SCFAs) and mucin components in stool samples of 40 healthy subjects, 49 ulcerative colitis (UC) patients, and 44 Crohn's disease (CD) patients from Japan.

FINDINGS: Levels of n-butyrate were significantly lower in stools of both CD and UC patients than in stools of healthy subjects. Correlation analysis identified seven bacterial species positively correlated with n-butyrate levels; the major n-butyrate producer, Faecalibacterium prausnitzii, was particularly underrepresented in CD patients, but not in UC patients. In UC patients, there were inverse correlations between mucin O-glycan levels and the production of SCFAs, such as n-butyrate, suggesting that mucin O-glycans serve as an endogenous fermentation substrate for n-butyrate production. Indeed, mucin-fed rodents exhibited enhanced n-butyrate production, leading to the expansion of RORgt+Treg cells and IgA-producing cells in colonic lamina propria. Microbial utilisation of mucin-associated O-glycans was significantly reduced in n-butyrate-deficient UC patients.

INTERPRETATION: Mucin O-glycans facilitate symbiosynthesis of n-butyrate by gut microbiota. Abnormal mucin utilisation may lead to reduced n-butyrate production in UC patients. FUND: Japan Society for the Promotion of Science, Health Labour Sciences Research Grant, AMED-Crest, AMED, Yakult Foundation, Keio Gijuku Academic Development Funds, The Aashi Grass Foundation, and The Canon Foundation.},
}

Adult
Animals
Biomarkers
Butyrates/metabolism
Case-Control Studies
Female
Gastrointestinal Microbiome
*Homeostasis
Humans
*Immunity, Mucosal
Inflammatory Bowel Diseases/etiology/metabolism/pathology
Intestinal Mucosa/*immunology/*metabolism
Male
Metagenome
Metagenomics
Mice
Middle Aged
Mucins/*metabolism
Polysaccharides/*metabolism
Symbiosis

@article {pmid32200314,
year = {2020},
author = {Wang, Y and Hu, Y and Liu, F and Cao, J and Lv, N and Zhu, B and Zhang, G and Gao, GF},
title = {Integrated metagenomic and metatranscriptomic profiling reveals differentially expressed resistomes in human, chicken, and pig gut microbiomes.},
journal = {Environment international},
volume = {138},
number = {},
pages = {105649},
doi = {10.1016/j.envint.2020.105649},
pmid = {32200314},
issn = {1873-6750},
abstract = {Gut microbiota is a reservoir of antibiotic resistance genes (ARGs). Yet, limited information is available regarding the presence (metagenomic DNA level) and expression profiles (metatranscriptomic RNA level) of ARGs in gut microbiota. Here, we used both metagenomic and metatranscriptomic approaches to comprehensively reveal the abundance, diversity, and expression of ARGs in human, chicken, and pig gut microbiomes in China. Based on deep sequencing data and ARG databases, a total of 330 ARGs associated with 21 antibiotic classes were identified in 18 human, chicken, and pig fecal samples. Metatranscriptomic analysis revealed that 49.4, 66.5, and 56.6% of ARGs identified in human, chicken, and pig gut microbiota, respectively, were expressed, indicating that a large proportion of ARGs were not transcriptionally active. Further analysis demonstrated that transcript abundance of tetracycline, aminoglycoside, and beta-lactam resistance genes was mainly contributed by acquired ARGs. We also found that various biocide, chemical, and metal resistance genes were actively transcribed in human and animal guts. The combination of metagenomic and metatranscriptomic analysis in this study allowed us to specifically link ARGs to their transcripts, providing a comprehensive view of the prevalence and expression of ARGs in gut microbiota. Taken together, these data deepen our understanding of the distribution, evolution, and dissemination of ARGs and metal resistance genes in human, chicken, and pig gut microbiota.},
}

@article {pmid32200249,
year = {2020},
author = {Santos, A and Rachid, C and Pacheco, AB and Magalhães, V},
title = {Biotic and abiotic factors affect microcystin-LR concentrations in water/sediment interface.},
journal = {Microbiological research},
volume = {236},
number = {},
pages = {126452},
doi = {10.1016/j.micres.2020.126452},
pmid = {32200249},
issn = {1618-0623},
abstract = {Harmful cyanobacterial blooms are increasingly common in aquatic environments. This can lead to higher concentrations of cyanotoxins, such as microcystins (MCs), posing a great risk to diverse organisms, including humans. MCs are among the most commonly reported cyanotoxins in freshwater environments worldwide, where they may have different fates. MCs can adsorb to suspended particles into the water column and deposit onto the sediment where they can be affected by physical factors (e.g. winds in shallow lakes causing sediment resuspension) or biological factors (e.g. biodegradation). Here we focused on the conditions of a coastal shallow lagoon contaminated by MCs aiming to estimate the return of pre-existing MCs from the sediment to the water column, to evaluate the adsorption of dissolved MC-LR to the sediment and to verify the occurrence of biodegradation. In experiments with sediment, desorption and adsorption were tested under the influence of temperature, pH and aeration, reproducing conditions observed in the lagoon. MC-desorption was not detected under the tested conditions. Spiking MC-LR into lagoon water samples in the presence of sediment resulted in a 50 % reduction of soluble MC-LR concentration in control conditions (25 °C, pH 8.0, no aeration). Increasing temperature (45 °C) or introducing aeration further stimulated MC-LR removal from the water. Biodegradation was observed in sediment samples and interstitial water (even with tetracycline). The composition of the bacterial community differed in sediment and interstitial water: major phyla were Chloroflexi, Proteobacteria, Firmicutes, and OP3. From the assigned OTUs, we identified genera already described as MC degrading bacteria. Thus, the sediment is a key factor influencing the fate of MC-LR in this shallow coastal lake contributing to stable adsorption and biodegradation.},
}

@article {pmid32200181,
year = {2020},
author = {Samson, R and Rajput, V and Shah, M and Yadav, R and Sarode, P and Dastager, SG and Dharne, MS and Khairnar, K},
title = {Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities.},
journal = {Chemosphere},
volume = {252},
number = {},
pages = {126507},
doi = {10.1016/j.chemosphere.2020.126507},
pmid = {32200181},
issn = {1879-1298},
abstract = {River confluences are interesting ecological niche with limited information in respect of the structure and the functions of diverse microbial communities. Fungi are gaining global attention as promising biological spectacles for defining the trophic status of riverine systems. We condense existing knowledge in confluence diversity in two Indian rivers (i.e. Ganges and Yamuna), by combining sediment metagenomics using long read aided MinION nanopore sequencing. A total of 63 OTU's were observed, of which top 20 OTU's were considered based on relative abundance of each OTU at a particular location. Fungal genera such as Aspergillus, Penicillium, Kluveromyces, Lodderomyces, and Nakaseomyces were deciphered as potential bio indicators of river pollution and eutrophication in the confluent zone. In silico functional gene analysis uncovered hits for neurodegenerative diseases and xenobiotic degradation potential, supporting bioindication of river pollution in wake of anthropogenic intervention.},
}

@article {pmid32200157,
year = {2020},
author = {Strubbia, S and Schaeffer, J and Besnard, A and Wacrenier, C and Le Mennec, C and Garry, P and Desdouits, M and Le Guyader, FS},
title = {Metagenomic to evaluate norovirus genomic diversity in oysters: Impact on hexamer selection and targeted capture-based enrichment.},
journal = {International journal of food microbiology},
volume = {323},
number = {},
pages = {108588},
doi = {10.1016/j.ijfoodmicro.2020.108588},
pmid = {32200157},
issn = {1879-3460},
abstract = {Human virus transmission through food consumption has been identified since many years and the international trade increases the risk of dissemination of viral pathogens. The development of metagenomic approach holds many promises for the surveillance of viruses in food and water. This work aimed to analyze norovirus diversity and to evaluate strain-dependent accumulation patterns in three oyster types by using a metagenomic approach. Different hexamer sets to prime cDNA were evaluated before capture-based approach to enhance virus reads recovery during deep sequencing. The study includes the use of technical replicates of artificially contaminated oysters and the analysis of multiple negatives controls. Results showed a clear impact of the hexamer set used for cDNA synthesis. A set of In-house designed (I-HD) hexamers, selected to lower mollusk amplification, gave promising results in terms of viral reads abundancy. However, the best correlation between CT values, thus concentrations, and number of reads was observed using random hexamers. Random hexamers also provided the highest numbers of reads and allowed the identification of sequence of different human enteric viruses. Regarding human norovirus, different genogroups and genotypes were identified among contigs longer than 500 bp. Two full genomes and six sequences longer than 3600 bases were obtained allowing a precise strain identification. The use of technical triplicates was found valuable to increase the chances to sequence viral strains present at low concentrations. Analyzing viral contamination in shellfish samples is quite challenging, however this work demonstrates that the recovery of full genome or long contigs, allowing clear identification of viral strains is possible.},
}

@article {pmid32199388,
year = {2020},
author = {Bilal, M and Wang, Z and Cui, J and Ferreira, LFR and Bharagava, RN and Iqbal, HMN},
title = {Environmental impact of lignocellulosic wastes and their effective exploitation as smart carriers - A drive towards greener and eco-friendlier biocatalytic systems.},
journal = {The Science of the total environment},
volume = {722},
number = {},
pages = {137903},
doi = {10.1016/j.scitotenv.2020.137903},
pmid = {32199388},
issn = {1879-1026},
abstract = {In recent years, lignocellulosic wastes have gathered much attention due to increasing economic, social, environmental apprehensions, global climate change and depleted fossil fuel reserves. The unsuitable management of lignocellulosic materials and related organic wastes poses serious environmental burden and causes pollution. On the other hand, lignocellulosic wastes hold significant economic potential and can be employed as promising catalytic supports because of impressing traits such as surface area, porous structure, and occurrence of many chemical moieties (i.e., carboxyl, amino, thiol, hydroxyl, and phosphate groups). In the current literature, scarce information is available on this important and highly valuable aspect of lignocellulosic wastes as smart carriers for immobilization. Thus, to fulfill this literature gap, herein, an effort has been made to signify the value generation aspects of lignocellulosic wastes. Literature assessment spotlighted that all these waste materials display high potential for immobilizing enzyme because of their low cost, bio-renewable, and sustainable nature. Enzyme immobilization has gained recognition as a highly useful technology to improve enzyme properties such as catalytic stability, performance, and repeatability. The application of carrier-supported biocatalysts has been a theme of considerable research, for the past three decades, in the bio-catalysis field. Nonetheless, the type of support matrix plays a key role in the immobilization process due to its influential impact on the physicochemical characteristics of the as-synthesized biocatalytic system. In the past, an array of various organic, inorganic, and composite materials has been used as carriers to formulate efficient and stable biocatalysts. This review is envisioned to provide recent progress and development on the use of different agricultural wastes (such as coconut fiber, sugarcane bagasse, corn and rice wastes, and Brewers' spent grain) as support materials for enzyme immobilization. In summary, the effective utilization of lignocellulosic wastes to develop multi-functional biocatalysts is not only economical but also reduce environmental problems of unsuitable management of organic wastes and drive up the application of biocatalytic technology in the industry.},
}

@article {pmid32199187,
year = {2020},
author = {Tang, Y and Dai, X and Dong, B and Guo, Y and Dai, L},
title = {Humification in extracellular polymeric substances (EPS) dominates methane release and EPS reconstruction during the sludge stabilization of high-solid anaerobic digestion.},
journal = {Water research},
volume = {175},
number = {},
pages = {115686},
doi = {10.1016/j.watres.2020.115686},
pmid = {32199187},
issn = {1879-2448},
abstract = {High-solid anaerobic digestion (HAD) can directly treat dewatered sewage sludge (total solid content ≥15%) with superior volume efficiency. Sludge stabilization during HAD is expected to achieve by throughout organic degradation and conversion towards methane-rich biogas release and humic formation. Sewage sludge is the combination of microbial zoogleas and theirs adsorption of organic and inorganic matter, in which the extracellular polymeric substances (EPS) account 60-80% of total sludge organic matter, inevitably participating most extracellular metabolic pathways. The interactions between EPS transformation and genetically annotated metabolic pathways were found in this research. In brief, noticing the highly cross-linked structures in EPS with major active components of humic substances (HS) and protein (PN), as PN hydrolysis and decomposition in EPS were enhanced in the high-solid anaerobic condition, the exposure of aromatic groups and sites in HS were considerable. HS release was the main factor shifting the electron exchange capacity and activity, which aided in energy metabolism of sludge microorganisms involved in redox reactions, especially the methanogenesis, thus in turn facilitating the PN degradation; Then, the screened humic groups and active protein derives might act as the beneficial precursors to regenerate neo-humic structures, whose significant bridging effect and signal role on stimulating amino acid biosynthesis, member transport and metallic complexation could further contribute to proteolytic condensation and EPS reconstruction. Hence, the in-depth sludge stabilization mechanism during HAD process was established for developing enlightening strategies.},
}

@article {pmid32198176,
year = {2020},
author = {Kanik, M and Munro-Ehrlich, M and Fernandes-Martins, MC and Payne, D and Gianoulias, K and Keller, L and Kubacki, A and Lindsay, MR and Baxter, BK and Vanden Berg, MD and Colman, DR and Boyd, ES},
title = {Unexpected abundance and diversity of phototrophs in mats from morphologically variable microbialites in Great Salt Lake, Utah.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.00165-20},
pmid = {32198176},
issn = {1098-5336},
abstract = {Microbial mat communities are associated with extensive (∼700 km2) and morphologically variable carbonate structures, termed microbialites, in the hypersaline Great Salt Lake (GSL), Utah. However, whether the composition of GSL mat communities co-varies with microbialite morphology and lake environment is unknown. Moreover, the potential adaptations that allow the establishment of these extensive mat communities at high salinity (14-17% total salts) are poorly understood. To address these questions, microbial mats were sampled from seven locations in the south arm of GSL representing different lake environments and microbialite morphologies. Despite the morphological differences, microbialite-associated mats were taxonomically similar and were dominated by the cyanobacterium Euhalothece and several heterotrophic bacteria. Metagenomic sequencing of a representative mat revealed Euhalothece and subdominant Thiohalocapsa populations that encode the Calvin cycle and nitrogenase, suggesting they supply fixed carbon and nitrogen to heterotrophic bacteria. Fifteen of the next sixteen most abundant taxa are inferred to be aerobic heterotrophs and surprisingly encode reaction center, rhodopsin, and/or bacteriochlorophyll biosynthesis proteins, suggesting aerobic photoheterotrophic (APH) capabilities. Importantly, proteins involved in APH are enriched in the GSL community relative to microbialite mat communities from lower salinity environments. These findings indicate that the ability to integrate light into energy metabolism is a key adaptation allowing for robust mat development in the hypersaline GSL.IMPORTANCEThe earliest evidence of life on Earth is from organosedimentary structures, termed microbialites, preserved in 3.481 Ga rocks. Phototrophic microbial mats form in association with ∼700 km2 expanse of morphologically diverse microbialites in the hypersaline Great Salt Lake, Utah. Here we show taxonomically similar microbial mat communities are associated with morphologically diverse microbialites across the lake. Metagenomic sequencing reveals an abundance and diversity of autotrophic and heterotrophic taxa capable of harvesting light energy to drive metabolism. The unexpected abundance of and diversity in, the mechanisms of harvesting light energy observed in GSL mat populations likely functions to minimize niche overlap among co-inhabiting taxa, provide a mechanism(s) to increase energy yield and osmotic balance during salt stress, and enhance fitness. Together, these physiological benefits promote the formation of robust mats that, in turn, influence the formation of morphologically diverse microbialite structures that can be imprinted in the rock record.},
}

@article {pmid32198072,
year = {2020},
author = {Wang, Y and Zhou, Y and Xiao, X and Zheng, J and Zhou, H},
title = {Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {103737},
doi = {10.1016/j.jprot.2020.103737},
pmid = {32198072},
issn = {1876-7737},
abstract = {The gut microbiota is the largest and most complex microbial community in the human body. Host-gut microbiota interactions have significant implications on health and disease. The development of genome-sequencing technologies, especially the application of next-generation sequencing (NGS), has accelerated the study of the gut microbiota. Most gut microbiota studies rely on 16S rRNA sequencing, metagenomics, and metatranscriptomics, but metaproteomics, based on mass spectrometry (MS), provides functional information on the signaling and metabolic pathways in the gut microbiota. This review is intended to introduce different research methods to study the gut microbiota, with a specific focus on the current progress and application of metaproteomics. SIGNIFICANCE: The gut microbiota plays a key role in human health and disease. In this review, different research methods are described and compared in the field of the gut microbiota. Among these research methods, metaproteomics reveals the taxonomy and functionality of the gut microbiota, especially the functional pathways associated with diseases. Thus, the current progress and application of metaproteomics are summarized, in order to enhance a comprehensive depiction of metaproteomics.},
}

@article {pmid32197656,
year = {2020},
author = {Dai, Z and Sevillano-Rivera, MC and Calus, ST and Bautista-de Los Santos, QM and Eren, AM and van der Wielen, PWJJ and Ijaz, UZ and Pinto, AJ},
title = {Disinfection exhibits systematic impacts on the drinking water microbiome.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {42},
doi = {10.1186/s40168-020-00813-0},
pmid = {32197656},
issn = {2049-2618},
support = {1749530//National Science Foundation/ ; EP/M016811/1//Engineering and Physical Sciences Research Council/ ; NE/L011956/1//Natural Environmental Research Council (GB)/ ; },
abstract = {Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without using a disinfectant. The impact of these contrasting approaches on the drinking water microbiome is not systematically understood. We use genome-resolved metagenomics to compare the structure, metabolic traits, and population genomes of drinking water microbiome samples from bulk drinking water across multiple full-scale disinfected and non-disinfected drinking water systems. Microbial communities cluster at the structural- and functional potential-level based on the presence/absence of a disinfectant residual. Disinfectant residual alone explained 17 and 6.5% of the variance in structure and functional potential of the drinking water microbiome, respectively, despite including multiple drinking water systems with variable source waters and source water communities and treatment strategies. The drinking water microbiome is structurally and functionally less diverse and variable across disinfected compared to non-disinfected systems. While bacteria were the most abundant domain, archaea and eukaryota were more abundant in non-disinfected and disinfected systems, respectively. Community-level differences in functional potential were driven by enrichment of genes associated with carbon and nitrogen fixation in non-disinfected systems and γ-aminobutyrate metabolism in disinfected systems likely associated with the recycling of amino acids. Genome-level analyses for a subset of phylogenetically-related microorganisms suggests that disinfection selects for microorganisms capable of using fatty acids, presumably from microbial decay products, via the glyoxylate cycle. Overall, we find that disinfection exhibits systematic selective pressures on the drinking water microbiome and may select for microorganisms able to utilize microbial decay products originating from disinfection-inactivated microorganisms. Video abstract.},
}

@article {pmid32197644,
year = {2020},
author = {Böhm, ME and Razavi, M and Marathe, NP and Flach, CF and Larsson, DGJ},
title = {Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {41},
doi = {10.1186/s40168-020-00814-z},
pmid = {32197644},
issn = {2049-2618},
support = {2018-02835//Vetenskapsrådet/ ; 2018-05771//Vetenskapsrådet/ ; 2018-00787//Svenska Forskningsrådet Formas/ ; },
abstract = {BACKGROUND: New antibiotic resistance determinants are generally discovered too late, long after they have irreversibly emerged in pathogens and spread widely. Early discovery of resistance genes, before or soon after their transfer to pathogens could allow more effective measures to monitor and reduce spread, and facilitate genetics-based diagnostics.

RESULTS: We modified a functional metagenomics approach followed by in silico filtering of known resistance genes to discover novel, mobilised resistance genes in class 1 integrons in wastewater-impacted environments. We identified an integron-borne gene cassette encoding a protein that conveys high-level resistance against aminoglycosides with a garosamine moiety when expressed in E. coli. The gene is named gar (garosamine-specific aminoglycoside resistance) after its specificity. It contains none of the functional domains of known aminoglycoside modifying enzymes, but bears characteristics of a kinase. By searching public databases, we found that the gene occurs in three sequenced, multi-resistant clinical isolates (two Pseudomonas aeruginosa and one Luteimonas sp.) from Italy and China, respectively, as well as in two food-borne Salmonella enterica isolates from the USA. In all cases, gar has escaped discovery until now.

CONCLUSION: To the best of our knowledge, this is the first time a novel resistance gene, present in clinical isolates, has been discovered by exploring the environmental microbiome. The gar gene has spread horizontally to different species on at least three continents, further limiting treatment options for bacterial infections. Its specificity to garosamine-containing aminoglycosides may reduce the usefulness of the newest semisynthetic aminoglycoside plazomicin, which is designed to avoid common aminoglycoside resistance mechanisms. Since the gene appears to be not yet common in the clinics, the data presented here enables early surveillance and maybe even mitigation of its spread.},
}

@article {pmid32197504,
year = {2020},
author = {Zhimo, VY and Biasi, A and Kumar, A and Feygenberg, O and Salim, S and Vero, S and Wisniewski, M and Droby, S},
title = {Yeasts and Bacterial Consortia from Kefir Grains Are Effective Biocontrol Agents of Postharvest Diseases of Fruits.},
journal = {Microorganisms},
volume = {8},
number = {3},
pages = {},
doi = {10.3390/microorganisms8030428},
pmid = {32197504},
issn = {2076-2607},
abstract = {Fungal pathogens in fruits and vegetables cause significant losses during handling, transportation, and storage. Biological control with microbial antagonists replacing the use of chemical fungicides is a major approach in postharvest disease control, and several products based on single antagonists have been developed but have limitations related to reduced and inconsistent performance under commercial conditions. One possible approach to enhance the biocontrol efficacy is to broaden the spectrum of the antagonistic action by employing compatible microbial consortia. Here, we explore commercial kefir grains, a natural probiotic microbial consortium, by culture-dependent and metagenomic approaches and observed a rich diversity of co-existing yeasts and bacterial population. We report effective inhibition of the postharvest pathogen Penicillium expansum on apple by using the grains in its fresh commercial and milk-activated forms. We observed few candidate bacteria and yeasts from the kefir grains that grew together over successive enrichment cycles, and these mixed fermentation cultures showed enhanced biocontrol activities as compared to the fresh commercial or milk-activated grains. We also report several individual species of bacteria and yeasts with biocontrol activities against Penicillium rots on apple and grapefruit. These species with antagonistic properties could be further exploited to develop a synthetic consortium to achieve enhanced antagonistic effects against a wide range of postharvest pathogens.},
}

@article {pmid32197299,
year = {2020},
author = {Lázaro-Perona, F and Dahdouh, E and Román-Soto, S and Jiménez-Rodríguez, S and Rodríguez-Antolín, C and de la Calle, F and Agrifoglio, A and Membrillo, FJ and García-Rodríguez, J and Mingorance, J},
title = {Metagenomic Detection of Two Vientoviruses in a Human Sputum Sample.},
journal = {Viruses},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/v12030327},
pmid = {32197299},
issn = {1999-4915},
support = {DTS/1500171//Instituto de Salud Carlos III/ ; VIRUSCAN FETPROACT-2016-731868//European Comission/ ; H2020-MSCA-IF-2017-796084//European Comission/ ; Youth Employment Initiative//Comunidad de Madrid, Consejería de Educación, Juventud y Deporte/ ; Youth Employment Initiative//European Social Fund/ ; },
abstract = {We used metagenomics to analyze one sputum sample from a patient with symptoms of a respiratory infection that yielded negative results for all pathogens tested. We detected two viral genomes that could be assembled and showed sequence similarity to redondoviruses, a recently described group within the CRESS-DNA viruses. One hundred sputum samples were screened for the presence of these viruses using specific primers. One sample was positive for the same two viruses, and another was positive for one of them. These findings raise questions about a possible role of redondoviruses in respiratory infections in humans.},
}

@article {pmid32197188,
year = {2020},
author = {Feng, S and Liu, F and Zhu, S and Feng, P and Wang, Z and Yuan, Z and Shang, C and Chen, H},
title = {Performance of a microalgal-bacterial consortium system for the treatment of dairy-derived liquid digestate and biomass production.},
journal = {Bioresource technology},
volume = {306},
number = {},
pages = {123101},
doi = {10.1016/j.biortech.2020.123101},
pmid = {32197188},
issn = {1873-2976},
abstract = {To enhance the treatment performance of dairy-derived liquid digestate (DLD) using microalgal-bacterial consortium system composed of Chlorella vulgaris and indigenous bacteria (CV), activated sludge was introduced to form a new microalgal-bacterial consortium system (Co-culture). The activated sludge shortened the lag phase and increased the specific growth rate of C. vulgaris (0.56 d-1). The biomass yield in the Co-culture was 2.72 g L-1, which was lower than that in the CV (3.24 g L-1), but the Co-culture had an improved COD (chemical oxygen demand) removal (25.26%) compared to the CV (13.59%). Quantitative PCR and metagenomic analyses demonstrated that microalgae also promoted bacterial growth, but influenced differently on the bacterial communities of indigenous bacteria and activated sludge. Compared with indigenous bacteria, activated sludge was more prone to forming a favorable symbiosis with C. vulgaris. These findings contribute to the construction of efficient microalgal-bacterial consortium system in wastewater treatment.},
}

@article {pmid32196626,
year = {2020},
author = {Nicoletti, A and Ponziani, FR and Nardella, E and Ianiro, G and Gasbarrini, A and Zileri Dal Verme, L},
title = {Biliary tract microbiota: a new kid on the block of liver diseases?.},
journal = {European review for medical and pharmacological sciences},
volume = {24},
number = {5},
pages = {2750-2775},
doi = {10.26355/eurrev_202003_20548},
pmid = {32196626},
issn = {2284-0729},
abstract = {The microbiome plays a crucial role in maintaining the homeostasis of the organism. Recent evidence has provided novel insights for understanding the interaction between the microbiota and the host. However, the vast majority of such studies have analyzed the interactions taking place in the intestinal tract. The biliary tree has traditionally been considered sterile under normal conditions. However, the advent of metagenomic techniques has revealed an unexpectedly rich bacterial community in the biliary tract. Associations between specific microbiological patterns and inflammatory biliary diseases and cancer have been recently described. Hence, biliary dysbiosis may be a primary trigger in the pathogenesis of biliary diseases. In particular, recent studies have suggested that microorganisms could play a significant role in the development of gallstones, pathogenesis of autoimmune cholangiopathies and biliary carcinogenesis. Moreover, the intimate connection between the biliary tract, liver and pancreas, could reveal hidden influences on the development of diseases of these organs. Further studies are needed to deepen the comprehension of the influence of the biliary microbiota in human pathology. This knowledge could lead to the formulation of strategies for modulating the biliary microbiota in order to treat and prevent these pathological conditions.},
}

@article {pmid32196510,
year = {2020},
author = {Farhana, L and Sarkar, S and Nangia-Makker, P and Yu, Y and Khosla, P and Levi, E and Azmi, A and Majumdar, APN},
title = {Natural agents inhibit colon cancer cell proliferation and alter microbial diversity in mice.},
journal = {PloS one},
volume = {15},
number = {3},
pages = {e0229823},
doi = {10.1371/journal.pone.0229823},
pmid = {32196510},
issn = {1932-6203},
abstract = {The current study was undertaken to investigate the effect of differentially formulated polyphenolic compound Essential Turmeric Oil-Curcumin (ETO-Cur), and Tocotrienol-rich fraction (TRF) of vitamin E isomers on colorectal cancer (CRC) cells that produce aggressive tumors. Combinations of ETO-Cur and TRF were used to determine the combinatorial effects of ETO-Cur and TRF-mediated inhibition of growth of CRC cells in vitro and HCT-116 cells xenograft in SCID mice. 16S rRNA gene sequence profiling was performed to determine the outcome of gut microbial communities in mice feces between control and ETO-Cur-TRF groups. Bacterial identifications were validated by performing SYBR-based Real Time (RT) PCR. For metagenomics analysis to characterize the microbial communities, multiple software/tools were used, including Quantitative Insights into Microbial Ecology (QIIME) processing tool. We found ETO-Cur and TRF to synergize and that the combination of ETO-Cur-TRF significantly inhibited growth of HCT-116 xenografts in SCID mice. This was associated with a marked alteration in microbial communities and increased microbial OTU (operation taxonomic unit) number. The relative abundance of taxa was increased and the level of microbial diversity after 34 days of combinatorial treatment was found to be 44% higher over the control. Shifting of microbial family composition was observed in ETO-Cur-TRF treated mice as evidenced by marked reductions in Bacteroidaceae, Ruminococcaceae, Clostridiales, Firmicutes and Parabacteroids families, compared to controls. Interestingly, during the inhibition of tumor growth in ETO-Cur treated mice, probiotic Lactobacillaceae and Bifidobacteriaceae were increased by 20-fold and 6-fold, respectively. The relative abundance of anti-inflammatory Clostridium XIVa was also increased in ETO-Cur-TRF treated mice when compared with the control. Our data suggest that ETO-Cur-TRF show synergistic effects in inhibiting colorectal cancer cell proliferation in vitro and in mouse xenografts in vivo, and might induce changes in microbial diversity in mice.},
}

@article {pmid32196448,
year = {2020},
author = {Boutin, S and Dalpke, AH},
title = {The microbiome: a reservoir to discover new antimicrobials agents.},
journal = {Current topics in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/1568026620666200320112731},
pmid = {32196448},
issn = {1873-4294},
abstract = {Nature offered mankind the first golden era of discovery of novel antimicrobials based on the ability of eukaryotes or micro-organisms to produce such compounds. The microbial world proved to be a huge reservoir of such antimicrobial compounds which play important functional roles in every environment. However, most of those organisms are still uncultivable in the classical way and therefore the use of extended culture or DNA based methods (metagenomics) to discover novel compounds promises usefulness. In the past decades, the advances in next generation sequencing and bioinformatics revealed the enormous diversity of the microbial worlds and the functional repertoire available for studies. Thus, data-mining becomes of particular interest in the context of the increased need for new antibiotics due to antimicrobial resistance and the rush in antimicrobial discovery. In this review, we will present an overview of the environmental sources to discover new natural compounds from the microbiome, the culture-based and culture independent (metagenomic) approaches that have been developed to identify new antimicrobials, the input of those methods in the field and their limitations.},
}

@article {pmid32196394,
year = {2020},
author = {Liu, G and Wu, C and Abrams, WR and Li, Y},
title = {Structural and Functional Characteristics of the Microbiome in Deep-Dentin Caries.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {22034520913248},
doi = {10.1177/0022034520913248},
pmid = {32196394},
issn = {1544-0591},
abstract = {Dental caries is a cariogenic bacteria-mediated, fermentable carbohydrate-driven dynamic disease. The new ecological hypothesis for dentin caries suggests that an alteration in the microbial community and the presence of specific metabolic pathway genes contribute to the initiation and progression of caries. This study aimed to determine the structural and functional characteristics of a microbial community of human deep-dentin carious lesions. Sixteen deep-dentin carious lesions were obtained from the first permanent molars of 8 patients aged 9 to 18 y. Shotgun metagenomic sequencing was used to measure the microbial composition and abundance at the phylum, class, order, family, genus, and species levels. Functional analysis of the DNA sequencing data set was also performed and compared among different layers of the lesions using DIAMOND software against the Kyoto Encyclopedia of Genes and Genomes database. This study found that in the deep-dentin carious lesions, Actinobacteria (35.8%) and Firmicutes (31.2%) were the most prevalent phyla, followed by Bacteroidetes (13.6%), Proteobacteria (3.6%), and Fusobacteria (2.5%). The microbial composition varied among the individuals, but there were no significant differences in the distribution of the relative microbial abundance between the superficial layers and the deep layers. Although 14.5% of the top 10 taxa were identified as Lactobacillus at the genus level, only 25% of the deep-dentin carious samples showed Lactobacillus as the most abundant genus. Other abundant taxa included Actinomyces (10.5%), Olsenella (9.4%), Prevotella (8.8%), Propionibacterium (7.2%), Streptococcus (3.9%), Selenomonas (3.7%), Corynebacterium (1.9%), Leptotrichia (1.4%), and Parascardovia (1.1%). The most abundant pathway identified in the KEGG database was the metabolic pathway containing 101,427 annotated genes, which consisted of 51.4% of all annotated genes. The carbohydrate metabolism pathway, amino acid metabolism, and membrane transport were the functional traits of the level 2 pathways. These findings suggest that the potent interaction within the microbial communities in deep-dentin carious lesions may play a fundamental role in caries etiology.},
}

@article {pmid32196076,
year = {2020},
author = {Deyett, E and Rolshausen, PE},
title = {Endophytic Microbial Assemblage in Grapevine.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaa053},
pmid = {32196076},
issn = {1574-6941},
abstract = {The plant vascular system has remained an under-explored niche despite its potential for hosting beneficial microbes. The aim of this work was to determine the origin of the microbial endophytes inhabiting grapevine. We focused on a single commercial vineyard in California over a two-year period and used an amplicon metagenomics approach to profile the bacterial (16S -V4) and fungal (ITS) communities of the microbiome across a continuum of six grapevine compartments; bulk soil, rhizosphere, root, cordon, cane and sap. Our data supported that roots are a bottleneck to microbial richness and that they are mostly colonized with soilborne microbes, including possible plant growth promoting bacteria recruited by the host, but also saprohytic and pathogenic fungal invaders. A core group of taxa was identified throughout the vine, however there were clear partitioning of the microbiome based on host's niche. Above and below ground plant tissues displayed distinct microbial fingerprints and were intermixed in a limited capacity mostly by way of the plant sap. We discuss how cultural practices and human contact may shape the endosphere microbiome and identify potential channels for transmission of its residents.},
}

@article {pmid32194518,
year = {2020},
author = {Mumo, NN and Mamati, GE and Ateka, EM and Rimberia, FK and Asudi, GO and Boykin, LM and Machuka, EM and Njuguna, JN and Pelle, R and Stomeo, F},
title = {Metagenomic Analysis of Plant Viruses Associated With Papaya Ringspot Disease in Carica papaya L. in Kenya.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {205},
doi = {10.3389/fmicb.2020.00205},
pmid = {32194518},
issn = {1664-302X},
abstract = {Carica papaya L. is an important fruit crop grown by small- and large-scale farmers in Kenya for local and export markets. However, its production is constrained by papaya ringspot disease (PRSD). The disease is believed to be caused by papaya ringspot virus (PRSV). Previous attempts to detect PRSV in papaya plants showing PRSD symptoms, using enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR) procedures with primers specific to PRSV, have not yielded conclusive results. Therefore, the nature of viruses responsible for PRSD was elucidated in papaya leaves collected from 22 counties through Illumina MiSeq next-generation sequencing (NGS) and validated by RT-PCR and Sanger sequencing. Viruses were detected in 38 out of the 48 leaf samples sequenced. Sequence analysis revealed the presence of four viruses: a Potyvirus named Moroccan watermelon mosaic virus (MWMV) and three viruses belonging to the genus Carlavirus. The Carlaviruses include cowpea mild mottle virus (CpMMV) and two putative Carlaviruses-closely related but distinct from cucumber vein-clearing virus (CuVCV) with amino acid and nucleotide sequence identities of 75.7-78.1 and 63.6-67.6%, respectively, in the coat protein genes. In reference to typical symptoms observed in the infected plants, the two putative Carlaviruses were named papaya mottle-associated virus (PaMV) and papaya mild mottle-associated virus (PaMMV). Surprisingly, and in contrast to previous studies conducted in other parts of world, PRSV was not detected. The majority of the viruses were detected as single viral infections, while a few were found to be infecting alongside another virus (for example, MWMV and PaMV). Furthermore, the NGS and RT-PCR analysis identified MWMV as being strongly associated with ringspot symptoms in infected papaya fruits. This study has provided the first complete genome sequences of these viruses isolated from papaya in Kenya, together with primers for their detection-thus proving to be an important step towards the design of long-term, sustainable disease management strategies.},
}

@article {pmid32194513,
year = {2020},
author = {Zhang, M and Chen, H and Liu, L and Xu, L and Wang, X and Chang, L and Chang, Q and Lu, G and Jiang, J and Zhu, L},
title = {The Changes in the Frog Gut Microbiome and Its Putative Oxygen-Related Phenotypes Accompanying the Development of Gastrointestinal Complexity and Dietary Shift.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {162},
doi = {10.3389/fmicb.2020.00162},
pmid = {32194513},
issn = {1664-302X},
abstract = {There are many examples of symbiotic and reciprocal relationships in ecological systems; animal gut microbiome-host interactions are one such kind of bidirectional and complex relationship. Here, we utilized several approaches (16S rRNA gene sequencing, metagenomics, and transcriptomics) to explore potential gut microbiome-host interactions accompanying the development of gastrointestinal complexity and a dietary shift from metamorphosis to maturity in ornamented pygmy frogs (Microhyla fissipes). We identified the possible coevolution between a particular gut microbial group (increased putative fat-digesting Erysipelotrichaceae and chitin-digesting Bacteroides and Ruminococcaceae) and the host dietary shift [from herbivore to insectivore (high proportion of dietary chitin and fat)] during metamorphosis. We also found that the remodeling and complexity of the gastrointestinal system during metamorphosis might have a profound effect on the gut microbial community (decreasing facultative anaerobic Proteobacteria and increasing anaerobic Firmicutes) and its putative oxygen-related phenotypes. Moreover, a high proportion of chitin-digesting bacteria and increased carbohydrate metabolism by gut microbiomes at the climax of metamorphosis would help the frog's nutrition and energy needs during metamorphosis and development. Considering the increased expression of particular host genes (e.g., chitinase) in juvenile frogs, we speculate that host plays an important role in amphibian metamorphosis, and their symbiotic gut microbiome may help in this process by providing the nutrition and energy needs. We provide this basic information for the amphibian conservation and managements.},
}

@article {pmid32193781,
year = {2020},
author = {Li, Y and He, XZ and Li, MH and Li, B and Yang, MJ and Xie, Y and Zhang, Y and Ma, XJ},
title = {Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11262-020-01746-4},
pmid = {32193781},
issn = {1572-994X},
support = {2018ZX10711001//China Mega-Projects for Infectious Disease/ ; 2017ZX10104001//China Mega-Projects for Infectious Disease/ ; 2018ZX10713-002//China Mega-Projects for Infectious Disease/ ; },
abstract = {The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses timely makes it a powerful tool for public health emergency response. Third-generation sequencing (TGS) offers advantages in speed and length of detection over second-generation sequencing (SGS). Here, we presented the end-to-end workflows for both Oxford Nanopore MinION and Pacbio Sequel on a viral disease emergency event, along with Ion Torrent PGM as a reference. A specific pipeline for comparative analysis on viral genomes recovered by each platform was assembled, given the high errors of base-calling for TGS platforms. All the three platforms successfully identified and recovered at least 85% Norovirus GII genomes. Oxford Nanopore MinION spent the least sample-to-answer turnaround time with relatively low but enough accuracy for taxonomy classification. Pacbio Sequel recovered the most accurate viral genome, while spending the longest time. Overall, Nanopore metagenomics can rapidly characterize viruses, and Pacbio Sequel can accurately recover viruses. This study provides a framework for designing the appropriate experiments that are likely to lead to accurate and rapid virus emergency response.},
}

@article {pmid32193482,
year = {2020},
author = {Ghanbari Maman, L and Palizban, F and Fallah Atanaki, F and Elmi Ghiasi, N and Ariaeenejad, S and Ghaffari, MR and Hosseini Salekdeh, G and Kavousi, K},
title = {Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {4995},
doi = {10.1038/s41598-020-61942-y},
pmid = {32193482},
issn = {2045-2322},
abstract = {Rumen microbial environment hosts a variety of microorganisms that interact with each other to carry out the feed digestion and generation of several by-products especially methane, which plays an essential role in global warming as a greenhouse gas. However, due to its multi-factorial nature, the exact cause of methane production in the rumen has not yet been fully determined. The current study is an attempt to use system modeling to analyze the relationship between interacting components of rumen microbiome and its role in methane production. Metagenomic data of sheep rumen, with equal numbers of high methane yield (HMY) and low methane yield (LMY) samples, were used. As a well-known approach for the systematic comparative study of complex traits, the co-abundance networks were constructed in both operational taxonomic unit (OTU) and gene levels. A gene-catalog of 1,444 different rumen microbial strains was developed as a reference to measure gene abundances. The results from both types of co-abundance networks showed that methanogens, which are the main ruminal source for methanogenesis, need other microbial species to accomplish the task of methane production through producing the main precursor molecules like H2 and acetate for methanogenesis pathway as their byproducts. KEGG Orthology(KO) analysis of the current study shows that the metabolism and growth rate of methanogens will be increased due to the higher rate of the metabolism and carbohydrate/fiber digestion pathways in the hidden elements. This finding proposes that any ruminant methane yield alteration strategy should consider complex interactions of rumen microbiome components as one tightly integrated unit rather than several separate parts.},
}

@article {pmid32193245,
year = {2020},
author = {Valdés, N and Gonzalez, A and Garcia, V and Tello, M},
title = {Analysis of the Microbiome of Rainbow Trout (Oncorhynchus mykiss) Exposed to the Pathogen Flavobacterium psychrophilum 10094.},
journal = {Microbiology resource announcements},
volume = {9},
number = {12},
pages = {},
doi = {10.1128/MRA.01562-19},
pmid = {32193245},
issn = {2576-098X},
abstract = {Rainbow trout that were resistant or susceptible to Flavobacterium psychrophilum infection were compared with respect to their microbial composition by using 16S rRNA V3-V4 sequencing. The differences occurred in gills, where resistant fish displayed a greater abundance of the phylum Proteobacteria and a smaller proportion of Firmicutes relative to those of susceptible fish.},
}

@article {pmid32193237,
year = {2020},
author = {Marques, M and Borges, N and Silva, SG and da Rocha, UN and Lago-Lestón, A and Keller-Costa, T and Costa, R},
title = {Metagenome-Assembled Genome Sequences of Three Uncultured Planktomarina sp. Strains from the Northeast Atlantic Ocean.},
journal = {Microbiology resource announcements},
volume = {9},
number = {12},
pages = {},
doi = {10.1128/MRA.00127-20},
pmid = {32193237},
issn = {2576-098X},
abstract = {We report three metagenome-assembled genomes (MAGs) of Planktomarina strains from coastal seawater (Portugal) to help illuminate the functions of understudied Rhodobacteraceae bacteria in marine environments. The MAGs encode proteins involved in aerobic anoxygenic photosynthesis and a versatile carbohydrate metabolism, strengthening the role of Planktomarina species in oceanic carbon cycling.},
}

@article {pmid32193113,
year = {2020},
author = {Tian, H and Xu, X and Qu, J and Li, H and Hu, Y and Huang, L and He, W and Li, B},
title = {Biodegradation of phenolic compounds in high saline wastewater by biofilms adhering on aerated membranes.},
journal = {Journal of hazardous materials},
volume = {392},
number = {},
pages = {122463},
doi = {10.1016/j.jhazmat.2020.122463},
pmid = {32193113},
issn = {1873-3336},
abstract = {High saline phenolic wastewater is a typical toxic and refractory industrial wastewater. A single membrane-aerated biofilm reactor (MABR) was used to treat wastewater containing phenol, p-nitrophenol and hydroquinone under increasing phenolic loading and salinity conditions. More than 95 % of phenolic compounds were removed, and a removal efficiency of 8.9 g/m2 d for total phenolic (TP) contents was achieved under conditions with 32 g/L of salt and 763 mg/L of influent TP contents. The microbial diversity, structure and function of a biofilm exposed to different conditions were investigated by high-throughput 16S rRNA gene sequencing and metagenomics. Salinity and specific TP loading substantially affected the bacterial community. Gammaproteobacteria, Actinobacteria and Betaproteobacteria contributed more to initial phenolic compound degradation than other classes, with Pseudomonas and Rhodococcus as the main contributing genera. The key phenolic-degrading genes of different metabolic pathways were explored, and their relative abundance was strengthened with increasing phenolic loading and salinity. The diverse cooperation and competition patterns of these microorganisms further promoted the high removal efficiency of multiple phenolic contaminants in the biofilms. These results demonstrate the feasibility of MABR for degrading multiple phenolic compounds in high saline wastewater.},
}

@article {pmid32192536,
year = {2020},
author = {Kavagutti, VS and Andrei, AŞ and Mehrshad, M and Salcher, MM and Ghai, R},
title = {Correction to: Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {40},
doi = {10.1186/s40168-020-00828-7},
pmid = {32192536},
issn = {2049-2618},
abstract = {Following publication of the original article [1], the authors reported that an affiliation of the first author was missing.},
}

@article {pmid32192451,
year = {2020},
author = {Hasan, MR and Sundaram, MS and Sundararaju, S and Tsui, KM and Karim, MY and Roscoe, D and Imam, O and Janahi, MA and Thomas, E and Dobson, S and Tan, R and Tang, P and Lopez, AP},
title = {Unusual accumulation of a wide array of antimicrobial resistance mechanisms in a patient with cytomegalovirus-associated hemophagocytic lymphohistiocytosis: a case report.},
journal = {BMC infectious diseases},
volume = {20},
number = {1},
pages = {237},
doi = {10.1186/s12879-020-04966-z},
pmid = {32192451},
issn = {1471-2334},
support = {SIRF_200026//Sidra Medicine/ ; SIRF_200040//Sidra Medicine/ ; },
abstract = {BACKGROUND: Infections with multidrug-resistant organisms (MDRO) pose a serious threat to patients with dysregulated immunity such as in hemophagocytic lymphohistiocytosis (HLH), but such infections have rarely been comprehensively characterized. Here, we present a fatal case of HLH secondary to cytomegalovirus (CMV) infection complicated by both anti-viral drug resistance and sepsis from multiple MDROs including pandrug-resistant superbug bacteria.

CASE PRESENTATION: A previously healthy, six-year-old boy presented with a 45-day history of fever prior to a diagnosis of hemophagocytic lymphohistiocytosis and hemorrhagic colitis, both associated with CMV. On hospital admission, the patient was found to be colonized with multiple, multidrug-resistant (MDR) bacteria including vancomycin-resistant enterococci (VRE) and carbapenamase-producing organisms (CPO). He eventually developed respiratory, urine and bloodstream infections with highly drug-resistant, including pandrug-resistant bacteria, which could not be controlled by antibiotic treatment. Antiviral therapy also failed to contain his CMV infection and the patient succumbed to overwhelming bacterial and viral infection. Whole genome sequencing (WGS) of the MDR bacteria and metagenomic analysis of his blood sample revealed an unusual accumulation of a wide range of antimicrobial resistance mechanisms in a single patient, including antiviral resistance to ganciclovir, and resistance mechanisms to all currently available antibiotics.

CONCLUSIONS: The case highlights both the risk of acquiring MDR superbugs and the severity of these infections in HLH patients.},
}

@article {pmid32191703,
year = {2020},
author = {Gautreau, G and Bazin, A and Gachet, M and Planel, R and Burlot, L and Dubois, M and Perrin, A and Médigue, C and Calteau, A and Cruveiller, S and Matias, C and Ambroise, C and Rocha, EPC and Vallenet, D},
title = {PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.},
journal = {PLoS computational biology},
volume = {16},
number = {3},
pages = {e1007732},
doi = {10.1371/journal.pcbi.1007732},
pmid = {32191703},
issn = {1553-7358},
abstract = {The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species. These methods usually lack multivariate statistical models to infer the partitions and the optimal number of classes and don't account for genome organization. We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. Our method, named PPanGGOLiN, partitions nodes using an Expectation-Maximization algorithm based on multivariate Bernoulli Mixture Model coupled with a Markov Random Field. This approach takes into account the topology of the graph and the presence/absence of genes in pangenomes to classify gene families into persistent, cloud, and one or several shell partitions. By analyzing the partitioned pangenome graphs of isolate genomes from 439 species and metagenome-assembled genomes from 78 species, we demonstrate that our method is effective in estimating the persistent genome. Interestingly, it shows that the shell genome is a key element to understand genome dynamics, presumably because it reflects how genes present at intermediate frequencies drive adaptation of species, and its proportion in genomes is independent of genome size. The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative genomics. The software is freely available at https://github.com/labgem/PPanGGOLiN.},
}

@article {pmid32190998,
year = {2020},
author = {Naboka, YL and Gudima, IA and Mordanov, SV and Krakhotkin, DV and Ilyash, AV and Kogan, MI and Ibishev, KS},
title = {[Virusuria as a component of the urine microbiota and its significance for assessing the health of the urinary tract: a descriptive clinical study].},
journal = {Urologiia (Moscow, Russia : 1999)},
volume = {},
number = {1},
pages = {12-18},
pmid = {32190998},
issn = {1728-2985},
abstract = {AIM: To determine the frequency of occurrence of oportunistic pathogenic bacterial flora and viral pathogens in the urine of healthy people with the establishment of the association between them.

MATERIALS AND METHODS: 40 healthy sexually active women and men were examined, which are divided by gender into equivalent groups: Group I - healthy women (n=19), Group II - healthy men (n=21). The age of the subjects ranged from 20 to 25 years, the average age was 22.4+/-1.2 years. In both groups, the average portion of morning urine was taken for a study after a proper hygienic procedure with self-urination of the subjects in a sterile plastic container (Sterile Uricol for urine sample collection "HiMedia"). In addition to the nutrient media regulated by the Clinical Guidelines, additional HiMedia chromogenic media were used to cultivate facultative anaerobic (FAB) and non-clostridial anaerobic bacteria (NAB). Detection of viruses was performed by PCR with detection in "real time". DNA isolation was carried out by the sorption method using the AmpliPrime DNA-Sorb-B ("NextBio") kit from urine samples, with preliminary concentration.

RESULTS: In all 40 cases, normative leukocyturia was detected in the urine. According to the results of bacteriological examination of urine, healthy men and women in all cases found aerobic-anaerobic associations. Coagulase-negative staphylococci (CNS) and Corynebacterium spp. Dominated in the cluster of aerobic taxa of microbiota. (75.0%, 55.0% respectively). The spectrum of CNS was represented by five species: S.epidermidis (30.0%), S.haemolyticus (27.5%), and S.warneri (25.0%), S.saprophyticus and S.lentus (15.0%). Enterococcus spp. were recorded in the urine in 32.5% of cases. Representatives of the Enterobacteriaceae family were represented by 4 taxa: E. coli (10.0%), Klebsiella spp., Proteus spp. (5.0% each), Enterobacter spp., Citrobacter spp. (2.5%). In a cluster of anaerobic bacteria in the urine, Eubacterium spp. (60.0%) and almost half of healthy individuals recorded Lactobacillus spp. and Peptococcus spp. (42.5% each). When analyzing the frequencies of detection of various microbiota taxa, it was found that women significantly more frequently recorded urine Corynebacterium spp., Eubacterium spp. and Lactobacillus spp., as well as Enterococcus spp. and Peptococcus spp. Peptostreptococcus spp. and Veillonella spp. were significantly more often determined (p<0.05) in the urine of men. HHV6 (10.0%), HPV18 and B19 parvovirus (2,5%) were determined in the urine of healthy people. It should be noted that the studied viruses were more often recorded in men, in particular, HPV18 and parvovirus B19 - only in men, and HHV6 more often in men (7.5%), less often in women (2.5%). Significant associations of some genera of microorganisms with the sex of the participants were revealed for E. faecalis and Lactobacillus spp., which were more often found in the urine of healthy women Reliably significant associations were found for three taxa: viruses HPV6, HPV18 and parvoviruses B19 (16.7%) were determined in the presence of Bacteroides spp., Bifidobacterium spp., and Prevotella spp., in urine. Accordingly, in 83.3% of cases, these viruses were detected in the absence of the above-listed taxa of microorganisms in the urine.

CONCLUSIONS: The normal urinary microbiota of healthy women and men has differences: Lactobacillus spp and Candida spp are absent in the urine of men while Streptococcus spp in urine of women. HHV6, HPV18, parvoviruses B19 are found in urine of healthy people and more often in men. Data about the virobiota and microbiota of urine in healthy people can highlight on the pathogenesis of urinary tract infections of various localization and develop targeted approaches in personalized therapy of this group of diseases.},
}

@article {pmid32190917,
year = {2020},
author = {Gotoh, Y and Chiba, K and Sekiyama, Y and Okada, K and Hayashi, T and Misawa, N},
title = {16S rRNA-based amplicon analysis of changes in the bacterial population in the lesions of papillomatous digital dermatitis in dairy cattle after topical treatment with allyl isothiocyanate.},
journal = {Microbiology and immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1348-0421.12786},
pmid = {32190917},
issn = {1348-0421},
abstract = {Papillomatous digital dermatitis (PDD) is a foot disease causing lameness in dairy cattle. It is regarded as a polymicrobial infection, although its etiology is not fully understood. PDD is treated by the topical or systemic administration of antibiotics such as lincomycin (LCM); however, the milk of the cows cannot be marketed during the treatment and withdrawal period due to the residual antibiotics in milk. Allyl isothiocyanate (AITC), an extract of Wasabia japonica (known as wasabi or Japanese horseradish) widely employed as a food additive, can be used as an alternative antimicrobial agent that overcomes this problem. We previously showed that AITC is as effective as LCM in PDD treatment. Here, using the samples obtained in the previous clinical study, we analyzed changes in the bacterial population in the PDD-associated microbiota after AITC treatment and compared it with that of LCM treatment by means of 16S rRNA-based amplicon analysis. Treatment induced major changes in the bacterial population, and Treponema species, which have been regarded as the major causative agents of PDD, were efficiently eliminated by both agents. However, the AITC-treated samples exhibited higher diversity compared with pretreatment samples, but this trend was not observed for LCM treatment, probably reflecting different antibacterial activities of the two agents. Importantly, this analysis detected population changes before morphological changes in PDD lesions (clinical signs of healing) became evident, indicating that 16S rRNA-based amplicon analysis represents an efficient strategy for analyzing and monitoring the treatment efficiency of PDD as well as other polymicrobial diseases. This article is protected by copyright. All rights reserved.},
}

@article {pmid32190661,
year = {2020},
author = {Sha, Y and Hu, J and Shi, B and Dingkao, R and Wang, J and Li, S and Zhang, W and Luo, Y and Liu, X},
title = {Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages.},
journal = {BioMed research international},
volume = {2020},
number = {},
pages = {3482692},
doi = {10.1155/2020/3482692},
pmid = {32190661},
issn = {2314-6141},
abstract = {A cattle-yak, which is a hybrid between a yak (Bos grunniens) and cattle (Bos taurus), is an important livestock animal, but basic questions regarding its physiology and environmental adaptation remain unanswered. To address this issue, the present study examined the species composition and functional characteristics of rumen microorganisms in the cattle-yak of different ages (2 and 3 years old) by metagenomic analysis. We found that rumen microbial community composition was similar at the two ages. Firmicutes, Fibrobacteres, Euryarchaeota, Bacteroidetes, and Proteobacteria were the predominant phyla, with Firmicutes accounting for the highest percentage of bacteria in 2-year-old (48%) and 3-year-old (46%) animals. Bacterial species involved in lignocellulose degradation were detected in the rumen of adult cattle-yaks including Ruminococcus flavefaciens, Ruminococcus albus, Fibrobacter succinogenes, and Prevotella ruminicola, with F. succinogenes being the most abundant. A total of 145,489 genes were annotated according to the Carbohydrate-active Enzyme database, which identified glycoside hydrolases as the most highly represented enzyme family. Further functional annotation revealed specific microflora and genes in the adult rumen that are potentially related to plateau adaptability. These results could explain the heterosis of the cattle-yak and provide insight into mechanisms of physiologic adaptation in plateau animals.},
}

@article {pmid32190648,
year = {2020},
author = {Li, K and Peng, W and Zhou, Y and Ren, Y and Zhao, J and Fu, X and Nie, Y},
title = {Host Genetic and Environmental Factors Shape the Composition and Function of Gut Microbiota in Populations Living at High Altitude.},
journal = {BioMed research international},
volume = {2020},
number = {},
pages = {1482109},
doi = {10.1155/2020/1482109},
pmid = {32190648},
issn = {2314-6141},
abstract = {The human gut microbiota is affected by genetic and environmental factors. It remains unclear how host genetic and environmental factors affect the composition and function of gut microbiota in populations living at high altitudes. We used a metagenome-wide analysis to investigate the gut microbiota composition in 15 native Tibetans and 12 Hans living on the Tibetan Plateau. The composition of gut microbiota differed significantly between these two groups (P < 0.05). The Planctomycetes was the most abundant phyla both in native Tibetans and in Hans. Furthermore, the most relatively abundant phyla for native Tibetans were Bacteroidetes (15.66%), Firmicutes (11.10%), Proteobacteria (1.32%), Actinobacteria (1.10%), and Tenericutes (0.35%), while the most relatively abundant phyla for Hans were Bacteroidetes (16.28%), Firmicutes (8.41%), Proteobacteria (2.93%), Actinobacteria (0.49%), and Cyanobacteria (0.21%). The abundance of the majority of genera was significantly higher in Tibetans than in Hans (P < 0.01). The number of microbial genes was 4.9 times higher in Tibetans than in Hans. The metabolic pathways and clusters of orthologous groups differed significantly between the two populations (P < 0.05). The abundance of carbohydrate-active enzyme modules and antibiotic resistance genes was significantly lower in Tibetans compared to Hans (P < 0.05). Our results suggest that different genetic factors (race) and environmental factors (diets and consumption of antibiotics) may play important roles in shaping the composition and function of gut microbiota in populations living at high altitudes.},
}