@article {pmid30659861,
year = {2019},
author = {Hamza, IA and Bibby, K},
title = {Critical Issues in Application of Molecular Methods to Environmental Virology.},
journal = {Journal of virological methods},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jviromet.2019.01.008},
pmid = {30659861},
issn = {1879-0984},
abstract = {Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.},
}

@article {pmid30659857,
year = {2019},
author = {Hu, HL and Guo, LY and Wu, HL and Feng, WY and Chen, TM and Liu, G},
title = {Evaluation of next-generation sequencing for the pathogenic diagnosis of children brain abscesses.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jinf.2019.01.003},
pmid = {30659857},
issn = {1532-2742},
abstract = {In this study, we applied metagenomic next-generation sequencing (mNGS) to detect the causative pathogens in brain abscess samples from 4 pediatric patients. NGS could offer unbiased sequencing and rapid diagnosis of causative pathogens, moreover, it could detect multiple pathogenic microorganisms from abscess samples. In our study, Fusobacterium nucleatum, and Streptococcus intermedius or combinations of them were found in 3/4 of polymicrobial brain abscesses. Internal organ abscesses are illustrative of the shortcomings of bacterial culture. NGS has the ability to identify both common and rare pathogens without any prior suspicious needed, and is able to offer a new platform for quantification of all detected microorganisms. Our study displayed the possible potential that NGS is about to provide the diagnostic tools that can characterize even the most complex microbial communities during brain abscesses and is less affected by prior antibiotic exposure.},
}

@article {pmid30659724,
year = {2019},
author = {Turgay, E and Steinum, TM and Colquhoun, D and Karataş, S},
title = {Environmental biofilm communities associated with early-stage common dentex (Dentex dentex) culture.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jam.14205},
pmid = {30659724},
issn = {1365-2672},
abstract = {AIMS: To describe the biofilm microbiota associated with various feeding phases during larval common dentex (Dentex dentex) culture.

METHODS AND RESULTS: A targeted metagenomic (metagenetic) study was performed by means of 16S rRNA gene based PCR and NextGen pyrosequencing. The resulting dataset was scrutinized with microbial community analysis software (R packages) using R/Rstudio. While median observed and estimated alpha-diversities were 171 ± 38 and 207 ± 27 taxa, respectively, 72.1-85.8% of individual biofilm communities comprised only 27 to 46 taxa. Members of the genus Methylobacterium and family Rhodobacteraceae dominated biofilms formed during all feeding phases while genera Nannochloropsis and Tetraselmis microalgae were major constituents of biofilms during rotifer live feeding. Both potential fish pathogenic genera e.g. Vibrio and putatively probiotic taxa e.g. Phaeobacter gallaeciensis were identified.

CONCLUSIONS: Relatively stable biofilm communities were identified during each feeding phase but varied significantly between feeding phases, most likely in response to the introduction of live feed/microalgae associated bacteria into rearing tanks.

The structure of the bacterial communities identified represent a 'template' for successful larval dentex culture and provides a foundation for future investigations into failed production cycles. This article is protected by copyright. All rights reserved.},
}

@article {pmid30658995,
year = {2019},
author = {Hildebrand, F and Moitinho-Silva, L and Blasche, S and Jahn, MTT and Gossmann, TI and Heuerta Cepas, J and Hercog, R and Luetge, M and Bahram, M and Pryszlak, A and Alves, RJ and Waszak, SM and Zhu, A and Ye, L and Costea, PI and Aalvink, S and Belzer, C and Forslund, SK and Sunagawa, S and Hentschel, U and Merten, C and Patil, KR and Benes, V and Bork, P},
title = {Antibiotics-induced monodominance of a novel gut bacterial order.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2018-317715},
pmid = {30658995},
issn = {1468-3288},
abstract = {OBJECTIVE: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species.

DESIGN: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria.

RESULTS: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, UBorkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals.

CONCLUSION: The bloom of UB. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.},
}

@article {pmid30658982,
year = {2019},
author = {Jiao, S and Chen, W and Wei, G},
title = {Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02523-18},
pmid = {30658982},
issn = {1098-5336},
abstract = {Lacking knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of different plant growth were explored via sequencing of the 16S rRNA amplicon and shotgun metagenomics. Soil microbial alpha-diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles compared with functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals strong resilience of soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion.Importance Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon-degradation and metal-tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.},
}

@article {pmid30658981,
year = {2019},
author = {Williams, TJ and Allen, MA and Liao, Y and Raftery, MJ and Cavicchioli, R},
title = {Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics and Metagenomics.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02935-18},
pmid = {30658981},
issn = {1098-5336},
abstract = {The canonical pathway for sucrose metabolism in haloarchaea utilizes a modified Embden-Meyerhof-Parnas pathway (EMP), in which ketohexokinase and 1-phosphofructokinase phosphorylate fructose released from sucrose hydrolysis. However, our survey of haloarchaeal genomes determined that ketohexokinase and 1-phosphofructokinase genes were not present in all species known to utilize fructose and sucrose, thereby indicating that alternative mechanisms exist for fructose metabolism. A fructokinase gene was identified in the majority of fructose- and sucrose-utilizing species, whereas only a small number possessed a ketohexokinase gene. Analysis of a range of hypersaline metagenomes revealed that haloarchaeal fructokinase genes were far more abundant (37 times) than haloarchaeal ketohexokinase genes. We used proteomics on Halohasta litchfieldiae (which encodes fructokinase) and identified changes in protein abundance that relate to growth on sucrose. Proteins inferred to be involved in sucrose metabolism included fructokinase, a carbohydrate primary transporter, a putative sucrose hydrolase, and two uncharacterized carbohydrate-related proteins encoded in the same gene cluster as fructokinase and the transporter. Homologs of these proteins were present in the genomes of all haloarchaea that use sugars for growth. Enzymes involved in the semi-phosphorylative Entner-Doudoroff pathway also had higher abundance in sucrose-grown Hht. litchfieldiae cells, consistent with this pathway functioning in the catabolism of the glucose moiety of sucrose. The study revises the current understanding of fundamental pathways for sugar utilization in haloarchaea, and proposes alternatives to the modified EMP pathway used by haloarchaea for sucrose and fructose utilization.IMPORTANCE Our ability to infer the function that microorganisms perform in the environment is predicated on assumptions about metabolic capacity. When using genomic or metagenomic data, metabolic capacity is inferred from genetic potential. Here we investigate the pathways by which haloarchaea utilize sucrose. The canonical haloarchaeal pathway for fructose metabolism involving ketohexokinase only occurs in a small proportion of haloarchaeal genomes and is underrepresented in metagenomes. Instead, fructokinase genes are present in the majority of genomes/metagenomes. In addition to genomic and metagenomic analyses, we used proteomics on Halohasta litchfieldiae (which encodes fructokinase but lacks ketohexokinase) and identified changes in protein abundance that related to growth on sucrose. In this way, we identified novel proteins implicated in sucrose metabolism in haloarchaea, comprising a transporter and various catabolic enzymes (including proteins that are annotated as hypothetical).},
}

@article {pmid30658973,
year = {2019},
author = {Malmuthuge, N and Liang, G and Griebel, PJ and Guan, LL},
title = {Taxonomic and functional composition of the small intestinal microbiome in neonatal calves provide a framework for understanding early life gut health.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02534-18},
pmid = {30658973},
issn = {1098-5336},
abstract = {A lack of information on the intestinal microbiome of neonatal calves prevents the use of microbial intervention strategies to improve calf gut health. This study profiled the taxonomic and functional composition of the small intestinal luminal microbiome of neonatal calves using whole genome sequencing of metagenome, aiming to understand the dynamics of microbial establishment during the early life. Despite highly individualized microbial communities, we identified two distinct taxonomic-based clusters from the collective luminal microbiomes comprising either a high level of Lactobacillus or Bacteroides Among the clustered microbiomes, Lactobacillus-dominant ileal microbiomes had significantly lower abundances of Bacteroides, Prevotella, Roseburia, Ruminococcus, and Veillonella compared to the Bacteroides-dominated ileal microbiomes. In addition, the upregulated ileal genes of the Lactobacillus-dominant calves were related to leukocyte and lymphocyte chemotaxis, the cytokine/chemokine-mediated signaling pathway, and inflammatory responses, while the upregulated ileal genes of the Bacteroides-dominant calves were related to cell adhesion, response to stimulus, cell communication and regulation of MAPK cascades. The functional profiles of the luminal microbiomes also revealed two distinct clusters consisting of functions related to either high protein metabolism or sulfur metabolism. A lower abundance of Bifidobacterium and a higher abundance of sulfur-reducing bacteria (SRB) were observed in the sulfur metabolism-dominant cluster (0.2±0.1%) compared to the protein metabolism-dominant cluster (12.6±5.7%), suggesting an antagonistic relationship between SRB and Bifidobacterium, which both compete for cysteine. These distinct taxonomic and functional clusters may provide a framework to further analyze interactions between the intestinal microbiome and the immune function and health of neonatal calves.Importance Dietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-term impacts on hosts. Currently, our understanding on early gut microbiome of neonatal calves is limited to 16S rRNA gene amplicon based microbial profiling, which is a barrier to develop dietary interventions to improve calf gut health. The use of metagenome sequencing based approach in the present study revealed high individual animal variation in taxonomic and functional abundance of intestinal microbiome and potential impacts of early microbiome on mucosal immune responses during the pre-weaning period. During this developmental period, age- and diet-related changes in microbial diversity, richness, density and the abundance taxa and functions were observed. A correlation based approach to further explore the individual animal variation revealed potential enterotypes that can be linked to calf gut health, which may pave the way to developing strategies to manipulate the microbiome and improve calf health.},
}

@article {pmid30658727,
year = {2019},
author = {Sarin, SK and Pande, A and Schnabl, B},
title = {Microbiome as a therapeutic target in alcohol-related liver disease.},
journal = {Journal of hepatology},
volume = {70},
number = {2},
pages = {260-272},
doi = {10.1016/j.jhep.2018.10.019},
pmid = {30658727},
issn = {1600-0641},
abstract = {Alcohol-related liver disease is associated with significant changes in gut microbial composition. The transmissibility of ethanol-induced liver disease has been demonstrated using faecal microbiota transfer in preclinical models. This technique has also led to improved survival in patients with severe alcoholic hepatitis, suggesting that changes in the composition and function of the gut microbiota are causatively linked to alcohol-related liver disease. A major mechanism by which gut microbiota influence the development of alcohol-related liver disease is through a leaky intestinal barrier. This permits translocation of viable bacteria and microbial products to the liver, where they induce and promote inflammation, as well as contribute to hepatocyte death and the fibrotic response. In addition, gut dysbiosis is associated with changes in the metabolic function of the intestinal microbiota, bile acid composition and circulation, immune dysregulation during onset and progression of alcohol-related liver disease. Findings from preclinical and human studies will be used to demonstrate how alcohol causes intestinal pathology and contributes to alcohol-related liver disease and how the latter is self-perpetuating. Additionally, we summarise the effects of untargeted treatment approaches on the gut microbiota, such as diet, probiotics, antibiotics and faecal microbial transplantation in alcohol-related liver disease. We further discuss how targeted approaches can restore intestinal homeostasis and improve alcohol-related liver disease. These approaches are likely to add to the therapeutic options for alcohol-related liver disease independently or in conjunction with steroids.},
}

@article {pmid30658400,
year = {2019},
author = {Liew, WP and Mohd-Redzwan, S and Than, LTL},
title = {Gut Microbiota Profiling of Aflatoxin B1-Induced Rats Treated with Lactobacillus casei Shirota.},
journal = {Toxins},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/toxins11010049},
pmid = {30658400},
issn = {2072-6651},
support = {GP-IPS/2018/9613100//Universiti Putra Malaysia/ ; },
abstract = {Aflatoxin B1 (AFB1) is a ubiquitous carcinogenic food contaminant. Gut microbiota is of vital importance for the host's health, regrettably, limited studies have reported the effects of xenobiotic toxins towards gut microbiota. Thus, the present study aims to investigate the interactions between AFB1 and the gut microbiota. Besides, an AFB1-binding microorganism, Lactobacillus casei Shirota (Lcs) was tested on its ability to ameliorate the changes on gut microbiota induced by AFB1. The fecal contents of three groups of rats included an untreated control group, an AFB1 group, as well as an Lcs + AFB1 group, were analyzed. Using the MiSeq platform, the PCR products of 16S rDNA gene extracted from the feces were subjected to next-generation sequencing. The alpha diversity index (Shannon) showed that the richness of communities increased significantly in the Lcs + AFB1 group compared to the control and AFB1 groups. Meanwhile, beta diversity indices demonstrated that AFB1 group significantly deviated from the control and Lcs + AFB1 groups. AFB1-exposed rats were especially high in Alloprevotella spp. abundance. Such alteration in the bacterial composition might give an insight on the interactions of AFB1 towards gut microbiota and how Lcs plays its role in detoxification of AFB1.},
}

@article {pmid30658055,
year = {2019},
author = {Pellock, SJ and Walton, WG and Ervin, SM and Torres-Rivera, D and Creekmore, BC and Bergan, G and Dunn, ZD and Li, B and Tripathy, A and Redinbo, MR},
title = {Discovery and Characterization of FMN-Binding β-Glucuronidases in the Human Gut Microbiome.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmb.2019.01.013},
pmid = {30658055},
issn = {1089-8638},
abstract = {The human gut microbiota encodes β-glucuronidases (GUS) that play key roles in health and disease via the metabolism of glucuronate-containing carbohydrates and drugs. Hundreds of putative bacterial GUS enzymes have been identified by metagenomic analysis of the human gut microbiome, but less than 10% have characterized structures and functions. Here we describe a set of unique gut microbial GUS enzymes that bind flavin mononucleotide (FMN). First, we show using mass spectrometry, isothermal titration calorimetry, and x-ray crystallography that a purified GUS from the gut commensal microbe Faecalibacterium prausnitzii binds to FMN on a surface groove located 30 Å away from the active site. Second, utilizing structural and functional data from this FMN-binding GUS, we analyzed the 279 unique GUS sequences from the human microbiome project database and identified 14 putative FMN-binding GUSs. We characterized four of these hits and solved the structure of two, the GUSs from Ruminococcus gnavus and Roseburia hominis, which confirmed that these are FMN binders. Third, binding and kinetic analysis of the FMN-binding site mutants of these five GUSs show that they utilize a conserved site to bind FMN that is not essential for GUS activity, but can affect KM. Lastly, a comprehensive structural review of the PDB reveals that the FMN-binding site employed by these enzymes is unlike any structurally characterized FMN-binders to date. These findings reveal the first instance of an FMN-binding glycoside hydrolase and suggest a potential link between FMN and carbohydrate metabolism in the human gut microbiota.},
}

@article {pmid30657979,
year = {2019},
author = {Liu, J and Lian, Q and Chen, Y and Qi, J},
title = {Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz017},
pmid = {30657979},
issn = {1362-4962},
abstract = {Metagenomic studies, greatly promoted by the fast development of next-generation sequencing (NGS) technologies, uncover complex structures of microbial communities and their interactions with environment. As the majority of microbes lack information of genome sequences, it is essential to assemble prokaryotic genomes ab initio aiming to retrieve complete coding genes from various metabolic pathways. The complex nature of microbial composition and the burden of handling a vast amount of metagenomic data, bring great challenges to the development of effective and efficient bioinformatic tools. Here we present a protein assembler (MetaPA), based on de Bruijn graph searching on oligopeptide spaces and can be applied on both metagenomic and metatranscriptomic sequencing data. When public homologous protein sequences are involved to guide the assembling procedures, MetaPA assembles 85% of total proteins in complete sequences with high precision of 83% on real high-throughput sequencing datasets. Application of MetaPA on metatranscriptomic data successfully identifies the majority of actively transcribed genes validated in related studies. The results suggest that MetaPA has a good potential in both metagenomic and metatranscriptomic studies to characterize the composition and abundance of microbiota.},
}

@article {pmid30657007,
year = {2019},
author = {Machiavelli, A and Duarte, RTD and Pires, MMS and Zarate-Bladés, CR and Pinto, AR},
title = {The impact of in utero HIV exposure on gut microbiota, inflammation, and microbial translocation.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/19490976.2018.1560768},
pmid = {30657007},
issn = {1949-0984},
abstract = {HIV-exposed but uninfected (HEU) children represent a growing population and show a significantly higher number of infectious diseases, several immune alterations, compromised growth, and increased mortality rates when compared to HIV-unexposed children. Considering the impact that the gut microbiota has on general host homeostasis and immune system development and modulation, we hypothesized that HEU children present altered gut microbiota that is linked to the increased morbidity and the immune system disorders faced by them. Our experiments revealed no differences in beta and alpha diversity of the gut microbiota between HEU and unexposed children or between HIV-infected and uninfected mothers. However, there were differences in the abundance of several taxa from the gut microbiota between HEU and unexposed children and between HIV-infected and uninfected mothers. Functional prediction based on 16S rRNA sequences also indicated differences between HEU and unexposed children and between infected and uninfected mothers. In addition, we detected no differences between HEU and unexposed children in relation to weight, weight-for-age z scores, albumin serum levels, or microbial translocation and inflammation markers. In summary, HIV-infected mothers and their HIV-exposed children present alterations in the abundance of several taxa in the gut microbiome and the predicted functional metagenome when compared to uninfected mothers and unexposed children. Knowledge about the gut microbiome of HEU children in different settings is essential in order to determine better treatments for this susceptible population.},
}

@article {pmid30656204,
year = {2019},
author = {Sadaiappan, B and Prasannakumar, C and Subramanian, K and Subramanian, M},
title = {Metagenomic data of vertical distribution and abundance of bacterial diversity in the hypersaline sediments of Mad Boon-mangrove ecosystem, Bay of Bengal.},
journal = {Data in brief},
volume = {22},
number = {},
pages = {716-721},
doi = {10.1016/j.dib.2018.12.028},
pmid = {30656204},
issn = {2352-3409},
abstract = {Bacterial diversity studies in hypersaline soil often yield novel organisms and contribute to our understanding of this extreme environment. Soil from Mad Boon is previously uncharacterized, with dense mangrove forest in one side and hypersaline soil in another side of backwater located in Southeast coast of Tamil Nadu, India. We surveyed to characterize the structure and diversity of the bacterial community. Samples were collected in a partially vegetated upland, exposed backwater sedimentation and water-logged location. In this study, we investigate the bacterial community structure using pyrosequence analysis of the V5- V9 gene region. After quality checks a total of 3919, 7298 and 7399 reads were obtained. About 42 phyla were observed, among them Proteobacteria were dominant phylum followed by Acidobacteria, Firmicutes and Chloroflexi. Classes including Deltaproteobacteria and Gammaproteobacteriawere observed. All sequences generated in this study were submitted to NCBI SRA under the accession numbers SRR627695, SRR63011 and SRR631012.},
}

@article {pmid30656069,
year = {2019},
author = {Barajas, HR and Romero, MF and Martínez-Sánchez, S and Alcaraz, LD},
title = {Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e6233},
doi = {10.7717/peerj.6233},
pmid = {30656069},
issn = {2167-8359},
abstract = {Background: The Streptococcus genus is relevant to both public health and food safety because of its ability to cause pathogenic infections. It is well-represented (>100 genomes) in publicly available databases. Streptococci are ubiquitous, with multiple sources of isolation, from human pathogens to dairy products. The Streptococcus genus has traditionally been classified by morphology, serum types, the 16S ribosomal RNA (rRNA) gene, and multi-locus sequence types subject to in-depth comparative genomic analysis.

Methods: Core and pan-genomes described the genomic diversity of 108 strains belonging to 16 Streptococcus species. The core genome nucleotide diversity was calculated and compared to phylogenomic distances within the genus Streptococcus. The core genome was also used as a resource to recruit metagenomic fragment reads from streptococci dominated environments. A conventional 16S rRNA gene phylogeny reconstruction was used as a reference to compare the resulting dendrograms of average nucleotide identity (ANI) and genome similarity score (GSS) dendrograms.

Results: The core genome, in this work, consists of 404 proteins that are shared by all 108 Streptococcus. The average identity of the pairwise compared core proteins decreases proportionally to GSS lower scores, across species. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). The GSS is a distance metric that can reflect evolutionary history comparing orthologous proteins. Additionally, GSS resulted in the most useful metric for genus and species comparisons, where ANI metrics failed due to false positives when comparing different species.

Discussion: Understanding of genomic variability and species relatedness is the goal of tools like GSS, which makes use of the maximum pairwise shared orthologous sequences for its calculation. It allows for long evolutionary distances (above species) to be included because of the use of amino acid alignment scores, rather than nucleotides, and normalizing by positive matches. Newly sequenced species and strains could be easily placed into GSS dendrograms to infer overall genomic relatedness. The GSS is not restricted to ubiquitous conservancy of gene features; thus, it reflects the mosaic-structure and dynamism of gene acquisition and loss in bacterial genomes.},
}

@article {pmid30655087,
year = {2019},
author = {Markowski, MC and Boorjian, SA and Burton, JP and Hahn, NM and Ingersoll, MA and Vareki, SM and Pal, SK and Sfanos, KS},
title = {The Microbiome and Genitourinary Cancer: A Collaborative Review.},
journal = {European urology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.eururo.2018.12.043},
pmid = {30655087},
issn = {1873-7560},
abstract = {CONTEXT: The recent discovery of the existence of a human genitourinary microbiome has led to the investigation of its role in mediating the pathogenesis of genitourinary malignancies, including bladder, kidney, and prostate cancers. Furthermore, although it is largely recognized that members of the gastrointestinal microbiota are actively involved in drug metabolism, new studies demonstrate additional roles and the potential necessity of the gastrointestinal microbiota in dictating cancer treatment response.

OBJECTIVE: To summarize the current evidence of a mechanistic role for the genitourinary and gastrointestinal microbiome in genitourinary cancer initiation and treatment response.

EVIDENCE ACQUISITION: We conducted a literature search up to October 2018. Search terms included microbiome, microbiota, urinary microbiome, bladder cancer, urothelial carcinoma, renal cell carcinoma, kidney cancer, testicular cancer, and prostate cancer.

EVIDENCE SYNTHESIS: There is preliminary evidence to implicate the members of the genitourinary microbiota as causative factors or cofactors in genitourinary malignancy. Likewise, the current evidence for gastrointestinal microbes in dictating cancer treatment response is mainly correlative; however, we provide examples where therapeutic agents used for the treatment of genitourinary cancers are affected by the human-associated microbiota, or vice versa. Clinical trials, such as fecal microbiota transplant to increase the efficacy of immunotherapy, are currently underway.

CONCLUSIONS: The role of the microbiome in genitourinary cancer is an emerging field that merits further studies. Translating microbiome research into clinical action will require incorporation of microbiome surveillance into ongoing and future clinical trials as well as expansion of studies to include metagenomic sequencing and metabolomics.

PATIENT SUMMARY: This review covers recent evidence that microbial populations that reside in the genitourinary tract-and were previously not known to exist-may influence the development of genitourinary malignancies including bladder, kidney, and prostate cancers. Furthermore, microbial populations that exist at sites outside of the genitourinary tract, such as those that reside in our gut, may influence cancer development and/or treatment response.},
}

@article {pmid29445130,
year = {2018},
author = {Liu, Y and Zhou, Z and Pan, J and Baker, BJ and Gu, JD and Li, M},
title = {Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota.},
journal = {The ISME journal},
volume = {12},
number = {4},
pages = {1021-1031},
pmid = {29445130},
issn = {1751-7370},
mesh = {Archaea/classification/*genetics/isolation & purification/metabolism ; Carbon/metabolism ; Carbon Cycle ; Eukaryota/genetics ; *Genome, Archaeal ; Genomics ; Geologic Sediments/microbiology ; Metagenome ; Photosynthesis ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {Thorarchaeota are a new archaeal phylum within the Asgard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudflat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, fix inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen fixation, nitrite reduction, and arsenic detoxification. Interestingly, these Thorarchaeotal genomes are inferred to contain the tetrahydromethanopterin and tetrahydrofolate Wood-Ljungdahl (WL) pathways for CO2 reduction, and the latter WL pathway appears to have originated from bacteria. These archaea are predicted to be able to use various inorganic and organic carbon sources, possessing genes inferred to encode ribulose bisphosphate carboxylase-like proteins (normally without RuBisCO activity) and a near-complete Calvin-Benson-Bassham cycle. The existence of eukaryotic selenocysteine insertion sequences and many genes for proteins previously considered eukaryote-specific in Thorarchaeota genomes provide new insights into their evolutionary roles in the origin of eukaryotic cellular complexity. Resolving the metabolic capacities of these enigmatic archaea and their origins will enhance our understanding of the origins of eukaryotes and their roles in ecosystems.},
}

Archaea/classification/*genetics/isolation & purification/metabolism
Carbon/metabolism
Carbon Cycle
Eukaryota/genetics
*Genome, Archaeal
Genomics
Geologic Sediments/microbiology
Metagenome
Photosynthesis
Phylogeny
Ribulose-Bisphosphate Carboxylase/genetics

@article {pmid30654102,
year = {2019},
author = {Akyol, Ç and Ince, O and Bozan, M and Ozbayram, EG and Ince, B},
title = {Fungal bioaugmentation of anaerobic digesters fed with lignocellulosic biomass: What to expect from anaerobic fungus Orpinomyces sp.},
journal = {Bioresource technology},
volume = {277},
number = {},
pages = {1-10},
doi = {10.1016/j.biortech.2019.01.024},
pmid = {30654102},
issn = {1873-2976},
abstract = {Energy-efficient biogas reactors are often designed and operated mimicking natural microbial ecosystems such as the digestive tracts of ruminants. Anaerobic fungi play a crucial role in the degradation of lignocellulose-rich fiber thanks to their high cellulolytic activity. Fungal bioaugmentation is therefore at the heart of our understanding of enhancing anaerobic digestion (AD). The efficiency of bioaugmentation with anaerobic fungus Orpinomyces sp. was evaluated in lignocellulose-based AD configurations. Fungal bioaugmentation increased the methane yield by 15-33% during anaerobic co-digestion of cow manure and selected cereal crops/straws. Harvesting stage of the crops was a decisive parameter to influence methane production together with fungal bioaugmentation. A more efficient fermentation process in the bioaugmented digesters was distinguished by relatively-higher abundance of Synergistetes, which was mainly represented by the genus Anaerobaculum. On the contrary, the composition of the methanogenic archaea did not change, and the majority of methanogens was assigned to Methanosarcina.},
}

@article {pmid30652494,
year = {2019},
author = {Kalantar, KL and Moazed, F and Christenson, SC and Wilson, J and Deiss, T and Belzer, A and Vessel, K and Caldera, S and Jauregui, A and Bolourchi, S and DeRisi, JL and Calfee, CS and Langelier, C},
title = {A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota.},
journal = {American journal of physiology. Lung cellular and molecular physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajplung.00476.2018},
pmid = {30652494},
issn = {1522-1504},
abstract = {Accurate and informative microbiologic testing is essential for guiding diagnosis and management of pneumonia in critically ill patients. Sampling of tracheal aspirate (TA) is less invasive compared to mini-bronchoalveolar lavage (mBAL) and is now recommended as a frontline diagnostic approach in mechanically ventilated patients, despite the historical belief that TA was suboptimal due to contamination from oral microbes. Advancements in metagenomic next generation sequencing (mNGS) now permit assessment of airway microbiota without a need for culture, and as such provide an opportunity to examine differences between mBAL and TA at a resolution previously unachievable. Here, we engaged shotgun mNGS to quantitatively assess the airway microbiome in matched mBAL and TA specimens from a prospective cohort of critically ill adults. We observed moderate differences betweensampletypes across all subjects, however we found significant compositional similarity in subjects with bacterial pneumonia, whose microbial communities were characterized by a dominant pathogen. In addition, we found that both mBAL and TA were similar in terms of microbialrelative abundance, abundance of oropharyngeal taxa, and microbial diversity. Our findings suggest that TA sampling provides a similar assessment of airway microbiota as more invasive testing by mBAL, and that this similarity is most significant in the setting of bacterial pneumonia.},
}

@article {pmid30651609,
year = {2019},
author = {Boyd, JA and Jungbluth, SP and Leu, AO and Evans, PN and Woodcroft, BJ and Chadwick, GL and Orphan, VJ and Amend, JP and Rappé, MS and Tyson, GW},
title = {Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-018-0343-2},
pmid = {30651609},
issn = {1751-7370},
support = {DE-SC0010580//U.S. Department of Energy (DOE)/ ; DE-SC0016440//U.S. Department of Energy (DOE)/ ; DE-SC0016469//U.S. Department of Energy (DOE)/ ; DE-SC0016469//U.S. Department of Energy (DOE)/ ; DE-170100428//Department of Education and Training | Australian Research Council (ARC)/ ; DE-160100248//Department of Education and Training | Australian Research Council (ARC)/ ; MCB06-04014//National Science Foundation (NSF)/ ; },
abstract = {The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane, and potentially propane. The number of archaeal clades encoding the MCR continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; Ca. Polytropus marinifundus gen. nov. sp. nov.) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Ca. Bathyarchaeota and Ca. Syntrophoarchaeum MAGs. Ca. P. marinifundus is basal to members of the class Archaeoglobi, and encodes the genes for β-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. Ca. P. marinifundus also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. Phylogenetic analysis suggests that the Ca. P. marinifundus MCR operons were horizontally transferred, changing our understanding of the evolution and distribution of this complex in the Archaea.},
}

@article {pmid30651402,
year = {2019},
author = {Mu, A and Kwong, JC and Isles, NS and Gonçalves da Silva, A and Schultz, MB and Ballard, SA and Lane, CR and Carter, GP and Williamson, DA and Seemann, T and Stinear, TP and Howden, BP},
title = {Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing.},
journal = {mSphere},
volume = {4},
number = {1},
pages = {},
doi = {10.1128/mSphere.00529-18},
pmid = {30651402},
issn = {2379-5042},
abstract = {Culture-independent methods that target genome fragments have shown promise in identifying certain pathogens, but the holy grail of comprehensive pathogen genome detection from microbiologically complex samples for subsequent forensic analyses remains a challenge. In the context of an investigation of a nosocomial outbreak, we used shotgun metagenomic sequencing of a human fecal sample and a neural network algorithm based on tetranucleotide frequency profiling to reconstruct microbial genomes and tested the same approach using rectal swabs from a second patient. The approach rapidly and readily detected the genome of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in the patient fecal specimen and in the rectal swab sample, achieving a level of strain resolution that was sufficient for confident transmission inference during a highly clonal outbreak. The analysis also detected previously unrecognized colonization of the patient by vancomycin-resistant Enterococcus faecium, another multidrug-resistant bacterium.IMPORTANCE The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms.},
}

@article {pmid30649386,
year = {2019},
author = {Van Gompel, L and Luiken, REC and Sarrazin, S and Munk, P and Knudsen, BE and Hansen, RB and Bossers, A and Aarestrup, FM and Dewulf, J and Wagenaar, JA and Mevius, DJ and Schmitt, H and Heederik, DJJ and Dorado-García, A and Smit, LAM and , },
title = {The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1093/jac/dky518},
pmid = {30649386},
issn = {1460-2091},
abstract = {Objectives: Previous studies in food-producing animals have shown associations between antimicrobial use (AMU) and resistance (AMR) in specifically isolated bacterial species. Multi-country data are scarce and only describe between-country differences. Here we investigate associations between the pig faecal mobile resistome and characteristics at the farm-level across Europe.

Methods: A cross-sectional study was conducted among 176 conventional pig farms from nine European countries. Twenty-five faecal samples from fattening pigs were pooled per farm and acquired resistomes were determined using shotgun metagenomics and the Resfinder reference database, i.e. the full collection of horizontally acquired AMR genes (ARGs). Normalized fragments resistance genes per kilobase reference per million bacterial fragments (FPKM) were calculated. Specific farm-level data (AMU, biosecurity) were collected. Random-effects meta-analyses were performed by country, relating farm-level data to relative ARG abundances (FPKM).

Results: Total AMU during fattening was positively associated with total ARG (total FPKM). Positive associations were particularly observed between widely used macrolides and tetracyclines, and ARGs corresponding to the respective antimicrobial classes. Significant AMU-ARG associations were not found for β-lactams and only few colistin ARGs were found, despite high use of these antimicrobial classes in younger pigs. Increased internal biosecurity was directly related to higher abundances of ARGs mainly encoding macrolide resistance. These effects of biosecurity were independent of AMU in mutually adjusted models.

Conclusions: Using resistome data in association studies is unprecedented and adds accuracy and new insights to previously observed AMU-AMR associations. Major components of the pig resistome are positively and independently associated with on-farm AMU and biosecurity conditions.},
}

@article {pmid30649204,
year = {2019},
author = {Saha, S and Johnson, J and Pal, S and Weinstock, G and Rajasekaran, S},
title = {MSC: a metagenomic sequence classification algorithm.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/bty1071},
pmid = {30649204},
issn = {1367-4811},
abstract = {Motivation: Metagenomics is the study of genetic materials directly sampled from natural habitats. It has the potential to reveal previously hidden diversity of microscopic life largely due to the existence of highly parallel and low-cost next-generation sequencing (NGS) technology. Conventional approaches align metagenomic reads onto known reference genomes to identify microbes in the sample. Since such a collection of reference genomes is very large, the approach often needs high-end computing machines with large memory which is not often available to researchers. Alternative approaches follow an alignment-free methodology where the presence of a microbe is predicted using the information about the unique k-mers present in the microbe genomes. However, such approaches suffer from high false positives due to trading off the value of k with the computational resources. In this article we propose a highly efficient metagenomic sequence classification algorithm (MSC) that is a hybrid of both approaches. Instead of aligning reads to the full genomes, MSC aligns reads onto a set of carefully chosen, shorter and highly discriminating model sequences built from the unique k-mers of each of the target sequences.

Results: Microbiome researchers are generally interested in two objectives of a taxonomic classifier: 1) to detect prevalence, i.e., the taxa present in a sample, and 2) to estimate their relative abundances. MSC is primarily designed to detect prevalence and experimental results show that MSC is indeed a more effective and efficient algorithm compared to the other state-of-the-art algorithms in terms of accuracy, memory, and runtime. Moreover, MSC outputs an approximate estimate of the abundances.

Availability: The implementations are freely available for non-commercial purposes. They can be downloaded from https://drive.google.com/open?id=1XirkAamkQ3ltWvI1W1igYQFusp9DHtVl.},
}

@article {pmid30649168,
year = {2019},
author = {Griffith, JC and Morgan, XC},
title = {Invited Commentary: Improving accessibility of the Human Microbiome Project data through integration with R/Bioconductor.},
journal = {American journal of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/aje/kwz007},
pmid = {30649168},
issn = {1476-6256},
abstract = {Alterations in the composition of the microbiota have been implicated in many diseases. The Human Microbiome Project (HMP) provides a comprehensive reference dataset of the "normal" human microbiome of 242 healthy adults at five major body sites. The HMP used both 16S ribosomal RNA gene sequencing and whole-genome metagenomic sequencing to profile the subjects' microbial communities. However, accessing and analyzing the HMP dataset still presents technical and bioinformatic challenges, as researchers must import the microbiome data, integrate phylogenetic trees, and access and merge public and restricted metadata. In this issue, the HMP16SData R/Bioconductor package developed by Schiffer and colleagues (Am J Epidemiol. XXX; XX (XX): XX-XXX) greatly simplifies access to the HMP data by combining 16S taxonomic abundance data, public patient metadata, and phylogenetic trees as a single data object. The authors also provide an interface for users with approved dbGaP projects to easily retrieve and merge the controlled-access HMP metadata. This package has a broad range of appeal to researchers across disciplines and with various levels of expertise in using R and/or other statistical tools. This will translate to improved data accessibility for public health research, with data from healthy individuals serving as a reference for disease-associated studies.},
}

@article {pmid30649062,
year = {2019},
author = {Sessa, L and Reddel, S and Manno, E and Quagliariello, A and Cotugno, N and Del Chierico, F and Amodio, D and Capponi, C and Leone, F and Bernardi, S and Rossi, P and Putignani, L and Palma, P},
title = {Distinct gut microbiota profile in ART-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.},
journal = {AIDS (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/QAD.0000000000002131},
pmid = {30649062},
issn = {1473-5571},
abstract = {OBJECTIVE: Persistent inflammation and higher risk to develop cardiovascular diseases (CVDs) still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota (GM) profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART.

DESIGN: Cross-sectional study including sixty-one ART-treated PHIV (age range 3-30 years old) and seventy-one age-matched healthy controls (CTRL). Blood and stool sample were collected at the same time and analyzed for GM composition and plasma biomarkers.

METHODS: GM composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, SI and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4+ and CD8+T-cells.

RESULTS: We identified two distinct GM profiles (group A and B) among PHIV. No different clinical parameters (age, sex, ethnicity, clinical class), dietary and sexual habits were found between the groups. The group A showed a relative dominance of Akkermansia muciniphila (A.muciniphila), whereas GM of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of sE-selectin (p = 0.0296), ICAM-1 (p = 0.0028), VCAM-1 (p = 0.0230), IL-6 (p = 0.0247) and sCD14 (p = 0.0142) in group A compared to group B.

CONCLUSIONS: Distinctive GM profiles are differently associated with inflammation, MT and VEA. Future studies are needed in order to understand the role of A.muciniphila and risk to develop CVDs in PHIV.},
}

@article {pmid30648419,
year = {2019},
author = {BenIsrael, M and Wanner, P and Aravena, R and Parker, BL and Haack, EA and Tsao, DT and Dunfield, KE},
title = {Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/15226514.2018.1523873},
pmid = {30648419},
issn = {1549-7879},
abstract = {Biodegradation is an important mechanism of action of phytoremediation systems, but performance evaluation is challenging. We applied metagenomic molecular approaches and compound-specific stable carbon isotope analysis to assess biodegradation of toluene in the vadose zone at an urban pilot field system where hybrid poplars were planted to remediate legacy impacts to an underlying shallow fractured bedrock aquifer. Carbon isotope ratios were compared spatio-temporally between toluene dissolved in groundwater and in the vapor phase. Enrichment of 13C from toluene in the vapor phase compared to groundwater provided evidence for biodegradation in the vadose zone. Total bacterial abundance (16S rRNA) and abundance and expression of degradation genes were determined in rhizosphere soil (DNA and RNA) and roots (DNA) using quantitative PCR. Relative abundances of degraders in the rhizosphere were on average higher at greater depths, except for enrichment of PHE-encoding communities that more strongly followed patterns of toluene concentrations detected. Quantification of RMO and PHE gene transcripts supported observations of active aerobic toluene degradation. Finally, spatially-variable numbers of toluene degraders were detected in poplar roots. We present multiple lines of evidence for biodegradation in the vadose zone at this site, contributing to our understanding of mechanisms of action of the phytoremediation system.},
}

@article {pmid30648011,
year = {2019},
author = {Susi, H and Filloux, D and Frilander, MJ and Roumagnac, P and Laine, AL},
title = {Diverse and variable virus communities in wild plant populations revealed by metagenomic tools.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6140},
doi = {10.7717/peerj.6140},
pmid = {30648011},
issn = {2167-8359},
abstract = {Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.},
}

@article {pmid30647460,
year = {2019},
author = {Rubin-Blum, M and Antony, CP and Sayavedra, L and Martínez-Pérez, C and Birgel, D and Peckmann, J and Wu, YC and Cardenas, P and MacDonald, I and Marcon, Y and Sahling, H and Hentschel, U and Dubilier, N},
title = {Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-019-0346-7},
pmid = {30647460},
issn = {1751-7370},
support = {N/A//Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation)/ ; 679849//EC | Horizon 2020 (Horizon 2020 - Research and Innovation Framework Programme)/ ; 679849//EC | European Research Council (ERC)/ ; GBMF3811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
abstract = {Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 clade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host-symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.},
}

@article {pmid30541441,
year = {2018},
author = {Zhu, J and Guo, Y and Su, K and Liu, Z and Ren, Z and Li, K and Guo, X},
title = {Construction of a highly saturated Genetic Map for Vitis by Next-generation Restriction Site-associated DNA Sequencing.},
journal = {BMC plant biology},
volume = {18},
number = {1},
pages = {347},
doi = {10.1186/s12870-018-1575-z},
pmid = {30541441},
issn = {1471-2229},
support = {31372021, 31572085//National Natural Science Foundation of China/ ; },
mesh = {*Chromosome Mapping/methods ; Chromosomes, Plant/genetics ; Genes, Plant/*genetics ; Genetic Markers/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait, Heritable ; Restriction Mapping/*methods ; Vitis/*genetics ; },
abstract = {BACKGROUND: High-saturate molecular linkage maps are an important tool in studies on plant molecular biology and assisted breeding. Development of a large set of single nucleotide polymorphisms (SNPs) via next-generation sequencing (NGS)-based methods, restriction-site associated DNA sequencing (RAD-seq), and the generation of a highly saturated genetic map help improve fine mapping of quantitative trait loci (QTL).

RESULTS: We generated a highly saturated genetic map to identify significant traits in two elite grape cultivars and 176 F1 plants. In total, 1,426,967 high-quality restriction site-associated DNA tags were detected; 51,365, 23,683, and 70,061 markers were assessed in 19 linkage groups (LGs) for the maternal, paternal, and integrated maps, respectively. Our map was highly saturated in terms of marker density and average "Gap ≤ 5 cM" percentage.

CONCLUSIONS: In this study, RAD-seq of 176 F1 plants and their parents yielded 8,481,484 SNPs and 1,646,131 InDel markers, of which 65,229 and 4832, respectively, were used to construct a highly saturated genetic map for grapevine. This map is expected to facilitate genetic studies on grapevine, including an evaluation of grapevine and deciphering the genetic basis of economically and agronomically important traits. Our findings provide basic essential genetic data the grapevine genetic research community, which will lead to improvements in grapevine breeding.},
}

*Chromosome Mapping/methods
Chromosomes, Plant/genetics
Genes, Plant/*genetics
Genetic Markers/genetics
High-Throughput Nucleotide Sequencing/methods
Metagenomics
Polymorphism, Single Nucleotide/genetics
Quantitative Trait, Heritable
Restriction Mapping/*methods
Vitis/*genetics

@article {pmid29902438,
year = {2018},
author = {Milshteyn, A and Colosimo, DA and Brady, SF},
title = {Accessing Bioactive Natural Products from the Human Microbiome.},
journal = {Cell host & microbe},
volume = {23},
number = {6},
pages = {725-736},
doi = {10.1016/j.chom.2018.05.013},
pmid = {29902438},
issn = {1934-6069},
support = {R01 AT009562/AT/NCCIH NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/metabolism ; Bacteria/genetics/metabolism ; Biological Products/*metabolism/*pharmacology ; Humans ; Indoles/metabolism ; Metabolomics ; Metagenomics ; Microbial Interactions ; Microbiota/genetics/*physiology ; Multigene Family ; Peptides, Cyclic/metabolism ; Pyrrolidonecarboxylic Acid/metabolism ; Thiazolidines/metabolism ; },
abstract = {Natural products have long played a pivotal role in the development of therapeutics for a variety of diseases. Traditionally, soil and marine environments have provided a rich reservoir from which diverse chemical scaffolds could be discovered. Recently, the human microbiome has been recognized as a promising niche from which secondary metabolites with therapeutic potential have begun to be isolated. In this Review, we address how the expansive history of identifying bacterial natural products in other environments is informing the approaches being brought to bear on the study of the human microbiota. We also touch on how these tools can lead to insights about microbe-microbe and host-microbe interactions and help generate biological hypotheses that may lead to developments of new therapeutic modalities.},
}

Anti-Bacterial Agents/metabolism
Bacteria/genetics/metabolism
Biological Products/*metabolism/*pharmacology
Humans
Indoles/metabolism
Metabolomics
Metagenomics
Microbial Interactions
Microbiota/genetics/*physiology
Multigene Family
Peptides, Cyclic/metabolism
Pyrrolidonecarboxylic Acid/metabolism
Thiazolidines/metabolism

@article {pmid29405826,
year = {2018},
author = {Huang, YY and Martínez-Del Campo, A and Balskus, EP},
title = {Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity.},
journal = {Gut microbes},
volume = {9},
number = {5},
pages = {437-451},
pmid = {29405826},
issn = {1949-0984},
mesh = {Anaerobiosis ; Bacteria/classification/*enzymology/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Hydro-Lyases/genetics/*metabolism ; Hydroxyproline/chemistry/*metabolism ; Metabolic Networks and Pathways ; Metagenome ; Microbiota ; Phylogeny ; },
abstract = {The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ1-pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.},
}

Anaerobiosis
Bacteria/classification/*enzymology/genetics/metabolism
Bacterial Proteins/genetics/*metabolism
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology
Humans
Hydro-Lyases/genetics/*metabolism
Hydroxyproline/chemistry/*metabolism
Metabolic Networks and Pathways
Metagenome
Microbiota
Phylogeny

@article {pmid29216773,
year = {2017},
author = {Eulenstein, O and Ding, Q and Al-Mubaid, H},
title = {Foreword.},
journal = {Journal of bioinformatics and computational biology},
volume = {15},
number = {6},
pages = {1702004},
doi = {10.1142/S0219720017020048},
pmid = {29216773},
issn = {1757-6334},
mesh = {Algorithms ; Computational Biology/*methods ; Congresses as Topic ; *Metagenome ; *Phylogeny ; RNA/chemistry ; },
}

Algorithms
Computational Biology/*methods
Congresses as Topic
*Metagenome
*Phylogeny
RNA/chemistry

@article {pmid30645605,
year = {2019},
author = {Kim, SH and Kang, PA and Han, K and Lee, SW and Rhee, S},
title = {Crystal structure of chloramphenicol-metabolizing enzyme EstDL136 from a metagenome.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210298},
doi = {10.1371/journal.pone.0210298},
pmid = {30645605},
issn = {1932-6203},
abstract = {Metagenomes often convey novel biological activities and therefore have gained considerable attention for use in biotechnological applications. Recently, metagenome-derived EstDL136 was found to possess chloramphenicol (Cm)-metabolizing features. Sequence analysis showed EstDL136 to be a member of the hormone-sensitive lipase (HSL) family with an Asp-His-Ser catalytic triad and a notable substrate specificity. In this study, we determined the crystal structures of EstDL136 and in a complex with Cm. Consistent with the high sequence similarity, the structure of EstDL136 is homologous to that of the HSL family. The active site of EstDL136 is a relatively shallow pocket that could accommodate Cm as a substrate as opposed to the long acyl chain substrates typical of the HSL family. Mutational analyses further suggested that several residues in the vicinity of the active site play roles in the Cm-binding of EstDL136. These results provide structural and functional insights into a metagenome-derived EstDL136.},
}

@article {pmid30644013,
year = {2019},
author = {Wang, G and Ren, Y and Ng, TB and Streit, WR and Ye, X},
title = {High-throughput amplicon sequencing demonstrates extensive diversity of xylanase genes in the sediment of soda lake Dabusu.},
journal = {Biotechnology letters},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10529-019-02646-w},
pmid = {30644013},
issn = {1573-6776},
support = {31301406//National Natural Science Foundation of China/ ; 2014FJPT02//the Marine Biological Engineering Platform for Innovative Services/ ; 2017-3059//China Scholarship Council/ ; },
abstract = {OBJECTIVE: To explore the diversity of glycoside hydrolase family 10 xylanase genes in the sediment of soda lake Dabusu by using high-throughput amplicon sequencing based on the Illumina HiSeq2500 platform.

RESULTS: A total of 227,420 clean reads, representing approximately 49.5 M bp, were obtained. Operational taxonomic unit (OTU) classification, with a 95% sequence identity cut-off, resulted in 467 OTUs with 392 annotated as GH10 xylanase, exhibiting 35-99% protein sequence identity with their closest-related xylanases in GenBank. Above 75% of the total OTUs demonstrated less than 80% identity with known xylanases. In addition, xylanases derived from the sediment were found to be affiliated to 12 different phyla, with Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and Basidiomycota being the dominant phyla. Moreover, barcode sequence had a major effect on abundance with only a minor effect on diversity.

CONCLUSIONS: High-throughput amplicon sequencing offers insight into xylanase gene diversity at a substantially higher resolution and lesser cost than library cloning and Sanger sequencing, facilitating a more thorough understanding of xylanase distribution and ecology.},
}

@article {pmid30643883,
year = {2019},
author = {Franco Filho, LC and Barata, RR and Cardoso, JF and Massafra, JMV and Lemos, PDS and Casseb, LMN and Cruz, ACR and Nunes, MRT},
title = {Metagenomic Analysis of Samples from Three Bat Species Collected in the Amazon Rain Forest.},
journal = {Microbiology resource announcements},
volume = {8},
number = {2},
pages = {},
doi = {10.1128/MRA.01422-18},
pmid = {30643883},
issn = {2576-098X},
abstract = {We report here the sequencing of five microbiome samples collected from different bat species in the Amazon rain forest. All contigs matching virus sequences were assigned to members of the Retroviridae family, while the bacterial contigs matched several bacterial species mostly belonging to the Proteobacteria phylum.},
}

@article {pmid30643240,
year = {2019},
author = {Nakamoto, N and Sasaki, N and Aoki, R and Miyamoto, K and Suda, W and Teratani, T and Suzuki, T and Koda, Y and Chu, PS and Taniki, N and Yamaguchi, A and Kanamori, M and Kamada, N and Hattori, M and Ashida, H and Sakamoto, M and Atarashi, K and Narushima, S and Yoshimura, A and Honda, K and Sato, T and Kanai, T},
title = {Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-018-0333-1},
pmid = {30643240},
issn = {2058-5276},
abstract = {Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease and its frequent complication with ulcerative colitis highlights the pathogenic role of epithelial barrier dysfunction. Intestinal barrier dysfunction has been implicated in the pathogenesis of PSC, yet its underlying mechanism remains unknown. Here, we identify Klebsiella pneumonia in the microbiota of patients with PSC and demonstrate that K. pneumoniae disrupts the epithelial barrier to initiate bacterial translocation and liver inflammatory responses. Gnotobiotic mice inoculated with PSC-derived microbiota exhibited T helper 17 (TH17) cell responses in the liver and increased susceptibility to hepatobiliary injuries. Bacterial culture of mesenteric lymph nodes in these mice isolated K. pneumoniae, Proteus mirabilis and Enterococcus gallinarum, which were prevalently detected in patients with PSC. A bacterial-organoid co-culture system visualized the epithelial-damaging effect of PSC-derived K. pneumoniae that was associated with bacterial translocation and susceptibility to TH17-mediated hepatobiliary injuries. We also show that antibiotic treatment ameliorated the TH17 immune response induced by PSC-derived microbiota. These results highlight the role of pathobionts in intestinal barrier dysfunction and liver inflammation, providing insights into therapeutic strategies for PSC.},
}

@article {pmid30643213,
year = {2019},
author = {Ronda, C and Chen, SP and Cabral, V and Yaung, SJ and Wang, HH},
title = {Metagenomic engineering of the mammalian gut microbiome in situ.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41592-018-0301-y},
pmid = {30643213},
issn = {1548-7105},
abstract = {Engineering of microbial communities in open environments remains challenging. Here we describe a platform used to identify and modify genetically tractable mammalian microbiota by engineering community-wide horizontal gene transfer events in situ. With this approach, we demonstrate that diverse taxa in the mouse gut microbiome can be modified directly with a desired genetic payload. In situ microbiome engineering in living animals allows novel capabilities to be introduced into established communities in their native milieu.},
}

@article {pmid30643200,
year = {2019},
author = {González, JM and Hernández, L and Manzano, I and Pedrós-Alió, C},
title = {Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-019-0347-6},
pmid = {30643200},
issn = {1751-7370},
abstract = {Dimethylsulfoniopropionate (DMSP) is produced mainly by phytoplankton and bacteria. It is relatively abundant and ubiquitous in the marine environment, where bacterioplankton make use of it readily as both carbon and sulfur sources. In one transformation pathway, part of the molecule becomes dimethylsulfide (DMS), which escapes into the atmosphere and plays an important role in the sulfur exchange between oceans and atmosphere. Through its other dominant catabolic pathway, bacteria are able to use it as sulfur source. During the past few years, a number of genes involved in its transformation have been characterized. Identifying genes in taxonomic groups not amenable to conventional methods of cultivation is challenging. Indeed, functional annotation of genes in environmental studies is not straightforward, considering that particular taxa are not well represented in the available sequence databases. Furthermore, many genes belong to families of paralogs with similar sequences but perhaps different functions. In this study, we develop in silico approaches to infer protein function of an environmentally important gene (dmdA) that carries out the first step in the sulfur assimilation from DMSP. The method combines a set of tools to annotate a targeted gene in genome databases and metagenome assemblies. The method will be useful to identify genes that carry out key biochemical processes in the environment.},
}

@article {pmid30642389,
year = {2019},
author = {Li, F and Hitch, TCA and Chen, Y and Creevey, CJ and Guan, LL},
title = {Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {6},
doi = {10.1186/s40168-019-0618-5},
pmid = {30642389},
issn = {2049-2618},
support = {BB/E/W/10964A01 and BBS/OS/GC/000011B//BBSRC/ ; 2013R029R//Alberta Livestock and Meat Agency/ ; 2015P008R//Alberta Livestock and Meat Agency/ ; Discovery//Natural Sciences and Engineering Research Council of Canada/ ; Doctoral Scholarship//Alberta Innovates - Technology Futures/ ; Scholarship//GPLER/ ; },
abstract = {BACKGROUND: Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome.

RESULTS: Rumen metagenomes were more closely clustered together and thus more conserved among individuals than metatranscriptomes, suggesting that inter-individual functional variations at the RNA level were higher than those at the DNA level. However, while mRNA enrichment significantly increased the sequencing depth of mRNA and generated similar functional profiles to total RNA-based metatranscriptomics, it led to biased abundance estimation of several transcripts. We observed divergent rumen microbial composition (metatranscriptomic level) and functional potentials (metagenomic level) among three breeds, but differences in functional activity (metatranscriptomic level) were less apparent. Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes) were detected between cattle with high and low feed efficiency, and most of them were breed-specific.

CONCLUSIONS: Metatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts.},
}

@article {pmid30642268,
year = {2019},
author = {Aiemjoy, K and Altan, E and Aragie, S and Fry, DM and Phan, TG and Deng, X and Chanyalew, M and Tadesse, Z and Callahan, EK and Delwart, E and Keenan, JD},
title = {Viral species richness and composition in young children with loose or watery stool in Ethiopia.},
journal = {BMC infectious diseases},
volume = {19},
number = {1},
pages = {53},
doi = {10.1186/s12879-019-3674-3},
pmid = {30642268},
issn = {1471-2334},
support = {F31 HD088070-01A1//National Institute of Child Health and Human Development/ ; U10 EY016214//National Eye Institute/ ; R01 HL105770//National Heart, Lung, and Blood Institute/ ; },
abstract = {BACKGROUND: Stool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease.

METHODS: We examine the pediatric enteric virome across stool consistencies to evaluate differences in richness and community composition using fecal samples collected from children aged 0 to 5 years participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling.

RESULTS: Of 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The median age of children with stool samples was 36 months. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman's r = - 0.45, p = 0.013). The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95%CI 3.9, 7.7).

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

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

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

@article {pmid30294753,
year = {2018},
author = {Reis, AC and Čvančarová, M and Liu, Y and Lenz, M and Hettich, T and Kolvenbach, BA and Corvini, PF and Nunes, OC},
title = {Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP.},
journal = {Applied microbiology and biotechnology},
volume = {102},
number = {23},
pages = {10299-10314},
doi = {10.1007/s00253-018-9411-9},
pmid = {30294753},
issn = {1432-0614},
support = {160332//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CH)/ ; SFRH/BD/95814/2013//Fundação para a Ciência e a Tecnologia/ ; UID/EQU/00511/2013 - POCI-01-0145-FEDER-006939//Fundação para a Ciência e a Tecnologia/ ; NORTE-01-0145-FEDER-000005//Comissão de Coordenação e Desenvolvimento Regional do Norte/ ; },
mesh = {Achromobacter denitrificans/*metabolism ; Actinobacteria/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Biodegradation, Environmental ; Cloning, Molecular ; Gene Expression Regulation, Bacterial ; Gene Library ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/microbiology ; Sulfamethoxazole/*metabolism ; },
abstract = {In the last decade, biological degradation and mineralization of antibiotics have been increasingly reported feats of environmental bacteria. The most extensively described example is that of sulfonamides that can be degraded by several members of Actinobacteria and Proteobacteria. Previously, we reported sulfamethoxazole (SMX) degradation and partial mineralization by Achromobacter denitrificans strain PR1, isolated from activated sludge. However, further studies revealed an apparent instability of this metabolic trait in this strain. Here, we investigated this instability and describe the finding of a low-abundance and slow-growing actinobacterium, thriving only in co-culture with strain PR1. This organism, named GP, shared highest 16S rRNA gene sequence similarity (94.6-96.9%) with the type strains of validly described species of the genus Leucobacter. This microbial consortium was found to harbor a homolog to the sulfonamide monooxygenase gene (sadA) also found in other sulfonamide-degrading bacteria. This gene is overexpressed in the presence of the antibiotic, and evidence suggests that it codes for a group D flavin monooxygenase responsible for the ipso-hydroxylation of SMX. Additional side reactions were also detected comprising an NIH shift and a Baeyer-Villiger rearrangement, which indicate an inefficient biological transformation of these antibiotics in the environment. This work contributes to further our knowledge in the degradation of this ubiquitous micropollutant by environmental bacteria.},
}

Achromobacter denitrificans/*metabolism
Actinobacteria/*metabolism
Bacterial Proteins/genetics/metabolism
*Biodegradation, Environmental
Cloning, Molecular
Gene Expression Regulation, Bacterial
Gene Library
Metagenomics
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Sewage/microbiology
Sulfamethoxazole/*metabolism

@article {pmid30640944,
year = {2019},
author = {Hjelmsø, MH and Mollerup, S and Jensen, RH and Pietroni, C and Lukjancenko, O and Schultz, AC and Aarestrup, FM and Hansen, AJ},
title = {Metagenomic analysis of viruses in toilet waste from long distance flights-A new procedure for global infectious disease surveillance.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210368},
doi = {10.1371/journal.pone.0210368},
pmid = {30640944},
issn = {1932-6203},
abstract = {Human viral pathogens are a major public health threat. Reliable information that accurately describes and characterizes the global occurrence and transmission of human viruses is essential to support national and global priority setting, public health actions, and treatment decisions. However, large areas of the globe are currently without surveillance due to limited health care infrastructure and lack of international cooperation. We propose a novel surveillance strategy, using metagenomic analysis of toilet material from international air flights as a method for worldwide viral disease surveillance. The aim of this study was to design, implement, and evaluate a method for viral analysis of airplane toilet waste enabling simultaneous detection and quantification of a wide range of human viral pathogens. Toilet waste from 19 international airplanes was analyzed for viral content, using viral capture probes followed by high-throughput sequencing. Numerous human pathogens were detected including enteric and respiratory viruses. Several geographic trends were observed with samples originating from South Asia having significantly higher viral species richness as well as higher abundances of salivirus A, aichivirus A and enterovirus B, compared to samples originating from North Asia and North America. In addition, certain city specific trends were observed, including high numbers of rotaviruses in airplanes departing from Islamabad. Based on this study we believe that central sampling and analysis at international airports could be a useful supplement for global viral surveillance, valuable for outbreak detection and for guiding public health resources.},
}

@article {pmid30640905,
year = {2019},
author = {Ravi, A and Ereqat, S and Al-Jawabreh, A and Abdeen, Z and Abu Shamma, O and Hall, H and Pallen, MJ and Nasereddin, A},
title = {Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus.},
journal = {PLoS neglected tropical diseases},
volume = {13},
number = {1},
pages = {e0006805},
doi = {10.1371/journal.pntd.0006805},
pmid = {30640905},
issn = {1935-2735},
abstract = {BACKGROUND: Across the world, ticks act as vectors of human and animal pathogens. Ticks rely on bacterial endosymbionts, which often share close and complex evolutionary links with tick-borne pathogens. As the prevalence, diversity and virulence potential of tick-borne agents remain poorly understood, there is a pressing need for microbial surveillance of ticks as potential disease vectors.

We developed a two-stage protocol that includes 16S-amplicon screening of pooled samples of hard ticks collected from dogs, sheep and camels in Palestine, followed by shotgun metagenomics on individual ticks to detect and characterise tick-borne pathogens and endosymbionts. Two ticks isolated from sheep yielded an abundance of reads from the genus Rickettsia, which were assembled into draft genomes. One of the resulting genomes was highly similar to Rickettsia massiliae strain MTU5. Analysis of signature genes showed that the other represents the first genome sequence of the potential pathogen Candidatus Rickettsia barbariae. Ticks from a dog and a sheep yielded draft genome sequences of Coxiella strains. A sheep tick yielded sequences from the sheep pathogen Anaplasma ovis, while Hyalomma ticks from camels yielded sequences belonging to Francisella-like endosymbionts. From the metagenome of a dog tick from Jericho, we generated a genome sequence of a canine parvovirus.

SIGNIFICANCE: Here, we have shown how a cost-effective two-stage protocol can be used to detect and characterise tick-borne pathogens and endosymbionts. In recovering genome sequences from an unexpected pathogen (canine parvovirus) and a previously unsequenced pathogen (Candidatus Rickettsia barbariae), we demonstrate the open-ended nature of metagenomics. We also provide evidence that ticks can carry canine parvovirus, raising the possibility that ticks might contribute to the spread of this troublesome virus.},
}

@article {pmid30640566,
year = {2019},
author = {Dubourg, G and Raoult, D and Fenollar, F},
title = {Emerging methodologies for pathogen identification in bloodstream infections: an update.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2019.1568241},
pmid = {30640566},
issn = {1744-8352},
abstract = {INTRODUCTION: Bloodstream infections (BSIs) remain a major public health burden worldwide, particularly in high-income countries as they are associated with a significant mortality rate. As early administration of appropriate antimicrobial therapy is a major prognostic factor, there remain unmet needs for shortening BSI diagnosis. Current blood cultures (BC) processing to identify pathogens involved in BSI is not compatible with such delays, although it remains the gold standard. Areas covered: Herein, we review and discuss emerging or ongoing assessed methodologies dedicated to shorten the identification of microorganisms involved in BSI and published since 2015. A particular focus on the economical and clinical impact of these approaches is provided when hindsight is sufficient. Methods to shorten antibiotic susceptibility testing are also reviewed. Expert commentary: Post-culture approaches have encountered a huge success as they are reliable, fast and easy to implement in the laboratory. In particular, the MALDI-TOF MS was shown to be a cost-effective method when combined with antimicrobial stewardship policies. However, further research is needed to optimize methods performed on whole blood in particular next generation sequencing methods, as they represent an opportunity to substantially improve management of high-risk patients.},
}

@article {pmid30639767,
year = {2019},
author = {Davis, WJ and Amses, KR and Benny, GL and Carter-House, D and Chang, Y and Grigoriev, I and Smith, ME and Spatafora, JW and Stajich, JE and James, TY},
title = {Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ympev.2019.01.006},
pmid = {30639767},
issn = {1095-9513},
abstract = {Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.},
}

@article {pmid30637962,
year = {2019},
author = {Asante, J and Osei Sekyere, J},
title = {Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: Advances and applications.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12735},
pmid = {30637962},
issn = {1758-2229},
abstract = {Our inability to cultivate most micro-organisms, specifically bacteria, in the laboratory has for many years restricted our view and understanding of the bacterial meta-resistome in all living and non-living environments. As a result, reservoirs, sources, and distribution of antibiotic resistance genes (ARGS) and antibiotic-producers, as well as the effects of human activity and antibiotics on the selection and dissemination of ARGs were not well comprehended. With the advances made in the fields of metagenomics and metatranscriptomics, many of the hitherto little-understood concepts are becoming clearer. Further, the discovery of antibiotics such as lugdinin and lactocillin from the human microbiota, buttressed the importance of these new fields. Metagenomics and metatranscriptomics are becoming important clinical diagnostic tools for screening and detecting pathogens and ARGs, assessing the effects of antibiotics, other xenobiotics, and human activity on the environment, characterizing the microbiome and the environmental resistome with lesser turnaround time and decreasing cost, as well as discovering antibiotic-producers. However, challenges with accurate binning, skewed ARGs databases, detection of less abundant and allelic variants of ARGs, and efficient mobilome characterization remain. Ongoing efforts in long-read, phased- and single-cell sequencing, strain-resolved binning, chromosomal-conformation capture, DNA-methylation binning, and deep-learning bioinformatic approaches offer promising prospects in reconstructing complete strain-level genomes and mobilomes from metagenomes. This article is protected by copyright. All rights reserved.},
}

@article {pmid30637337,
year = {2018},
author = {Bayer, K and Jahn, MT and Slaby, BM and Moitinho-Silva, L and Hentschel, U},
title = {Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00150-18},
pmid = {30637337},
issn = {2379-5077},
abstract = {Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae, and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features of Chloroflexi sponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism, and respiration. Clade-specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, but only amino acid utilization by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding components involved in cofactor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by the fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM) method. Carbohydrate degradation potential was reported previously for "Candidatus Poribacteria" and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus, sponge microbes may not only provide nutrients to the sponge host, but they may also contribute to dissolved organic matter (DOM) recycling and primary productivity in reef ecosystems via a pathway termed the sponge loop. IMPORTANCEChloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought.},
}

@article {pmid30636420,
year = {2019},
author = {Gunasekera, SP and Meyer, JL and Ding, Y and Abboud, KA and Luo, D and Campbell, JE and Angerhofer, A and Goodsell, JL and Raymundo, LJ and Liu, J and Ye, T and Luesch, H and Teplitski, M and Paul, VJ},
title = {Chemical and Metagenomic Studies of the Lethal Black Band Disease of Corals Reveal Two Broadly Distributed, Redox-Sensitive Mixed Polyketide/Peptide Macrocycles.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.8b00804},
pmid = {30636420},
issn = {1520-6025},
abstract = {Black band disease (BBD), a lethal, polymicrobial disease consortium dominated by the cyanobacterium Roseofilum reptotaenium, kills many species of corals worldwide. To uncover chemical signals or cytotoxins that could be important in proliferation of Roseofilum and the BBD layer, we examined the secondary metabolites present in geographically diverse collections of BBD from Caribbean and Pacific coral reefs. Looekeyolide A (1), a 20-membered macrocyclic compound formed by a 16-carbon polyketide chain, 2-deamino-2-hydroxymethionine, and d-leucine, and its autoxidation product looekeyolide B (2) were extracted as major compounds (∼1 mg g-1 dry wt) from more than a dozen field-collected BBD samples. Looekeyolides A and B were also produced by a nonaxenic R. reptotaenium culture under laboratory conditions at similar concentrations. R. reptotaenium genomes that were constructed from four different metagenomic data sets contained a unique nonribosomal peptide/polyketide biosynthetic cluster that is likely responsible for the biosynthesis of the looekeyolides. Looekeyolide A, which readily oxidizes to looekeyolide B, may play a biological role in reducing H2O2 and other reactive oxygen species that could occur in the BBD layer as it overgrows and destroys coral tissue.},
}

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

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

@article {pmid30024981,
year = {2018},
author = {Douglass, AP and Offei, B and Braun-Galleani, S and Coughlan, AY and Martos, AAR and Ortiz-Merino, RA and Byrne, KP and Wolfe, KH},
title = {Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names.},
journal = {PLoS pathogens},
volume = {14},
number = {7},
pages = {e1007138},
pmid = {30024981},
issn = {1553-7374},
support = {105341/Z/14/Z//Wellcome Trust/United Kingdom ; },
mesh = {Candida/*classification/*genetics ; *Metagenomics ; Phylogeny ; Pichia/*classification/*genetics ; },
abstract = {We investigated genomic diversity of a yeast species that is both an opportunistic pathogen and an important industrial yeast. Under the name Candida krusei, it is responsible for about 2% of yeast infections caused by Candida species in humans. Bloodstream infections with C. krusei are problematic because most isolates are fluconazole-resistant. Under the names Pichia kudriavzevii, Issatchenkia orientalis and Candida glycerinogenes, the same yeast, including genetically modified strains, is used for industrial-scale production of glycerol and succinate. It is also used to make some fermented foods. Here, we sequenced the type strains of C. krusei (CBS573T) and P. kudriavzevii (CBS5147T), as well as 30 other clinical and environmental isolates. Our results show conclusively that they are the same species, with collinear genomes 99.6% identical in DNA sequence. Phylogenetic analysis of SNPs does not segregate clinical and environmental isolates into separate clades, suggesting that C. krusei infections are frequently acquired from the environment. Reduced resistance of strains to fluconazole correlates with the presence of one gene instead of two at the ABC11-ABC1 tandem locus. Most isolates are diploid, but one-quarter are triploid. Loss of heterozygosity is common, including at the mating-type locus. Our PacBio/Illumina assembly of the 10.8 Mb CBS573T genome is resolved into 5 complete chromosomes, and was annotated using RNAseq support. Each of the 5 centromeres is a 35 kb gene desert containing a large inverted repeat. This species is a member of the genus Pichia and family Pichiaceae (the methylotrophic yeasts clade), and so is only distantly related to other pathogenic Candida species.},
}

Candida/*classification/*genetics
*Metagenomics
Phylogeny
Pichia/*classification/*genetics

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

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

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

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

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

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

@article {pmid30635385,
year = {2019},
author = {Fredriksen, L and Stokke, R and Jensen, MS and Westereng, B and Jameson, JK and Steen, IH and Eijsink, VGH},
title = {Discovery of a thermostable GH10 xylanase with broad substrate specificity from the Arctic Mid-Ocean Ridge vent system.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02970-18},
pmid = {30635385},
issn = {1098-5336},
abstract = {A two-domain GH10 xylanase encoding gene (amor_gh10a) was discovered from a metagenomic dataset, generated after in situ incubation of a lignocellulosic substrate in hot sediments on the sea floor of the Arctic Mid-Ocean Ridge (AMOR). AMOR_GH10A comprises a signal peptide, a carbohydrate-binding module belonging to a previously uncharacterized family, and a catalytic glycosyl hydrolase (GH10) domain. The enzyme shares the highest sequence identity (42%) with a hypothetical protein from Verrucomicrobia bacterium, and its GH10 domain shares low identity (24-28%) with functionally characterized xylanases. Purified AMOR_GH10A showed thermophilic and halophilic properties and was active towards various xylans. Uniquely, the enzyme showed high activity towards amorphous cellulose, glucomannan, and xyloglucan and was more active towards cellopentaose than towards xylopentaose. Binding assays showed that the N-terminal domain of this broad-specificity GH10 binds strongly to amorphous cellulose, as well as to microcrystalline cellulose, birchwood glucuronoxylan, barley β-glucan and konjac glucomannan, confirming its classification as a novel CBM (CBM85).ImportanceHot springs at the sea bottom harbor unique biodiversity and are a promising source of enzymes with interesting properties. We describe the functional characterization of a thermophilic and halophilic multi-domain xylanase originating from the Arctic Mid-Ocean Ridge vent system, belonging to the well-studied family 10 of glycosyl hydrolases (GH10). This xylanase, AMOR_GH10A, has a surprisingly wide substrate range and is more active towards cellopentaose compared to xylopentaose. This substrate promiscuity is unique for the GH10 family and could prove useful in industrial applications. Emphasizing the versatility of AMOR_GH10A, its N-terminal domain binds to both xylans and glycans, while not showing significant sequence similarities to any known carbohydrate-binding module (CBM) in the CAZy database. Thus, this N-terminal domain lays the foundation for the new CBM85 family.},
}

@article {pmid30635078,
year = {2019},
author = {Zhao, L and Rosario, K and Breitbart, M and Duffy, S},
title = {Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range.},
journal = {Advances in virus research},
volume = {103},
number = {},
pages = {71-133},
doi = {10.1016/bs.aivir.2018.10.001},
pmid = {30635078},
issn = {1557-8399},
abstract = {While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.},
}

@article {pmid30635058,
year = {2019},
author = {Simon, JC and Marchesi, JR and Mougel, C and Selosse, MA},
title = {Host-microbiota interactions: from holobiont theory to analysis.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {5},
doi = {10.1186/s40168-019-0619-4},
pmid = {30635058},
issn = {2049-2618},
abstract = {In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series "Host-microbiota interactions: from holobiont theory to analysis," we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.},
}

@article {pmid30635018,
year = {2019},
author = {Akorli, J and Namaali, PA and Ametsi, GW and Egyirifa, RK and Pels, NAP},
title = {Generational conservation of composition and diversity of field-acquired midgut microbiota in Anopheles gambiae (sensu lato) during colonization in the laboratory.},
journal = {Parasites & vectors},
volume = {12},
number = {1},
pages = {27},
doi = {10.1186/s13071-019-3287-0},
pmid = {30635018},
issn = {1756-3305},
support = {DEL-15-007: Awandare//DELTAS Africa/ ; },
abstract = {BACKGROUND: The gut microbiota is known to play a role in a mosquito vector's life history, a subject of increasing research. Laboratory experiments are essential for such studies and require laboratory colonies. In this study, the conservation of field-obtained midgut microbiota was evaluated in laboratory-reared Anopheles gambiae (s.l.) mosquitoes continuously hatched in water from field breeding habitats.

METHODS: Pupae and late instars were obtained from the field and reared, and the emerged adults were blood-fed. The eggs obtained from them were hatched in either water from the field or in dechlorinated tap water. The mosquito colonies were maintained for 10 generations. Midguts of female adults from unfed F0 (emerging from field-caught pupae and larvae), F5 and F10 were dissected out and genomic DNA was extracted for 16S metagenomic sequencing. The sequences were compared to investigate the diversity and bacterial compositional differences using ANCOM and correlation clustering methods.

RESULTS: Less than 10% of the bacterial families identified had differential relative abundances between generational groups and accounted for 46% of the variation observed. Although diversity reduced in F10 mosquitoes during laboratory colonization (Shannon-Weaver; P-value < 0.05), 50% of bacterial genera were conserved in those bred continuously in field-water compared to 38% in those bred in dechlorinated tap water.

CONCLUSIONS: To our knowledge, this study is the first report on the assessment of gut bacterial community of mosquitoes during laboratory colonization and recommends the use of water from the natural breeding habitats if they are intended for microbiota research.},
}

@article {pmid30635006,
year = {2019},
author = {Brinkmann, A and Hekimoğlu, O and Dinçer, E and Hagedorn, P and Nitsche, A and Ergünay, K},
title = {A cross-sectional screening by next-generation sequencing reveals Rickettsia, Coxiella, Francisella, Borrelia, Babesia, Theileria and Hemolivia species in ticks from Anatolia.},
journal = {Parasites & vectors},
volume = {12},
number = {1},
pages = {26},
doi = {10.1186/s13071-018-3277-7},
pmid = {30635006},
issn = {1756-3305},
support = {not applicable//Alexander von Humboldt-Stiftung (DE)/ ; },
abstract = {BACKGROUND: Ticks participate as arthropod vectors in the transmission of pathogenic microorganisms to humans. Several tick-borne infections have reemerged, along with newly described agents of unexplored pathogenicity. In an attempt to expand current information on tick-associated bacteria and protozoans, we performed a cross-sectional screening of ticks, using next-generation sequencing. Ticks seeking hosts and infesting domestic animals were collected in four provinces across the Aegean, Mediterranean and Central Anatolia regions of Turkey and analyzed by commonly used procedures and platforms.

RESULTS: Two hundred and eighty ticks comprising 10 species were evaluated in 40 pools. Contigs from tick-associated microorganisms were detected in 22 (55%) questing and 4 feeding (10%) tick pools, with multiple microorganisms identified in 12 pools. Rickettsia 16S ribosomal RNA gene, gltA, sca1 and ompA sequences were present in 7 pools (17.5%), comprising feeding Haemaphysalis parva and questing/hunting Rhipicephalus bursa, Rhipicephalus sanguineus (sensu lato) and Hyalomma marginatum specimens. A near-complete genome and conjugative plasmid of a Rickettsia hoogstraalii strain could be characterized in questing Ha. parva. Coxiella-like endosymbionts were identified in pools of questing (12/40) as well as feeding (4/40) ticks of the genera Rhipicephalus, Haemaphysalis and Hyalomma. Francisella-like endosymbionts were also detected in 22.5% (9/40) of the pools that comprise hunting Hyalomma ticks in 8 pools. Coxiella-like and Francisella-like endosymbionts formed phylogenetically distinct clusters associated with their tick hosts. Borrelia turcica was characterized in 5% (2/40) of the pools, comprising hunting Hyalomma aegyptium ticks. Co-infection of Coxiella-like endosymbiont and Babesia was noted in a questing R. sanguineus (s.l.) specimen. Furthermore, protozoan 18S rRNA gene sequences were detected in 4 pools of questing/hunting ticks (10%) and identified as Babesia ovis, Hemolivia mauritanica, Babesia and Theileria spp.

CONCLUSIONS: Our metagenomic approach enabled identification of diverse pathogenic and non-pathogenic microorganisms in questing and feeding ticks in Anatolia.},
}

@article {pmid30632609,
year = {2019},
author = {Hamada, T and Nowak, JA and Milner, DA and Song, M and Ogino, S},
title = {Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms.},
journal = {The Journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1002/path.5236},
pmid = {30632609},
issn = {1096-9896},
abstract = {Molecular pathological epidemiology (MPE) is an integrative transdisciplinary field that addresses heterogeneous effects of exogenous and endogenous factors (collectively termed "exposures"), including microorganisms, on disease occurrence and consequence utilising molecular pathological signatures of the disease. In parallel with the paradigm of precision medicine, findings from MPE research can provide aetiological insights into tailored strategies of disease prevention and treatment. Due to the availability of molecular pathological tests on tumours, the MPE approach has been utilised predominantly in research on cancers including breast, lung, prostate, and colorectal carcinomas. Mounting evidence indicates that the microbiome (inclusive of viruses, bacteria, fungi, and parasites) plays an important role in a variety of human diseases including neoplasms. An alteration of the microbiome may be not only a cause of neoplasia but also an informative biomarker that indicates or mediates the association of an epidemiological exposure with health conditions and outcomes. To adequately educate and train investigators in this emerging area, we herein propose the integration of microbiology into the MPE model (termed "microbiology-MPE"), which can improve our understanding of the complex interactions of environment, tumour cells, the immune system, and microbes in the tumour microenvironment during the carcinogenic process. Using this approach, we can examine how lifestyle factors, dietary patterns, medications, environmental exposures, and germline genetics influence cancer development and progression through impacting the microbial communities in the human body. Further integration of other disciplines (e.g. pharmacology, immunology, nutrition) into microbiology-MPE would expand this developing research frontier. With the advent of high-throughput next-generation sequencing technologies, researchers now have increasing access to large-scale metagenomics as well as other omics data (e.g. genomics, epigenomics, proteomics, and metabolomics) in population-based research. The integrative field of microbiology-MPE will open new opportunities for personalised medicine and public health.},
}

@article {pmid30632017,
year = {2019},
author = {Altan, E and Seguin, MA and Leutenegger, CM and Phan, TG and Deng, X and Delwart, E},
title = {Nasal virome of dogs with respiratory infection signs include novel taupapillomaviruses.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11262-019-01634-6},
pmid = {30632017},
issn = {1572-994X},
support = {5149.14//Blood Systems Research Institute/ ; },
abstract = {Using viral metagenomics, we characterized the mammalian virome of nasal swabs from 57 dogs with unexplained signs of respiratory infection showing mostly negative results using the IDEXX Canine Respiratory Disease RealPCR™ Panel. We identified canine parainfluenza virus 5, canine respiratory coronavirus, carnivore bocaparvovirus 3, canine circovirus and canine papillomavirus 9. Novel canine taupapillomaviruses (CPV21-23) were also identified in 3 dogs and their complete genome sequenced showing L1 nucleotide identity ranging from 68.4 to 70.3% to their closest taupapillomavirus relative. Taupapillomavirus were the only mammalian viral nucleic acids detected in two affected dogs, while a third dog was coinfected with low levels of canine parainfluenza 5. A role for these taupapillomavirues in canine respiratory disease remains to be determined.},
}

@article {pmid30631958,
year = {2019},
author = {Haddad-Boubaker, S and Joffret, ML and Pérot, P and Bessaud, M and Meddeb, Z and Touzi, H and Delpeyroux, F and Triki, H and Eloit, M},
title = {Metagenomic analysis identifies human adenovirus 31 in children with acute flaccid paralysis in Tunisia.},
journal = {Archives of virology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00705-018-04141-5},
pmid = {30631958},
issn = {1432-8798},
support = {ANR-10-LABX-62-IBEID//Instituto Nacional de Biotecnologia Estrutural e Química Medicinal em Doenças Infecciosas (BR)/ ; S-CM15010-05B//Fondation Total/ ; },
abstract = {A variety of viruses can cause acute flaccid paralysis (AFP). However, the causative agent, sometimes, remains undetermined. Metagenomics helps in identifying viruses not diagnosed by conventional methods. Stool samples from AFP (n = 104) and non-AFP (n = 114) cases that tested enterovirus-negative by WHO standard methods were investigated. A metagenomics approach, first used on five pools of four samples each, revealed the presence of adenovirus sequences. Amplification in A549 cells and full-genome sequencing were used for complete virus identification and for designing a PCR assay to screen individual related samples. Metagenomic analysis showed that adenovirus sequences that were closely to the A31 and A61 genotypes were the most abundant. Two out of the corresponding 20 individual samples were found positive by PCR, and isolates were obtained in cell culture. Phylogenetic analysis based on complete genome sequences showed that the viruses belong to HAdV-A31 genotype (98-100% nucleotide sequence identity). PCR analysis of stool samples from all AFP and non-AFP cases revealed that a larger proportion of the positive samples were from AFP cases (17.3%) than from non-AFP cases (2.4%). These results open the way to studies aiming to test a possible role of HAdV-A31 in the pathogenesis of AFP.},
}

@article {pmid30631769,
year = {2018},
author = {Klaumann, F and Correa-Fiz, F and Franzo, G and Sibila, M and Núñez, JI and Segalés, J},
title = {Current Knowledge on Porcine circovirus 3 (PCV-3): A Novel Virus With a Yet Unknown Impact on the Swine Industry.},
journal = {Frontiers in veterinary science},
volume = {5},
number = {},
pages = {315},
doi = {10.3389/fvets.2018.00315},
pmid = {30631769},
issn = {2297-1769},
abstract = {Porcine circovirus 3 (PCV-3) is a recently described virus belonging to the family Circoviridae. It represents the third member of genus Circovirus able to infect swine, together with PCV-1, considered non-pathogenic, and PCV-2, one of the most economically relevant viruses for the swine worldwide industry. PCV-3 was originally found by metagenomics analyses in 2015 in tissues of pigs suffering from porcine dermatitis and nephropathy syndrome, reproductive failure, myocarditis and multisystemic inflammation. The lack of other common pathogens as potential infectious agents of these conditions prompted the suspicion that PCV-3 might etiologically be involved in disease occurrence. Subsequently, viral genome was detected in apparently healthy pigs, and retrospective studies indicated that PCV-3 was already present in pigs by early 1990s. In fact, current evidence suggests that PCV-3 is a rather widespread virus worldwide. Recently, the virus DNA has also been found in wild boar, expanding the scope of infection susceptibility among the Suidae family; also, the potential reservoir role of this species for the domestic pig has been proposed. Phylogenetic studies with available PCV-3 partial and complete sequences from around the world have revealed high nucleotide identity (>96%), although two main groups and several subclusters have been described as well. Moreover, it has been proposed the existence of a most common ancestor dated around 50 years ago. Taking into account the economic importance and the well-known effects of PCV-2 on the swine industry, a new member of the same family like PCV-3 should not be neglected. Studies on epidemiology, pathogenesis, immunity and diagnosis are guaranteed in the next few years. Therefore, the present review will update the current knowledge and future trends of research on PCV-3.},
}

@article {pmid30631651,
year = {2019},
author = {Gardner, PP and Watson, RJ and Morgan, XC and Draper, JL and Finn, RD and Morales, SE and Stott, MB},
title = {Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6160},
doi = {10.7717/peerj.6160},
pmid = {30631651},
issn = {2167-8359},
abstract = {Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.},
}

@article {pmid30631318,
year = {2018},
author = {Shao, L and Ling, Z and Chen, D and Liu, Y and Yang, F and Li, L},
title = {Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3166},
doi = {10.3389/fmicb.2018.03166},
pmid = {30631318},
issn = {1664-302X},
abstract = {Early detection and effective interventions for liver cirrhosis (LC) remain an urgent unmet clinical need. Inspired from intestinal disorders in LC patients, we investigated the associations between gut microbiome and disease progression based on a raw metagenomic dataset of 47 healthy controls, 49 compensated, and 46 decompensated LC patients from our previous study, and a metabolomic dataset of urine samples from the same controls/patients using ultra-performance liquid chromatography/mass spectrophotometry system. It was found that the combination and relative abundance of gut microbiome, the inter-microbiome regulatory networks, and the microbiome-host correlation patterns varied during disease progression. The significant reduction of bacteria involved in fermentation of plant cell wall polysaccharides and resistant starch (such as Alistipes sp. HG5, Clostridium thermocellum) contributed to the reduced supply of energy sources, the disorganized self-feeding and cross-feeding networks and the thriving of some opportunistic pathogens in genus Veillonella. The marked decrease of butyrate-producing bacteria and increase of Ruminococcus gnavus implicated in degradation of elements from the mucus layer provided an explanation for the impaired intestinal barrier function and systematic inflammation in LC patients. Our results pave the way for further developments in early detection and intervention of LC targeting on gut microbiome.},
}

@article {pmid30631102,
year = {2019},
author = {Weiland-Bräuer, N and Fischer, MA and Pinnow, N and Schmitz, RA},
title = {Potential role of host-derived quorum quenching in modulating bacterial colonization in the moon jellyfish Aurelia aurita.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {34},
doi = {10.1038/s41598-018-37321-z},
pmid = {30631102},
issn = {2045-2322},
abstract = {Multicellular organisms can be regarded as metaorganisms, comprising of a macroscopic host interacting with associated microorganisms. Within this alliance, the host has to ensure attracting beneficial bacteria and defending against pathogens to establish and maintain a healthy homeostasis. Here, we obtained several lines of evidence arguing that Aurelia aurita uses interference with bacterial quorum sensing (QS) - quorum quenching (QQ) - as one host defense mechanism. Three A. aurita-derived proteins interfering with bacterial QS were identified by functionally screening a metagenomic library constructed from medusa-derived mucus. Native expression patterns of these host open reading frames (ORFs) differed in the diverse life stages (associated with different microbiota) pointing to a specific role in establishing the developmental stage-specific microbiota. Highly increased expression of all QQ-ORFs in germ-free animals further indicates their impact on the microbiota. Moreover, incubation of native animals with pathogenic bacteria induced expression of the identified QQ-ORFs arguing for a host defense strategy against confronting bacteria by interference with bacterial QS. In agreement, immobilized recombinant QQ proteins induced restructuring of polyp-associated microbiota through changing abundance and operational taxonomic unit composition. Thus, we hypothesize that additional to the immune system host-derived QQ-activities potentially control bacterial colonization.},
}

@article {pmid30630933,
year = {2019},
author = {Jiang, X and Hall, AB and Arthur, TD and Plichta, DR and Covington, CT and Poyet, M and Crothers, J and Moses, PL and Tolonen, AC and Vlamakis, H and Alm, EJ and Xavier, RJ},
title = {Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut.},
journal = {Science (New York, N.Y.)},
volume = {363},
number = {6423},
pages = {181-187},
doi = {10.1126/science.aau5238},
pmid = {30630933},
issn = {1095-9203},
abstract = {Phase variation, the reversible alternation between genetic states, enables infection by pathogens and colonization by commensals. However, the diversity of phase variation remains underexplored. We developed the PhaseFinder algorithm to quantify DNA inversion-mediated phase variation. A systematic search of 54,875 bacterial genomes identified 4686 intergenic invertible DNA regions (invertons), revealing an enrichment in host-associated bacteria. Invertons containing promoters often regulate extracellular products, underscoring the importance of surface diversity for gut colonization. We found invertons containing promoters regulating antibiotic resistance genes that shift to the ON orientation after antibiotic treatment in human metagenomic data and in vitro, thereby mitigating the cost of antibiotic resistance. We observed that the orientations of some invertons diverge after fecal microbiota transplant, potentially as a result of individual-specific selective forces.},
}

@article {pmid30629718,
year = {2019},
author = {Gruenstaeudl, M and Hartmaring, Y},
title = {EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210347},
doi = {10.1371/journal.pone.0210347},
pmid = {30629718},
issn = {1932-6203},
abstract = {BACKGROUND: The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant and fungal DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant and fungal DNA barcoding.

METHODS: A Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called 'checklists') for a subsequent upload to the annotated sequence section of the European Nucleotide Archive (ENA). The software tool, titled 'EMBL2checklists', automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates files that can be uploaded via the interactive Webin submission system of ENA.

RESULTS: EMBL2checklists provides a simple, platform-independent tool that automates the conversion of common DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in four recent investigations, including plant phylogenetic and fungal metagenomic studies.

DISCUSSION: EMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant and fungal biologists without bioinformatics expertise to generate submission-ready checklists from common DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.},
}

@article {pmid30629604,
year = {2019},
author = {Mayday, MY and Khan, LM and Chow, ED and Zinter, MS and DeRisi, JL},
title = {Miniaturization and optimization of 384-well compatible RNA sequencing library preparation.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0206194},
doi = {10.1371/journal.pone.0206194},
pmid = {30629604},
issn = {1932-6203},
abstract = {Preparation of high-quality sequencing libraries is a costly and time-consuming component of metagenomic next generation sequencing (mNGS). While the overall cost of sequencing has dropped significantly over recent years, the reagents needed to prepare sequencing samples are likely to become the dominant expense in the process. Furthermore, libraries prepared by hand are subject to human variability and needless waste due to limitations of manual pipetting volumes. Reduction of reaction volumes, combined with sub-microliter automated dispensing of reagents without consumable pipette tips, has the potential to provide significant advantages. Here, we describe the integration of several instruments, including the Labcyte Echo 525 acoustic liquid handler and the iSeq and NovaSeq Illumina sequencing platforms, to miniaturize and automate mNGS library preparation, significantly reducing the cost and the time required to prepare samples. Through the use of External RNA Controls Consortium (ERCC) spike-in RNAs, we demonstrated the fidelity of the miniaturized preparation to be equivalent to full volume reactions. Furthermore, detection of viral and microbial species from cell culture and patient samples was also maintained in the miniaturized libraries. For 384-well mNGS library preparations, we achieved cost savings of over 80% in materials and reagents alone, and reduced preparation time by 90% compared to manual approaches, without compromising quality or representation within the library.},
}

@article {pmid30629185,
year = {2019},
author = {Stewart, CJ and Mansbach, JM and Ajami, NJ and Petrosino, JF and Zhu, Z and Liang, L and Camargo, CA and Hasegawa, K},
title = {Serum metabolome is associated with nasopharyngeal microbiota and disease severity among infants with bronchiolitis.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiz021},
pmid = {30629185},
issn = {1537-6613},
abstract = {Background: Emerging evidence suggests relations of nasopharyngeal metabolome and microbiota with bronchiolitis severity. However, the influence of host systemic metabolism on disease pathobiology remains unclear. We aimed to examine metabolome profiles and their association with higher severity, defined by use of positive pressure ventilation (PPV), in infants hospitalized for bronchiolitis.

Methods: In 140 infants with bronchiolitis, metabolomic profiling was performed on serum: n=70 in the training dataset and n=70 independent samples in the test dataset. We also profiled the nasopharyngeal airway microbiota and examined its association with the serum metabolites.

Results: Serum metabolome profiles differed by bronchiolitis severity (P<0.001). In total, 20 metabolites in the training dataset were significantly associated with the risk of PPV and 18 metabolites remained significant following adjustment for confounders (FDR<0.10). Phosphatidylcholine metabolites were associated with higher risks of PPV use, while metabolites from the plasmalogen sub-pathway were associated with lower risks. The test dataset validated these findings (FDR<0.05). Streptococcus abundance was positively associated with metabolites that are associated with higher risks of PPV.

Conclusions: Serum metabolomic signatures were associated with both the nasopharyngeal microbiota and bronchiolitis severity. Our findings advance research into the complex interrelations between airway microbiome, host systemic response, and pathobiology of bronchiolitis.},
}

@article {pmid30627872,
year = {2019},
author = {Wang, Q and Wang, K and Wu, W and Giannoulatou, E and Ho, JWK and Li, L},
title = {Host and microbiome multi-omics integration: applications and methodologies.},
journal = {Biophysical reviews},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12551-018-0491-7},
pmid = {30627872},
issn = {1867-2450},
support = {81330011, 81330014, 81790631, 81790633, 81570512, and 81121002//National Natural Science Foundation of China/ ; 81721091//Science Fund for Creative Research Groups/ ; 100848//National Heart Foundation of Australia/ ; 101204//National Heart Foundation of Australia/ ; },
abstract = {The study of the microbial community-the microbiome-associated with a human host is a maturing research field. It is increasingly clear that the composition of the human's microbiome is associated with various diseases such as gastrointestinal diseases, liver diseases and metabolic diseases. Using high-throughput technologies such as next-generation sequencing and mass spectrometry-based metabolomics, we are able to comprehensively sequence the microbiome-the metagenome-and associate these data with the genomic, epigenomics, transcriptomic and metabolic profile of the host. Our review summarises the application of integrating host omics with microbiome as well as the analytical methods and related tools applied in these studies. In addition, potential future directions are discussed.},
}

@article {pmid30626904,
year = {2019},
author = {Delgado, B and Bach, A and Guasch, I and González, C and Elcoso, G and Pryce, JE and Gonzalez-Recio, O},
title = {Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11},
doi = {10.1038/s41598-018-36673-w},
pmid = {30626904},
issn = {2045-2322},
abstract = {The current research was carried out to determine the associations between the rumen microbiota and traits related with feed efficiency in a Holstein cattle population (n = 30) using whole metagenome sequencing. Improving feed efficiency (FE) is important for a more sustainable livestock production. The variability for the efficiency of feed utilization in ruminants is partially controlled by the gastrointestinal microbiota. Modulating the microbiota composition can promote a more sustainable and efficient livestock. This study revealed that most efficient cows had larger relative abundance of Bacteroidetes (P = 0.041) and Prevotella (P = 0.003), while lower, but non-significant (P = 0.119), relative abundance of Firmicutes. Methanobacteria (P = 0.004) and Methanobrevibacter (P = 0.003) were also less abundant in the high-efficiency cows. A de novo metagenome assembly was carried out using de Bruijn graphs in MEGAHIT resulting in 496,375 contigs. An agnostic pre-selection of microbial contigs allowed high classification accuracy for FE and intake levels using hierarchical classification. These microbial contigs were also able to predict FE and intake levels with accuracy of 0.19 and 0.39, respectively, in an independent population (n = 31). Nonetheless, a larger potential accuracy up to 0.69 was foreseen in this study for datasets that allowed a larger statistical power. Enrichment analyses showed that genes within these contigs were mainly involved in fatty acids and cellulose degradation pathways. The findings indicated that there are differences between the microbiota compositions of high and low-efficiency animals both at the taxonomical and gene levels. These differences are even more evident in terms of intake levels. Some of these differences remain even between populations under different diets and environments, and can provide information on the feed utilization performance without information on the individual intake level.},
}

@article {pmid30626868,
year = {2019},
author = {Singh, R and Chandrashekharappa, S and Bodduluri, SR and Baby, BV and Hegde, B and Kotla, NG and Hiwale, AA and Saiyed, T and Patel, P and Vijay-Kumar, M and Langille, MGI and Douglas, GM and Cheng, X and Rouchka, EC and Waigel, SJ and Dryden, GW and Alatassi, H and Zhang, HG and Haribabu, B and Vemula, PK and Jala, VR},
title = {Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {89},
doi = {10.1038/s41467-018-07859-7},
pmid = {30626868},
issn = {2041-1723},
abstract = {The importance of gut microbiota in human health and pathophysiology is undisputable. Despite the abundance of metagenomics data, the functional dynamics of gut microbiota in human health and disease remain elusive. Urolithin A (UroA), a major microbial metabolite derived from polyphenolics of berries and pomegranate fruits displays anti-inflammatory, anti-oxidative, and anti-ageing activities. Here, we show that UroA and its potent synthetic analogue (UAS03) significantly enhance gut barrier function and inhibit unwarranted inflammation. We demonstrate that UroA and UAS03 exert their barrier functions through activation of aryl hydrocarbon receptor (AhR)- nuclear factor erythroid 2-related factor 2 (Nrf2)-dependent pathways to upregulate epithelial tight junction proteins. Importantly, treatment with these compounds attenuated colitis in pre-clinical models by remedying barrier dysfunction in addition to anti-inflammatory activities. Cumulatively, the results highlight how microbial metabolites provide two-pronged beneficial activities at gut epithelium by enhancing barrier functions and reducing inflammation to protect from colonic diseases.},
}

@article {pmid30626052,
year = {2019},
author = {Cheong, DE and Park, SY and Lim, HD and Kim, GJ},
title = {An Alternative Platform for Protein Expression Using an Innate Whole Expression Module from Metagenomic DNA.},
journal = {Microorganisms},
volume = {7},
number = {1},
pages = {},
doi = {10.3390/microorganisms7010009},
pmid = {30626052},
issn = {2076-2607},
support = {NRF-2017030616//The Intelligent Synthetic Biology Center program of the National Research Foundation (NRF) funded by the Ministry of Science/ ; 20170305//ICT & Future Planning and by a grant from the Marine Biotechnology Program funded by the Ministry of Oceans and Fisheries, Korea/ ; 2017R1D1A1B03035338//Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Education/ ; },
abstract = {Many integrated gene clusters beyond a single genetic element are commonly trapped as the result of promoter traps in (meta)genomic DNA libraries. Generally, a single element, which is mainly the promoter, is deduced from the resulting gene clusters and employed to construct a new expression vector. However, expression patterns of target proteins under the incorporated promoter are often inconsistent with those shown in clones harboring plasmids with gene clusters. These results suggest that the integrated set of gene clusters with diverse cis- and trans-acting elements is evolutionarily tuned as a complete set for gene expression, and is an expression module with all the components for the expression of a nested open reading frame (ORF). This possibility is further supported by truncation and/or serial deletion analysis of this module in which the expression of the nested ORF is highly fluctuated or reduced frequently, despite being supported by plentiful cis-acting elements in the spanning regions around the ORF such as the promoter, ribosome binding site (RBS), terminator, and 3'-/5'-UTRs for gene expression. Here, we examined whether an innate module with a naturally overexpressed gene could be considered as a scaffold for an expression system. For a proof-of-principle study, we mined a complete expression module with an innately overexpressed ORF in E. coli from a metagenomics DNA library, and incorporated it into a vector that had no regulatory element for expressing the insert. We obtained successful expression of several inserts such as MBP, GFPuv, β-glucosidase, and esterase using this simple construct without tuning and codon optimization of the target insert.},
}

@article {pmid30626002,
year = {2019},
author = {Rechenberger, J and Samaras, P and Jarzab, A and Behr, J and Frejno, M and Djukovic, A and Sanz, J and González-Barberá, EM and Salavert, M and López-Hontangas, JL and Xavier, KB and Debrauwer, L and Rolain, JM and Sanz, M and Garcia-Garcera, M and Wilhelm, M and Ubeda, C and Kuster, B},
title = {Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae.},
journal = {Proteomes},
volume = {7},
number = {1},
pages = {},
doi = {10.3390/proteomes7010002},
pmid = {30626002},
issn = {2227-7382},
support = {031L0089//Bundesministerium für Bildung und Forschung/ ; },
abstract = {The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date, and the first metaproteomic study addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable future addition to the analysis of patient cohorts.},
}

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

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

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

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

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

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

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

@article {pmid30625356,
year = {2019},
author = {Jia, ML and Zhong, XL and Lin, ZW and Dong, BX and Li, G},
title = {Expression and characterization of an esterase belonging to a new family via isolation from a metagenomic library of paper mill sludge.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijbiomac.2019.01.025},
pmid = {30625356},
issn = {1879-0003},
abstract = {A new bacterial lipolytic enzyme Est903 was obtained from paper mill sludge via metagenomic approach. Est903 displayed moderate similarities to two lipolytic enzymes from Rhodopirellula islandica and contained a distinctive pentapeptide motif (GFSAG) that differed from those of all known fourteen families of bacterial lipolytic enzymes. Est903 was regarded as from a new bacterial lipolytic enzyme family through multiple sequence alignment and phylogenetic analysis. The recombinant Est903 showed the highest activity for ρ-nitrophenol butyrate. The pH optimum and temperature optimum of the recombinant enzyme was 9.0 and 51 °C, respectively. Also, this enzyme displayed moderate thermostability, high activity under alkaline conditions, and good tolerance against several organic solvents. In addition, the compatibility test and washing performance analysis revealed that Est903 had good compatibility with commercial laundry detergent and high cleaning ability of oil stains. These good properties make Est903 a potential candidate in organic synthesis or detergent industry.},
}

@article {pmid30624643,
year = {2019},
author = {Baldrian, P},
title = {The known and the unknown in soil microbial ecology.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz005},
pmid = {30624643},
issn = {1574-6941},
abstract = {The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions. Also the analysis of processes exemplified by enzyme activity measurements is still imperfect. In the future, it is important to look at soil at a finer detail to obtain a better picture on the properties of individual microbes, their in situ interactions, metabolic rates and activity at a scale relevant to individual microbes. Scaling up is needed as well to get answers at ecosystem or biome levels and to enable global modelling. The recent development of novel tools including metabolomics, identification of genomes in metagenomics sequencing datasets or collection of trait data have the potential to bring soil ecology further. It will, however, always remain a highly demanding scientific discipline.},
}

@article {pmid30623484,
year = {2019},
author = {Zhai, J and Knox, K and Twigg, HL and Zhou, H and Zhou, JJ},
title = {Exact variance component tests for longitudinal microbiome studies.},
journal = {Genetic epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/gepi.22185},
pmid = {30623484},
issn = {1098-2272},
support = {DMS-1645093//National Science Foundation/ ; GM105785//National Institute of General Medical Sciences/ ; GM053275//National Institute of General Medical Sciences/ ; HG006139//National Human Genome Research Institute/ ; K01DK106116//National Institute of Diabetes and Digestive and Kidney Diseases/ ; New Investigator Award//Arizona Biomedical Research Commission/ ; },
abstract = {In metagenomic studies, testing the association between microbiome composition and clinical outcomes translates to testing the nullity of variance components. Motivated by a lung human immunodeficiency virus (HIV) microbiome project, we study longitudinal microbiome data by using variance component models with more than two variance components. Current testing strategies only apply to models with exactly two variance components and when sample sizes are large. Therefore, they are not applicable to longitudinal microbiome studies. In this paper, we propose exact tests (score test, likelihood ratio test, and restricted likelihood ratio test) to (a) test the association of the overall microbiome composition in a longitudinal design and (b) detect the association of one specific microbiome cluster while adjusting for the effects from related clusters. Our approach combines the exact tests for null hypothesis with a single variance component with a strategy of reducing multiple variance components to a single one. Simulation studies demonstrate that our method has a correct type I error rate and superior power compared to existing methods at small sample sizes and weak signals. Finally, we apply our method to a longitudinal pulmonary microbiome study of HIV-infected patients and reveal two interesting genera Prevotella and Veillonella associated with forced vital capacity. Our findings shed light on the impact of the lung microbiome on HIV complexities. The method is implemented in the open-source, high-performance computing language Julia and is freely available at https://github.com/JingZhai63/VCmicrobiome.},
}

@article {pmid30623233,
year = {2019},
author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS},
title = {Chinese liver fluke Clonorchis sinensis infection changes the gut microbiome and increases probiotic Lactobacillus in mice.},
journal = {Parasitology research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00436-018-6179-x},
pmid = {30623233},
issn = {1432-1955},
support = {NRF-2016R1A2B4016194//National Research Foundation of Korea/ ; 2011-0012166//National Research Foundation of Korea/ ; },
abstract = {Chinese liver fluke Clonorchis sinensis changes the host's immune system. Recently, it has been reported that helminths including C. sinensis can ameliorate immune-related diseases such as allergy. In addition, recent studies showed that helminth infection can alleviate immune-mediated disorders by altering the gut microbiome. However, changes in the gut microbiome due to C. sinensis have not been reported yet. In this study, changes in the gut microbiome of C57BL/6 mice infected with C. sinensis metacercariae were evaluated over time. Stool was analyzed by 16S rRNA amplicon analysis using high-throughput sequencing technology. There was no apparent difference in species richness and diversity between the infected and control groups. However, the composition of the microbiome was different between the infected and control groups at 20 days and 30 days post-infection, and the difference disappeared at 50 days post-infection. In particular, this microbiome alteration was associated with a change in the relative abundance of genus Lactobacillus and the probiotic Lactobacillus species that are known to have an immune-modulation role in immune-mediated diseases.},
}

@article {pmid30623212,
year = {2019},
author = {de Sousa, AGG and Tomasino, MP and Duarte, P and Fernández-Méndez, M and Assmy, P and Ribeiro, H and Surkont, J and Leite, RB and Pereira-Leal, JB and Torgo, L and Magalhães, C},
title = {Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-01314-2},
pmid = {30623212},
issn = {1432-184X},
support = {244646//Research Council of Norway/ ; NORTE-01-0145-FEDER-000031//Structured Program of R&D&I MarInfo/ ; Arktis 2030//Norwegian Ministries of Foreign Affairs and Climate and Environment/ ; NITROLIMIT - PTDC 2017 - PTDC/CTA-AMB/30997/2017//Funda??o para a Ci?ncia e a Tecnologia/ ; },
abstract = {One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.},
}

@article {pmid30622518,
year = {2018},
author = {Fujiwara, K and Iwanami, T and Fujikawa, T},
title = {Alterations of Candidatus Liberibacter asiaticus-Associated Microbiota Decrease Survival of Ca. L. asiaticus in in vitro Assays.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3089},
doi = {10.3389/fmicb.2018.03089},
pmid = {30622518},
issn = {1664-302X},
abstract = {Phloem-inhabiting bacterial phytopathogens often have smaller genomes than other bacterial phytopathogens. It is thought that they depend on both other phloem microbiota and phloem nutrients for colonization of the host. However, the mechanism underlying associations between phloem-inhabiting phytopathogens and other phloem microbiota are poorly understood. Here, we demonstrate that the survival of Candidatus Liberibacter asiaticus (CLas), a cause of huanglongbing (citrus greening disease), depends on interplay with a specific subset of CLas-associated microbiota. CLas was not susceptible to oxytetracycline in vitro. However, oxytetracycline treatment eliminated a particular sub-community dominated by the Comamonadaceae, Flavobacteriaceae, Microbacteriaceae, and Pseudomonadaceae, decreasing CLas survival. We speculate that CLas uses ecological services derived from CLas-associated microbiota to colonize the host and to construct a pathogen-associated community that stimulates disease development.},
}

@article {pmid30622259,
year = {2019},
author = {Karkman, A and Pärnänen, K and Larsson, DGJ},
title = {Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {80},
doi = {10.1038/s41467-018-07992-3},
pmid = {30622259},
issn = {2041-1723},
abstract = {Discharge of treated sewage leads to release of antibiotic resistant bacteria, resistance genes and antibiotic residues to the environment. However, it is unclear whether increased abundance of antibiotic resistance genes in sewage and sewage-impacted environments is due to on-site selection pressure by residual antibiotics, or is simply a result of fecal contamination with resistant bacteria. Here we analyze relative resistance gene abundance and accompanying extent of fecal pollution in publicly available metagenomic data, using crAssphage sequences as a marker of human fecal contamination (crAssphage is a bacteriophage that is exceptionally abundant in, and specific to, human feces). We find that the presence of resistance genes can largely be explained by fecal pollution, with no clear signs of selection in the environment, with the exception of environments polluted by very high levels of antibiotics from manufacturing, where selection is evident. Our results demonstrate the necessity to take into account fecal pollution levels to avoid making erroneous assumptions regarding environmental selection of antibiotic resistance.},
}

@article {pmid30622080,
year = {2019},
author = {Cota-Ruiz, K and López de Los Santos, Y and Hernández-Viezcas, JA and Delgado-Rios, M and Peralta-Videa, JR and Gardea-Torresdey, JL},
title = {A comparative metagenomic and spectroscopic analysis of soils from an international point of entry between the US and Mexico.},
journal = {Environment international},
volume = {123},
number = {},
pages = {558-566},
doi = {10.1016/j.envint.2018.12.055},
pmid = {30622080},
issn = {1873-6750},
abstract = {The Paso del Norte region is characterized by its dynamic industries and active agriculture. Throughout the years, urban and agricultural soils from this region have been exposed to xenobiotics, heavy metals, and excess of hydrocarbons. In this study, samples of urban [domestic workshops (DW)] and agricultural-intended (AI) soils from different sites of Ciudad Juárez, Mexico were evaluated for their fertility, element content, and microbial diversity. Chemical analyses showed that nitrites, nitrates, P, K, Mg, and Mn were predominantly higher in AI soils, compared to DW soils (p ≤ 0.05). The composition of soil microbial communities showed that Proteobacteria phylum was the most abundant in both soils (67%, p ≤ 0.05). In AI soils, Paracoccus denitrificans was reduced (p ≤ 0.05), concurring with an increment in nitrates, while the content of nitrogen was negatively correlated with the rhizobium group (r2 = -0.65, p ≤ 0.05). In DW soils, the Firmicutes phylum represented up to ~25%, and the relative abundance of Proteobacteria strongly correlated with a higher Cu content (r2 = 0.99, p ≤ 0.0001). The monotypic genus Sulfuricurvum was found only in oil-contaminated soil samples. Finally, all samples showed the presence of the recently created phylum Candidatus saccharibacteria. These results describe the productivity parameters of AI soils and its correlation to the microbial diversity, which are very important to understand and potentiate the productivity of soils. The data also suggest that soils impacted with hydrocarbons and metal(oid)s allow the reproduction of microorganisms with the potential to alleviate contaminated sites.},
}

@article {pmid30621881,
year = {2019},
author = {Jagadeesan, B and Gerner-Smidt, P and Allard, MW and Leuillet, S and Winkler, A and Xiao, Y and Chaffron, S and Van Der Vossen, J and Tang, S and Katase, M and McClure, P and Kimura, B and Ching Chai, L and Chapman, J and Grant, K},
title = {The use of next generation sequencing for improving food safety: Translation into practice.},
journal = {Food microbiology},
volume = {79},
number = {},
pages = {96-115},
doi = {10.1016/j.fm.2018.11.005},
pmid = {30621881},
issn = {1095-9998},
abstract = {Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.},
}

@article {pmid30621868,
year = {2019},
author = {Ottesen, A and Ramachandran, P and Reed, E and Gu, G and Gorham, S and Ducharme, D and Newell, M and Rideout, S and Turini, T and Hill, T and Strain, E and Brown, E},
title = {Metagenome tracking biogeographic agroecology: Phytobiota of tomatoes from Virginia, Maryland, North Carolina and California.},
journal = {Food microbiology},
volume = {79},
number = {},
pages = {132-136},
doi = {10.1016/j.fm.2018.12.001},
pmid = {30621868},
issn = {1095-9998},
abstract = {Describing baseline microbiota associated with agricultural commodities in the field is an important step towards improving our understanding of a wide range of important objectives from plant pathology and horticultural sustainability, to food safety. Environmental pressures on plants (wind, dust, drought, water, temperature) vary by geography and characterizing the impact of these variable pressures on phyllosphere microbiota will contribute to improved stewardship of fresh produce for both plant and human health. A higher resolution understanding of the incidence of human pathogens on food plants and co-occurring phytobiota using metagenomic approaches (metagenome tracking) may contribute to improved source attribution and risk assessment in cases where human pathogens become introduced to agro-ecologies. Between 1990 and 2007, as many as 1990 culture-confirmed Salmonella illnesses were linked to tomatoes from as many as 12 multistate outbreaks (Bell et al., 2012; Bell et al., 2015; Bennett et al., 2014; CDC, 2004; CDC, 2007; Greene et al., 2005a; Gruszynski et al., 2014). When possible, source attribution for these incidents revealed a biogeographic trend, most events were associated with eastern growing regions. To improve our understanding of potential biogeographically linked trends in contamination of tomatoes by Salmonella, we profiled microbiota from the surfaces of tomatoes from Virginia, Maryland, North Carolina and California. Bacterial profiles from California tomatoes were completely different than those of Maryland, Virginia and North Carolina (which were highly similar to each other). A statistically significant enrichment of Firmicutes taxa was observed in California phytobiota compared to the three eastern states. Rhizobiaceae, Sphingobacteriaceae and Xanthobacteraceae were the most abundant bacterial families associated with tomatoes grown in eastern states. These baseline metagenomic profiles of phyllosphere microbiota may contribute to improved understanding of how certain ecologies provide supportive resources for human pathogens on plants and how components of certain agro-ecologies may play a role in the introduction of human pathogens to plants.},
}

@article {pmid30621867,
year = {2019},
author = {Marino, M and Dubsky de Wittenau, G and Saccà, E and Cattonaro, F and Spadotto, A and Innocente, N and Radovic, S and Piasentier, E and Marroni, F},
title = {Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese.},
journal = {Food microbiology},
volume = {79},
number = {},
pages = {123-131},
doi = {10.1016/j.fm.2018.12.007},
pmid = {30621867},
issn = {1095-9998},
abstract = {The microbiota of different types of Italian high-moisture Mozzarella cheese produced using cow or buffalo milk, acidified with natural or selected cultures, and sampled at the dairy or at the mass market, was evaluated using a Next Generation Sequencing approach, in order to identify possible drivers of the bacterial diversity. Cow Mozzarella and buffalo Mozzarella acidified with commercial cultures were dominated by Streptococcus thermophilus, while buffalo samples acidified with natural whey cultures showed similar prevalence of L. delbrueckii subsp. bulgaricus, L. helveticus and S. thermophilus. Moreover, several species of non-starter lactic acid bacteria were frequently detected. The diversity in cow Mozzarella microbiota was much higher than that of water buffalo samples. Cluster analysis clearly separated cow's cheeses from buffalo's ones, the former having a higher prevalence of psychrophilic taxa, and the latter of Lactobacillus and Streptococcus. A higher prevalence of psychrophilic species and potential spoilers was observed in samples collected at the mass retail, suggesting that longer exposures to cooling temperatures and longer production-to-consumption times could significantly affect microbiota diversity. Our results could help in detecting some kind of thermal abuse during the production or storage of mozzarella cheese.},
}

@article {pmid30621760,
year = {2018},
author = {Gerner, SM and Rattei, T and Graf, AB},
title = {Assessment of urban microbiome assemblies with the help of targeted in silico gold standards.},
journal = {Biology direct},
volume = {13},
number = {1},
pages = {22},
doi = {10.1186/s13062-018-0225-6},
pmid = {30621760},
issn = {1745-6150},
support = {Call 19-19 Project UrbanMetagenApp//MA23/ ; },
abstract = {BACKGROUND: Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metagenome samples. The only in silico approach that allows us to find unknown species, is the assembly and classification of draft genomes from a metagenomic dataset. In this study we (1) investigate the applicability of an assembly and binning approach for urban metagenome datasets, and (2) develop a new method for the generation of in silico gold standards to better understand the specific challenges of such datasets and provide a guide in the selection of available software.

RESULTS: We applied combinations of three assembly (Megahit, SPAdes and MetaSPAdes) and three binning tools (MaxBin, MetaBAT and CONCOCT) to whole genome shotgun datasets from the CAMDA 2017 Challenge. Complex in silico gold standards with a simulated bacterial fraction were generated for representative samples of each surface type and city. Using these gold standards, we found the combination of SPAdes and MetaBAT to be optimal for urban metagenome datasets by providing the best trade-off between the number of high-quality genome draft bins (MIMAG standards) retrieved, the least amount of misassemblies and contamination. The assembled draft genomes included known species like Propionibacterium acnes but also novel species according to respective ANI values.

CONCLUSIONS: In our work, we showed that, even for datasets with high diversity and low sequencing depth from urban environments, assembly and binning-based methods can provide high-quality genome drafts. Of vital importance to retrieve high-quality genome drafts is sequence depth but even more so a high proportion of the bacterial sequence fraction too achieve high coverage for bacterial genomes. In contrast to read-based methods relying on database knowledge, genome-centric methods as applied in this study can provide valuable information about unknown species and strains as well as functional contributions of single community members within a sample. Furthermore, we present a method for the generation of sample-specific highly complex in silico gold standards.

REVIEWERS: This article was reviewed by Craig Herbold, Serghei Mangul and Yana Bromberg.},
}

@article {pmid30621600,
year = {2019},
author = {Imhann, F and Van der Velde, KJ and Barbieri, R and Alberts, R and Voskuil, MD and Vich Vila, A and Collij, V and Spekhorst, LM and der Sloot Kwj, V and Peters, V and Van Dullemen, HM and Visschedijk, MC and Eam, F and Swertz, MA and Dijkstra, G and Weersma, RK},
title = {The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1.},
journal = {BMC gastroenterology},
volume = {19},
number = {1},
pages = {5},
doi = {10.1186/s12876-018-0917-5},
pmid = {30621600},
issn = {1471-230X},
support = {016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 92.003.577//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; MLDS D16-14//Maag Lever Darm Stichting/ ; CD14-04//Maag Lever Darm Stichting (NL)/ ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal tract. Patients with IBD can experience a wide range of symptoms, but the pathophysiological mechanisms that cause these individual differences in clinical presentation remain largely unknown. In consequence, IBD is currently classified into subtypes using clinical characteristics. If we are to develop a more targeted treatment approach, molecular subtypes of IBD need to be discovered that can be used as new drug targets. To achieve this, we need multiple layers of molecular data generated from the same IBD patients.

CONSTRUCTION AND CONTENT: We initiated the 1000IBD project (https://1000ibd.org) to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, we have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1215 participants have been enrolled in the project and enrolment is on-going. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing.

UTILITY AND DISCUSSION: All molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive (https://ega-archive.org , accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. Future releases will comprise many more additional phenotypes and -omics data layers. 1000IBD data can be used by other researchers as a replication cohort, a dataset to test new software tools, or a dataset for applying new statistical models.

CONCLUSIONS: We report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets.},
}

@article {pmid30620035,
year = {2019},
author = {Huo, L and Hug, JJ and Fu, C and Bian, X and Zhang, Y and Müller, R},
title = {Heterologous expression of bacterial natural product biosynthetic pathways.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/c8np00091c},
pmid = {30620035},
issn = {1460-4752},
abstract = {Covering: 2013 to June 2018Heterologous expression of natural product biosynthetic pathways is of increasing interest in microbial biotechnology, drug discovery and optimization. It empowers not only the robust production of valuable biomolecules in more amenable heterologous hosts but also permits the generation of novel analogs through biosynthetic engineering. This strategy also facilitates the discovery of novel bioactive compounds following the functional expression of cryptic biosynthetic gene clusters (BGCs) from fastidious original producers or metagenomic DNA in surrogate hosts, thus facilitating genome mining in the post-genomic era. This review discusses recent advances and trends pertaining to the heterologous production of bacterial natural products, with an emphasis on new techniques, heterologous hosts, and novel chemistry since 2013.},
}

@article {pmid30619927,
year = {2019},
author = {Kadnikov, VV and Mardanov, AV and Frank, YA and Beletsky, AV and Karnachuk, OV and Ravin, NV},
title = {Genomes of three bacteriophages from the deep subsurface aquifer.},
journal = {Data in brief},
volume = {22},
number = {},
pages = {488-491},
doi = {10.1016/j.dib.2018.12.045},
pmid = {30619927},
issn = {2352-3409},
abstract = {Viral particles have been detected in the underground biosphere where they could be one of the main factors impacting microbial diversity, biogeochemistry and evolution. To characterize the viral component in the deep subsurface biosphere, we sequenced the metagenome of subsurface aquifer located in the Tomsk region of Russia, sampled via 2.8-km-deep borehole 5P. The de novo assembly of metagenomics sequences yielded three circular genomes assigned to bacteriophages of the order Caudovirales. The annotated genome sequences of these bacteriophages have been deposited in the GenBank database under the accession numbers MK113949, MK113950 and MK113951.},
}

@article {pmid30619848,
year = {2018},
author = {Nishiyama, E and Higashi, K and Mori, H and Suda, K and Nakamura, H and Omori, S and Maruyama, S and Hongoh, Y and Kurokawa, K},
title = {The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {6},
number = {},
pages = {202},
doi = {10.3389/fbioe.2018.00202},
pmid = {30619848},
issn = {2296-4185},
abstract = {Diverse microorganisms specifically inhabit extreme environments, such as hot springs and deep-sea hydrothermal vents. To test the hypothesis that the microbial community structure is predictable based on environmental factors characteristic of such extreme environments, we conducted correlation analyses of microbial taxa/functions and environmental factors using metagenomic and 61 types of physicochemical data of water samples from nine hot springs in the Kirishima area (Kyusyu, Japan), where hot springs with diverse chemical properties are distributed in a relatively narrow area. Our metagenomic analysis revealed that the samples can be classified into two major types dominated by either phylum Crenarchaeota or phylum Aquificae. The correlation analysis showed that Crenarchaeota dominated in nutrient-rich environments with high concentrations of ions and total carbons, whereas Aquificae dominated in nutrient-poor environments with low ion concentrations. These environmental factors were also important explanatory variables in the generalized linear models constructed to predict the abundances of Crenarchaeota or Aquificae. Functional enrichment analysis of genes also revealed that the separation of the two major types is primarily attributable to genes involved in autotrophic carbon fixation, sulfate metabolism and nitrate reduction. Our results suggested that Aquificae and Crenarchaeota play a vital role in the Kirishima hot spring water ecosystem through their metabolic pathways adapted to each environment. Our findings provide a basis to predict microbial community structures in hot springs from environmental parameters, and also provide clues for the exploration of biological resources in extreme environments.},
}

@article {pmid30619804,
year = {2018},
author = {Bachmann, NL and Rockett, RJ and Timms, VJ and Sintchenko, V},
title = {Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics.},
journal = {Frontiers in public health},
volume = {6},
number = {},
pages = {363},
doi = {10.3389/fpubh.2018.00363},
pmid = {30619804},
issn = {2296-2565},
abstract = {Whole genome sequencing (WGS) plays an increasing role in communicable disease control through high-resolution outbreak tracing, laboratory surveillance and diagnostics. However, WGS has traditionally relied on microbial culture in order to obtain pathogen specific DNA for sequencing. This has severely limited the application of whole genome sequencing on pathogens with fastidious culturing requirements. In addition, the widespread adoption of culture-independent diagnostic tests has reduced availability of cultured isolates for confirmatory testing and surveillance. These recent developments have created demand for the implementation of techniques enabling direct sequencing of microbial genomes in clinical samples without having to culture an isolate. However, sequencing of specific organisms from clinical samples can be affected by high levels of contaminating DNA from the host and other commensal microorganisms. Several methods have been introduced for selective lysis of host cells and/or separate specific organisms from a clinical sample. This review examines the different approaches for sample preparation that have been used in diagnostic and public health laboratories for metagenomic sequencing.},
}

@article {pmid30619779,
year = {2018},
author = {Hu, YL and Pang, W and Huang, Y and Zhang, Y and Zhang, CJ},
title = {The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {433},
doi = {10.3389/fcimb.2018.00433},
pmid = {30619779},
issn = {2235-2988},
abstract = {Objective: Dysbiosis of gastric microbiota such as Helicobacter pylori plays a significant role in pathogenesis and progression of gastric cancer. Our aim was to evaluate the composition and functional effects of gastric microbiota in superficial gastritis (SG) and advanced gastric adenocarcinoma (GC). Methods: We carried out shotgun metagenomic sequencing on gastric wash samples from 6 patients with GC and 5 patients with SG. The taxonomic composition was profiled using MetaPhlAn2 and functional gene pathway was profiled using HUMAnN2. Differences in microbial composition and pathways between the two patient groups were assessed via LEfSe. Results: The gastric microbiota in GC patients was characterized by reduced species richness, enrichment of 13 bacterial taxa and depletion of 31 taxa (q < 0.05). The most representative taxa which were abundant in GC corresponded to the commensals or opportunistic pathogens that usually colonize the oral cavity, including genera Neisseria, Alloprevotella, and Aggregatibacter, species Streptococcus_mitis_oralis_pneumoniae and strain Porphyromonas_endodontalis.t_GCF_000174815. Each of the three GC-associated genera could separate GC from SG completely. In particular, Sphingobium yanoikuyae, a bacterium capable of degrading carcinogenic compounds, was depleted in GC. Functionally, pathways associated with the biosynthesis of lipopolysaccharide (LPS) and L-arginine were enriched in GC, whereas pathways involved in the fermentation of short chain fatty acids (SCFAs) and branched amino acid metabolism were more abundant in SG. Conclusions: Our results present new alterations in the gastric microbiome in patients with GC from a whole-genome perspective, suggesting that microbiome composition and function can be used for prognosis and diagnosis of GC.},
}

@article {pmid30619503,
year = {2018},
author = {Cai, FF and Zhou, WJ and Wu, R and Su, SB},
title = {Systems biology approaches in the study of Chinese herbal formulae.},
journal = {Chinese medicine},
volume = {13},
number = {},
pages = {65},
doi = {10.1186/s13020-018-0221-x},
pmid = {30619503},
issn = {1749-8546},
abstract = {Systems biology is an academic field that attempts to integrate different levels of information to understand how biological systems function. It is the study of the composition of all components of a biological system and their interactions under specific conditions. The core of systems biology is holistic and systematic research, which is different from the manner of thinking and research of all other branches of biology to date. Chinese herbal formulae (CHF) are the main form of Chinese medicine and are composed of single Chinese herbal medicines (CHMs) with pharmacological and pharmacodynamic compatibility. When single CHMs are combined into CHF, the result is different from the original effect of a single drug and can be better adapted to more diseases with complex symptoms. CHF represent a complex system with multiple components, targets and effects. Therefore, the use of systems biology is conducive to revealing the complex characteristics of CHF. With the rapid development of omics technologies, systems biology has been widely and increasingly applied to the study of the basis of the pharmacological substances, action targets and mechanisms of CHF. To meet the challenges of multiomics synthesis-intensive studies and system dynamics research in CHF, this paper reviews the common techniques of genomics, transcriptomics, proteomics, metabolomics, and metagenomics and their applications in research on CHF.},
}

@article {pmid30619215,
year = {2018},
author = {Han, M and Yang, P and Zhong, C and Ning, K},
title = {The Human Gut Virome in Hypertension.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3150},
doi = {10.3389/fmicb.2018.03150},
pmid = {30619215},
issn = {1664-302X},
abstract = {Objectives: Previous studies have reported that the gut microbiome has an important link with the development of hypertension. Though previous researches have focused on the links of gut bacteria with hypertension, little has been known about the linkage of gut viruses to hypertension and the development of hypertension, largely due to the lack of data mining tools for such investigation. In this work, we have analyzed 196 fecal metagenomic data related to hypertension aiming to profile the gut virome and link the gut virome to pre-hypertension and hypertension. Design: Here, we have applied a statistically sound method for mining of gut virome data and linking gut virome to hypertension. We characterized the viral composition and bacterial composition of 196 samples, identified the viral-type of each sample and linked gut virome to hypertension. Results: We stratified these 196 fecal samples into two viral-types and selected 32 viruses as the biomarkers for these groups. We found that viruses could have a superior resolution and discrimination power than bacteria for differentiation of healthy samples and pre-hypertension samples, as well as hypertension samples. Moreover, as to the co-occurrence networks linking viruses and bacteria, we found increasingly pervasive virus-bacteria linkages from healthy people to pre-hypertension people to hypertension patients. Conclusion: Overall, our results have shown ample indications of the link between human gut virome and hypertension, and could help provide microbial solutions toward early diagnoses of hypertension.},
}

@article {pmid30619209,
year = {2018},
author = {Suzuki, S and Nealson, KH and Ishii, S},
title = {Genomic and in-situ Transcriptomic Characterization of the Candidate Phylum NPL-UPL2 From Highly Alkaline Highly Reducing Serpentinized Groundwater.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3141},
doi = {10.3389/fmicb.2018.03141},
pmid = {30619209},
issn = {1664-302X},
abstract = {Serpentinization is a process whereby water interacts with reduced mantle rock called peridotite to produce a new suite of minerals (e.g., serpentine), a highly alkaline fluid, and hydrogen. In previous reports, we identified abundance of microbes of the candidate phylum NPL-UPA2 in a serpentinization site called The Cedars. Here, we report the first metagenome assembled genome (MAG) of the candidate phylum as well as the in-situ gene expression. The MAG of the phylum NPL-UPA2, named Unc8, is only about 1 Mbp and its biosynthetic properties suggest it should be capable of independent growth. In keeping with the highly reducing niche of Unc8, its genome encodes none of the known oxidative stress response genes including superoxide dismutases. With regard to energy metabolism, the MAG of Unc8 encodes all enzymes for Wood-Ljungdahl acetogenesis pathway, a ferredoxin:NAD+ oxidoreductase (Rnf) and electron carriers for flavin-based electron bifurcation (Etf, Hdr). Furthermore, the transcriptome of Unc8 in the waters of The Cedars showed enhanced levels of gene expression in the key enzymes of the Wood-Ljungdahl pathway [e.g., Carbon monoxide dehydrogenase /Acetyl-CoA synthase complex (CODH/ACS), Rnf, Acetyl-CoA synthetase (Acd)], which indicated that the Unc8 is an acetogen. However, the MAG of Unc8 encoded no well-known hydrogenase genes, suggesting that the energy metabolism of Unc8 might be focused on CO as the carbon and energy sources for the acetate formation. Given that CO could be supplied via abiotic reaction associated with deep subsurface serpentinization, while available CO2 would be at extremely low concentrations in this high pH environment, CO-associated metabolism could provide advantageous approach. The CODH/ACS in Unc8 is a Bacteria/Archaea hybrid type of six-subunit complex and the electron carriers, Etf and Hdr, showed the highest similarity to those in Archaea, suggesting that archaeal methanogenic energy metabolism was incorporated into the bacterial acetogenesis in NPL-UPA2. Given that serpentinization systems are viewed as potential habitats for early life, and that acetogenesis via the Wood-Ljungdahl pathway is proposed as an energy metabolism of Last Universal Common Ancestor, a phylogenetically distinct acetogen from an early earth analog site may provide important insights in primordial lithotrophs and their habitat.},
}

@article {pmid30619206,
year = {2018},
author = {Guo, M and Chen, J and Li, Q and Fu, Y and Fan, G and Ma, J and Peng, L and Zeng, L and Chen, J and Wang, Y and Lee, SM},
title = {Dynamics of Gut Microbiome in Giant Panda Cubs Reveal Transitional Microbes and Pathways in Early Life.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3138},
doi = {10.3389/fmicb.2018.03138},
pmid = {30619206},
issn = {1664-302X},
abstract = {Adult giant pandas (Ailuropoda melanoleuca) express transitional characteristics in that they consume bamboos, despite their carnivore-like digestive tracts. Their genome contains no cellulolytic enzymes; therefore, understanding the development of the giant panda gut microbiome, especially in early life, is important for decoding the rules underlying gut microbial formation, inheritance and dietary transitions. With deep metagenomic sequencing, we investigated the gut microbiomes of two newborn giant panda brothers and their parents living in Macao, China, from 2016 to 2017. Both giant panda cubs exhibited progressive increases in gut microbial richness during growth, particularly from the 6th month after birth. Enterobacteriaceae dominated the gut microbial compositions in both adult giant pandas and cubs. A total of 583 co-abundance genes (CAGs) and about 79 metagenomic species (MGS) from bacteria or viruses displayed significant changes with age. Seven genera (Shewanella, Oblitimonas, Helicobacter, Haemophilus, Aeromonas, Listeria, and Fusobacterium) showed great importance with respect to gut microbial structural determination in the nursing stage of giant panda cubs. Furthermore, 10 orthologous gene functions and 44 pathways showed significant changes with age. Of the significant pathways, 16 from Escherichia, Klebsiella, Propionibacterium, Lactobacillus, and Lactococcus displayed marked differences between parents and their cubs at birth, while 29 pathways from Escherichia, Campylobacter and Lactobacillus exhibited significant increase in cubs from 6 to 9 months of age. In addition, oxidoreductases, transferases, and hydrolases dominated the significantly changed gut microbial enzymes during the growth of giant panda cubs, while few of them were involved in cellulose degradation. The findings indicated diet-stimulated gut microbiome transitions and the important role of Enterobacteriaceae in the guts of giant panda in early life.},
}

@article {pmid30619174,
year = {2018},
author = {Sharma, A and Schmidt, M and Kiesel, B and Mahato, NK and Cralle, L and Singh, Y and Richnow, HH and Gilbert, JA and Arnold, W and Lal, R},
title = {Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3095},
doi = {10.3389/fmicb.2018.03095},
pmid = {30619174},
issn = {1664-302X},
abstract = {Hot spring-associated viruses, particularly the archaeal viruses, remain under-examined compared to bacteriophages. Previous metagenomic studies of the Manikaran hot springs in India suggested an abundance of viral DNA, which prompted us to examine the virus-host (bacterial and archaeal) interactions in sediment and microbial mat samples collected from the thermal discharges. Here, we characterize the viruses (both bacterial and archaeal) from this Himalayan hot spring using both metagenomics assembly and electron microscopy. We utilized four shotgun samples from sediment (78-98°C) and two from microbial mats (50°C) to reconstruct 65 bacteriophage genomes (24-200 kb). We also identified 59 archaeal viruses that were notably abundant across the sediment samples. Whole-genome analyses of the reconstructed bacteriophage genomes revealed greater genomic conservation in sediments (65%) compared to microbial mats (49%). However, a minimal phage genome was still maintained across both sediment and microbial mats suggesting a common origin. To complement the metagenomic data, scanning-electron and helium-ion microscopy were used to reveal diverse morphotypes of Caudovirales and archaeal viruses. The genome level annotations provide further evidence for gene-level exchange between virus and host in these hot springs, and augments our knowledgebase for bacteriophages, archaeal viruses and Clustered Regularly Interspaced Short Palindromic Repeat cassettes, which provide a critical resource for studying viromes in extreme natural environments.},
}

@article {pmid30619142,
year = {2018},
author = {Nasko, DJ and Chopyk, J and Sakowski, EG and Ferrell, BD and Polson, SW and Wommack, KE},
title = {Family A DNA Polymerase Phylogeny Uncovers Diversity and Replication Gene Organization in the Virioplankton.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3053},
doi = {10.3389/fmicb.2018.03053},
pmid = {30619142},
issn = {1664-302X},
abstract = {Shotgun metagenomics, which allows for broad sampling of viral diversity, has uncovered genes that are widely distributed among virioplankton populations and show linkages to important biological features of unknown viruses. Over 25% of known dsDNA phage carry the DNA polymerase I (polA) gene, making it one of the most widely distributed phage genes. Because of its pivotal role in DNA replication, this enzyme is linked to phage lifecycle characteristics. Previous research has suggested that a single amino acid substitution might be predictive of viral lifestyle. In this study Chesapeake Bay virioplankton were sampled by shotgun metagenomic sequencing (using long and short read technologies). More polA sequences were predicted from this single viral metagenome (virome) than from 86 globally distributed virome libraries (ca. 2,100, and 1,200, respectively). The PolA peptides predicted from the Chesapeake Bay virome clustered with 69% of PolA peptides from global viromes; thus, remarkably the Chesapeake Bay virome captured the majority of known PolA peptide diversity in viruses. This deeply sequenced virome also expanded the diversity of PolA sequences, increasing the number of PolA clusters by 44%. Contigs containing polA sequences were also used to examine relationships between phylogenetic clades of PolA and other genes within unknown viral populations. Phylogenic analysis revealed five distinct groups of phages distinguished by the amino acids at their 762 (Escherichia coli IAI39 numbering) positions and replication genes. DNA polymerase I sequences from Tyr762 and Phe762 groups were most often neighbored by ring-shaped superfamily IV helicases and ribonucleotide reductases (RNRs). The Leu762 groups had non-ring shaped helicases from superfamily II and were further distinguished by an additional helicase gene from superfamily I and the lack of any identifiable RNR genes. Moreover, we found that the inclusion of ribonucleotide reductase associated with PolA helped to further differentiate phage diversity, chiefly within lytic podovirus populations. Altogether, these data show that DNA Polymerase I is a useful marker for observing the diversity and composition of the virioplankton and may be a driving factor in the divergence of phage replication components.},
}