@article {pmid30906284,
year = {2019},
author = {Cycoń, M and Mrozik, A and Piotrowska-Seget, Z},
title = {Antibiotics in the Soil Environment-Degradation and Their Impact on Microbial Activity and Diversity.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {338},
doi = {10.3389/fmicb.2019.00338},
pmid = {30906284},
issn = {1664-302X},
abstract = {Antibiotics play a key role in the management of infectious diseases in humans, animals, livestock, and aquacultures all over the world. The release of increasing amount of antibiotics into waters and soils creates a potential threat to all microorganisms in these environments. This review addresses issues related to the fate and degradation of antibiotics in soils and the impact of antibiotics on the structural, genetic and functional diversity of microbial communities. Due to the emergence of bacterial resistance to antibiotics, which is considered a worldwide public health problem, the abundance and diversity of antibiotic resistance genes (ARGs) in soils are also discussed. When antibiotic residues enter the soil, the main processes determining their persistence are sorption to organic particles and degradation/transformation. The wide range of DT50 values for antibiotic residues in soils shows that the processes governing persistence depend on a number of different factors, e.g., physico-chemical properties of the residue, characteristics of the soil, and climatic factors (temperature, rainfall, and humidity). The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups (i.e., Gram-negative bacteria, Gram-positive bacteria, and fungi) in microbial communities. Studies using methods based on analyses of nucleic acids prove that antibiotics alter the biodiversity of microbial communities and the presence of many types of ARGs in soil are affected by agricultural and human activities. It is worth emphasizing that studies on ARGs in soil have resulted in the discovery of new genes and enzymes responsible for bacterial resistance to antibiotics. However, many ambiguous results indicate that precise estimation of the impact of antibiotics on the activity and diversity of soil microbial communities is a great challenge.},
}

@article {pmid30905871,
year = {2019},
author = {Folch-Mallol, JL and Zárate, A and Sánchez-Reyes, A and López-Lara, IM},
title = {Expression, purification, and characterization of a metagenomic thioesterase from activated sludge involved in the degradation of acylCoA-derivatives.},
journal = {Protein expression and purification},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pep.2019.03.008},
pmid = {30905871},
issn = {1096-0279},
abstract = {Metagenomic libraries are a novel and powerful approach to seek for pathways involved in xenobiotic degradation, since this technique abolishes the need for cultivating microorganisms that otherwise would be overlooked if they cannot grow on standard laboratory media and conditions. In this paper, we describe the expression, purification and characterization of a novel metagenomic thioesterase which was described to be involved in phenylacetic acid degradation (A. Sánchez-Reyes, R. Batista-García, G. Valdés-García E. Ortiz, L. Perezgasga, A. Zárate-Romero, N. Pastor, J. L. Folch-Mallol, A Family 13 thioesterase isolated from an activated sludge metagenome: insights into aromatic compounds metabolism, Proteins 85 (2017) 1222-1237). According to similarity and phylogenetic analyses, the enzyme seems to belong to an Actinobacterium. Nevertheless, after a process of denaturation and refolding, the protein expressed in E. coli was obtained in an active form. New data concerning the substrate preferences for this enzyme are presented which suggest that this thioesterase could be involved in breaking the ester bond in the CoA-linear acyl derivatives of the phenylacetic acetic pathway.},
}

@article {pmid30904192,
year = {2019},
author = {Dubois, H and van Loo, G and Wullaert, A},
title = {Nucleic Acid Induced Interferon and Inflammasome Responses in Regulating Host Defense to Gastrointestinal Viruses.},
journal = {International review of cell and molecular biology},
volume = {345},
number = {},
pages = {137-171},
doi = {10.1016/bs.ircmb.2018.08.003},
pmid = {30904192},
issn = {1937-6448},
abstract = {The gut bacterial and fungal communities residing in the gastrointestinal tract have undisputed far-reaching effects in regulating host health. In the meantime, however, metagenomic sequencing efforts are revealing enteric viruses as the most abundant dimension of the intestinal gut ecosystem, and the first gut virome-wide association studies showed that inflammatory bowel disease as well as type 1 diabetes could be linked to the presence or absence of particular viral inhabitants in the intestine. In line with the genetic component of these human diseases, mouse model studies demonstrated how beneficial functions of a resident virus can switch to detrimental inflammatory effects in a genetically predisposed host. Such viral-induced intestinal immune disturbances are also recapitulated by several gastrointestinal infectious viruses such as rotavirus and human norovirus. This wide range of viral effects on intestinal immunity emphasizes the need for understanding the innate immune responses to gastrointestinal viruses. Numerous nucleic acid sensors such as DexD/H helicases and AIM2 serve as cytosolic viral guardians to induce antiviral interferon and/or pro-inflammatory inflammasome responses. In both cases, pioneering examples are emerging in which RNA helicases cooperate with particular Nod-like receptors to trigger these cellular responses to enteric viruses. Here we summarize the reported beneficial versus detrimental effects of enteric viruses in the intestinal immune system, and we zoom in on the mechanisms through which sensing of nucleic acids from these enteric viruses trigger interferon and inflammasome responses.},
}

@article {pmid30904077,
year = {2019},
author = {Grogan, MD and Bartow-McKenney, C and Flowers, L and Knight, SAB and Uberoi, A and Grice, EA},
title = {Research Techniques Made Simple: Profiling the Skin Microbiota.},
journal = {The Journal of investigative dermatology},
volume = {139},
number = {4},
pages = {747-752.e1},
doi = {10.1016/j.jid.2019.01.024},
pmid = {30904077},
issn = {1523-1747},
abstract = {Skin is colonized by microbial communities (microbiota) that participate in immune homeostasis, development and maintenance of barrier function, and protection from pathogens. The past decade has been marked by an increased interest in the skin microbiota and its role in cutaneous health and disease, in part due to advances in next-generation sequencing platforms that enable high-throughput, culture-independent detection of bacteria, fungi, and viruses. Various approaches, including bacterial 16S ribosomal RNA gene sequencing and metagenomic shotgun sequencing, have been applied to profile microbial communities colonizing healthy skin and diseased skin including atopic dermatitis, psoriasis, and acne, among others. Here, we provide an overview of culture-dependent and -independent approaches to profiling the skin microbiota and the types of questions that may be answered by each approach. We additionally highlight important study design considerations, selection of controls, interpretation of results, and limitations and challenges.},
}

@article {pmid30903144,
year = {2019},
author = {Lannes, R and Olsson-Francis, K and Lopez, P and Bapteste, E},
title = {Carbon fixation by marine ultra-small prokaryotes.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evz050},
pmid = {30903144},
issn = {1759-6653},
abstract = {Autotrophic carbon fixation is a crucial process for sustaining life on Earth. To date, six pathways, the Calvin-Benson-Bassham cycle, the reductive tricarboxylic acid cycle, the 3-hydroxypropionate bi-cycle, the Wood-Ljungdahl pathway, the dicarboxylate/4-hydroxybutyrate cycle, and the 4-hydroxybutyrate cycle have been described. Nanoorganisms, such as members of the Candidate Phyla Radiation (CPR) bacterial superphylum and the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohalorchaeota (DPANN) archaeal superphylum, could deeply impact carbon cycling and carbon fixation in ways that are still to be determined. CPR and DPANN are ubiquitous in the environment but understudied; their gene contents are not exhaustively described, and their metabolisms are not yet fully understood. Here, the completeness of each of the above pathways were quantified and tested for the presence of all key enzymes in a diversity of nanoorganisms across the World Ocean. The novel marine ultra-small prokaryotes was demonstrated to collectively harbor the genes required for carbon fixation, in particular the 'energetically efficient' DH pathway, and HBC pathways. This contrasted with the known carbon metabolic pathways associated with CPR memebers in aquifers, where they are described as degraders (Castelle 2015 et al., 2015, Castelle et al., 2018, Anantharaman et al., 2016). Our findings offer the possibility that nanoorganisms have a broader contribution to carbon fixation and cycling than currently assumed. Furthermore, CPR and DPANN are possibly not the only nanosized prokaryotes; therefore, the discovery of new autotrophic marine nanoorganisms, by future single cell genomics is anticipated.},
}

@article {pmid30902854,
year = {2019},
author = {Youssef, NH and Farag, IF and Hahn, CR and Jarett, J and Becraft, E and Eloe-Fadrosh, E and Lightfoot, J and Bourgeois, A and Cole, T and Ferrante, S and Truelock, M and Marsh, W and Jamaleddine, M and Ricketts, S and Simpson, R and McFadden, A and Hoff, W and Ravin, NV and Sievert, S and Stepanauskas, R and Woyke, T and Elshahed, M},
title = {Genomic characterization of candidate division LCP-89 reveals an atypical cell wall structure, microcompartment production, and dual respiratory and fermentative capacities.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.00110-19},
pmid = {30902854},
issn = {1098-5336},
abstract = {Recent experimental and bioinformatic advances enable the recovery of genomes belonging to yet-uncultured microbial lineages directly from environmental samples. Here, we report on the recovery and characterization of single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) representing candidate phylum LCP-89, previously defined based on 16S rRNA gene sequences. Analysis of LCP-89 genomes recovered from Zodletone spring, an anoxic spring in Oklahoma, predicts slow-growing, rod-shaped organisms. LCP-89 genomes encode genes for cell wall lipopolysaccharide (LPS) production but lack the entire machinery for peptidoglycan biosynthesis, suggesting an atypical cell wall structure. Genomes, however, encode for S-layer homology domain-containing proteins, as well as for the biosynthesis of CMP-legionaminate, inferring the possession of an S-layer glycoprotein. A near complete chemotaxis machinery coupled to the absence of flagellar synthesis and assembly genes argue for the utilization of alternative types of motility. A strict anaerobic lifestyle is predicted, with dual respiratory (nitrite ammonification) and fermentative capacities. Predicted substrates include a wide range of sugars, sugar alcohols, and few amino acids. The capability of rhamnose metabolism is confirmed by the identification of bacterial microcompartment genes to sequester the generated toxic intermediates. Comparative genomic analysis identified differences in oxygen sensitivities, respiratory capabilities, substrate utilization preferences, and fermentation end products between LCP-89 genomes, and those belonging to its four sister phyla (Calditrichota, SM32-31, AABM5-125-24, and KSB1) within the broader FCB superphylum. Our results provide a detailed characterization of members of the candidate division LCP-89, and highlight the importance of reconciling 16S rRNA-based and genome-based phylogenies.Importance. Our understanding of the metabolic capacities, physiological preferences, and ecological roles of yet-uncultured microbial phyla is rapidly expanding. Two distinct approaches are currently being utilized for characterizing microbial communities in nature: amplicon-based 16S rRNA gene surveys for community characterization, and metagenomics/single cell genomics for detailed metabolic reconstruction. The occurrence of multiple, yet-uncultured bacterial phyla has been documented using 16S rRNA surveys, and obtaining genome representatives of these yet-uncultured lineages is critical to our understanding of the role of yet-uncultured organisms in nature. This study provides a genomics-based analysis highlighting the structural features and metabolic capacities of a yet-uncultured bacterial phylum (LCP-89) previously identified in 16S rRNA surveys for which no prior genomes have been described. Our analysis identifies several interesting structural features for members of this phylum e.g. lack of peptidoglycan biosynthetic machinery and ability to form bacterial microcompartments. Predicted metabolic capabilities include degradation of a wide range of sugars, anaerobic respiratory capacity, as well as fermentative capacities. In addition to the detailed structural and metabolic analysis provided for candidate division LCP-89, this effort represents an additional step towards a unified scheme for microbial taxonomy by reconciling 16S rRNA gene-based and genomics-based taxonomic outlines.},
}

@article {pmid30902785,
year = {2019},
author = {Kumar, R and Mishra, A and Jha, B},
title = {Bacterial community structure and functional diversity in subsurface seawater from the western coastal ecosystem of the Arabian Sea, India.},
journal = {Gene},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.gene.2019.02.099},
pmid = {30902785},
issn = {1879-0038},
abstract = {The present study revealed the spatial variability of bacteria in relation to physicochemical variations at four different locations (Diu - DIU, Veraval - VER, Porbandar - POR and Okha - OKH) along the Gujarat coast (Arabian Sea, India). The natural habitat was analyzed for temperature, salinity, pH, total dissolved solids, total organic content, total inorganic content, biological oxygen demand, conductivity and total dissolved oxygen. The lowest salinity and conductivity were observed at the VER site, whereas the highest salinity and conductivity were measured with OKH samples. In contrast, the pH was slightly alkaline at all of the sites. The VER site contained the maximum total dissolved solids (TDS), total carbon (TC), total organic carbon (TOC), and total inorganic carbon (TIC), while OKH showed the maximum dissolve oxygen (DO), biological oxygen demand (BOD), pH, temperature, conductivity, and salinity. The physicochemical characteristics showed that the Gujarat coast is alkaline and has a nutrient heterogeneous nature. Average well color development (AWCD) values, calculated using Biolog EcoPlates, showed that the microbial community from VER contained the highest metabolic activities and could metabolize all 31 substrates, followed by DIU > OKH > POR samples. In contrast, the abundance of the bacterial community, determined by qRT-PCR, was maximum in OKH samples, followed by POR > DIU > VER samples. The Shannon and Simpson indices showed that DIU, POR and OKH seawater clone libraries were more diverse. Furthermore, Chao estimator revealed the high diversity of POR and DIU clone libraries. Interestingly, DIU and OKH did not share any common operational taxonomic units (OTUs), and overall, the maximum bacterial diversity was observed with the POR seawater sample. Moreover, these observations were supported by statistical analysis, such as canonical correspondence analysis (CCA) and principal component analysis (PCA). The molecular phylogeny revealed the dominance of Proteobacteria followed by Firmicutes. Within the Proteobacteria phylum, most of the sequences were affiliated with the Gammaproteobacteria class. In total, about 726 OTUs were observed from all four sites which covers 59.79% DIU, 87.5% VER, 50% POR and 98.83% OKH of samples. This study is the first report to describe physicochemical attributes and the bacterial diversity of the coastal area of Gujarat. The study will provide useful insights about bacterial diversity, distribution, and abundance, as well as their relationships with the habitat.},
}

@article {pmid30902113,
year = {2019},
author = {Clarke, EL and Taylor, LJ and Zhao, C and Connell, A and Lee, JJ and Fett, B and Bushman, FD and Bittinger, K},
title = {Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {46},
doi = {10.1186/s40168-019-0658-x},
pmid = {30902113},
issn = {2049-2618},
support = {U01HL112712//National Heart, Lung, and Blood Institute/ ; R01HL113252//National Heart, Lung, and Blood Institute/ ; R01HL113252//National Heart, Lung, and Blood Institute/ ; 4100068710//Pennsylvania Department of Health/ ; 4100068710//Pennsylvania Department of Health/ ; 4100068710//Pennsylvania Department of Health/ ; 4100068710//Pennsylvania Department of Health/ ; P30AI045008//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND: Analysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical steps include quality control, adapter trimming, host decontamination, metagenomic classification, read assembly, and alignment to reference genomes.

RESULTS: We present a modular and user-extensible pipeline called Sunbeam that performs these steps in a consistent and reproducible fashion. It can be installed in a single step, does not require administrative access to the host computer system, and can work with most cluster computing frameworks. We also introduce Komplexity, a software tool to eliminate potentially problematic, low-complexity nucleotide sequences from metagenomic data. A unique component of the Sunbeam pipeline is an easy-to-use extension framework that enables users to add custom processing or analysis steps directly to the workflow. The pipeline and its extension framework are well documented, in routine use, and regularly updated.

CONCLUSIONS: Sunbeam provides a foundation to build more in-depth analyses and to enable comparisons in metagenomic sequencing experiments by removing problematic, low-complexity reads and standardizing post-processing and analytical steps. Sunbeam is written in Python using the Snakemake workflow management software and is freely available at github.com/sunbeam-labs/sunbeam under the GPLv3.},
}

@article {pmid30901843,
year = {2019},
author = {Cortes, L and Wopereis, H and Tartiere, A and Piquenot, J and Gouw, JW and Tims, S and Knol, J and Chelsky, D},
title = {Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome.},
journal = {International journal of molecular sciences},
volume = {20},
number = {6},
pages = {},
doi = {10.3390/ijms20061430},
pmid = {30901843},
issn = {1422-0067},
abstract = {A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.},
}

@article {pmid30782659,
year = {2019},
author = {Klein, C and Gonzalez, D and Samwel, K and Kahesa, C and Mwaiselage, J and Aluthge, N and Fernando, S and West, JT and Wood, C and Angeletti, PC},
title = {Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions.},
journal = {mBio},
volume = {10},
number = {1},
pages = {},
doi = {10.1128/mBio.02785-18},
pmid = {30782659},
issn = {2150-7511},
mesh = {Bacteria/*classification/genetics ; Cervix Uteri/*microbiology/*pathology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; HIV Infections/*complications ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; Precancerous Conditions/*epidemiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tanzania/epidemiology ; Uterine Cervical Neoplasms/*epidemiology ; },
abstract = {Nearly all cervical cancers are causally associated with human papillomavirus (HPV). The burden of HPV-associated dysplasias in sub-Saharan Africa is influenced by HIV. To investigate the role of the bacterial microbiome in cervical dysplasia, cytobrush samples were collected directly from cervical lesions of 144 Tanzanian women. The V4 hypervariable region of the 16S rRNA gene was amplified and deep sequenced. Alpha diversity metrics (Chao1, PD whole tree, and operational taxonomic unit [OTU] estimates) displayed significantly higher bacterial richness in HIV-positive patients (P = 0.01) than in HIV-negative patients. In HIV-positive patients, there was higher bacterial richness in patients with high-grade squamous intraepithelial lesions (HSIL) (P = 0.13) than those without lesions. The most abundant OTUs associated with high-grade squamous intraepithelial lesions were Mycoplasmatales, Pseudomonadales, and Staphylococcus We suggest that a chronic mycoplasma infection of the cervix may contribute to HPV-dependent dysplasia by sustained inflammatory signals.IMPORTANCE HPV is known to be the causal agent in the majority of cervical cancers. However, the role of the cervical bacterial microbiome in cervical cancer is not clear. To investigate that possibility, we collected cervical cytobrush samples from 144 Tanzanian women and performed deep sequencing of bacterial 16S rRNA genes. We found that HIV-positive patients had greater bacterial richness (P = 0.01) than HIV-negative patients. We also observed that women with high-grade squamous intraepithelial lesions (HSIL) had greater cervical bacterial diversity than women with cytologically normal cervices. Data from our precise sampling of cervical lesions leads us to propose that Mycoplasma contributes to a cervical microbiome status that promotes HPV-related cervical lesions. These results suggest a greater influence of the bacterial microbiota on the outcome of HPV infection than previously thought.},
}

Bacteria/*classification/genetics
Cervix Uteri/*microbiology/*pathology
Cluster Analysis
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Female
HIV Infections/*complications
High-Throughput Nucleotide Sequencing
Humans
Metagenomics
*Microbiota
Phylogeny
Precancerous Conditions/*epidemiology
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Tanzania/epidemiology
Uterine Cervical Neoplasms/*epidemiology

@article {pmid29167556,
year = {2018},
author = {Del Bas, JM and Guirro, M and Boqué, N and Cereto, A and Ras, R and Crescenti, A and Caimari, A and Canela, N and Arola, L},
title = {Alterations in gut microbiota associated with a cafeteria diet and the physiological consequences in the host.},
journal = {International journal of obesity (2005)},
volume = {42},
number = {4},
pages = {746-754},
pmid = {29167556},
issn = {1476-5497},
mesh = {Animals ; Diet, High-Fat/*adverse effects ; Gastrointestinal Microbiome/genetics/*physiology ; Insulin Resistance ; Male ; Metabolic Networks and Pathways/physiology ; Metabolic Syndrome/metabolism ; Metagenome/genetics/physiology ; Obesity/*metabolism ; Organ Size/physiology ; Rats ; Rats, Wistar ; },
abstract = {OBJECTIVE: Gut microbiota have been described as key factors in the pathophysiology of obesity and different components of metabolic syndrome (MetS). The cafeteria diet (CAF)-fed rat is a preclinical model that reproduces most of the alterations found in human MetS by simulating a palatable human unbalanced diet. Our objective was to assess the effects of CAF on gut microbiota and their associations with different components of MetS in Wistar rats.

METHODS: Animals were fed a standard diet or CAF for 12 weeks. A partial least square-based methodology was used to reveal associations between gut microbiota, characterized by 16S ribosomal DNA gene sequencing, and biochemical, nutritional and physiological parameters.

RESULTS: CAF feeding resulted in obesity, dyslipidemia, insulin resistance and hepatic steatosis. These changes were accompanied by a significant decrease in gut bacterial diversity, decreased Firmicutes and an increase in Actinobacteria and Proteobacteria abundances, which were concomitant with increased endotoxemia. Associations of different genera with the intake of lipids and carbohydrates were opposed from those associated with the intake of fiber. Changes in gut microbiota were also associated with the different physiological effects of CAF, mainly increased adiposity and altered levels of plasma leptin and glycerol, consistent with altered adipose tissue metabolism. Also hepatic lipid accretion was associated with changes in microbiota, highlighting the relevance of gut microbiota homeostasis in the adipose-liver axis.

CONCLUSIONS: Overall, our results suggest that CAF feeding has a profound impact on the gut microbiome and, in turn, that these changes may be associated with important features of MetS.},
}

Animals
Diet, High-Fat/*adverse effects
Gastrointestinal Microbiome/genetics/*physiology
Insulin Resistance
Male
Metabolic Networks and Pathways/physiology
Metabolic Syndrome/metabolism
Metagenome/genetics/physiology
Obesity/*metabolism
Organ Size/physiology
Rats
Rats, Wistar

@article {pmid30901643,
year = {2019},
author = {Appolinario, LR and Tschoeke, D and Paixão, RVS and Venas, T and Calegario, G and Leomil, L and Silva, BS and Thompson, CC and Thompson, FL},
title = {Metagenomics sheds light on the metabolic repertoire of oil-biodegrading microbes of the South Atlantic Ocean.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {249},
number = {},
pages = {295-304},
doi = {10.1016/j.envpol.2019.03.007},
pmid = {30901643},
issn = {1873-6424},
abstract = {Unplanned oil spills during offshore oil production are a serious problem for the industry and the marine environment. Here we assess the biodegradation potential of marine microorganisms from three water depths in the Campos Basin (South Atlantic Ocean): (i) 5 m (surface), (ii) ∼80 m (chlorophyll maximum layer), and (iii) ∼1200 m (near the bottom). After incubating seawater samples with or without crude oil for 52 days, we used metagenomics and classic microbiology techniques to analyze microbial abundance and diversity, and measured physical-chemical parameters to better understand biodegradation processes. We observed increased microbial abundance and concomitant decreases in dissolved oxygen and hydrocarbon concentrations, indicating oil biodegradation in the three water depths treatments within approximately 27 days. An increase in metagenomic sequences of oil-degrading archaea, fungi, and bacteria (Alcanivorax, Alteromonas, Colwellia, Marinobacter, and Pseudomonas) accompanied by a significant increase in metagenomic sequences involved in the degradation of aromatic compounds indicate that crude oil promotes the growth of microorganisms with oil degradation potential. The abundance of genes involved in biodegrading benzene, toluene, ethylbenzene, xylene, alkanes, and poly-aromatic hydrocarbons peaked approximately 3 days after oil addition. All 12 novel metagenome-assembled genomes contained genes involved in hydrocarbon degradation, indicating the oil-degrading potential of planktonic microbes in the Campos Basin.},
}

@article {pmid30899254,
year = {2019},
author = {Willms, IM and Kamran, A and Aßmann, NF and Krone, D and Bolz, SH and Fiedler, F and Nacke, H},
title = {Discovery of Novel Antibiotic Resistance Determinants in Forest and Grassland Soil Metagenomes.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {460},
doi = {10.3389/fmicb.2019.00460},
pmid = {30899254},
issn = {1664-302X},
abstract = {Soil represents a significant reservoir of antibiotic resistance genes (ARGs), which can potentially spread across distinct ecosystems and be acquired by pathogens threatening human as well as animal health. Currently, information on the identity and diversity of these genes, enabling anticipation of possible future resistance development in clinical environments and the livestock sector, is lacking. In this study, we applied functional metagenomics to discover novel sulfonamide as well as tetracycline resistance genes in soils derived from forest and grassland. Screening of soil metagenomic libraries revealed a total of eight so far unknown ARGs. The recovered genes originate from phylogenetically diverse soil bacteria (e.g., Actinobacteria, Chloroflexi, or Proteobacteria) and encode proteins with a minimum identity of 46% to other antibiotic resistance determinants. In particular forest soil ecosystems have so far been neglected in studies focusing on antibiotic resistance. Here, we detected for the first time non-mobile dihydropteroate synthase (DHPS) genes conferring resistance to sulfonamides in forest soil with no history of exposure to these synthetic drugs. In total, three sulfonamide resistant DHPSs, differing in taxonomic origin, were discovered in beech or pine forest soil. This indicates that sulfonamide resistance naturally occurs in forest-resident soil bacterial communities. Besides forest soil-derived sulfonamide resistance proteins, we also identified a DHPS affiliated to Chloroflexi in grassland soil. This enzyme and the other recovered DHPSs confer reduced susceptibility toward sulfamethazine, which is widely used in food animal production. With respect to tetracycline resistance, four efflux proteins affiliated to the major facilitator superfamily (MFS) were identified. Noteworthy, one of these proteins also conferred reduced susceptibility toward lincomycin.},
}

@article {pmid30899180,
year = {2019},
author = {Hashem, A and Kumar, A and Al-Dbass, AM and Alqarawi, AA and Al-Arjani, AF and Singh, G and Farooq, M and Abd Allah, EF},
title = {Arbuscular mycorrhizal fungi and biochar improves drought tolerance in chickpea.},
journal = {Saudi journal of biological sciences},
volume = {26},
number = {3},
pages = {614-624},
doi = {10.1016/j.sjbs.2018.11.005},
pmid = {30899180},
issn = {1319-562X},
abstract = {Arbuscular mycorrhizal fungi (AMF) inoculation and biochar amendment has been reported to improve growth of several crop plants however their role in stress amelioration individually as well as in combination has not been worked out. This experiment was conducted to evaluate the application of AMF and biochar on the performance of chickpea under drought stress. The treatments included the individual as well as combined treatment of AMF and biochar to drought stressed and normal chickpea plants. Plants inoculation improved growth in terms of shoot and root length, leaf area and number of branches which was observed to show a steep decline due to drought stress. Drought declined the AMF colonization potential though biochar amendment ameliorated the negative effects of drought significantly by improving the spore population, number of mycelium, vesicle and arbuscules and the percentage of colonization as well. Increased chlorophyll synthesis in biochar and AMF treated plants was obvious, which lead to significant enhancement in the net photosynthetic efficiency. Drought stress also declined the relative water content (RWC) and membrane stability index (MSI), while treatment of biochar and AMF either individually or in combination mitigated the deleterious effects to considerable extent and caused a significant enhancement in RWC and MSI under normal conditions. Amendments with biochar and AMF inoculation increased the nitrogen fixation attributes including the number and weight of nodules, leghemoglobin content and activity of nitrate reductase enzyme leading to greater uptake and assimilation of nitrogen in them when compared to drought stressed plants. Drought stressed chickpea plants exhibited considerable reduction in uptake of nitrogen and phosphorous which was ameliorated by biochar and AMF treatments. It could be suggested that increase in growth and physiological attributes in chickpea due to biochar amendments and AMF inoculation under drought stress were plausibly due to their involvement in nitrogen and phosphorous uptake, chlorophyll synthesis and photosynthesis.},
}

@article {pmid30899033,
year = {2019},
author = {Reddel, S and Del Chierico, F and Quagliariello, A and Giancristoforo, S and Vernocchi, P and Russo, A and Fiocchi, A and Rossi, P and Putignani, L and El Hachem, M},
title = {Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {4996},
doi = {10.1038/s41598-019-41149-6},
pmid = {30899033},
issn = {2045-2322},
support = {201502P003534//Ministero della Salute (Ministry of Health, Italy)/ ; 201602P00370//Ministero della Salute (Ministry of Health, Italy)/ ; 201503X003570//Ministero della Salute (Ministry of Health, Italy)/ ; },
abstract = {Atopic dermatitis (AD) has been hypothesised to be associated with gut microbiota (GM) composition. We performed a comparative study of the GM profile of 19 AD children and 18 healthy individuals aimed at identifying bacterial biomarkers associated with the disease. The effect of probiotic intake (Bifidobacterium breve plus Lactobacillus salivarius) on the modulation of GM and the probiotic persistence in the GM were also evaluated. Faecal samples were analysed by real-time PCR and 16S rRNA targeted metagenomics. Although the probiotics, chosen for this study, did not shape the entire GM profile, we observed the ability of these species to pass through the gastrointestinal tract and to persist (only B. breve) in the GM. Moreover, the GM of patients compared to CTRLs showed a dysbiotic status characterised by an increase of Faecalibacterium, Oscillospira, Bacteroides, Parabacteroides and Sutterella and a reduction of short-chain fatty acid (SCFA)-producing bacteria (i.e., Bifidobacterium, Blautia, Coprococcus, Eubacterium and Propionibacterium). Taken togheter these results show an alteration in AD microbiota composition with the depletion or absence of some species, opening the way to future probiotic intervention studies.},
}

@article {pmid30898140,
year = {2019},
author = {Che, Y and Xia, Y and Liu, L and Li, AD and Yang, Y and Zhang, T},
title = {Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {44},
doi = {10.1186/s40168-019-0663-0},
pmid = {30898140},
issn = {2049-2618},
abstract = {BACKGROUND: Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown.

RESULTS: In this study, we combined Oxford Nanopore and Illumina metagenomics sequencing to comprehensively uncover the resistome context of influent, activated sludge, and effluent of three WWTPs and simultaneously track the hosts of the ARGs. The results showed that most of the ARGs detected in all compartments of the WWTPs were carried by plasmids. Transposons and integrons also showed higher prevalence on plasmids than on the ARG-carrying chromosome. Notably, integrative and conjugative elements (ICEs) carrying five types of ARGs were detected, and they may play an important role in facilitating the transfer of ARGs, particularly for tetracycline and macrolide-lincosamide-streptogramin (MLS). A broad spectrum of ARGs carried by plasmids (29 subtypes) and ICEs (4 subtypes) was persistent across the WWTPs. Host tracking showed a variety of antibiotic-resistant bacteria in the effluent, suggesting the high potential for their dissemination into receiving environments. Importantly, phenotype-genotype analysis confirmed the significant role of conjugative plasmids in facilitating the survival and persistence of multidrug-resistant bacteria in the WWTPs. At last, the consistency in the quantitative results for major ARGs types revealed by Nanopore and Illumina sequencing platforms demonstrated the feasibility of Nanopore sequencing for resistome quantification.

CONCLUSION: Overall, these findings substantially expand our current knowledge of resistome in WWTPs, and help establish a baseline analysis framework to study ARGs in the environment.},
}

@article {pmid30781951,
year = {2019},
author = {Vuoristo, KS and Fredriksen, L and Oftebro, M and Arntzen, MØ and Aarstad, OA and Stokke, R and Steen, IH and Hansen, LD and Schüller, RB and Aachmann, FL and Horn, SJ and Eijsink, VGH},
title = {Production, Characterization, and Application of an Alginate Lyase, AMOR_PL7A, from Hot Vents in the Arctic Mid-Ocean Ridge.},
journal = {Journal of agricultural and food chemistry},
volume = {67},
number = {10},
pages = {2936-2945},
doi = {10.1021/acs.jafc.8b07190},
pmid = {30781951},
issn = {1520-5118},
mesh = {Arctic Regions ; Bacteria/classification/*enzymology/genetics/isolation & purification ; Bacterial Proteins/*chemistry/genetics/metabolism ; Biocatalysis ; Enzyme Stability ; Hydrogen-Ion Concentration ; Hydrothermal Vents/chemistry/*microbiology ; Kinetics ; Metagenomics ; Phaeophyta/chemistry ; Phylogeny ; Polysaccharide-Lyases/*chemistry/genetics/metabolism ; Polysaccharides/chemistry ; Seaweed/chemistry ; Substrate Specificity ; Temperature ; },
abstract = {Enzymatic depolymerization of seaweed polysaccharides is gaining interest for the production of functional oligosaccharides and fermentable sugars. We describe a thermostable alginate lyase belonging to Polysaccharide Lyase family 7 (PL7), which can be used to degrade brown seaweed, Saccharina latissima, at conditions also suitable for a commercial cellulase cocktail (Cellic CTec2). This enzyme, AMOR_PL7A, is a β-d-mannuronate specific (EC 4.2.2.3) endoacting alginate lyase, which degrades alginate and poly mannuronate within a broad range of pH, temperature and salinity. At 65 °C and pH 6.0, its Km and kcat values for sodium alginate are 0.51 ± 0.09 mg/mL and 7.8 ± 0.3 s-1 respectively. Degradation of seaweed with blends of Cellic CTec2 and AMOR_PL7A at 55 °C in seawater showed that the lyase efficiently reduces viscosity and increases glucose solublization. Thus, AMOR_PL7A may be useful in development of efficient protocols for enzymatic seaweed processing.},
}

Arctic Regions
Bacteria/classification/*enzymology/genetics/isolation & purification
Bacterial Proteins/*chemistry/genetics/metabolism
Biocatalysis
Enzyme Stability
Hydrogen-Ion Concentration
Hydrothermal Vents/chemistry/*microbiology
Kinetics
Metagenomics
Phaeophyta/chemistry
Phylogeny
Polysaccharide-Lyases/*chemistry/genetics/metabolism
Polysaccharides/chemistry
Seaweed/chemistry
Substrate Specificity
Temperature

@article {pmid30289885,
year = {2018},
author = {Callister, SJ and McCue, LA and Boaro, AA and LaMarche, B and White, RA and Brown, JM and Ahring, BK},
title = {Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0204831},
pmid = {30289885},
issn = {1932-6203},
mesh = {Acetates/chemistry ; Anaerobiosis ; Animals ; Bacteria/*classification/genetics/isolation & purification/metabolism ; Bacterial Proteins/*analysis ; Bioreactors/*microbiology ; Caproates/chemistry ; Cattle ; Cellulose ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fermentation ; Metabolomics ; Metagenomics/methods ; Propionates/chemistry ; Proteomics/methods ; RNA, Ribosomal, 16S/*genetics ; Rumen/microbiology ; },
abstract = {Proteins, metabolites, and 16S rRNA measurements were used to examine the community structure and functional relationships within a cellulose degrading anaerobic bioreactor. The bioreactor was seeded with bovine rumen fluid and operated with a 4 day hydraulic retention time on cellulose (avicel) as sole carbon and energy source. The reactor performance and microbial community structure was monitored during the establishment of the cellulose-degrading community. After stable operation was established in the bioreactor, the mixing intensity was increased in order to investigate the effect of a physical disruption of the microbial community structure. Finally, the original conditions were re-established to understand the stability of the microbial community after a perturbation. All factors measured were found to be inter-correlated during these three distinct phases of operation (establishment, perturbation and re-establishment). In particular, the return of community structure and function to pre-perturbed conditions suggests that propionate fermentation and acetate utilization were the explanatory factors for community establishment and re-establishment.},
}

Acetates/chemistry
Anaerobiosis
Animals
Bacteria/*classification/genetics/isolation & purification/metabolism
Bacterial Proteins/*analysis
Bioreactors/*microbiology
Caproates/chemistry
Cattle
Cellulose
DNA, Bacterial/genetics
DNA, Ribosomal/genetics
Fermentation
Metabolomics
Metagenomics/methods
Propionates/chemistry
Proteomics/methods
RNA, Ribosomal, 16S/*genetics
Rumen/microbiology

@article {pmid30895843,
year = {2019},
author = {Hadjadj, L and Baron, SA and Diene, SM and Rolain, JM},
title = {How to discover new antibiotic resistance genes?.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/14737159.2019.1592678},
pmid = {30895843},
issn = {1744-8352},
abstract = {INTRODUCTION: Antibiotic resistance (AR) is a worldwide concern and the description of AR have been discovered mainly because of their implications in human medicine. Since the recent burden of whole-genome sequencing of microorganisms, the number of new AR genes (ARGs) have dramatically increased over the last decade. Areas covered: In this review, we will describe the different methods that could be used to characterize new ARGs using classic or innovative methods. First, we will focus on the biochemical methods, then we will develop on molecular methods, next-generation sequencing and bioinformatics approaches. The use of various methods, including cloning, mutagenesis, transposon mutagenesis, functional genomics, whole genome sequencing, metagenomic and functional metagenomics will be reviewed here, outlining the advantages and drawbacks of each method. Bioinformatics softwares used for resistome analysis and protein modeling will be also described. Expert opinion: Biological experiments and bioinformatics analysis are complementary. Nowadays, the ARGs described only account for the tip of the iceberg of all existing resistance mechanisms. The multiplication of the ecosystems studied allows us to find a large reservoir of AR mechanisms. Furthermore, the adaptation ability of bacteria facing new antibiotics promises a constant discovery of new AR mechanisms.},
}

@article {pmid30895406,
year = {2019},
author = {Nguyen, VD and Nguyen, TT and Pham, TT and Packianather, M and Le, CH},
title = {Molecular screening and genetic diversity analysis of anticancer Azurin-encoding and Azurin-like genes in human gut microbiome deduced through cultivation-dependent and cultivation-independent studies.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10123-019-00070-8},
pmid = {30895406},
issn = {1618-1905},
support = {106-YS.04-2014.40//National Foundation for Science and Technology Development/ ; },
abstract = {Azurin, a bacteriocin produced by a human gut bacterium Pseudomonas aeruginosa, can reveal selectively cytotoxic and induce apoptosis in cancer cells. After overcoming two phase I trials, a functional region of Azurin called p28 has been approved as a drug for the treatment of brain tumor glioma by FDA. The present study aims to improve a screening procedure and assess genetic diversity of Azurin genes in P. aeruginosa and Azurin-like genes in the gut microbiome of a specific population in Vietnam and global populations. Firstly, both cultivation-dependent and cultivation-independent techniques based on genomic and metagenomic DNAs extracted from fecal samples of the healthy specific population were performed and optimized to detect Azurin genes. Secondly, the Azurin gene sequences were analyzed and compared with global populations by using bioinformatics tools. Finally, the screening procedure improved from the first step was applied for screening Azurin-like genes, followed by the protein synthesis and NCI in vitro screening for anticancer activity. As a result, this study has successfully optimized the annealing temperatures to amplify DNAs for screening Azurin genes and applying to Azurin-like genes from human gut microbiota. The novelty of this study is the first of its kind to classify Azurin genes into five different genotypes at a global scale and confirm the potential anticancer activity of three Azurin-like synthetic proteins (Cnazu1, Dlazu11, and Ruazu12). The results contribute to the procedure development applied for screening anticancer proteins from human microbiome and a comprehensive understanding of their therapeutic response at a genetic level.},
}

@article {pmid30894435,
year = {2019},
author = {Majta, J and Odrzywolek, K and Milanovic, B and Hubar, V and Wrobel, S and Strycharz-Angrecka, E and Wojciechowski, S and Milanowska, K},
title = {Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population.},
journal = {mSphere},
volume = {4},
number = {2},
pages = {},
doi = {10.1128/mSphereDirect.00152-19},
pmid = {30894435},
issn = {2379-5042},
abstract = {A variety of autoimmune and allergy events are becoming increasingly common, especially in Western countries. Some pieces of research link such conditions with the composition of microbiota during infancy. In this period, the predominant form of nutrition for gut microbiota is oligosaccharides from human milk (HMO). A number of gut-colonizing strains, such as Bifidobacterium and Bacteroides, are able to utilize HMO, but only some Bifidobacterium strains have evolved to digest the specific composition of human oligosaccharides. Differences in the proportions of the two genera that are able to utilize HMO have already been associated with the frequency of allergies and autoimmune diseases in the Finnish and the Russian populations. Our results show that differences in terms of the taxonomic annotation do not explain the reason for the differences in the Bifidobacterium/Bacteroides ratio between the Finnish and the Russian populations. In this paper, we present the results of function-level analysis. Unlike the typical workflow for gene abundance analysis, BiomeScout technology explains the differences in the Bifidobacterium/Bacteroides ratio. Our research shows the differences in the abundances of the two enzymes that are crucial for the utilization of short type 1 oligosaccharides.IMPORTANCE Knowing the limitations of taxonomy-based research, there is an emerging need for the development of higher-resolution techniques. The significance of this research is demonstrated by the novel method used for the analysis of function-level metagenomes. BiomeScout-the presented technology-utilizes proprietary algorithms for the detection of differences between functionalities present in metagenomic samples.},
}

@article {pmid30894139,
year = {2019},
author = {Szafrańska, AK and Junker, V and Steglich, M and Nübel, U},
title = {Rapid cell division of Staphylococcus aureus during colonization of the human nose.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {229},
doi = {10.1186/s12864-019-5604-6},
pmid = {30894139},
issn = {1471-2164},
support = {643476//Horizon 2020 Framework Programme/ ; },
abstract = {BACKGROUND: Staphylococcus aureus is an important opportunistic pathogen and a commensal bacterium, thriving in the nasal cavities of 20% of the human population. Little is known about the dynamics of asymptomatic colonization and the occasional transition to infectious disease.

RESULTS: In this study, we inferred that S. aureus cells replicate every one to three hours on average while colonizing the human nose, based on two independent lines of genomic evidence. First, we collected nasal swab samples from human subjects, extracted and sequenced metagenomic DNA, and analyzed the distribution of sequencing coverage along the staphylococcal chromosome. Calibration of this data by comparison to a laboratory culture enabled measuring S. aureus cell division rates in nasal samples. Second, we applied mutation accumulation experiments paired with genome sequencing to measure spontaneous mutation rates at a genome scale. Relating these mutation rates to annual evolutionary rates confirmed that nasal S. aureus continuously pass several thousand cell divisions per year when averaged over large, globally distributed populations and over many years, corresponding to generation times of less than two hours.

CONCLUSIONS: The cell division rates we determined were higher than the fastest documented rates during fulminant disease progression (in a mouse model of systemic infection) and much higher than those previously measured in expectorated sputum from cystic fibrosis patients. This paper supplies absolute in-vivo generation times for an important bacterial commensal, indicating that colonization of the human upper respiratory tract is characterized by a highly dynamic equilibrium between bacterial growth and removal.},
}

@article {pmid30894059,
year = {2019},
author = {Bjørkhaug, ST and Aanes, H and Neupane, SP and Bramness, JG and Malvik, S and Henriksen, C and Skar, V and Medhus, AW and Valeur, J},
title = {Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/19490976.2019.1580097},
pmid = {30894059},
issn = {1949-0984},
abstract = {Excessive alcohol intake can alter the gut microbiota, which may underlie the pathophysiology of alcohol-related diseases. We examined gut microbiota composition and functions in patients with alcohol overconsumption for >10 years, compared to a control group of patients with a history of no or low alcohol intake. Faecal microbiota composition was assessed by 16S rRNA sequencing. Gut microbiota functions were evaluated by quantification of short-chain fatty acids (SCFAs) and predictive metagenome profiling (PICRUSt). Twenty-four patients, mean age 64.8 years (19 males), with alcohol overconsumption, and 18 control patients, mean age 58.2 years (14 males) were included. The two groups were comparable regarding basic clinical variables. Nutritional assessment revealed lower total score on the screening tool Mini Nutritional Assessment, lower muscle mass as assessed by handgrip strength, and lower plasma vitamin C levels in the alcohol overconsumption group. Bacteria from phylum Proteobacteria were found in higher relative abundance, while bacteria from genus Faecalibacterium were found in lower relative abundance in the group of alcohol overconsumers. The group also had higher levels of the genera Sutterella, Holdemania and Clostridium, and lower concentration and percentage of butyric acid. When applying PICRUSt to predict the metagenomic composition, we found that genes related to invasion of epithelial cells were more common in the group of alcohol overconsumers. We conclude that gut microbiota composition and functions in patients with alcohol overconsumption differ from patients with low consumption of alcohol, and seem to be skewed into a putative pro-inflammatory direction.},
}

@article {pmid30893890,
year = {2019},
author = {Tatsika, S and Karamanoli, K and Karayanni, H and Genitsaris, S},
title = {Metagenomic Characterization of Bacterial Communities on Ready-to-Eat Vegetables and Effects of Household Washing on their Diversity and Composition.},
journal = {Pathogens (Basel, Switzerland)},
volume = {8},
number = {1},
pages = {},
doi = {10.3390/pathogens8010037},
pmid = {30893890},
issn = {2076-0817},
abstract = {Ready-to-eat (RTE) leafy salad vegetables are considered foods that can be consumed immediately at the point of sale without further treatment. The aim of the study was to investigate the bacterial community composition of RTE salads at the point of consumption and the changes in bacterial diversity and composition associated with different household washing treatments. The bacterial microbiomes of rocket and spinach leaves were examined by means of 16S rRNA gene high-throughput sequencing. Overall, 886 Operational Taxonomic Units (OTUs) were detected in the salads' leaves. Proteobacteria was the most diverse high-level taxonomic group followed by Bacteroidetes and Firmicutes. Although they were processed at the same production facilities, rocket showed different bacterial community composition than spinach salads, mainly attributed to the different contributions of Proteobacteria and Bacteroidetes to the total OTU number. The tested household decontamination treatments proved inefficient in changing the bacterial community composition in both RTE salads. Furthermore, storage duration of the salads at refrigeration temperatures affected the microbiome, by decreasing the bacterial richness and promoting the dominance of psychrotropic bacteria. Finally, both salads were found to be a reservoir of opportunistic human pathogens, while washing methods usually applied at home proved to be inefficient in their removal.},
}

@article {pmid30009332,
year = {2019},
author = {Bag, S and Ghosh, TS and Banerjee, S and Mehta, O and Verma, J and Dayal, M and Desigamani, A and Kumar, P and Saha, B and Kedia, S and Ahuja, V and Ramamurthy, T and Das, B},
title = {Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota.},
journal = {Microbial ecology},
volume = {77},
number = {2},
pages = {546-557},
doi = {10.1007/s00248-018-1228-7},
pmid = {30009332},
issn = {1432-184X},
support = {BT/MB/THSTI/HMC-SFC/2011//Department of Biotechnology , Ministry of Science and Technology/ ; },
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/isolation & purification ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Genotype ; Humans ; Interspersed Repetitive Sequences/genetics ; Metagenome/genetics ; Microbial Sensitivity Tests ; *Phenotype ; *Symbiosis ; Transformation, Genetic/genetics ; Vibrio cholerae/genetics ; Whole Genome Sequencing ; },
abstract = {Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections. Resistant phenotype is very common in enteric bacteria. The most common mechanisms of AMR are enzymatic modifications to the antimicrobials or their target molecules. In enteric bacteria, most of the resistance traits are acquired by horizontal gene transfer from closely or distantly related bacterial population. AMR traits are generally linked with mobile genetic elements (MGEs) and could rapidly disseminate to the bacterial species through horizontal gene transfer (HGT) from a pool of resistance genes. Although prevalence of AMR genes among pathogenic bacteria is widely studied in the interest of infectious disease management, the resistance profile and the genetic traits that encode resistance to the commensal microbiota residing in the gut of healthy humans are not well-studied. In the present study, we have characterized AMR phenotypes and genotypes of five dominant commensal enteric bacteria isolated from the gut of healthy Indians. Our study revealed that like pathogenic bacteria, enteric commensals are also multidrug-resistant. The genes encoding antibiotic resistance are physically linked with MGEs and could disseminate vertically to the progeny and laterally to the distantly related microbial species. Consequently, the AMR genes present in the chromosome of commensal gut bacteria could be a potential source of resistance functions for other enteric pathogens.},
}

Anti-Bacterial Agents/pharmacology
Bacteria/drug effects/genetics/isolation & purification
DNA Transposable Elements/genetics
Drug Resistance, Bacterial/*genetics
Feces/microbiology
Gastrointestinal Microbiome/drug effects/*genetics
Gene Transfer, Horizontal/genetics
Genes, Bacterial/*genetics
Genome, Bacterial
Genotype
Humans
Interspersed Repetitive Sequences/genetics
Metagenome/genetics
Microbial Sensitivity Tests
*Phenotype
*Symbiosis
Transformation, Genetic/genetics
Vibrio cholerae/genetics
Whole Genome Sequencing

@article {pmid29177936,
year = {2018},
author = {Reid, G},
title = {Is bacterial vaginosis a disease?.},
journal = {Applied microbiology and biotechnology},
volume = {102},
number = {2},
pages = {553-558},
doi = {10.1007/s00253-017-8659-9},
pmid = {29177936},
issn = {1432-0614},
mesh = {*Disease Management ; *Dysbiosis ; Female ; Humans ; Metagenome ; Microbiota ; Probiotics/therapeutic use ; Vagina/*microbiology/physiopathology ; Vaginosis, Bacterial/diagnosis/*physiopathology/prevention & control/therapy ; },
abstract = {Bacterial vaginosis (BV) has been described as a disease, a disorder, a vaginal inflammation, an infection, a microbial dysbiosis, a condition, and in some women, a normal situation. In order to fit the definition of a disease, BV would have to be a disorder of function that produces specific signs or symptoms or affects the vagina in an aberrant way. Yet, there is little consistency in patients reporting signs and symptoms when BV is diagnosed, nor the appearance of aberrations to the vagina. If BV is not a disease, there are implications for its management and coverage of treatment costs, and for the conclusions drawn in a multitude of previous studies. It is time for BV to be redefined and for the various subsets to be given a separate terminology with specific methods of diagnosis and appropriate treatment and preventive strategies.},
}

*Disease Management
*Dysbiosis
Female
Humans
Metagenome
Microbiota
Probiotics/therapeutic use
Vagina/*microbiology/physiopathology
Vaginosis, Bacterial/diagnosis/*physiopathology/prevention & control/therapy

@article {pmid28827587,
year = {2017},
author = {Kinross, J and Mirnezami, R and Alexander, J and Brown, R and Scott, A and Galea, D and Veselkov, K and Goldin, R and Darzi, A and Nicholson, J and Marchesi, JR},
title = {A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8979},
pmid = {28827587},
issn = {2045-2322},
mesh = {Cluster Analysis ; Colorectal Neoplasms/*microbiology/*pathology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*chemistry/*microbiology ; Magnetic Resonance Spectroscopy ; *Metabolome ; Metabolomics ; Metagenomics ; Microbiota ; Phylogeny ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Colon cancer induces a state of mucosal dysbiosis with associated niche specific changes in the gut microbiota. However, the key metabolic functions of these bacteria remain unclear. We performed a prospective observational study in patients undergoing elective surgery for colon cancer without mechanical bowel preparation (n = 18). Using 16 S rRNA gene sequencing we demonstrated that microbiota ecology appears to be cancer stage-specific and strongly associated with histological features of poor prognosis. Fusobacteria (p < 0.007) and ε- Proteobacteria (p < 0.01) were enriched on tumour when compared to adjacent normal mucosal tissue, and fusobacteria and β-Proteobacteria levels increased with advancing cancer stage (p = 0.014 and 0.002 respecitvely). Metabonomic analysis using 1H Magic Angle Spinning Nuclear Magnetic Resonsance (MAS-NMR) spectroscopy, demonstrated increased abundance of taurine, isoglutamine, choline, lactate, phenylalanine and tyrosine and decreased levels of lipids and triglycerides in tumour relative to adjacent healthy tissue. Network analysis revealed that bacteria associated with poor prognostic features were not responsible for the modification of the cancer mucosal metabonome. Thus the colon cancer mucosal microbiome evolves with cancer stage to meet the demands of cancer metabolism. Passenger microbiota may play a role in the maintenance of cancer mucosal metabolic homeostasis but these metabolic functions may not be stage specific.},
}

Cluster Analysis
Colorectal Neoplasms/*microbiology/*pathology
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
*Gastrointestinal Microbiome
Humans
Intestinal Mucosa/*chemistry/*microbiology
Magnetic Resonance Spectroscopy
*Metabolome
Metabolomics
Metagenomics
Microbiota
Phylogeny
Prospective Studies
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid30891366,
year = {2019},
author = {Wainaina, JM and Ateka, E and Makori, T and Kehoe, MA and Boykin, LM},
title = {A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6465},
doi = {10.7717/peerj.6465},
pmid = {30891366},
issn = {2167-8359},
abstract = {Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I-III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV and PVBV indicate that these viruses have likely been underreported due to the unavailability of diagnostic tools.},
}

@article {pmid30891034,
year = {2019},
author = {Bello-Gil, D and Audebert, C and Olivera-Ardid, S and Pérez-Cruz, M and Even, G and Khasbiullina, N and Gantois, N and Shilova, N and Merlin, S and Costa, C and Bovin, N and Mañez, R},
title = {The Formation of Glycan-Specific Natural Antibodies Repertoire in GalT-KO Mice Is Determined by Gut Microbiota.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {342},
doi = {10.3389/fimmu.2019.00342},
pmid = {30891034},
issn = {1664-3224},
abstract = {Gut commensal bacteria are known to have a significant role in regulating the innate and adaptive immune homeostasis. Alterations in the intestinal microbial composition have been associated with several disease states, including autoimmune and inflammatory conditions. However, it is not entirely clear how commensal gut microbiota modulate and contribute to the systemic immunity, and whether circulating elements of the host immune system could regulate the microbiome. Thus, we have studied the diversity and abundance of specific taxons in the gut microbiota of inbred GalT-KO mice during 7 months of animal life by metagenetic high-throughput sequencing (16S rRNA gene, variable regions V3-V5). The repertoire of glycan-specific natural antibodies, obtained by printed glycan array technology, was then associated with the microbial diversity for each animal by metagenome-wide association studies (MWAS). Our data show that the orders clostridiales (most abundant), bacteriodales, lactobacillales, and deferribacterales may be associated with the development of the final repertoire of natural anti-glycan antibodies in GalT-KO mice. The main changes in microbiota diversity (month-2 and month-3) were related to important changes in levels and repertoire of natural anti-glycan antibodies in these mice. Additionally, significant positive and negative associations were found between the gut microbiota and the pattern of specific anti-glycan antibodies. Regarding individual features, the gut microbiota and the corresponding repertoire of natural anti-glycan antibodies showed differences among the examined animals. We also found redundancy in different taxa associated with the development of specific anti-glycan antibodies. Differences in microbial diversity did not, therefore, necessarily influence the overall functional output of the gut microbiome of GalT-KO mice. In summary, the repertoire of natural anti-carbohydrate antibodies may be partially determined by the continuous antigenic stimulation produced by the gut bacterial population of each GalT-KO mouse. Small differences in gut microbiota diversity could determine different repertoire and levels of natural anti-glycan antibodies and consequently might induce different immune responses to pathogens or other potential threats.},
}

@article {pmid30890906,
year = {2019},
author = {Hewel, C and Kaiser, J and Wierczeiko, A and Linke, J and Reinhardt, C and Endres, K and Gerber, S},
title = {Common miRNA Patterns of Alzheimer's Disease and Parkinson's Disease and Their Putative Impact on Commensal Gut Microbiota.},
journal = {Frontiers in neuroscience},
volume = {13},
number = {},
pages = {113},
doi = {10.3389/fnins.2019.00113},
pmid = {30890906},
issn = {1662-4548},
abstract = {With the rise of Next-Generation-Sequencing (NGS) methods, Micro-RNAs (miRNAs) have achieved an important position in the research landscape and have been found to present valuable diagnostic tools in various diseases such as multiple sclerosis or lung cancer. There is also emerging evidence that miRNAs play an important role in the pathogenesis of neurodegenerative diseases such as Alzheimer's disease (AD) or Parkinson's disease (PD). Apparently, these diseases come along with changes in miRNA expression patterns which led to attempts from researchers to use these small RNA species from several body fluids for a better diagnosis and in order to observe disease progression. Additionally, it became evident that microbial commensals might play an important role for pathology development and were shown to have a significantly different composition in patients suffering from neurodegeneration compared with healthy controls. As it could recently be shown that secreted miRNAs are able to enter microbial organisms, it is conceivable that the host's miRNA might affect the gut microbial ecosystem. As such, miRNAs may inherit a central role in shaping the "diseased microbiome" and thereby mutually act on the characteristics of these neurodegenerative diseases. We have therefore (1) compiled a list of miRNAs known to be associated with AD and/or PD, (2) performed an in silico target screen for binding sites of these miRNA on human gut metagenome sequences and (3) evaluated the hit list for interesting matches potentially relevant to the etiology of AD and or PD. The examination of protein identifiers connected to bacterial secretion system, lipopolysaccharide biosynthesis and biofilm formation revealed an overlap of 37 bacterial proteins that were targeted by human miRNAs. The identified links of miRNAs to the biological processes of bacteria connected to AD and PD have yet to be validated via in vivo experiments. However, our results show a promising new approach for understanding aspects of these neurodegenerative diseases in light of the regulation of the microbiome.},
}

@article {pmid30890181,
year = {2019},
author = {Zheng, T and Li, J and Ni, Y and Kang, K and Misiakou, MA and Imamovic, L and Chow, BKC and Rode, AA and Bytzer, P and Sommer, M and Panagiotou, G},
title = {Mining, analyzing, and integrating viral signals from metagenomic data.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {42},
doi = {10.1186/s40168-019-0657-y},
pmid = {30890181},
issn = {2049-2618},
support = {H2020-MSCA-ITN-2018 813781//Deutsche Forschungsgemeinschaft/ ; 638902//H2020 European Research Council/ ; 282004//the European Union PF7 (Health-2011-single-stage)/ ; R140-2013-13496//The Lundbeck Foundation/ ; NNF10CC1016517//the Novo Nordisk Foundation/ ; },
abstract = {BACKGROUND: Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagenomic sequencing data. Here we employed the random forest algorithm to develop VirMiner, a web-based phage contig prediction tool especially sensitive for high-abundances phage contigs, trained and validated by paired metagenomic and phagenomic sequencing data from the human gut flora.

RESULTS: VirMiner achieved 41.06% ± 17.51% sensitivity and 81.91% ± 4.04% specificity in the prediction of phage contigs. In particular, for the high-abundance phage contigs, VirMiner outperformed other tools (VirFinder and VirSorter) with much higher sensitivity (65.23% ± 16.94%) than VirFinder (34.63% ± 17.96%) and VirSorter (18.75% ± 15.23%) at almost the same specificity. Moreover, VirMiner provides the most comprehensive phage analysis pipeline which is comprised of metagenomic raw reads processing, functional annotation, phage contig identification, and phage-host relationship prediction (CRISPR-spacer recognition) and supports two-group comparison when the input (metagenomic sequence data) includes different conditions (e.g., case and control). Application of VirMiner to an independent cohort of human gut metagenomes obtained from individuals treated with antibiotics revealed that 122 KEGG orthology and 118 Pfam groups had significantly differential abundance in the pre-treatment samples compared to samples at the end of antibiotic administration, including clustered regularly interspaced short palindromic repeats (CRISPR), multidrug resistance, and protein transport. The VirMiner webserver is available at http://sbb.hku.hk/VirMiner/ .

CONCLUSIONS: We developed a comprehensive tool for phage prediction and analysis for metagenomic samples. Compared to VirSorter and VirFinder-the most widely used tools-VirMiner is able to capture more high-abundance phage contigs which could play key roles in infecting bacteria and modulating microbial community dynamics.

TRIAL REGISTRATION: The European Union Clinical Trials Register, EudraCT Number: 2013-003378-28 . Registered on 9 April 2014.},
}

@article {pmid30700713,
year = {2019},
author = {Coutinho, FH and Silveira, CB and Gregoracci, GB and Thompson, CC and Edwards, RA and Brussaard, CPD and Dutilh, BE and Thompson, FL},
title = {Reply to: Caution in inferring viral strategies from abundance correlations in marine metagenomes.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {502},
doi = {10.1038/s41467-018-08286-4},
pmid = {30700713},
issn = {2041-1723},
mesh = {*Metagenome ; Phylogeny ; },
}

*Metagenome
Phylogeny

@article {pmid30674644,
year = {2019},
author = {He, S and Lau, MP and Linz, AM and Roden, EE and McMahon, KD},
title = {Extracellular Electron Transfer May Be an Overlooked Contribution to Pelagic Respiration in Humic-Rich Freshwater Lakes.},
journal = {mSphere},
volume = {4},
number = {1},
pages = {},
doi = {10.1128/mSphere.00436-18},
pmid = {30674644},
issn = {2379-5042},
mesh = {Carbon/metabolism ; *Electron Transport ; *Energy Metabolism ; Fresh Water/*microbiology ; Humic Substances ; Iron/metabolism ; Lakes/*microbiology ; *Metagenome ; },
abstract = {Humic lakes and ponds receive large amounts of terrestrial carbon and are important components of the global carbon cycle, yet how their redox cycling influences the carbon budget is not fully understood. Here we compared metagenomes obtained from a humic bog and a clear-water eutrophic lake and found a much larger number of genes that might be involved in extracellular electron transfer (EET) for iron redox reactions and humic substance (HS) reduction in the bog than in the clear-water lake, consistent with the much higher iron and HS levels in the bog. These genes were particularly rich in the bog's anoxic hypolimnion and were found in diverse bacterial lineages, some of which are relatives of known iron oxidizers or iron-HS reducers. We hypothesize that HS may be a previously overlooked electron acceptor and that EET-enabled redox cycling may be important in pelagic respiration and greenhouse gas budget in humic-rich freshwater lakes.},
}

Carbon/metabolism
*Electron Transport
*Energy Metabolism
Fresh Water/*microbiology
Humic Substances
Iron/metabolism
Lakes/*microbiology
*Metagenome

@article {pmid30655514,
year = {2019},
author = {Tully, BJ},
title = {Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {271},
doi = {10.1038/s41467-018-07840-4},
pmid = {30655514},
issn = {2041-1723},
mesh = {Aquatic Organisms/genetics/*metabolism ; Ecology/*methods ; Euryarchaeota/genetics/*metabolism ; Genome, Archaeal/*genetics ; Genomics ; *Metagenomics ; Phototrophic Processes ; Phylogeny ; Rhodopsins, Microbial/metabolism ; Seawater/microbiology ; },
abstract = {Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world, and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present a comparative genomic analysis of 250 MGII genomes, providing a comprehensive investigation of these mesophilic archaea. This analysis identifies 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera reveals distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins, common in all other subclades.},
}

Aquatic Organisms/genetics/*metabolism
Ecology/*methods
Euryarchaeota/genetics/*metabolism
Genome, Archaeal/*genetics
Genomics
*Metagenomics
Phototrophic Processes
Phylogeny
Rhodopsins, Microbial/metabolism
Seawater/microbiology

@article {pmid30578263,
year = {2019},
author = {Wegner, CE and Gaspar, M and Geesink, P and Herrmann, M and Marz, M and Küsel, K},
title = {Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {5},
pages = {},
doi = {10.1128/AEM.02346-18},
pmid = {30578263},
issn = {1098-5336},
abstract = {Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbor autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-omic profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes, and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, and ammonium oxidation [anammox]) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), depending on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Being dominated by a few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, and Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome depending on the availability of oxygen and inorganic electron donors, like ammonium.IMPORTANCE Groundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage, and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than does hydrochemistry.},
}

@article {pmid30204780,
year = {2018},
author = {Wang, T and Yu, L and Xu, C and Pan, K and Mo, M and Duan, M and Zhang, Y and Xiong, H},
title = {Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0203503},
pmid = {30204780},
issn = {1932-6203},
mesh = {Adult ; Asian Continental Ancestry Group ; China ; Fatigue Syndrome, Chronic/*microbiology ; *Fusobacteria/classification/genetics ; Humans ; *Metagenome ; *Microbiota ; Mouth/*microbiology ; },
abstract = {Host-microbe interactions have been implicated in the pathogenesis of chronic fatigue syndrome (CFS), but whether the oral microbiome is altered in CFS patients is unknown. We explored alterations of the oral microbiome in Chinese Han CFS patients using 16S rRNA gene sequencing and alterations in the functional potential of the oral microbiome using PICRUSt. We found that Shannon and Simpson diversity indices were not different in CFS patients compared to healthy controls, but the overall oral microbiome composition was different (MANOVA, p < 0.01). CFS patients had a higher relative abundance of Fusobacteria compared with healthy controls. Further, the genera Leptotrichia, Prevotella, and Fusobacterium were enriched and Haemophilus, Veillonella, and Porphyromonas were depleted in CFS patients compared to healthy controls. Functional analysis from inferred metagenomes showed that bacterial genera altered in CFS patients were primarily associated with amino acid and energy metabolism. Our findings demonstrate that the oral microbiome in CFS patients is different from healthy controls, and these differences lead to shifts in functional pathways with implications for CFS pathogenesis. These findings increase our understanding of the relationship between the oral microbiota and CFS, which will advance our understanding of CFS pathogenesis and may contribute to future improvements in treatment and diagnosis.},
}

Adult
Asian Continental Ancestry Group
China
Fatigue Syndrome, Chronic/*microbiology
*Fusobacteria/classification/genetics
Humans
*Metagenome
*Microbiota
Mouth/*microbiology

@article {pmid29176284,
year = {2017},
author = {},
title = {.},
journal = {Nihon Rinsho Men'eki Gakkai kaishi = Japanese journal of clinical immunology},
volume = {40},
number = {4},
pages = {258a},
doi = {10.2177/jsci.40.258a},
pmid = {29176284},
issn = {1349-7413},
mesh = {Animals ; Autoimmune Diseases/microbiology ; Cardiovascular Diseases/microbiology ; Dysbiosis ; Epigenomics ; Gastrointestinal Microbiome/*genetics/immunology/physiology ; Host-Pathogen Interactions ; Humans ; Inflammatory Bowel Diseases/microbiology ; Metabolic Diseases/microbiology ; Metabolome ; Metagenome ; Transcriptome ; },
}

Animals
Autoimmune Diseases/microbiology
Cardiovascular Diseases/microbiology
Dysbiosis
Epigenomics
Gastrointestinal Microbiome/*genetics/immunology/physiology
Host-Pathogen Interactions
Humans
Inflammatory Bowel Diseases/microbiology
Metabolic Diseases/microbiology
Metabolome
Metagenome
Transcriptome

@article {pmid28710395,
year = {2017},
author = {Gong, H and Shi, Y and Xiao, X and Cao, P and Wu, C and Tao, L and Hou, D and Wang, Y and Zhou, L},
title = {Alterations of microbiota structure in the larynx relevant to laryngeal carcinoma.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {5507},
pmid = {28710395},
issn = {2045-2322},
mesh = {Adult ; Aged ; Bacteria/*classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Laryngeal Neoplasms/*microbiology ; Male ; Metagenomics/*methods ; Middle Aged ; Pharynx/*microbiology ; Phylogeny ; Polyps/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The microbial communities that inhabit the laryngeal mucosa build stable microenvironments and have the potential to influence the health of the human throat. However, the associations between the microbiota structure and laryngeal carcinoma remain uncertain. Here, we explored this question by comparing the laryngeal microbiota structure in laryngeal cancer patients with that in control subjects with vocal cord polyps through high-throughput pyrosequencing. Overall, the genera Streptococcus, Fusobacterium, and Prevotella were prevalent bacterial populations in the laryngeal niche. Tumor tissue samples and normal tissues adjacent to the tumor sites (NATs) were collected from 31 laryngeal cancer patients, and the bacterial communities in laryngeal cancer patients were compared with control samples from 32 subjects. A comparison of the laryngeal communities in the tumor tissues and the NATs showed higher α-diversity in cancer patients than in control subjects, and the relative abundances of seven bacterial genera differed among the three groups of samples. Furthermore, the relative abundances of ten bacterial genera in laryngeal cancer patients differed substantially from those in control subjects. These findings indicate that the laryngeal microbiota profiles are altered in laryngeal cancer patients, suggesting that a disturbance of the microbiota structure might be relevant to laryngeal cancer.},
}

Adult
Aged
Bacteria/*classification/genetics/isolation & purification
DNA, Bacterial/genetics
DNA, Ribosomal/genetics
Female
High-Throughput Nucleotide Sequencing
Humans
Laryngeal Neoplasms/*microbiology
Male
Metagenomics/*methods
Middle Aged
Pharynx/*microbiology
Phylogeny
Polyps/*microbiology
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid30889229,
year = {2019},
author = {Portillo, A and Palomar, AM and de Toro, M and Santibáñez, S and Santibáñez, P and Oteo, JA},
title = {Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213384},
doi = {10.1371/journal.pone.0213384},
pmid = {30889229},
issn = {1932-6203},
abstract = {OBJECTIVE: The aim of this study was to characterize the bacterial microbiome of hard ticks with affinity to bite humans in La Rioja (North of Spain).

METHODS: A total of 88 adult ticks (22 Rhipicephalus sanguineus sensu lato, 27 Haemaphysalis punctata, 30 Dermacentor marginatus and 9 Ixodes ricinus) and 120 I. ricinus nymphs (CRETAV collection, La Rioja, Spain), representing the main anthropophilic species in our environment, were subjected to a metagenomic analysis of the V3-V4 region of the 16S rRNA gene using an Illumina MiSeq platform. Data obtained with Greengenes database were refined with BLAST. Four groups of samples were defined, according to the four tick species.

RESULTS: Proteobacteria was the predominant phylum observed in all groups. Gammaproteobacteria was the most abundant class, followed by Alphaproteobacteria for R. sanguineus, H. punctata and D. marginatus but the relative abundance of reads for these classes was reversed for I. ricinus. This tick species showed more than 46% reads corresponding to 'not assigned' OTUs (Greengenes), and >97% of them corresponded to 'Candidatus Midichloriaceae' using BLAST. Within Rickettsiales, 'Candidatus Midichloria', Rickettsia, Ehrlichia, 'Candidatus Neoehrlichia' and Wolbachia were detected. I. ricinus was the most alpha-diverse species. Regarding beta-diversity, I. ricinus and H. punctata samples grouped according to their tick species but microbial communities of some R. sanguineus and D. marginatus specimens clustered together.

CONCLUSIONS: The metagenomics approach seems useful to discover the spectrum of tick-related bacteria. More studies are needed to identify and differentiate bacterial species, and to improve the knowledge of tick-borne diseases in Spain.},
}

@article {pmid30887877,
year = {2019},
author = {Polzin, J and Arevalo, P and Nussbaumer, T and Polz, MF and Bright, M},
title = {Polyclonal symbiont populations in hydrothermal vent tubeworms and the environment.},
journal = {Proceedings. Biological sciences},
volume = {286},
number = {1896},
pages = {20181281},
doi = {10.1098/rspb.2018.1281},
pmid = {30887877},
issn = {1471-2954},
abstract = {Horizontally transmitted symbioses usually house multiple and variable symbiont genotypes that are acquired from a much more diverse environmental pool via partner choice mechanisms. However, in the deep-sea hydrothermal vent tubeworm Riftia pachyptila (Vestimentifera, Siboglinidae), it has been suggested that the Candidatus Endoriftia persephone symbiont is monoclonal. Here, we show with high-coverage metagenomics that adult R. pachyptila house a polyclonal symbiont population consisting of one dominant and several low-frequency variants. This dominance of one genotype is confirmed by multilocus gene sequencing of amplified housekeeping genes in a broad range of host individuals where three out of four loci (atpA, uvrD and recA) revealed no genomic differences, while one locus (gyrB) was more diverse in adults than in juveniles. We also analysed a metagenome of free-living Endoriftia and found that the free-living population showed greater sequence variability than the host-associated population. Most juveniles and adults shared a specific dominant genotype, while other genotypes can dominate in few individuals. We suggest that although generally permissive, partner choice is selective enough to restrict uptake of some genotypes present in the environment.},
}

@article {pmid30887686,
year = {2019},
author = {Weyrich, LS and Farrer, AG and Eisenhofer, R and Arriola, LA and Young, J and Selway, CA and Handsley-Davis, M and Adler, C and Breen, J and Cooper, A},
title = {Laboratory contamination over time during low-biomass sample analysis.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13011},
pmid = {30887686},
issn = {1755-0998},
abstract = {Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g. skin swabs, tissue biopsies, ice, water, degraded forensic samples, or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over five years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a homemade silica-based extraction method, commonly used to analyse low-endogenous samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to the modern molecular biology laboratories, and changed over time according to researchers, month, and season. The commercial kit contained higher microbial diversity and several human-associated taxa in comparison to the homemade silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: 1) extraction blank controls should be included and sequenced with every batch of extractions and 2) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study. This article is protected by copyright. All rights reserved.},
}

@article {pmid30886779,
year = {2019},
author = {Eisenhofer, R and Weyrich, LS},
title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6594},
doi = {10.7717/peerj.6594},
pmid = {30886779},
issn = {2167-8359},
abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.},
}

@article {pmid30886772,
year = {2019},
author = {Jiang, H and Zhang, X and Li, L and Ma, J and He, N and Liu, H and Han, R and Li, H and Wu, Z and Chen, J},
title = {Identification of Austwickia chelonae as cause of cutaneous granuloma in endangered crocodile lizards using metataxonomics.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6574},
doi = {10.7717/peerj.6574},
pmid = {30886772},
issn = {2167-8359},
abstract = {The crocodile lizard (Shinisaurus crocodilurus Ahl, 1930) is an endangered reptile species, and in recent years many have died from diseases, especially the rescued and breeding individuals. However, pathogens underlying these diseases are unclear. In this study, we report our effort in rapidly identifying and isolating the pathogen that causes high mortality in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. The typical symptom is cutaneous granuloma in the infected crocodile lizards. Metagenomic next-generation sequencing (mNGS) is a comprehensive approach for sequence-based identification of pathogenic microbes. In this study, 16S rDNA based mNGS was used for rapid identification of pathogens, and microscopy and microbe isolation were used to confirm the results. Austwickia chelonae was identified to be the dominant pathogen in the granuloma using 16S rDNA based mNGS. Chinese skinks were used as an animal model to verify the pathogenicity of A. chelonae to fulfill Koch's postulates. As expected, subcutaneous inoculation of A. chelonae induced granulomas in the healthy Chinese skinks and the A. chelonae was re-isolated from the induced granulomas. Therefore, A. chelonae was the primary pathogen that caused this high mortality disease, cutaneous granuloma, in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. Antibiotics analysis demonstrated that A. chelonae was sensitive to cephalothin, minocycline and ampicillin, but not to kanamycin, gentamicin, streptomycin and clarithromycin, suggesting a possible treatment for the infected crocodile lizards. However, surgical resection of the nodules as early as possible was recommended. This study is the first report of pathogenic analysis in crocodile lizards and provides a reference for disease control and conservations of the endangered crocodile lizards and other reptiles. In addition, this study indicated that mNGS of lesions could be used to detect the pathogens in animals with benefits in speed and convenient.},
}

@article {pmid30886359,
year = {2019},
author = {Lee, KS and Palatinszky, M and Pereira, FC and Nguyen, J and Fernandez, VI and Mueller, AJ and Menolascina, F and Daims, H and Berry, D and Wagner, M and Stocker, R},
title = {An automated Raman-based platform for the sorting of live cells by functional properties.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-019-0394-9},
pmid = {30886359},
issn = {2058-5276},
abstract = {Stable-isotope probing is widely used to study the function of microbial taxa in their natural environment, but sorting of isotopically labelled microbial cells from complex samples for subsequent genomic analysis or cultivation is still in its early infancy. Here, we introduce an optofluidic platform for automated sorting of stable-isotope-probing-labelled microbial cells, combining microfluidics, optical tweezing and Raman microspectroscopy, which yields live cells suitable for subsequent single-cell genomics, mini-metagenomics or cultivation. We describe the design and optimization of this Raman-activated cell-sorting approach, illustrate its operation with four model bacteria (two intestinal, one soil and one marine) and demonstrate its high sorting accuracy (98.3 ± 1.7%), throughput (200-500 cells h-1; 3.3-8.3 cells min-1) and compatibility with cultivation. Application of this sorting approach for the metagenomic characterization of bacteria involved in mucin degradation in the mouse colon revealed a diverse consortium of bacteria, including several members of the underexplored family Muribaculaceae, highlighting both the complexity of this niche and the potential of Raman-activated cell sorting for identifying key players in targeted processes.},
}

@article {pmid30885807,
year = {2019},
author = {Murray, AK and Zhang, L and Snape, J and Gaze, WH},
title = {Comparing the selective and co-selective effects of different antimicrobials in bacterial communities.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijantimicag.2019.03.001},
pmid = {30885807},
issn = {1872-7913},
abstract = {Bacterial communities are exposed to a cocktail of antimicrobial agents, including antibiotics, heavy metals and biocidal antimicrobials such as quaternary ammonium compounds (QACs). The extent to which these compounds may select or co-select for antimicrobial resistance (AMR) is not fully understood. In this study, human associated, wastewater derived, bacterial communities were exposed to either benzalkonium chloride (BAC), ciprofloxacin or trimethoprim at sub-point of use concentrations for one week, in order to determine selective and co-selective potential. Metagenome analyses were performed to determine effects on bacterial community structure and prevalence of antibiotic resistance genes (ARGs) and metal or biocide resistance genes (MBRGS). Ciprofloxacin had the greatest co-selective potential, significantly enriching for resistance mechanisms to multiple antibiotic classes. Conversely, BAC exposure significantly reduced relative abundance of ARGs and MBRGS, including the well characterised qac efflux genes. However, BAC exposure significantly impacted bacterial community structure. This suggests BAC and potentially other QACs did not play as significant a role in co-selection for AMR relative to antibiotics such as ciprofloxacin at below point of use concentrations in this study. This approach can be used to identify priority compounds for further study, to better understand evolution of AMR in bacterial communities exposed to sub-point of use concentrations of antimicrobials.},
}

@article {pmid30885780,
year = {2019},
author = {Zuo, X and Deguchi, Y and Xu, W and Liu, Y and Li, HS and Wei, D and Tian, R and Chen, W and Xu, M and Yang, Y and Gao, S and Jaoude, JC and Liu, F and Chrieki, SP and Moussalli, MJ and Gagea, M and Sebastian, MM and Zheng, X and Tan, D and Broaddus, R and Wang, J and Ajami, NJ and Swennes, AG and Watowich, SS and Shureiqi, I},
title = {PPARD and Interferon gamma Promote Transformation of Gastric Progenitor Cells and Tumorigenesis in Mice.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2019.03.018},
pmid = {30885780},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: The peroxisome proliferator activated receptor delta (PPARD) regulates cell metabolism, proliferation, and inflammation and has been associated with gastric and other cancers. Villin-positive epithelial cells are a small population of quiescent gastric progenitor cells. We expressed PPARD from a villin promoter to investigate the role of these cells and PPARD in development of gastric cancer.

METHODS: We analyzed gastric tissues from mice that express the Ppard (PPARD1 and PPARD2 mice) from a villin promoter, and mice that did not carry this transgene (controls), by histology and immunohistochemistry. We performed cell lineage tracing experiments and analyzed the microbiomes, chemokine and cytokine production, and immune cells and transcriptomes of stomachs of these mice. We also performed immunohistochemical analysis of PPARD levels in in 2 sets of human gastric tissue microarrays.

RESULTS: Thirty-eight percent of PPARD mice developed spontaneous, invasive gastric adenocarcinomas, with severe chronic inflammation. Levels of PPARD were increased in human gastric cancer tissues, compared with non-tumor tissues, and associated with gastric cancer stage and grade. We found an inverse correlation between level of PPARD in tumor tissue and patients survival time. Gastric microbiomes from PPARD and control mice did not differ significantly. Lineage-tracing experiments identified villin-expressing gastric progenitor cells (VGPCs) as the origin of gastric tumors in PPARD mice. In these mice, PPARD upregulated CCL20 and CXCL1, which increased infiltration of the gastric mucosa by immune cells. Immune cell production of inflammatory cytokines promoted chronic gastric inflammation and expansion and transformation of VGPCs, leading to tumorigenesis. We identified a positive-feedback loop between PPARD and interferon gamma signaling that sustained gastric inflammation to induce VGPC transformation and gastric carcinogenesis.

CONCLUSIONS: We found PPARD overexpression in VPGCs to result in inflammation, dysplasia, and tumor formation. PPARD and VGPCs might be therapeutic targets for stomach cancer.},
}

@article {pmid30885720,
year = {2019},
author = {LaPierre, N and Ju, CJ and Zhou, G and Wang, W},
title = {MetaPheno: A Critical Evaluation of Deep Learning and Machine Learning in Metagenome-Based Disease Prediction.},
journal = {Methods (San Diego, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymeth.2019.03.003},
pmid = {30885720},
issn = {1095-9130},
abstract = {The human microbiome plays a number of critical roles, impacting almost every aspect of human health and well-being. Conditions in the microbiome have been linked to a num-ber of significant diseases. Additionally, revolutions in sequencing technology have led to a rapid increase in publicly-available sequencing data. Consequently, there have been grow-ing efforts to predict disease status from metagenomic sequencing data, with a proliferation of new approaches in the last few years. Some of these efforts have explored utilizing a powerful form of machine learning called deep learning, which has been applied successfully in several biological domains. Here, we review some of these methods and the algorithms that they are based on, with a particular focus on deep learning methods. We also per-form a deeper analysis of Type 2 Diabetes and obesity datasets that have eluded improved results, using a variety of machine learning and feature extraction methods. We conclude by offering perspectives on study design considerations that may impact results and future directions the field can take to improve results and offer more valuable conclusions. The scripts and extracted features for the analyses conducted in this paper are available via GitHub: https://github.com/nlapier2/metapheno.},
}

@article {pmid30885689,
year = {2019},
author = {Hildonen, M and Kodama, M and Puetz, L and Gilbert, MTP and Limborg, MT},
title = {A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss).},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mimet.2019.03.010},
pmid = {30885689},
issn = {1872-8359},
abstract = {Immediate freezing is perhaps the most preferred method used for preserving gut microbial samples, but research on sample preservation has been principally based around samples from mammalian species, and little is known about the advantages or disadvantages relating to different storage methods for fish guts. Fish gut samples may pose additional challenges due to the different chemical and enzymatic profile, as well as the higher water content, which might affect the yield and purity of DNA recovered. To explore this, we took gut content and mucosal scrape samples from 10 rainbow trout (Oncorhynchus mykiss), and tested whether different preservation methods have any effect on the ability to construct high quality genomic libraries for shotgun and 16S rRNA gene sequencing. Four different storage methods were compared for the gut content samples (immediate freezing on dry ice, 96% ethanol, RNAlater and DNA/RNA shield), while two different methods were compared for mucosal scrape samples (96% ethanol and RNAlater). The samples were thereafter stored at -80 °C. Our findings concluded that 96% ethanol outperforms the other storage methods when considering DNA quantity, quality, cost and labor. Ethanol works consistently well for both gut content and mucosal scrape samples, and enables construction of DNA sequencing libraries of sufficient quantity and with a fragment length distribution suitable for shotgun sequencing. Two main conclusions from our study are i) sample storage optimisation is an important part of establishing a microbiome research program in a new species or sample type system, and ii) 96% ethanol is the preferred method for storing rainbow trout gut content and mucosal scrape samples.},
}

@article {pmid30885626,
year = {2019},
author = {Oberbach, A and Friedrich, M and Lehmann, S and Schlichting, N and Kullnick, Y and Gräber, S and Buschmann, T and Hagl, C and Bagaev, E and , and , and , },
title = {Bacterial infiltration in structural heart valve disease.},
journal = {The Journal of thoracic and cardiovascular surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtcvs.2019.02.019},
pmid = {30885626},
issn = {1097-685X},
abstract = {OBJECTIVES: The pathology of structural valvular heart disease (sVHD) ranges from basic diseases of rheumatologic origin to chronic degenerative remodeling processes after acute bacterial infections. Molecular genetic methods allow detection of the complete microbial spectrum in heart valve tissues independent of microbiological cultivation. In particular, whole-metagenome analysis is a sensitive and highly specific analytical method that allows a deeper insight into the pathogenicity of the diseases. In the present study we assessed the pathogen spectrum in heart valve tissue from 25 sVHD patients using molecular and microbiological methods.

METHODS: Twenty-five sVHD patients were selected randomly from an observational cohort study (March 2016 to January 2017). The explanted native heart valves were examined using microbiological methods and immunohistological structural analysis. In addition, the bacterial metagenome of the heart valve tissue was determined using next-generation sequencing.

RESULTS: The use of sonication as a pretreatment of valve tissue from 4 sVHD patients permitted successful detection of Clostridium difficile, Enterococcus faecalis, Staphylococcus saccharolyticus, and Staphylococcus haemolyticus using microbial cultivation. Histological staining revealed intramural localization. Metagenome analysis identified a higher rate of bacterial infiltration in 52% of cases. The pathogen spectrum included both gram-positive and gram-negative bacteria.

CONCLUSIONS: Microbiological and molecular biological studies are necessary to detect the spectrum of bacteria in a calcified heart valve. Metagenome analysis is a valid method to gain new insight into the polymicrobial pathophysiology of sVHD. Our results suggest that an undetected proportion of sVHD might be triggered by chronic inflammation or influenced by secondary bacterial infiltration.},
}

@article {pmid30885397,
year = {2019},
author = {Ashokan, A and Papanicolas, LE and Leong, LEX and Theodossi, M and Daniel, S and Wesselingh, SL and Rogers, GB and Gordon, DL},
title = {Case report: Identification of intra-laboratory blood culture contamination with Staphylococcus aureus by whole genome sequencing.},
journal = {Diagnostic microbiology and infectious disease},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.diagmicrobio.2019.02.016},
pmid = {30885397},
issn = {1879-0070},
abstract = {Staphylococcus aureus in blood cultures is rarely considered a contaminant. We report a case of intra-laboratory contamination between blood culture bottles which was confirmed by whole genome sequencing, highlighting the importance of molecular analysis in the clinical laboratory setting.},
}

@article {pmid30885294,
year = {2019},
author = {Prodan, A and Levin, E and Nieuwdorp, M},
title = {Does disease start in the mouth, the gut or both?.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
doi = {10.7554/eLife.45931},
pmid = {30885294},
issn = {2050-084X},
abstract = {Oral bacteria colonize the gut more frequently than previously thought.},
}

@article {pmid30885224,
year = {2019},
author = {Liu, P and Qiu, Y and Xing, C and Zhou, JH and Yang, WH and Wang, Q and Li, JY and Han, X and Zhang, YZ and Ge, XY},
title = {Detection and genome characterization of two novel papillomaviruses and a novel polyomavirus in tree shrew (Tupaia belangeri chinensis) in China.},
journal = {Virology journal},
volume = {16},
number = {1},
pages = {35},
doi = {10.1186/s12985-019-1141-9},
pmid = {30885224},
issn = {1743-422X},
support = {2017YFD0500104//National Key Research and Development Program of China/ ; 31470260//National Natural Science Foundation of China/ ; 81401672//National Natural Science Foundation of China/ ; 81660558//National Natural Science Foundation of China/ ; 2017RS3017//Hu-Xiang Youth Talents Scholar Program of Hunan Province/ ; },
abstract = {BACKGROUND: Papillomaviruses (PVs) and polyomaviruses (PyVs) infect diverse vertebrates including human and cause a broad spectrum of outcomes from asymptomatic infection to severe disease. There has been no PV and only one PyV detected in tree shrews, though the genomic properties of tree shrews are highly similar to those of the primates.

METHODS: Swab and organ samples of tree shrews collected in the Yunnan Province of China, were tested by viral metagenomic analysis and random PCR to detect the presence of PVs and PyVs. By PCR amplification using specific primers, cloning, sequencing and assembling, genomes of two PVs and one PyV were identified in the samples.

RESULTS: Two novel PVs and a novel PyV, named tree shrew papillomavirus 1 and 2 (TbelPV1 and TbelPV2) and polyomavirus 1 (TbelPyV1) were characterized in the Chinese tree shrew (Tupaia belangeri chinensis). The genomes of TbelPV1, TbelPV2, and TbelPyV1 are 7410 bp, 7526 bp, and 4982 bp in size, respectively. The TbelPV1 genome contains 7 putative open-reading frames (ORFs) coding for viral proteins E1, E2, E4, E6, E7, L1, and L2; the TbelPV2 genome contains 6 ORFs coding for viral proteins E1, E2, E6, E7, L1, and L2; and the TbelPyV1 genome codes for the typical small and large T antigens of PyV, as well as the VP1, VP2, and VP3 capsid proteins. Genomic comparison and phylogenetic analysis indicated that TbelPV1 and TbelPV2 represented 2 novel PV genera of Papillomaviridae, and TbelPyV1 represented a new species of genus Alphapolyomavirus. Our epidemiologic study indicated that TbelPV1 and TbelPV2 were both detected in oral swabs, while TbelPyV1 was detected in oral swabs and spleens.

CONCLUSION: Two novel PVs (TbelPV1 and TbelPV2) and a novel PyV (TbelPyV) were discovered in tree shrews and their genomes were characterized. TbelPV1, TbelPV2, and TbelPyV1 have the highest similarity to Human papillomavirus type 63, Ursus maritimus papillomavirus 1, and Human polyomavirus 9, respectively. TbelPV1 and TbelPV2 only showed oral tropism, while TbelPyV1 showed oral and spleen tropism.},
}

@article {pmid30885206,
year = {2019},
author = {Ziko, L and Saqr, AA and Ouf, A and Gimpel, M and Aziz, RK and Neubauer, P and Siam, R},
title = {Antibacterial and anticancer activities of orphan biosynthetic gene clusters from Atlantis II Red Sea brine pool.},
journal = {Microbial cell factories},
volume = {18},
number = {1},
pages = {56},
doi = {10.1186/s12934-019-1103-3},
pmid = {30885206},
issn = {1475-2859},
abstract = {BACKGROUND: Cancer and infectious diseases are problematic because of continuous emergence of drug resistance. One way to address this enormous global health threat is bioprospecting the unlikeliest environments, such as extreme marine niches, which have tremendous biodiversity that is barely explored. One such environment is the Red Sea brine pool, Atlantis II Deep (ATII). Here, we functionally screened a fosmid library of metagenomic DNA isolated from the ATII lower convective layer (LCL) for antibacterial and anticancer activities.

RESULTS: Selected clones, 14-7E and 10-2G, displayed antibacterial effects on the marine strain Bacillus sp. Cc6. Moreover, whole cell lysates from 14-7E and 10-2G exhibited decreased cell viability against MCF-7 (39.1% ± 6.6, 42% ± 8.1 at 50% v/v) and U2OS cells (35.7% ± 1.9, 79.9% ± 5.9 at 50% v/v), respectively. By sequencing the insert DNA from 14-7E and 10-2G, we identified two putative orphan biosynthetic gene clusters. Both clusters harbored putative ATP-binding cassette (ABC) transporter permeases and S-adenosylmethionine-related genes. Interestingly, the biosynthetic gene cluster identified on 14-7E is of archaeal origin and harbors a putative transcription factor. Several identified genes may be responsible for the observed antibacterial and anticancer activities. The 14-7E biosynthetic gene cluster may be encoding enzymes producing a specialized metabolite (effect of detected genes involved in C-C bond formation and glycosylation). The bioactivity may also be due to predicted subtilases encoded by this cluster. The 10-2G cluster harbored putative glycosyltransferase and non-ribosomal peptide synthase genes; thus the observed activity of this clone could be caused by a bioactive peptide.

CONCLUSIONS: The ATII LCL prokaryotic metagenome hosts putative orphan biosynthetic gene clusters that confer antibiotic and anticancer effects. Further biochemical studies should characterize the detected bioactive components, and the potential use of 14-7E metabolite for antibiosis and 10-2G metabolite as a selective anti-breast cancer drug.},
}

@article {pmid30884876,
year = {2019},
author = {Pu, G and Zeng, D and Mo, L and Liao, J and Chen, X},
title = {Artificial Light at Night Alleviates the Negative Effect of Pb on Freshwater Ecosystems.},
journal = {International journal of molecular sciences},
volume = {20},
number = {6},
pages = {},
doi = {10.3390/ijms20061343},
pmid = {30884876},
issn = {1422-0067},
abstract = {Artificial light at night (ALAN) is an increasing phenomenon worldwide that can cause a series of biological and ecological effects, yet little is known about its potential interaction with other stressors in aquatic ecosystems. Here, we tested whether the impact of lead (Pb) on litter decomposition was altered by ALAN exposure using an indoor microcosm experiment. The results showed that ALAN exposure alone significantly increased leaf litter decomposition, decreased the lignin content of leaf litter, and altered fungal community composition and structure. The decomposition rate was 51% higher in Pb with ALAN exposure treatments than in Pb without ALAN treatments, resulting in increased microbial biomass, β-glucosidase (β-G) activity, and the enhanced correlation between β-G and litter decomposition rate. These results indicate that the negative effect of Pb on leaf litter decomposition in aquatic ecosystems may be alleviated by ALAN. In addition, ALAN exposure also alters the correlation among fungi associated with leaf litter decomposition. In summary, this study expands our understanding of Pb toxicity on litter decomposition in freshwater ecosystems and highlights the importance of considering ALAN when assessing environmental metal pollutions.},
}

@article {pmid30747106,
year = {2019},
author = {Schmidt, TS and Hayward, MR and Coelho, LP and Li, SS and Costea, PI and Voigt, AY and Wirbel, J and Maistrenko, OM and Alves, RJ and Bergsten, E and de Beaufort, C and Sobhani, I and Heintz-Buschart, A and Sunagawa, S and Zeller, G and Wilmes, P and Bork, P},
title = {Extensive transmission of microbes along the gastrointestinal tract.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
doi = {10.7554/eLife.42693},
pmid = {30747106},
issn = {2050-084X},
support = {CORE/15/BM/10404093//Fonds National de la Recherche Luxembourg/ ; ERC-AdG-669830//H2020 European Research Council/ ; 661019//H2020 Marie Skłodowska-Curie Actions/ ; de.NBI #031A537B//German Network for Bioinformatics Infrastructure/ ; de.NBI #031A537B//German Network Bioinformatics/ ; },
abstract = {The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to the intestine is considered a rare aberrant event, and a hallmark of disease. By studying salivary and fecal microbial strain populations of 310 species in 470 individuals from five countries, we found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals. We found evidence for a vast majority of oral species to be transferable, with increased levels of transmission in colorectal cancer and rheumatoid arthritis patients and, more generally, for species described as opportunistic pathogens. This establishes the oral cavity as an endogenous reservoir for gut microbial strains, and oral-fecal transmission as an important process that shapes the gastrointestinal microbiome in health and disease.},
}

@article {pmid30690359,
year = {2019},
author = {Qiao, R and Sheng, C and Lu, Y and Zhang, Y and Ren, H and Lemos, B},
title = {Microplastics induce intestinal inflammation, oxidative stress, and disorders of metabolome and microbiome in zebrafish.},
journal = {The Science of the total environment},
volume = {662},
number = {},
pages = {246-253},
doi = {10.1016/j.scitotenv.2019.01.245},
pmid = {30690359},
issn = {1879-1026},
mesh = {Animals ; Dose-Response Relationship, Drug ; Dysbiosis/chemically induced/immunology/*physiopathology ; Fish Diseases/chemically induced/*immunology/physiopathology ; Gastrointestinal Microbiome/drug effects ; Inflammation/chemically induced/*immunology ; Intestines/immunology/physiology ; Metabolome/drug effects ; Metagenomics ; Oxidative Stress/drug effects ; Polystyrenes/*adverse effects/metabolism ; Random Allocation ; Toxicity Tests, Chronic ; Water Pollutants, Chemical/*adverse effects/metabolism ; *Zebrafish/metabolism/microbiology ; },
abstract = {Microplastics (MPs) can be ingested by a variety of species and mainly accumulate in the gut. However, the consequences of MPs exposure in the gut are largely unknown. Here we evaluated the impacts of MPs exposure in zebrafish gut. Animals were experimentally exposed to polystyrene MPs (5-μm beads; 50 μg/L and 500 μg/L) for 21 days and monitored for alterations in tissue histology, enzymatic biomarkers, gut microbiome and metabolomic responses. Inflammation and oxidative stress were observed in the zebrafish gut after exposed to MPs. Furthermore, significant alterations in the gut microbiome and tissue metabolic profiles were observed, with most of these were associated with oxidative stress, inflammation and lipid metabolism. This study provides evidence that MPs exposure causes gut damage as well as alterations in gut metabolome and microbiome, yielding novel insights into the consequences of MPs exposure.},
}

Animals
Dose-Response Relationship, Drug
Dysbiosis/chemically induced/immunology/*physiopathology
Fish Diseases/chemically induced/*immunology/physiopathology
Gastrointestinal Microbiome/drug effects
Inflammation/chemically induced/*immunology
Intestines/immunology/physiology
Metabolome/drug effects
Metagenomics
Oxidative Stress/drug effects
Polystyrenes/*adverse effects/metabolism
Random Allocation
Toxicity Tests, Chronic
Water Pollutants, Chemical/*adverse effects/metabolism
*Zebrafish/metabolism/microbiology

@article {pmid29884754,
year = {2018},
author = {Lugli, GA and Mancino, W and Milani, C and Duranti, S and Turroni, F and van Sinderen, D and Ventura, M},
title = {Reconstruction of the Bifidobacterial Pan-Secretome Reveals the Network of Extracellular Interactions between Bifidobacteria and the Infant Gut.},
journal = {Applied and environmental microbiology},
volume = {84},
number = {16},
pages = {},
pmid = {29884754},
issn = {1098-5336},
abstract = {The repertoire of secreted proteins decoded by a microorganism represents proteins released from or associated with the cell surface. In gut commensals, such as bifidobacteria, these proteins are perceived to be functionally relevant, as they regulate the interaction with the gut environment. In the current study, we screened the predicted proteome of over 300 bifidobacterial strains among the currently recognized bifidobacterial species to generate a comprehensive database encompassing bifidobacterial extracellular proteins. A glycobiome analysis of this predicted bifidobacterial secretome revealed that a correlation exists between particular bifidobacterial species and their capability to hydrolyze human milk oligosaccharides (HMOs) and intestinal glycoconjugates, such as mucin. Furthermore, an exploration of metatranscriptomic data sets of the infant gut microbiota allowed the evaluation of the expression of bifidobacterial genes encoding extracellular proteins, represented by ABC transporter substrate-binding proteins and glycoside hydrolases enzymes involved in the degradation of human milk oligosaccharides and mucin. Overall, this study provides insights into how bifidobacteria interact with their natural yet highly complex environment, the infant gut.IMPORTANCE The ecological success of bifidobacteria relies on the activity of extracellular proteins that are involved in the metabolism of nutrients and the interaction with the environment. To date, information on secreted proteins encoded by bifidobacteria is incomplete and just related to few species. In this study, we reconstructed the bifidobacterial pan-secretome, revealing extracellular proteins that modulate the interaction of bifidobacteria with their natural environment. Furthermore, a survey of the secretion systems between bifidobacterial genomes allowed the identification of a conserved Sec-dependent secretion machinery in all the analyzed genomes and the Tat protein translocation system in the chromosomes of 23 strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium aesculapii.},
}

@article {pmid29684640,
year = {2018},
author = {Oddes, S and Zelig, A and Kaplan, N},
title = {Three invariant Hi-C interaction patterns: Applications to genome assembly.},
journal = {Methods (San Diego, Calif.)},
volume = {142},
number = {},
pages = {89-99},
doi = {10.1016/j.ymeth.2018.04.013},
pmid = {29684640},
issn = {1095-9130},
mesh = {Animals ; Chromosome Mapping/instrumentation/*methods ; DNA/chemistry/genetics ; Genome/genetics ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; Humans ; Imaging, Three-Dimensional/instrumentation/methods ; Metagenomics/instrumentation/*methods ; *Models, Genetic ; Models, Statistical ; Molecular Imaging/instrumentation/methods ; Molecular Sequence Annotation/*methods ; Nucleic Acid Conformation ; Sequence Analysis, DNA/instrumentation/methods ; },
abstract = {Assembly of reference-quality genomes from next-generation sequencing data is a key challenge in genomics. Recently, we and others have shown that Hi-C data can be used to address several outstanding challenges in the field of genome assembly. This principle has since been developed in academia and industry, and has been used in the assembly of several major genomes. In this paper, we explore the central principles underlying Hi-C-based assembly approaches, by quantitatively defining and characterizing three invariant Hi-C interaction patterns on which these approaches can build: Intrachromosomal interaction enrichment, distance-dependent interaction decay and local interaction smoothness. Specifically, we evaluate to what degree each invariant pattern holds on a single locus level in different species, cell types and Hi-C map resolutions. We find that these patterns are generally consistent across species and cell types but are affected by sequencing depth, and that matrix balancing improves consistency of loci with all three invariant patterns. Finally, we overview current Hi-C-based assembly approaches in light of these invariant patterns and demonstrate how local interaction smoothness can be used to easily detect scaffolding errors in extremely sparse Hi-C maps. We suggest that simultaneously considering all three invariant patterns may lead to better Hi-C-based genome assembly methods.},
}

Animals
Chromosome Mapping/instrumentation/*methods
DNA/chemistry/genetics
Genome/genetics
High-Throughput Nucleotide Sequencing/instrumentation/*methods
Humans
Imaging, Three-Dimensional/instrumentation/methods
Metagenomics/instrumentation/*methods
*Models, Genetic
Models, Statistical
Molecular Imaging/instrumentation/methods
Molecular Sequence Annotation/*methods
Nucleic Acid Conformation
Sequence Analysis, DNA/instrumentation/methods

@article {pmid30882592,
year = {2019},
author = {Ikawa, T and Watanabe, Y and Okuzaki, D and Goto, N and Okamura, N and Yamanishi, K and Higashino, T and Yamanishi, H and Okamura, H and Higashino, H},
title = {A new approach to identifying hypertension-associated genes in the mesenteric artery of spontaneously hypertensive rats and stroke-prone spontaneously hypertensive rats.},
journal = {Journal of hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/HJH.0000000000002083},
pmid = {30882592},
issn = {1473-5598},
abstract = {OBJECTIVE: Hypertension is one of the most prevalent diseases in humans who live a modern lifestyle. Alongside more effective care, clarification of the genetic background of hypertension is urgently required. Gene expression in mesenteric resistance arteries of spontaneously hypertensive rats (SHR), stroke-prone SHR (SHRSP) and two types of renal hypertensive Wistar Kyoto rats (WKY), two kidneys and one clip renal hypertensive rat (2K1C) and one kidney and one clip renal hypertensive rat (1K1C), was compared using DNA microarrays.

METHODS: We used a simultaneous equation and comparative selection method to identify genes associated with hypertension using the Reactome analysis tool and GenBank database.

RESULTS: The expression of 298 genes was altered between SHR and WKY (44 upregulated and 254 downregulated), while the expression of 290 genes was altered between SHRSP and WKY (83 upregulated and 207 downregulated). For SHRSP versus SHR, the expression of 60 genes was altered (36 upregulated and 24 downregulated). Several genes expressed in SHR and SHRSP were also expressed in the renovascular hypertensive 2K1C and 1K1C rats, indicative of the existence of hyper-renin and/or hypervolemic pathophysiological changes in SHR and SHRSP.

CONCLUSION: The overexpression of Kcnq1, Crlf1, Alb and Xirp1 and the inhibition of Galr2, Kcnh1, Ache, Chrm2 and Slc5a7 expression may indicate that a relationship exists between these genes and the cause and/or worsening of hypertension in SHR and SHRSP.This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0.},
}

@article {pmid30881924,
year = {2019},
author = {Tribble, GD and Angelov, N and Weltman, R and Wang, BY and Eswaran, SV and Gay, IC and Parthasarathy, K and Dao, DV and Richardson, KN and Ismail, NM and Sharina, IG and Hyde, ER and Ajami, NJ and Petrosino, JF and Bryan, NS},
title = {Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {39},
doi = {10.3389/fcimb.2019.00039},
pmid = {30881924},
issn = {2235-2988},
abstract = {The oral microbiome has the potential to provide an important symbiotic function in human blood pressure physiology by contributing to the generation of nitric oxide (NO), an essential cardiovascular signaling molecule. NO is produced by the human body via conversion of arginine to NO by endogenous nitric oxide synthase (eNOS) but eNOS activity varies by subject. Oral microbial communities are proposed to supplement host NO production by reducing dietary nitrate to nitrite via bacterial nitrate reductases. Unreduced dietary nitrate is delivered to the oral cavity in saliva, a physiological process termed the enterosalivary circulation of nitrate. Previous studies demonstrated that disruption of enterosalivary circulation via use of oral antiseptics resulted in increases in systolic blood pressure. These previous studies did not include detailed information on the oral health of enrolled subjects. Using 16S rRNA gene sequencing and analysis, we determined whether introduction of chlorhexidine antiseptic mouthwash for 1 week was associated with changes in tongue bacterial communities and resting systolic blood pressure in healthy normotensive individuals with documented oral hygiene behaviors and free of oral disease. Tongue cleaning frequency was a predictor of chlorhexidine-induced changes in systolic blood pressure and tongue microbiome composition. Twice-daily chlorhexidine usage was associated with a significant increase in systolic blood pressure after 1 week of use and recovery from use resulted in an enrichment in nitrate-reducing bacteria on the tongue. Individuals with relatively high levels of bacterial nitrite reductases had lower resting systolic blood pressure. These results further support the concept of a symbiotic oral microbiome contributing to human health via the enterosalivary nitrate-nitrite-NO pathway. These data suggest that management of the tongue microbiome by regular cleaning together with adequate dietary intake of nitrate provide an opportunity for the improvement of resting systolic blood pressure.},
}

@article {pmid30878035,
year = {2019},
author = {Rowe, WP and Carrieri, AP and Alcon-Giner, C and Caim, S and Shaw, A and Sim, K and Kroll, JS and Hall, LJ and Pyzer-Knapp, EO and Winn, MD},
title = {Streaming histogram sketching for rapid microbiome analytics.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {40},
doi = {10.1186/s40168-019-0653-2},
pmid = {30878035},
issn = {2049-2618},
support = {100/974/C/13/Z//Wellcome Trust/United Kingdom ; BB/M011216/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; None//Winnicott Foundation/ ; },
abstract = {BACKGROUND: The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research, allowing for the design of new studies, augmentation of novel datasets and reanalysis of published works. This vast amount of microbiome data, as well as the widespread proliferation of microbiome research and the looming era of clinical metagenomics, means there is an urgent need to develop analytics that can process huge amounts of data in a short amount of time. To address this need, we propose a new method for tyrhe compact representation of microbiome sequencing data using similarity-preserving sketches of streaming k-mer spectra. These sketches allow for dissimilarity estimation, rapid microbiome catalogue searching and classification of microbiome samples in near real time.

RESULTS: We apply streaming histogram sketching to microbiome samples as a form of dimensionality reduction, creating a compressed 'histosketch' that can efficiently represent microbiome k-mer spectra. Using public microbiome datasets, we show that histosketches can be clustered by sample type using the pairwise Jaccard similarity estimation, consequently allowing for rapid microbiome similarity searches via a locality sensitive hashing indexing scheme. Furthermore, we use a 'real life' example to show that histosketches can train machine learning classifiers to accurately label microbiome samples. Specifically, using a collection of 108 novel microbiome samples from a cohort of premature neonates, we trained and tested a random forest classifier that could accurately predict whether the neonate had received antibiotic treatment (97% accuracy, 96% precision) and could subsequently be used to classify microbiome data streams in less than 3 s.

CONCLUSIONS: Our method offers a new approach to rapidly process microbiome data streams, allowing samples to be rapidly clustered, indexed and classified. We also provide our implementation, Histosketching Using Little K-mers (HULK), which can histosketch a typical 2 GB microbiome in 50 s on a standard laptop using four cores, with the sketch occupying 3000 bytes of disk space. (https://github.com/will-rowe/hulk).},
}

@article {pmid30877015,
year = {2019},
author = {Gómez-Acata, ES and Centeno, CM and Falcón, LI},
title = {Methods for extracting 'omes from microbialites.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mimet.2019.02.014},
pmid = {30877015},
issn = {1872-8359},
abstract = {Microbialites are organo-sedimentary structures formed by complex microbial communities that interact with abiotic factors to form carbonate rich fabrics. Extraction of DNA or total RNA from microbialites can be difficult because of the high carbonate mineral concentration and exopolymeric substances. The methods employed until now include substances such as cetyltrimethylammonium bromide, sodium dodecyl sulfate, xanthogenate, lysozyme and proteinase K, as well as mechanical disruption. Additionally, several commercial kits have been used to improve DNA and total RNA extraction. This minireview presents different methods applied for DNA and RNA extraction from microbialites and discusses their advantages and disadvantages. Moreover, extraction of all 'omes (DNA, RNA, Protein, Lipids, polar metabolites) using multiomic extraction methods (MPlex), as well as the state of art for extraction of viruses from microbialites, are also discussed.},
}

@article {pmid30875864,
year = {2019},
author = {Uritskiy, G and DiRuggiero, J},
title = {Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome.},
journal = {Genes},
volume = {10},
number = {3},
pages = {},
doi = {10.3390/genes10030220},
pmid = {30875864},
issn = {2073-4425},
support = {NNX15AP18G//National Aeronautics and Space Administration/ ; DEB1556574//National Science Foundation/ ; },
abstract = {In the past decades, the study of microbial life through shotgun metagenomic sequencing has rapidly expanded our understanding of environmental, synthetic, and clinical microbial communities. Here, we review how shotgun metagenomics has affected the field of halophilic microbial ecology, including functional potential reconstruction, virus⁻host interactions, pathway selection, strain dispersal, and novel genome discoveries. However, there still remain pitfalls and limitations from conventional metagenomic analysis being applied to halophilic microbial communities. Deconvolution of halophilic metagenomes has been difficult due to the high G + C content of these microbiomes and their high intraspecific diversity, which has made both metagenomic assembly and binning a challenge. Halophiles are also underrepresented in public genome databases, which in turn slows progress. With this in mind, this review proposes experimental and analytical strategies to overcome the challenges specific to the halophilic microbiome, from experimental designs to data acquisition and the computational analysis of metagenomic sequences. Finally, we speculate about the potential applications of other next-generation sequencing technologies in halophilic communities. RNA sequencing, long-read technologies, and chromosome conformation assays, not initially intended for microbiomes, are becoming available in the study of microbial communities. Together with recent analytical advancements, these new methods and technologies have the potential to rapidly advance the field of halophile research.},
}

@article {pmid30875404,
year = {2019},
author = {Kumar, S and Suyal, DC and Yadav, A and Shouche, Y and Goel, R},
title = {Microbial diversity and soil physiochemical characteristic of higher altitude.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213844},
doi = {10.1371/journal.pone.0213844},
pmid = {30875404},
issn = {1932-6203},
abstract = {Altitude is the major factor affecting both biodiversity and soil physiochemical properties of soil ecosystems. In order to understand the effect of altitude on soil physiochemical properties and bacterial diversity across the Himalayan cold desert, high altitude Gangotri soil ecosystem was studied and compared with the moderate altitude Kandakhal soil. Soil physiochemical analysis showed that altitude was positively correlated with soil pH, organic matter and total nitrogen content. However soil mineral nutrients and soil phosphorus were negatively correlated to the altitude. RT-PCR based analysis revealed the decreased bacterial and diazotrophic abundance at high altitude. Metagenomic study showed that Proteobacteria, Acidobacteria and Actinobacteria were dominant bacteria phyla at high altitude soil while Bacteroidetes and Fermicutes were found dominant at low altitude. High ratio of Gram-negative to Gram positive bacteria at Gangotri suggests the selective proliferation of Gram negative bacteria at high altitude with decrease in Gram positive bacteria. Moreover, Alphaproteobacteria was found more abundant at high altitude while the opposite was true for Betaproteobacteria. Abundance of Cytophaga, Flavobacterium and Bacteroides (CFB) were also found comparatively high at high altitude. Presence of many taxonomically unclassified sequences in Gangotri soil indicates the presence of novel bacterial diversity at high altitude. Further, isolation of bacteria through indigenously designed diffusion chamber revealed the existence of bacteria which has been documented in unculturable study of WIH (Western Indian Himalaya) but never been cultivated from WIH. Nevertheless, diverse functional free-living psychrotrophic diazotrophs were isolated only from the high altitude Gangotri soil. Molecular characterization revealed them as Arthrobacter humicola, Brevibacillus invocatus, Pseudomonas mandelii and Pseudomonas helmanticensis. Thus, this study documented the bacterial and psychrophilic diazotrophic diversity at high altitude and is an effort for exploration of low temperature bacteria in agricultural productivity with the target for sustainable hill agriculture.},
}

@article {pmid30875247,
year = {2019},
author = {Taylor, SL and Leong, LEX and Mobegi, FM and Choo, JM and Wesselingh, S and Yang, IA and Upham, JW and Reynolds, PN and Hodge, S and James, AL and Jenkins, C and Peters, MJ and Baraket, M and Marks, GB and Gibson, PG and Rogers, GB and Simpson, JL},
title = {Long-Term Azithromycin Reduces Haemophilus influenzae and Increases Antibiotic Resistance in Severe Asthma.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.201809-1739OC},
pmid = {30875247},
issn = {1535-4970},
abstract = {Rationale The macrolide antibiotic, azithromycin, reduces exacerbations in adults with persistent symptomatic asthma. However, owing to the pleotropic properties of macrolides, unintended bacteriological consequences such as augmented pathogen colonization or dissemination of antibiotic-resistant organisms can occur, calling into question the long-term safety of azithromycin maintenance therapy. Objectives To assess the effects of azithromycin on the airway microbiota, pathogen abundance, and carriage of antibiotic-resistance genes. Methods 16S rRNA sequencing and quantitative PCR (qPCR) were performed to assess the effect of azithromycin on sputum microbiology from participants of the AMAZES trial: a 48-week, double-blind, placebo-controlled trial of thrice-weekly 500mg oral azithromycin in adults with persistent uncontrolled asthma. Pooled-template shotgun metagenomic sequencing, qPCR, and isolate whole genome sequencing were performed to assess antibiotic resistance. Measurements and Main Results Paired sputum was available from 61 patients (n=34 placebo, n=27 azithromycin). Azithromycin did not affect bacterial load (p=0.37) but did significantly decrease Faith's bacterial diversity (p=0.026) and Haemophilus influenzae load (p<0.001). Azithromycin did not significantly affect levels of Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa or Moraxella catarrhalis. Of the 89 antibiotic resistance genes detected, macrolide resistance genes (erm(B), erm(F), msr(E), mef(A), and mel) and tetracycline resistance genes (tet(M) and tet(W)) were increased significantly. Conclusions In patients with persistent uncontrolled asthma, addition of azithromycin reduced airway H. influenzae load, with no changes to total or pathogenic bacterial loads. Macrolide resistance increased, reflecting previous studies. These results highlight the need for studies assessing the efficacy of non-antibiotic macrolides as long-term therapy for patients with persistent uncontrolled asthma.},
}

@article {pmid30875042,
year = {2019},
author = {Epp, LS and Zimmermann, HH and Stoof-Leichsenring, KR},
title = {Sampling and Extraction of Ancient DNA from Sediments.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {31-44},
doi = {10.1007/978-1-4939-9176-1_5},
pmid = {30875042},
issn = {1940-6029},
abstract = {Environmental DNA preserved in sediments is rapidly gaining importance as a tool in paleoecology. Sampling procedures for sedimentary ancient DNA (sedaDNA) have to be well planned to ensure clean subsampling of the inside of sediment cores and avoid introducing contamination. Additionally, ancient DNA extraction protocols may need to be optimized for the recovery of DNA from sediments, which may contain inhibitors. Here we describe procedures for subsampling both nonfrozen and frozen sediment cores, and we describe an efficient method for ancient DNA extraction from such samples.},
}

@article {pmid30875036,
year = {2019},
author = {Al-Masaudi, S and El Kaoutari, A and Drula, E and Redwan, EM and Lombard, V and Henrissat, B},
title = {A metagenomics investigation of carbohydrate-active enzymes along the goat and camel intestinal tract.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10123-019-00068-2},
pmid = {30875036},
issn = {1618-1905},
support = {67/130/35-HiCi//Deanship of Scientific Research, King Abdulaziz University, Jeddah/ ; },
abstract = {Studies of the digestive microbiota of ruminant animals most often focus on the bacterial diversity in the rumen or the feces of the animals, but little is known about the diversity and functions of their distal intestine. Here, the bacterial microbiota of the distal intestinal tract of two goats and two camels was investigated by metagenomics techniques. The bacterial taxonomic diversity and carbohydrate-active enzyme profile were estimated for samples taken from the small intestine, the large intestine, and the rectum of each animal. The bacterial diversity and abundance in the small intestine were lower than in the rectal and large intestinal samples. Analysis of the carbohydrate-active enzyme profiles at each site revealed a comparatively low abundance of enzymes targeting xylan and cellulose in all animals examined, similar to what has been reported earlier for sheep and therefore suggesting that plant cell wall digestion probably takes place elsewhere, such as in the rumen.},
}

@article {pmid30873724,
year = {2019},
author = {Zhang, M and Hill, JE and Fernando, C and Alexander, TW and Timsit, E and van der Meer, F and Huang, Y},
title = {Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease.},
journal = {Transboundary and emerging diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/tbed.13172},
pmid = {30873724},
issn = {1865-1682},
abstract = {Bovine respiratory disease (BRD) causes considerable economic losses in North America. The pathogenesis involves interactions between bacteria, viruses, environment and management factors. Primary viral infection can increase the risk of secondary fatal bacterial infection. The objective of this study was to use metagenomic sequencing to characterize the respiratory viromes of paired nasal swabs and tracheal washes from western Canadian feedlot cattle, with or without BRD. A total of 116 cattle (116 nasal swabs and 116 tracheal washes) were analyzed. The presence of influenza D virus (IDV), bovine rhinitis A virus (BRAV), bovine rhinitis B virus (BRBV), bovine coronavirus (BCV) and bovine respiratory syncytial virus (BRSV) was associated with BRD. Agreement between identification of viruses in nasal swabs and tracheal washes was generally weak, indicating that sampling location may affect detection of infection. This study reported several viruses for the first time in Canada and provides a basis for further studies investigating candidate viruses important to the prevention of BRD. This article is protected by copyright. All rights reserved.},
}

@article {pmid30872807,
year = {2019},
author = {Thomas, F and Corre, E and Cébron, A},
title = {Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-019-0394-z},
pmid = {30872807},
issn = {1751-7370},
support = {ANR-13-JSV7-0007_01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-13-JSV7-0007_01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.},
}

@article {pmid30872803,
year = {2019},
author = {Fones, EM and Colman, DR and Kraus, EA and Nothaft, DB and Poudel, S and Rempfert, KR and Spear, JR and Templeton, AS and Boyd, ES},
title = {Physiological adaptations to serpentinization in the Samail Ophiolite, Oman.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-019-0391-2},
pmid = {30872803},
issn = {1751-7370},
abstract = {Hydration of ultramafic rock during the geologic process of serpentinization can generate reduced substrates that microorganisms may use to fuel their carbon and energy metabolisms. However, serpentinizing environments also place multiple constraints on microbial life by generating highly reduced hyperalkaline waters that are limited in dissolved inorganic carbon. To better understand how microbial life persists under these conditions, we performed geochemical measurements on waters from a serpentinizing environment and subjected planktonic microbial cells to metagenomic and physiological analyses. Metabolic potential inferred from metagenomes correlated with fluid type, and genes involved in anaerobic metabolisms were enriched in hyperalkaline waters. The abundance of planktonic cells and their rates of utilization of select single-carbon compounds were lower in hyperalkaline waters than alkaline waters. However, the ratios of substrate assimilation to dissimilation were higher in hyperalkaline waters than alkaline waters, which may represent adaptation to minimize energetic and physiologic stress imposed by highly reducing, carbon-limited conditions. Consistent with this hypothesis, estimated genome sizes and average oxidation states of carbon in inferred proteomes were lower in hyperalkaline waters than in alkaline waters. These data suggest that microorganisms inhabiting serpentinized waters exhibit a unique suite of physiological adaptations that allow for their persistence under these polyextremophilic conditions.},
}

@article {pmid30871469,
year = {2019},
author = {Perz, AI and Giles, CB and Brown, CA and Porter, H and Roopnarinesingh, X and Wren, JD},
title = {MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations.},
journal = {BMC bioinformatics},
volume = {20},
number = {Suppl 2},
pages = {96},
doi = {10.1186/s12859-019-2623-x},
pmid = {30871469},
issn = {1471-2105},
abstract = {BACKGROUND: The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments. This could be a potentially powerful way to interpret new experiments, by identifying common themes and causes behind changes in species abundance.

RESULTS: We propose a novel framework for comparing microbial shifts between conditions. Using data from one of the largest human metagenome projects to date, the American Gut Project (AGP), we obtain differential abundance vectors for microbes using experimental condition information provided with the AGP metadata, such as patient age, dietary habits, or health status. We show it can be used to identify similar and opposing shifts in microbial species, and infer putative interactions between microbes. Our results show that groups of shifts with similar effects on microbiome can be identified and that similar dietary interventions display similar microbial abundance shifts.

CONCLUSIONS: Without comparison to prior data, it is difficult for experimentalists to know if their observed changes in species abundance have been observed by others, both in their conditions and in others they would never consider comparable. Yet, this can be a very important contextual factor in interpreting the significance of a shift. We've proposed and tested an algorithmic solution to this problem, which also allows for comparing the metagenomic signature shifts between conditions in the existing body of data.},
}

@article {pmid30871459,
year = {2019},
author = {Thrash, A and Arick, M and Barbato, RA and Jones, RM and Douglas, TA and Esdale, J and Perkins, EJ and Garcia-Reyero, N},
title = {Keanu: a novel visualization tool to explore biodiversity in metagenomes.},
journal = {BMC bioinformatics},
volume = {20},
number = {Suppl 2},
pages = {103},
doi = {10.1186/s12859-019-2629-4},
pmid = {30871459},
issn = {1471-2105},
abstract = {BACKGROUND: One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, especially with metagenomics data or data suspected to be contaminated. Here, we describe the development and application of a command-line tool, Keanu, for visualizing and exploring sample content in metagenomics data. We developed Keanu as an interactive tool to make viewing complex data easier.

RESULTS: Keanu, a tool for exploring sequence content, helps a user to understand the presence and abundance of organisms in a sample by analyzing alignments against a database that contains taxonomy data and displaying them in an interactive web page. The content of a sample can be presented either as a collapsible tree, with node size indicating abundance, or as a bilevel partition graph, with arc size indicating abundance. Here, we illustrate how Keanu works by exploring shotgun metagenomics data from a sample collected from a bluff that contained paleosols and a krotovina in an alpine site in Ft. Greely, Alaska.

CONCLUSIONS: Keanu provides a simple means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu .},
}

@article {pmid30871224,
year = {2019},
author = {Gurwara, S and Ajami, NJ and Jang, A and Hessel, FC and Chen, L and Plew, S and Wang, Z and Graham, DY and Hair, C and White, DL and Kramer, J and Kourkoumpetis, T and Hoffman, K and Cole, R and Hou, J and Husain, N and Jarbrink-Sehgal, M and Hernaez, R and Kanwal, F and Ketwaroo, G and Shah, R and Velez, M and Natarajan, Y and El-Serag, HB and Petrosino, JF and Jiao, L},
title = {Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon.},
journal = {Nutrients},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/nu11030613},
pmid = {30871224},
issn = {2072-6643},
support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; 1000//Gillson Longenbaugh Foundation/ ; 0000//Golfers Against Cancer/ ; },
abstract = {One carbon (1C) metabolism nutrients influence epigenetic regulation and they are supplied by diet and synthesized by gut microbiota. We examined the association between dietary consumption of methyl donors (methionine, betaine and choline) and B vitamins (folate, B2, B6, and B12) and the community composition and structure of the colonic mucosa-associated gut microbiota determined by 16S rRNA gene sequencing in 97 colonic biopsies of 35 men. We used the food frequency questionnaire to assess daily consumption of nutrients, and the UPARSE and SILVA databases for operational taxonomic unit classification. The difference in bacterial diversity and taxonomic relative abundance were compared between low versus high consumption of these nutrients. False discover rate (FDR) adjusted p value < 0.05 indicated statistical significance. The bacterial richness and composition differed significantly by the consumption of folate and B vitamins (p < 0.001). Compared with higher consumption, a lower consumption of these nutrients was associated with a lower abundance of Akkermansia (folate), Roseburia (vitamin B2), and Faecalibacterium (vitamins B2, B6, and B12) but a higher abundance of Erysipelatoclostridium (vitamin B2) (FDR p values < 0.05). The community composition and structure of the colonic bacteria differed significantly by dietary consumption of folate and B vitamins.},
}

@article {pmid30871085,
year = {2019},
author = {Lin, JH and Wu, ZY and Gong, L and Wong, CH and Chao, WC and Yen, CM and Wang, CP and Wei, CL and Huang, YT and Liu, PY},
title = {Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing.},
journal = {Journal of clinical medicine},
volume = {8},
number = {3},
pages = {},
doi = {10.3390/jcm8030351},
pmid = {30871085},
issn = {2077-0383},
support = {TCVGH-1083901B//Taichung Veterans General Hospital/ ; },
abstract = {Brain abscess is a severe infectious disease with high mortality and mobility. Although culture-based techniques have been widely used for the investigation of microbial composition of brain abscess, these approaches are inherent biased. Recent studies using 16S ribosomal sequencing approaches revealed high complexity of the bacterial community involved in brain abscess but fail to detect fungal and viral composition. In the study, both culture-independent nanopore metagenomic sequencing and culture-based whole-genome sequencing using both the Illumina and the Nanopore platforms were conducted to investigate the microbial composition and genomic characterization in brain abscess. Culture-independent metagenomic sequencing revealed not only a larger taxonomic diversity of bacteria but also the presence of fungi and virus communities. The culture-based whole-genome sequencing identified a novel species in Prevotella and reconstructs a Streptococcus constellatus with a high GC-skew genome. Antibiotic-resistance genes CfxA and ErmF associated with resistance to penicillin and clindamycin were also identified in culture-based and culture-free sequencing. This study implies current understanding of brain abscess need to consider the broader diversity of microorganisms.},
}

@article {pmid30609875,
year = {2019},
author = {Waseem, H and Jameel, S and Ali, J and Saleem Ur Rehman, H and Tauseef, I and Farooq, U and Jamal, A and Ali, MI},
title = {Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {1},
pages = {},
doi = {10.3390/molecules24010163},
pmid = {30609875},
issn = {1420-3049},
mesh = {Anti-Infective Agents/*pharmacology ; Computational Biology/methods ; Data Analysis ; *Drug Resistance, Microbial ; *Environmental Microbiology ; Gastrointestinal Microbiome ; Genes, Bacterial ; *High-Throughput Screening Assays ; Humans ; Metagenome ; Metagenomics/methods ; Quality Control ; *Real-Time Polymerase Chain Reaction ; },
abstract = {Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGenTM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.},
}

Anti-Infective Agents/*pharmacology
Computational Biology/methods
Data Analysis
*Drug Resistance, Microbial
*Environmental Microbiology
Gastrointestinal Microbiome
Genes, Bacterial
*High-Throughput Screening Assays
Humans
Metagenome
Metagenomics/methods
Quality Control
*Real-Time Polymerase Chain Reaction

@article {pmid29611114,
year = {2018},
author = {Wang, J and Chen, L and Zhao, N and Xu, X and Xu, Y and Zhu, B},
title = {Of genes and microbes: solving the intricacies in host genomes.},
journal = {Protein & cell},
volume = {9},
number = {5},
pages = {446-461},
pmid = {29611114},
issn = {1674-8018},
mesh = {Animals ; Biomedical Research ; *Genes ; *Genetic Variation ; *Genome ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenomics ; *Microbiota ; },
abstract = {Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.},
}

Animals
Biomedical Research
*Genes
*Genetic Variation
*Genome
Host-Pathogen Interactions/*genetics
Humans
Metagenomics
*Microbiota

@article {pmid28827532,
year = {2017},
author = {Jiang, J and Song, Z and Yang, X and Mao, Z and Nie, X and Guo, H and Peng, X},
title = {Microbial community analysis of apple rhizosphere around Bohai Gulf.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8918},
pmid = {28827532},
issn = {2045-2322},
mesh = {Biodiversity ; Environment ; Malus/*microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Plant Roots/microbiology ; *Rhizosphere ; *Soil Microbiology ; },
abstract = {Bohai Gulf is the main area for apple tree cultivation in China. Consecutive replanting significantly affects the yield and quality of apple trees in this area. Microecological imbalance in apple trees' rhizospheres caused by variation in the soil microbial community is considered the primary cause of apple replant disease (ARD). This study analysed the microbial communities of the rhizospheres of perennial apple trees (PAT) and apple tree saplings under replanting (ATS) around Bohai Gulf using high-throughput sequencing. The results revealed increased populations of typical pathogenic fungi Verticillium and bacteria Xanthomonadaceae, and decreased populations of beneficial bacterial populations Pseudomonas and Bacillus with replanting, suggesting that competition between pathogens and beneficial microbes varies according to the ratio of pathogens to beneficial microbes in rhizosphere soil under the replanting system. Meanwhile, replanting was accompanied by an increase in the antagonistic bacteria Arthrobacter and fungus Chaetomium, suggesting that increased numbers of pathogens can lead to more instances of antagonism. Redundancy analysis (RDA) revealed site position and the main soil properties (pH, organic matter, available N, available K, available P, and moisture) affected the microbial community composition. It found clear differences in soil microbial communities and demonstrated a better understanding of the causes for ARD.},
}

Biodiversity
Environment
Malus/*microbiology
Metagenome
Metagenomics
*Microbiota
Plant Roots/microbiology
*Rhizosphere
*Soil Microbiology

@article {pmid28821872,
year = {2017},
author = {Nakagawa, S and Saito, H and Tame, A and Hirai, M and Yamaguchi, H and Sunata, T and Aida, M and Muto, H and Sawayama, S and Takaki, Y},
title = {Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8764},
pmid = {28821872},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; Fish Diseases/microbiology ; Helicobacter/*classification/*genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Starfish/*microbiology ; },
abstract = {Marine invertebrates associate with diverse microorganisms. Microorganisms even inhabit coelomic fluid (CF), namely, the fluid filling the main body cavity of echinoderms. The CF microbiota potentially impacts host health and disease. Here, we analysed the CF microbiota in two common coastal starfish species, Patiria pectinifera and Asterias amurensis. Although microbial community structures were highly variable among individual starfish, those of P. pectinifera were compositionally similar to those in the surrounding seawater. By contrast, many A. amurensis individuals harboured unique microbes in the CF, which was dominated by the unclassified Thiotrichales or previously unknown Helicobacter-related taxon. In some individuals, the Helicobacter-related taxon was the most abundant genus-level taxon, accounting for up to 97.3% of reads obtained from the CF microbial community. Fluorescence in situ hybridization using a Helicobacter-related-taxon-specific probe suggested that probe-reactive cells in A. amurensis were spiral-shaped, morphologically similar to known Helicobacter species. Electron microscopy revealed that the spiral cells had a prosthecate-like polar appendage that has never been reported in Helicobacter species. Although culture of Helicobacter-related taxon was unsuccessful, this is the first report of the dominance of a Helicobacter-related taxon in invertebrates and non-digestive organs, reshaping our knowledge of the phylogeography of Helicobacter-related taxa.},
}

Animals
*Biodiversity
Fish Diseases/microbiology
Helicobacter/*classification/*genetics
Metagenome
Metagenomics/methods
*Microbiota
Phylogeography
RNA, Ribosomal, 16S/genetics
Starfish/*microbiology

@article {pmid28821814,
year = {2017},
author = {Fang, D and Shi, D and Lv, L and Gu, S and Wu, W and Chen, Y and Guo, J and Li, A and Hu, X and Guo, F and Ye, J and Li, Y and Li, L},
title = {Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8770},
pmid = {28821814},
issn = {2045-2322},
mesh = {Animals ; Bifidobacterium/*physiology ; Bifidobacterium pseudocatenulatum/*physiology ; Cytokines/blood/metabolism ; Galactosamine/*adverse effects ; Gastrointestinal Microbiome/*drug effects ; Inflammation Mediators/blood/metabolism ; Intestinal Mucosa/drug effects/metabolism/pathology ; Liver Diseases/*etiology/metabolism/pathology ; Male ; Metagenome ; Metagenomics ; Models, Biological ; Rats ; },
abstract = {The gut microbiota is altered in liver diseases, and several probiotics have been shown to reduce the degree of liver damage. We hypothesized that oral administration of specific Bifidobacterium strains isolated from healthy guts could attenuate liver injury. Five strains were tested in this study. Acute liver injury was induced by D-galactosamine after pretreating Sprague-Dawley rats with the Bifidobacterium strains, and liver function, liver and ileum histology, plasma cytokines, bacterial translocation and the gut microbiome were assessed. Two strains, Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10, conferred liver protection, as well as alleviated the increase in plasma M-CSF, MIP-1α and MCP-1 and bacterial translocation. They also ameliorated ileal mucosal injury and gut flora dysbiosis, especially the enrichment of the opportunistic pathogen Parasutterella and the depletion of the SCFA-producing bacteria Anaerostipes, Coprococcus and Clostridium XI. Negative correlations were found between MIP-1α / MCP-1 and Odoribacter (LI09 group) and MIP-1α / M-CSF and Flavonifractor (LI10 group). Our results indicate that the liver protection effects might be mediated through gut microbiota modification, which thus affect the host immune profile. The desirable characteristics of these two strains may enable them to serve as potential probiotics for the prevention or adjuvant treatment of liver injury.},
}

Animals
Bifidobacterium/*physiology
Bifidobacterium pseudocatenulatum/*physiology
Cytokines/blood/metabolism
Galactosamine/*adverse effects
Gastrointestinal Microbiome/*drug effects
Inflammation Mediators/blood/metabolism
Intestinal Mucosa/drug effects/metabolism/pathology
Liver Diseases/*etiology/metabolism/pathology
Male
Metagenome
Metagenomics
Models, Biological
Rats

@article {pmid30868805,
year = {2019},
author = {Liu, ZX and Xu, J and Sun, W and Shi, YH and Chen, SL},
title = {[Application of DNA metabarcoding in species identification of Chinese herbal medicines].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {44},
number = {1},
pages = {1-8},
doi = {10.19540/j.cnki.cjcmm.2019.0001},
pmid = {30868805},
issn = {1001-5302},
abstract = {DNA metabarcoding,one rapid and robust method using specific standard DNA fragments,has been widely used for rapid species identification of a bulk sample through high-throughput sequencing technologies.While it has been widely used in the studies of metagenomics,animal and plant biodiversity,it has gradually come to be used as a profitable method in species identification of mixed Chinese herbal medicines.In this paper,we mainly summarize the current studies of the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines.Moreover,high-throughput sequencing technologies adopted in those studies,such as Sanger,the next-generation,and third-generation sequencing technologies,are discussed.It is conducted to provide a theoretical guidance for the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines and in more other biodiversity studies.},
}

@article {pmid30867546,
year = {2019},
author = {Smith, AR and Kieft, B and Mueller, R and Fisk, MR and Mason, OU and Popa, R and Colwell, FS},
title = {Carbon fixation and energy metabolisms of a subseafloor olivine biofilm.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-019-0385-0},
pmid = {30867546},
issn = {1751-7370},
abstract = {Earth's largest aquifer ecosystem resides in igneous oceanic crust, where chemosynthesis and water-rock reactions provide the carbon and energy that support an active deep biosphere. The Calvin Cycle is the predominant carbon fixation pathway in cool, oxic, crust; however, the energy and carbon metabolisms in the deep thermal basaltic aquifer are poorly understood. Anaerobic carbon fixation pathways such as the Wood-Ljungdahl pathway, which uses hydrogen (H2) and CO2, may be common in thermal aquifers since water-rock reactions can produce H2 in hydrothermal environments and bicarbonate is abundant in seawater. To test this, we reconstructed the metabolisms of eleven bacterial and archaeal metagenome-assembled genomes from an olivine biofilm obtained from a Juan de Fuca Ridge basaltic aquifer. We found that the dominant carbon fixation pathway was the Wood-Ljungdahl pathway, which was present in seven of the eight bacterial genomes. Anaerobic respiration appears to be driven by sulfate reduction, and one bacterial genome contained a complete nitrogen fixation pathway. This study reveals the potential pathways for carbon and energy flux in the deep anoxic thermal aquifer ecosystem, and suggests that ancient H2-based chemolithoautotrophy, which once dominated Earth's early biosphere, may thus remain one of the dominant metabolisms in the suboceanic aquifer today.},
}

@article {pmid30867542,
year = {2019},
author = {Amato, P and Besaury, L and Joly, M and Penaud, B and Deguillaume, L and Delort, AM},
title = {Metatranscriptomic exploration of microbial functioning in clouds.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {4383},
doi = {10.1038/s41598-019-41032-4},
pmid = {30867542},
issn = {2045-2322},
support = {ANR-15-CE01-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-DFG-14-CE35-005-02//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Clouds constitute the uppermost layer of the biosphere. They host diverse communities whose functioning remains obscure, although biological activity potentially participates to atmospheric chemical and physical processes. In order to gain information on the metabolic functioning of microbial communities in clouds, we conducted coordinated metagenomics/metatranscriptomics profiling of cloud water microbial communities. Samples were collected from a high altitude atmospheric station in France and examined for biological content after untargeted amplification of nucleic acids. Living microorganisms, essentially bacteria, maintained transcriptional and translational activities and expressed many known complementary physiological responses intended to fight oxidants, osmotic variations and cold. These included activities of oxidant detoxification and regulation, synthesis of osmoprotectants/cryoprotectants, modifications of membranes, iron uptake. Consistently these energy-demanding processes were fueled by central metabolic routes involved in oxidative stress response and redox homeostasis management, such as pentose phosphate and glyoxylate pathways. Elevated binding and transmembrane ion transports demonstrated important interactions between cells and their cloud droplet chemical environments. In addition, polysaccharides, potentially beneficial for survival like exopolysaccharides, biosurfactants and adhesins, were synthesized. Our results support a biological influence on cloud physical and chemical processes, acting notably on the oxidant capacity, iron speciation and availability, amino-acids distribution and carbon and nitrogen fates.},
}

@article {pmid30867497,
year = {2019},
author = {Tu, P and Gao, B and Chi, L and Lai, Y and Bian, X and Ru, H and Lu, K},
title = {Subchronic low-dose 2,4-D exposure changed plasma acylcarnitine levels and induced gut microbiome perturbations in mice.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {4363},
doi = {10.1038/s41598-019-40776-3},
pmid = {30867497},
issn = {2045-2322},
support = {R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R01ES024950//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; },
abstract = {The gut microbiota critically confers various health benefits, whereas environmental chemicals can affect its constitution and functionality thereby increasing disease risk. In the present study, we aim to evaluate the toxic effects of a wildly-used herbicide 2,4-D (2,4-dichlorophenoxyacetic acid) on the gut microbiome and host using an occupationally relevant dose. A mouse model was used combined with metagenomic sequencing and metabolomic profiling to examine the alterations induced by subchronic low-dose 2,4-D exposure in fecal and plasma samples. The metagenomics results revealed a distinct gut microbial community with profound changes in diverse microbial pathways including urea degradation, amino acid and carbohydrate metabolism in 2,4-D-treated mice. Moreover, the metabolomics results revealed that the metabolic profiles in treatment group were differentiated from control group in both fecal and plasma samples. Toxic effects on the host of 2,4-D at an occupationally relevant dose were observed indicated by decreased acylcarnitine levels in plasma. These findings indicated that 2,4-D can cause toxicity and substantially impact the gut microbiome in mice at occupationally relevant doses, inferring that the relationship between environmental contaminants and microbiota is largely underestimated calling for more comprehensive consideration of the toxicity of occupational exposures.},
}

@article {pmid30867308,
year = {2019},
author = {Chong, R and Shi, M and Grueber, CE and Holmes, EC and Hogg, CJ and Belov, K and Barrs, VR},
title = {Fecal viral diversity of captive and wild Tasmanian devils characterized using virion-enriched metagenomics and meta-transcriptomics.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JVI.00205-19},
pmid = {30867308},
issn = {1098-5514},
abstract = {The Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumour disease (DFTD). While research on DFTD has been extensive, little is known about viruses in devils, and whether any are of potential conservation relevance for this endangered species. Using both metagenomics based on virion enrichment and sequence-independent amplification (virion-enriched metagenomics) and meta-transcriptomics based on bulk RNA sequencing, we characterized and compared the fecal viromes of captive and wild devils. A total of 54 fecal samples collected from 2 captive and 4 wild populations were processed for virome characterization using both approaches. In total, 24 novel marsupial-related viruses, comprising a sapelovirus, astroviruses, rotaviruses, picobirnaviruses, parvoviruses, papillomaviruses, polyomaviruses and a gammaherpesvirus were identified, as well as known mammalian pathogens such as rabbit haemorrhagic disease virus 2. Captive devils showed significantly lower viral diversity than wild devils. Comparison of the two virus discovery approaches revealed substantial differences in the number and types of viruses detected, with meta-transcriptomics better suited for RNA viruses and virion-enriched metagenomics largely identifying more DNA viruses. Thus, the viral communities revealed by virion-enriched metagenomics and meta-transcriptomics were not interchangeable and neither approach was able to detect all viruses present. An integrated approach using both virion-enriched metagenomics and meta-transcriptomics constitutes a powerful tool for obtaining a complete overview of both the taxonomic and functional profiles of viral communities within a sample.Importance: The Tasmanian devil is an iconic Australian marsupial that has suffered an 80% population decline due to a contagious cancer, devil facial tumour disease, along with other threats. Until now, viral discovery in this species has been confined to one gammaherpesvirus (DaHV-2), for which captivity was identified as a significant risk factor. Our discovery of 24 novel marsupial-associated RNA and DNA viruses, and that viral diversity is lower in captive than wild devils, has greatly expanded our knowledge of gut-associated viruses in devils and provides important baseline information that will contribute to the conservation and captive management of this endangered species. Our results also revealed that a combination of virion-enriched metagenomics and meta-transcriptomics may be a more comprehensive approach for virome characterization than either method alone. Our results thus provide a springboard for continuous improvements in the way we study complex viral communities.},
}

@article {pmid30866812,
year = {2019},
author = {Das, P and Babaei, P and Nielsen, J},
title = {Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {208},
doi = {10.1186/s12864-019-5591-7},
pmid = {30866812},
issn = {1471-2164},
support = {HEALTH-F4-2012-305312//METACARDIS/ ; },
abstract = {BACKGROUND: Human gut microbial communities have been known to produce vitamins, which are subsequently absorbed by the host in the large intestine. However, the relationship between species with vitamin pathway associated functional features or their gene abundance in different states of health and disease is lacking. Here, we analyzed shotgun fecal metagenomes of individuals from four different countries for genes that are involved in vitamin biosynthetic pathways and transport mechanisms and corresponding species' abundance.

RESULTS: We found that the prevalence of these genes were found to be distributed across the dominant phyla of gut species. The number of positive correlations were high between species harboring genes related to vitamin biosynthetic pathways and transporter mechanisms than that with either alone. Although, the range of total gene abundances remained constant across healthy populations at the global level, species composition and their presence for metabolic pathway related genes determine the abundance and functional genetic content of vitamin metabolism. Based on metatranscriptomics data, the equation between abundance of vitamin-biosynthetic enzymes and vitamin-dependent enzymes suggests that the production and utilization potential of these enzymes seems way more complex usage allocations than just mere direct linear associations.

CONCLUSIONS: Our findings provide a rationale to examine and disentangle the interrelationship between B-vitamin dosage (dietary or microbe-mediated) on gut microbial members and the host, in the gut microbiota of individuals with under- or overnutrition.},
}

@article {pmid30866778,
year = {2019},
author = {Li, J and Cui, L and Deng, X and Yu, X and Zhang, Z and Yang, Z and Delwart, E and Zhang, W and Hua, X},
title = {Canine bufavirus in faeces and plasma of dogs with diarrhoea, China.},
journal = {Emerging microbes & infections},
volume = {8},
number = {1},
pages = {245-247},
doi = {10.1080/22221751.2018.1563457},
pmid = {30866778},
issn = {2222-1751},
}

@article {pmid30866714,
year = {2019},
author = {Park, H and Laffin, MR and Jovel, J and Millan, B and Hyun, JE and Hotte, N and Kao, D and Madsen, KL},
title = {The success of fecal microbial transplantation in Clostridium difficile infection correlates with bacteriophage relative abundance in the donor: a retrospective cohort study.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/19490976.2019.1586037},
pmid = {30866714},
issn = {1949-0984},
abstract = {BACKGROUND: Fecal microbial transplantation (FMT) is used in the treatment of relapsing Clostridium difficile infection (rCDI). Failure rate for FMT is as high as 10% but the mechanisms contributing to a failed FMT are not understood. We utilized metagenomic data to identify the role of bacteria and bacteriophages on FMT success.

RESULTS: Subjects with rCDI (n = 19) received FMT from volunteer donors (n = 7) via colonoscopy. Twelve patients fully recovered after a single FMT, while seven patients required a subsequent FMT. DNA was extracted from patient and donor stool samples for shotgun metagenomic analysis. Metagenomics libraries were analyzed focusing on bacterial taxonomy and bacteriophage sequences. Gammaproteobacteria were dominant in rCDI patients prior to FMT largely due to elevated levels of Klebsiella and Escherichia. A successful FMT led to increased levels of Clostridia and Bacteroidia and a reduction in Gammaproteobacteria. In contrast, a failed FMT led to no significant changes in bacterial composition. Bacteriophages were classified during whole metagenomic analysis of each sample and were markedly different between rCDI patients, donors, and a healthy control cohort (n = 96). Bacteriophage sequence reads were increased in CDI patients compared with donors and healthy controls. Successful FMT donors had higher bacteriophage α-diversity and lower relative abundance compared to the donors of a failed initial FMT.

CONCLUSIONS: In this retrospective analysis, FMTs with increased bacteriophage α-diversity were more likely to successfully treat rCDI. In addition, the relative number of bacteriophage reads was lower in donations leading to a successful FMT. These results suggest that bacteriophage abundance may have some role in determining the relative success of FMT.},
}

@article {pmid30866521,
year = {2019},
author = {François, S and Mutuel, D and Duncan, AB and Rodrigues, LR and Danzelle, C and Lefevre, S and Santos, I and Frayssinet, M and Fernandez, E and Filloux, D and Roumagnac, P and Froissart, R and Ogliastro, M},
title = {A New Prevalent Densovirus Discovered in Acari. Insight from Metagenomics in Viral Communities Associated with Two-Spotted Mite (Tetranychus urticae) Populations.},
journal = {Viruses},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/v11030233},
pmid = {30866521},
issn = {1999-4915},
abstract = {Viral metagenomics and high throughput sequence mining have revealed unexpected diversity, and the potential presence, of parvoviruses in animals from all phyla. Among arthropods, this diversity highlights the poor knowledge that we have regarding the evolutionary history of densoviruses. The aim of this study was to explore densovirus diversity in a small arthropod pest belonging to Acari, the two-spotted spider mite Tetranychus urticae, while using viral metagenomics based on virus-enrichment. Here, we present the viromes obtained from T. urticae laboratory populations made of contigs that are attributed to nine new potential viral species, including the complete sequence of a novel densovirus. The genome of this densovirus has an ambisens genomic organization and an unusually compact size with particularly small non-structural proteins and a predicted major capsid protein that lacks the typical PLA2 motif that is common to all ambidensoviruses described so far. In addition, we showed that this new densovirus had a wide prevalence across populations of mite species tested and a genomic diversity that likely correlates with the host phylogeny. In particular, we observed a low densovirus genomic diversity between the laboratory and natural populations, which suggests that virus within-species evolution is probably slower than initially thought. Lastly, we showed that this novel densovirus can be inoculated to the host plant following feeding by infected mites, and circulate through the plant vascular system. These findings offer new insights into densovirus prevalence, evolution, and ecology.},
}

@article {pmid30866512,
year = {2019},
author = {Amor Stander, E and Williams, W and Rautenbach, F and Le Roes-Hill, M and Mgwatyu, Y and Marnewick, J and Hesse, U},
title = {Visualization of Aspalathin in Rooibos (Aspalathus linearis) Plant and Herbal Tea Extracts Using Thin-Layer Chromatography.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {5},
pages = {},
doi = {10.3390/molecules24050938},
pmid = {30866512},
issn = {1420-3049},
support = {CSUR150714125961//National Research Foundation/ ; },
abstract = {Aspalathin, the main polyphenol of rooibos (Aspalathus linearis), is associated with diverse health promoting properties of the tea. During fermentation, aspalathin is oxidized and concentrations are significantly reduced. Standardized methods for quality control of rooibos products do not investigate aspalathin, since current techniques of aspalathin detection require expensive equipment and expertise. Here, we describe a simple and fast thin-layer chromatography (TLC) method that can reproducibly visualize aspalathin in rooibos herbal tea and plant extracts at a limit of detection (LOD) equal to 178.7 ng and a limit of quantification (LOQ) equal to 541.6 ng. Aspalathin is a rare compound, so far only found in A. linearis and its (rare) sister species A. pendula. Therefore, aspalathin could serve as a marker compound for authentication and quality control of rooibos products, and the described TLC method represents a cost-effective approach for high-throughput screening of plant and herbal tea extracts.},
}

@article {pmid30594064,
year = {2019},
author = {Procopio, N and Ghignone, S and Williams, A and Chamberlain, A and Mello, A and Buckley, M},
title = {Metabarcoding to investigate changes in soil microbial communities within forensic burial contexts.},
journal = {Forensic science international. Genetics},
volume = {39},
number = {},
pages = {73-85},
doi = {10.1016/j.fsigen.2018.12.002},
pmid = {30594064},
issn = {1878-0326},
mesh = {Animals ; Burial ; DNA Barcoding, Taxonomic/*methods ; Forensic Sciences ; Metagenomics/methods ; Microbiota/*genetics ; Models, Animal ; Polymerase Chain Reaction ; *Postmortem Changes ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Swine ; },
abstract = {The estimation of the time elapsed since death (post-mortem interval, or PMI) is one of the key themes that forensic scientists have to address frequently. However, the estimation of PMI still suffers from poor accuracy and biases especially when decomposition stages are prolonged, so further improvements in methods for PMI estimation are desirable. Soil microbial communities associated with decomposing bodies have been shown to be good candidates for the estimation of the PMI of exposed bodies. Nevertheless, further research is required to better understand the bacterial succession associated with decomposition of buried carcasses in order to test its reliability and applicability for the estimation of PMI and to better understand the dynamics involved with decomposition within this particular scenario. Therefore we explored the succession of soil microbial communities associated with four decomposing pig carcasses (from one to six months PMI) using a metabarcoding approach. The sequencing of the bacterial 16S rRNA variable region 4 (V4) revealed trends linking particular microbial taxa with specific PMIs, and notably an increase in Proteobacteria, Firmicutes and Bacteroidetes at specific PMIs as well as a decrease in Acidobacteria. Our results, in accordance with previous studies conducted on exposed bodies of different mammalian species (including humans), also showed a general reduction of the taxonomic richness from two months PMI onwards, as well as an incomplete re-establishment of the starting soil microbial conditions after six months PMI. We also found specific mammal-derived taxa, such as Bacteroides spp., being still present in the soil after six months PMI. As such, this study serves as a baseline for additional research to allow the characterisation of biomarkers associated with specific PMIs. Due to the similarity between the results presented here and those reported in other types of decomposition studies we believe that the metabarcoding approach has considerable potential in the estimation of the PMI, particularly to clarify cases involving heavily skeletonised bodies or for the investigation of clandestine graves in which the carcass has been moved from its original place of deposition.},
}

Animals
Burial
DNA Barcoding, Taxonomic/*methods
Forensic Sciences
Metagenomics/methods
Microbiota/*genetics
Models, Animal
Polymerase Chain Reaction
*Postmortem Changes
RNA, Ribosomal, 16S
*Soil Microbiology
Swine

@article {pmid30496170,
year = {2018},
author = {Shoko, R and Manasa, J and Maphosa, M and Mbanga, J and Mudziwapasi, R and Nembaware, V and Sanyika, WT and Tinago, T and Chikwambi, Z and Mawere, C and Matimba, A and Mugumbate, G and Mufandaedza, J and Mulder, N and Patterton, H},
title = {Strategies and opportunities for promoting bioinformatics in Zimbabwe.},
journal = {PLoS computational biology},
volume = {14},
number = {11},
pages = {e1006480},
doi = {10.1371/journal.pcbi.1006480},
pmid = {30496170},
issn = {1553-7358},
mesh = {*Computational Biology ; Food Supply ; Health Status Indicators ; Humans ; Interprofessional Relations ; Metagenomics ; Zimbabwe/epidemiology ; },
}

*Computational Biology
Food Supply
Health Status Indicators
Humans
Interprofessional Relations
Metagenomics
Zimbabwe/epidemiology

@article {pmid30864784,
year = {2019},
author = {Zhang, W and Gu, J and Li, Y and Lin, L and Wang, P and Wang, C and Qian, B and Wang, H and Niu, L and Wang, L and Zhang, H and Gao, Y and Zhu, M and Fang, S},
title = {New Insights into Sediment Transport in Interconnected River-Lake Systems Through Tracing Microorganisms.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.8b07334},
pmid = {30864784},
issn = {1520-5851},
abstract = {A growing awareness of the wider environmental significance of diffuse sediment pollution in interconnected river-lake systems has generated the need for reliable provenance information. Owing to their insufficient ability to distinguish between multiple sources, common sediment source apportionment methods would rarely be a practical solution. Based on the inseparable relationships between sediment and adsorbed microorganisms, community-based microbial source tracking may be a novel method of identifying dominant sediment sources in the era of high-throughput sequencing. Dongting Lake was selected as a study area as it receives considerable sediment import from its inflowing rivers during the flood season. This study was conducted to characterize the bacterial community composition of sediment samples from the inflow-river estuaries and quantify their sediment microbe contributions to the central lake. Metagenomic analysis revealed that the community compositions of source sediment samples were significantly different, allowing specific sources to be identified with the machine learning classification program SourceTracker. Modified analysis using SourceTracker found that the major contributors to three major lake districts were the Songzi, Zishui, and Xinqiang Rivers. The impacts of hydrodynamic conditions on source apportionment were further verified, and suggested the practicability of this method to offer a systematic and comprehensive understanding of sediment sources, pathways, and transport dynamics. Finally, a novel framework for sediment source-tracking was established to develop effective sediment management and control strategies in river-lake systems.},
}

@article {pmid30864339,
year = {2019},
author = {Gürsoy, G and Harmanci, A and Tang, H and Ayday, E and Brenner, SE},
title = {When Biology Gets Personal: Hidden Challenges of Privacy and Ethics in Biological Big Data.},
journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing},
volume = {24},
number = {},
pages = {386-390},
pmid = {30864339},
issn = {2335-6936},
abstract = {High-throughput technologies for biological data acquisition are advancing at an increasing pace. Most prominently, the decreasing cost of DNA sequencing has led to an exponential growth of sequence information, including individual human genomes. This session of the 2019 Pacific Symposium on Biocomputing presents the distinctive privacy and ethical challenges related to the generation, storage, processing, study, and sharing of individuals' biological data generated by multitude of technologies including but not limited to genomics, proteomics, metagenomics, bioimaging, biosensors, and personal health trackers. The mission is to bring together computational biologists, experimental biologists, computer scientists, ethicists, and policy and lawmakers to share ideas, discuss the challenges related to biological data and privacy.},
}

@article {pmid30864326,
year = {2019},
author = {Han, W and Ye, Y},
title = {A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data.},
journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing},
volume = {24},
number = {},
pages = {236-247},
pmid = {30864326},
issn = {2335-6936},
abstract = {The microbiome research is going through an evolutionary transition from focusing on the characterization of reference microbiomes associated with different environments/hosts to the translational applications, including using microbiome for disease diagnosis, improving the effcacy of cancer treatments, and prevention of diseases (e.g., using probiotics). Microbial markers have been identified from microbiome data derived from cohorts of patients with different diseases, treatment responsiveness, etc, and often predictors based on these markers were built for predicting host phenotype given a microbiome dataset (e.g., to predict if a person has type 2 diabetes given his or her microbiome data). Unfortunately, these microbial markers and predictors are often not published so are not reusable by others. In this paper, we report the curation of a repository of microbial marker genes and predictors built from these markers for microbiome-based prediction of host phenotype, and a computational pipeline called Mi2P (from Microbiome to Phenotype) for using the repository. As an initial effort, we focus on microbial marker genes related to two diseases, type 2 diabetes and liver cirrhosis, and immunotherapy efficacy for two types of cancer, non-small-cell lung cancer (NSCLC) and renal cell carcinoma (RCC). We characterized the marker genes from metagenomic data using our recently developed subtractive assembly approach. We showed that predictors built from these microbial marker genes can provide fast and reasonably accurate prediction of host phenotype given microbiome data. As understanding and making use of microbiome data (our second genome) is becoming vital as we move forward in this age of precision health and precision medicine, we believe that such a repository will be useful for enabling translational applications of microbiome data.},
}

@article {pmid30864226,
year = {2019},
author = {Zhang, Y and Zhao, R and Shi, D and Sun, S and Ren, H and Zhao, H and Wu, W and Jin, L and Sheng, J and Shi, Y},
title = {Characterization of the Circulating Microbiome in Acute-on-chronic Liver Failure Associated with Hepatitis B.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1111/liv.14097},
pmid = {30864226},
issn = {1478-3231},
abstract = {BACKGROUND: Patients with hepatitis B-related acute-on-chronic liver failure (HB-ACLF) may have an increased circulating microbial burden. This study aimed to assess circulating microbial load and composition and to explore the association between the circulating microbiome and both systemic inflammation and clinical outcome in HB-ACLF.

METHODS: Plasma from 50 HB-ACLF patients, 23 healthy controls (HCs) and 25 patients with compensated liver cirrhosis (C-LC) was analyzed for chemokines/cytokines and bacterial DNA and further analysed by 16S rDNApyrosequencing. Linear discriminant analysis effect size (LEfSe) and inferred metagenomics analyses were performed.

RESULTS: The circulating bacterial DNA was significantly increased in HB-ACLF patients compared to that in the control groups. The overall microbial diversity was significantly decreased in HB-ACLF patients. HB-ACLF patients were enriched with Moraxellaceae, Sulfurovum, Comamonas, and Burkholderiaceae but were depleted in Actinobacteria, Deinococcus-Thermus, Alphaproteobacteria, Xanthomonadaceae and Enterobacteriaceae compared to controls. Networkanalysis revealed a direct positive correlation between Burkholderiaceae and chemokine IP-10 in HB-ACLF patients. The relative abundance of Prevotellaceae independently predicted 28-day mortality. Inferred functional metagenomics predicted an enrichment of bacteria with genes related to methane, alanine, aspartate, glutamate, pyrimidine, purine and energy metabolism.

CONCLUSIONS: HB-ACLF patients display increased circulating microbial burden, altered microbiome composition and a shift in microbiome functionality. The alteration in circulating microbiota is associated with systemic inflammation (SI) and clinical outcome in HB-ACLF. This article is protected by copyright. All rights reserved.},
}

@article {pmid30863724,
year = {2019},
author = {Iyer, LR and Verma, AK and Paul, J and Bhattacharya, A},
title = {Phagocytosis of Gut Bacteria by Entamoeba histolytica.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {34},
doi = {10.3389/fcimb.2019.00034},
pmid = {30863724},
issn = {2235-2988},
abstract = {The protist parasite Entamoeba histolytica causes amoebiasis, a major public health problem in developing countries. Only a small fraction of patients infected with the parasite display invasive disease involving colon or extra intestinal tissues such as liver. E. histolytica exists as two distinct forms, cysts, the infective form, and trophozoites, that are responsible for disease pathology. The latter multiply in the large intestine occasionally causing disease. The large intestine in humans is populated by a number of different bacterial communities and amoebic cells grow in their midst using some as food material. Several studies have shown relationship between bacteria and E. histolytica growth and virulence. However, an understanding of this relationship in human gut environment is not clear. We have investigated the possibility that there may be specific interaction of amoeba with different bacteria present in the gut environment by using a metagenomic pipe line. This was done by incubating bacteria isolated from human fecal material with E. histolytica and then identifying the bacterial population isolated from amoebic cells using a rRNA based metagenomic approach. Our results show that the parasite prefers a few bacterial species. One of these species is Lactobacillus ruminus which has never shown to be associated with E. histolytica.},
}

@article {pmid30863691,
year = {2019},
author = {Gupta, V and Singh, I and Kumar, P and Rasool, S and Verma, V},
title = {A hydrolase with esterase activity expressed from a fosmid gene bank prepared from DNA of a North West Himalayan glacier frozen soil sample.},
journal = {3 Biotech},
volume = {9},
number = {3},
pages = {107},
doi = {10.1007/s13205-019-1621-z},
pmid = {30863691},
issn = {2190-572X},
abstract = {Screening of 20,000 clones of a fosmid gene bank, constructed from DNA extracted from North West Himalaya (NWH) glacier soil sample, using functional approach identified 10 esterase/lipase-producing clones. Of these, a clone designated pFG43 with an insert size of 45 kb which produced the highest concentration of enzyme (467.43 U/mg) was sequenced. Clone pFG43 contained 61 open reading frames (ORF) and of these an ORF of 1155 bp designated ME-003, was found to be closely related to a hydrolase from Acidobacteria sps (77% sequence identity and E value = 1e-164) and subsequently identified as a putative cocaine esterase. ORF ME-003 was amplified and sub-cloned using a TA vector system into E. coli (DH5α). The purified recombinant enzyme with a molecular weight of 43 kDa had optimal activity at 40 °C, pH 6 and the highest activity with shorter chain fatty acids than with higher chain length fatty acids. There is insignificant effect of inhibitors on the enzyme activity of ME-003, except PMSF which completely inhibited its activity. ME-003 activity was also inhibited in the presence of copper oxide but remained stable in presence of other metal ions. The enzyme activity was also inhibited in the presence of organic solvents; however, in the presence of 10% isopropanol, 12% of enzymatic activity was retained. Among various detergents, SDS completely inhibited enzymatic activity. The recombinant enzyme also shows enantio-specific activity against the racemic drug intermediates/precursors and exhibited 90% ee against racemic 1-phenyl ethanol and fluoxetine.},
}

@article {pmid30863681,
year = {2019},
author = {Klimina, KM and Kasianov, AS and Poluektova, EU and Emelyanov, KV and Voroshilova, VN and Zakharevich, NV and Kudryavtseva, AV and Makeev, VJ and Danilenko, VN},
title = {Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6554},
doi = {10.7717/peerj.6554},
pmid = {30863681},
issn = {2167-8359},
abstract = {Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota are not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human GM. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human GM we developed TAGMA (toxin antitoxin genes for metagenomes analyses) software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strains of Lactobacillus and Bifidobacterium in metagenomes.},
}

@article {pmid30863388,
year = {2019},
author = {Yang, W and Wang, L and Hu, Q and Pei, F and Mugambi, MA},
title = {Identification of Bacterial Composition in Freeze-Dried Agaricus bisporus During Storage and the Resultant Odor Deterioration.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {349},
doi = {10.3389/fmicb.2019.00349},
pmid = {30863388},
issn = {1664-302X},
abstract = {Moisture absorption and bacterial growth are critical factors for quality deterioration of freeze-dried Agaricus bisporus. In order to explore the bacterial composition and the resultant odor changes in freeze-dried A. bisporus during storage under three typical conditions (RT: 25°C, 55% RH; HT: 37°C, 85% RH; AT: ambient temperature), bacterial diversity and communities were analyzed using metagenomics. Moreover, volatile compounds were determined using SPME-GC-MS. The results demonstrated that the bacterial composition in freeze-dried A. bisporus was dominated by Pseudomonas, followed by Rhizobium and Pedobacter. In addition, Mucilaginibacter, Flavobacterium, and Thermus were a few other genera more dominant in HT samples, Chryseobacterium was the other genera more dominant in AT samples, while, Sphingobacterium and Chryseobacterium were a few other genera more dominant in RT samples. Furthermore, the increase of benzaldehyde content in HT samples may have been induced by the growth of Pseudomonads and the esters production in RT and AT samples might have been induced by Chryseobacterium. This study provided comprehensive information on exogenous bacterial composition and the resultant odor in freeze-dried A. bisporus. These results may be a theoretical basis for quality control and quick quality detection based on volatiles of freeze-dried A. bisporus.},
}

@article {pmid30863381,
year = {2019},
author = {Takhampunya, R and Korkusol, A and Pongpichit, C and Yodin, K and Rungrojn, A and Chanarat, N and Promsathaporn, S and Monkanna, T and Thaloengsok, S and Tippayachai, B and Kumfao, N and Richards, AL and Davidson, SA},
title = {Metagenomic Approach to Characterizing Disease Epidemiology in a Disease-Endemic Environment in Northern Thailand.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {319},
doi = {10.3389/fmicb.2019.00319},
pmid = {30863381},
issn = {1664-302X},
abstract = {In this study, we used a metagenomic approach to analyze bacterial communities from diverse populations (humans, animals, and vectors) to investigate the role of these microorganisms as causative agents of disease in human and animal populations. Wild rodents and ectoparasites were collected from 2014 to 2018 in Nan province, Thailand where scrub typhus is highly endemic. Samples from undifferentiated febrile illness (UFI) patients were obtained from a local hospital. A total of 200 UFI patient samples were obtained and 309 rodents and 420 pools of ectoparasites were collected from rodents (n = 285) and domestic animals (n = 135). The bacterial 16S rRNA gene was amplified and sequenced with the Illumina. Real-time PCR and Sanger sequencing were used to confirm the next-generation sequencing (NGS) results and to characterize pathogen species. Several pathogens were detected by NGS in all populations studied and the most common pathogens identified included Bartonella spp., Rickettsia spp., Leptospira spp., and Orientia tsutsugamushi. Interestingly, Anaplasma spp. was detected in patient, rodent and tick populations, although they were not previously known to cause human disease from this region. Candidatus Neoehrlichia, Neorickettsia spp., Borrelia spp., and Ehrlichia spp. were detected in rodents and their associated ectoparasites. The same O. tsutsugamushi genotypes were shared among UFI patients, rodents, and chiggers in a single district indicating that the chiggers found on rodents were also likely responsible for transmitting to people. Serological testing using immunofluorescence assays in UFI samples showed high prevalence (IgM/IgG) of Rickettsia and Orientia pathogens, most notably among samples collected during September-November. Additionally, a higher number of seropositive samples belonged to patients in the working age population (20-60 years old). The results presented in this study demonstrate that the increased risk of human infection or exposure to chiggers and their associated pathogen (O. tsutsugamushi) resulted in part from two important factors; working age group and seasons for rice cultivation and harvesting. Evidence of pathogen exposure was shown to occur as there was seropositivity (IgG) in UFI patients for bartonellosis as well as for anaplasmosis. Using a metagenomic approach, this study demonstrated the circulation and transmission of several pathogens in the environment, some of which are known causative agents of illness in human populations.},
}